[MOBY-guts] biomoby commit
Dennis Wang
dwang at pub.open-bio.org
Mon Jul 18 16:53:49 UTC 2005
dwang
Mon Jul 18 12:53:49 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv16261/Perl/MOBY/Adaptor/moby
Modified Files:
queryapi.pm
Log Message:
All routines that are implementated in mysql.pm now exists in queryapi interface
moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/07/13 18:19:09 1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/07/18 16:53:49 1.4
@@ -108,44 +108,67 @@
}
-
+# general query subroutine
+# parameters:
+# statement - a string SQL statement
+# bind_values - an array of values to be bound to the parameters
+# returns:
+# resultset - reference to an array containing ARRAY references
+sub general_query{
+ die "general_query not implemented in adaptor\n";
+}
+
#
-# authority table functions
+# collection_input table functions
#
-sub query_authority{
-
-
+sub query_collection_input{
+ die "query_collection_input not implemented in adaptor\n";
}
-sub insert_authority{
-
+sub insert_collection_input {
+ 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 $id;
+ #}
}
-sub delete_authority{
-
+sub delete_collection_input{
+ die "delete_collection_input not implemented in adaptor\n";
}
-
#
-# service_instance table functions
+# collection_output table fuctions
#
-sub query_service_instance {
- die "query_service_instance not implemented in adaptor\n";
+sub query_collection_output{
+ die "query_collection_output not implemented in adaptor\n";
}
-sub insert_service_instance {
- die "insert_service_instance not implemented in adaptor\n";
+sub insert_collection_output {
+ die "insert_collection_output not implemented in adaptor\n";
+ #my ($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 $id;
+ #}
}
-sub delete_service_intance{
-
+sub delete_collection_output{
+ die "delete_collection_output not implemented in adaptor\n";
}
-
+
#
# simple_output table functions
#
sub query_simple_input{
-
+ die "query_simple_input not implemented in adaptor\n";
}
sub insert_simple_input {
@@ -171,14 +194,14 @@
}
sub delete_simple_input{
-
+ die "delete_simple_input not implemented in adaptor\n";
}
#
# simple_output table functions
#
sub query_simple_output{
-
+ die "query_simple_output not implemented in adaptor\n";
}
sub insert_simple_output {
@@ -205,178 +228,214 @@
}
sub delete_simple_output{
-
-}
-
-#
-# collection_input table functions
-#
-sub query_collection_input{
-
+ die "delete_simple_output not implemented in adaptor\n";
}
-sub insert_collection_input {
- die "insert_collection_input not implemented in adaptor\n";
- #my ($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 $id;
- #}
-}
-
-sub delete_collection_input{
-
-}
-
-#
-# collection_output table fuctions
-#
-sub query_collection_output{
-
+# secondary_input table functions
+sub query_secondary_input{
+ die "query_secondary_input not implemented in adaptor\n";
}
-sub insert_collection_output {
- die "insert_collection_output not implemented in adaptor\n";
- #my ($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_secondary_input{
+ die "insert_secondary_input not implemented in adaptor\n";
}
-sub delete_collection_output{
-
+sub delete_secondary_input{
+ die "delete_secondary_input not implemented in adaptor\n";
}
#
# object table functions
#
sub query_object{
-
+ die "query_object not implemented in adaptor\n";
}
sub insert_object{
-
+ die "insert_object not implemented in adaptor\n";
}
sub delete_object{
-
+ die "delete_object not implemented in adaptor\n";
}
#
# object_term2term table functions
#
sub query_object_term2term{
-
+ die "query_object_term2term not implemented in adaptor\n";
}
sub insert_object_term2term{
-
+ die "insert_object_term2term not implemented in adaptor\n";
}
sub delete_object_term2term{
-
+ die "delete_object_term2term not implemented in adaptor\n";
}
#
-# relationship table functions
+# service_instance table functions
#
-sub query_relationship{
-
+sub query_service_instance {
+ die "query_service_instance not implemented in adaptor\n";
}
-sub insert_relationship{
-
