[MOBY-guts] biomoby commit
Dennis Wang
dwang at pub.open-bio.org
Tue Aug 30 23:01:27 UTC 2005
dwang
Tue Aug 30 19:01:27 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby
In directory pub.open-bio.org:/tmp/cvs-serv28848/Perl/MOBY/Adaptor/moby
Modified Files:
queryapi.pm
Log Message:
adjusted formating in queryapi documentation
moby-live/Perl/MOBY/Adaptor/moby queryapi.pm,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/08/26 21:33:24 1.28
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi.pm 2005/08/30 23:01:27 1.29
@@ -442,7 +442,7 @@
Usage : my $un = $API->delete_simple_input(%args)
Function : Deletes Simple inputs according to the service instance, or collection input
Args : service_instance_lsid => String,
- collection_input_id => Integer
+ collection_input_id => Integer
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
@@ -461,7 +461,7 @@
Usage : my $un = $API->query_simple_output(%args)
Function : Executes a query for Simple outputs according to the service instance or collection output
Args : service_instance_lsid => String,
- collection_output_id => Integer
+ collection_output_id => Integer
Returns : listref of hashrefs:
[{simple_output_id => Integer,
object_type_uri => String,
@@ -499,7 +499,7 @@
Usage : my $un = $API->delete_simple_output(%args)
Function : Deletes Simple outputs according to the service instance, or collection output
Args : service_instance_lsid => String,
- collection_output_id => Integer
+ collection_output_id => Integer
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error
@@ -558,8 +558,8 @@
Function : Deletes a Secondary input from the database
Args : service_instance_lsid => String
Returns : ($err, $errstr)
- $err = 1 if there was an delete error, 0 if successful
- $errstr = String error message if there was an error
+ $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{
@@ -576,12 +576,12 @@
Function : Executes a query for objects in the database
Args : type => String - lsid or a term identifying a particular object
Returns : listref of hashrefs:
- [{object_id => Integer,
- object_lsid => String,
- object_type => String,
- description => String,
- authority => String,
- contact_email => String}, ...]
+ [{object_id => Integer,
+ object_lsid => String,
+ object_type => String,
+ description => String,
+ authority => String,
+ contact_email => String}, ...]
Notes : Only allows querying by lsid or type term
=cut
sub query_object{
@@ -594,10 +594,10 @@
Usage : my $un = $API->insert_object(%args)
Function : Inserts an object into the database
Args : object_type => String,
- object_lsid => String,
- description => String,
- authority => String,
- contact_email => String
+ object_lsid => String,
+ description => String,
+ authority => String,
+ contact_email => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -613,8 +613,8 @@
Function : Deletes an object and any relationships it has from the database
Args : type => String - lsid or term identifying a particular object
Returns : ($err, $errstr)
- $err = 1 if there was an delete error, 0 if successful
- $errstr = String error message if there was an error
+ $err = 1 if there was an delete error, 0 if successful
+ $errstr = String error message if there was an error
=cut
sub delete_object{
@@ -631,11 +631,11 @@
Function : Executes a query for object relationships in the database
Args : type => String - lsid or a term identifying a particular object
Returns : listref of hashrefs:
- [{assertion_id => Integer,
- relationship_type => String,
- object1_id => String,
- object2_id => String,
- object2_articlename => String}, ...]
+ [{assertion_id => Integer,
+ relationship_type => String,
+ object1_id => String,
+ object2_id => String,
+ object2_articlename => String}, ...]
Notes : Only allows querying by lsid or type term
=cut
sub query_object_term2term{
@@ -648,9 +648,9 @@
Usage : my $un = $API->insert_object_term2term(%args)
Function : Inserts an object relationship into the database
Args : relationship_type => String,
- object1_id => String,
- object2_id => String,
- object2_articlename => String
+ object1_id => String,
+ object2_id => String,
+ object2_articlename => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -673,29 +673,29 @@
Usage : my $un = $API->query_service_instance(%args)
Function : Executes a query for service instances in the database
Args : 0 or more:
- service_instance_id => Integer
- category => String
- servicename => String
- service_type_uri => String
- 'authority.authority_uri' => String - IMPORTANT notice use of quotes to avoid conflict with perl special operator '.'
