[MOBY-guts] biomoby commit
Dennis Wang
dwang at pub.open-bio.org
Wed Aug 31 22:28:22 UTC 2005
dwang
Wed Aug 31 18:28:22 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv1593/Perl/MOBY/Adaptor/moby
Modified Files:
queryapi.pm
Log Message:
line formating for pod lines
moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/08/30 23:01:27 1.29
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/08/31 22:28:22 1.30
@@ -303,7 +303,9 @@
one hashref for each collection that service consumes
Notes : the fact that it returns a collection_input_id is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub query_collection_input{
die "query_collection_input not implemented in adaptor\n";
}
@@ -318,7 +320,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_collection_input {
die "insert_collection_input not implemented in adaptor\n";
}
@@ -332,8 +336,11 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
-
+
+
=cut
+
+
sub delete_collection_input{
die "delete_collection_input not implemented in adaptor\n";
}
@@ -341,6 +348,7 @@
#
# collection_output table fuctions
#
+
=head2 query_collection_output
Title : query_collection_output
@@ -352,7 +360,9 @@
article_name => String,
service_instance_id => Integer}, ...]
Notes : Only allows querying by lsid or type term, so service_instance_id is retrieved from lsid or term
+
=cut
+
sub query_collection_output{
die "query_collection_output not implemented in adaptor\n";
}
@@ -367,7 +377,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_collection_output {
die "insert_collection_output not implemented in adaptor\n";
#my ($self, %args) = @_;
@@ -390,7 +402,9 @@
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
+
=cut
+
sub delete_collection_output{
die "delete_collection_output not implemented in adaptor\n";
}
@@ -413,7 +427,9 @@
service_instance_id => Integer,
collection_input_id => Integer}, ...]
Notes : Only allows querying by lsid or type term, so service_instance_id is retrieved from lsid or term
+
=cut
+
sub query_simple_input{
die "query_simple_input not implemented in adaptor\n";
}
@@ -431,7 +447,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_simple_input {
die "insert_simple_input not implemented in adaptor\n";
}
@@ -445,9 +463,11 @@
collection_input_id => Integer
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
- $errstr = String error message if there was an error
-
+ $errstr = String error message if there was an error
+
=cut
+
+
sub delete_simple_input{
die "delete_simple_input not implemented in adaptor\n";
}
@@ -455,6 +475,7 @@
#
# simple_output table functions
#
+
=head2 query_simple_output
Title : query_simple_output
@@ -470,7 +491,9 @@
service_instance_id => Integer,
collection_output_id => Integer}, ...]
Notes : Only allows querying by lsid or type term, so service_instance_id is retrieved from lsid or term
+
=cut
+
sub query_simple_output{
die "query_simple_output not implemented in adaptor\n";
}
@@ -488,7 +511,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_simple_output {
die "insert_simple_output not implemented in adaptor\n";
}
@@ -503,13 +528,15 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
-
+
=cut
+
sub delete_simple_output{
die "delete_simple_output not implemented in adaptor\n";
}
# secondary_input table functions
+
=head2 query_secondary_input
Title : query_secondary_input
@@ -526,7 +553,9 @@
article_name => String,
service_instance_id => Integer}, ...]
Notes : Only allows querying by lsid or type term, so service_instance_id is retrieved from lsid or term
+
=cut
+
sub query_secondary_input{
die "query_secondary_input not implemented in adaptor\n";
}
@@ -546,7 +575,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_secondary_input{
die "insert_secondary_input not implemented in adaptor\n";
}
@@ -560,8 +591,9 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
-
+
=cut
+
sub delete_secondary_input{
die "delete_secondary_input not implemented in adaptor\n";
}
@@ -569,6 +601,7 @@
#
# object table functions
#
+
=head2 query_object
Title : query_object
@@ -583,7 +616,9 @@
authority => String,
contact_email => String}, ...]
