diff --git a/dependencies.json b/dependencies.json index fb1cbf2..4d0b8cb 100644 --- a/dependencies.json +++ b/dependencies.json @@ -1,4 +1,8 @@ [ { + "module_name" : "cb_annotation_ontology_api", + "type" : "sdk", + "version_tag" : "dev" +}, { "module_name" : "DataFileUtil", "type" : "sdk", "version_tag" : "release" diff --git a/lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py b/lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py index fd0728c..442b3f9 100644 --- a/lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py +++ b/lib/ModelSEEDReconstruction/ModelSEEDReconstructionImpl.py @@ -37,9 +37,6 @@ class ModelSEEDReconstruction: GIT_COMMIT_HASH = "" #BEGIN_CLASS_HEADER - from installed_clients.DataFileUtilClient import DataFileUtil - from installed_clients.KBaseReportClient import KBaseReport - from installed_clients.WorkspaceClient import Workspace #END_CLASS_HEADER # config contains contents of config file in a hash or None if it couldn't diff --git a/lib/installed_clients/cb_annotation_ontology_apiClient.py b/lib/installed_clients/cb_annotation_ontology_apiClient.py new file mode 100644 index 0000000..5037078 --- /dev/null +++ b/lib/installed_clients/cb_annotation_ontology_apiClient.py @@ -0,0 +1,96 @@ +# -*- coding: utf-8 -*- +############################################################ +# +# Autogenerated by the KBase type compiler - +# any changes made here will be overwritten +# +############################################################ + +from __future__ import print_function +# the following is a hack to get the baseclient to import whether we're in a +# package or not. This makes pep8 unhappy hence the annotations. +try: + # baseclient and this client are in a package + from .baseclient import BaseClient as _BaseClient # @UnusedImport +except ImportError: + # no they aren't + from baseclient import BaseClient as _BaseClient # @Reimport + + +class cb_annotation_ontology_api(object): + + def __init__( + self, url=None, timeout=30 * 60, user_id=None, + password=None, token=None, ignore_authrc=False, + trust_all_ssl_certificates=False, + auth_svc='https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login', + service_ver='dev', + async_job_check_time_ms=100, async_job_check_time_scale_percent=150, + async_job_check_max_time_ms=300000): + if url is None: + raise ValueError('A url is required') + self._service_ver = service_ver + self._client = _BaseClient( + url, timeout=timeout, user_id=user_id, password=password, + token=token, ignore_authrc=ignore_authrc, + trust_all_ssl_certificates=trust_all_ssl_certificates, + auth_svc=auth_svc, + async_job_check_time_ms=async_job_check_time_ms, + async_job_check_time_scale_percent=async_job_check_time_scale_percent, + async_job_check_max_time_ms=async_job_check_max_time_ms) + + def get_annotation_ontology_events(self, params, context=None): + """ + Retrieves annotation ontology events in a standardized form cleaning up inconsistencies in underlying data + :param params: instance of type "GetAnnotationOntologyEventsParams" + -> structure: parameter "input_ref" of String, parameter + "input_workspace" of String, parameter "query_events" of list of + String, parameter "query_genes" of list of String, parameter + "standardize_modelseed_ids" of Long + :returns: instance of type "GetAnnotationOntologyEventsOutput" -> + structure: parameter "events" of list of type + "AnnotationOntologyEvent" -> structure: parameter "event_id" of + String, parameter "description" of String, parameter "ontology_id" + of String, parameter "method" of String, parameter + "method_version" of String, parameter "timestamp" of String, + parameter "feature_types" of mapping from String to String, + parameter "ontology_terms" of mapping from String to list of type + "AnnotationOntologyTerm" -> structure: parameter "term" of String, + parameter "modelseed_ids" of list of String, parameter + "evidence_only" of Long, parameter "evidence" of type "Evidence" + -> structure: parameter "reference" of tuple of size 2: parameter + "entity_type" of String, parameter "ref_entity" of String, + parameter "scores" of mapping from String to Double + """ + return self._client.run_job('cb_annotation_ontology_api.get_annotation_ontology_events', + [params], self._service_ver, context) + + def add_annotation_ontology_events(self, params, context=None): + """ + Adds a new annotation ontology event to a genome or AMA + :param params: instance of type "AddAnnotationOntologyEventsParams" + -> structure: parameter "input_ref" of String, parameter + "input_workspace" of String, parameter "output_name" of String, + parameter "output_workspace" of String, parameter "clear_existing" + of Long, parameter "overwrite_matching" of Long, parameter + "events" of list of type "AnnotationOntologyEvent" -> structure: + parameter "event_id" of String, parameter "description" of String, + parameter "ontology_id" of String, parameter "method" of String, + parameter "method_version" of String, parameter "timestamp" of + String, parameter "feature_types" of mapping from String to + String, parameter "ontology_terms" of mapping from String to list + of type "AnnotationOntologyTerm" -> structure: parameter "term" of + String, parameter "modelseed_ids" of list of String, parameter + "evidence_only" of Long, parameter "evidence" of type "Evidence" + -> structure: parameter "reference" of tuple of size 2: parameter + "entity_type" of String, parameter "ref_entity" of String, + parameter "scores" of mapping from String to Double + :returns: instance of type "AddAnnotationOntologyEventsOutput" -> + structure: parameter "output_ref" of String + """ + return self._client.run_job('cb_annotation_ontology_api.add_annotation_ontology_events', + [params], self._service_ver, context) + + def status(self, context=None): + return self._client.run_job('cb_annotation_ontology_api.status', + [], self._service_ver, context)