NAME
MOBY::Adaptor::moby::queryapi - An interface definition for MOBY Central underlying data-stores
SYNOPSIS
use MOBY::Adaptor::moby::queryapi::mysql # implements this interface def
my $m = MOBY::Adaptor::moby::queryapi::mysql->new(
username => 'user',
password => 'pass',
dbname => 'mobycentral',
port => '3306',
sourcetype => 'DBD::mysql');
my $objectid = $m->insert_object(
{object_type => "MyObject"},
{description => "this represents a foo bar"},
{authority => "www.example.org"},
{contact_email, 'me@example.org'})DESCRIPTION
This is an interface definition. There is NO implementation in this module with the exception that certain calls to required parameters have get/setter functions in this module (that can be overridden)
AUTHORS
Mark Wilkinson markw_at_ illuminae dot com Dennis Wang oikisai _at_ hotmail dot com BioMOBY Project: http://www.biomoby.org
METHODS
new
Title : new
Usage : my $MOBY = MOBY::Client::Central->new(%args)
Function : connect to one or more MOBY-Central
registries for searching
Returns : MOBY::Client::Central object
Args :
Notes : username
Title : username
Usage : my $un = $API->username($arg)
Function : get/set username (if required)
Returns : String (username)
Args : String (username) - optional.password
Title : password
Usage : my $un = $API->password($arg)
Function : get/set password (if required)
Returns : String (password)
Args : String (password) - optional.dbname
Title : dbname
Usage : my $un = $API->dbname($arg)
Function : get/set dbname (if required)
Returns : String (dbname)
Args : String (dbname) - optional.port
Title : port
Usage : my $un = $API->port($arg)
Function : get/set port (if required)
Returns : String (port)
Args : String (port) - optional.proxy
Title : proxy
Usage : my $un = $API->proxy($arg)
Function : get/set proxy (if required)
Returns : String (proxy)
Args : String (proxy) - optional.sourcetype
Title : sourcetype
Usage : my $un = $API->sourcetype($arg)
Function : get/set string name of sourcetype (e.g. mySQL)
Returns : String (sourcetype)
Args : String (sourcetype) - optional.driver
Title : driver
Usage : my $un = $API->driver($arg)
Function : get/set string name of DSI driver module (e.g. DBI:mySQL)
Returns : String (driver)
Args : String (driver) - optional.url
Title : url
Usage : my $un = $API->url($arg)
Function : get/set url (if required)
Returns : String (url)
Args : String (url) - optional.dbh
Title : dbh
Usage : my $un = $API->dbh($arg)
Function : get/set database handle (if required)
Returns : Database handle in whatever object is appropriate for sourcetype
Args : Database handle in whatever object is appropriate for sourcetypequery_collection_input
Title : query_collection_input
Usage : my $un = $API->query_collection_input(%arg)
Function : get the collection input information for a given service
Args : service_lsid => String
Returns : listref of hashrefs:
[{collection_input_id => Integer
article_name => String}, ...]
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...insert_collection_input
Title : insert_collection_input
Usage : my $un = $API->insert_collection_input(%args)
Function : Inserts a Collection input into the database
Args : article_name => String,
service_instance_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...delete_collection_input
Title : delete_collection_input
Usage : my $un = $API->delete_collection_input(%args)
Function : Deletes Collection inputs according to the service instance
Args : service_instance_lsid => String,
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error query_collection_output
Title : query_collection_output
Usage : my $un = $API->query_collection_output(%args)
Function : Executes a query for Collection outputs according to the service instance
Args : service_instance_lsid => String,
Returns : listref of hashrefs:
[{collection_output_id => Integer,
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 terminsert_collection_output
Title : insert_collection_output
Usage : my $un = $API->insert_collection_output(%args)
Function : Inserts a Collection output into the database
Args : article_name => String,
service_instance_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...delete_collection_output
Title : delete_collection_output
Usage : my $un = $API->delete_collection_output(%args)
Function : Deletes Collection outputs according to the service instance
Args : service_instance_lsid => String,
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error query_simple_input
Title : query_simple_input
Usage : my $un = $API->query_simple_input(%args)
Function : Executes a query for Simple inputs according to the service instance or collection output
Args : service_instance_lsid => String,
collection_input_id => Integer
Returns : listref of hashrefs:
[{simple_input_id => Integer,
object_type_uri => String,
namespace_type_uris => String,
article_name => String,
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 terminsert_simple_input
Title : insert_simple_input
Usage : my $un = $API->insert_simple_input(%args)
Function : Inserts a Simple input into the database
Args : object_type_uri => String,
namespace_type_uris => String,
article_name => String,
service_instance_lsid => String,
collection_input_id => Integer
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...delete_simple_input
Title : delete_simple_input
Usage : my $un = $API->delete_simple_input(%args)
Function : Deletes Simple inputs according to the service instance, or collection input
Args : service_instance_lsid => String,
