Input XML :
<registerService>
- <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' ; currently only 'moby' services are fully supported -->
+ <Category>moby</Category> <!-- one of 'moby', 'cgi', 'wsdl' ; currently only 'moby' and 'wsdl' services are fully supported -->
<serviceName>YourServiceNameHere</serviceName>
<serviceType>TypeOntologyTerm</serviceType>
<authURI>your.URI.here</authURI>
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.113
retrieving revision 1.114
diff -u -r1.113 -r1.114
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/11/24 18:06:45 1.113
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 00:23:23 1.114
@@ -873,25 +873,27 @@
=over 2
-=item * in "moby" services, the input and output messaging structure is defined by the BioMOBY API, and the services use data Objects that are defined in the Class ontology as inheriting from the root "Object" Class. For "soap" services, there is additional flexibility:
+=item * in "moby" services, the input and output messaging structure is defined by the BioMOBY API, and the services use data Objects that are defined in the Class ontology as inheriting from the root "Object" Class.
+
+=item * For "soap" services, there is additional flexibility:
=over 2
-=item * Similar to a "moby" service, your "soap" service must consume/produce ontologically valid named data-types in order to be discovered by registry searches. As such, you _must_ register a single unique name for any non-MOBY input or output data Classes, regardless of the actual complexity of the input/output message.
+=item * Similar to a "moby" service, your "soap" service must consume/produce named data types. These are represented as LSID's
-=item * Do this using the registerObjectClass call of MOBY Central; To ensure uniqueness and LSID compatibilty of data class names, you must name your data using the following format: your.authURI:dataClassName
+=item * YOU DO NOT NEED TO REGISTER THESE DATA TYPES in MOBY Central; it is up to you what your LSID's represent, and MOBY Central WILL NOT try to resolve them!
-=item * remember, you may use any MOBY Object as your input/output (i.e. any Class Ontology term that inherits from Object) so long as you follow the MOBY message structure for that input or output.
+=item * You may mix ontologies when describing your service - i.e. you may freely use any MOBY Object as your input or (XOR) your output and use a non-MOBY object (LSID) for the alternate so long as you follow the MOBY message structure for the parameter that uses the MOBY Object
-=item * You may register, for example, a service that consumes a non-MOBY data Class and outputs a MOBY data class, so long as you follow the MOBY Messaging format for the output data
+=over 2
-=item * You may register, for example, a service that consumes a MOBY data Class and outputs a non-MOBY data class, so long as you follow the MOBY Messaging format for the ihput data
+=item * You may register, for example, a service that consumes a non-MOBY data Class and outputs a MOBY data class, so long as you follow the MOBY Messaging format for the output data
-=item * NOTE: Nether of the cases above are considred MOBY services, and are therefore described in the category of "soap" service
+=item * You may register, for example, a service that consumes a MOBY data Class and outputs a non-MOBY data class, so long as you follow the MOBY Messaging format for the input data
-=item * When registering a non-MOBY data Class name, it DOES NOT have any "Relationship" component (see registerObjectClass API)
+=item * NOTE: Nether of the cases above are considered MOBY services, and are therefore described in the category of "soap" service
-=item * non-MOBY inputs or outputs are described as a single Primary, Simple article of your new named type.
+=back
=back
@@ -903,6 +905,7 @@
=back
+=back
Input XML :
@@ -1079,17 +1082,18 @@
foreach (keys %objects_to_be_validated){
my ($valid, $message, $URI) = $OS->objectExists(term => $_);
- return &_error("$message","$URI") unless ($valid);
+ return &_error("$message","$URI") unless ($valid || (($_ =~ /urn:lsid/i) && !($_ =~ /urn:lsid:biomoby.org/i))); # either valid, or a non-moby LSID
}
- $debug && &_LOG("\n\n\aall objects okay\n");
+
+ $debug && &_LOG("\n\n\aall objects okay - either valid MOBY objects, or LSID's\n");
$OS = MOBY::OntologyServer->new(ontology => 'service');
my ($valid, $message, $URI) = $OS->serviceExists(term => $serviceType);
- return &_error("$message","$URI") unless ($valid);
+ print STDERR "\n\nChecking $URI\n\n";
+ return &_error("$message","$URI") unless ($valid || (($serviceType =~ /urn:lsid/i) && !($serviceType =~ /urn:lsid:biomoby.org/i))); # either valid, or a non-MOBY LSID
+ print STDERR "\n\nChecking $URI OK!!\n\n";
# right, registration should be successful now!
- # "soap" services may only have one input and one output
-
my $SVC = MOBY::service_instance->new(
category => $Category,
servicename => $serviceName,
@@ -1158,8 +1162,8 @@
($_->getNodeType == TEXT_NODE) && ($object_type = $_->toString);
}
my ($success, $message, $typeURI) = $OE->objectExists(term => $object_type);
- unless ($success) {
- $SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist");
+ if ((!($success) && ($object_type =~ /urn:lsid:biomoby.org/i)) || (!($success) && !($object_type =~ /urn:lsid/i))) { # if the object doesn't exist, and it isn't an LSID
+ $SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist, and is not an LSID");
} # kill it all unless this was successful!
my $namespace_string;
@@ -1169,10 +1173,11 @@
for (my $n = 0; $n<$num_ns;++$n) {
foreach my $name ($namespaces->item($n)->getChildNodes) {
if ($name->getNodeType == TEXT_NODE) {
- my ($success, $message, $URI) = $OE->namespaceExists(term => $name->toString);
- unless ($success) {
+ my $term = $name->toString;
+ my ($success, $message, $URI) = $OE->namespaceExists(term => $term);
+ if ((!($success) && ($term =~ /urn:lsid:biomoby.org/i)) || (!($success) && !($term =~ /urn:lsid/i))) { # if the object doesn't exist, and it isn't an LSID
$SVC->DELETE_THYSELF;
- return (-1,"namespace: " . $name->toString . " doesn't exist");
+ return (-1,"namespace: $term doesn't exist and is not an LSID");
}
$namespace_string .=$URI.",";
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/11/24 17:25:49 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30
@@ -171,9 +171,13 @@
my ($self, %args) = @_;
my $term = $args{term};
$term =~ s/^moby://; # if the term is namespaced, then remove that
-
- return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'object');
my $sth;
+ return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'object');
+
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objecttype/)){
+ return (1, "external ontology", $term);
+ }
+
if ($term =~ /^urn\:lsid/){
$sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?");
} else {
@@ -204,6 +208,10 @@
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objectclass/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -265,11 +273,15 @@
return (0, "WRONG ONTOLOGY",'') unless ($self->ontology eq 'object');
my $term = $args{term};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objectclass/)){
+ return (0, "can't delete from external ontology", $term);
+ }
+
my $LSID;
unless ($term =~ /urn\:lsid/){$LSID = $self->getObjectURI($term)} else {$LSID=$term}
return (0, q{Object type $term cannot be resolved to an LSID},"") unless $LSID;
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select object_id, object_lsid from object where object_type = ?},undef,$term);
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select object_id, object_lsid from object where object_lsid = ?},undef,$LSID);
# object1_id ISA object2_id?
my (@isa) = $self->dbh->selectrow_array(q{select * from object_term2term where object2_id = ?},undef, $id);
if (scalar @isa){
@@ -415,6 +427,10 @@
my $term = $args{term};
$term =~ s/^moby://; # if the term is namespaced, then remove that
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){
+ return (1, "external ontology", $term);
+ }
+
my $sth;
if ($term =~ /^urn\:lsid/){
$sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?");
@@ -446,6 +462,10 @@
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -475,11 +495,17 @@
my ($self, %args) = @_;
return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'service');
my $term = $args{term};
- my $LSID;
- unless ($term =~ /urn\:lsid/){$LSID = $self->getServiceURI($term)} else {$LSID=$term}
- return (0, q{Service type $term cannot be resolved to an LSID},"") unless $LSID;
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select service_id, service_lsid from service where service_type = ?},undef,$term);
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){
+ return (0, "can't delete from external ontology", $term);
+ }
+
+ my $LSID;
+ unless ($term =~ /^urn:lsid:biomoby.org:servicetype/){$LSID = $self->getServiceURI($term)} else {$LSID=$term}
+ return (0, q{Service type $term cannot be resolved to an LSID in the MOBY ontologies},"") unless $LSID;
+
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select service_id, service_lsid from service where service_lsid = ?}, undef, $LSID);
+
if (!defined $id){
return (0, q{Service type $term does not exist in the ontology},$lsid);
}
@@ -514,7 +540,11 @@
$term =~ s/^moby://; # if the term is namespaced, then remove that
my $sth;
- if ($term =~ /^urn\:lsid/){
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){
+ return (1, "external ontology", $term);
+ }
+
+ if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?");
} else {
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?");
@@ -540,10 +570,14 @@
#authority => $auth,
#contact_email => $email);
return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'namespace');
- return (0, "requires a object type node",'') unless ($args{node});
+ return (0, "requires a namespace type node",'') unless ($args{node});
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -575,8 +609,12 @@
my $LSID;
unless ($term =~ /urn\:lsid/){$LSID = $self->getNamespaceURI($term)} else {$LSID=$term}
return (0, q{Namespace type $term cannot be resolved to an LSID},"") unless $LSID;
+
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){
+ return (0, "cannot delete a term from an external ontology", $term);
+ }
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select namespace_id, namespace_lsid from namespace where namespace_type = ?},undef,$term);
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select namespace_id, namespace_lsid from namespace where namespace_lsid = ?},undef,$LSID);
unless ($id){return (0, q{Namespace type $term does not exist in the ontology},$lsid)}
# service1_id ISA service2_id?
@@ -839,7 +877,7 @@
sub setURI {
my ($self, $id) = @_;
my $URI;
- $id = lc($id);
+ # $id = lc($id);
if ($self->ontology eq 'object'){
$URI = "urn:lsid:biomoby.org:objectclass:$id"
} elsif ($self->ontology eq 'namespace'){
@@ -847,7 +885,7 @@
} elsif ($self->ontology eq 'service'){
$URI = "urn:lsid:biomoby.org:servicetype:$id"
} elsif ($self->ontology eq 'relationship'){
- $URI = "urn:lsid:biomoby.org:servicetype:$id"
+ $URI = "urn:lsid:biomoby.org:relationshiptype:$id"
} else {
$URI = 0
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2003/05/08 15:08:03 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2003/12/02 00:23:23 1.3
@@ -197,8 +197,8 @@
if ($self->service_type){
my $OE = MOBY::OntologyServer->new(ontology => 'service');
my ($success, $message, $servicetypeURI) = $OE->serviceExists(term => $self->service_type);
- unless ($success){return undef}
- $self->service_type_uri($servicetypeURI);
+ unless (($success || (($self->service_type =~ /urn:lsid/i) && !($self->service_type =~ /urn:lsid:biomoby.org/i)))){return undef}
+ ($self->service_type =~ /urn:lsid/)?$self->service_type_uri($self->service_type):$self->service_type_uri($servicetypeURI);
}
my ($serviceid, $category, $name, $typeURI, $authid,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist?
From mwilkinson at pub.open-bio.org Mon Dec 1 19:57:15 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Dec 1 19:57:39 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312020057.hB20vFsF021742@pub.open-bio.org>
mwilkinson
Mon Dec 1 19:57:15 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21719/MOBY
Modified Files:
Central.html Central.pm
Log Message:
I just remembered that Martin objected to me calling the non-MOBY services 'soap' services, so I now call them 'wsdl' services. Also fixed some more documentation errors, and fixed an error in the test suite.
moby-live/Perl/MOBY Central.html,1.10,1.11 Central.pm,1.114,1.115
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:23:23 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:57:15 1.11
@@ -27,7 +27,6 @@
...Registration Object...
-
Input XML :
-- <deregisterNamespace> - <namespaceType>MyNamespace</namespaceType> - </deregisterNamespace>-
Ouptut XML :
-...Registration Object...
--
input: listref; (articleName may be undef)
input =>[
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.63
retrieving revision 1.64
diff -u -r1.63 -r1.64
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:23:23 1.63
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:57:15 1.64
@@ -621,8 +621,8 @@
authURI => $authURI,
contactEmail => "your@mail.address",
description => $human_readable_description,
- category => "moby" | "cgi" | "soap" (currently only moby supported)
- URL => $URL_TO_SERVICE
+ category => "moby" | "cgi" | "wsdl" (currently only moby and wsdl supported)
+ URL => $URL_TO_SERVICE (or URL to WSDL document for wsdl-type services)
input: listref; (articleName may be undef)
input =>[
@@ -670,8 +670,8 @@
my $email = $a{contactEmail}; $email ||="";
my $URL = $a{URL}; $URL ||="";
my $desc = $a{description}; $desc ||="";
- my $Category = lc($a{Category}); $Category ||="moby";
- return $self->errorRegXML("Only MOBY Service Categories are currently allowed") unless ($Category eq 'moby');
+ my $Category = lc($a{category}); chomp $Category; $Category ||="";
+ return $self->errorRegXML("Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category") unless (($Category eq 'moby') || ($Category eq 'wsdl'));
return $self->errorRegXML("All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary") unless (
$name && $type && $authURI && $email && $URL && $desc && $Category);
@@ -685,7 +685,7 @@
$authURI
$email ";
- if ($Category eq "moby") {
+ if ($Category eq "moby" || $Category eq 'soap') {
my %SEC;
if ($a{'secondary'} && ref($a{'secondary'} =~ /hash/i)){
%SEC = %{$a{secondary}}
@@ -778,7 +778,7 @@
}
$message .= "\n";
$message .= "";
- } else { return $self->errorRegXML("cannot register services with a client initialized with multiple registries")}
+ } else { return $self->errorRegXML("only 'moby' and 'wsdl' service types are allowed to be registered at this time.")}
#elsif ($Category eq "cgi") {
# my $IN = $a{input};
From mwilkinson at pub.open-bio.org Mon Dec 1 20:08:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Dec 1 20:08:47 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312020108.hB218O1t021842@pub.open-bio.org>
mwilkinson
Mon Dec 1 20:08:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21819/Perl/MOBY
Modified Files:
Central.html Central.pm
Log Message:
still calling Collection articles 'Complex' articles. This is confusing. It is now consistent thorughout the documentation
moby-live/Perl/MOBY Central.html,1.11,1.12 Central.pm,1.115,1.116
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:57:15 1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 01:08:24 1.12
@@ -304,12 +304,10 @@
Input XML :
@@ -372,13 +378,13 @@
human readable COMPREHENSIVE description of your service]]>
</Description>
<Input>
- <!-- zero or more Primary (Simple and/or Complex) articles -->
+ <!-- zero or more Primary (Simple and/or Collection) articles -->
</Input>
<secondaryArticles>
<!-- zero or more INPUT Secondary articles -->
</secondaryArticles>
<Output>
- <!-- zero or more Primary (Simple and/or Complex) articles -->
+ <!-- zero or more Primary (Simple and/or Collection) articles -->
</Output>
</registerService>
@@ -553,10 +559,10 @@
<contactEmail>your@email.address</contactEmail>
<URL>http://endpoint.of.service</URL>;
<Input>
- <!-- one or more Simple and/or Complex Primary articles -->
+ <!-- one or more Simple and/or Collection Primary articles -->
</Input>
<Output>
- <!-- one or more Simple and/or Complex Primary articles -->
+ <!-- one or more Simple and/or Collection Primary articles -->
</Output>
<secondaryArticles>
<!-- one or more Secondary articles -->
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.115
retrieving revision 1.116
diff -u -r1.115 -r1.116
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 00:57:15 1.115
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 01:08:24 1.116
@@ -905,13 +905,13 @@
human readable COMPREHENSIVE description of your service]]>
-
+
@@ -1019,13 +1019,12 @@
# http://URL.to.your/CGI.pl
# your.URI.here
#
-#
+#
#
#
#
-#
#
#
@@ -1119,7 +1118,7 @@
my $dbh = $SVC->dbh;
return (-1,'Bad node') unless $node->getNodeType == ELEMENT_NODE;
- # this is a Simple or a Complex object
+ # this is a Simple or a Collection object
my $simp_coll = $node->getTagName;
$debug && &_LOG("TAGNAME in $inout _registerArticle is $simp_coll");
@@ -1431,10 +1430,10 @@
your@email.address
http://endpoint.of.service
-
+
From mwilkinson at pub.open-bio.org Tue Dec 9 16:06:51 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 9 16:06:25 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092106.hB9L6pJU028188@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:06:51 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28169/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
added a generic server-side parser to CommonSubs that should basically do all of the work for you and be compatible with the 0.6 API. Not yet documented; just testing on my own services first.
moby-live/Perl/MOBY CommonSubs.pm,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/12 16:47:16 1.28
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:06:51 1.29
@@ -143,9 +143,17 @@
use XML::DOM;
use MOBY::CrossReference;
use MOBY::Client::OntologyServer;
+use strict;
+use warnings;
-@ISA = qw(Exporter);
-@EXPORT_OK = qw(
+use constant COLLECTION => 1;
+use constant SIMPLE => 2;
+use constant BE_NICE => 1;
+use constant BE_STRICT => 0;
+
+our @ISA = qw(Exporter);
+our @EXPORT = qw(COLLECTION SIMPLE BE_NICE BE_STRICT);
+our @EXPORT_OK = qw(
getSimpleArticleIDs
getSimpleArticleNamespaceURI
simpleResponse
@@ -165,8 +173,13 @@
extractResponseArticles
getResponseArticles
getCrossReferences
+ genericServiceInputParser
+ COLLECTION
+ SIMPLE
+ BE_NICE
+ BE_STRICT
);
-%EXPORT_TAGS =(all => [qw(
+our %EXPORT_TAGS =(all => [qw(
getSimpleArticleIDs
getSimpleArticleNamespaceURI
simpleResponse
@@ -186,9 +199,39 @@
extractResponseArticles
getResponseArticles
getCrossReferences
+ genericServiceInputParser
+ COLLECTION
+ SIMPLE
+ BE_NICE
+ BE_STRICT
)]);
+
+sub genericServiceInputParser {
+ my ($message, $namespaces) = @_; # get the incoming MOBY query XML
+ my @inputs; # set empty response
+ my @queries = getInputs($message); # returns XML::DOM nodes
+
+ foreach my $query(@queries){
+ my $queryID = getInputID($query); # get the queryID attribute of the queryInput
+ my @input_articles = getArticles($query); # get the Simple/Collection articles making up this query
+ foreach my $input(@input_articles){ # input is a listref
+ my ($articleName, $article) = @{$input}; # get the named article
+ my $simple = isSimpleArticle($article); # articles may be simple or collection
+ my $collection = isCollectionArticle($article);
+ if ($collection){
+ my @simples = getCollectedSimples($article);
+ push @inputs, [COLLECTION,$queryID, \@simples];
+
+ } elsif ($simple){
+ push @inputs, [SIMPLE,$queryID,$simple];
+ }
+ }
+ }
+ return @inputs;
+}
+
#################################################
##################################
##################################
@@ -482,7 +525,7 @@
sub getInputs {
my ($XML) = @_;
-
+ my $moby;
unless (ref($XML) =~ /XML\:\:DOM/){
my $parser = new XML::DOM::Parser;
my $doc = $parser->parse($XML);
@@ -573,7 +616,7 @@
return undef unless $moby->getNodeType == ELEMENT_NODE;
return undef unless ($moby->getTagName =~ /queryInput/ || $moby->getTagName =~ /queryResponse/);
my @articles;
- foreach $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
+ foreach my $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
next unless $child->getNodeType == ELEMENT_NODE; # ignore whitespace
next unless ($child->getTagName =~ /Simple/ || $child->getTagName =~ /Collection/);
my $articleName = $child->getAttribute('articleName');
@@ -608,7 +651,7 @@
return undef unless ($moby->getTagName =~ /Collection/);
my @articles;
- foreach $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
+ foreach my $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
next unless $child->getNodeType == ELEMENT_NODE; # ignore whitespace
next unless ($child->getTagName =~ /Simple/);
push @articles, $child; # take the child elements, which are
$term
$def
")
} else {
- $response .= simpleResponse("")
+ $MOBY_RESPONSE .= simpleResponse("")
}
}
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
From mwilkinson at pub.open-bio.org Tue Dec 9 16:23:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 9 16:22:57 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092123.hB9LNOTl028369@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:23:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28350/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
dumb dumb dumb dumb
moby-live/Perl/MOBY CommonSubs.pm,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:06:51 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:23:24 1.30
@@ -209,7 +209,7 @@
sub genericServiceInputParser {
- my ($message, $namespaces) = @_; # get the incoming MOBY query XML
+ my ($message) = @_; # get the incoming MOBY query XML
my @inputs; # set empty response
my @queries = getInputs($message); # returns XML::DOM nodes
@@ -225,7 +225,7 @@
push @inputs, [COLLECTION,$queryID, \@simples];
} elsif ($simple){
- push @inputs, [SIMPLE,$queryID,$simple];
+ push @inputs, [SIMPLE,$queryID,$article];
}
}
}
From mwilkinson at pub.open-bio.org Tue Dec 9 16:30:33 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 9 16:30:05 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092130.hB9LUXWW028465@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:30:33 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28446/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
dumb dumb dumb dumb
moby-live/Perl/MOBY CommonSubs.pm,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:23:24 1.30
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:30:33 1.31
@@ -168,6 +168,7 @@
extractRawContent
collectionResponse
validateNamespaces
+ validateThisNamespace
isSimpleArticle
isCollectionArticle
extractResponseArticles
@@ -194,6 +195,7 @@
extractRawContent
collectionResponse
validateNamespaces
+ validateThisNamespace
isSimpleArticle
isCollectionArticle
extractResponseArticles
From mwilkinson at pub.open-bio.org Tue Dec 9 16:38:39 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 9 16:38:11 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092138.hB9LcdU5028578@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:38:39 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28559/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
initialize possibly undef values
moby-live/Perl/MOBY CommonSubs.pm,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:30:33 1.31
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:38:39 1.32
@@ -370,8 +370,12 @@
sub simpleResponse {
my ($data, $articleName, $qID) = @_; # articleName optional
- $data ||='';
$qID = &_getQueryID($qID) if ref($qID) =~ /XML::DOM/; # in case they send the DOM instead of the ID
+
+ $data ||=''; # initialize to avoid uninit value errors
+ $qID ||="";
+ $articleName ||="";
+
if ($articleName) {
return "
From mwilkinson at pub.open-bio.org Tue Dec 9 17:24:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 9 17:23:35 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092224.hB9MO3AB028801@pub.open-bio.org>
mwilkinson
Tue Dec 9 17:24:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv28763/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
updating my GO services to be 0.6 compliant and a bit more readable
moby-live/Perl/scripts/Services LocalServices.pm,1.37,1.38
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -u -r1.37 -r1.38
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/09 21:06:51 1.37
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/09 22:24:03 1.38
@@ -10,6 +10,7 @@
use SOAP::Lite;
use DBI;
use DBD::mysql;
+use GO::AppHandle;
use MIME::Base64;
use XML::DOM;
use MOBY::Client::OntologyServer;
@@ -24,85 +25,60 @@
#getNodeContentWithArticle
use vars qw(@ISA);
-@ISA = qw(SOAP::Server::Parameters); # uncomment this line if you want access to the SOM as the
- # last parameter passed to the subroutine
sub getGoTerm {
my ($caller, $message) = @_;
my $MOBY_RESPONSE;
- my (@inputs)= genericServiceInputParser($message, []); # ([SIMPLE, $queryID, $simple],...)
+ my (@inputs)= genericServiceInputParser($message); # ([SIMPLE, $queryID, $simple],...)
return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- my @validNS = validateNamespaces(); # ONLY do this if you are intending to be namespace aware!
+ my @validNS = validateNamespaces("GO"); # ONLY do this if you are intending to be namespace aware!
+
+ my $dbh = _dbAccess('go');
+ die "can't connect to GO database\n" unless $dbh;
+ my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
- my @accessions;
foreach (@inputs){
my ($articleType, $ID, $input) = @{$_};
unless ($articleType == SIMPLE){
- $MOBY_RESPONSE .= simpleResponse("", "", $ID) ;
+ $MOBY_RESPONSE .= simpleResponse("", "Collection_Article_Not_allowed_as_input", $ID);
next;
} else {
my $ns = getSimpleArticleNamespaceURI($input);
- ((push @accessions, undef) && (next)) unless validateThisNamespace($ns, @validNS);
- push @accessions, defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):1;
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $accession = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ unless (defined($accession)){
+ $MOBY_RESPONSE .= simpleResponse("", "Invalid_Accession", $ID);
+ next;
+ }
+ unless ($accession =~/^GO:/){
+ $accession = "GO:$accession"; # we still haven't decided on whether id's should include the prefix...
+ }
+ $sth->execute($accession);
+ my ($term, $def) = $sth->fetchrow_array;
+ if ($term){
+ $MOBY_RESPONSE .= simpleResponse("
+
+ $term
+ $def
+ ", "GO_Term_From_ID", $ID)
+ } else {
+ $MOBY_RESPONSE .= simpleResponse("", "NO_Term_Found", $ID)
+ }
}
}
- my $dbh = _dbAccess('go');
- die "can't connect to GO database\n" unless $dbh;
- my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
- foreach my $acc(@accessions){
- unless ($acc =~/^GO:/){
- $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
- }
- $sth->execute($acc);
- my ($term, $def) = $sth->fetchrow_array;
- if ($term){
- $MOBY_RESPONSE .= simpleResponse("
-
- $term
- $def
- ")
- } else {
- $MOBY_RESPONSE .= simpleResponse("")
- }
- }
return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
-
sub getGoTermAssociations {
+ my ($caller, $message) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($message); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- my $SOM = pop;
- my ($self, $data) = @_;
- my $response = "";
- my @accessions;
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'GO');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace GO does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data);
- foreach (@input_nodes){
- my ($input) = @{$_}; # this service only allows one input per query, so take the first
- my $ns = getSimpleArticleNamespaceURI($input);
- push @accessions, undef unless $ns eq $VALID_NAMESPACE; # if we have been sent an invalid namespace, then stack an undef as a response
- my ($id) = getSimpleArticleIDs($ns, [$input]);
- if (defined $id){
- push @accessions, $id;
- } else {
- push @accessions, undef;
- }
- }
-
- use DBI;
- use DBD::mysql;
my $dbh = _dbAccess('go');
- die "can't connecvt to database\n" unless $dbh;
+ die "can't connect to database\n" unless $dbh;
my $sth = $dbh->prepare("
select
gp.symbol,
@@ -125,27 +101,39 @@
and a.is_not = 0
and t.id = d.term_id
order by species_id");
-
- foreach my $acc(@accessions){
- unless ($acc =~/^GO:/){
- $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
- }
- my @simples;
- $sth->execute($acc);
- while (my ($symb, $sp, $namsp, $type, $name, $def) = $sth->fetchrow_array){
- my $response_data .= "\n";
- push @simples, $response_data;
+
+ my @validNS = validateNamespaces("GO"); # ONLY do this if you are intending to be namespace aware!
+
+ foreach (@inputs){
+ my ($articleType, $ID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= collectionResponse([], "Collection_Article_Input_Invalid", $ID) ;
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= $MOBY_RESPONSE .= collectionResponse([], "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $acc, defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ unless (defined($acc)){
+ $MOBY_RESPONSE .= collectionResponse([], "Invalid_Accession", $ID);
+ next;
+ }
+ unless ($acc =~/^GO:/){
+ $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
+ }
+ my @simples;
+ $sth->execute($acc);
+ while (my ($symb, $sp, $namsp, $type, $name, $def) = $sth->fetchrow_array){
+ my $response_data .= "\n";
+ push @simples, $response_data;
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples,"Known_GO_Term_Associations",$ID); # after all images have been collected, create the collection
}
- $response .= collectionResponse(\@simples); # after all images have been collected, create the collection
}
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
@@ -153,67 +141,51 @@
sub RetrieveGOFromKeywords {
my $SOM = pop;
my ($self, $query) = @_;
- use GO::AppHandle;
-
- my $ua = new LWP::UserAgent;
- my $req = new HTTP::Request GET => 'http://www.godatabase.org/dev/database/server.cfg';
- my $res = $ua->request($req);
+ # INITIALIZE CONNECTION TO GO DB
my $host; my $dbname;
$host = "sin.lbl.gov";
$dbname = "go";
-# if ($res->is_success) {
- # my $resp = $res->content;
- # if ($resp =~ /(\w+)\@(\S+)/){
- # $host = $2;
- # $dbname= $1;
- # } else {
- # return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- # }
- #}
my %connect_hash;
$connect_hash{-dbname}=$dbname;
$connect_hash{-dbhost}=$host;
-
my $GO_API = GO::AppHandle->connect(%connect_hash);
unless ($GO_API){
return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
}
+ # DB is now initialized
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'Global_Keyword');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace Global_Keyword does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($query); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- # now start analyzing the input data
- my @input_nodes = getInputArticles($query); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my $response;
- foreach (@input_nodes){
- my $input = $_->[0]; # we only allow one input object per query
- my ($kw) = getSimpleArticleIDs($VALID_NAMESPACE, [$input]);
- ($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
- my @terms = @{$GO_API->get_terms({search=>"$kw"})};
- next unless($terms[0]);
- my @simples;
- foreach my $term(@terms){
- my $acc = $term->public_acc;
- my $def = $term->definition;
- my $name = $term->name;
- push @simples, "
-
-
- $name
- $def
- ";
+ my @validNS = validateNamespaces("Global_Keyword"); # ONLY do this if you are intending to be namespace aware!
+ foreach (@inputs){
+ my ($articleType, $ID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= collectionResponse([], "Collection_Input_Invalid", $ID) ;
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= collectionResponse([], "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $kw = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ ($MOBY_RESPONSE .= collectionResponse([], "No_Keyword", $ID) && (next)) unless defined $kw;
+ ($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
+ my @terms = @{$GO_API->get_terms({search=>"$kw"})};
+ next unless($terms[0]);
+ my @simples;
+ foreach my $term(@terms){
+ my $acc = $term->public_acc;
+ my $def = $term->definition;
+ my $name = $term->name;
+ push @simples, "
+ $name
+ $def
+ ";
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples, "GO_terms_from_keywords", $ID);
}
- $response .= collectionResponse(\@simples);
- }
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ }
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
From mwilkinson at pub.open-bio.org Tue Dec 9 17:24:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 9 17:23:36 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092224.hB9MO30d028782@pub.open-bio.org>
mwilkinson
Tue Dec 9 17:24:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28763/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
updating my GO services to be 0.6 compliant and a bit more readable
moby-live/Perl/MOBY CommonSubs.pm,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:38:39 1.32
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 22:24:03 1.33
@@ -248,16 +248,16 @@
function : to get the IDs of simple articles that are in the given namespace
usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
args : (in order)
- $Namespace - (required) a namespace stringfrom the MOBY namespace ontology
+ $Namespace - (required) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care
\@Simples - (required) a listref of Simple XML::DOM nodes
i.e. the XML::DOM representing an XML structure like this:
- note : it will return *only* the ids that are in the given namespace
+ note : it will return *only* the ids that are in the given namespace, if you provide one
but since you are required to return an output for every input
(even if it is invalid) this routine will return undef for
- those articles that are not in that namespace
+ those articles in the list that are not in that namespace so you can keep track
=cut
@@ -271,45 +271,52 @@
my @input_nodes = @{$input_nodes};
my $OS = MOBY::Client::OntologyServer->new;
my ($s, $m);
- ($s, $m, $desired_namespace) = $OS->namespaceExists(term => $desired_namespace); # returns (success, message, lsid)
- return undef unless $s; # bail if not successful
+ if ($desired_namespace){
+ ($s, $m, $desired_namespace) = $OS->namespaceExists(term => $desired_namespace); # returns (success, message, lsid)
+ unless ($s){ # bail if not successful
+ print STDERR "MOBY::CommonSubs WARNING ** the namespace $desired_namespace does not exist in the MOBY ontology, and is not a valid LSID\n";
+ return undef;
+ }
+ }
- my @accessions;
+ my @ids;
foreach my $in(@input_nodes){
#$in = "
- note : it will return *only* the ids that are in the given namespace, if you provide one
- but since you are required to return an output for every input
- (even if it is invalid) this routine will return undef for
- those articles in the list that are not in that namespace so you can keep track
+ note : If you provide a namespace, it will return *only* the ids that are in the given namespace,
+ but will return 'undef' for any articles in the WRONG namespace so that you get an
+ equivalent number of outputs to inputs.
+
+ Note that if you call this with a single argument, this is assumed to
+ be \@Articles, so you will get ALL id's regardless of namespace!
=cut
sub getSimpleArticleIDs {
my ($desired_namespace, $input_nodes) = @_;
- return undef unless $input_nodes;
+ if ($desired_namespace && !($input_nodes)){ # if called with ONE argument, then these are the input nodes!