- url => String
- 'service_instance.contact_email' => String - Again IMPORTANT use of quotes
- authoritative => Integer
- description => String
- signatureURL => String
- lsid => String
- Returns : listref of hashrefs:
- [{service_instance_id => Integer,
- category => String,
- servicename => String,
- service_type_uri => String,
- authority.authority_uri => String,
- url => String,
- service_instance.contact_email => String,
- authoritative => Integer,
- description => String,
- signatureURL => String,
- lsid => String}, ...]
+ service_instance_id => Integer
+ category => String
+ servicename => String
+ service_type_uri => String
+ 'authority.authority_uri' => String - IMPORTANT notice use of quotes to avoid conflict with perl special operator '.'
+ url => String
+ 'service_instance.contact_email' => String - Again IMPORTANT use of quotes
+ authoritative => Integer
+ description => String
+ signatureURL => String
+ lsid => String
+ Returns : listref of hashrefs:
+ [{service_instance_id => Integer,
+ category => String,
+ servicename => String,
+ service_type_uri => String,
+ authority.authority_uri => String,
+ url => String,
+ service_instance.contact_email => String,
+ authoritative => Integer,
+ description => String,
+ signatureURL => String,
+ lsid => String}, ...]
Notes : Allows querying by multiple conditions joined by 'and'
=cut
sub query_service_instance {
@@ -707,10 +707,10 @@
Title : query_service_existence
Usage : my $un = $API->query_service_existence(%args)
Function : Executes a query to check if the service exists in the database
- Args : servicename => String
- authority_uri => String
+ Args : servicename => String
+ authority_uri => String
Returns : 1 if service exists
- 0 if no such service instance
+ 0 if no such service instance
Notes : Only allows querying by URI of the authority and service name
=cut
sub query_service_existence{
@@ -729,15 +729,15 @@
Usage : my $un = $API->insert_service_instance(%args)
Function : Inserts a service instance into the database
Args : category => String,
- servicename => String,
- service_type_uri => String,
- authority_uri => String,
- url => String,
- contact_email => String,
- authoritative => Integer,
- description => String,
- signatureURL => String,
- lsid => String
+ servicename => String,
+ service_type_uri => String,
+ authority_uri => String,
+ url => String,
+ contact_email => String,
+ authoritative => Integer,
+ description => String,
+ signatureURL => String,
+ lsid => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -753,8 +753,8 @@
Function : Deletes a service instance from the database
Args : service_instance_lsid => String
Returns : ($err, $errstr)
- $err = 1 if there was an delete error, 0 if successful
- $errstr = String error message if there was an error
+ $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{
@@ -771,9 +771,9 @@
Function : Executes a query for authorities in the database
Args : authority_uri => String
Returns : listref of hashrefs:
- [{authority_common_name => String,
- authority_uri => String,
- contact_email => String}, ...]
+ [{authority_common_name => String,
+ authority_uri => String,
+ contact_email => String}, ...]
Notes : Only allows querying by URI of the authority
=cut
sub query_authority{
@@ -787,7 +787,7 @@
Function : Gets all unique authority URIs from the database
Args : no arguments
Returns : listref of hashrefs:
- [{authority_uri => String}]
+ [{authority_uri => String}]
=cut
sub get_all_authorities{
@@ -800,8 +800,8 @@
Usage : my $un = $API->insert_authority(%args)
Function : Inserts an authority into the database
Args : authority_common_name => String,
- authority_uri => String,
- contact_email => String
+ authority_uri => String,
+ contact_email => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -825,12 +825,12 @@
Function : Executes a query for service class
Args : type => String - either service_type or service_lsid
Returns : listref of hashrefs:
- [{service_id => Integer,
- service_lsid => String,
- service_type => String,
- description => String,
- authority => String,
- contact_email => String}, ...]