collection_input_id => Integer
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an errorquery_simple_output
Title : query_simple_output
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
Returns : listref of hashrefs:
[{simple_output_id => Integer,
object_type_uri => String,
namespace_type_uris => String,
article_name => String,
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 terminsert_simple_output
Title : insert_simple_output
Usage : my $un = $API->insert_simple_output(%args)
Function : Inserts a Simple output into the database
Args : object_type_uri => String,
namespace_type_uris => String,
article_name => String,
service_instance_lsid => String,
collection_output_id => Integer
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...delete_simple_output
Title : delete_simple_output
Usage : my $un = $API->delete_simple_output(%args)
Function : Deletes Simple outputs according to the service instance, or collection output
Args : service_instance_lsid => String,
collection_output_id => Integer
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error query_secondary_input
Title : query_secondary_input
Usage : my $un = $API->query_secondary_input(%args)
Function : Executes a query for Secondary input articles in the database
Args : service_instance_lsid => String
Returns : listref of hashrefs:
[{secondary_input_id => Integer,
default_value => String,
maximum_value => Float,
minimum_value => Float,
enum_value => String,
datatype => String,
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 terminsert_secondary_input
Title : insert_secondary_input
Usage : my $un = $API->insert_secondar_input(%args)
Function : Inserts a Secondary input into the database
Args : default_value => String,
maximum_value => Float,
minimum_value => Float,
enum_value => String,
datatype => String,
article_name => String,
service_instance_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...delete_secondary_input
Title : delete_secondary_input
Usage : my $un = $API->delete_secondary_input(%args)
Function : Deletes a Secondary input from the database
Args : service_instance_lsid => String
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error query_object
Title : query_object
Usage : my $un = $API->query_object(%args)
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}, ...]
Notes : Only allows querying by lsid or type terminsert_object
Title : insert_object
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
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...delete_object
Title : delete_object
Usage : my $un = $API->delete_object(%args)
Function : Deletes an object and any relationships it has from the database
Args : type => String - lsid or term identifying a particular object
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error query_object_term2term
Title : query_object_term2term
Usage : my $un = $API->query_object_term2term(%args)
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}, ...]
Notes : Only allows querying by lsid or type terminsert_object_term2term
Title : insert_object_term2term
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
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...query_service_instance
Title : query_service_instance
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}, ...]
Notes : Allows querying by multiple conditions joined by 'and'query_service_existence
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
Returns : 1 if service exists
0 if no such service instance
Notes : Only allows querying by URI of the authority and service nameinsert_service_instance
Title : insert_service_instance
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
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...delete_service_instance
Title : delete_service_instance
Usage : my $un = $API->delete_service_instance(%args)
Function : Deletes a service instance from the database
Args : service_instance_lsid => String
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 if successful
$errstr = String error message if there was an error query_authority
Title : query_authority
Usage : my $un = $API->query_authority(%args)
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}, ...]
Notes : Only allows querying by URI of the authorityget_all_authorities
Title : get_all_authorities
Usage : my $un = $API->get_all_authorities()
Function : Gets all unique authority URIs from the database
Args : no arguments
Returns : listref of hashrefs:
[{authority_uri => String}]insert_authority
Title : insert_authority
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
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...query_service
Title : query_service
Usage : my $un = $API->query_service(%args)
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}, ...]
Notes : the fact that it returns an service_id is bad since this
is only useful to an SQL-based API...insert_service
Title : insert_service
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
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...delete_service
Title : delete_service
Usage : my $un = $API->delete_service(%args)
Function : Deletes a service from the database
Args : service_lsid => String
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 otherwise
$errstr = String error message if there was an error query_service_term2term
Title : query_service_term2term
Usage : my $un = $API->query_service_term2term(%args)
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}, ...]