+ $input_nodes = $desired_namespace;
+ $desired_namespace = undef;
+ }
$input_nodes = [$input_nodes] unless ref($input_nodes) =~ /ARRAY/; # be flexible!
return undef unless scalar @{$input_nodes};
@@ -281,6 +286,7 @@
my @ids;
foreach my $in(@input_nodes){
+ next unless $in;
#$in = "
+
+
+
+ ";
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my $gb = SHoundGetGenBankff($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
+ $MOBY_RESPONSE .= "
+
+
+
+ ";
+ }
}
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $response .= simpleResponse("
-
- $length
- ");
- } else {
- $response .= simpleResponse("");
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+}
+
+sub GenbankAccVirtualSequenceRetrieve {
+ my ($self, $data) = @_;
+
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ (($MOBY_RESPONSE .= simpleResponse("", "no_input_object", $qID)) && (next)) unless (defined $input);
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse([], "Invalid_Namespace", $qID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my ($acc) = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ ($MOBY_RESPONSE .= collectionResponse([], "No_Accession_provided", $qID) && (next)) unless defined $acc;
+ use Bio::DB::GenBank;
+ my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
+ my $seq = $gb->get_Seq_by_acc($acc);
+ my $length;
+ if ($seq){$length = $seq->length;}
+ if ($length){
+ $MOBY_RESPONSE .= simpleResponse("
+
+ $length
+ ", "", $qID);
+ } else {
+ $MOBY_RESPONSE .= simpleResponse("", "sequence_has_no_length", $qID);
+ }
}
}
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
+
sub GenbankAccSequenceRetrieve {
my ($self, $data) = @_;
my $response; my @accessions;
From mwilkinson at pub.open-bio.org Wed Dec 10 17:34:36 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Dec 10 17:34:02 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102234.hBAMYaZc032738@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:34:36 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv32719/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
small changes to service output
moby-live/Perl/scripts/Services LocalServices.pm,1.41,1.42
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:22:03 1.41
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:34:36 1.42
@@ -70,7 +70,7 @@
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub getGoTermAssociations {
@@ -135,7 +135,7 @@
$MOBY_RESPONSE .= collectionResponse(\@simples,"Known_GO_Term_Associations",$ID); # after all images have been collected, create the collection
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -187,7 +187,7 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "GO_terms_from_keywords", $ID);
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -223,7 +223,7 @@
# do your thing here!
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub MOBYSHoundGetGenBankff {
@@ -281,8 +281,8 @@
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ #print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub GenbankAccVirtualSequenceRetrieve {
From mwilkinson at pub.open-bio.org Wed Dec 10 17:40:57 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Dec 10 17:40:23 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102240.hBAMevNm000374@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:40:56 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv355/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
Doh. Use the output format you dummy
moby-live/Perl/scripts/Services LocalServices.pm,1.42,1.43
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:34:36 1.42
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:40:56 1.43
@@ -262,21 +262,23 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+ $MOBY_RESPONSE .= simpleResponse("
- ";
+ ",
+ "", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+ $MOBY_RESPONSE .= simpleResponse("
- ";
+ ",
+ "", $qID);
}
}
}
From mwilkinson at pub.open-bio.org Wed Dec 10 17:45:12 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Dec 10 17:44:36 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102245.hBAMjCKF000512@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:45:12 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv493/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
missed one
moby-live/Perl/scripts/Services LocalServices.pm,1.43,1.44
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -u -r1.43 -r1.44
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:40:56 1.43
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:45:11 1.44
@@ -256,7 +256,7 @@
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my $gb = SHoundGetGenBankff($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+
+
+
+ ",
+ "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my $gb = SHoundGetGenBankff($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ",
+ "", $qID);
+ }
+ }
}
+ $aa = SHoundFini();
+ #print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
-sub MOBYSHoundGetGenBankff {
+sub _makeSeqObj {
+ my ($id) = @_;
+ my $gb = SHoundGetGenBankff($id);
+ return undef unless $gb;
+ my $gbio = IO::String->new($gb);
+ my $sio = Bio::SeqIO->new(-fh => \*$gbio, '-format' => 'genbank');
+ my $seq = $sio->next_seq;
+ return ($seq, $seq->length, $seq->seq);
+}
+
+sub MOBYSHoundGetGenBankVirtSequence {
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
@@ -254,30 +345,167 @@
my ($identifier) = getSimpleArticleIDs($input);
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
- my $gb = SHoundGetGenBankff($identifier);
+ my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+ ".($SEQ->length)."
+ ", "", $qID);
+ } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ my $gi = SHoundFindAcc($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ".($SEQ->length)."
+ ",
+ "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ".($SEQ->length)."
+ ",
+ "", $qID);
+ }
+ }
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub MOBYSHoundGetGenBankWhateverSequence {
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+
+ my %objtype = ('dna', "DNASequence", 'rna', "RNASequence", 'protein', "AminoAcidSequence");
+
+ my $aa = SHoundInit("TRUE", "MOBY_SHoundGetGenBankff_Service"); # initialize SeqHound
+ $aa = SHoundIsInited(); # confirm initialization
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter) unless $aa eq "TRUE";
+
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my %validNS;
+ foreach (qw(NCBI_Acc NCBI_gi PIR Swiss-Prot EMBL PDB)){
+ my ($valid) = validateNamespaces($_); # we are going to ignore anything that is invalid
+ $validNS{$_} = $valid;
+ }
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && (defined($input))){ # we only accept simple inputs to this service
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send back a blank response for this queryID
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $qID)) && next) unless validateThisNamespace($ns, values(%validNS)); # return blank if they have sent us a namespace we don't understand
+ my ($identifier) = getSimpleArticleIDs($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
+ if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
+ my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ my $objType = $objtype{$SEQ->alphabet};
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$identifier'>
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ my $gi = SHoundFindAcc($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my $objType = $objtype{$SEQ->alphabet};
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
+
+
+
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my $objType = $objtype{$SEQ->alphabet};
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
+
+
+
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ }
+ }
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub MOBYSHoundGetGenBankFasta {
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+
+ my $aa = SHoundInit("TRUE", "MOBY_SHoundGetGenBankff_Service"); # initialize SeqHound
+ $aa = SHoundIsInited(); # confirm initialization
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter) unless $aa eq "TRUE";
+
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my %validNS;
+ foreach (qw(NCBI_Acc NCBI_gi PIR Swiss-Prot EMBL PDB)){
+ my ($valid) = validateNamespaces($_); # we are going to ignore anything that is invalid
+ $validNS{$_} = $valid;
+ }
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && (defined($input))){ # we only accept simple inputs to this service
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send back a blank response for this queryID
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $qID)) && next) unless validateThisNamespace($ns, values(%validNS)); # return blank if they have sent us a namespace we don't understand
+ my ($identifier) = getSimpleArticleIDs($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
+
+ if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
+ my $gb = SHoundGetFasta($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("
+ $MOBY_RESPONSE .= simpleResponse("
- ",
+ ",
"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
- my $gb = SHoundGetGenBankff($gi);
+ my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("
+ $MOBY_RESPONSE .= simpleResponse("
- ",
+ ",
"", $qID);
}
}
@@ -287,6 +515,7 @@
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
+
sub GenbankAccVirtualSequenceRetrieve {
my ($self, $data) = @_;
From mwilkinson at pub.open-bio.org Thu Dec 11 13:08:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Dec 11 13:07:35 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312111808.hBBI8EdB004309@pub.open-bio.org>
mwilkinson
Thu Dec 11 13:08:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv4290
Modified Files:
MOBY-Client05.cgi
Log Message:
added Xrefs to my new services. Small change in the client program to improve readability
moby-live/Perl/scripts MOBY-Client05.cgi,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi 2003/11/06 16:42:41 1.25
+++ /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi 2003/12/11 18:08:14 1.26
@@ -1,6 +1,6 @@
#!/usr/bin/perl -w
use strict;
-use lib '/usr/local/apache/cgi-bin/MOBY05';
+use lib '/usr/local/apache/cgi-bin/BIO/moby-live/Perl';
use MOBY::Client::Central;
use MOBY::Client::Service;
@@ -466,11 +466,15 @@
my $output = "(";
foreach my $param(@{$objs}){
if ($param->isSimple){
- $output .= "Simple:".($param->objectType)." ,";
+ my $type = (($param->objectType =~ /\:(\S+)$/) && $1);
+ $type = $param->objectType unless $type;
+ $output .= "Simple: $type ,";
} else {
$output .= "Collection:[";
foreach my $simp(@{$param->Simples}){
- $output .= ($simp->objectType).",";
+ my $type = (($simp->objectType =~ /\:(\S+)$/) && $1);
+ $type = $simp->objectType unless $type;
+ $output .= "$type,";
}
chop $output;
$output .="],";
From mwilkinson at pub.open-bio.org Thu Dec 11 13:08:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Dec 11 13:07:39 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312111808.hBBI8EFh004328@pub.open-bio.org>
mwilkinson
Thu Dec 11 13:08:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv4290/Services
Modified Files:
LocalServices.pm
Log Message:
added Xrefs to my new services. Small change in the client program to improve readability
moby-live/Perl/scripts/Services LocalServices.pm,1.45,1.46
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 15:36:38 1.45
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:08:14 1.46
@@ -9,6 +9,7 @@
use strict;
use SeqHound;
use SOAP::Lite;
+use Bio::SeqIO;
use DBI;
use DBD::mysql;
use GO::AppHandle;
@@ -317,6 +318,16 @@
return ($seq, $seq->length, $seq->seq);
}
+sub _getXrefs {
+ my ($seq) = @_; # bioperl seq object
+ #my $gi = $seq->primary_id; # e.g. 163483
+ #print STDERR "\n\n*********************$ gi\n\n";
+ my $acc = $seq->accession; # e.g. A123434
+ my $kw = $seq->species->binomial; # e.g. mus musculus
+ my $taxon = $seq->species->ncbi_taxid; # e.g. 1234
+ return ($acc, $kw, $taxon);
+}
+
sub MOBYSHoundGetGenBankVirtSequence {
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
@@ -346,39 +357,53 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
- (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("
- ".($SEQ->length)."
- ", "", $qID);
+
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .=" \n".($SEQ->length)."
+
-
-
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
- ".($SEQ->length)."
- ",
- "", $qID);
+ ".($SEQ->length)."
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("
-
-
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
- ".($SEQ->length)."
- ",
- "", $qID);
+ ".($SEQ->length)."
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
}
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+# print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -413,43 +438,59 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$identifier'>
- ".($SEQ->length)."
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .=" \n".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
} elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
-
-
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
-
-
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
}
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+# print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -516,335 +557,6 @@
}
-sub GenbankAccVirtualSequenceRetrieve {
- my ($self, $data) = @_;
-
- my $MOBY_RESPONSE;
- my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
-
- my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
-
- foreach (@inputs){
- my ($articleType, $qID, $input) = @{$_};
- unless ($articleType == SIMPLE){
- $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
- next;
- } else {
- (($MOBY_RESPONSE .= simpleResponse("", "no_input_object", $qID)) && (next)) unless (defined $input);
- my $ns = getSimpleArticleNamespaceURI($input);
- (($MOBY_RESPONSE .= simpleResponse([], "Invalid_Namespace", $qID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
- my ($acc) = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
- ($MOBY_RESPONSE .= collectionResponse([], "No_Accession_provided", $qID) && (next)) unless defined $acc;
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $MOBY_RESPONSE .= simpleResponse("
-
- $length
- ", "", $qID);
- } else {
- $MOBY_RESPONSE .= simpleResponse("", "sequence_has_no_length", $qID);
- }
- }
- }
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
-}
-
-sub GenbankAccSequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_Acc');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;my $sequence;
- if ($seq){$length = $seq->length;$sequence = $seq->seq}
- if ($length){
- $response .= simpleResponse("
-
- $length
- $sequence
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-}
-sub GenbankGIVirtualSequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_gi');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_gi($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $response .= simpleResponse("
-
- $length
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-}
-
-sub GenbankGISequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_gi');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_gi($acc); # get the sequence object for each gi
- my $length;my $sequence;
- if ($seq){$length = $seq->length;$sequence = $seq->seq} # if it exists, get the length and sequence
- if ($length){ # and construct the response
- $response .= simpleResponse("
-
- $length
- $sequence
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse;
-}
-#=================================================
-#=================================================
-#=================================================
-
-sub GenbankCompleteSequenceRetrieve {
-
-# this service is registered as consuming NCBI_Acc OR NCBI_gi
-# and producing GenericSequence objects. However, it will
-# actually produce DNA, RNA or PRotein objects, as appropriate
-# and will produce a cross-reference block as well
-
- my ($self, $data) = @_;
- my $response; my @gis;
-
- my ($GB_Acc_LSID, $GB_gi_LSID) = validateNamespaces('NCBI_Acc', 'NCBI_gi');
- unless ($GB_Acc_LSID && $GB_gi_LSID){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc or NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- foreach my $node(@inputs){
-
- my $namespace_LSID = getSimpleArticleNamespaceURI($node); # get the LSID of the namespace for this input object
- unless (($namespace_LSID eq $GB_Acc_LSID) || ($namespace_LSID eq $GB_gi_LSID)){ # validate the namespace
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if bad namespace
- next;
- }
-
- my ($ID)= getSimpleArticleIDs($namespace_LSID, [$node]); # get the ID within this namespace
- unless (defined $ID){ # send a blank if we failed to get an id,
- $response .= simpleResponse(""); # because we have to send one response per input
- next;
- }
-
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string'); # now that we have a namespace and ID, we are ready to retrieve
- my $seq;
- if ($namespace_LSID eq $GB_Acc_LSID){ # if the namespace is a genbank Accession thebn
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the accession
- } elsif ($namespace_LSID eq $GB_gi_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_gi($ID); # get the sequence object for the gi
- } else {
- $response .= simpleResponse(""); # if it is neither,then send a blank as required by the API
- next;
- }
-
- my $length;my $sequence;
- if ($seq){
- $length = $seq->length;$sequence = $seq->seq; # if it exists, get the length and sequence
- } else {
- $response .= simpleResponse(""); # if we got nada, then send a blank as required
- next;
- }
-
- my $gi = $seq->primary_id; # e.g. 163483
- my $acc = $seq->accession; # e.g. A123434
- my $kw = $seq->species->binomial; # e.g. mus musculus
- my $moltype = $seq->alphabet; # 'dna', 'rna', 'protein'
- my $taxon = $seq->species->ncbi_taxid; # e.g. 1234
-
- my $ObjectType="GenericSequence"; # set it as the generic as default
- if ($moltype eq 'dna'){$ObjectType = "DNASequence"} # set to DNA
- elsif ($moltype eq 'rna'){$ObjectType = "RNASequence"} # set to RNA
- elsif ($moltype eq 'protein'){$ObjectType = "AminoAcidSequence"} # set to Protein
-
- if ($length){ # and construct the response; luckily, all of these objects have exactly the same structure :-)
- my $tempresponse .= "
-
- ";
- if ($taxon){ $tempresponse .=""}
- if ($kw){$tempresponse .=""}
- if ($acc && !($namespace_LSID eq $GB_Acc_LSID)){$tempresponse .=""}
- if ($gi && !($namespace_LSID eq $GB_gi_LSID)){$tempresponse .=""}
- $tempresponse .="
- $length
- $sequence
- ";
- $response .= simpleResponse($tempresponse);
- } else {
- $response .= simpleResponse(""); # if we failed to get a sequence length, then something weird happened, so just ignore it
- }
- }
- my $fullresponse = responseHeader() . $response . responseFooter(); # add the headers and footers
- my $SOAPResponse = SOAP::Data->type('base64' => $fullresponse); # base 64 encode it (optional)
- return $SOAPResponse;
-}
-
-
-sub GenbankRecordRetrieve {
- use Bio::SeqIO;
- use IO::String;
- my ($self, $data) = @_;
- my $response; # prepare a variable to hold the responses
-
- # Step 1 - validate the namespaces you plan to accept as input
- my ($GB_Acc_LSID, $GB_gi_LSID, $EMBL_LSID) = validateNamespaces('NCBI_Acc', 'NCBI_gi', 'EMBL');
- unless ($GB_Acc_LSID && $GB_gi_LSID && $EMBL_LSID){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc, NCBI_gi, or EMBL_LSID that we are expecting does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # Step 2 - get your input objects
- # in this case, we have registered as accepting
- # only simple inputs (not collections), therefore
- # we can insist on that constraint.
- my @inputs = getInputArticles($data); # returns ([SimpleDOM], [SimpleDOM],...), each represents a unique query input
- foreach my $node(@inputs){
- # do a bit of simple validation
- # the next 12 lines or so are ~cut-n-paste for every service
- unless (isSimpleArticle($node)){ # we only allow Simple inputs to this service, ignore anything else
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if it fails
- next;
- }
- my $namespace_LSID = getSimpleArticleNamespaceURI($node); # get the LSID of the namespace for this input object
- unless (($namespace_LSID eq $GB_Acc_LSID) || ($namespace_LSID eq $GB_gi_LSID) || $namespace_LSID eq $EMBL_LSID){ # validate the namespace
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if bad namespace
- next;
- }
- my ($ID)= getSimpleArticleIDs($namespace_LSID, [$node]); # get the ID within this namespace
- unless (defined $ID){ # send a blank if we failed to get an id,
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if there is no id (?!?)
- next;
- }
-
- # Now, do the analysis
- use Bio::DB::GenBank;
- use Bio::DB::EMBL;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string'); # now that we have a namespace and ID, we are ready to retrieve
- my $emb = new Bio::DB::EMBL(-retrievaltype => 'io_string');
- my $seq;
- if ($namespace_LSID eq $GB_Acc_LSID){ # if the namespace is a genbank Accession thebn
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the accession
- } elsif ($namespace_LSID eq $GB_gi_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_gi($ID); # get the sequence object for the gi
- } elsif ($namespace_LSID eq $EMBL_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the gi
- } else {
- $response .= simpleResponse(""); # if it is neither,then send a blank as required by the API
- next;
- }
-
- my $string;
- my $stringio = IO::String->new($string);
- my $out = Bio::SeqIO->new('-fh' => $stringio,
- '-format' => 'genbank');
- # output goes into $string
- $out->write_seq($seq);
- $response .= simpleResponse("
-
+
-
+
",
"", $qID);
} else {
@@ -295,9 +295,9 @@
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
}
@@ -359,12 +359,12 @@
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "\n";
+ my $tempresponse = "\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
- $tempresponse .=" \n".($SEQ->length)."
+ $tempresponse .="\n".($SEQ->length)."
\n\n";
+ my $tempresponse = "\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -389,13 +389,13 @@
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "\n\n";
+ my $tempresponse = "\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -441,12 +441,12 @@
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
- $tempresponse .=" \n".($SEQ->length)."
+ $tempresponse .="\n".($SEQ->length)."
".($SEQ->seq)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
@@ -457,13 +457,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
".($SEQ->seq)."
";
@@ -475,13 +475,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
".($SEQ->seq)."
";
@@ -532,9 +532,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
} else {
@@ -543,9 +543,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
}
From mwilkinson at pub.open-bio.org Thu Dec 11 17:30:53 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu Dec 11 17:30:13 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312112230.hBBMUrFG005178@pub.open-bio.org>
mwilkinson
Thu Dec 11 17:30:53 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv5159/Services
Modified Files:
LocalServices.pm
Log Message:
two more services dealing with taxon data
moby-live/Perl/scripts/Services LocalServices.pm,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:22:02 1.47
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 22:30:53 1.48
@@ -46,13 +46,13 @@
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
foreach (@inputs){
my ($articleType, $qID, $input) = @{$_};
- unless ($articleType == SIMPLE){
+ unless (($articleType == SIMPLE) && ($input)){
$MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
next;
} else {
@@ -69,6 +69,97 @@
##################################################
##################################################
+sub getTaxChildNodes { # WORKS
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= collectionResponse([], "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= collectionResponse([], "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $children = SHoundGetTaxChildNodes($identifier);
+ $MOBY_RESPONSE .= collectionResponse([], "nothing_found", $qID) unless ($children);
+ my @children = split ",", $children;
+ my @simples;
+ foreach my $taxon (@children){
+ next unless $taxon;
+ $taxon =~ s/\s//g;
+ push @simples, "";
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= simpleResponse("", "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $parent = SHoundGetTaxParent($identifier);
+ $MOBY_RESPONSE .= simpleResponse("", "nothing_found", $qID) unless ($parent);
+ $parent && ($MOBY_RESPONSE .= simpleResponse("", "", $qID));
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+
+sub getTaxNameFromTaxID{ # WORKS
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= simpleResponse("", "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $name = SHoundGetTaxNameFromTaxID($identifier);
+ $MOBY_RESPONSE .= simpleResponse("", "nothing_found", $qID) unless ($name);
+ $name && ($MOBY_RESPONSE .= simpleResponse("
+
+
+ $name ", "", $qID));
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
sub getGoTerm {
my ($caller, $message) = @_;
From mwilkinson at pub.open-bio.org Fri Dec 12 14:22:45 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri Dec 12 14:21:59 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312121922.hBCJMikJ009022@pub.open-bio.org>
mwilkinson
Fri Dec 12 14:22:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv9003/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
making GMOD moby server revealed a commonsubs error. removed the deprecated services from my CGI client
moby-live/Perl/MOBY CommonSubs.pm,1.34,1.35
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.34
retrieving revision 1.35
diff -u -r1.34 -r1.35
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/10 22:22:03 1.34
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/12 19:22:44 1.35
@@ -397,7 +397,7 @@
";
} elsif($data) {
return "
-
+
$data
";
From mwilkinson at pub.open-bio.org Fri Dec 12 14:22:45 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri Dec 12 14:21:59 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312121922.hBCJMjo6009041@pub.open-bio.org>
mwilkinson
Fri Dec 12 14:22:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv9003/Perl/scripts
Modified Files:
Services.cgi
Log Message:
making GMOD moby server revealed a commonsubs error. removed the deprecated services from my CGI client
moby-live/Perl/scripts Services.cgi,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services.cgi,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/scripts/Services.cgi 2003/10/17 21:29:52 1.4
+++ /home/repository/moby/moby-live/Perl/scripts/Services.cgi 2003/12/12 19:22:44 1.5
@@ -2,8 +2,13 @@
# _________________________________________________________________
use SOAP::Transport::HTTP;
use lib "/usr/local/apache/cgi-bin";
+use lib "/usr/local/apache/cgi-bin/MOBY05";
+use lib "/usr/local/apache/cgi-bin/BIO/go-dev/perl-api";
use lib "/usr/local/apache/cgi-bin/BIO/moby-live/Perl";
-use lib "/usr/local/apache/cgi-bin/BIO/core/Perl";
+use lib '/usr/local/apache/cgi-bin/bioperl/core';
+use lib '/usr/local/apache/cgi-bin/Services/';
+use Bio::SeqIO::genbank;
+use GO::AppHandle;
use Services::LocalServices;
use strict;
@@ -12,13 +17,13 @@
$x->dispatch_with({
'http://biomoby.org/#getGoTerm' => 'Services::LocalServices',
'http://biomoby.org/#getGoTermAssociations' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankAccVirtualSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankAccSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankGIVirtualSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankGISequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankCompleteSequenceRetrieve' => 'Services::LocalServices',
'http://biomoby.org/#RetrieveGOFromKeywords' => 'Services::LocalServices',
'http://biomoby.org/#getDragonMutantImages' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankff' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankFasta' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankWhateverSequence' => 'Services::LocalServices',
+'http://biomoby.org/#getTaxNameFromTaxID' => 'Services::LocalServices',
+'http://biomoby.org/#getTaxChildNodes' => 'Services::LocalServices',
});
$x->handle;
From mwilkinson at pub.open-bio.org Tue Dec 16 15:46:40 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue Dec 16 15:45:28 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312162046.hBGKke7h000685@pub.open-bio.org>
mwilkinson
Tue Dec 16 15:46:40 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv665/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
corrected the SeqHound call for EMBL accession numbers Added a new service that wraps the SeqHound SHoundGetTaxParent function to retrieve the taxonomic parents of a given taxon id.
moby-live/Perl/scripts/Services LocalServices.pm,1.48,1.49
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 22:30:53 1.48
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/16 20:46:40 1.49
@@ -17,15 +17,31 @@
use MIME::Base64;
use XML::DOM;
use MOBY::Client::OntologyServer;
-use MOBY::CommonSubs qw(:all); # this provides the
-# subroutines:
-#getSimpleArticleIDs
-#getSimpleArticleNamespaceURI
-#simpleResponse
-#responseHeader
-#responseFooter
-#getInputArticles
-#getNodeContentWithArticle
+use MOBY::CommonSubs qw(:all); # this provides the following vars and functions
+ #getSimpleArticleIDs
+ #getSimpleArticleNamespaceURI
+ #simpleResponse
+ #responseHeader
+ #responseFooter
+ #getInputArticles
+ #getInputs
+ #getInputID
+ #getArticles
+ #getCollectedSimples
+ #getNodeContentWithArticle
+ #extractRawContent
+ #collectionResponse
+ #validateNamespaces
+ #validateThisNamespace
+ #isSimpleArticle
+ #isCollectionArticle
+ #extractResponseArticles
+ #getResponseArticles
+ #getCrossReferences
+ #genericServiceInputParser
+ #COLLECTION
+ #SIMPLE
+
my $debug = 1;
use vars qw(@ISA);
@@ -103,7 +119,7 @@
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
-sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+sub getTaxParent { # now it works.
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
@@ -327,14 +343,6 @@
# ===============================================
# = Genbank Retrieval Scripts =
# = =
-# = Note: The two VirtualSequenceRetrieve's =
-# = and two SequenceRetrieves below could=
-# = have been registered as two services =
-# = instead of four, by simply =
-# = registering each under two different =
-# = namespaces (Acc and gi) instead of =
-# = having a single service for each =
-# = namespace =
# ===============================================
@@ -369,7 +377,7 @@
my $gb = SHoundGetGenBankff($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
- } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ } elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -541,7 +549,7 @@
".($SEQ->seq)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
- } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ } elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -617,7 +625,7 @@
my $gb = SHoundGetFasta($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
An HTML attachment was scrubbed...
URL: http://portal.open-bio.org/pipermail/moby-guts/attachments/20031222/3a20bb44/attachment.htm
From mwilkinson at pub.open-bio.org Fri Dec 26 17:01:31 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri Dec 26 17:03:54 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312262201.hBQM1VtN026461@pub.open-bio.org>
mwilkinson
Fri Dec 26 17:01:31 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv26442/Perl/MOBY/Client
Modified Files:
Central.pm
Log Message:
duh! If you pass identical objects to the ISA routine, CLEARLY it should return TRUE!!
moby-live/Perl/MOBY/Client Central.pm,1.64,1.65
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -r1.64 -r1.65
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:57:15 1.64
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/26 22:01:31 1.65
@@ -1383,6 +1383,7 @@
sub ISA {
my ($self, $class1, $class2) = @_;
+ return 1 if (($class1 eq $class2) || ("moby:$class1" eq $class2) || ($class1 eq "moby:$class2"));
my $OS = MOBY::Client::OntologyServer->new;
my ($s, $d, $lsid1) = $OS->objectExists(term => $class1);
return 0 unless $s;
From mwilkinson at pub.open-bio.org Sat Dec 27 08:55:20 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat Dec 27 08:57:39 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271355.hBRDtKVf028530@pub.open-bio.org>
mwilkinson
Sat Dec 27 08:55:20 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv28511/Perl/MOBY/Client
Modified Files:
Central.pm
Log Message:
serious performance issues revealed by the new Gbrowse moby client program. The ISA call of MOB::Clien:Central requires two CGI calls, a SOAP call, which itself results in two CGI calls, and a myriad of independent database calls to traverse the ontology. It ended up being >1 second per call,which was unacceptable for many situations where you just need a quick answer to a 'what the heck is this' question. Started client-side caching of the ontology and LSID terms in Client::Central to speed things up. It is now only slow the first time, and <.05 seconds per call thereafter. It does show how critical the need is to start storing the ontology in memory on the server side, though.
moby-live/Perl/MOBY/Client Central.pm,1.65,1.66
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.65
retrieving revision 1.66
diff -u -r1.65 -r1.66
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/26 22:01:31 1.65
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 13:55:20 1.66
@@ -1385,13 +1385,27 @@
my ($self, $class1, $class2) = @_;
return 1 if (($class1 eq $class2) || ("moby:$class1" eq $class2) || ($class1 eq "moby:$class2"));
my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $d, $lsid1) = $OS->objectExists(term => $class1);
- return 0 unless $s;
- my ($s2, $d2, $lsid2) = $OS->objectExists(term => $class2);
- return 0 unless $s2;
- my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1);
- my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'};
- foreach (@$lsids){
+ my ($lsid1, $lsid2);
+ unless ($lsid1 = $self->{LSID_CACHE}->{$class1}){
+ my ($s, $d, $lsid) = $OS->objectExists(term => $class1);
+ $self->{LSID_CACHE}->{$class1} = $lsid;
+ $lsid1 = $lsid;
+ return 0 unless $s;
+ }
+ unless ($lsid2 = $self->{LSID_CACHE}->{$class2}){
+ my ($s, $d, $lsid) = $OS->objectExists(term => $class2);
+ $self->{LSID_CACHE}->{$class2} = $lsid;
+ $lsid2 = $lsid;
+ return 0 unless $s;
+ }
+ my @lsids;
+ unless ($self->{"ISA_CACHE"}->{"$lsid1"} && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){
+ my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1, Relationships => ['ISA']);
+ my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'};
+ @lsids = @$lsids;
+ }
+ $self->{"ISA_CACHE"}->{"$lsid1"} = [@lsids];
+ foreach (@lsids){
return 1 if $_ eq $lsid2;
}
return 0;
From mwilkinson at pub.open-bio.org Sat Dec 27 10:12:32 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat Dec 27 10:14:50 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271512.hBRFCWeV028733@pub.open-bio.org>
mwilkinson
Sat Dec 27 10:12:31 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28714/Perl/MOBY
Modified Files:
Central.pm
Log Message:
Gbrowse client reveals another MOBY Central bug. Searching for services where you provide an invalid namespace as a parameter should NOT find ALL services, it should find NO services.