Notes : Only allows querying by lsid or type term
+
=cut
+
sub query_object{
die "query_object not implemented in adaptor\n";
}
@@ -601,7 +636,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_object{
die "insert_object not implemented in adaptor\n";
}
@@ -615,8 +652,9 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
-
+
=cut
+
sub delete_object{
die "delete_object not implemented in adaptor\n";
}
@@ -624,6 +662,7 @@
#
# object_term2term table functions
#
+
=head2 query_object_term2term
Title : query_object_term2term
@@ -637,7 +676,9 @@
object2_id => String,
object2_articlename => String}, ...]
Notes : Only allows querying by lsid or type term
+
=cut
+
sub query_object_term2term{
die "query_object_term2term not implemented in adaptor\n";
}
@@ -654,7 +695,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_object_term2term{
die "insert_object_term2term not implemented in adaptor\n";
}
@@ -667,6 +710,7 @@
#
# service_instance table functions
#
+
=head2 query_service_instance
Title : query_service_instance
@@ -697,7 +741,9 @@
signatureURL => String,
lsid => String}, ...]
Notes : Allows querying by multiple conditions joined by 'and'
+
=cut
+
sub query_service_instance {
die "query_service_instance not implemented in adaptor\n";
}
@@ -712,7 +758,9 @@
Returns : 1 if service exists
0 if no such service instance
Notes : Only allows querying by URI of the authority and service name
+
=cut
+
sub query_service_existence{
die "query_service_existence not implemented in adaptor\n";
}
@@ -741,7 +789,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_service_instance {
die "insert_service_instance not implemented in adaptor\n";
}
@@ -755,8 +805,11 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
-
+
+
=cut
+
+
sub delete_service_intance{
die "delete_service_intance not implemented in adaptor\n";
}
@@ -764,6 +817,7 @@
#
# authority table functions
#
+
=head2 query_authority
Title : query_authority
@@ -775,7 +829,9 @@
authority_uri => String,
contact_email => String}, ...]
Notes : Only allows querying by URI of the authority
+
=cut
+
sub query_authority{
die "query_authority not implemented in adaptor\n";
}
@@ -789,7 +845,10 @@
Returns : listref of hashrefs:
[{authority_uri => String}]
+
=cut
+
+
sub get_all_authorities{
die "get_all_authorities not implemented in adaptor\n";
}
@@ -805,7 +864,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_authority{
die "insert_authority not implemented in adaptor\n";
}
@@ -818,6 +879,7 @@
#
# service table fuctions
#
+
=head2 query_service
Title : query_service
@@ -833,7 +895,9 @@
contact_email => String}, ...]
Notes : the fact that it returns an service_id is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub query_service{
die "query_service not implemented in adaptor\n";
}
@@ -851,7 +915,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_service{
die "insert_service not implemented in adaptor\n";
}
@@ -865,8 +931,10 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 otherwise
$errstr = String error message if there was an error
-
+
+
=cut
+
sub delete_service{
die "delete_service not implemented in adaptor\n";
}
@@ -874,6 +942,7 @@
#
# service_term2term table functions
#
+
=head2 query_service_term2term
Title : query_service_term2term
@@ -887,7 +956,9 @@
service2_id => String}, ...]
Notes : the fact that it returns an service ids is bad since this
is only useful to an SQL-based API...should return lsids
+
=cut
+
sub query_service_term2term{
die "query_service_term2term not implemented in adaptor\n";
}
@@ -903,12 +974,15 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_service_term2term{
die "insert_service_term2term not implemented in adaptor\n";
}
# private subroutine in mysql api
+
sub delete_service_term2term{
die "delete_service_term2term not implemented in adaptor\n";
}
@@ -916,6 +990,7 @@
#
# relationship table functions
#
+
=head2 query_relationship
Title : query_relationship
@@ -935,7 +1010,9 @@
one hashref for each relationship
Notes : the fact that it returns a relationship_id is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub query_relationship{
die "query_relationship not implemented in adaptor\n";
}
@@ -953,6 +1030,7 @@
#
# namespace table functions
#
+
=head2 query_namespace
Title : query_namespace
@@ -966,8 +1044,9 @@
description => String,
authority => String,
contact_email => String}, ...]
