[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Fri Jul 9 00:21:53 UTC 2004
mwilkinson
Thu Jul 8 20:21:53 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv5633/MOBY/Adaptor/moby
Modified Files:
queryapi.pm
Log Message:
more refactoring of code to get SQL out of mobycentral. Also created two new subroutines for Martin and Ben to add their XSD-generating code such that the WSDL from MOBY Central will be valid
moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/06/24 22:32:39 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2004/07/09 00:21:53 1.2
@@ -16,12 +16,7 @@
dbname => [undef, 'read/write'],
port => [undef, 'read/write'],
proxy => [undef, 'read/write'],
- sourcetype => ["MOBY::Adaptor::moby::queryapi::mysql", 'read/write'],
- url => [undef, 'read/write'],
- _implementation => [undef, 'read/write'], # this is the implementation of the API, e.g. mysql
-
- dbh => [undef, 'read/write'], # once all the calls are converttd remove this! It should not be accessible from outside!!!
-
+ url => [undef, 'read/write'],
);
#_____________________________________________________________
@@ -41,10 +36,56 @@
}
# List of names of all specified object attributes
- sub _standard_keys {
+ sub _standard_keys_a {
keys %_attr_data;
}
+ sub username {
+ my ($self, $arg) = @_;
+ $self->{username} = $arg if defined $arg;
+ return $self->{username};
+ }
+ sub password {
+ my ($self, $arg) = @_;
+ $self->{password} = $arg if defined $arg;
+ return $self->{password};
+ }
+ sub dbname {
+ my ($self, $arg) = @_;
+ $self->{dbname} = $arg if defined $arg;
+ return $self->{dbname};
+ }
+ sub port {
+ my ($self, $arg) = @_;
+ $self->{port} = $arg if defined $arg;
+ return $self->{port};
+ }
+ sub proxy {
+ my ($self, $arg) = @_;
+ $self->{proxy} = $arg if defined $arg;
+ return $self->{proxy};
+ }
+ sub sourcetype {
+ my ($self, $arg) = @_;
+ $self->{sourcetype} = $arg if defined $arg;
+ return $self->{sourcetype};
+ }
+ sub url {
+ my ($self, $arg) = @_;
+ $self->{url} = $arg if defined $arg;
+ return $self->{url};
+ }
+ sub _implementation {
+ my ($self, $arg) = @_;
+ $self->{'_implementation'} = $arg if defined $arg;
+ return $self->{'_implementation'};
+ }
+ sub dbh {
+ my ($self, $arg) = @_;
+ $self->{dbh} = $arg if defined $arg;
+ return $self->{dbh};
+ }
+
}
sub new {
@@ -54,7 +95,7 @@
my $self = bless {}, $class;
- foreach my $attrname ( $self->_standard_keys ) {
+ foreach my $attrname ( $self->_standard_keys_a ) {
if (exists $args{$attrname} && defined $args{$attrname}) {
$self->{$attrname} = $args{$attrname} }
elsif ($caller_is_obj) {
@@ -62,95 +103,88 @@
else {
$self->{$attrname} = $self->_default_for($attrname) }
}
-
- my $source = $self->sourcetype;
- my $datasource = $source->new(adaptor => $self);
- unless ($datasource) {
- print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n";
- return undef;
- }
- $self->_implementation($datasource);
-
- # the lines below should be removed, since this should be pushed down into the implementation
- ##############################################################
- unless ($datasource->dbh) {
- print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n";
- return undef;
- }
-
- $self->dbh($datasource->dbh);
- #############################################################
-
return $self;
}
sub insert_collection_input {
- my ($self, %args) = @_;
- my $dbh = $self->dbh;
- if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){
- # this should be dropped down into the mysql.pm module?? probably...
- $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name}));
- my $id=$self->dbh->{mysql_insertid};
- return $id;
- }
+ die "insert_collection_input not implemented in adaptor\n";
+ #my ($self, %args) = @_;
+ #my $dbh = $self->dbh;
+ #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){
+ # # this should be dropped down into the mysql.pm module?? probably...
+ # $self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name}));
+ # my $id=$self->dbh->{mysql_insertid};
+ # return $id;
+ #}
}
sub insert_collection_output {
- my ($self, %args) = @_;
- my $dbh = $self->dbh;
- if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){
- # this should be dropped down into the mysql.pm module?? probably...
- $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name}));
- my $id=$self->dbh->{mysql_insertid};
- return $id;
- }
+ die "insert_collection_output not implemented in adaptor\n";
+ #my ($self, %args) = @_;
+ #my $dbh = $self->dbh;
+ #if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){
+ # # this should be dropped down into the mysql.pm module?? probably...