moby-live/Perl/MOBY Central.pm,1.118,1.119
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.118
retrieving revision 1.119
diff -u -r1.118 -r1.119
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/22 17:21:16 1.118
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119
@@ -1849,7 +1849,7 @@
next unless ($_->getNodeType == TEXT_NODE);
my $name = $_->toString; chomp $name;
my ($success, $message, $URI) = $OS->namespaceExists(term => $name);
- ($URI) && push @namespaces, $URI;
+ $URI?(push @namespaces, $URI):(push @namespaces, "__MOBY__INVALID__NAMESPACE__");
}
}
return ($objectURI, \@namespaces);
From mwilkinson at pub.open-bio.org Sat Dec 27 12:41:32 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat Dec 27 12:43:51 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271741.hBRHfWiQ029662@pub.open-bio.org>
mwilkinson
Sat Dec 27 12:41:32 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv29639/Perl/MOBY/Client
Modified Files:
Central.html Central.pm
Log Message:
more tweaks for the Gbrowse project. Create getter/setter methods for the LSID and ISA caches in MOBY::Client::Central so that they can be called from outside of the module itself. This will allow us to build external tools that play with these caches. This may not seem useful at the moment since we only have CGI based clients, so the cache is erased every time we make a call, but once we have a standalone client it will be very useful
moby-live/Perl/MOBY/Client Central.html,1.13,1.14 Central.pm,1.66,1.67
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/02 00:57:15 1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/27 17:41:32 1.14
@@ -2,7 +2,7 @@
MOBY::Client::Central - a client side wrapper for MOBY Central
-
+
@@ -20,8 +20,8 @@
- new
- - registerObject a.k.a registerObjectClass
- - deregisterObject a.k.a. deregisterObjectClass
+ - registerObject a.k.a registerObjectClass
+ - deregisterObject a.k.a. deregisterObjectClass
- retrieveObjectDefinition
- registerServiceType
- deregisterServiceType
@@ -41,6 +41,8 @@
- Relationships
- ISA
- DUMP
+ - LSID_CACHE
+ - ISA_CACHE
-
Title : registerObject ; registerObjectClass
Usage : $REG = $MOBY->registerObject(%args)
@@ -154,7 +156,7 @@
[Object1, articleName]]}
-
Title : deregisterObject ; deregisterObjectClass Usage : $REG = $MOBY->deregisterObject(%args) @@ -430,6 +432,27 @@ Function : DUMP the mysql for the current MOBY Central database Returns : text Args : $reg - name of MOBY Central you want to use if not default+
+
++ Title : LSID_CACHE + Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid) + Function : get/set LSID from the cache + Returns : lsid as a scalar + Args : the term for which you have/want an lsid, + and optionally the lsid to set.+
+
++ Title : ISA_CACHE + Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) + Function : get/set the ISA relationships in the cache + Returns : listref of ISA relationships. The resulting + list is IN ORDER from term to root. + Args : the term for which you have/want the ISA parentage, + and optionally the parentage listref to set.=================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.66 retrieving revision 1.67 diff -u -r1.66 -r1.67 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 13:55:20 1.66 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 17:41:32 1.67 @@ -213,6 +213,7 @@ } } + sub new { my ($caller, %args) = @_; @@ -1342,6 +1343,7 @@ } + sub _relationshipsPayload{ my ($payload) = @_; return undef unless $payload; @@ -1388,23 +1390,23 @@ my ($lsid1, $lsid2); unless ($lsid1 = $self->{LSID_CACHE}->{$class1}){ my ($s, $d, $lsid) = $OS->objectExists(term => $class1); - $self->{LSID_CACHE}->{$class1} = $lsid; + $self->LSID_CACHE($class1, $lsid); $lsid1 = $lsid; return 0 unless $s; } unless ($lsid2 = $self->{LSID_CACHE}->{$class2}){ my ($s, $d, $lsid) = $OS->objectExists(term => $class2); - $self->{LSID_CACHE}->{$class2} = $lsid; + $self->LSID_CACHE($class2, $lsid); $lsid2 = $lsid; return 0 unless $s; } my @lsids; - unless ($self->{"ISA_CACHE"}->{"$lsid1"} && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){ + unless ($self->ISA_CACHE($lsid1) && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){ my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1, Relationships => ['ISA']); my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'}; @lsids = @$lsids; } - $self->{"ISA_CACHE"}->{"$lsid1"} = [@lsids]; + $self->ISA_CACHE($lsid1, [@lsids]); foreach (@lsids){ return 1 if $_ eq $lsid2; } @@ -1507,6 +1509,61 @@ return \@Services; } + +=head2 LSID_CACHE + + Title : LSID_CACHE + Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid) + Function : get/set LSID from the cache + Returns : lsid as a scalar + Args : the term for which you have/want an lsid, + and optionally the lsid to set. + +=cut + + +sub LSID_CACHE { + my ($self, $term, $lsid) = @_; + if ($term && $lsid){ + $self->{LSID_CACHE}->{$term} = $lsid; + return $self->{LSID_CACHE}->{$term}; + } elsif ($term){ + return $self->{LSID_CACHE}->{$term}; + } else { + return undef + } +} + + +=head2 ISA_CACHE + + Title : ISA_CACHE + Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) + Function : get/set the ISA relationships in the cache + Returns : listref of ISA relationships. The resulting + list is IN ORDER from term to root. + Args : the term for which you have/want the ISA parentage, + and optionally the parentage listref to set. + +=cut + +sub ISA_CACHE { + my ($self, $term, $isas) = @_; + return [] if $isas && !(ref($isas)=~/ARRAY/); + if ($term && $isas){ + while (scalar(@$isas)){ + $self->{ISA_CACHE}->{$term} = [@$isas]; + $term = shift(@$isas); + } + return $self->{ISA_CACHE}->{$term}; + } elsif ($term){ + return $self->{ISA_CACHE}->{$term}; + } else { + return [] + } +} + + sub parseRegXML { #
+
+
Title : LSID_CACHE @@ -446,13 +450,15 @@From mwilkinson at pub.open-bio.org Sat Dec 27 15:15:45 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sat Dec 27 15:18:02 2003 Subject: [MOBY-guts] biomoby commit Message-ID: <200312272015.hBRKFjpJ030037@pub.open-bio.org> mwilkinson Sat Dec 27 15:15:45 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv30014/Perl/MOBY Modified Files: CommonSubs.pm CommonSubs.html Log Message: Gbrowse client needed a new utility routine in CommonSubs. This will take a list of 'known' Object ontology nodes and check it against the parentage of an in-hand object type, returning to you the term from your list that is DEEPEST in the ontology in the ISA parentage of your in-hand object. Why? (you might ask) Well, because when you want to assign renderers to objects you want the most complex renderer possible to deal with your in-hand object, so if you have rendrers for a variety of base object types, you want to chose the one that is best able to deal with whatever you have in-hand, thus you want the node closest to your object type moby-live/Perl/MOBY CommonSubs.pm,1.36,1.37 CommonSubs.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.36 retrieving revision 1.37 diff -u -r1.36 -r1.37 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/22 19:57:04 1.36 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:15:45 1.37 @@ -175,6 +175,7 @@ getResponseArticles getCrossReferences genericServiceInputParser + whichDeepestParentObject COLLECTION SIMPLE BE_NICE @@ -202,6 +203,7 @@ getResponseArticles getCrossReferences genericServiceInputParser + whichDeepestParentObject COLLECTION SIMPLE BE_NICE @@ -1071,6 +1073,43 @@ return @XREFS; } + + +=head2 whichDeepestParentObject + + name : whichDeepestParentObject + function : select the parent node from nodeList that is + closest to the querynode + usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + args : $CENTRAL - your MOBY::Client::Central object + $queryNode - the node I am interested in + \@nodelist - the list of nodes that I know about + returns : an ontology term as a scalar, or undef if there + is no parent of this node in the nodelist + +=cut + + +sub whichDeepestParentObject { + use MOBY::Client::OntologyServer; + my ($CENTRAL, $queryTerm, $termlist) = @_; + return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); + my %nodeLSIDs; + foreach (@$termlist){ # get list of known LSIDs + my $lsid = $CENTRAL->ObjLSID($_); + $nodeLSIDs{$lsid}=1; + } + my $queryLSID = $CENTRAL->ObjLSID($queryTerm); + return undef unless keys(%nodeLSIDs); + my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already + return undef unless $isa; # this should return true or we are in BIIIG trouble! + my @lsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root + while (my $thisnode = shift @lsids){ # @isas are lsid's + return $thisnode if $nodeLSIDs{$thisnode}; + } + return undef +} + sub _makeXrefType { my ($xref) = @_; my $ns = $xref->getAttributeNode('namespace'); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/11/08 17:21:31 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:15:45 1.7 @@ -4,7 +4,7 @@ISA_CACHE
- Title : ISA_CACHE - Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) - Function : get/set the ISA relationships in the cache - Returns : listref of ISA relationships. The resulting - list is IN ORDER from term to root. - Args : the term for which you have/want the ISA parentage, - and optionally the parentage listref to set.+ Title : ISA_CACHE + Usage : @lsids = $MOBY->ISA_CACHE($lsid, \@isas) + Function : get/set the ISA relationships in the cache + Returns : list of ISA relationships. The ISA list + is IN ORDER from, excluding the term itself, to + root Object. Base Object returns an empty list. + Args : The LSID for which you have/want the ISA parentage, + and optionally the parentage listref to set. + Note : WHAT COMES BACK ARE LSIDs!!!
+
+ name : extractRawContent + function : pass me an article (Simple, or Collection) and I'll give you the + content AS A STRING - i.e. the raw XML of the contained MOBY Object(s) + usage : extractRawContent($simple) + input : the one element of the output from getArticles + returns : string+
+
name : validateNamespaces
@@ -427,7 +442,16 @@
presumptive namespaces; undef for each namespace that was invalid
-
+ name : validateThisNamespace + function : checks a given namespace against a list of valid namespaces + usage : $valid = validateThisNamespace($ns, @validNS); + args : ordered list of the namespace of interest and the list of valid NS's + returns : boolean+
+
+
name : getResponseArticles
function : get the DOM nodes corresponding to individual
@@ -461,6 +485,19 @@
}
}
}
++
++ name : whichDeepestParentObject + function : select the parent node from nodeList that is + closest to the querynode + usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + args : $CENTRAL - your MOBY::Client::Central object + $queryNode - the node I am interested in + \@nodelist - the list of nodes that I know about + returns : an ontology term as a scalar, or undef if there + is no parent of this node in the nodelistFrom mwilkinson at pub.open-bio.org Sat Dec 27 15:24:52 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sat Dec 27 15:27:09 2003 Subject: [MOBY-guts] biomoby commit Message-ID: <200312272024.hBRKOqJS030126@pub.open-bio.org> mwilkinson Sat Dec 27 15:24:52 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv30103/Perl/MOBY Modified Files: CommonSubs.html CommonSubs.pm Log Message: changed my mind and decided to return both the object name as well as its LSID, since the latter is a bit arcane sometimes. moby-live/Perl/MOBY CommonSubs.html,1.7,1.8 CommonSubs.pm,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:15:45 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:24:52 1.8 @@ -492,10 +492,10 @@ name : whichDeepestParentObject function : select the parent node from nodeList that is closest to the querynode - usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + usage : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList) args : $CENTRAL - your MOBY::Client::Central object - $queryNode - the node I am interested in - \@nodelist - the list of nodes that I know about + $queryTerm - the object type I am interested in + \@termlist - the list of object types that I know about returns : an ontology term as a scalar, or undef if there is no parent of this node in the nodelist =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:15:45 1.37 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38 @@ -1080,10 +1080,10 @@ name : whichDeepestParentObject function : select the parent node from nodeList that is closest to the querynode - usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + usage : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList) args : $CENTRAL - your MOBY::Client::Central object - $queryNode - the node I am interested in - \@nodelist - the list of nodes that I know about + $queryTerm - the object type I am interested in + \@termlist - the list of object types that I know about returns : an ontology term as a scalar, or undef if there is no parent of this node in the nodelist @@ -1093,21 +1093,21 @@ sub whichDeepestParentObject { use MOBY::Client::OntologyServer; my ($CENTRAL, $queryTerm, $termlist) = @_; - return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); + return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); my %nodeLSIDs; foreach (@$termlist){ # get list of known LSIDs my $lsid = $CENTRAL->ObjLSID($_); - $nodeLSIDs{$lsid}=1; + $nodeLSIDs{$lsid}=$_; } my $queryLSID = $CENTRAL->ObjLSID($queryTerm); - return undef unless keys(%nodeLSIDs); + return (undef, undef) unless keys(%nodeLSIDs); my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already - return undef unless $isa; # this should return true or we are in BIIIG trouble! - my @lsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root - while (my $thisnode = shift @lsids){ # @isas are lsid's - return $thisnode if $nodeLSIDs{$thisnode}; + return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble! + my @ISAlsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root + while (my $thislsid = shift @ISAlsids){ # @isas are lsid's + return ($nodeLSIDs{$thislsid},$thislsid) if $nodeLSIDs{$thislsid}; } - return undef + return (undef, undef); } sub _makeXrefType { From mwilkinson at pub.open-bio.org Sun Dec 28 15:41:59 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun Dec 28 15:44:10 2003 Subject: [MOBY-guts] biomoby commit Message-ID: <200312282041.hBSKfx4X009349@pub.open-bio.org> mwilkinson Sun Dec 28 15:41:59 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv9318/MOBY Modified Files: Central.pm CommonSubs.pm OntologyServer.pm simple_input.pm Log Message: making MOBY Central case-sensitive for LSIDs. I might have missed a few places. please let me know if you find any. moby-live/Perl/MOBY Central.pm,1.119,1.120 CommonSubs.pm,1.38,1.39 OntologyServer.pm,1.30,1.31 simple_input.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.119 retrieving revision 1.120 diff -u -r1.119 -r1.120 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/28 20:41:59 1.120 @@ -758,7 +758,7 @@ my $dbh = MOBY::central_db_connection->new->dbh; - my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where namespace_type_uris like '%$existingURI%'"); + my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where INSTR(namespace_type_uris,'$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -768,7 +768,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where INSTR(namespace_type_uris,'$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -778,7 +778,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where INSTR(namespace_type_uris, '$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -788,7 +788,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where INSTR(namespace_type_uris, '$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -1699,7 +1699,7 @@ my $nsquery; foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's - $nsquery .=" OR namespace_type_uris like '%$ns%' "; + $nsquery .=" OR INSTR(namespace_type_uris, '$ns') "; } if ($nsquery){ $nsquery =~ s/OR//; # just the first @@ -1754,7 +1754,7 @@ my $nsquery; foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's - $nsquery .=" OR namespace_type_uris like '%$ns%' "; + $nsquery .=" OR INSTR(namespace_type_uris, '$ns') "; } if ($nsquery){ $nsquery =~ s/^\sOR//; # just the first =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.38 retrieving revision 1.39 diff -u -r1.38 -r1.39 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39 @@ -1074,7 +1074,6 @@ } - =head2 whichDeepestParentObject name : whichDeepestParentObject @@ -1084,8 +1083,12 @@ args : $CENTRAL - your MOBY::Client::Central object $queryTerm - the object type I am interested in \@termlist - the list of object types that I know about - returns : an ontology term as a scalar, or undef if there - is no parent of this node in the nodelist + returns : an ontology term and LSID as a scalar, or undef if there + is no parent of this node in the nodelist. + (note that it will only return the term if you give it + term names in the @termList. If you give it + LSID's in the termList, then both the parameters + returned will be LSID's - it doesn't back-translate...) =cut =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30 +++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31 @@ -179,7 +179,7 @@ } if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?"); + $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where INSTR(object_lsid, ?)"); } else { $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_type = ?"); } @@ -326,7 +326,7 @@ return (0, "requires both term and ontology arguments\n",'') unless (defined($term) && defined($ont)); my $sth; if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_lsid = ? and ontology=?"); + $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where INSTR(relationship_lsid,?) and ontology=?"); } else { $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_type = ? and ontology=?"); } @@ -433,7 +433,7 @@ my $sth; if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?"); + $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where INSTR(service_lsid, ?)"); } else { $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_type = ?"); } @@ -545,7 +545,7 @@ } if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){ - $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?"); + $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where INSTR(namespace_lsid, ?)"); } else { $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?"); } @@ -691,7 +691,7 @@ sub getObjectCommonName { my ($self, $URI) = @_; return undef unless $URI =~ /urn\:lsid/; - my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_id = ?}, undef, $URI); + my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_lsid = ?}, undef, $URI); return $name?$name:$URI; } @@ -702,7 +702,7 @@ sub getNamespaceCommonName { my ($self, $URI) = @_; return undef unless $URI =~ /urn\:lsid/; - my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_id = ?}, undef, $URI); + my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_lsid = ?}, undef, $URI); return $name?$name:$URI; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/05/07 19:20:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/12/28 20:41:59 1.2 @@ -14,7 +14,7 @@ =head1 SYNOPSIS - use MOBY::authority; + use MOBY::simple_input; my $Instance = MOBY::simple_input->new( object_type => "Sequence", namespaces => ["genbank/gi", "genbank/Acc"], From mwilkinson at pub.open-bio.org Sun Dec 28 21:43:43 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun Dec 28 21:45:52 2003 Subject: [MOBY-guts] biomoby commit Message-ID: <200312290243.hBT2hhlC010292@pub.open-bio.org> mwilkinson Sun Dec 28 21:43:43 EST 2003 Update of /home/repository/moby/moby-live In directory pub.open-bio.org:/tmp/cvs-serv10273 Modified Files: README Log Message: just testing the new cron on biomoby.org moby-live README,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/README 2003/02/19 21:12:16 1.3 +++ /home/repository/moby/moby-live/README 2003/12/29 02:43:43 1.4 @@ -1,3 +1,4 @@ +test README # # Revision History From mwilkinson at pub.open-bio.org Tue Dec 30 15:03:54 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Dec 30 15:05:52 2003 Subject: [MOBY-guts] biomoby commit Message-ID: <200312302003.hBUK3sN1016258@pub.open-bio.org> mwilkinson Tue Dec 30 15:03:54 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16239/Perl/MOBY Modified Files: OntologyServer.pm Log Message: changing the case of the LSID's buggered up the Relationships call of the OntologyServer. I noticed this when the Gbrowse MOBY browser stopped working. moby-live/Perl/MOBY OntologyServer.pm,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31 +++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/30 20:03:54 1.32 @@ -801,13 +801,13 @@ $term = $self->getObjectURI($term); } my %results; - while (($term ne 'urn:lsid:biomoby.org:objectclass:object') && ($term ne 'urn:lsid:biomoby.org:servicetype:service')){ + while (($term ne 'urn:lsid:biomoby.org:objectclass:Object') && ($term ne 'urn:lsid:biomoby.org:servicetype:Service')){ my $defs = $self->_doRelationshipsQuery($ontology, $term, $relationship, $direction); my $lsid; my $rel; foreach (@{$defs}){ $lsid = $_->[0]; $rel = $_->[1]; - $debug && _LOG("\t\tADDING RELATIONSHIP $_ : $lsid to $rel\n"); + $debug && _LOG("\t\tADDING RELATIONSHIP $_ : $lsid to $rel\n"); push @{$results{$rel}}, $lsid; } last unless ($expand); From mwilkinson at pub.open-bio.org Tue Dec 30 15:21:31 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Dec 30 15:23:29 2003 Subject: [MOBY-guts] biomoby commit Message-ID: <200312302021.hBUKLVww016376@pub.open-bio.org> mwilkinson Tue Dec 30 15:21:31 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16357/Perl/MOBY Modified Files: CommonSubs.pm Log Message: whichDeepestParentObject should return right away if it finds an object in the list you provided it. Before this would actualy return Object if you gave it the exact object type as part of the search moby-live/Perl/MOBY CommonSubs.pm,1.39,1.40 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.39 retrieving revision 1.40 diff -u -r1.39 -r1.40 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/30 20:21:30 1.40 @@ -1098,11 +1098,12 @@ my ($CENTRAL, $queryTerm, $termlist) = @_; return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); my %nodeLSIDs; + my $queryLSID = $CENTRAL->ObjLSID($queryTerm); foreach (@$termlist){ # get list of known LSIDs my $lsid = $CENTRAL->ObjLSID($_); - $nodeLSIDs{$lsid}=$_; + return ($_, $lsid) if ($lsid eq $queryLSID); # of course, if we find it in the list, then return it right away! + $nodeLSIDs{$lsid}=$_; } - my $queryLSID = $CENTRAL->ObjLSID($queryTerm); return (undef, undef) unless keys(%nodeLSIDs); my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble! From mwilkinson at pub.open-bio.org Mon Dec 1 19:23:23 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 1 Dec 2003 19:23:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312020023.hB20NNax021442@pub.open-bio.org> mwilkinson Mon Dec 1 19:23:23 EST 2003 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv21426/Perl Removed Files: MOBY.pm Log Message: lots of changes to allow registration of arbitrary SOAP services. MOBY Central expects such services to register their inputs and outputs as LSIDs. They can similarly be discovered using LSID's. A mix of MOBY and non-MOBY inputs and outputs is allowed, but has not been tested. The URL component of the registration is the URL to the WSDL document describing the service. moby-live/Perl MOBY.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/RCS/MOBY.pm,v: No such file or directory From mwilkinson at pub.open-bio.org Mon Dec 1 19:23:23 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 1 Dec 2003 19:23:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312020023.hB20NNC9021529@pub.open-bio.org> mwilkinson Mon Dec 1 19:23:23 EST 2003 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21426/Perl/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: lots of changes to allow registration of arbitrary SOAP services. MOBY Central expects such services to register their inputs and outputs as LSIDs. They can similarly be discovered using LSID's. A mix of MOBY and non-MOBY inputs and outputs is allowed, but has not been tested. The URL component of the registration is the URL to the WSDL document describing the service. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2003/07/04 16:12:37 1.11 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2003/12/02 00:23:23 1.12 @@ -23,7 +23,12 @@ } -my $C = MOBY::Client::Central->new(); +my $C = MOBY::Client::Central->new( +#Registries => { +# mobycentral => {URL => 'http://localhost/cgi-bin/MOBY-Central.pl', +# URI => 'http://localhost/MOBY/Central'} +# } +); #reg first object class From mwilkinson at pub.open-bio.org Mon Dec 1 19:23:23 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 1 Dec 2003 19:23:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312020023.hB20NNoQ021508@pub.open-bio.org> mwilkinson Mon Dec 1 19:23:23 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv21426/Perl/MOBY/Client Modified Files: Central.html Central.pm CollectionArticle.pm SimpleArticle.pm Log Message: lots of changes to allow registration of arbitrary SOAP services. MOBY Central expects such services to register their inputs and outputs as LSIDs. They can similarly be discovered using LSID's. A mix of MOBY and non-MOBY inputs and outputs is allowed, but has not been tested. The URL component of the registration is the URL to the WSDL document describing the service. moby-live/Perl/MOBY/Client Central.html,1.11,1.12 Central.pm,1.62,1.63 CollectionArticle.pm,1.5,1.6 SimpleArticle.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/10/22 14:29:09 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/02 00:23:23 1.12 @@ -409,7 +409,7 @@ Relationships => \@relationship_types (optional, 'all' if parameter is missing) Registry => $registry_name (optional) - expandRelationships (NOT YET IMPLEMENTED) + expandRelationships => [1/0] (optional)
Input XML :
<registerService>
- <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' ; currently only 'moby' services are fully supported -->
+ <Category>moby</Category> <!-- one of 'moby', 'cgi', 'wsdl' ; currently only 'moby' and 'wsdl' services are fully supported -->
<serviceName>YourServiceNameHere</serviceName>
<serviceType>TypeOntologyTerm</serviceType>
<authURI>your.URI.here</authURI>
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.113
retrieving revision 1.114
diff -u -r1.113 -r1.114
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/11/24 18:06:45 1.113
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 00:23:23 1.114
@@ -873,25 +873,27 @@
=over 2
-=item * in "moby" services, the input and output messaging structure is defined by the BioMOBY API, and the services use data Objects that are defined in the Class ontology as inheriting from the root "Object" Class. For "soap" services, there is additional flexibility:
+=item * in "moby" services, the input and output messaging structure is defined by the BioMOBY API, and the services use data Objects that are defined in the Class ontology as inheriting from the root "Object" Class.
+
+=item * For "soap" services, there is additional flexibility:
=over 2
-=item * Similar to a "moby" service, your "soap" service must consume/produce ontologically valid named data-types in order to be discovered by registry searches. As such, you _must_ register a single unique name for any non-MOBY input or output data Classes, regardless of the actual complexity of the input/output message.
+=item * Similar to a "moby" service, your "soap" service must consume/produce named data types. These are represented as LSID's
-=item * Do this using the registerObjectClass call of MOBY Central; To ensure uniqueness and LSID compatibilty of data class names, you must name your data using the following format: your.authURI:dataClassName
+=item * YOU DO NOT NEED TO REGISTER THESE DATA TYPES in MOBY Central; it is up to you what your LSID's represent, and MOBY Central WILL NOT try to resolve them!
-=item * remember, you may use any MOBY Object as your input/output (i.e. any Class Ontology term that inherits from Object) so long as you follow the MOBY message structure for that input or output.
+=item * You may mix ontologies when describing your service - i.e. you may freely use any MOBY Object as your input or (XOR) your output and use a non-MOBY object (LSID) for the alternate so long as you follow the MOBY message structure for the parameter that uses the MOBY Object
-=item * You may register, for example, a service that consumes a non-MOBY data Class and outputs a MOBY data class, so long as you follow the MOBY Messaging format for the output data
+=over 2
-=item * You may register, for example, a service that consumes a MOBY data Class and outputs a non-MOBY data class, so long as you follow the MOBY Messaging format for the ihput data
+=item * You may register, for example, a service that consumes a non-MOBY data Class and outputs a MOBY data class, so long as you follow the MOBY Messaging format for the output data
-=item * NOTE: Nether of the cases above are considred MOBY services, and are therefore described in the category of "soap" service
+=item * You may register, for example, a service that consumes a MOBY data Class and outputs a non-MOBY data class, so long as you follow the MOBY Messaging format for the input data
-=item * When registering a non-MOBY data Class name, it DOES NOT have any "Relationship" component (see registerObjectClass API)
+=item * NOTE: Nether of the cases above are considered MOBY services, and are therefore described in the category of "soap" service
-=item * non-MOBY inputs or outputs are described as a single Primary, Simple article of your new named type.
+=back
=back
@@ -903,6 +905,7 @@
=back
+=back
Input XML :
@@ -1079,17 +1082,18 @@
foreach (keys %objects_to_be_validated){
my ($valid, $message, $URI) = $OS->objectExists(term => $_);
- return &_error("$message","$URI") unless ($valid);
+ return &_error("$message","$URI") unless ($valid || (($_ =~ /urn:lsid/i) && !($_ =~ /urn:lsid:biomoby.org/i))); # either valid, or a non-moby LSID
}
- $debug && &_LOG("\n\n\aall objects okay\n");
+
+ $debug && &_LOG("\n\n\aall objects okay - either valid MOBY objects, or LSID's\n");
$OS = MOBY::OntologyServer->new(ontology => 'service');
my ($valid, $message, $URI) = $OS->serviceExists(term => $serviceType);
- return &_error("$message","$URI") unless ($valid);
+ print STDERR "\n\nChecking $URI\n\n";
+ return &_error("$message","$URI") unless ($valid || (($serviceType =~ /urn:lsid/i) && !($serviceType =~ /urn:lsid:biomoby.org/i))); # either valid, or a non-MOBY LSID
+ print STDERR "\n\nChecking $URI OK!!\n\n";
# right, registration should be successful now!
- # "soap" services may only have one input and one output
-
my $SVC = MOBY::service_instance->new(
category => $Category,
servicename => $serviceName,
@@ -1158,8 +1162,8 @@
($_->getNodeType == TEXT_NODE) && ($object_type = $_->toString);
}
my ($success, $message, $typeURI) = $OE->objectExists(term => $object_type);
- unless ($success) {
- $SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist");
+ if ((!($success) && ($object_type =~ /urn:lsid:biomoby.org/i)) || (!($success) && !($object_type =~ /urn:lsid/i))) { # if the object doesn't exist, and it isn't an LSID
+ $SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist, and is not an LSID");
} # kill it all unless this was successful!
my $namespace_string;
@@ -1169,10 +1173,11 @@
for (my $n = 0; $n<$num_ns;++$n) {
foreach my $name ($namespaces->item($n)->getChildNodes) {
if ($name->getNodeType == TEXT_NODE) {
- my ($success, $message, $URI) = $OE->namespaceExists(term => $name->toString);
- unless ($success) {
+ my $term = $name->toString;
+ my ($success, $message, $URI) = $OE->namespaceExists(term => $term);
+ if ((!($success) && ($term =~ /urn:lsid:biomoby.org/i)) || (!($success) && !($term =~ /urn:lsid/i))) { # if the object doesn't exist, and it isn't an LSID
$SVC->DELETE_THYSELF;
- return (-1,"namespace: " . $name->toString . " doesn't exist");
+ return (-1,"namespace: $term doesn't exist and is not an LSID");
}
$namespace_string .=$URI.",";
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/11/24 17:25:49 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30
@@ -171,9 +171,13 @@
my ($self, %args) = @_;
my $term = $args{term};
$term =~ s/^moby://; # if the term is namespaced, then remove that
-
- return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'object');
my $sth;
+ return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'object');
+
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objecttype/)){
+ return (1, "external ontology", $term);
+ }
+
if ($term =~ /^urn\:lsid/){
$sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?");
} else {
@@ -204,6 +208,10 @@
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objectclass/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -265,11 +273,15 @@
return (0, "WRONG ONTOLOGY",'') unless ($self->ontology eq 'object');
my $term = $args{term};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objectclass/)){
+ return (0, "can't delete from external ontology", $term);
+ }
+
my $LSID;
unless ($term =~ /urn\:lsid/){$LSID = $self->getObjectURI($term)} else {$LSID=$term}
return (0, q{Object type $term cannot be resolved to an LSID},"") unless $LSID;
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select object_id, object_lsid from object where object_type = ?},undef,$term);
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select object_id, object_lsid from object where object_lsid = ?},undef,$LSID);
# object1_id ISA object2_id?
my (@isa) = $self->dbh->selectrow_array(q{select * from object_term2term where object2_id = ?},undef, $id);
if (scalar @isa){
@@ -415,6 +427,10 @@
my $term = $args{term};
$term =~ s/^moby://; # if the term is namespaced, then remove that
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){
+ return (1, "external ontology", $term);
+ }
+
my $sth;
if ($term =~ /^urn\:lsid/){
$sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?");
@@ -446,6 +462,10 @@
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -475,11 +495,17 @@
my ($self, %args) = @_;
return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'service');
my $term = $args{term};
- my $LSID;
- unless ($term =~ /urn\:lsid/){$LSID = $self->getServiceURI($term)} else {$LSID=$term}
- return (0, q{Service type $term cannot be resolved to an LSID},"") unless $LSID;
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select service_id, service_lsid from service where service_type = ?},undef,$term);
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){
+ return (0, "can't delete from external ontology", $term);
+ }
+
+ my $LSID;
+ unless ($term =~ /^urn:lsid:biomoby.org:servicetype/){$LSID = $self->getServiceURI($term)} else {$LSID=$term}
+ return (0, q{Service type $term cannot be resolved to an LSID in the MOBY ontologies},"") unless $LSID;
+
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select service_id, service_lsid from service where service_lsid = ?}, undef, $LSID);
+
if (!defined $id){
return (0, q{Service type $term does not exist in the ontology},$lsid);
}
@@ -514,7 +540,11 @@
$term =~ s/^moby://; # if the term is namespaced, then remove that
my $sth;
- if ($term =~ /^urn\:lsid/){
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){
+ return (1, "external ontology", $term);
+ }
+
+ if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?");
} else {
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?");
@@ -540,10 +570,14 @@
#authority => $auth,
#contact_email => $email);
return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'namespace');
- return (0, "requires a object type node",'') unless ($args{node});
+ return (0, "requires a namespace type node",'') unless ($args{node});
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -575,8 +609,12 @@
my $LSID;
unless ($term =~ /urn\:lsid/){$LSID = $self->getNamespaceURI($term)} else {$LSID=$term}
return (0, q{Namespace type $term cannot be resolved to an LSID},"") unless $LSID;
+
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){
+ return (0, "cannot delete a term from an external ontology", $term);
+ }
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select namespace_id, namespace_lsid from namespace where namespace_type = ?},undef,$term);
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select namespace_id, namespace_lsid from namespace where namespace_lsid = ?},undef,$LSID);
unless ($id){return (0, q{Namespace type $term does not exist in the ontology},$lsid)}
# service1_id ISA service2_id?
@@ -839,7 +877,7 @@
sub setURI {
my ($self, $id) = @_;
my $URI;
- $id = lc($id);
+ # $id = lc($id);
if ($self->ontology eq 'object'){
$URI = "urn:lsid:biomoby.org:objectclass:$id"
} elsif ($self->ontology eq 'namespace'){
@@ -847,7 +885,7 @@
} elsif ($self->ontology eq 'service'){
$URI = "urn:lsid:biomoby.org:servicetype:$id"
} elsif ($self->ontology eq 'relationship'){
- $URI = "urn:lsid:biomoby.org:servicetype:$id"
+ $URI = "urn:lsid:biomoby.org:relationshiptype:$id"
} else {
$URI = 0
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2003/05/08 15:08:03 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2003/12/02 00:23:23 1.3
@@ -197,8 +197,8 @@
if ($self->service_type){
my $OE = MOBY::OntologyServer->new(ontology => 'service');
my ($success, $message, $servicetypeURI) = $OE->serviceExists(term => $self->service_type);
- unless ($success){return undef}
- $self->service_type_uri($servicetypeURI);
+ unless (($success || (($self->service_type =~ /urn:lsid/i) && !($self->service_type =~ /urn:lsid:biomoby.org/i)))){return undef}
+ ($self->service_type =~ /urn:lsid/)?$self->service_type_uri($self->service_type):$self->service_type_uri($servicetypeURI);
}
my ($serviceid, $category, $name, $typeURI, $authid,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist?
From mwilkinson at pub.open-bio.org Mon Dec 1 19:57:15 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 1 Dec 2003 19:57:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312020057.hB20vFsF021742@pub.open-bio.org>
mwilkinson
Mon Dec 1 19:57:15 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21719/MOBY
Modified Files:
Central.html Central.pm
Log Message:
I just remembered that Martin objected to me calling the non-MOBY services 'soap' services, so I now call them 'wsdl' services. Also fixed some more documentation errors, and fixed an error in the test suite.
moby-live/Perl/MOBY Central.html,1.10,1.11 Central.pm,1.114,1.115
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:23:23 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:57:15 1.11
@@ -27,7 +27,6 @@
...Registration Object...
-
Input XML :
-- <deregisterNamespace> - <namespaceType>MyNamespace</namespaceType> - </deregisterNamespace>-
Ouptut XML :
-...Registration Object...