+ [{service_id => Integer,
+ service_lsid => String,
+ service_type => String,
+ description => String,
+ authority => String,
+ 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
@@ -844,10 +844,10 @@
Usage : my $un = $API->insert_service(%args)
Function : Inserts a service class into the database
Args : service_type => String,
- service_lsid => String,
- description => String,
- authority => String,
- contact_email => String
+ service_lsid => String,
+ description => String,
+ authority => String,
+ contact_email => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -863,8 +863,8 @@
Function : Deletes a service from the database
Args : service_lsid => String
Returns : ($err, $errstr)
- $err = 1 if there was an delete error, 0 otherwise
- $errstr = String error message if there was an error
+ $err = 1 if there was an delete error, 0 otherwise
+ $errstr = String error message if there was an error
=cut
sub delete_service{
@@ -881,10 +881,10 @@
Function : Executes a query for service relationships
Args : type => String - either service_type or service_lsid
Returns : listref of hashrefs:
- [{assertion_id => Integer,
- relationship_type => String,
- service1_id => String,
- service2_id => String}, ...]
+ [{assertion_id => Integer,
+ relationship_type => String,
+ service1_id => String,
+ 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
@@ -898,8 +898,8 @@
Usage : my $un = $API->insert_service_term2term(%args)
Function : Inserts a service relationship
Args : relationship_type => String,
- service1_type => String,
- service2_type => String
+ service1_type => String,
+ service2_type => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -921,18 +921,18 @@
Title : query_relationship
Usage : my $un = $API->query_relationship(%args)
Function : Executes a query for a relationship in an ontology
- Args : type => String,
- ontology => String
+ Args : type => String,
+ ontology => String
Returns : listref of hashrefs:
[{relationship_id => Integer,
- relationship_lsid => String,
- relationship_type => String,
- container => Integer,
- description => String,
- authority => String,
- contact_email => String,
- ontology => String}, ...]
- one hashref for each relationship
+ relationship_lsid => String,
+ relationship_type => String,
+ container => Integer,
+ description => String,
+ authority => String,
+ contact_email => String,
+ ontology => String}, ...]
+ 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
@@ -960,12 +960,12 @@
Function : Executes a query for namespace instances in the database
Args : type => String - either lsid or term for a particular namespace
Returns : listref of hashrefs:
- [{namespace_id => Integer,
- namespace_lsid => String,
- namespace_type => String,
- description => String,
- authority => String,
- contact_email => String}, ...]
+ [{namespace_id => Integer,
+ namespace_lsid => String,
+ namespace_type => String,
+ description => String,
+ authority => String,
+ contact_email => String}, ...]
=cut
sub query_namespace{
@@ -978,10 +978,10 @@
Usage : my $un = $API->insert_namespace(%args)
Function : Deletes a namespace instance from the database
Args : namespace_type => String,
- namespace_lsid => String,
- description => String,
- authority => String,
- contact_email => String
+ namespace_lsid => String,
+ description => String,
+ authority => String,
+ contact_email => String
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...
@@ -997,8 +997,8 @@
Function : Deletes a namespace instance from the database
Args : type => String - lsid or namespace term identifying a particular namespace
Returns : ($err, $errstr)
- $err = 1 if there was an delete error, 0 otherwise
- $errstr = String error message if there was an error
+ $err = 1 if there was an delete error, 0 otherwise
+ $errstr = String error message if there was an error
=cut
sub delete_namespace{
@@ -1012,10 +1012,10 @@
Function : Execute a query for namespaces_term2term
Args : type => String - namespace_type you are checking for
Returns : listref of hashrefs:
- [{assertion_id => Integer,
- relationship_type => String,
- namespace1_id => String,
- namespace2_id => String}, ...]
+ [{assertion_id => Integer,
+ relationship_type => String,
+ namespace1_id => String,
+ namespace2_id => String}, ...]