+ # $self->dbh->do("insert into collection_output (service_instance_id, article_name) values (?,?)", undef, ($args{service_instance}, $args{article_name}));
+ # my $id=$self->dbh->{mysql_insertid};
+ # return $id;
+ #}
}
sub insert_simple_input {
- my ($self, %args) = @_;
- my $dbh = $self->dbh;
-
- $dbh->do("insert into simple_input
- (object_type_uri,
- namespace_type_uris,
- article_name,
- service_instance_id,
- collection_input_id)
- values (?,?,?,?,?)",
- undef,
- ($args{object_type_uri},
- $args{namespace_type_uris},
- $args{article_name},
- $args{service_instance_id},
- $args{collection_input_id}));
- my $id=$dbh->{mysql_insertid};
- return $id;
+ die "insert_simple_input not implemented in adaptor\n";
+ #my ($self, %args) = @_;
+ #my $dbh = $self->dbh;
+ #
+ #$dbh->do("insert into simple_input
+ # (object_type_uri,
+ # namespace_type_uris,
+ # article_name,
+ # service_instance_id,
+ # collection_input_id)
+ # values (?,?,?,?,?)",
+ # undef,
+ # ($args{object_type_uri},
+ # $args{namespace_type_uris},
+ # $args{article_name},
+ # $args{service_instance_id},
+ # $args{collection_input_id}));
+ #my $id=$dbh->{mysql_insertid};
+ #return $id;
}
sub insert_simple_output {
- my ($self, %args) = @_;
- my $dbh = $self->dbh;
-
- $dbh->do("insert into simple_output
- (object_type_uri,
- namespace_type_uris,
- article_name,
- service_instance_id,
- collection_output_id)
- values (?,?,?,?,?)",
- undef,
- ($args{object_type_uri},
- $args{namespace_type_uris},
- $args{article_name},
- $args{service_instance_id},
- $args{collection_output_id}));
- my $id=$dbh->{mysql_insertid};
- return $id;
+ die "insert_simple_output not implemented in adaptor\n";
+ #my ($self, %args) = @_;
+ #my $dbh = $self->dbh;
+ #
+ #$dbh->do("insert into simple_output
+ # (object_type_uri,
+ # namespace_type_uris,
+ # article_name,
+ # service_instance_id,
+ # collection_output_id)
+ # values (?,?,?,?,?)",
+ # undef,
+ # ($args{object_type_uri},
+ # $args{namespace_type_uris},
+ # $args{article_name},
+ # $args{service_instance_id},
+ # $args{collection_output_id}));
+ #my $id=$dbh->{mysql_insertid};
+ #return $id;
}
+sub query_service_instance {
+ die "query_service_instance not implemented in adaptor\n";
+}
+
+sub insert_service_instance {
+ die "insert_service_instance not implemented in adaptor\n";
+}
+
sub _dump {
my ($self) = @_;
@@ -160,37 +194,37 @@
}
sub DESTROY {}
-
-sub AUTOLOAD {
- no strict "refs";
- my ($self, $newval) = @_;
-
- $AUTOLOAD =~ /.*::(\w+)/;
-
- my $attr=$1;
- if ($self->_accessible($attr,'write')) {
-
- *{$AUTOLOAD} = sub {
- if (defined $_[1]) { $_[0]->{$attr} = $_[1] }
- return $_[0]->{$attr};
- }; ### end of created subroutine
-
-### this is called first time only
- if (defined $newval) {
- $self->{$attr} = $newval
- }
- return $self->{$attr};
-
- } elsif ($self->_accessible($attr,'read')) {
-
- *{$AUTOLOAD} = sub {
- return $_[0]->{$attr} }; ### end of created subroutine
- return $self->{$attr} }
-
-
- # Must have been a mistake then...
- croak "No such method: $AUTOLOAD";
-}
-
+#
+#sub AUTOLOAD {
+# no strict "refs";
+# my ($self, $newval) = @_;
+#
+# $AUTOLOAD =~ /.*::(\w+)/;
+#
+# my $attr=$1;
+# if ($self->_accessible($attr,'write')) {
+#
+# *{$AUTOLOAD} = sub {
+# if (defined $_[1]) { $_[0]->{$attr} = $_[1] }
+# return $_[0]->{$attr};
+# }; ### end of created subroutine
+#
+#### this is called first time only
+# if (defined $newval) {
+# $self->{$attr} = $newval
+# }
+# return $self->{$attr};
+#
+# } elsif ($self->_accessible($attr,'read')) {
+#
+# *{$AUTOLOAD} = sub {
+# return $_[0]->{$attr} }; ### end of created subroutine
+# return $self->{$attr} }
+#
+#
+# # Must have been a mistake then...
+# croak "No such method: $AUTOLOAD";
+#}
+#
1;
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