--
input: listref; (articleName may be undef)
input =>[
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.63
retrieving revision 1.64
diff -u -r1.63 -r1.64
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:23:23 1.63
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:57:15 1.64
@@ -621,8 +621,8 @@
authURI => $authURI,
contactEmail => "your at mail.address",
description => $human_readable_description,
- category => "moby" | "cgi" | "soap" (currently only moby supported)
- URL => $URL_TO_SERVICE
+ category => "moby" | "cgi" | "wsdl" (currently only moby and wsdl supported)
+ URL => $URL_TO_SERVICE (or URL to WSDL document for wsdl-type services)
input: listref; (articleName may be undef)
input =>[
@@ -670,8 +670,8 @@
my $email = $a{contactEmail}; $email ||="";
my $URL = $a{URL}; $URL ||="";
my $desc = $a{description}; $desc ||="";
- my $Category = lc($a{Category}); $Category ||="moby";
- return $self->errorRegXML("Only MOBY Service Categories are currently allowed") unless ($Category eq 'moby');
+ my $Category = lc($a{category}); chomp $Category; $Category ||="";
+ return $self->errorRegXML("Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category") unless (($Category eq 'moby') || ($Category eq 'wsdl'));
return $self->errorRegXML("All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary") unless (
$name && $type && $authURI && $email && $URL && $desc && $Category);
@@ -685,7 +685,7 @@
$authURI
$email ";
- if ($Category eq "moby") {
+ if ($Category eq "moby" || $Category eq 'soap') {
my %SEC;
if ($a{'secondary'} && ref($a{'secondary'} =~ /hash/i)){
%SEC = %{$a{secondary}}
@@ -778,7 +778,7 @@
}
$message .= "\n";
$message .= "";
- } else { return $self->errorRegXML("cannot register services with a client initialized with multiple registries")}
+ } else { return $self->errorRegXML("only 'moby' and 'wsdl' service types are allowed to be registered at this time.")}
#elsif ($Category eq "cgi") {
# my $IN = $a{input};
From mwilkinson at pub.open-bio.org Mon Dec 1 20:08:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 1 Dec 2003 20:08:24 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312020108.hB218O1t021842@pub.open-bio.org>
mwilkinson
Mon Dec 1 20:08:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21819/Perl/MOBY
Modified Files:
Central.html Central.pm
Log Message:
still calling Collection articles 'Complex' articles. This is confusing. It is now consistent thorughout the documentation
moby-live/Perl/MOBY Central.html,1.11,1.12 Central.pm,1.115,1.116
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:57:15 1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 01:08:24 1.12
@@ -304,12 +304,10 @@
Input XML :
@@ -372,13 +378,13 @@
human readable COMPREHENSIVE description of your service]]>
</Description>
<Input>
- <!-- zero or more Primary (Simple and/or Complex) articles -->
+ <!-- zero or more Primary (Simple and/or Collection) articles -->
</Input>
<secondaryArticles>
<!-- zero or more INPUT Secondary articles -->
</secondaryArticles>
<Output>
- <!-- zero or more Primary (Simple and/or Complex) articles -->
+ <!-- zero or more Primary (Simple and/or Collection) articles -->
</Output>
</registerService>
@@ -553,10 +559,10 @@
<contactEmail>your at email.address</contactEmail>
<URL>http://endpoint.of.service</URL>;
<Input>
- <!-- one or more Simple and/or Complex Primary articles -->
+ <!-- one or more Simple and/or Collection Primary articles -->
</Input>
<Output>
- <!-- one or more Simple and/or Complex Primary articles -->
+ <!-- one or more Simple and/or Collection Primary articles -->
</Output>
<secondaryArticles>
<!-- one or more Secondary articles -->
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.115
retrieving revision 1.116
diff -u -r1.115 -r1.116
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 00:57:15 1.115
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 01:08:24 1.116
@@ -905,13 +905,13 @@
human readable COMPREHENSIVE description of your service]]>
-
+
@@ -1019,13 +1019,12 @@
# http://URL.to.your/CGI.pl
# your.URI.here
#
-#
+#
#
#
#
-#
#
#
@@ -1119,7 +1118,7 @@
my $dbh = $SVC->dbh;
return (-1,'Bad node') unless $node->getNodeType == ELEMENT_NODE;
- # this is a Simple or a Complex object
+ # this is a Simple or a Collection object
my $simp_coll = $node->getTagName;
$debug && &_LOG("TAGNAME in $inout _registerArticle is $simp_coll");
@@ -1431,10 +1430,10 @@
your at email.address
http://endpoint.of.service
-
+
From mwilkinson at pub.open-bio.org Tue Dec 9 16:06:51 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:06:51 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092106.hB9L6pJU028188@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:06:51 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28169/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
added a generic server-side parser to CommonSubs that should basically do all of the work for you and be compatible with the 0.6 API. Not yet documented; just testing on my own services first.
moby-live/Perl/MOBY CommonSubs.pm,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/12 16:47:16 1.28
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:06:51 1.29
@@ -143,9 +143,17 @@
use XML::DOM;
use MOBY::CrossReference;
use MOBY::Client::OntologyServer;
+use strict;
+use warnings;
- at ISA = qw(Exporter);
- at EXPORT_OK = qw(
+use constant COLLECTION => 1;
+use constant SIMPLE => 2;
+use constant BE_NICE => 1;
+use constant BE_STRICT => 0;
+
+our @ISA = qw(Exporter);
+our @EXPORT = qw(COLLECTION SIMPLE BE_NICE BE_STRICT);
+our @EXPORT_OK = qw(
getSimpleArticleIDs
getSimpleArticleNamespaceURI
simpleResponse
@@ -165,8 +173,13 @@
extractResponseArticles
getResponseArticles
getCrossReferences
+ genericServiceInputParser
+ COLLECTION
+ SIMPLE
+ BE_NICE
+ BE_STRICT
);
-%EXPORT_TAGS =(all => [qw(
+our %EXPORT_TAGS =(all => [qw(
getSimpleArticleIDs
getSimpleArticleNamespaceURI
simpleResponse
@@ -186,9 +199,39 @@
extractResponseArticles
getResponseArticles
getCrossReferences
+ genericServiceInputParser
+ COLLECTION
+ SIMPLE
+ BE_NICE
+ BE_STRICT
)]);
+
+sub genericServiceInputParser {
+ my ($message, $namespaces) = @_; # get the incoming MOBY query XML
+ my @inputs; # set empty response
+ my @queries = getInputs($message); # returns XML::DOM nodes
+
+ foreach my $query(@queries){
+ my $queryID = getInputID($query); # get the queryID attribute of the queryInput
+ my @input_articles = getArticles($query); # get the Simple/Collection articles making up this query
+ foreach my $input(@input_articles){ # input is a listref
+ my ($articleName, $article) = @{$input}; # get the named article
+ my $simple = isSimpleArticle($article); # articles may be simple or collection
+ my $collection = isCollectionArticle($article);
+ if ($collection){
+ my @simples = getCollectedSimples($article);
+ push @inputs, [COLLECTION,$queryID, \@simples];
+
+ } elsif ($simple){
+ push @inputs, [SIMPLE,$queryID,$simple];
+ }
+ }
+ }
+ return @inputs;
+}
+
#################################################
##################################
##################################
@@ -482,7 +525,7 @@
sub getInputs {
my ($XML) = @_;
-
+ my $moby;
unless (ref($XML) =~ /XML\:\:DOM/){
my $parser = new XML::DOM::Parser;
my $doc = $parser->parse($XML);
@@ -573,7 +616,7 @@
return undef unless $moby->getNodeType == ELEMENT_NODE;
return undef unless ($moby->getTagName =~ /queryInput/ || $moby->getTagName =~ /queryResponse/);
my @articles;
- foreach $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
+ foreach my $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
next unless $child->getNodeType == ELEMENT_NODE; # ignore whitespace
next unless ($child->getTagName =~ /Simple/ || $child->getTagName =~ /Collection/);
my $articleName = $child->getAttribute('articleName');
@@ -608,7 +651,7 @@
return undef unless ($moby->getTagName =~ /Collection/);
my @articles;
- foreach $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
+ foreach my $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
next unless $child->getNodeType == ELEMENT_NODE; # ignore whitespace
next unless ($child->getTagName =~ /Simple/);
push @articles, $child; # take the child elements, which are
$term
$def
")
} else {
- $response .= simpleResponse("")
+ $MOBY_RESPONSE .= simpleResponse("")
}
}
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
From mwilkinson at pub.open-bio.org Tue Dec 9 16:23:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:23:24 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092123.hB9LNOTl028369@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:23:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28350/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
dumb dumb dumb dumb
moby-live/Perl/MOBY CommonSubs.pm,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:06:51 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:23:24 1.30
@@ -209,7 +209,7 @@
sub genericServiceInputParser {
- my ($message, $namespaces) = @_; # get the incoming MOBY query XML
+ my ($message) = @_; # get the incoming MOBY query XML
my @inputs; # set empty response
my @queries = getInputs($message); # returns XML::DOM nodes
@@ -225,7 +225,7 @@
push @inputs, [COLLECTION,$queryID, \@simples];
} elsif ($simple){
- push @inputs, [SIMPLE,$queryID,$simple];
+ push @inputs, [SIMPLE,$queryID,$article];
}
}
}
From mwilkinson at pub.open-bio.org Tue Dec 9 16:30:33 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:30:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092130.hB9LUXWW028465@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:30:33 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28446/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
dumb dumb dumb dumb
moby-live/Perl/MOBY CommonSubs.pm,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:23:24 1.30
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:30:33 1.31
@@ -168,6 +168,7 @@
extractRawContent
collectionResponse
validateNamespaces
+ validateThisNamespace
isSimpleArticle
isCollectionArticle
extractResponseArticles
@@ -194,6 +195,7 @@
extractRawContent
collectionResponse
validateNamespaces
+ validateThisNamespace
isSimpleArticle
isCollectionArticle
extractResponseArticles
From mwilkinson at pub.open-bio.org Tue Dec 9 16:38:39 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:38:39 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092138.hB9LcdU5028578@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:38:39 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28559/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
initialize possibly undef values
moby-live/Perl/MOBY CommonSubs.pm,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:30:33 1.31
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:38:39 1.32
@@ -370,8 +370,12 @@
sub simpleResponse {
my ($data, $articleName, $qID) = @_; # articleName optional
- $data ||='';
$qID = &_getQueryID($qID) if ref($qID) =~ /XML::DOM/; # in case they send the DOM instead of the ID
+
+ $data ||=''; # initialize to avoid uninit value errors
+ $qID ||="";
+ $articleName ||="";
+
if ($articleName) {
return "
From mwilkinson at pub.open-bio.org Tue Dec 9 17:24:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 17:24:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092224.hB9MO3AB028801@pub.open-bio.org>
mwilkinson
Tue Dec 9 17:24:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv28763/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
updating my GO services to be 0.6 compliant and a bit more readable
moby-live/Perl/scripts/Services LocalServices.pm,1.37,1.38
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -u -r1.37 -r1.38
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/09 21:06:51 1.37
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/09 22:24:03 1.38
@@ -10,6 +10,7 @@
use SOAP::Lite;
use DBI;
use DBD::mysql;
+use GO::AppHandle;
use MIME::Base64;
use XML::DOM;
use MOBY::Client::OntologyServer;
@@ -24,85 +25,60 @@
#getNodeContentWithArticle
use vars qw(@ISA);
- at ISA = qw(SOAP::Server::Parameters); # uncomment this line if you want access to the SOM as the
- # last parameter passed to the subroutine
sub getGoTerm {
my ($caller, $message) = @_;
my $MOBY_RESPONSE;
- my (@inputs)= genericServiceInputParser($message, []); # ([SIMPLE, $queryID, $simple],...)
+ my (@inputs)= genericServiceInputParser($message); # ([SIMPLE, $queryID, $simple],...)
return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- my @validNS = validateNamespaces(); # ONLY do this if you are intending to be namespace aware!
+ my @validNS = validateNamespaces("GO"); # ONLY do this if you are intending to be namespace aware!
+
+ my $dbh = _dbAccess('go');
+ die "can't connect to GO database\n" unless $dbh;
+ my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
- my @accessions;
foreach (@inputs){
my ($articleType, $ID, $input) = @{$_};
unless ($articleType == SIMPLE){
- $MOBY_RESPONSE .= simpleResponse("", "", $ID) ;
+ $MOBY_RESPONSE .= simpleResponse("", "Collection_Article_Not_allowed_as_input", $ID);
next;
} else {
my $ns = getSimpleArticleNamespaceURI($input);
- ((push @accessions, undef) && (next)) unless validateThisNamespace($ns, @validNS);
- push @accessions, defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):1;
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $accession = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ unless (defined($accession)){
+ $MOBY_RESPONSE .= simpleResponse("", "Invalid_Accession", $ID);
+ next;
+ }
+ unless ($accession =~/^GO:/){
+ $accession = "GO:$accession"; # we still haven't decided on whether id's should include the prefix...
+ }
+ $sth->execute($accession);
+ my ($term, $def) = $sth->fetchrow_array;
+ if ($term){
+ $MOBY_RESPONSE .= simpleResponse("
+
+ $term
+ $def
+ ", "GO_Term_From_ID", $ID)
+ } else {
+ $MOBY_RESPONSE .= simpleResponse("", "NO_Term_Found", $ID)
+ }
}
}
- my $dbh = _dbAccess('go');
- die "can't connect to GO database\n" unless $dbh;
- my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
- foreach my $acc(@accessions){
- unless ($acc =~/^GO:/){
- $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
- }
- $sth->execute($acc);
- my ($term, $def) = $sth->fetchrow_array;
- if ($term){
- $MOBY_RESPONSE .= simpleResponse("
-
- $term
- $def
- ")
- } else {
- $MOBY_RESPONSE .= simpleResponse("")
- }
- }
return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
-
sub getGoTermAssociations {
+ my ($caller, $message) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($message); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- my $SOM = pop;
- my ($self, $data) = @_;
- my $response = "";
- my @accessions;
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'GO');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace GO does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data);
- foreach (@input_nodes){
- my ($input) = @{$_}; # this service only allows one input per query, so take the first
- my $ns = getSimpleArticleNamespaceURI($input);
- push @accessions, undef unless $ns eq $VALID_NAMESPACE; # if we have been sent an invalid namespace, then stack an undef as a response
- my ($id) = getSimpleArticleIDs($ns, [$input]);
- if (defined $id){
- push @accessions, $id;
- } else {
- push @accessions, undef;
- }
- }
-
- use DBI;
- use DBD::mysql;
my $dbh = _dbAccess('go');
- die "can't connecvt to database\n" unless $dbh;
+ die "can't connect to database\n" unless $dbh;
my $sth = $dbh->prepare("
select
gp.symbol,
@@ -125,27 +101,39 @@
and a.is_not = 0
and t.id = d.term_id
order by species_id");
-
- foreach my $acc(@accessions){
- unless ($acc =~/^GO:/){
- $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
- }
- my @simples;
- $sth->execute($acc);
- while (my ($symb, $sp, $namsp, $type, $name, $def) = $sth->fetchrow_array){
- my $response_data .= "\n";
- push @simples, $response_data;
+
+ my @validNS = validateNamespaces("GO"); # ONLY do this if you are intending to be namespace aware!
+
+ foreach (@inputs){
+ my ($articleType, $ID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= collectionResponse([], "Collection_Article_Input_Invalid", $ID) ;
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= $MOBY_RESPONSE .= collectionResponse([], "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $acc, defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ unless (defined($acc)){
+ $MOBY_RESPONSE .= collectionResponse([], "Invalid_Accession", $ID);
+ next;
+ }
+ unless ($acc =~/^GO:/){
+ $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
+ }
+ my @simples;
+ $sth->execute($acc);
+ while (my ($symb, $sp, $namsp, $type, $name, $def) = $sth->fetchrow_array){
+ my $response_data .= "\n";
+ push @simples, $response_data;
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples,"Known_GO_Term_Associations",$ID); # after all images have been collected, create the collection
}
- $response .= collectionResponse(\@simples); # after all images have been collected, create the collection
}
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
@@ -153,67 +141,51 @@
sub RetrieveGOFromKeywords {
my $SOM = pop;
my ($self, $query) = @_;
- use GO::AppHandle;
-
- my $ua = new LWP::UserAgent;
- my $req = new HTTP::Request GET => 'http://www.godatabase.org/dev/database/server.cfg';
- my $res = $ua->request($req);
+ # INITIALIZE CONNECTION TO GO DB
my $host; my $dbname;
$host = "sin.lbl.gov";
$dbname = "go";
-# if ($res->is_success) {
- # my $resp = $res->content;
- # if ($resp =~ /(\w+)\@(\S+)/){
- # $host = $2;
- # $dbname= $1;
- # } else {
- # return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- # }
- #}
my %connect_hash;
$connect_hash{-dbname}=$dbname;
$connect_hash{-dbhost}=$host;
-
my $GO_API = GO::AppHandle->connect(%connect_hash);
unless ($GO_API){
return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
}
+ # DB is now initialized
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'Global_Keyword');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace Global_Keyword does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($query); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- # now start analyzing the input data
- my @input_nodes = getInputArticles($query); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my $response;
- foreach (@input_nodes){
- my $input = $_->[0]; # we only allow one input object per query
- my ($kw) = getSimpleArticleIDs($VALID_NAMESPACE, [$input]);
- ($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
- my @terms = @{$GO_API->get_terms({search=>"$kw"})};
- next unless($terms[0]);
- my @simples;
- foreach my $term(@terms){
- my $acc = $term->public_acc;
- my $def = $term->definition;
- my $name = $term->name;
- push @simples, "
-
-
- $name
- $def
- ";
+ my @validNS = validateNamespaces("Global_Keyword"); # ONLY do this if you are intending to be namespace aware!
+ foreach (@inputs){
+ my ($articleType, $ID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= collectionResponse([], "Collection_Input_Invalid", $ID) ;
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= collectionResponse([], "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $kw = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ ($MOBY_RESPONSE .= collectionResponse([], "No_Keyword", $ID) && (next)) unless defined $kw;
+ ($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
+ my @terms = @{$GO_API->get_terms({search=>"$kw"})};
+ next unless($terms[0]);
+ my @simples;
+ foreach my $term(@terms){
+ my $acc = $term->public_acc;
+ my $def = $term->definition;
+ my $name = $term->name;
+ push @simples, "
+ $name
+ $def
+ ";
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples, "GO_terms_from_keywords", $ID);
}
- $response .= collectionResponse(\@simples);
- }
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ }
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
From mwilkinson at pub.open-bio.org Tue Dec 9 17:24:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 17:24:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092224.hB9MO30d028782@pub.open-bio.org>
mwilkinson
Tue Dec 9 17:24:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28763/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
updating my GO services to be 0.6 compliant and a bit more readable
moby-live/Perl/MOBY CommonSubs.pm,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:38:39 1.32
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 22:24:03 1.33
@@ -248,16 +248,16 @@
function : to get the IDs of simple articles that are in the given namespace
usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
args : (in order)
- $Namespace - (required) a namespace stringfrom the MOBY namespace ontology
+ $Namespace - (required) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care
\@Simples - (required) a listref of Simple XML::DOM nodes
i.e. the XML::DOM representing an XML structure like this:
- note : it will return *only* the ids that are in the given namespace
+ note : it will return *only* the ids that are in the given namespace, if you provide one
but since you are required to return an output for every input
(even if it is invalid) this routine will return undef for
- those articles that are not in that namespace
+ those articles in the list that are not in that namespace so you can keep track
=cut
@@ -271,45 +271,52 @@
my @input_nodes = @{$input_nodes};
my $OS = MOBY::Client::OntologyServer->new;
my ($s, $m);
- ($s, $m, $desired_namespace) = $OS->namespaceExists(term => $desired_namespace); # returns (success, message, lsid)
- return undef unless $s; # bail if not successful
+ if ($desired_namespace){
+ ($s, $m, $desired_namespace) = $OS->namespaceExists(term => $desired_namespace); # returns (success, message, lsid)
+ unless ($s){ # bail if not successful
+ print STDERR "MOBY::CommonSubs WARNING ** the namespace $desired_namespace does not exist in the MOBY ontology, and is not a valid LSID\n";
+ return undef;
+ }
+ }
- my @accessions;
+ my @ids;
foreach my $in(@input_nodes){
#$in = "
- note : it will return *only* the ids that are in the given namespace, if you provide one
- but since you are required to return an output for every input
- (even if it is invalid) this routine will return undef for
- those articles in the list that are not in that namespace so you can keep track
+ note : If you provide a namespace, it will return *only* the ids that are in the given namespace,
+ but will return 'undef' for any articles in the WRONG namespace so that you get an
+ equivalent number of outputs to inputs.
+
+ Note that if you call this with a single argument, this is assumed to
+ be \@Articles, so you will get ALL id's regardless of namespace!
=cut
sub getSimpleArticleIDs {
my ($desired_namespace, $input_nodes) = @_;
- return undef unless $input_nodes;
+ if ($desired_namespace && !($input_nodes)){ # if called with ONE argument, then these are the input nodes!
+ $input_nodes = $desired_namespace;
+ $desired_namespace = undef;
+ }
$input_nodes = [$input_nodes] unless ref($input_nodes) =~ /ARRAY/; # be flexible!
return undef unless scalar @{$input_nodes};
@@ -281,6 +286,7 @@
my @ids;
foreach my $in(@input_nodes){
+ next unless $in;
#$in = "
+
+
+
+ ";
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my $gb = SHoundGetGenBankff($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
+ $MOBY_RESPONSE .= "
+
+
+
+ ";
+ }
}
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $response .= simpleResponse("
-
- $length
- ");
- } else {
- $response .= simpleResponse("");
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+}
+
+sub GenbankAccVirtualSequenceRetrieve {
+ my ($self, $data) = @_;
+
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ (($MOBY_RESPONSE .= simpleResponse("", "no_input_object", $qID)) && (next)) unless (defined $input);
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse([], "Invalid_Namespace", $qID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my ($acc) = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ ($MOBY_RESPONSE .= collectionResponse([], "No_Accession_provided", $qID) && (next)) unless defined $acc;
+ use Bio::DB::GenBank;
+ my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
+ my $seq = $gb->get_Seq_by_acc($acc);
+ my $length;
+ if ($seq){$length = $seq->length;}
+ if ($length){
+ $MOBY_RESPONSE .= simpleResponse("
+
+ $length
+ ", "", $qID);
+ } else {
+ $MOBY_RESPONSE .= simpleResponse("", "sequence_has_no_length", $qID);
+ }
}
}
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
+
sub GenbankAccSequenceRetrieve {
my ($self, $data) = @_;
my $response; my @accessions;
From mwilkinson at pub.open-bio.org Wed Dec 10 17:34:36 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 10 Dec 2003 17:34:36 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102234.hBAMYaZc032738@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:34:36 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv32719/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
small changes to service output
moby-live/Perl/scripts/Services LocalServices.pm,1.41,1.42
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:22:03 1.41
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:34:36 1.42
@@ -70,7 +70,7 @@
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub getGoTermAssociations {
@@ -135,7 +135,7 @@
$MOBY_RESPONSE .= collectionResponse(\@simples,"Known_GO_Term_Associations",$ID); # after all images have been collected, create the collection
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -187,7 +187,7 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "GO_terms_from_keywords", $ID);
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -223,7 +223,7 @@
# do your thing here!
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub MOBYSHoundGetGenBankff {
@@ -281,8 +281,8 @@
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ #print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub GenbankAccVirtualSequenceRetrieve {
From mwilkinson at pub.open-bio.org Wed Dec 10 17:40:57 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 10 Dec 2003 17:40:57 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102240.hBAMevNm000374@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:40:56 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv355/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
Doh. Use the output format you dummy
moby-live/Perl/scripts/Services LocalServices.pm,1.42,1.43
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:34:36 1.42
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:40:56 1.43
@@ -262,21 +262,23 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+ $MOBY_RESPONSE .= simpleResponse("
- ";
+ ",
+ "", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+ $MOBY_RESPONSE .= simpleResponse("
- ";
+ ",
+ "", $qID);
}
}
}
From mwilkinson at pub.open-bio.org Wed Dec 10 17:45:12 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 10 Dec 2003 17:45:12 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102245.hBAMjCKF000512@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:45:12 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv493/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
missed one
moby-live/Perl/scripts/Services LocalServices.pm,1.43,1.44
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -u -r1.43 -r1.44
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:40:56 1.43
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:45:11 1.44
@@ -256,7 +256,7 @@
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my $gb = SHoundGetGenBankff($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+
+
+
+ ",
+ "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my $gb = SHoundGetGenBankff($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ",
+ "", $qID);
+ }
+ }
}
+ $aa = SHoundFini();
+ #print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
-sub MOBYSHoundGetGenBankff {
+sub _makeSeqObj {
+ my ($id) = @_;
+ my $gb = SHoundGetGenBankff($id);
+ return undef unless $gb;
+ my $gbio = IO::String->new($gb);
+ my $sio = Bio::SeqIO->new(-fh => \*$gbio, '-format' => 'genbank');
+ my $seq = $sio->next_seq;
+ return ($seq, $seq->length, $seq->seq);
+}
+
+sub MOBYSHoundGetGenBankVirtSequence {
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
@@ -254,30 +345,167 @@
my ($identifier) = getSimpleArticleIDs($input);
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
- my $gb = SHoundGetGenBankff($identifier);
+ my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+ ".($SEQ->length)."
+ ", "", $qID);
+ } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ my $gi = SHoundFindAcc($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ".($SEQ->length)."
+ ",
+ "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ".($SEQ->length)."
+ ",
+ "", $qID);
+ }
+ }
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub MOBYSHoundGetGenBankWhateverSequence {
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+
+ my %objtype = ('dna', "DNASequence", 'rna', "RNASequence", 'protein', "AminoAcidSequence");
+
+ my $aa = SHoundInit("TRUE", "MOBY_SHoundGetGenBankff_Service"); # initialize SeqHound
+ $aa = SHoundIsInited(); # confirm initialization
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter) unless $aa eq "TRUE";
+
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my %validNS;
+ foreach (qw(NCBI_Acc NCBI_gi PIR Swiss-Prot EMBL PDB)){
+ my ($valid) = validateNamespaces($_); # we are going to ignore anything that is invalid
+ $validNS{$_} = $valid;
+ }
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && (defined($input))){ # we only accept simple inputs to this service
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send back a blank response for this queryID
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $qID)) && next) unless validateThisNamespace($ns, values(%validNS)); # return blank if they have sent us a namespace we don't understand
+ my ($identifier) = getSimpleArticleIDs($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
+ if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
+ my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ my $objType = $objtype{$SEQ->alphabet};
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$identifier'>
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ my $gi = SHoundFindAcc($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my $objType = $objtype{$SEQ->alphabet};
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
+
+
+
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my $objType = $objtype{$SEQ->alphabet};
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
+
+
+
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ }
+ }
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub MOBYSHoundGetGenBankFasta {
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+
+ my $aa = SHoundInit("TRUE", "MOBY_SHoundGetGenBankff_Service"); # initialize SeqHound
+ $aa = SHoundIsInited(); # confirm initialization
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter) unless $aa eq "TRUE";
+
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my %validNS;
+ foreach (qw(NCBI_Acc NCBI_gi PIR Swiss-Prot EMBL PDB)){
+ my ($valid) = validateNamespaces($_); # we are going to ignore anything that is invalid
+ $validNS{$_} = $valid;
+ }
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && (defined($input))){ # we only accept simple inputs to this service
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send back a blank response for this queryID
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $qID)) && next) unless validateThisNamespace($ns, values(%validNS)); # return blank if they have sent us a namespace we don't understand
+ my ($identifier) = getSimpleArticleIDs($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
+
+ if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
+ my $gb = SHoundGetFasta($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("
+ $MOBY_RESPONSE .= simpleResponse("
- ",
+ ",
"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
- my $gb = SHoundGetGenBankff($gi);
+ my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("
+ $MOBY_RESPONSE .= simpleResponse("
- ",
+ ",
"", $qID);
}
}
@@ -287,6 +515,7 @@
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
+
sub GenbankAccVirtualSequenceRetrieve {
my ($self, $data) = @_;
From mwilkinson at pub.open-bio.org Thu Dec 11 13:08:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 11 Dec 2003 13:08:14 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312111808.hBBI8EdB004309@pub.open-bio.org>
mwilkinson
Thu Dec 11 13:08:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv4290
Modified Files:
MOBY-Client05.cgi
Log Message:
added Xrefs to my new services. Small change in the client program to improve readability
moby-live/Perl/scripts MOBY-Client05.cgi,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi 2003/11/06 16:42:41 1.25
+++ /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi 2003/12/11 18:08:14 1.26
@@ -1,6 +1,6 @@
#!/usr/bin/perl -w
use strict;
-use lib '/usr/local/apache/cgi-bin/MOBY05';
+use lib '/usr/local/apache/cgi-bin/BIO/moby-live/Perl';
use MOBY::Client::Central;
use MOBY::Client::Service;
@@ -466,11 +466,15 @@
my $output = "(";
foreach my $param(@{$objs}){
if ($param->isSimple){
- $output .= "Simple:".($param->objectType)." ,";
+ my $type = (($param->objectType =~ /\:(\S+)$/) && $1);
+ $type = $param->objectType unless $type;
+ $output .= "Simple: $type ,";
} else {
$output .= "Collection:[";
foreach my $simp(@{$param->Simples}){
- $output .= ($simp->objectType).",";
+ my $type = (($simp->objectType =~ /\:(\S+)$/) && $1);
+ $type = $simp->objectType unless $type;
+ $output .= "$type,";
}
chop $output;
$output .="],";
From mwilkinson at pub.open-bio.org Thu Dec 11 13:08:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 11 Dec 2003 13:08:14 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312111808.hBBI8EFh004328@pub.open-bio.org>
mwilkinson
Thu Dec 11 13:08:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv4290/Services
Modified Files:
LocalServices.pm
Log Message:
added Xrefs to my new services. Small change in the client program to improve readability
moby-live/Perl/scripts/Services LocalServices.pm,1.45,1.46
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 15:36:38 1.45
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:08:14 1.46
@@ -9,6 +9,7 @@
use strict;
use SeqHound;
use SOAP::Lite;
+use Bio::SeqIO;
use DBI;
use DBD::mysql;
use GO::AppHandle;
@@ -317,6 +318,16 @@
return ($seq, $seq->length, $seq->seq);
}
+sub _getXrefs {
+ my ($seq) = @_; # bioperl seq object
+ #my $gi = $seq->primary_id; # e.g. 163483
+ #print STDERR "\n\n*********************$ gi\n\n";
+ my $acc = $seq->accession; # e.g. A123434
+ my $kw = $seq->species->binomial; # e.g. mus musculus
+ my $taxon = $seq->species->ncbi_taxid; # e.g. 1234
+ return ($acc, $kw, $taxon);
+}
+
sub MOBYSHoundGetGenBankVirtSequence {
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
@@ -346,39 +357,53 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
- (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("
- ".($SEQ->length)."
- ", "", $qID);
+
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .=" \n".($SEQ->length)."
+
-
-
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
- ".($SEQ->length)."
- ",
- "", $qID);
+ ".($SEQ->length)."
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("
-
-
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
- ".($SEQ->length)."
- ",
- "", $qID);
+ ".($SEQ->length)."
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
}
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+# print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -413,43 +438,59 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$identifier'>
- ".($SEQ->length)."