Notes : namespace1_id and namespace2_id will be lsids
=cut
@@ -1042,9 +1042,9 @@
Function : Execute a custom query for objects that are used by some service
Args : type => String - either namespace_lsid or namespace_term
Returns : a list:
- ($err, $errstr)
- $err = 1 if namespace is used by a service, 0 otherwise
- $errstr = contains the error message
+ ($err, $errstr)
+ $err = 1 if namespace is used by a service, 0 otherwise
+ $errstr = contains the error message
=cut
# custom query subroutine for Moby::Central.pm->deregisterObjectClass()
@@ -1059,9 +1059,9 @@
Function : Execute a custom query for namespaces that are used by some service
Args : type => String - either namespace_lsid or namespace_term
Returns : a list:
- ($err, $errstr)
- $err = 1 if namespace is used by a service, 0 otherwise
- $errstr = contains the error message
+ ($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()
@@ -1077,20 +1077,20 @@
Args : keywords => listref (of keywords)
Returns : listref of hashrefs:
[{service_instance_id => Integer,
- category => String,
- servicename => String,
- service_type_uri => String,
- authority_id => Integer,
- url => String,
- contact_email => String,
- authoritative => String,
+ category => String,
+ servicename => String,
+ service_type_uri => String,
+ authority_id => Integer,
+ url => String,
+ contact_email => String,
+ authoritative => String,
description => String,
- signatureURL => String,
- lsid => String}, ...]
+ signatureURL => String,
+ lsid => String}, ...]
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
+ Keywords are assumed to be joined by "OR" for the query
=cut
# custom query routine for Moby::Central.pm -> findService()
@@ -1103,9 +1103,9 @@
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
- namespaceURIs => array-ref - reference to an array of namespace URIs
+ Args : inout => String - to specify if input or output
+ ancestor_string => String - values that occur in object_type_uri
+ namespaceURIs => array-ref - reference to an array of namespace URIs
Returns : listref of hashrefs:
[{service_instance_id => Integer,
namespace_type_uris => String}, ...]
@@ -1123,9 +1123,9 @@
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
- namespaceURIs => array-ref - reference to an array of namespace URIs
+ Args : inout => String - to specify if input or output
+ objectURI => String - value that binds to object_type_uri
+ namespaceURIs => array-ref - reference to an array of namespace URIs
Returns : listref of hashrefs:
[{service_instance_id => Integer,
namespace_type_uris => String}, ...]
@@ -1147,7 +1147,7 @@
Returns : listref of hashrefs:
[{authority_uri => String,
servicename => String}, ...]
- one hashref for each service
+ one hashref for each service
=cut
# custom query subroutine for Moby::Central.pm->RetrieveServiceNames
@@ -1161,10 +1161,10 @@
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
+ term => String - bindvalue for OntologyEntry.term
Returns : listref of hashrefs:
[{term => String}, ...]
- one hashref for each parent
+ one hashref for each parent
=cut
# custom query for Moby::Central.pm->_flatten
@@ -1180,13 +1180,13 @@
Args : type => String - either an object name or LSID
Returns : listref of hashrefs:
[{relationship_type => String,
- object_type => String,
+ object_type => String,
object_lsid => String,
- description => String,
- authority => String,
- contact_email => String,
+ description => String,
+ authority => String,
+ contact_email => String,
object2_articlename => String}, ...]
- one hashref for each relationship between two objects
+ 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
@@ -1201,13 +1201,13 @@
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
- term => String - a bind value for lsid
- relationship => String - a bind value for relationship_type
+ Args : direction => String - direction in the ontology (eg. 'root')
+ ontology => String - name of the table ontology
+ term => String - a bind value for lsid
+ relationship => String - a bind value for relationship_type
Returns : reference to array containing array-refs representing the result set:
- [[String lsid, String relationship_type], ...]
- each array-ref represents one row
+ [[String lsid, String relationship_type], ...]
+ each array-ref represents one row
Notes : Only returns distinct lsids from $ontology and relationship_type from $ontology_term2term
=cut
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