Notes : the fact that it returns an service ids is bad since this
is only useful to an SQL-based API...should return lsidsinsert_service_term2term
Title : insert_service_term2term
Usage : my $un = $API->insert_service_term2term(%args)
Function : Inserts a service relationship
Args : relationship_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...query_relationship
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
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
Notes : the fact that it returns a relationship_id is bad since this
is only useful to an SQL-based API...query_namespace
Title : query_namespace
Usage : my $un = $API->query_namespace(%args)
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}, ...]insert_namespace
Title : insert_namespace
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
Returns : Integer insertid
Notes : the fact that it returns an insertid is bad since this
is only useful to an SQL-based API...delete_namespace
Title : delete_namespace
Usage : my $un = $API->delete_namespace(%args)
Function : Deletes a namespace instance from the database
Args : type => String - lsid or namespace term identifying a particular namespace
Returns : ($err, $errstr)
$err = 1 if there was an delete error, 0 otherwise
$errstr = String error message if there was an error query_namespace_term2term
Title : query_namespace_term2term
Usage : my $un = $API->query_namespace_term2term(%args)
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}, ...]
Notes : namespace1_id and namespace2_id will be lsids check_object_usage
Title : check_object_usage
Usage : my $un = $API->check_object_usage(%args)
Function : Execute a custom query for objects that are used by some service
Args : type => String - either namespace_lsid or namespace_term
Returns : a list:
($err, $errstr)
$err = 1 if namespace is used by a service, 0 otherwise
$errstr = contains the error message check_namespace_usage
Title : check_namespace_usage
Usage : my $un = $API->check_namespace_usage(%args)
Function : Execute a custom query for namespaces that are used by some service
Args : type => String - either namespace_lsid or namespace_term
Returns : a list:
($err, $errstr)
$err = 1 if namespace is used by a service, 0 otherwise
$errstr = contains the error message check_keywords
Title : check_keywords
Usage : my $un = $API->check_keywords(%args)
Function : Execute a custom query for services with keywords in its description
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,
description => 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 find_by_simple
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
Returns : listref of hashrefs:
[{service_instance_id => Integer,
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...find_by_collection
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
Returns : listref of hashrefs:
[{service_instance_id => Integer,
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...get_service_names
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:
[{authority_uri => String,
servicename => String}, ...]
one hashref for each serviceget_parent_terms
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
Returns : listref of hashrefs:
[{term => String}, ...]
one hashref for each parentget_object_relationships
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 : type => String - either an object name or LSID
Returns : listref of hashrefs:
[{relationship_type => String,
object_type => String,
object_lsid => String,
description => String,
authority => String,
contact_email => String,
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_term2termget_relationship
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
Returns : reference to array containing array-refs representing the result set:
[[String lsid, String relationship_type], ...]
each array-ref represents one row
Notes : Only returns distinct lsids from $ontology and relationship_type from $ontology_term2termget_all_relationships
Title : get_all_relationships
Usage : my $un = $API->get_all_relationships(%args)
Function : Execute a query for all relationships represented in $ontology_term2term
Args : direction => String - direction in the ontology (either 'root' or 'leaves')
ontology => String - name of the table ontology
Returns : reference to hash with the following structure:
$resultHash->{String relationship_type}->{Integer key_entity_id} = <VALUE>
The structure of <VALUE> depends on relationship_type and direction:
HAS/HASA :
<VALUE> = @([Integer value_entity_id, String articleName, Integer assertion_id])
ISA, leaves :
<VALUE> = @(Integer value_entity_id)
ISA, root :
<VALUE> = Integer value_entity_id
Notes : The hash is built 'direction-aware', that is for
- root : key_entity_id = ${ontology}1_id, value_entity_id = ${ontology}2_id
- leaves: key_entity_id = ${ontology}2_id, value_entity_id = ${ontology}1_id
The structure of the result hash is a bit complex because it is specifically
designed for usage by MOBY::OntolgyServer::Relationships
The result hash contains the entire table ${ontology}_term2term in order to
reduce DB interaction in the ontology explorationget_details_for_id_list
Title : get_deails_for_id_list
Usage : my $un = $API->get_all_relationships($ontology, $field_list, $id_list)
Function : Retrieve details specified in @$field_list from $ontology for ids in @$id_list
Args : $ontology => String - name of the table ontology
$field_list => Reference to array of Strings representing table fields in $ontology
$id_list => Reference to array of Integers representing ${ontology}_ids
Returns : reference to hash with the following structure:
$resultHash->{Integer ${ontology}_id}->{String field_name} = field_value
Notes : This function is generic with respect to which details (fields) are retrieved, but
is restricted to those tables whose name is identical to the ontology name (i.e.
currently 'object', 'service', 'namespace' and 'relationship')
Makes use of the 'select ... from ... where ... in (<LIST>)' statement syntax
in order to reduce the number of DB interactions
Used in MOBY::OntologyServer::Relationships, but maybe useful for other purposes...