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .=" \n".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
} elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
-
-
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
-
-
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
}
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+# print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -516,335 +557,6 @@
}
-sub GenbankAccVirtualSequenceRetrieve {
- my ($self, $data) = @_;
-
- my $MOBY_RESPONSE;
- my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
-
- my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
-
- foreach (@inputs){
- my ($articleType, $qID, $input) = @{$_};
- unless ($articleType == SIMPLE){
- $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
- next;
- } else {
- (($MOBY_RESPONSE .= simpleResponse("", "no_input_object", $qID)) && (next)) unless (defined $input);
- my $ns = getSimpleArticleNamespaceURI($input);
- (($MOBY_RESPONSE .= simpleResponse([], "Invalid_Namespace", $qID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
- my ($acc) = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
- ($MOBY_RESPONSE .= collectionResponse([], "No_Accession_provided", $qID) && (next)) unless defined $acc;
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $MOBY_RESPONSE .= simpleResponse("
-
- $length
- ", "", $qID);
- } else {
- $MOBY_RESPONSE .= simpleResponse("", "sequence_has_no_length", $qID);
- }
- }
- }
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
-}
-
-sub GenbankAccSequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_Acc');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;my $sequence;
- if ($seq){$length = $seq->length;$sequence = $seq->seq}
- if ($length){
- $response .= simpleResponse("
-
- $length
- $sequence
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-}
-sub GenbankGIVirtualSequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_gi');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_gi($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $response .= simpleResponse("
-
- $length
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-}
-
-sub GenbankGISequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_gi');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_gi($acc); # get the sequence object for each gi
- my $length;my $sequence;
- if ($seq){$length = $seq->length;$sequence = $seq->seq} # if it exists, get the length and sequence
- if ($length){ # and construct the response
- $response .= simpleResponse("
-
- $length
- $sequence
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse;
-}
-#=================================================
-#=================================================
-#=================================================
-
-sub GenbankCompleteSequenceRetrieve {
-
-# this service is registered as consuming NCBI_Acc OR NCBI_gi
-# and producing GenericSequence objects. However, it will
-# actually produce DNA, RNA or PRotein objects, as appropriate
-# and will produce a cross-reference block as well
-
- my ($self, $data) = @_;
- my $response; my @gis;
-
- my ($GB_Acc_LSID, $GB_gi_LSID) = validateNamespaces('NCBI_Acc', 'NCBI_gi');
- unless ($GB_Acc_LSID && $GB_gi_LSID){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc or NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- foreach my $node(@inputs){
-
- my $namespace_LSID = getSimpleArticleNamespaceURI($node); # get the LSID of the namespace for this input object
- unless (($namespace_LSID eq $GB_Acc_LSID) || ($namespace_LSID eq $GB_gi_LSID)){ # validate the namespace
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if bad namespace
- next;
- }
-
- my ($ID)= getSimpleArticleIDs($namespace_LSID, [$node]); # get the ID within this namespace
- unless (defined $ID){ # send a blank if we failed to get an id,
- $response .= simpleResponse(""); # because we have to send one response per input
- next;
- }
-
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string'); # now that we have a namespace and ID, we are ready to retrieve
- my $seq;
- if ($namespace_LSID eq $GB_Acc_LSID){ # if the namespace is a genbank Accession thebn
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the accession
- } elsif ($namespace_LSID eq $GB_gi_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_gi($ID); # get the sequence object for the gi
- } else {
- $response .= simpleResponse(""); # if it is neither,then send a blank as required by the API
- next;
- }
-
- my $length;my $sequence;
- if ($seq){
- $length = $seq->length;$sequence = $seq->seq; # if it exists, get the length and sequence
- } else {
- $response .= simpleResponse(""); # if we got nada, then send a blank as required
- next;
- }
-
- my $gi = $seq->primary_id; # e.g. 163483
- my $acc = $seq->accession; # e.g. A123434
- my $kw = $seq->species->binomial; # e.g. mus musculus
- my $moltype = $seq->alphabet; # 'dna', 'rna', 'protein'
- my $taxon = $seq->species->ncbi_taxid; # e.g. 1234
-
- my $ObjectType="GenericSequence"; # set it as the generic as default
- if ($moltype eq 'dna'){$ObjectType = "DNASequence"} # set to DNA
- elsif ($moltype eq 'rna'){$ObjectType = "RNASequence"} # set to RNA
- elsif ($moltype eq 'protein'){$ObjectType = "AminoAcidSequence"} # set to Protein
-
- if ($length){ # and construct the response; luckily, all of these objects have exactly the same structure :-)
- my $tempresponse .= "
-
- ";
- if ($taxon){ $tempresponse .=""}
- if ($kw){$tempresponse .=""}
- if ($acc && !($namespace_LSID eq $GB_Acc_LSID)){$tempresponse .=""}
- if ($gi && !($namespace_LSID eq $GB_gi_LSID)){$tempresponse .=""}
- $tempresponse .="
- $length
- $sequence
- ";
- $response .= simpleResponse($tempresponse);
- } else {
- $response .= simpleResponse(""); # if we failed to get a sequence length, then something weird happened, so just ignore it
- }
- }
- my $fullresponse = responseHeader() . $response . responseFooter(); # add the headers and footers
- my $SOAPResponse = SOAP::Data->type('base64' => $fullresponse); # base 64 encode it (optional)
- return $SOAPResponse;
-}
-
-
-sub GenbankRecordRetrieve {
- use Bio::SeqIO;
- use IO::String;
- my ($self, $data) = @_;
- my $response; # prepare a variable to hold the responses
-
- # Step 1 - validate the namespaces you plan to accept as input
- my ($GB_Acc_LSID, $GB_gi_LSID, $EMBL_LSID) = validateNamespaces('NCBI_Acc', 'NCBI_gi', 'EMBL');
- unless ($GB_Acc_LSID && $GB_gi_LSID && $EMBL_LSID){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc, NCBI_gi, or EMBL_LSID that we are expecting does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # Step 2 - get your input objects
- # in this case, we have registered as accepting
- # only simple inputs (not collections), therefore
- # we can insist on that constraint.
- my @inputs = getInputArticles($data); # returns ([SimpleDOM], [SimpleDOM],...), each represents a unique query input
- foreach my $node(@inputs){
- # do a bit of simple validation
- # the next 12 lines or so are ~cut-n-paste for every service
- unless (isSimpleArticle($node)){ # we only allow Simple inputs to this service, ignore anything else
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if it fails
- next;
- }
- my $namespace_LSID = getSimpleArticleNamespaceURI($node); # get the LSID of the namespace for this input object
- unless (($namespace_LSID eq $GB_Acc_LSID) || ($namespace_LSID eq $GB_gi_LSID) || $namespace_LSID eq $EMBL_LSID){ # validate the namespace
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if bad namespace
- next;
- }
- my ($ID)= getSimpleArticleIDs($namespace_LSID, [$node]); # get the ID within this namespace
- unless (defined $ID){ # send a blank if we failed to get an id,
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if there is no id (?!?)
- next;
- }
-
- # Now, do the analysis
- use Bio::DB::GenBank;
- use Bio::DB::EMBL;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string'); # now that we have a namespace and ID, we are ready to retrieve
- my $emb = new Bio::DB::EMBL(-retrievaltype => 'io_string');
- my $seq;
- if ($namespace_LSID eq $GB_Acc_LSID){ # if the namespace is a genbank Accession thebn
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the accession
- } elsif ($namespace_LSID eq $GB_gi_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_gi($ID); # get the sequence object for the gi
- } elsif ($namespace_LSID eq $EMBL_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the gi
- } else {
- $response .= simpleResponse(""); # if it is neither,then send a blank as required by the API
- next;
- }
-
- my $string;
- my $stringio = IO::String->new($string);
- my $out = Bio::SeqIO->new('-fh' => $stringio,
- '-format' => 'genbank');
- # output goes into $string
- $out->write_seq($seq);
- $response .= simpleResponse("
-
+
-
+
",
"", $qID);
} else {
@@ -295,9 +295,9 @@
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
}
@@ -359,12 +359,12 @@
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "\n";
+ my $tempresponse = "\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
- $tempresponse .=" \n".($SEQ->length)."
+ $tempresponse .="\n".($SEQ->length)."
\n\n";
+ my $tempresponse = "\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -389,13 +389,13 @@
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "\n\n";
+ my $tempresponse = "\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -441,12 +441,12 @@
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
- $tempresponse .=" \n".($SEQ->length)."
+ $tempresponse .="\n".($SEQ->length)."
".($SEQ->seq)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
@@ -457,13 +457,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
".($SEQ->seq)."
";
@@ -475,13 +475,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
".($SEQ->seq)."
";
@@ -532,9 +532,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
} else {
@@ -543,9 +543,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
}
From mwilkinson at pub.open-bio.org Thu Dec 11 17:30:53 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 11 Dec 2003 17:30:53 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312112230.hBBMUrFG005178@pub.open-bio.org>
mwilkinson
Thu Dec 11 17:30:53 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv5159/Services
Modified Files:
LocalServices.pm
Log Message:
two more services dealing with taxon data
moby-live/Perl/scripts/Services LocalServices.pm,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:22:02 1.47
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 22:30:53 1.48
@@ -46,13 +46,13 @@
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
foreach (@inputs){
my ($articleType, $qID, $input) = @{$_};
- unless ($articleType == SIMPLE){
+ unless (($articleType == SIMPLE) && ($input)){
$MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
next;
} else {
@@ -69,6 +69,97 @@
##################################################
##################################################
+sub getTaxChildNodes { # WORKS
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= collectionResponse([], "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= collectionResponse([], "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $children = SHoundGetTaxChildNodes($identifier);
+ $MOBY_RESPONSE .= collectionResponse([], "nothing_found", $qID) unless ($children);
+ my @children = split ",", $children;
+ my @simples;
+ foreach my $taxon (@children){
+ next unless $taxon;
+ $taxon =~ s/\s//g;
+ push @simples, "";
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= simpleResponse("", "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $parent = SHoundGetTaxParent($identifier);
+ $MOBY_RESPONSE .= simpleResponse("", "nothing_found", $qID) unless ($parent);
+ $parent && ($MOBY_RESPONSE .= simpleResponse("", "", $qID));
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+
+sub getTaxNameFromTaxID{ # WORKS
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= simpleResponse("", "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $name = SHoundGetTaxNameFromTaxID($identifier);
+ $MOBY_RESPONSE .= simpleResponse("", "nothing_found", $qID) unless ($name);
+ $name && ($MOBY_RESPONSE .= simpleResponse("
+
+
+ $name ", "", $qID));
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
sub getGoTerm {
my ($caller, $message) = @_;
From mwilkinson at pub.open-bio.org Fri Dec 12 14:22:45 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 12 Dec 2003 14:22:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312121922.hBCJMikJ009022@pub.open-bio.org>
mwilkinson
Fri Dec 12 14:22:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv9003/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
making GMOD moby server revealed a commonsubs error. removed the deprecated services from my CGI client
moby-live/Perl/MOBY CommonSubs.pm,1.34,1.35
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.34
retrieving revision 1.35
diff -u -r1.34 -r1.35
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/10 22:22:03 1.34
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/12 19:22:44 1.35
@@ -397,7 +397,7 @@
";
} elsif($data) {
return "
-
+
$data
";
From mwilkinson at pub.open-bio.org Fri Dec 12 14:22:45 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 12 Dec 2003 14:22:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312121922.hBCJMjo6009041@pub.open-bio.org>
mwilkinson
Fri Dec 12 14:22:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv9003/Perl/scripts
Modified Files:
Services.cgi
Log Message:
making GMOD moby server revealed a commonsubs error. removed the deprecated services from my CGI client
moby-live/Perl/scripts Services.cgi,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services.cgi,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/scripts/Services.cgi 2003/10/17 21:29:52 1.4
+++ /home/repository/moby/moby-live/Perl/scripts/Services.cgi 2003/12/12 19:22:44 1.5
@@ -2,8 +2,13 @@
# _________________________________________________________________
use SOAP::Transport::HTTP;
use lib "/usr/local/apache/cgi-bin";
+use lib "/usr/local/apache/cgi-bin/MOBY05";
+use lib "/usr/local/apache/cgi-bin/BIO/go-dev/perl-api";
use lib "/usr/local/apache/cgi-bin/BIO/moby-live/Perl";
-use lib "/usr/local/apache/cgi-bin/BIO/core/Perl";
+use lib '/usr/local/apache/cgi-bin/bioperl/core';
+use lib '/usr/local/apache/cgi-bin/Services/';
+use Bio::SeqIO::genbank;
+use GO::AppHandle;
use Services::LocalServices;
use strict;
@@ -12,13 +17,13 @@
$x->dispatch_with({
'http://biomoby.org/#getGoTerm' => 'Services::LocalServices',
'http://biomoby.org/#getGoTermAssociations' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankAccVirtualSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankAccSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankGIVirtualSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankGISequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankCompleteSequenceRetrieve' => 'Services::LocalServices',
'http://biomoby.org/#RetrieveGOFromKeywords' => 'Services::LocalServices',
'http://biomoby.org/#getDragonMutantImages' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankff' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankFasta' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankWhateverSequence' => 'Services::LocalServices',
+'http://biomoby.org/#getTaxNameFromTaxID' => 'Services::LocalServices',
+'http://biomoby.org/#getTaxChildNodes' => 'Services::LocalServices',
});
$x->handle;
From mwilkinson at pub.open-bio.org Tue Dec 16 15:46:40 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 16 Dec 2003 15:46:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312162046.hBGKke7h000685@pub.open-bio.org>
mwilkinson
Tue Dec 16 15:46:40 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv665/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
corrected the SeqHound call for EMBL accession numbers Added a new service that wraps the SeqHound SHoundGetTaxParent function to retrieve the taxonomic parents of a given taxon id.
moby-live/Perl/scripts/Services LocalServices.pm,1.48,1.49
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 22:30:53 1.48
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/16 20:46:40 1.49
@@ -17,15 +17,31 @@
use MIME::Base64;
use XML::DOM;
use MOBY::Client::OntologyServer;
-use MOBY::CommonSubs qw(:all); # this provides the
-# subroutines:
-#getSimpleArticleIDs
-#getSimpleArticleNamespaceURI
-#simpleResponse
-#responseHeader
-#responseFooter
-#getInputArticles
-#getNodeContentWithArticle
+use MOBY::CommonSubs qw(:all); # this provides the following vars and functions
+ #getSimpleArticleIDs
+ #getSimpleArticleNamespaceURI
+ #simpleResponse
+ #responseHeader
+ #responseFooter
+ #getInputArticles
+ #getInputs
+ #getInputID
+ #getArticles
+ #getCollectedSimples
+ #getNodeContentWithArticle
+ #extractRawContent
+ #collectionResponse
+ #validateNamespaces
+ #validateThisNamespace
+ #isSimpleArticle
+ #isCollectionArticle
+ #extractResponseArticles
+ #getResponseArticles
+ #getCrossReferences
+ #genericServiceInputParser
+ #COLLECTION
+ #SIMPLE
+
my $debug = 1;
use vars qw(@ISA);
@@ -103,7 +119,7 @@
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
-sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+sub getTaxParent { # now it works.
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
@@ -327,14 +343,6 @@
# ===============================================
# = Genbank Retrieval Scripts =
# = =
-# = Note: The two VirtualSequenceRetrieve's =
-# = and two SequenceRetrieves below could=
-# = have been registered as two services =
-# = instead of four, by simply =
-# = registering each under two different =
-# = namespaces (Acc and gi) instead of =
-# = having a single service for each =
-# = namespace =
# ===============================================
@@ -369,7 +377,7 @@
my $gb = SHoundGetGenBankff($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
- } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ } elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -541,7 +549,7 @@
".($SEQ->seq)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
- } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ } elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -617,7 +625,7 @@
my $gb = SHoundGetFasta($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
An HTML attachment was scrubbed...
URL: http://biomoby.org/pipermail/moby-guts/attachments/20031222/3a20bb44/attachment.html
From mwilkinson at pub.open-bio.org Fri Dec 26 17:01:31 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 26 Dec 2003 17:01:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312262201.hBQM1VtN026461@pub.open-bio.org>
mwilkinson
Fri Dec 26 17:01:31 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv26442/Perl/MOBY/Client
Modified Files:
Central.pm
Log Message:
duh! If you pass identical objects to the ISA routine, CLEARLY it should return TRUE!!
moby-live/Perl/MOBY/Client Central.pm,1.64,1.65
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -r1.64 -r1.65
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:57:15 1.64
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/26 22:01:31 1.65
@@ -1383,6 +1383,7 @@
sub ISA {
my ($self, $class1, $class2) = @_;
+ return 1 if (($class1 eq $class2) || ("moby:$class1" eq $class2) || ($class1 eq "moby:$class2"));
my $OS = MOBY::Client::OntologyServer->new;
my ($s, $d, $lsid1) = $OS->objectExists(term => $class1);
return 0 unless $s;
From mwilkinson at pub.open-bio.org Sat Dec 27 08:55:20 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat, 27 Dec 2003 08:55:20 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271355.hBRDtKVf028530@pub.open-bio.org>
mwilkinson
Sat Dec 27 08:55:20 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv28511/Perl/MOBY/Client
Modified Files:
Central.pm
Log Message:
serious performance issues revealed by the new Gbrowse moby client program. The ISA call of MOB::Clien:Central requires two CGI calls, a SOAP call, which itself results in two CGI calls, and a myriad of independent database calls to traverse the ontology. It ended up being >1 second per call,which was unacceptable for many situations where you just need a quick answer to a 'what the heck is this' question. Started client-side caching of the ontology and LSID terms in Client::Central to speed things up. It is now only slow the first time, and <.05 seconds per call thereafter. It does show how critical the need is to start storing the ontology in memory on the server side, though.
moby-live/Perl/MOBY/Client Central.pm,1.65,1.66
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.65
retrieving revision 1.66
diff -u -r1.65 -r1.66
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/26 22:01:31 1.65
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 13:55:20 1.66
@@ -1385,13 +1385,27 @@
my ($self, $class1, $class2) = @_;
return 1 if (($class1 eq $class2) || ("moby:$class1" eq $class2) || ($class1 eq "moby:$class2"));
my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $d, $lsid1) = $OS->objectExists(term => $class1);
- return 0 unless $s;
- my ($s2, $d2, $lsid2) = $OS->objectExists(term => $class2);
- return 0 unless $s2;
- my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1);
- my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'};
- foreach (@$lsids){
+ my ($lsid1, $lsid2);
+ unless ($lsid1 = $self->{LSID_CACHE}->{$class1}){
+ my ($s, $d, $lsid) = $OS->objectExists(term => $class1);
+ $self->{LSID_CACHE}->{$class1} = $lsid;
+ $lsid1 = $lsid;
+ return 0 unless $s;
+ }
+ unless ($lsid2 = $self->{LSID_CACHE}->{$class2}){
+ my ($s, $d, $lsid) = $OS->objectExists(term => $class2);
+ $self->{LSID_CACHE}->{$class2} = $lsid;
+ $lsid2 = $lsid;
+ return 0 unless $s;
+ }
+ my @lsids;
+ unless ($self->{"ISA_CACHE"}->{"$lsid1"} && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){
+ my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1, Relationships => ['ISA']);
+ my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'};
+ @lsids = @$lsids;
+ }
+ $self->{"ISA_CACHE"}->{"$lsid1"} = [@lsids];
+ foreach (@lsids){
return 1 if $_ eq $lsid2;
}
return 0;
From mwilkinson at pub.open-bio.org Sat Dec 27 10:12:32 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat, 27 Dec 2003 10:12:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271512.hBRFCWeV028733@pub.open-bio.org>
mwilkinson
Sat Dec 27 10:12:31 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28714/Perl/MOBY
Modified Files:
Central.pm
Log Message:
Gbrowse client reveals another MOBY Central bug. Searching for services where you provide an invalid namespace as a parameter should NOT find ALL services, it should find NO services.
moby-live/Perl/MOBY Central.pm,1.118,1.119
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.118
retrieving revision 1.119
diff -u -r1.118 -r1.119
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/22 17:21:16 1.118
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119
@@ -1849,7 +1849,7 @@
next unless ($_->getNodeType == TEXT_NODE);
my $name = $_->toString; chomp $name;
my ($success, $message, $URI) = $OS->namespaceExists(term => $name);
- ($URI) && push @namespaces, $URI;
+ $URI?(push @namespaces, $URI):(push @namespaces, "__MOBY__INVALID__NAMESPACE__");
}
}
return ($objectURI, \@namespaces);
From mwilkinson at pub.open-bio.org Sat Dec 27 12:41:32 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat, 27 Dec 2003 12:41:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271741.hBRHfWiQ029662@pub.open-bio.org>
mwilkinson
Sat Dec 27 12:41:32 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv29639/Perl/MOBY/Client
Modified Files:
Central.html Central.pm
Log Message:
more tweaks for the Gbrowse project. Create getter/setter methods for the LSID and ISA caches in MOBY::Client::Central so that they can be called from outside of the module itself. This will allow us to build external tools that play with these caches. This may not seem useful at the moment since we only have CGI based clients, so the cache is erased every time we make a call, but once we have a standalone client it will be very useful
moby-live/Perl/MOBY/Client Central.html,1.13,1.14 Central.pm,1.66,1.67
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/02 00:57:15 1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/27 17:41:32 1.14
@@ -2,7 +2,7 @@
MOBY::Client::Central - a client side wrapper for MOBY Central
-
+
@@ -20,8 +20,8 @@
- new
- - registerObject a.k.a registerObjectClass
- - deregisterObject a.k.a. deregisterObjectClass
+ - registerObject a.k.a registerObjectClass
+ - deregisterObject a.k.a. deregisterObjectClass
- retrieveObjectDefinition
- registerServiceType
- deregisterServiceType
@@ -41,6 +41,8 @@
- Relationships
- ISA
- DUMP
+ - LSID_CACHE
+ - ISA_CACHE
-
Title : registerObject ; registerObjectClass
Usage : $REG = $MOBY->registerObject(%args)
@@ -154,7 +156,7 @@
[Object1, articleName]]}
-
Title : deregisterObject ; deregisterObjectClass Usage : $REG = $MOBY->deregisterObject(%args) @@ -430,6 +432,27 @@ Function : DUMP the mysql for the current MOBY Central database Returns : text Args : $reg - name of MOBY Central you want to use if not default+
+
++ Title : LSID_CACHE + Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid) + Function : get/set LSID from the cache + Returns : lsid as a scalar + Args : the term for which you have/want an lsid, + and optionally the lsid to set.+
+
++ Title : ISA_CACHE + Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) + Function : get/set the ISA relationships in the cache + Returns : listref of ISA relationships. The resulting + list is IN ORDER from term to root. + Args : the term for which you have/want the ISA parentage, + and optionally the parentage listref to set.=================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.66 retrieving revision 1.67 diff -u -r1.66 -r1.67 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 13:55:20 1.66 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 17:41:32 1.67 @@ -213,6 +213,7 @@ } } + sub new { my ($caller, %args) = @_; @@ -1342,6 +1343,7 @@ } + sub _relationshipsPayload{ my ($payload) = @_; return undef unless $payload; @@ -1388,23 +1390,23 @@ my ($lsid1, $lsid2); unless ($lsid1 = $self->{LSID_CACHE}->{$class1}){ my ($s, $d, $lsid) = $OS->objectExists(term => $class1); - $self->{LSID_CACHE}->{$class1} = $lsid; + $self->LSID_CACHE($class1, $lsid); $lsid1 = $lsid; return 0 unless $s; } unless ($lsid2 = $self->{LSID_CACHE}->{$class2}){ my ($s, $d, $lsid) = $OS->objectExists(term => $class2); - $self->{LSID_CACHE}->{$class2} = $lsid; + $self->LSID_CACHE($class2, $lsid); $lsid2 = $lsid; return 0 unless $s; } my @lsids; - unless ($self->{"ISA_CACHE"}->{"$lsid1"} && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){ + unless ($self->ISA_CACHE($lsid1) && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){ my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1, Relationships => ['ISA']); my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'}; @lsids = @$lsids; } - $self->{"ISA_CACHE"}->{"$lsid1"} = [@lsids]; + $self->ISA_CACHE($lsid1, [@lsids]); foreach (@lsids){ return 1 if $_ eq $lsid2; } @@ -1507,6 +1509,61 @@ return \@Services; } + +=head2 LSID_CACHE + + Title : LSID_CACHE + Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid) + Function : get/set LSID from the cache + Returns : lsid as a scalar + Args : the term for which you have/want an lsid, + and optionally the lsid to set. + +=cut + + +sub LSID_CACHE { + my ($self, $term, $lsid) = @_; + if ($term && $lsid){ + $self->{LSID_CACHE}->{$term} = $lsid; + return $self->{LSID_CACHE}->{$term}; + } elsif ($term){ + return $self->{LSID_CACHE}->{$term}; + } else { + return undef + } +} + + +=head2 ISA_CACHE + + Title : ISA_CACHE + Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) + Function : get/set the ISA relationships in the cache + Returns : listref of ISA relationships. The resulting + list is IN ORDER from term to root. + Args : the term for which you have/want the ISA parentage, + and optionally the parentage listref to set. + +=cut + +sub ISA_CACHE { + my ($self, $term, $isas) = @_; + return [] if $isas && !(ref($isas)=~/ARRAY/); + if ($term && $isas){ + while (scalar(@$isas)){ + $self->{ISA_CACHE}->{$term} = [@$isas]; + $term = shift(@$isas); + } + return $self->{ISA_CACHE}->{$term}; + } elsif ($term){ + return $self->{ISA_CACHE}->{$term}; + } else { + return [] + } +} + + sub parseRegXML { #
+
+
Title : LSID_CACHE @@ -446,13 +450,15 @@From mwilkinson at pub.open-bio.org Sat Dec 27 15:15:45 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sat, 27 Dec 2003 15:15:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312272015.hBRKFjpJ030037@pub.open-bio.org> mwilkinson Sat Dec 27 15:15:45 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv30014/Perl/MOBY Modified Files: CommonSubs.pm CommonSubs.html Log Message: Gbrowse client needed a new utility routine in CommonSubs. This will take a list of 'known' Object ontology nodes and check it against the parentage of an in-hand object type, returning to you the term from your list that is DEEPEST in the ontology in the ISA parentage of your in-hand object. Why? (you might ask) Well, because when you want to assign renderers to objects you want the most complex renderer possible to deal with your in-hand object, so if you have rendrers for a variety of base object types, you want to chose the one that is best able to deal with whatever you have in-hand, thus you want the node closest to your object type moby-live/Perl/MOBY CommonSubs.pm,1.36,1.37 CommonSubs.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.36 retrieving revision 1.37 diff -u -r1.36 -r1.37 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/22 19:57:04 1.36 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:15:45 1.37 @@ -175,6 +175,7 @@ getResponseArticles getCrossReferences genericServiceInputParser + whichDeepestParentObject COLLECTION SIMPLE BE_NICE @@ -202,6 +203,7 @@ getResponseArticles getCrossReferences genericServiceInputParser + whichDeepestParentObject COLLECTION SIMPLE BE_NICE @@ -1071,6 +1073,43 @@ return @XREFS; } + + +=head2 whichDeepestParentObject + + name : whichDeepestParentObject + function : select the parent node from nodeList that is + closest to the querynode + usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + args : $CENTRAL - your MOBY::Client::Central object + $queryNode - the node I am interested in + \@nodelist - the list of nodes that I know about + returns : an ontology term as a scalar, or undef if there + is no parent of this node in the nodelist + +=cut + + +sub whichDeepestParentObject { + use MOBY::Client::OntologyServer; + my ($CENTRAL, $queryTerm, $termlist) = @_; + return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); + my %nodeLSIDs; + foreach (@$termlist){ # get list of known LSIDs + my $lsid = $CENTRAL->ObjLSID($_); + $nodeLSIDs{$lsid}=1; + } + my $queryLSID = $CENTRAL->ObjLSID($queryTerm); + return undef unless keys(%nodeLSIDs); + my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already + return undef unless $isa; # this should return true or we are in BIIIG trouble! + my @lsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root + while (my $thisnode = shift @lsids){ # @isas are lsid's + return $thisnode if $nodeLSIDs{$thisnode}; + } + return undef +} + sub _makeXrefType { my ($xref) = @_; my $ns = $xref->getAttributeNode('namespace'); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/11/08 17:21:31 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:15:45 1.7 @@ -4,7 +4,7 @@ISA_CACHE
- Title : ISA_CACHE - Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) - Function : get/set the ISA relationships in the cache - Returns : listref of ISA relationships. The resulting - list is IN ORDER from term to root. - Args : the term for which you have/want the ISA parentage, - and optionally the parentage listref to set.+ Title : ISA_CACHE + Usage : @lsids = $MOBY->ISA_CACHE($lsid, \@isas) + Function : get/set the ISA relationships in the cache + Returns : list of ISA relationships. The ISA list + is IN ORDER from, excluding the term itself, to + root Object. Base Object returns an empty list. + Args : The LSID for which you have/want the ISA parentage, + and optionally the parentage listref to set. + Note : WHAT COMES BACK ARE LSIDs!!!
