[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Tue Jul 26 23:32:48 UTC 2005
mwilkinson
Tue Jul 26 19:32:48 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv25766/MOBY/Adaptor/moby
Modified Files:
queryapi.pm
Log Message:
adaptor API should now be complete
moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/07/26 21:55:28 1.15
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/07/26 23:32:48 1.16
@@ -613,10 +613,10 @@
die "check_object_usage not implemented in adaptor\n";
}
-=head2 checkNamespaceUsedByService
+=head2 check_namespace_usage
- Title : checkNamespaceUsedByService
- Usage : my $un = $API->checkNamespaceUsedByService(%args)
+ Title : check_namespace_usage
+ Usage : my $un = $API->check_namespace_usage(%args)
Function : Execute a custom query for namespaces that are used by some service
Args : namespace_type_uris => String - namespace_type_uris you are checking for
term => String - the type of the namespace
@@ -627,16 +627,16 @@
=cut
# custom query routine for Moby::Central.pm -> deregisterNamespace()
-sub checkNamespaceUsedByService{
- die "checkNamespaceUsedByService not implemented in adaptor\n";
+sub check_namespace_usage{
+ die "check_namespace_usage not implemented in adaptor\n";
}
-=head2 checkKeywords
+=head2 check_keywords
- Title : checkKeywords
- Usage : my $un = $API->checkKeywords(%args)
+ Title : check_keywords
+ Usage : my $un = $API->check_keywords(%args)
Function : Execute a custom query for services with keywords in its description
- Args : findme => hashref - hash contains an array of keywords
+ Args : keywords => listref (of keywords)
Returns : listref of hashrefs:
[{service_instance_id => Integer,
category => String,
@@ -652,17 +652,18 @@
Each hash represents a service
Notes : the fact that it returns a service_instance_id is bad since this
is only useful to an SQL-based API...
-
+ Keywords are assumed to be joined by "OR" for the query
+
=cut
# custom query routine for Moby::Central.pm -> findService()
-sub checkKeywords{
- die "checkKeywords not implemented in adaptor\n";
+sub check_keywords{
+ die "check_keywords not implemented in adaptor\n";
}
-=head2 getFromSimple
+=head2 find_by_simple
- Title : getFromSimple
- Usage : my $un = $API->getFromSimple(%args)
+ Title : find_by_simple
+ Usage : my $un = $API->find_by_simple(%args)
Function : Execute a custom query for service ids in simple_input/output
Args : inout => String - to specify if input or output
ancestor_string => String - values that occur in object_type_uri
@@ -675,14 +676,14 @@
=cut
# custom query subroutine for Moby::Central.pm->_searchForSimple()
-sub getFromSimple{
- die "getFromSimple not implemented in adaptor\n";
+sub find_by_simple{
+ die "find_by_simple not implemented in adaptor\n";
}
-=head2 getFromCollection
+=head2 find_by_collection
- Title : getFromCollection
- Usage : my $un = $API->getFromCollection(%args)
+ Title : find_by_collection
+ Usage : my $un = $API->find_by_collection(%args)
Function : Execute a custom query for service ids from collections
Args : inout => String - to specify if input or output
objectURI => String - value that binds to object_type_uri
@@ -695,14 +696,14 @@
=cut
# custom query subroutine for Moby::Central.pm->_searchForCollection()
-sub getFromCollection{
- die "getFromCollection not implemented in adaptor\n";
+sub find_by_collection{
+ die "find_by_collection not implemented in adaptor\n";
}
-=head2 getServiceNames
+=head2 get_service_names
- Title : getServiceNames
- Usage : my $un = $API->getServiceNames(%args)
+ Title : get_service_names
+ Usage : my $un = $API->get_service_names(%args)
Function : Execute a query for all service names
Args : no inputs needed
Returns : listref of hashrefs:
@@ -712,14 +713,14 @@
=cut
# custom query subroutine for Moby::Central.pm->RetrieveServiceNames
-sub getServiceNames{
- die "getServiceNames not implemented in adaptor\n";
+sub get_service_names{
+ die "get_service_names not implemented in adaptor\n";
}
-=head2 getParentTerms
+=head2 get_parent_terms
- Title : getParentTerms
- Usage : my $un = $API->getParentTerms(%args)
+ Title : get_parent_terms
+ Usage : my $un = $API->get_parent_terms(%args)
Function : From a given term, traverse the ontology and get all parent terms
Args : relationship_type_id => Integer - a bind value for relationship_type_id on an underlying SQL-based data source
term => String - bindvalue for OntologyEntry.term
@@ -729,16 +730,16 @@
=cut
# custom query for Moby::Central.pm->_flatten
-sub getParentTerms{
- die "getParentTerms not implemented in adaptor\n";
+sub get_parent_terms{
+ die "get_parent_terms not implemented in adaptor\n";
}
-=head2 getObjectRelationships
+=head2 get_object_relationships
- Title : getObjectRelationships
- Usage : my $un = $API->getObjectRelationships(%args)
+ Title : get_object_relationships
+ Usage : my $un = $API->get_object_relationships(%args)
Function : Execute a query for objects that have relationships with other objects
- Args : object1_id => Integer - a bind value for object1_id on an underlying SQL-based data source
+ Args : type => String - either an object name or LSID
Returns : listref of hashrefs:
[{relationship_type => String,
object_lsid => String,
@@ -749,14 +750,14 @@
=cut
# 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";
+sub get_object_relationships{
+ die "get_object_relationships not implemented in adaptor\n";
}
-=head2 getRelationship
+=head2 get_relationship
- Title : getRelationship
- Usage : my $un = $API->getRelationships(%args)
+ Title : get_relationship
+ Usage : my $un = $API->get_relationship(%args)
Function : Execute a query for a relationship between two ontologies
Args : direction => String - direction in the ontology (eg. 'root')
ontology => String - name of the table ontology
@@ -770,8 +771,8 @@
=cut
# 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 get_relationship{
+ die "get_relationship not implemented in adaptor\n";
}
# Not quite sure what this does...
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