Adding annotation ontology API client

Author: cshenry

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"

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

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)