+
+ name : extractRawContent + function : pass me an article (Simple, or Collection) and I'll give you the + content AS A STRING - i.e. the raw XML of the contained MOBY Object(s) + usage : extractRawContent($simple) + input : the one element of the output from getArticles + returns : string+
+
name : validateNamespaces
@@ -427,7 +442,16 @@
presumptive namespaces; undef for each namespace that was invalid
-
+ name : validateThisNamespace + function : checks a given namespace against a list of valid namespaces + usage : $valid = validateThisNamespace($ns, @validNS); + args : ordered list of the namespace of interest and the list of valid NS's + returns : boolean+
+
+
name : getResponseArticles
function : get the DOM nodes corresponding to individual
@@ -461,6 +485,19 @@
}
}
}
++
++ name : whichDeepestParentObject + function : select the parent node from nodeList that is + closest to the querynode + usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + args : $CENTRAL - your MOBY::Client::Central object + $queryNode - the node I am interested in + \@nodelist - the list of nodes that I know about + returns : an ontology term as a scalar, or undef if there + is no parent of this node in the nodelistFrom mwilkinson at pub.open-bio.org Sat Dec 27 15:24:52 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sat, 27 Dec 2003 15:24:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312272024.hBRKOqJS030126@pub.open-bio.org> mwilkinson Sat Dec 27 15:24:52 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv30103/Perl/MOBY Modified Files: CommonSubs.html CommonSubs.pm Log Message: changed my mind and decided to return both the object name as well as its LSID, since the latter is a bit arcane sometimes. moby-live/Perl/MOBY CommonSubs.html,1.7,1.8 CommonSubs.pm,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:15:45 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:24:52 1.8 @@ -492,10 +492,10 @@ name : whichDeepestParentObject function : select the parent node from nodeList that is closest to the querynode - usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + usage : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList) args : $CENTRAL - your MOBY::Client::Central object - $queryNode - the node I am interested in - \@nodelist - the list of nodes that I know about + $queryTerm - the object type I am interested in + \@termlist - the list of object types that I know about returns : an ontology term as a scalar, or undef if there is no parent of this node in the nodelist =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:15:45 1.37 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38 @@ -1080,10 +1080,10 @@ name : whichDeepestParentObject function : select the parent node from nodeList that is closest to the querynode - usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + usage : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList) args : $CENTRAL - your MOBY::Client::Central object - $queryNode - the node I am interested in - \@nodelist - the list of nodes that I know about + $queryTerm - the object type I am interested in + \@termlist - the list of object types that I know about returns : an ontology term as a scalar, or undef if there is no parent of this node in the nodelist @@ -1093,21 +1093,21 @@ sub whichDeepestParentObject { use MOBY::Client::OntologyServer; my ($CENTRAL, $queryTerm, $termlist) = @_; - return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); + return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); my %nodeLSIDs; foreach (@$termlist){ # get list of known LSIDs my $lsid = $CENTRAL->ObjLSID($_); - $nodeLSIDs{$lsid}=1; + $nodeLSIDs{$lsid}=$_; } my $queryLSID = $CENTRAL->ObjLSID($queryTerm); - return undef unless keys(%nodeLSIDs); + return (undef, undef) unless keys(%nodeLSIDs); my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already - return undef unless $isa; # this should return true or we are in BIIIG trouble! - my @lsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root - while (my $thisnode = shift @lsids){ # @isas are lsid's - return $thisnode if $nodeLSIDs{$thisnode}; + return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble! + my @ISAlsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root + while (my $thislsid = shift @ISAlsids){ # @isas are lsid's + return ($nodeLSIDs{$thislsid},$thislsid) if $nodeLSIDs{$thislsid}; } - return undef + return (undef, undef); } sub _makeXrefType { From mwilkinson at pub.open-bio.org Sun Dec 28 15:41:59 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 28 Dec 2003 15:41:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312282041.hBSKfx4X009349@pub.open-bio.org> mwilkinson Sun Dec 28 15:41:59 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv9318/MOBY Modified Files: Central.pm CommonSubs.pm OntologyServer.pm simple_input.pm Log Message: making MOBY Central case-sensitive for LSIDs. I might have missed a few places. please let me know if you find any. moby-live/Perl/MOBY Central.pm,1.119,1.120 CommonSubs.pm,1.38,1.39 OntologyServer.pm,1.30,1.31 simple_input.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.119 retrieving revision 1.120 diff -u -r1.119 -r1.120 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/28 20:41:59 1.120 @@ -758,7 +758,7 @@ my $dbh = MOBY::central_db_connection->new->dbh; - my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where namespace_type_uris like '%$existingURI%'"); + my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where INSTR(namespace_type_uris,'$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -768,7 +768,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where INSTR(namespace_type_uris,'$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -778,7 +778,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where INSTR(namespace_type_uris, '$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -788,7 +788,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where INSTR(namespace_type_uris, '$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -1699,7 +1699,7 @@ my $nsquery; foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's - $nsquery .=" OR namespace_type_uris like '%$ns%' "; + $nsquery .=" OR INSTR(namespace_type_uris, '$ns') "; } if ($nsquery){ $nsquery =~ s/OR//; # just the first @@ -1754,7 +1754,7 @@ my $nsquery; foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's - $nsquery .=" OR namespace_type_uris like '%$ns%' "; + $nsquery .=" OR INSTR(namespace_type_uris, '$ns') "; } if ($nsquery){ $nsquery =~ s/^\sOR//; # just the first =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.38 retrieving revision 1.39 diff -u -r1.38 -r1.39 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39 @@ -1074,7 +1074,6 @@ } - =head2 whichDeepestParentObject name : whichDeepestParentObject @@ -1084,8 +1083,12 @@ args : $CENTRAL - your MOBY::Client::Central object $queryTerm - the object type I am interested in \@termlist - the list of object types that I know about - returns : an ontology term as a scalar, or undef if there - is no parent of this node in the nodelist + returns : an ontology term and LSID as a scalar, or undef if there + is no parent of this node in the nodelist. + (note that it will only return the term if you give it + term names in the @termList. If you give it + LSID's in the termList, then both the parameters + returned will be LSID's - it doesn't back-translate...) =cut =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30 +++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31 @@ -179,7 +179,7 @@ } if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?"); + $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where INSTR(object_lsid, ?)"); } else { $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_type = ?"); } @@ -326,7 +326,7 @@ return (0, "requires both term and ontology arguments\n",'') unless (defined($term) && defined($ont)); my $sth; if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_lsid = ? and ontology=?"); + $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where INSTR(relationship_lsid,?) and ontology=?"); } else { $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_type = ? and ontology=?"); } @@ -433,7 +433,7 @@ my $sth; if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?"); + $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where INSTR(service_lsid, ?)"); } else { $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_type = ?"); } @@ -545,7 +545,7 @@ } if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){ - $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?"); + $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where INSTR(namespace_lsid, ?)"); } else { $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?"); } @@ -691,7 +691,7 @@ sub getObjectCommonName { my ($self, $URI) = @_; return undef unless $URI =~ /urn\:lsid/; - my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_id = ?}, undef, $URI); + my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_lsid = ?}, undef, $URI); return $name?$name:$URI; } @@ -702,7 +702,7 @@ sub getNamespaceCommonName { my ($self, $URI) = @_; return undef unless $URI =~ /urn\:lsid/; - my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_id = ?}, undef, $URI); + my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_lsid = ?}, undef, $URI); return $name?$name:$URI; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/05/07 19:20:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/12/28 20:41:59 1.2 @@ -14,7 +14,7 @@ =head1 SYNOPSIS - use MOBY::authority; + use MOBY::simple_input; my $Instance = MOBY::simple_input->new( object_type => "Sequence", namespaces => ["genbank/gi", "genbank/Acc"], From mwilkinson at pub.open-bio.org Sun Dec 28 21:43:43 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 28 Dec 2003 21:43:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312290243.hBT2hhlC010292@pub.open-bio.org> mwilkinson Sun Dec 28 21:43:43 EST 2003 Update of /home/repository/moby/moby-live In directory pub.open-bio.org:/tmp/cvs-serv10273 Modified Files: README Log Message: just testing the new cron on biomoby.org moby-live README,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/README 2003/02/19 21:12:16 1.3 +++ /home/repository/moby/moby-live/README 2003/12/29 02:43:43 1.4 @@ -1,3 +1,4 @@ +test README # # Revision History From mwilkinson at pub.open-bio.org Tue Dec 30 15:03:54 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 30 Dec 2003 15:03:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312302003.hBUK3sN1016258@pub.open-bio.org> mwilkinson Tue Dec 30 15:03:54 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16239/Perl/MOBY Modified Files: OntologyServer.pm Log Message: changing the case of the LSID's buggered up the Relationships call of the OntologyServer. I noticed this when the Gbrowse MOBY browser stopped working. moby-live/Perl/MOBY OntologyServer.pm,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31 +++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/30 20:03:54 1.32 @@ -801,13 +801,13 @@ $term = $self->getObjectURI($term); } my %results; - while (($term ne 'urn:lsid:biomoby.org:objectclass:object') && ($term ne 'urn:lsid:biomoby.org:servicetype:service')){ + while (($term ne 'urn:lsid:biomoby.org:objectclass:Object') && ($term ne 'urn:lsid:biomoby.org:servicetype:Service')){ my $defs = $self->_doRelationshipsQuery($ontology, $term, $relationship, $direction); my $lsid; my $rel; foreach (@{$defs}){ $lsid = $_->[0]; $rel = $_->[1]; - $debug && _LOG("\t\tADDING RELATIONSHIP $_ : $lsid to $rel\n"); + $debug && _LOG("\t\tADDING RELATIONSHIP $_ : $lsid to $rel\n"); push @{$results{$rel}}, $lsid; } last unless ($expand); From mwilkinson at pub.open-bio.org Tue Dec 30 15:21:31 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 30 Dec 2003 15:21:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312302021.hBUKLVww016376@pub.open-bio.org> mwilkinson Tue Dec 30 15:21:31 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16357/Perl/MOBY Modified Files: CommonSubs.pm Log Message: whichDeepestParentObject should return right away if it finds an object in the list you provided it. Before this would actualy return Object if you gave it the exact object type as part of the search moby-live/Perl/MOBY CommonSubs.pm,1.39,1.40 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.39 retrieving revision 1.40 diff -u -r1.39 -r1.40 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/30 20:21:30 1.40 @@ -1098,11 +1098,12 @@ my ($CENTRAL, $queryTerm, $termlist) = @_; return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); my %nodeLSIDs; + my $queryLSID = $CENTRAL->ObjLSID($queryTerm); foreach (@$termlist){ # get list of known LSIDs my $lsid = $CENTRAL->ObjLSID($_); - $nodeLSIDs{$lsid}=$_; + return ($_, $lsid) if ($lsid eq $queryLSID); # of course, if we find it in the list, then return it right away! + $nodeLSIDs{$lsid}=$_; } - my $queryLSID = $CENTRAL->ObjLSID($queryTerm); return (undef, undef) unless keys(%nodeLSIDs); my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble! From mwilkinson at pub.open-bio.org Tue Dec 2 00:23:23 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 1 Dec 2003 19:23:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312020023.hB20NNax021442@pub.open-bio.org> mwilkinson Mon Dec 1 19:23:23 EST 2003 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv21426/Perl Removed Files: MOBY.pm Log Message: lots of changes to allow registration of arbitrary SOAP services. MOBY Central expects such services to register their inputs and outputs as LSIDs. They can similarly be discovered using LSID's. A mix of MOBY and non-MOBY inputs and outputs is allowed, but has not been tested. The URL component of the registration is the URL to the WSDL document describing the service. moby-live/Perl MOBY.pm,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Perl/RCS/MOBY.pm,v: No such file or directory From mwilkinson at pub.open-bio.org Tue Dec 2 00:23:23 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 1 Dec 2003 19:23:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312020023.hB20NNC9021529@pub.open-bio.org> mwilkinson Mon Dec 1 19:23:23 EST 2003 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv21426/Perl/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: lots of changes to allow registration of arbitrary SOAP services. MOBY Central expects such services to register their inputs and outputs as LSIDs. They can similarly be discovered using LSID's. A mix of MOBY and non-MOBY inputs and outputs is allowed, but has not been tested. The URL component of the registration is the URL to the WSDL document describing the service. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2003/07/04 16:12:37 1.11 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2003/12/02 00:23:23 1.12 @@ -23,7 +23,12 @@ } -my $C = MOBY::Client::Central->new(); +my $C = MOBY::Client::Central->new( +#Registries => { +# mobycentral => {URL => 'http://localhost/cgi-bin/MOBY-Central.pl', +# URI => 'http://localhost/MOBY/Central'} +# } +); #reg first object class From mwilkinson at pub.open-bio.org Tue Dec 2 00:23:23 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 1 Dec 2003 19:23:23 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312020023.hB20NNoQ021508@pub.open-bio.org> mwilkinson Mon Dec 1 19:23:23 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv21426/Perl/MOBY/Client Modified Files: Central.html Central.pm CollectionArticle.pm SimpleArticle.pm Log Message: lots of changes to allow registration of arbitrary SOAP services. MOBY Central expects such services to register their inputs and outputs as LSIDs. They can similarly be discovered using LSID's. A mix of MOBY and non-MOBY inputs and outputs is allowed, but has not been tested. The URL component of the registration is the URL to the WSDL document describing the service. moby-live/Perl/MOBY/Client Central.html,1.11,1.12 Central.pm,1.62,1.63 CollectionArticle.pm,1.5,1.6 SimpleArticle.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/10/22 14:29:09 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/02 00:23:23 1.12 @@ -409,7 +409,7 @@ Relationships => \@relationship_types (optional, 'all' if parameter is missing) Registry => $registry_name (optional) - expandRelationships (NOT YET IMPLEMENTED) + expandRelationships => [1/0] (optional)
Input XML :
<registerService>
- <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' ; currently only 'moby' services are fully supported -->
+ <Category>moby</Category> <!-- one of 'moby', 'cgi', 'wsdl' ; currently only 'moby' and 'wsdl' services are fully supported -->
<serviceName>YourServiceNameHere</serviceName>
<serviceType>TypeOntologyTerm</serviceType>
<authURI>your.URI.here</authURI>
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.113
retrieving revision 1.114
diff -u -r1.113 -r1.114
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/11/24 18:06:45 1.113
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 00:23:23 1.114
@@ -873,25 +873,27 @@
=over 2
-=item * in "moby" services, the input and output messaging structure is defined by the BioMOBY API, and the services use data Objects that are defined in the Class ontology as inheriting from the root "Object" Class. For "soap" services, there is additional flexibility:
+=item * in "moby" services, the input and output messaging structure is defined by the BioMOBY API, and the services use data Objects that are defined in the Class ontology as inheriting from the root "Object" Class.
+
+=item * For "soap" services, there is additional flexibility:
=over 2
-=item * Similar to a "moby" service, your "soap" service must consume/produce ontologically valid named data-types in order to be discovered by registry searches. As such, you _must_ register a single unique name for any non-MOBY input or output data Classes, regardless of the actual complexity of the input/output message.
+=item * Similar to a "moby" service, your "soap" service must consume/produce named data types. These are represented as LSID's
-=item * Do this using the registerObjectClass call of MOBY Central; To ensure uniqueness and LSID compatibilty of data class names, you must name your data using the following format: your.authURI:dataClassName
+=item * YOU DO NOT NEED TO REGISTER THESE DATA TYPES in MOBY Central; it is up to you what your LSID's represent, and MOBY Central WILL NOT try to resolve them!
-=item * remember, you may use any MOBY Object as your input/output (i.e. any Class Ontology term that inherits from Object) so long as you follow the MOBY message structure for that input or output.
+=item * You may mix ontologies when describing your service - i.e. you may freely use any MOBY Object as your input or (XOR) your output and use a non-MOBY object (LSID) for the alternate so long as you follow the MOBY message structure for the parameter that uses the MOBY Object
-=item * You may register, for example, a service that consumes a non-MOBY data Class and outputs a MOBY data class, so long as you follow the MOBY Messaging format for the output data
+=over 2
-=item * You may register, for example, a service that consumes a MOBY data Class and outputs a non-MOBY data class, so long as you follow the MOBY Messaging format for the ihput data
+=item * You may register, for example, a service that consumes a non-MOBY data Class and outputs a MOBY data class, so long as you follow the MOBY Messaging format for the output data
-=item * NOTE: Nether of the cases above are considred MOBY services, and are therefore described in the category of "soap" service
+=item * You may register, for example, a service that consumes a MOBY data Class and outputs a non-MOBY data class, so long as you follow the MOBY Messaging format for the input data
-=item * When registering a non-MOBY data Class name, it DOES NOT have any "Relationship" component (see registerObjectClass API)
+=item * NOTE: Nether of the cases above are considered MOBY services, and are therefore described in the category of "soap" service
-=item * non-MOBY inputs or outputs are described as a single Primary, Simple article of your new named type.
+=back
=back
@@ -903,6 +905,7 @@
=back
+=back
Input XML :
@@ -1079,17 +1082,18 @@
foreach (keys %objects_to_be_validated){
my ($valid, $message, $URI) = $OS->objectExists(term => $_);
- return &_error("$message","$URI") unless ($valid);
+ return &_error("$message","$URI") unless ($valid || (($_ =~ /urn:lsid/i) && !($_ =~ /urn:lsid:biomoby.org/i))); # either valid, or a non-moby LSID
}
- $debug && &_LOG("\n\n\aall objects okay\n");
+
+ $debug && &_LOG("\n\n\aall objects okay - either valid MOBY objects, or LSID's\n");
$OS = MOBY::OntologyServer->new(ontology => 'service');
my ($valid, $message, $URI) = $OS->serviceExists(term => $serviceType);
- return &_error("$message","$URI") unless ($valid);
+ print STDERR "\n\nChecking $URI\n\n";
+ return &_error("$message","$URI") unless ($valid || (($serviceType =~ /urn:lsid/i) && !($serviceType =~ /urn:lsid:biomoby.org/i))); # either valid, or a non-MOBY LSID
+ print STDERR "\n\nChecking $URI OK!!\n\n";
# right, registration should be successful now!
- # "soap" services may only have one input and one output
-
my $SVC = MOBY::service_instance->new(
category => $Category,
servicename => $serviceName,
@@ -1158,8 +1162,8 @@
($_->getNodeType == TEXT_NODE) && ($object_type = $_->toString);
}
my ($success, $message, $typeURI) = $OE->objectExists(term => $object_type);
- unless ($success) {
- $SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist");
+ if ((!($success) && ($object_type =~ /urn:lsid:biomoby.org/i)) || (!($success) && !($object_type =~ /urn:lsid/i))) { # if the object doesn't exist, and it isn't an LSID
+ $SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist, and is not an LSID");
} # kill it all unless this was successful!
my $namespace_string;
@@ -1169,10 +1173,11 @@
for (my $n = 0; $n<$num_ns;++$n) {
foreach my $name ($namespaces->item($n)->getChildNodes) {
if ($name->getNodeType == TEXT_NODE) {
- my ($success, $message, $URI) = $OE->namespaceExists(term => $name->toString);
- unless ($success) {
+ my $term = $name->toString;
+ my ($success, $message, $URI) = $OE->namespaceExists(term => $term);
+ if ((!($success) && ($term =~ /urn:lsid:biomoby.org/i)) || (!($success) && !($term =~ /urn:lsid/i))) { # if the object doesn't exist, and it isn't an LSID
$SVC->DELETE_THYSELF;
- return (-1,"namespace: " . $name->toString . " doesn't exist");
+ return (-1,"namespace: $term doesn't exist and is not an LSID");
}
$namespace_string .=$URI.",";
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/11/24 17:25:49 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30
@@ -171,9 +171,13 @@
my ($self, %args) = @_;
my $term = $args{term};
$term =~ s/^moby://; # if the term is namespaced, then remove that
-
- return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'object');
my $sth;
+ return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'object');
+
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objecttype/)){
+ return (1, "external ontology", $term);
+ }
+
if ($term =~ /^urn\:lsid/){
$sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?");
} else {
@@ -204,6 +208,10 @@
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objectclass/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -265,11 +273,15 @@
return (0, "WRONG ONTOLOGY",'') unless ($self->ontology eq 'object');
my $term = $args{term};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objectclass/)){
+ return (0, "can't delete from external ontology", $term);
+ }
+
my $LSID;
unless ($term =~ /urn\:lsid/){$LSID = $self->getObjectURI($term)} else {$LSID=$term}
return (0, q{Object type $term cannot be resolved to an LSID},"") unless $LSID;
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select object_id, object_lsid from object where object_type = ?},undef,$term);
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select object_id, object_lsid from object where object_lsid = ?},undef,$LSID);
# object1_id ISA object2_id?
my (@isa) = $self->dbh->selectrow_array(q{select * from object_term2term where object2_id = ?},undef, $id);
if (scalar @isa){
@@ -415,6 +427,10 @@
my $term = $args{term};
$term =~ s/^moby://; # if the term is namespaced, then remove that
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){
+ return (1, "external ontology", $term);
+ }
+
my $sth;
if ($term =~ /^urn\:lsid/){
$sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?");
@@ -446,6 +462,10 @@
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -475,11 +495,17 @@
my ($self, %args) = @_;
return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'service');
my $term = $args{term};
- my $LSID;
- unless ($term =~ /urn\:lsid/){$LSID = $self->getServiceURI($term)} else {$LSID=$term}
- return (0, q{Service type $term cannot be resolved to an LSID},"") unless $LSID;
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select service_id, service_lsid from service where service_type = ?},undef,$term);
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:servicetype/)){
+ return (0, "can't delete from external ontology", $term);
+ }
+
+ my $LSID;
+ unless ($term =~ /^urn:lsid:biomoby.org:servicetype/){$LSID = $self->getServiceURI($term)} else {$LSID=$term}
+ return (0, q{Service type $term cannot be resolved to an LSID in the MOBY ontologies},"") unless $LSID;
+
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select service_id, service_lsid from service where service_lsid = ?}, undef, $LSID);
+
if (!defined $id){
return (0, q{Service type $term does not exist in the ontology},$lsid);
}
@@ -514,7 +540,11 @@
$term =~ s/^moby://; # if the term is namespaced, then remove that
my $sth;
- if ($term =~ /^urn\:lsid/){
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){
+ return (1, "external ontology", $term);
+ }
+
+ if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?");
} else {
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?");
@@ -540,10 +570,14 @@
#authority => $auth,
#contact_email => $email);
return (0, "WRONG ONTOLOGY!",'') unless ($self->ontology eq 'namespace');
- return (0, "requires a object type node",'') unless ($args{node});
+ return (0, "requires a namespace type node",'') unless ($args{node});
return (0, "requires an authURI ",'') unless ($args{authority});
return (0, "requires a contact email address",'') unless ($args{contact_email});
return (0, "requires a object description",'') unless ($args{description});
+ my $term = $args{node};
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){ # if it is an LSID, but not a MOBY LSID, than barf
+ return (0, "can't create a term in a non-MOBY ontology!", $term);
+ }
my $LSID = ($args{'node'} =~ /urn\:lsid/)?$args{'node'}:$self->setURI($args{'node'});
unless ($LSID){return (0, "Failed during creation of an LSID",'')}
@@ -575,8 +609,12 @@
my $LSID;
unless ($term =~ /urn\:lsid/){$LSID = $self->getNamespaceURI($term)} else {$LSID=$term}
return (0, q{Namespace type $term cannot be resolved to an LSID},"") unless $LSID;
+
+ if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:namespacetype/)){
+ return (0, "cannot delete a term from an external ontology", $term);
+ }
- my ($id, $lsid) = $self->dbh->selectrow_array(q{select namespace_id, namespace_lsid from namespace where namespace_type = ?},undef,$term);
+ my ($id, $lsid) = $self->dbh->selectrow_array(q{select namespace_id, namespace_lsid from namespace where namespace_lsid = ?},undef,$LSID);
unless ($id){return (0, q{Namespace type $term does not exist in the ontology},$lsid)}
# service1_id ISA service2_id?
@@ -839,7 +877,7 @@
sub setURI {
my ($self, $id) = @_;
my $URI;
- $id = lc($id);
+ # $id = lc($id);
if ($self->ontology eq 'object'){
$URI = "urn:lsid:biomoby.org:objectclass:$id"
} elsif ($self->ontology eq 'namespace'){
@@ -847,7 +885,7 @@
} elsif ($self->ontology eq 'service'){
$URI = "urn:lsid:biomoby.org:servicetype:$id"
} elsif ($self->ontology eq 'relationship'){
- $URI = "urn:lsid:biomoby.org:servicetype:$id"
+ $URI = "urn:lsid:biomoby.org:relationshiptype:$id"
} else {
$URI = 0
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2003/05/08 15:08:03 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2003/12/02 00:23:23 1.3
@@ -197,8 +197,8 @@
if ($self->service_type){
my $OE = MOBY::OntologyServer->new(ontology => 'service');
my ($success, $message, $servicetypeURI) = $OE->serviceExists(term => $self->service_type);
- unless ($success){return undef}
- $self->service_type_uri($servicetypeURI);
+ unless (($success || (($self->service_type =~ /urn:lsid/i) && !($self->service_type =~ /urn:lsid:biomoby.org/i)))){return undef}
+ ($self->service_type =~ /urn:lsid/)?$self->service_type_uri($self->service_type):$self->service_type_uri($servicetypeURI);
}
my ($serviceid, $category, $name, $typeURI, $authid,$url,$email,$authoritative,$desc) = $dbh->selectrow_array( # does this service already exist?
From mwilkinson at pub.open-bio.org Tue Dec 2 00:57:15 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 1 Dec 2003 19:57:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312020057.hB20vFsF021742@pub.open-bio.org>
mwilkinson
Mon Dec 1 19:57:15 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21719/MOBY
Modified Files:
Central.html Central.pm
Log Message:
I just remembered that Martin objected to me calling the non-MOBY services 'soap' services, so I now call them 'wsdl' services. Also fixed some more documentation errors, and fixed an error in the test suite.
moby-live/Perl/MOBY Central.html,1.10,1.11 Central.pm,1.114,1.115
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:23:23 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:57:15 1.11
@@ -27,7 +27,6 @@
...Registration Object...
-
Input XML :
-- <deregisterNamespace> - <namespaceType>MyNamespace</namespaceType> - </deregisterNamespace>-
Ouptut XML :
-...Registration Object...
--
input: listref; (articleName may be undef)
input =>[
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.63
retrieving revision 1.64
diff -u -r1.63 -r1.64
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:23:23 1.63
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:57:15 1.64
@@ -621,8 +621,8 @@
authURI => $authURI,
contactEmail => "your at mail.address",
description => $human_readable_description,
- category => "moby" | "cgi" | "soap" (currently only moby supported)
- URL => $URL_TO_SERVICE
+ category => "moby" | "cgi" | "wsdl" (currently only moby and wsdl supported)
+ URL => $URL_TO_SERVICE (or URL to WSDL document for wsdl-type services)
input: listref; (articleName may be undef)
input =>[
@@ -670,8 +670,8 @@
my $email = $a{contactEmail}; $email ||="";
my $URL = $a{URL}; $URL ||="";
my $desc = $a{description}; $desc ||="";
- my $Category = lc($a{Category}); $Category ||="moby";
- return $self->errorRegXML("Only MOBY Service Categories are currently allowed") unless ($Category eq 'moby');
+ my $Category = lc($a{category}); chomp $Category; $Category ||="";
+ return $self->errorRegXML("Only 'moby' and 'wsdl' Service Categories are currently allowed - you gave me $Category") unless (($Category eq 'moby') || ($Category eq 'wsdl'));
return $self->errorRegXML("All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary") unless (
$name && $type && $authURI && $email && $URL && $desc && $Category);
@@ -685,7 +685,7 @@
$authURI
$email ";
- if ($Category eq "moby") {
+ if ($Category eq "moby" || $Category eq 'soap') {
my %SEC;
if ($a{'secondary'} && ref($a{'secondary'} =~ /hash/i)){
%SEC = %{$a{secondary}}
@@ -778,7 +778,7 @@
}
$message .= "\n";
$message .= "";
- } else { return $self->errorRegXML("cannot register services with a client initialized with multiple registries")}
+ } else { return $self->errorRegXML("only 'moby' and 'wsdl' service types are allowed to be registered at this time.")}
#elsif ($Category eq "cgi") {
# my $IN = $a{input};
From mwilkinson at pub.open-bio.org Tue Dec 2 01:08:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 1 Dec 2003 20:08:24 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312020108.hB218O1t021842@pub.open-bio.org>
mwilkinson
Mon Dec 1 20:08:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21819/Perl/MOBY
Modified Files:
Central.html Central.pm
Log Message:
still calling Collection articles 'Complex' articles. This is confusing. It is now consistent thorughout the documentation
moby-live/Perl/MOBY Central.html,1.11,1.12 Central.pm,1.115,1.116
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 00:57:15 1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.html 2003/12/02 01:08:24 1.12
@@ -304,12 +304,10 @@
Input XML :
@@ -372,13 +378,13 @@
human readable COMPREHENSIVE description of your service]]>
</Description>
<Input>
- <!-- zero or more Primary (Simple and/or Complex) articles -->
+ <!-- zero or more Primary (Simple and/or Collection) articles -->
</Input>
<secondaryArticles>
<!-- zero or more INPUT Secondary articles -->
</secondaryArticles>
<Output>
- <!-- zero or more Primary (Simple and/or Complex) articles -->
+ <!-- zero or more Primary (Simple and/or Collection) articles -->
</Output>
</registerService>
@@ -553,10 +559,10 @@
<contactEmail>your at email.address</contactEmail>
<URL>http://endpoint.of.service</URL>;
<Input>
- <!-- one or more Simple and/or Complex Primary articles -->
+ <!-- one or more Simple and/or Collection Primary articles -->
</Input>
<Output>
- <!-- one or more Simple and/or Complex Primary articles -->
+ <!-- one or more Simple and/or Collection Primary articles -->
</Output>
<secondaryArticles>
<!-- one or more Secondary articles -->
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.115
retrieving revision 1.116
diff -u -r1.115 -r1.116
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 00:57:15 1.115
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/02 01:08:24 1.116
@@ -905,13 +905,13 @@
human readable COMPREHENSIVE description of your service]]>
-
+
@@ -1019,13 +1019,12 @@
# http://URL.to.your/CGI.pl
# your.URI.here
#
-#
+#
#
#
#
-#
#
#
@@ -1119,7 +1118,7 @@
my $dbh = $SVC->dbh;
return (-1,'Bad node') unless $node->getNodeType == ELEMENT_NODE;
- # this is a Simple or a Complex object
+ # this is a Simple or a Collection object
my $simp_coll = $node->getTagName;
$debug && &_LOG("TAGNAME in $inout _registerArticle is $simp_coll");
@@ -1431,10 +1430,10 @@
your at email.address
http://endpoint.of.service
-
+
From mwilkinson at pub.open-bio.org Tue Dec 9 21:06:51 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:06:51 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092106.hB9L6pJU028188@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:06:51 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28169/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
added a generic server-side parser to CommonSubs that should basically do all of the work for you and be compatible with the 0.6 API. Not yet documented; just testing on my own services first.
moby-live/Perl/MOBY CommonSubs.pm,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/12 16:47:16 1.28
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:06:51 1.29
@@ -143,9 +143,17 @@
use XML::DOM;
use MOBY::CrossReference;
use MOBY::Client::OntologyServer;
+use strict;
+use warnings;
- at ISA = qw(Exporter);
- at EXPORT_OK = qw(
+use constant COLLECTION => 1;
+use constant SIMPLE => 2;
+use constant BE_NICE => 1;
+use constant BE_STRICT => 0;
+
+our @ISA = qw(Exporter);
+our @EXPORT = qw(COLLECTION SIMPLE BE_NICE BE_STRICT);
+our @EXPORT_OK = qw(
getSimpleArticleIDs
getSimpleArticleNamespaceURI
simpleResponse
@@ -165,8 +173,13 @@
extractResponseArticles
getResponseArticles
getCrossReferences
+ genericServiceInputParser
+ COLLECTION
+ SIMPLE
+ BE_NICE
+ BE_STRICT
);
-%EXPORT_TAGS =(all => [qw(
+our %EXPORT_TAGS =(all => [qw(
getSimpleArticleIDs
getSimpleArticleNamespaceURI
simpleResponse
@@ -186,9 +199,39 @@
extractResponseArticles
getResponseArticles
getCrossReferences
+ genericServiceInputParser
+ COLLECTION
+ SIMPLE
+ BE_NICE
+ BE_STRICT
)]);
+
+sub genericServiceInputParser {
+ my ($message, $namespaces) = @_; # get the incoming MOBY query XML
+ my @inputs; # set empty response
+ my @queries = getInputs($message); # returns XML::DOM nodes
+
+ foreach my $query(@queries){
+ my $queryID = getInputID($query); # get the queryID attribute of the queryInput
+ my @input_articles = getArticles($query); # get the Simple/Collection articles making up this query
+ foreach my $input(@input_articles){ # input is a listref
+ my ($articleName, $article) = @{$input}; # get the named article
+ my $simple = isSimpleArticle($article); # articles may be simple or collection
+ my $collection = isCollectionArticle($article);
+ if ($collection){
+ my @simples = getCollectedSimples($article);
+ push @inputs, [COLLECTION,$queryID, \@simples];
+
+ } elsif ($simple){
+ push @inputs, [SIMPLE,$queryID,$simple];
+ }
+ }
+ }
+ return @inputs;
+}
+
#################################################
##################################
##################################
@@ -482,7 +525,7 @@
sub getInputs {
my ($XML) = @_;
-
+ my $moby;
unless (ref($XML) =~ /XML\:\:DOM/){
my $parser = new XML::DOM::Parser;
my $doc = $parser->parse($XML);
@@ -573,7 +616,7 @@
return undef unless $moby->getNodeType == ELEMENT_NODE;
return undef unless ($moby->getTagName =~ /queryInput/ || $moby->getTagName =~ /queryResponse/);
my @articles;
- foreach $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
+ foreach my $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
next unless $child->getNodeType == ELEMENT_NODE; # ignore whitespace
next unless ($child->getTagName =~ /Simple/ || $child->getTagName =~ /Collection/);
my $articleName = $child->getAttribute('articleName');
@@ -608,7 +651,7 @@
return undef unless ($moby->getTagName =~ /Collection/);
my @articles;
- foreach $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
+ foreach my $child($moby->getChildNodes){ # there may be more than one Simple/Collection per input; iterate over them
next unless $child->getNodeType == ELEMENT_NODE; # ignore whitespace
next unless ($child->getTagName =~ /Simple/);
push @articles, $child; # take the child elements, which are
$term
$def
")
} else {
- $response .= simpleResponse("")
+ $MOBY_RESPONSE .= simpleResponse("")
}
}
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
From mwilkinson at pub.open-bio.org Tue Dec 9 21:23:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:23:24 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092123.hB9LNOTl028369@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:23:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28350/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
dumb dumb dumb dumb
moby-live/Perl/MOBY CommonSubs.pm,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:06:51 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:23:24 1.30
@@ -209,7 +209,7 @@
sub genericServiceInputParser {
- my ($message, $namespaces) = @_; # get the incoming MOBY query XML
+ my ($message) = @_; # get the incoming MOBY query XML
my @inputs; # set empty response
my @queries = getInputs($message); # returns XML::DOM nodes
@@ -225,7 +225,7 @@
push @inputs, [COLLECTION,$queryID, \@simples];
} elsif ($simple){
- push @inputs, [SIMPLE,$queryID,$simple];
+ push @inputs, [SIMPLE,$queryID,$article];
}
}
}
From mwilkinson at pub.open-bio.org Tue Dec 9 21:30:33 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:30:33 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092130.hB9LUXWW028465@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:30:33 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28446/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
dumb dumb dumb dumb
moby-live/Perl/MOBY CommonSubs.pm,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:23:24 1.30
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:30:33 1.31
@@ -168,6 +168,7 @@
extractRawContent
collectionResponse
validateNamespaces
+ validateThisNamespace
isSimpleArticle
isCollectionArticle
extractResponseArticles
@@ -194,6 +195,7 @@
extractRawContent
collectionResponse
validateNamespaces
+ validateThisNamespace
isSimpleArticle
isCollectionArticle
extractResponseArticles
From mwilkinson at pub.open-bio.org Tue Dec 9 21:38:39 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 16:38:39 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092138.hB9LcdU5028578@pub.open-bio.org>
mwilkinson
Tue Dec 9 16:38:39 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28559/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
initialize possibly undef values
moby-live/Perl/MOBY CommonSubs.pm,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:30:33 1.31
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:38:39 1.32
@@ -370,8 +370,12 @@
sub simpleResponse {
my ($data, $articleName, $qID) = @_; # articleName optional
- $data ||='';
$qID = &_getQueryID($qID) if ref($qID) =~ /XML::DOM/; # in case they send the DOM instead of the ID
+
+ $data ||=''; # initialize to avoid uninit value errors
+ $qID ||="";
+ $articleName ||="";
+
if ($articleName) {
return "
From mwilkinson at pub.open-bio.org Tue Dec 9 22:24:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 17:24:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092224.hB9MO3AB028801@pub.open-bio.org>
mwilkinson
Tue Dec 9 17:24:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv28763/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
updating my GO services to be 0.6 compliant and a bit more readable
moby-live/Perl/scripts/Services LocalServices.pm,1.37,1.38
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -u -r1.37 -r1.38
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/09 21:06:51 1.37
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/09 22:24:03 1.38
@@ -10,6 +10,7 @@
use SOAP::Lite;
use DBI;
use DBD::mysql;
+use GO::AppHandle;
use MIME::Base64;
use XML::DOM;
use MOBY::Client::OntologyServer;
@@ -24,85 +25,60 @@
#getNodeContentWithArticle
use vars qw(@ISA);
- at ISA = qw(SOAP::Server::Parameters); # uncomment this line if you want access to the SOM as the
- # last parameter passed to the subroutine
sub getGoTerm {
my ($caller, $message) = @_;
my $MOBY_RESPONSE;
- my (@inputs)= genericServiceInputParser($message, []); # ([SIMPLE, $queryID, $simple],...)
+ my (@inputs)= genericServiceInputParser($message); # ([SIMPLE, $queryID, $simple],...)
return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- my @validNS = validateNamespaces(); # ONLY do this if you are intending to be namespace aware!