+sub match_service_type_uri{
+ die "match_service_type_uri not implemented in adaptor\n";
}
-sub delete_relationship{
+sub insert_service_instance {
+ die "insert_service_instance not implemented in adaptor\n";
+}
+
+sub delete_service_intance{
+ die "delete_service_intance not implemented in adaptor\n";
+}
+#
+# authority table functions
+#
+sub query_authority{
+ die "query_authority not implemented in adaptor\n";
+}
+
+sub getUniqueAuthorityURI{
+ die "getUniqueAuthorityURI not implemented in adaptor\n";
+}
+
+sub insert_authority{
+ die "insert_authority not implemented in adaptor\n";
+}
+
+sub delete_authority{
+ die "delete_authority not implemented in adaptor\n";
}
#
# service table fuctions
#
sub query_service{
-
+ die "query_service not implemented in adaptor\n";
}
sub insert_service{
-
+ die "insert_service not implemented in adaptor\n";
}
sub delete_service{
-
+ die "delete_service not implemented in adaptor\n";
}
#
# service_term2term table functions
#
sub query_service_term2term{
-
+ die "query_service_term2term not implemented in adaptor\n";
}
sub insert_service_term2term{
-
+ die "insert_service_term2term not implemented in adaptor\n";
}
sub delete_service_term2term{
-
+ die "delete_service_term2term not implemented in adaptor\n";
+}
+
+#
+# relationship table functions
+#
+sub query_relationship{
+ die "query_relationship not implemented in adaptor\n";
+}
+
+sub insert_relationship{
+ die "insert_relationship not implemented in adaptor\n";
+}
+
+sub delete_relationship{
+ die "delete_relationship not implemented in adaptor\n";
}
#
# namespace table functions
#
sub query_namespace{
-
+ die "query_namespace not implemented in adaptor\n";
}
sub insert_namespace{
-
+ die "insert_namespace not implemented in adaptor\n";
}
sub delete_namespace{
-
+ die "delete_namespace not implemented in adaptor\n";
}
#
# namespace_term2term table functions
#
sub query_namespace_term2term{
-
+ die "query_namespace_term2term not implemented in adaptor\n";
}
sub insert_namespace_term2term{
-
+ die "insert_namespace_term2term not implemented in adaptor\n";
}
sub delete_namespace_term2term{
-
+ die "delete_namespace_term2term not implemented in adaptor\n";
}
-# secondary_input table functions
-sub query_secondary_input{
-
+# custom query subroutine for Moby::Central.pm->deregisterObjectClass()
+sub checkClassUsedByService{
+ die "checkClassUsedByService not implemented in adaptor\n";
}
-sub insert_secondary_input{
-
+# custom query routine for Moby::Central.pm -> deregisterNamespace()
+sub checkNamespaceUsedByService{
+ die "checkNamespaceUsedByService not implemented in adaptor\n";
}
-sub delete_secondary_input{
-
+# custom query routine for Moby::Central.pm -> findService()
+sub checkKeywords{
+ die "checkKeywords not implemented in adaptor\n";
}
-#
-# query term2term tables - queries relation between two tables
-#
-sub select_term2term{
-
+# custom query subroutine for Moby::Central.pm->_searchForSimple()
+sub getFromSimple{
+ die "getFromSimple not implemented in adaptor\n";
+}
+
+# custom query subroutine for Moby::Central.pm->_searchForCollection()
+sub getFromCollection{
+ die "getFromCollection not implemented in adaptor\n";
+}
+
+# custom query subroutine for Moby::Central.pm->RetrieveServiceNames
+sub getServiceNames{
+ die "getServiceNames not implemented in adaptor\n";
+}
+
+# custom query for Moby::Central.pm->_flatten
+sub getParentTerms{
+ die "getParentTerms not implemented in adaptor\n";
+}
+
+# custom query subroutine for selecting from object_term2term and object tables
+# used in Moby::OntologyServer.pm->retrieveObject()
+sub getObjectRelationships{
+ die "getObjectRelationships not implemented in adaptor\n";
+}
+
+# relationship query for any table used in Moby::OntologyServer->_doRelationshipQuery()
+# note: returns a reference to an array containing ARRAY references
+sub getRelationship{
+ die "getRelationship not implemented in adaptor\n";
+}
+
+sub _checkURI {
+ die "_checkURI not implemented in adaptor\n";
}
sub _dump {
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