-
+
=cut
+
sub query_namespace{
die "query_namespace not implemented in adaptor\n";
}
@@ -985,7 +1064,9 @@
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
+
=cut
+
sub insert_namespace{
die "insert_namespace not implemented in adaptor\n";
}
@@ -999,8 +1080,9 @@
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 otherwise
$errstr = String error message if there was an error
-
+
=cut
+
sub delete_namespace{
die "delete_namespace not implemented in adaptor\n";
}
@@ -1017,8 +1099,9 @@
namespace1_id => String,
namespace2_id => String}, ...]
Notes : namespace1_id and namespace2_id will be lsids
-
+
=cut
+
# namespace_term2term table functions
sub query_namespace_term2term{
die "query_namespace_term2term not implemented in adaptor\n";
@@ -1045,8 +1128,9 @@
($err, $errstr)
$err = 1 if namespace is used by a service, 0 otherwise
$errstr = contains the error message
-
+
=cut
+
# custom query subroutine for Moby::Central.pm->deregisterObjectClass()
sub check_object_usage{
die "check_object_usage not implemented in adaptor\n";
@@ -1062,8 +1146,9 @@
($err, $errstr)
$err = 1 if namespace is used by a service, 0 otherwise
$errstr = contains the error message
-
+
=cut
+
# custom query routine for Moby::Central.pm -> deregisterNamespace()
sub check_namespace_usage{
die "check_namespace_usage not implemented in adaptor\n";
@@ -1093,6 +1178,7 @@
Keywords are assumed to be joined by "OR" for the query
=cut
+
# custom query routine for Moby::Central.pm -> findService()
sub check_keywords{
die "check_keywords not implemented in adaptor\n";
@@ -1111,8 +1197,9 @@
namespace_type_uris => String}, ...]
Notes : the fact that it returns a service_instance_id is bad since this
is only useful to an SQL-based API...
-
+
=cut
+
# custom query subroutine for Moby::Central.pm->_searchForSimple()
sub find_by_simple{
die "find_by_simple not implemented in adaptor\n";
@@ -1131,8 +1218,9 @@
namespace_type_uris => String}, ...]
Notes : the fact that it returns a service_instance_id is bad since this
is only useful to an SQL-based API...
-
+
=cut
+
# custom query subroutine for Moby::Central.pm->_searchForCollection()
sub find_by_collection{
die "find_by_collection not implemented in adaptor\n";
@@ -1148,8 +1236,9 @@
[{authority_uri => String,
servicename => String}, ...]
one hashref for each service
-
+
=cut
+
# custom query subroutine for Moby::Central.pm->RetrieveServiceNames
sub get_service_names{
die "get_service_names not implemented in adaptor\n";
@@ -1165,8 +1254,9 @@
Returns : listref of hashrefs:
[{term => String}, ...]
one hashref for each parent
-
+
=cut
+
# custom query for Moby::Central.pm->_flatten
sub get_parent_terms{
die "get_parent_terms not implemented in adaptor\n";
@@ -1188,8 +1278,9 @@
object2_articlename => String}, ...]
one hashref for each relationship between two objects
Notes : relationship_type from object_term2term, object_lsid from object, and object2_articlename from object_term2term
-
+
=cut
+
# custom query subroutine for selecting from object_term2term and object tables
# used in Moby::OntologyServer.pm->retrieveObject()
sub get_object_relationships{
@@ -1211,6 +1302,7 @@
Notes : Only returns distinct lsids from $ontology and relationship_type from $ontology_term2term
=cut
+
# relationship query for any table used in Moby::OntologyServer->_doRelationshipQuery()
# note: returns a reference to an array containing ARRAY references
sub get_relationship{
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