+ my @validNS = validateNamespaces("GO"); # ONLY do this if you are intending to be namespace aware!
+
+ my $dbh = _dbAccess('go');
+ die "can't connect to GO database\n" unless $dbh;
+ my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
- my @accessions;
foreach (@inputs){
my ($articleType, $ID, $input) = @{$_};
unless ($articleType == SIMPLE){
- $MOBY_RESPONSE .= simpleResponse("", "", $ID) ;
+ $MOBY_RESPONSE .= simpleResponse("", "Collection_Article_Not_allowed_as_input", $ID);
next;
} else {
my $ns = getSimpleArticleNamespaceURI($input);
- ((push @accessions, undef) && (next)) unless validateThisNamespace($ns, @validNS);
- push @accessions, defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):1;
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $accession = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ unless (defined($accession)){
+ $MOBY_RESPONSE .= simpleResponse("", "Invalid_Accession", $ID);
+ next;
+ }
+ unless ($accession =~/^GO:/){
+ $accession = "GO:$accession"; # we still haven't decided on whether id's should include the prefix...
+ }
+ $sth->execute($accession);
+ my ($term, $def) = $sth->fetchrow_array;
+ if ($term){
+ $MOBY_RESPONSE .= simpleResponse("
+
+ $term
+ $def
+ ", "GO_Term_From_ID", $ID)
+ } else {
+ $MOBY_RESPONSE .= simpleResponse("", "NO_Term_Found", $ID)
+ }
}
}
- my $dbh = _dbAccess('go');
- die "can't connect to GO database\n" unless $dbh;
- my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
- foreach my $acc(@accessions){
- unless ($acc =~/^GO:/){
- $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
- }
- $sth->execute($acc);
- my ($term, $def) = $sth->fetchrow_array;
- if ($term){
- $MOBY_RESPONSE .= simpleResponse("
-
- $term
- $def
- ")
- } else {
- $MOBY_RESPONSE .= simpleResponse("")
- }
- }
return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
-
sub getGoTermAssociations {
+ my ($caller, $message) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($message); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- my $SOM = pop;
- my ($self, $data) = @_;
- my $response = "";
- my @accessions;
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'GO');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace GO does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data);
- foreach (@input_nodes){
- my ($input) = @{$_}; # this service only allows one input per query, so take the first
- my $ns = getSimpleArticleNamespaceURI($input);
- push @accessions, undef unless $ns eq $VALID_NAMESPACE; # if we have been sent an invalid namespace, then stack an undef as a response
- my ($id) = getSimpleArticleIDs($ns, [$input]);
- if (defined $id){
- push @accessions, $id;
- } else {
- push @accessions, undef;
- }
- }
-
- use DBI;
- use DBD::mysql;
my $dbh = _dbAccess('go');
- die "can't connecvt to database\n" unless $dbh;
+ die "can't connect to database\n" unless $dbh;
my $sth = $dbh->prepare("
select
gp.symbol,
@@ -125,27 +101,39 @@
and a.is_not = 0
and t.id = d.term_id
order by species_id");
-
- foreach my $acc(@accessions){
- unless ($acc =~/^GO:/){
- $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
- }
- my @simples;
- $sth->execute($acc);
- while (my ($symb, $sp, $namsp, $type, $name, $def) = $sth->fetchrow_array){
- my $response_data .= "\n";
- push @simples, $response_data;
+
+ my @validNS = validateNamespaces("GO"); # ONLY do this if you are intending to be namespace aware!
+
+ foreach (@inputs){
+ my ($articleType, $ID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= collectionResponse([], "Collection_Article_Input_Invalid", $ID) ;
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= $MOBY_RESPONSE .= collectionResponse([], "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $acc, defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ unless (defined($acc)){
+ $MOBY_RESPONSE .= collectionResponse([], "Invalid_Accession", $ID);
+ next;
+ }
+ unless ($acc =~/^GO:/){
+ $acc = "GO:$acc"; # we still haven't decided on whether id's should include the prefix...
+ }
+ my @simples;
+ $sth->execute($acc);
+ while (my ($symb, $sp, $namsp, $type, $name, $def) = $sth->fetchrow_array){
+ my $response_data .= "\n";
+ push @simples, $response_data;
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples,"Known_GO_Term_Associations",$ID); # after all images have been collected, create the collection
}
- $response .= collectionResponse(\@simples); # after all images have been collected, create the collection
}
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
@@ -153,67 +141,51 @@
sub RetrieveGOFromKeywords {
my $SOM = pop;
my ($self, $query) = @_;
- use GO::AppHandle;
-
- my $ua = new LWP::UserAgent;
- my $req = new HTTP::Request GET => 'http://www.godatabase.org/dev/database/server.cfg';
- my $res = $ua->request($req);
+ # INITIALIZE CONNECTION TO GO DB
my $host; my $dbname;
$host = "sin.lbl.gov";
$dbname = "go";
-# if ($res->is_success) {
- # my $resp = $res->content;
- # if ($resp =~ /(\w+)\@(\S+)/){
- # $host = $2;
- # $dbname= $1;
- # } else {
- # return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- # }
- #}
my %connect_hash;
$connect_hash{-dbname}=$dbname;
$connect_hash{-dbhost}=$host;
-
my $GO_API = GO::AppHandle->connect(%connect_hash);
unless ($GO_API){
return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
}
+ # DB is now initialized
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'Global_Keyword');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace Global_Keyword does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($query); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
- # now start analyzing the input data
- my @input_nodes = getInputArticles($query); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my $response;
- foreach (@input_nodes){
- my $input = $_->[0]; # we only allow one input object per query
- my ($kw) = getSimpleArticleIDs($VALID_NAMESPACE, [$input]);
- ($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
- my @terms = @{$GO_API->get_terms({search=>"$kw"})};
- next unless($terms[0]);
- my @simples;
- foreach my $term(@terms){
- my $acc = $term->public_acc;
- my $def = $term->definition;
- my $name = $term->name;
- push @simples, "
-
-
- $name
- $def
- ";
+ my @validNS = validateNamespaces("Global_Keyword"); # ONLY do this if you are intending to be namespace aware!
+ foreach (@inputs){
+ my ($articleType, $ID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= collectionResponse([], "Collection_Input_Invalid", $ID) ;
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= collectionResponse([], "Invalid_Namespace", $ID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my $kw = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ ($MOBY_RESPONSE .= collectionResponse([], "No_Keyword", $ID) && (next)) unless defined $kw;
+ ($kw) = (($kw =~ /^\s*(.*)\s*$/) && ($1));
+ my @terms = @{$GO_API->get_terms({search=>"$kw"})};
+ next unless($terms[0]);
+ my @simples;
+ foreach my $term(@terms){
+ my $acc = $term->public_acc;
+ my $def = $term->definition;
+ my $name = $term->name;
+ push @simples, "
+ $name
+ $def
+ ";
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples, "GO_terms_from_keywords", $ID);
}
- $response .= collectionResponse(\@simples);
- }
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ }
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
From mwilkinson at pub.open-bio.org Tue Dec 9 22:24:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 9 Dec 2003 17:24:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312092224.hB9MO30d028782@pub.open-bio.org>
mwilkinson
Tue Dec 9 17:24:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28763/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
updating my GO services to be 0.6 compliant and a bit more readable
moby-live/Perl/MOBY CommonSubs.pm,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 21:38:39 1.32
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/09 22:24:03 1.33
@@ -248,16 +248,16 @@
function : to get the IDs of simple articles that are in the given namespace
usage : my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
args : (in order)
- $Namespace - (required) a namespace stringfrom the MOBY namespace ontology
+ $Namespace - (required) a namespace stringfrom the MOBY namespace ontology, or undef if you don't care
\@Simples - (required) a listref of Simple XML::DOM nodes
i.e. the XML::DOM representing an XML structure like this:
- note : it will return *only* the ids that are in the given namespace
+ note : it will return *only* the ids that are in the given namespace, if you provide one
but since you are required to return an output for every input
(even if it is invalid) this routine will return undef for
- those articles that are not in that namespace
+ those articles in the list that are not in that namespace so you can keep track
=cut
@@ -271,45 +271,52 @@
my @input_nodes = @{$input_nodes};
my $OS = MOBY::Client::OntologyServer->new;
my ($s, $m);
- ($s, $m, $desired_namespace) = $OS->namespaceExists(term => $desired_namespace); # returns (success, message, lsid)
- return undef unless $s; # bail if not successful
+ if ($desired_namespace){
+ ($s, $m, $desired_namespace) = $OS->namespaceExists(term => $desired_namespace); # returns (success, message, lsid)
+ unless ($s){ # bail if not successful
+ print STDERR "MOBY::CommonSubs WARNING ** the namespace $desired_namespace does not exist in the MOBY ontology, and is not a valid LSID\n";
+ return undef;
+ }
+ }
- my @accessions;
+ my @ids;
foreach my $in(@input_nodes){
#$in = "
- note : it will return *only* the ids that are in the given namespace, if you provide one
- but since you are required to return an output for every input
- (even if it is invalid) this routine will return undef for
- those articles in the list that are not in that namespace so you can keep track
+ note : If you provide a namespace, it will return *only* the ids that are in the given namespace,
+ but will return 'undef' for any articles in the WRONG namespace so that you get an
+ equivalent number of outputs to inputs.
+
+ Note that if you call this with a single argument, this is assumed to
+ be \@Articles, so you will get ALL id's regardless of namespace!
=cut
sub getSimpleArticleIDs {
my ($desired_namespace, $input_nodes) = @_;
- return undef unless $input_nodes;
+ if ($desired_namespace && !($input_nodes)){ # if called with ONE argument, then these are the input nodes!
+ $input_nodes = $desired_namespace;
+ $desired_namespace = undef;
+ }
$input_nodes = [$input_nodes] unless ref($input_nodes) =~ /ARRAY/; # be flexible!
return undef unless scalar @{$input_nodes};
@@ -281,6 +286,7 @@
my @ids;
foreach my $in(@input_nodes){
+ next unless $in;
#$in = "
+
+
+
+ ";
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my $gb = SHoundGetGenBankff($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
+ $MOBY_RESPONSE .= "
+
+
+
+ ";
+ }
}
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $response .= simpleResponse("
-
- $length
- ");
- } else {
- $response .= simpleResponse("");
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+}
+
+sub GenbankAccVirtualSequenceRetrieve {
+ my ($self, $data) = @_;
+
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless ($articleType == SIMPLE){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ (($MOBY_RESPONSE .= simpleResponse("", "no_input_object", $qID)) && (next)) unless (defined $input);
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse([], "Invalid_Namespace", $qID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
+ my ($acc) = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
+ ($MOBY_RESPONSE .= collectionResponse([], "No_Accession_provided", $qID) && (next)) unless defined $acc;
+ use Bio::DB::GenBank;
+ my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
+ my $seq = $gb->get_Seq_by_acc($acc);
+ my $length;
+ if ($seq){$length = $seq->length;}
+ if ($length){
+ $MOBY_RESPONSE .= simpleResponse("
+
+ $length
+ ", "", $qID);
+ } else {
+ $MOBY_RESPONSE .= simpleResponse("", "sequence_has_no_length", $qID);
+ }
}
}
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
}
+
sub GenbankAccSequenceRetrieve {
my ($self, $data) = @_;
my $response; my @accessions;
From mwilkinson at pub.open-bio.org Wed Dec 10 22:34:36 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 10 Dec 2003 17:34:36 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102234.hBAMYaZc032738@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:34:36 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv32719/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
small changes to service output
moby-live/Perl/scripts/Services LocalServices.pm,1.41,1.42
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -r1.41 -r1.42
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:22:03 1.41
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:34:36 1.42
@@ -70,7 +70,7 @@
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub getGoTermAssociations {
@@ -135,7 +135,7 @@
$MOBY_RESPONSE .= collectionResponse(\@simples,"Known_GO_Term_Associations",$ID); # after all images have been collected, create the collection
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -187,7 +187,7 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "GO_terms_from_keywords", $ID);
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -223,7 +223,7 @@
# do your thing here!
}
}
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub MOBYSHoundGetGenBankff {
@@ -281,8 +281,8 @@
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
+ #print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
sub GenbankAccVirtualSequenceRetrieve {
From mwilkinson at pub.open-bio.org Wed Dec 10 22:40:57 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 10 Dec 2003 17:40:57 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102240.hBAMevNm000374@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:40:56 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv355/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
Doh. Use the output format you dummy
moby-live/Perl/scripts/Services LocalServices.pm,1.42,1.43
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -r1.42 -r1.43
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:34:36 1.42
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:40:56 1.43
@@ -262,21 +262,23 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+ $MOBY_RESPONSE .= simpleResponse("
- ";
+ ",
+ "", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+ $MOBY_RESPONSE .= simpleResponse("
- ";
+ ",
+ "", $qID);
}
}
}
From mwilkinson at pub.open-bio.org Wed Dec 10 22:45:12 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 10 Dec 2003 17:45:12 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312102245.hBAMjCKF000512@pub.open-bio.org>
mwilkinson
Wed Dec 10 17:45:12 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv493/Perl/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
missed one
moby-live/Perl/scripts/Services LocalServices.pm,1.43,1.44
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.43
retrieving revision 1.44
diff -u -r1.43 -r1.44
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:40:56 1.43
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/10 22:45:11 1.44
@@ -256,7 +256,7 @@
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my $gb = SHoundGetGenBankff($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= "
+
+
+
+ ",
+ "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my $gb = SHoundGetGenBankff($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ",
+ "", $qID);
+ }
+ }
}
+ $aa = SHoundFini();
+ #print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
-sub MOBYSHoundGetGenBankff {
+sub _makeSeqObj {
+ my ($id) = @_;
+ my $gb = SHoundGetGenBankff($id);
+ return undef unless $gb;
+ my $gbio = IO::String->new($gb);
+ my $sio = Bio::SeqIO->new(-fh => \*$gbio, '-format' => 'genbank');
+ my $seq = $sio->next_seq;
+ return ($seq, $seq->length, $seq->seq);
+}
+
+sub MOBYSHoundGetGenBankVirtSequence {
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
@@ -254,30 +345,167 @@
my ($identifier) = getSimpleArticleIDs($input);
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
- my $gb = SHoundGetGenBankff($identifier);
+ my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+ ".($SEQ->length)."
+ ", "", $qID);
+ } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ my $gi = SHoundFindAcc($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ".($SEQ->length)."
+ ",
+ "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("
+
+
+
+ ".($SEQ->length)."
+ ",
+ "", $qID);
+ }
+ }
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub MOBYSHoundGetGenBankWhateverSequence {
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+
+ my %objtype = ('dna', "DNASequence", 'rna', "RNASequence", 'protein', "AminoAcidSequence");
+
+ my $aa = SHoundInit("TRUE", "MOBY_SHoundGetGenBankff_Service"); # initialize SeqHound
+ $aa = SHoundIsInited(); # confirm initialization
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter) unless $aa eq "TRUE";
+
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my %validNS;
+ foreach (qw(NCBI_Acc NCBI_gi PIR Swiss-Prot EMBL PDB)){
+ my ($valid) = validateNamespaces($_); # we are going to ignore anything that is invalid
+ $validNS{$_} = $valid;
+ }
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && (defined($input))){ # we only accept simple inputs to this service
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send back a blank response for this queryID
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $qID)) && next) unless validateThisNamespace($ns, values(%validNS)); # return blank if they have sent us a namespace we don't understand
+ my ($identifier) = getSimpleArticleIDs($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
+ if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
+ my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ my $objType = $objtype{$SEQ->alphabet};
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$identifier'>
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ my $gi = SHoundFindAcc($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my $objType = $objtype{$SEQ->alphabet};
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
+
+
+
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ } else {
+ my $gi = SHoundFindName($identifier);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
+ my ($SEQ, $length, $seq) = _makeSeqObj($gi);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my $objType = $objtype{$SEQ->alphabet};
+ $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
+
+
+
+ ".($SEQ->length)."
+ ".($SEQ->seq)."
+ ", "", $qID);
+ }
+ }
+ }
+ $aa = SHoundFini();
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub MOBYSHoundGetGenBankFasta {
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+
+ my $aa = SHoundInit("TRUE", "MOBY_SHoundGetGenBankff_Service"); # initialize SeqHound
+ $aa = SHoundIsInited(); # confirm initialization
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter) unless $aa eq "TRUE";
+
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my %validNS;
+ foreach (qw(NCBI_Acc NCBI_gi PIR Swiss-Prot EMBL PDB)){
+ my ($valid) = validateNamespaces($_); # we are going to ignore anything that is invalid
+ $validNS{$_} = $valid;
+ }
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && (defined($input))){ # we only accept simple inputs to this service
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ; # send back a blank response for this queryID
+ next;
+ } else {
+ my $ns = getSimpleArticleNamespaceURI($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "Invalid_Namespace", $qID)) && next) unless validateThisNamespace($ns, values(%validNS)); # return blank if they have sent us a namespace we don't understand
+ my ($identifier) = getSimpleArticleIDs($input);
+ (($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
+
+ if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
+ my $gb = SHoundGetFasta($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("
+ $MOBY_RESPONSE .= simpleResponse("
- ",
+ ",
"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
- my $gb = SHoundGetGenBankff($gi);
+ my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("
+ $MOBY_RESPONSE .= simpleResponse("
- ",
+ ",
"", $qID);
}
}
@@ -287,6 +515,7 @@
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
+
sub GenbankAccVirtualSequenceRetrieve {
my ($self, $data) = @_;
From mwilkinson at pub.open-bio.org Thu Dec 11 18:08:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 11 Dec 2003 13:08:14 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312111808.hBBI8EdB004309@pub.open-bio.org>
mwilkinson
Thu Dec 11 13:08:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv4290
Modified Files:
MOBY-Client05.cgi
Log Message:
added Xrefs to my new services. Small change in the client program to improve readability
moby-live/Perl/scripts MOBY-Client05.cgi,1.25,1.26
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi 2003/11/06 16:42:41 1.25
+++ /home/repository/moby/moby-live/Perl/scripts/MOBY-Client05.cgi 2003/12/11 18:08:14 1.26
@@ -1,6 +1,6 @@
#!/usr/bin/perl -w
use strict;
-use lib '/usr/local/apache/cgi-bin/MOBY05';
+use lib '/usr/local/apache/cgi-bin/BIO/moby-live/Perl';
use MOBY::Client::Central;
use MOBY::Client::Service;
@@ -466,11 +466,15 @@
my $output = "(";
foreach my $param(@{$objs}){
if ($param->isSimple){
- $output .= "Simple:".($param->objectType)." ,";
+ my $type = (($param->objectType =~ /\:(\S+)$/) && $1);
+ $type = $param->objectType unless $type;
+ $output .= "Simple: $type ,";
} else {
$output .= "Collection:[";
foreach my $simp(@{$param->Simples}){
- $output .= ($simp->objectType).",";
+ my $type = (($simp->objectType =~ /\:(\S+)$/) && $1);
+ $type = $simp->objectType unless $type;
+ $output .= "$type,";
}
chop $output;
$output .="],";
From mwilkinson at pub.open-bio.org Thu Dec 11 18:08:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 11 Dec 2003 13:08:14 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312111808.hBBI8EFh004328@pub.open-bio.org>
mwilkinson
Thu Dec 11 13:08:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv4290/Services
Modified Files:
LocalServices.pm
Log Message:
added Xrefs to my new services. Small change in the client program to improve readability
moby-live/Perl/scripts/Services LocalServices.pm,1.45,1.46
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 15:36:38 1.45
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:08:14 1.46
@@ -9,6 +9,7 @@
use strict;
use SeqHound;
use SOAP::Lite;
+use Bio::SeqIO;
use DBI;
use DBD::mysql;
use GO::AppHandle;
@@ -317,6 +318,16 @@
return ($seq, $seq->length, $seq->seq);
}
+sub _getXrefs {
+ my ($seq) = @_; # bioperl seq object
+ #my $gi = $seq->primary_id; # e.g. 163483
+ #print STDERR "\n\n*********************$ gi\n\n";
+ my $acc = $seq->accession; # e.g. A123434
+ my $kw = $seq->species->binomial; # e.g. mus musculus
+ my $taxon = $seq->species->ncbi_taxid; # e.g. 1234
+ return ($acc, $kw, $taxon);
+}
+
sub MOBYSHoundGetGenBankVirtSequence {
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
@@ -346,39 +357,53 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
- (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("
- ".($SEQ->length)."
- ", "", $qID);
+
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .=" \n".($SEQ->length)."
+
-
-
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
- ".($SEQ->length)."
- ",
- "", $qID);
+ ".($SEQ->length)."
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("
-
-
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
+ my $tempresponse = "\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
- ".($SEQ->length)."
- ",
- "", $qID);
+ ".($SEQ->length)."
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
}
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+# print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -413,43 +438,59 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_Identifier_provided", $qID)) && next) unless $identifier;
if ($ns eq $validNS{'NCBI_gi'}){ # gi numbers are used natively by SeqHound
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$identifier'>
- ".($SEQ->length)."
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .=" \n".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
} elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
-
-
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
+ my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- $MOBY_RESPONSE .= simpleResponse("<$objType namespace='NCBI_gi' id='$gi'>
-
-
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ if ($taxon){ $tempresponse .="\n"}
+ if ($kw){$tempresponse .="\n"}
+ if ($acc){$tempresponse .="\n"}
+ $tempresponse .="\n";
+ $tempresponse .="
".($SEQ->length)."
".($SEQ->seq)."
- ", "", $qID);
+ ";
+ $MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
}
}
}
$aa = SHoundFini();
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+# print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -516,335 +557,6 @@
}
-sub GenbankAccVirtualSequenceRetrieve {
- my ($self, $data) = @_;
-
- my $MOBY_RESPONSE;
- my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
-
- my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
-
- foreach (@inputs){
- my ($articleType, $qID, $input) = @{$_};
- unless ($articleType == SIMPLE){
- $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
- next;
- } else {
- (($MOBY_RESPONSE .= simpleResponse("", "no_input_object", $qID)) && (next)) unless (defined $input);
- my $ns = getSimpleArticleNamespaceURI($input);
- (($MOBY_RESPONSE .= simpleResponse([], "Invalid_Namespace", $qID)) && (next)) unless validateThisNamespace($ns, @validNS); # only do this if you are truly validating namespaces
- my ($acc) = defined(getSimpleArticleIDs($ns, [$input]))?getSimpleArticleIDs($ns,[$input]):undef;
- ($MOBY_RESPONSE .= collectionResponse([], "No_Accession_provided", $qID) && (next)) unless defined $acc;
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $MOBY_RESPONSE .= simpleResponse("
-
- $length
- ", "", $qID);
- } else {
- $MOBY_RESPONSE .= simpleResponse("", "sequence_has_no_length", $qID);
- }
- }
- }
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter);
-}
-
-sub GenbankAccSequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_Acc');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_acc($acc);
- my $length;my $sequence;
- if ($seq){$length = $seq->length;$sequence = $seq->seq}
- if ($length){
- $response .= simpleResponse("
-
- $length
- $sequence
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-}
-sub GenbankGIVirtualSequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_gi');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_gi($acc);
- my $length;
- if ($seq){$length = $seq->length;}
- if ($length){
- $response .= simpleResponse("
-
- $length
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
-
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse
-}
-
-sub GenbankGISequenceRetrieve {
- my ($self, $data) = @_;
- my $response; my @accessions;
-
- # first, get the valid URI for the namespace that we accept
- my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $m, $VALID_NAMESPACE) = $OS->namespaceExists(term => 'NCBI_gi');
- unless ($VALID_NAMESPACE){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- @accessions = getSimpleArticleIDs($VALID_NAMESPACE, \@inputs);
- foreach my $acc(@accessions){
- unless (defined $acc){
- $response .= simpleResponse("");
- next;
- }
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
- my $seq = $gb->get_Seq_by_gi($acc); # get the sequence object for each gi
- my $length;my $sequence;
- if ($seq){$length = $seq->length;$sequence = $seq->seq} # if it exists, get the length and sequence
- if ($length){ # and construct the response
- $response .= simpleResponse("
-
- $length
- $sequence
- ");
- } else {
- $response .= simpleResponse("");
- }
- }
- $response = responseHeader() . $response . responseFooter();
- my $SOAPResponse = SOAP::Data->type('base64' => $response);
- return $SOAPResponse;
-}
-#=================================================
-#=================================================
-#=================================================
-
-sub GenbankCompleteSequenceRetrieve {
-
-# this service is registered as consuming NCBI_Acc OR NCBI_gi
-# and producing GenericSequence objects. However, it will
-# actually produce DNA, RNA or PRotein objects, as appropriate
-# and will produce a cross-reference block as well
-
- my ($self, $data) = @_;
- my $response; my @gis;
-
- my ($GB_Acc_LSID, $GB_gi_LSID) = validateNamespaces('NCBI_Acc', 'NCBI_gi');
- unless ($GB_Acc_LSID && $GB_gi_LSID){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc or NCBI_gi does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # now start analyzing the input data
- my @input_nodes = getInputArticles($data); # returns ([obj1, obj2], [obj3, obj4], [obj5], [obj6],...)
- my @inputs;
- foreach (@input_nodes){
- push @inputs, $_->[0]; # we only allow one input object per query
- }
- foreach my $node(@inputs){
-
- my $namespace_LSID = getSimpleArticleNamespaceURI($node); # get the LSID of the namespace for this input object
- unless (($namespace_LSID eq $GB_Acc_LSID) || ($namespace_LSID eq $GB_gi_LSID)){ # validate the namespace
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if bad namespace
- next;
- }
-
- my ($ID)= getSimpleArticleIDs($namespace_LSID, [$node]); # get the ID within this namespace
- unless (defined $ID){ # send a blank if we failed to get an id,
- $response .= simpleResponse(""); # because we have to send one response per input
- next;
- }
-
- use Bio::DB::GenBank;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string'); # now that we have a namespace and ID, we are ready to retrieve
- my $seq;
- if ($namespace_LSID eq $GB_Acc_LSID){ # if the namespace is a genbank Accession thebn
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the accession
- } elsif ($namespace_LSID eq $GB_gi_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_gi($ID); # get the sequence object for the gi
- } else {
- $response .= simpleResponse(""); # if it is neither,then send a blank as required by the API
- next;
- }
-
- my $length;my $sequence;
- if ($seq){
- $length = $seq->length;$sequence = $seq->seq; # if it exists, get the length and sequence
- } else {
- $response .= simpleResponse(""); # if we got nada, then send a blank as required
- next;
- }
-
- my $gi = $seq->primary_id; # e.g. 163483
- my $acc = $seq->accession; # e.g. A123434
- my $kw = $seq->species->binomial; # e.g. mus musculus
- my $moltype = $seq->alphabet; # 'dna', 'rna', 'protein'
- my $taxon = $seq->species->ncbi_taxid; # e.g. 1234
-
- my $ObjectType="GenericSequence"; # set it as the generic as default
- if ($moltype eq 'dna'){$ObjectType = "DNASequence"} # set to DNA
- elsif ($moltype eq 'rna'){$ObjectType = "RNASequence"} # set to RNA
- elsif ($moltype eq 'protein'){$ObjectType = "AminoAcidSequence"} # set to Protein
-
- if ($length){ # and construct the response; luckily, all of these objects have exactly the same structure :-)
- my $tempresponse .= "
-
- ";
- if ($taxon){ $tempresponse .=""}
- if ($kw){$tempresponse .=""}
- if ($acc && !($namespace_LSID eq $GB_Acc_LSID)){$tempresponse .=""}
- if ($gi && !($namespace_LSID eq $GB_gi_LSID)){$tempresponse .=""}
- $tempresponse .="
- $length
- $sequence
- ";
- $response .= simpleResponse($tempresponse);
- } else {
- $response .= simpleResponse(""); # if we failed to get a sequence length, then something weird happened, so just ignore it
- }
- }
- my $fullresponse = responseHeader() . $response . responseFooter(); # add the headers and footers
- my $SOAPResponse = SOAP::Data->type('base64' => $fullresponse); # base 64 encode it (optional)
- return $SOAPResponse;
-}
-
-
-sub GenbankRecordRetrieve {
- use Bio::SeqIO;
- use IO::String;
- my ($self, $data) = @_;
- my $response; # prepare a variable to hold the responses
-
- # Step 1 - validate the namespaces you plan to accept as input
- my ($GB_Acc_LSID, $GB_gi_LSID, $EMBL_LSID) = validateNamespaces('NCBI_Acc', 'NCBI_gi', 'EMBL');
- unless ($GB_Acc_LSID && $GB_gi_LSID && $EMBL_LSID){ # unless we could get the known namespace LSID's we should bail because somethign is very very wrong!
- print STDERR "the namespace NCBI_Acc, NCBI_gi, or EMBL_LSID that we are expecting does not exist in the MOBY namespace ontology\n";
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()); # base 64 encode it (optional)
- }
-
- # Step 2 - get your input objects
- # in this case, we have registered as accepting
- # only simple inputs (not collections), therefore
- # we can insist on that constraint.
- my @inputs = getInputArticles($data); # returns ([SimpleDOM], [SimpleDOM],...), each represents a unique query input
- foreach my $node(@inputs){
- # do a bit of simple validation
- # the next 12 lines or so are ~cut-n-paste for every service
- unless (isSimpleArticle($node)){ # we only allow Simple inputs to this service, ignore anything else
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if it fails
- next;
- }
- my $namespace_LSID = getSimpleArticleNamespaceURI($node); # get the LSID of the namespace for this input object
- unless (($namespace_LSID eq $GB_Acc_LSID) || ($namespace_LSID eq $GB_gi_LSID) || $namespace_LSID eq $EMBL_LSID){ # validate the namespace
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if bad namespace
- next;
- }
- my ($ID)= getSimpleArticleIDs($namespace_LSID, [$node]); # get the ID within this namespace
- unless (defined $ID){ # send a blank if we failed to get an id,
- $response .= simpleResponse(""); # because we have to send one response per input, send a blank if there is no id (?!?)
- next;
- }
-
- # Now, do the analysis
- use Bio::DB::GenBank;
- use Bio::DB::EMBL;
- my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string'); # now that we have a namespace and ID, we are ready to retrieve
- my $emb = new Bio::DB::EMBL(-retrievaltype => 'io_string');
- my $seq;
- if ($namespace_LSID eq $GB_Acc_LSID){ # if the namespace is a genbank Accession thebn
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the accession
- } elsif ($namespace_LSID eq $GB_gi_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_gi($ID); # get the sequence object for the gi
- } elsif ($namespace_LSID eq $EMBL_LSID) { # if the namespace is a genbank gi
- $seq = $gb->get_Seq_by_acc($ID); # get the sequence object for the gi
- } else {
- $response .= simpleResponse(""); # if it is neither,then send a blank as required by the API
- next;
- }
-
- my $string;
- my $stringio = IO::String->new($string);
- my $out = Bio::SeqIO->new('-fh' => $stringio,
- '-format' => 'genbank');
- # output goes into $string
- $out->write_seq($seq);
- $response .= simpleResponse("
-
+
-
+
",
"", $qID);
} else {
@@ -295,9 +295,9 @@
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
}
@@ -359,12 +359,12 @@
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "\n";
+ my $tempresponse = "\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
- $tempresponse .=" \n".($SEQ->length)."
+ $tempresponse .="\n".($SEQ->length)."
\n\n";
+ my $tempresponse = "\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -389,13 +389,13 @@
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "\n\n";
+ my $tempresponse = "\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -441,12 +441,12 @@
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'>\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
- $tempresponse .=" \n".($SEQ->length)."
+ $tempresponse .="\n".($SEQ->length)."
".($SEQ->seq)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
@@ -457,13 +457,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
".($SEQ->seq)."
";
@@ -475,13 +475,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n\n";
if ($taxon){ $tempresponse .="\n"}
if ($kw){$tempresponse .="\n"}
if ($acc){$tempresponse .="\n"}
$tempresponse .="\n";
$tempresponse .="
-
+
".($SEQ->length)."
".($SEQ->seq)."
";
@@ -532,9 +532,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
} else {
@@ -543,9 +543,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
-
+
-
+
",
"", $qID);
}
From mwilkinson at pub.open-bio.org Thu Dec 11 22:30:53 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 11 Dec 2003 17:30:53 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312112230.hBBMUrFG005178@pub.open-bio.org>
mwilkinson
Thu Dec 11 17:30:53 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv5159/Services
Modified Files:
LocalServices.pm
Log Message:
two more services dealing with taxon data
moby-live/Perl/scripts/Services LocalServices.pm,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:22:02 1.47
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 22:30:53 1.48
@@ -46,13 +46,13 @@
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
my @validNS = validateNamespaces("NCBI_Acc"); # ONLY do this if you are intending to be namespace aware!
foreach (@inputs){
my ($articleType, $qID, $input) = @{$_};
- unless ($articleType == SIMPLE){
+ unless (($articleType == SIMPLE) && ($input)){
$MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
next;
} else {
@@ -69,6 +69,97 @@
##################################################
##################################################
+sub getTaxChildNodes { # WORKS
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= collectionResponse([], "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= collectionResponse([], "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $children = SHoundGetTaxChildNodes($identifier);
+ $MOBY_RESPONSE .= collectionResponse([], "nothing_found", $qID) unless ($children);
+ my @children = split ",", $children;
+ my @simples;
+ foreach my $taxon (@children){
+ next unless $taxon;
+ $taxon =~ s/\s//g;
+ push @simples, "";
+ }
+ $MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= simpleResponse("", "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $parent = SHoundGetTaxParent($identifier);
+ $MOBY_RESPONSE .= simpleResponse("", "nothing_found", $qID) unless ($parent);
+ $parent && ($MOBY_RESPONSE .= simpleResponse("", "", $qID));
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
+
+
+sub getTaxNameFromTaxID{ # WORKS
+ my ($caller, $data) = @_;
+ my $MOBY_RESPONSE;
+ my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+ return SOAP::Data->type('base64' => responseHeader() . responseFooter()) unless (scalar(@inputs));
+
+ my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+ foreach (@inputs){
+ my ($articleType, $qID, $input) = @{$_};
+ unless (($articleType == SIMPLE) && ($input) ){
+ $MOBY_RESPONSE .= simpleResponse("", "", $qID) ;
+ next;
+ } else {
+ my $namespace = getSimpleArticleNamespaceURI($input);
+ my ($identifier) = getSimpleArticleIDs($input); # note array output!
+ $MOBY_RESPONSE .= simpleResponse("", "wrong_namespace", $qID) unless ($namespace eq $validNS);
+ my $name = SHoundGetTaxNameFromTaxID($identifier);
+ $MOBY_RESPONSE .= simpleResponse("", "nothing_found", $qID) unless ($name);
+ $name && ($MOBY_RESPONSE .= simpleResponse("
+
+
+ $name ", "", $qID));
+ }
+ }
+ print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
+}
sub getGoTerm {
my ($caller, $message) = @_;
From mwilkinson at pub.open-bio.org Fri Dec 12 19:22:45 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 12 Dec 2003 14:22:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312121922.hBCJMikJ009022@pub.open-bio.org>
mwilkinson
Fri Dec 12 14:22:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv9003/Perl/MOBY
Modified Files:
CommonSubs.pm
Log Message:
making GMOD moby server revealed a commonsubs error. removed the deprecated services from my CGI client
moby-live/Perl/MOBY CommonSubs.pm,1.34,1.35
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.34
retrieving revision 1.35
diff -u -r1.34 -r1.35
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/10 22:22:03 1.34
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/12 19:22:44 1.35
@@ -397,7 +397,7 @@
";
} elsif($data) {
return "
-
+
$data
";
From mwilkinson at pub.open-bio.org Fri Dec 12 19:22:45 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 12 Dec 2003 14:22:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312121922.hBCJMjo6009041@pub.open-bio.org>
mwilkinson
Fri Dec 12 14:22:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv9003/Perl/scripts
Modified Files:
Services.cgi
Log Message:
making GMOD moby server revealed a commonsubs error. removed the deprecated services from my CGI client
moby-live/Perl/scripts Services.cgi,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services.cgi,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/scripts/Services.cgi 2003/10/17 21:29:52 1.4
+++ /home/repository/moby/moby-live/Perl/scripts/Services.cgi 2003/12/12 19:22:44 1.5
@@ -2,8 +2,13 @@
# _________________________________________________________________
use SOAP::Transport::HTTP;
use lib "/usr/local/apache/cgi-bin";
+use lib "/usr/local/apache/cgi-bin/MOBY05";
+use lib "/usr/local/apache/cgi-bin/BIO/go-dev/perl-api";
use lib "/usr/local/apache/cgi-bin/BIO/moby-live/Perl";
-use lib "/usr/local/apache/cgi-bin/BIO/core/Perl";
+use lib '/usr/local/apache/cgi-bin/bioperl/core';
+use lib '/usr/local/apache/cgi-bin/Services/';
+use Bio::SeqIO::genbank;
+use GO::AppHandle;
use Services::LocalServices;
use strict;
@@ -12,13 +17,13 @@
$x->dispatch_with({
'http://biomoby.org/#getGoTerm' => 'Services::LocalServices',
'http://biomoby.org/#getGoTermAssociations' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankAccVirtualSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankAccSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankGIVirtualSequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankGISequenceRetrieve' => 'Services::LocalServices',
-'http://biomoby.org/#GenbankCompleteSequenceRetrieve' => 'Services::LocalServices',
'http://biomoby.org/#RetrieveGOFromKeywords' => 'Services::LocalServices',
'http://biomoby.org/#getDragonMutantImages' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankff' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankFasta' => 'Services::LocalServices',
+'http://biomoby.org/#MOBYSHoundGetGenBankWhateverSequence' => 'Services::LocalServices',
+'http://biomoby.org/#getTaxNameFromTaxID' => 'Services::LocalServices',
+'http://biomoby.org/#getTaxChildNodes' => 'Services::LocalServices',
});
$x->handle;
From mwilkinson at pub.open-bio.org Tue Dec 16 20:46:40 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 16 Dec 2003 15:46:40 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312162046.hBGKke7h000685@pub.open-bio.org>
mwilkinson
Tue Dec 16 15:46:40 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv665/scripts/Services
Modified Files:
LocalServices.pm
Log Message:
corrected the SeqHound call for EMBL accession numbers Added a new service that wraps the SeqHound SHoundGetTaxParent function to retrieve the taxonomic parents of a given taxon id.
moby-live/Perl/scripts/Services LocalServices.pm,1.48,1.49
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 22:30:53 1.48
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/16 20:46:40 1.49
@@ -17,15 +17,31 @@
use MIME::Base64;
use XML::DOM;
use MOBY::Client::OntologyServer;
-use MOBY::CommonSubs qw(:all); # this provides the
-# subroutines:
-#getSimpleArticleIDs
-#getSimpleArticleNamespaceURI
-#simpleResponse
-#responseHeader
-#responseFooter
-#getInputArticles
-#getNodeContentWithArticle
+use MOBY::CommonSubs qw(:all); # this provides the following vars and functions
+ #getSimpleArticleIDs
+ #getSimpleArticleNamespaceURI
+ #simpleResponse
+ #responseHeader
+ #responseFooter
+ #getInputArticles
+ #getInputs
+ #getInputID
+ #getArticles
+ #getCollectedSimples
+ #getNodeContentWithArticle
+ #extractRawContent
+ #collectionResponse
+ #validateNamespaces
+ #validateThisNamespace
+ #isSimpleArticle
+ #isCollectionArticle
+ #extractResponseArticles
+ #getResponseArticles
+ #getCrossReferences
+ #genericServiceInputParser
+ #COLLECTION
+ #SIMPLE
+
my $debug = 1;
use vars qw(@ISA);
@@ -103,7 +119,7 @@
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
-sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+sub getTaxParent { # now it works.
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
@@ -327,14 +343,6 @@
# ===============================================
# = Genbank Retrieval Scripts =
# = =
-# = Note: The two VirtualSequenceRetrieve's =
-# = and two SequenceRetrieves below could=
-# = have been registered as two services =
-# = instead of four, by simply =
-# = registering each under two different =
-# = namespaces (Acc and gi) instead of =
-# = having a single service for each =
-# = namespace =
# ===============================================
@@ -369,7 +377,7 @@
my $gb = SHoundGetGenBankff($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("".($SEQ->length)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
- } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ } elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -541,7 +549,7 @@
".($SEQ->seq)."
";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
- } elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
+ } elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
my $gi = SHoundFindAcc($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -617,7 +625,7 @@
my $gb = SHoundGetFasta($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("
An HTML attachment was scrubbed...
URL:
From mwilkinson at pub.open-bio.org Fri Dec 26 22:01:31 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Fri, 26 Dec 2003 17:01:31 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312262201.hBQM1VtN026461@pub.open-bio.org>
mwilkinson
Fri Dec 26 17:01:31 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv26442/Perl/MOBY/Client
Modified Files:
Central.pm
Log Message:
duh! If you pass identical objects to the ISA routine, CLEARLY it should return TRUE!!
moby-live/Perl/MOBY/Client Central.pm,1.64,1.65
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -r1.64 -r1.65
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/02 00:57:15 1.64
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/26 22:01:31 1.65
@@ -1383,6 +1383,7 @@
sub ISA {
my ($self, $class1, $class2) = @_;
+ return 1 if (($class1 eq $class2) || ("moby:$class1" eq $class2) || ($class1 eq "moby:$class2"));
my $OS = MOBY::Client::OntologyServer->new;
my ($s, $d, $lsid1) = $OS->objectExists(term => $class1);
return 0 unless $s;
From mwilkinson at pub.open-bio.org Sat Dec 27 13:55:20 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat, 27 Dec 2003 08:55:20 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271355.hBRDtKVf028530@pub.open-bio.org>
mwilkinson
Sat Dec 27 08:55:20 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv28511/Perl/MOBY/Client
Modified Files:
Central.pm
Log Message:
serious performance issues revealed by the new Gbrowse moby client program. The ISA call of MOB::Clien:Central requires two CGI calls, a SOAP call, which itself results in two CGI calls, and a myriad of independent database calls to traverse the ontology. It ended up being >1 second per call,which was unacceptable for many situations where you just need a quick answer to a 'what the heck is this' question. Started client-side caching of the ontology and LSID terms in Client::Central to speed things up. It is now only slow the first time, and <.05 seconds per call thereafter. It does show how critical the need is to start storing the ontology in memory on the server side, though.
moby-live/Perl/MOBY/Client Central.pm,1.65,1.66
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.65
retrieving revision 1.66
diff -u -r1.65 -r1.66
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/26 22:01:31 1.65
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 13:55:20 1.66
@@ -1385,13 +1385,27 @@
my ($self, $class1, $class2) = @_;
return 1 if (($class1 eq $class2) || ("moby:$class1" eq $class2) || ($class1 eq "moby:$class2"));
my $OS = MOBY::Client::OntologyServer->new;
- my ($s, $d, $lsid1) = $OS->objectExists(term => $class1);
- return 0 unless $s;
- my ($s2, $d2, $lsid2) = $OS->objectExists(term => $class2);
- return 0 unless $s2;
- my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1);
- my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'};
- foreach (@$lsids){
+ my ($lsid1, $lsid2);
+ unless ($lsid1 = $self->{LSID_CACHE}->{$class1}){
+ my ($s, $d, $lsid) = $OS->objectExists(term => $class1);
+ $self->{LSID_CACHE}->{$class1} = $lsid;
+ $lsid1 = $lsid;
+ return 0 unless $s;
+ }
+ unless ($lsid2 = $self->{LSID_CACHE}->{$class2}){
+ my ($s, $d, $lsid) = $OS->objectExists(term => $class2);
+ $self->{LSID_CACHE}->{$class2} = $lsid;
+ $lsid2 = $lsid;
+ return 0 unless $s;
+ }
+ my @lsids;
+ unless ($self->{"ISA_CACHE"}->{"$lsid1"} && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){
+ my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1, Relationships => ['ISA']);
+ my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'};
+ @lsids = @$lsids;
+ }
+ $self->{"ISA_CACHE"}->{"$lsid1"} = [@lsids];
+ foreach (@lsids){
return 1 if $_ eq $lsid2;
}
return 0;
From mwilkinson at pub.open-bio.org Sat Dec 27 15:12:32 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat, 27 Dec 2003 10:12:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271512.hBRFCWeV028733@pub.open-bio.org>
mwilkinson
Sat Dec 27 10:12:31 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv28714/Perl/MOBY
Modified Files:
Central.pm
Log Message:
Gbrowse client reveals another MOBY Central bug. Searching for services where you provide an invalid namespace as a parameter should NOT find ALL services, it should find NO services.
moby-live/Perl/MOBY Central.pm,1.118,1.119
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.118
retrieving revision 1.119
diff -u -r1.118 -r1.119
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/22 17:21:16 1.118
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119
@@ -1849,7 +1849,7 @@
next unless ($_->getNodeType == TEXT_NODE);
my $name = $_->toString; chomp $name;
my ($success, $message, $URI) = $OS->namespaceExists(term => $name);
- ($URI) && push @namespaces, $URI;
+ $URI?(push @namespaces, $URI):(push @namespaces, "__MOBY__INVALID__NAMESPACE__");
}
}
return ($objectURI, \@namespaces);
From mwilkinson at pub.open-bio.org Sat Dec 27 17:41:32 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Sat, 27 Dec 2003 12:41:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200312271741.hBRHfWiQ029662@pub.open-bio.org>
mwilkinson
Sat Dec 27 12:41:32 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv29639/Perl/MOBY/Client
Modified Files:
Central.html Central.pm
Log Message:
more tweaks for the Gbrowse project. Create getter/setter methods for the LSID and ISA caches in MOBY::Client::Central so that they can be called from outside of the module itself. This will allow us to build external tools that play with these caches. This may not seem useful at the moment since we only have CGI based clients, so the cache is erased every time we make a call, but once we have a standalone client it will be very useful
moby-live/Perl/MOBY/Client Central.html,1.13,1.14 Central.pm,1.66,1.67
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/02 00:57:15 1.13
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.html 2003/12/27 17:41:32 1.14
@@ -2,7 +2,7 @@
MOBY::Client::Central - a client side wrapper for MOBY Central
-
+
@@ -20,8 +20,8 @@
- new
- - registerObject a.k.a registerObjectClass
- - deregisterObject a.k.a. deregisterObjectClass
+ - registerObject a.k.a registerObjectClass
+ - deregisterObject a.k.a. deregisterObjectClass
- retrieveObjectDefinition
- registerServiceType
- deregisterServiceType
@@ -41,6 +41,8 @@
- Relationships
- ISA
- DUMP
+ - LSID_CACHE
+ - ISA_CACHE
-
Title : registerObject ; registerObjectClass
Usage : $REG = $MOBY->registerObject(%args)
@@ -154,7 +156,7 @@
[Object1, articleName]]}
-
Title : deregisterObject ; deregisterObjectClass Usage : $REG = $MOBY->deregisterObject(%args) @@ -430,6 +432,27 @@ Function : DUMP the mysql for the current MOBY Central database Returns : text Args : $reg - name of MOBY Central you want to use if not default+
+
++ Title : LSID_CACHE + Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid) + Function : get/set LSID from the cache + Returns : lsid as a scalar + Args : the term for which you have/want an lsid, + and optionally the lsid to set.+
+
++ Title : ISA_CACHE + Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) + Function : get/set the ISA relationships in the cache + Returns : listref of ISA relationships. The resulting + list is IN ORDER from term to root. + Args : the term for which you have/want the ISA parentage, + and optionally the parentage listref to set.=================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.66 retrieving revision 1.67 diff -u -r1.66 -r1.67 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 13:55:20 1.66 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/12/27 17:41:32 1.67 @@ -213,6 +213,7 @@ } } + sub new { my ($caller, %args) = @_; @@ -1342,6 +1343,7 @@ } + sub _relationshipsPayload{ my ($payload) = @_; return undef unless $payload; @@ -1388,23 +1390,23 @@ my ($lsid1, $lsid2); unless ($lsid1 = $self->{LSID_CACHE}->{$class1}){ my ($s, $d, $lsid) = $OS->objectExists(term => $class1); - $self->{LSID_CACHE}->{$class1} = $lsid; + $self->LSID_CACHE($class1, $lsid); $lsid1 = $lsid; return 0 unless $s; } unless ($lsid2 = $self->{LSID_CACHE}->{$class2}){ my ($s, $d, $lsid) = $OS->objectExists(term => $class2); - $self->{LSID_CACHE}->{$class2} = $lsid; + $self->LSID_CACHE($class2, $lsid); $lsid2 = $lsid; return 0 unless $s; } my @lsids; - unless ($self->{"ISA_CACHE"}->{"$lsid1"} && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){ + unless ($self->ISA_CACHE($lsid1) && (@lsids = @{$self->{"ISA_CACHE"}->{"$lsid1"}})){ my $resp = $self->Relationships(objectType => $lsid1, expandRelationship => 1, Relationships => ['ISA']); my $lsids = $resp->{'urn:lsid:biomoby.org:objectrelation:isa'}; @lsids = @$lsids; } - $self->{"ISA_CACHE"}->{"$lsid1"} = [@lsids]; + $self->ISA_CACHE($lsid1, [@lsids]); foreach (@lsids){ return 1 if $_ eq $lsid2; } @@ -1507,6 +1509,61 @@ return \@Services; } + +=head2 LSID_CACHE + + Title : LSID_CACHE + Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid) + Function : get/set LSID from the cache + Returns : lsid as a scalar + Args : the term for which you have/want an lsid, + and optionally the lsid to set. + +=cut + + +sub LSID_CACHE { + my ($self, $term, $lsid) = @_; + if ($term && $lsid){ + $self->{LSID_CACHE}->{$term} = $lsid; + return $self->{LSID_CACHE}->{$term}; + } elsif ($term){ + return $self->{LSID_CACHE}->{$term}; + } else { + return undef + } +} + + +=head2 ISA_CACHE + + Title : ISA_CACHE + Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) + Function : get/set the ISA relationships in the cache + Returns : listref of ISA relationships. The resulting + list is IN ORDER from term to root. + Args : the term for which you have/want the ISA parentage, + and optionally the parentage listref to set. + +=cut + +sub ISA_CACHE { + my ($self, $term, $isas) = @_; + return [] if $isas && !(ref($isas)=~/ARRAY/); + if ($term && $isas){ + while (scalar(@$isas)){ + $self->{ISA_CACHE}->{$term} = [@$isas]; + $term = shift(@$isas); + } + return $self->{ISA_CACHE}->{$term}; + } elsif ($term){ + return $self->{ISA_CACHE}->{$term}; + } else { + return [] + } +} + + sub parseRegXML { #
+
+
Title : LSID_CACHE @@ -446,13 +450,15 @@From mwilkinson at pub.open-bio.org Sat Dec 27 20:15:45 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sat, 27 Dec 2003 15:15:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312272015.hBRKFjpJ030037@pub.open-bio.org> mwilkinson Sat Dec 27 15:15:45 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv30014/Perl/MOBY Modified Files: CommonSubs.pm CommonSubs.html Log Message: Gbrowse client needed a new utility routine in CommonSubs. This will take a list of 'known' Object ontology nodes and check it against the parentage of an in-hand object type, returning to you the term from your list that is DEEPEST in the ontology in the ISA parentage of your in-hand object. Why? (you might ask) Well, because when you want to assign renderers to objects you want the most complex renderer possible to deal with your in-hand object, so if you have rendrers for a variety of base object types, you want to chose the one that is best able to deal with whatever you have in-hand, thus you want the node closest to your object type moby-live/Perl/MOBY CommonSubs.pm,1.36,1.37 CommonSubs.html,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.36 retrieving revision 1.37 diff -u -r1.36 -r1.37 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/22 19:57:04 1.36 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:15:45 1.37 @@ -175,6 +175,7 @@ getResponseArticles getCrossReferences genericServiceInputParser + whichDeepestParentObject COLLECTION SIMPLE BE_NICE @@ -202,6 +203,7 @@ getResponseArticles getCrossReferences genericServiceInputParser + whichDeepestParentObject COLLECTION SIMPLE BE_NICE @@ -1071,6 +1073,43 @@ return @XREFS; } + + +=head2 whichDeepestParentObject + + name : whichDeepestParentObject + function : select the parent node from nodeList that is + closest to the querynode + usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + args : $CENTRAL - your MOBY::Client::Central object + $queryNode - the node I am interested in + \@nodelist - the list of nodes that I know about + returns : an ontology term as a scalar, or undef if there + is no parent of this node in the nodelist + +=cut + + +sub whichDeepestParentObject { + use MOBY::Client::OntologyServer; + my ($CENTRAL, $queryTerm, $termlist) = @_; + return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); + my %nodeLSIDs; + foreach (@$termlist){ # get list of known LSIDs + my $lsid = $CENTRAL->ObjLSID($_); + $nodeLSIDs{$lsid}=1; + } + my $queryLSID = $CENTRAL->ObjLSID($queryTerm); + return undef unless keys(%nodeLSIDs); + my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already + return undef unless $isa; # this should return true or we are in BIIIG trouble! + my @lsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root + while (my $thisnode = shift @lsids){ # @isas are lsid's + return $thisnode if $nodeLSIDs{$thisnode}; + } + return undef +} + sub _makeXrefType { my ($xref) = @_; my $ns = $xref->getAttributeNode('namespace'); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/11/08 17:21:31 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:15:45 1.7 @@ -4,7 +4,7 @@ISA_CACHE
- Title : ISA_CACHE - Usage : $lsid = $MOBY->ISA_CACHE($term, \@isas) - Function : get/set the ISA relationships in the cache - Returns : listref of ISA relationships. The resulting - list is IN ORDER from term to root. - Args : the term for which you have/want the ISA parentage, - and optionally the parentage listref to set.+ Title : ISA_CACHE + Usage : @lsids = $MOBY->ISA_CACHE($lsid, \@isas) + Function : get/set the ISA relationships in the cache + Returns : list of ISA relationships. The ISA list + is IN ORDER from, excluding the term itself, to + root Object. Base Object returns an empty list. + Args : The LSID for which you have/want the ISA parentage, + and optionally the parentage listref to set. + Note : WHAT COMES BACK ARE LSIDs!!!
+
+ name : extractRawContent + function : pass me an article (Simple, or Collection) and I'll give you the + content AS A STRING - i.e. the raw XML of the contained MOBY Object(s) + usage : extractRawContent($simple) + input : the one element of the output from getArticles + returns : string+
+
name : validateNamespaces
@@ -427,7 +442,16 @@
presumptive namespaces; undef for each namespace that was invalid
-
+ name : validateThisNamespace + function : checks a given namespace against a list of valid namespaces + usage : $valid = validateThisNamespace($ns, @validNS); + args : ordered list of the namespace of interest and the list of valid NS's + returns : boolean+
+
+
name : getResponseArticles
function : get the DOM nodes corresponding to individual
@@ -461,6 +485,19 @@
}
}
}
++
++ name : whichDeepestParentObject + function : select the parent node from nodeList that is + closest to the querynode + usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + args : $CENTRAL - your MOBY::Client::Central object + $queryNode - the node I am interested in + \@nodelist - the list of nodes that I know about + returns : an ontology term as a scalar, or undef if there + is no parent of this node in the nodelistFrom mwilkinson at pub.open-bio.org Sat Dec 27 20:24:52 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sat, 27 Dec 2003 15:24:52 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312272024.hBRKOqJS030126@pub.open-bio.org> mwilkinson Sat Dec 27 15:24:52 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv30103/Perl/MOBY Modified Files: CommonSubs.html CommonSubs.pm Log Message: changed my mind and decided to return both the object name as well as its LSID, since the latter is a bit arcane sometimes. moby-live/Perl/MOBY CommonSubs.html,1.7,1.8 CommonSubs.pm,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:15:45 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/12/27 20:24:52 1.8 @@ -492,10 +492,10 @@ name : whichDeepestParentObject function : select the parent node from nodeList that is closest to the querynode - usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + usage : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList) args : $CENTRAL - your MOBY::Client::Central object - $queryNode - the node I am interested in - \@nodelist - the list of nodes that I know about + $queryTerm - the object type I am interested in + \@termlist - the list of object types that I know about returns : an ontology term as a scalar, or undef if there is no parent of this node in the nodelist =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:15:45 1.37 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38 @@ -1080,10 +1080,10 @@ name : whichDeepestParentObject function : select the parent node from nodeList that is closest to the querynode - usage : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList) + usage : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList) args : $CENTRAL - your MOBY::Client::Central object - $queryNode - the node I am interested in - \@nodelist - the list of nodes that I know about + $queryTerm - the object type I am interested in + \@termlist - the list of object types that I know about returns : an ontology term as a scalar, or undef if there is no parent of this node in the nodelist @@ -1093,21 +1093,21 @@ sub whichDeepestParentObject { use MOBY::Client::OntologyServer; my ($CENTRAL, $queryTerm, $termlist) = @_; - return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); + return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); my %nodeLSIDs; foreach (@$termlist){ # get list of known LSIDs my $lsid = $CENTRAL->ObjLSID($_); - $nodeLSIDs{$lsid}=1; + $nodeLSIDs{$lsid}=$_; } my $queryLSID = $CENTRAL->ObjLSID($queryTerm); - return undef unless keys(%nodeLSIDs); + return (undef, undef) unless keys(%nodeLSIDs); my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already - return undef unless $isa; # this should return true or we are in BIIIG trouble! - my @lsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root - while (my $thisnode = shift @lsids){ # @isas are lsid's - return $thisnode if $nodeLSIDs{$thisnode}; + return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble! + my @ISAlsids = $CENTRAL->ISA_CACHE($queryTerm); # returns **LSIDs** in order, so we can shift our way back to root + while (my $thislsid = shift @ISAlsids){ # @isas are lsid's + return ($nodeLSIDs{$thislsid},$thislsid) if $nodeLSIDs{$thislsid}; } - return undef + return (undef, undef); } sub _makeXrefType { From mwilkinson at pub.open-bio.org Sun Dec 28 20:41:59 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 28 Dec 2003 15:41:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312282041.hBSKfx4X009349@pub.open-bio.org> mwilkinson Sun Dec 28 15:41:59 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv9318/MOBY Modified Files: Central.pm CommonSubs.pm OntologyServer.pm simple_input.pm Log Message: making MOBY Central case-sensitive for LSIDs. I might have missed a few places. please let me know if you find any. moby-live/Perl/MOBY Central.pm,1.119,1.120 CommonSubs.pm,1.38,1.39 OntologyServer.pm,1.30,1.31 simple_input.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.119 retrieving revision 1.120 diff -u -r1.119 -r1.120 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/28 20:41:59 1.120 @@ -758,7 +758,7 @@ my $dbh = MOBY::central_db_connection->new->dbh; - my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where namespace_type_uris like '%$existingURI%'"); + my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where INSTR(namespace_type_uris,'$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -768,7 +768,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where INSTR(namespace_type_uris,'$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -778,7 +778,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where INSTR(namespace_type_uris, '$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -788,7 +788,7 @@ } } - $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where namespace_type_uris like '%$existingURI%'"); + $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where INSTR(namespace_type_uris, '$existingURI')"); $sth->execute; while (my ($id, $ns) = $sth->fetchrow_array()){ my @nss = split ",", $ns; @@ -1699,7 +1699,7 @@ my $nsquery; foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's - $nsquery .=" OR namespace_type_uris like '%$ns%' "; + $nsquery .=" OR INSTR(namespace_type_uris, '$ns') "; } if ($nsquery){ $nsquery =~ s/OR//; # just the first @@ -1754,7 +1754,7 @@ my $nsquery; foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's - $nsquery .=" OR namespace_type_uris like '%$ns%' "; + $nsquery .=" OR INSTR(namespace_type_uris, '$ns') "; } if ($nsquery){ $nsquery =~ s/^\sOR//; # just the first =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.38 retrieving revision 1.39 diff -u -r1.38 -r1.39 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39 @@ -1074,7 +1074,6 @@ } - =head2 whichDeepestParentObject name : whichDeepestParentObject @@ -1084,8 +1083,12 @@ args : $CENTRAL - your MOBY::Client::Central object $queryTerm - the object type I am interested in \@termlist - the list of object types that I know about - returns : an ontology term as a scalar, or undef if there - is no parent of this node in the nodelist + returns : an ontology term and LSID as a scalar, or undef if there + is no parent of this node in the nodelist. + (note that it will only return the term if you give it + term names in the @termList. If you give it + LSID's in the termList, then both the parameters + returned will be LSID's - it doesn't back-translate...) =cut =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30 +++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31 @@ -179,7 +179,7 @@ } if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?"); + $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where INSTR(object_lsid, ?)"); } else { $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_type = ?"); } @@ -326,7 +326,7 @@ return (0, "requires both term and ontology arguments\n",'') unless (defined($term) && defined($ont)); my $sth; if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_lsid = ? and ontology=?"); + $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where INSTR(relationship_lsid,?) and ontology=?"); } else { $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_type = ? and ontology=?"); } @@ -433,7 +433,7 @@ my $sth; if ($term =~ /^urn\:lsid/){ - $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?"); + $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where INSTR(service_lsid, ?)"); } else { $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_type = ?"); } @@ -545,7 +545,7 @@ } if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){ - $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?"); + $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where INSTR(namespace_lsid, ?)"); } else { $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?"); } @@ -691,7 +691,7 @@ sub getObjectCommonName { my ($self, $URI) = @_; return undef unless $URI =~ /urn\:lsid/; - my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_id = ?}, undef, $URI); + my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_lsid = ?}, undef, $URI); return $name?$name:$URI; } @@ -702,7 +702,7 @@ sub getNamespaceCommonName { my ($self, $URI) = @_; return undef unless $URI =~ /urn\:lsid/; - my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_id = ?}, undef, $URI); + my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_lsid = ?}, undef, $URI); return $name?$name:$URI; } =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/05/07 19:20:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/12/28 20:41:59 1.2 @@ -14,7 +14,7 @@ =head1 SYNOPSIS - use MOBY::authority; + use MOBY::simple_input; my $Instance = MOBY::simple_input->new( object_type => "Sequence", namespaces => ["genbank/gi", "genbank/Acc"], From mwilkinson at pub.open-bio.org Mon Dec 29 02:43:43 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Sun, 28 Dec 2003 21:43:43 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312290243.hBT2hhlC010292@pub.open-bio.org> mwilkinson Sun Dec 28 21:43:43 EST 2003 Update of /home/repository/moby/moby-live In directory pub.open-bio.org:/tmp/cvs-serv10273 Modified Files: README Log Message: just testing the new cron on biomoby.org moby-live README,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/README 2003/02/19 21:12:16 1.3 +++ /home/repository/moby/moby-live/README 2003/12/29 02:43:43 1.4 @@ -1,3 +1,4 @@ +test README # # Revision History From mwilkinson at pub.open-bio.org Tue Dec 30 20:03:54 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 30 Dec 2003 15:03:54 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312302003.hBUK3sN1016258@pub.open-bio.org> mwilkinson Tue Dec 30 15:03:54 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16239/Perl/MOBY Modified Files: OntologyServer.pm Log Message: changing the case of the LSID's buggered up the Relationships call of the OntologyServer. I noticed this when the Gbrowse MOBY browser stopped working. moby-live/Perl/MOBY OntologyServer.pm,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31 +++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/30 20:03:54 1.32 @@ -801,13 +801,13 @@ $term = $self->getObjectURI($term); } my %results; - while (($term ne 'urn:lsid:biomoby.org:objectclass:object') && ($term ne 'urn:lsid:biomoby.org:servicetype:service')){ + while (($term ne 'urn:lsid:biomoby.org:objectclass:Object') && ($term ne 'urn:lsid:biomoby.org:servicetype:Service')){ my $defs = $self->_doRelationshipsQuery($ontology, $term, $relationship, $direction); my $lsid; my $rel; foreach (@{$defs}){ $lsid = $_->[0]; $rel = $_->[1]; - $debug && _LOG("\t\tADDING RELATIONSHIP $_ : $lsid to $rel\n"); + $debug && _LOG("\t\tADDING RELATIONSHIP $_ : $lsid to $rel\n"); push @{$results{$rel}}, $lsid; } last unless ($expand); From mwilkinson at pub.open-bio.org Tue Dec 30 20:21:31 2003 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 30 Dec 2003 15:21:31 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200312302021.hBUKLVww016376@pub.open-bio.org> mwilkinson Tue Dec 30 15:21:31 EST 2003 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv16357/Perl/MOBY Modified Files: CommonSubs.pm Log Message: whichDeepestParentObject should return right away if it finds an object in the list you provided it. Before this would actualy return Object if you gave it the exact object type as part of the search moby-live/Perl/MOBY CommonSubs.pm,1.39,1.40 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v retrieving revision 1.39 retrieving revision 1.40 diff -u -r1.39 -r1.40 --- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39 +++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/30 20:21:30 1.40 @@ -1098,11 +1098,12 @@ my ($CENTRAL, $queryTerm, $termlist) = @_; return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/)); my %nodeLSIDs; + my $queryLSID = $CENTRAL->ObjLSID($queryTerm); foreach (@$termlist){ # get list of known LSIDs my $lsid = $CENTRAL->ObjLSID($_); - $nodeLSIDs{$lsid}=$_; + return ($_, $lsid) if ($lsid eq $queryLSID); # of course, if we find it in the list, then return it right away! + $nodeLSIDs{$lsid}=$_; } - my $queryLSID = $CENTRAL->ObjLSID($queryTerm); return (undef, undef) unless keys(%nodeLSIDs); my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble!