WS API HOME QL and new+legacy support for KBase zips

cobrakbase/Workspace/baseclient.py

@@ -55,14 +55,20 @@ def _get_token(user_id, password, auth_svc):
     return tok["token"]
 
 
-def _read_inifile(
-    file=_os.environ.get(  # @ReservedAssignment
-        "KB_DEPLOYMENT_CONFIG", _os.environ["HOME"] + "/.kbase_config"
-    )
-):
+def _read_inifile(file=None):
+    """
+    Filipe: hacked this portion to not crash on machines without HOME env var
+    @param file:
+    @return:
+    """
     # Another bandaid to read in the ~/.kbase_config file if one is present
     authdata = None
-    if _os.path.exists(file):
+    if file is None:
+        # @ReservedAssignment
+        if "HOME" in _os.environ:
+            file = _os.environ.get("KB_DEPLOYMENT_CONFIG", _os.environ["HOME"] + "/.kbase_config")
+
+    if file is not None and _os.path.exists(file):
         try:
             config = _ConfigParser()
             config.read(file)

cobrakbase/io/read_kbase_zip.py

@@ -33,15 +33,30 @@ def _read_kbase_zip(path):
 
 def load_kbase_zip_object(filename):
     item_info, item_data = _read_kbase_zip(filename)
-    data = {
-        'data': [
-            {
-                'info': item_info['metadata'][0],
-                'provenance': [item_info['provenance'][0]['provenance'][0]],
-                'data': item_data
-            }
-        ]
-    }
-
-    factory = KBaseObjectFactory()
-    return factory.create(data, None)
+    if item_info is None:
+        raise ValueError('invalid kbase zip file. unable to detect object workspace info')
+    if item_data is None:
+        raise ValueError('invalid kbase zip file. unable to detect object data')
+    legacy = 'info' not in item_info
+    if legacy:
+        data = {
+            'data': [
+                {
+                    'info': item_info['metadata'][0],
+                    'provenance': [item_info['provenance'][0]['provenance'][0]],
+                    'data': item_data
+                }
+            ]
+        }
+        KBaseObjectFactory().create(data, None)
+    else:
+        data = {
+            'data': [
+                {
+                    'info': item_info['info'],
+                    'provenance': [],
+                    'data': item_data
+                }
+            ]
+        }
+        return KBaseObjectFactory().create(data, None)

cobrakbase/kbase_catalog.py

@@ -1,7 +1,7 @@
 from cobrakbase.kbase_object_info import KBaseObjectInfo
 
 PROD_WS_MEDIA = 'KBaseMedia'
-PROD_WS_GENOMES = '?'
+PROD_WS_GENOMES = 'ReferenceDataManager'
 PROD_WS_TEMPLATES = 'NewKBaseModelTemplates'
 
 

cobrakbase/kbaseapi.py

@@ -284,9 +284,6 @@ def save_object(self, object_id, ws, object_type, data, meta=None):
             params["workspace"] = ws
         return KBaseObjectInfo(self.ws_client.save_objects(params)[0])
 
-    def save_model(self, object_id, ws, data):
-        return self.save_object(object_id, ws, "KBaseFBA.FBAModel", data)
-
     def list_objects(self, ws, object_type=None, include_metadata=False):
         """
         List objects of a workspace (i.e., narrative) with either numerical id (e.g., 12345)
@@ -308,28 +305,20 @@ def list_objects(self, ws, object_type=None, include_metadata=False):
             params["includeMetadata"] = 1
         return self.ws_client.list_objects(params)
 
+    def list_workspace(self, ws, object_type=None, include_metadata=False):
+        return [KBaseObjectInfo(i) for i in self.list_objects(ws, object_type, include_metadata)]
+
     def get_object_info(self, id_or_ref, workspace=None):
         ref_data = self.ws_client.get_object_info3(
-            {"objects": [self.process_workspace_identifiers(id_or_ref, workspace)],"includeMetadata":1}
+            {"objects": [self.process_workspace_identifiers(id_or_ref, workspace)], "includeMetadata": 1}
         )
         return KBaseObjectInfo(ref_data["infos"][0])
 
-    # TODO: this now seems obfuscated by get_object_info - can we delete this?
-    def get_object_info_from_ref(self, ref):
-        """
-        @deprecated get_object_info
-        """
-        return self.get_object_info(ref)
-
     def copy(self, from_id, from_ws, to_id, to_ws):
-        def copy_object(wclient, from_id, from_ws, to_id, to_ws):
-            params = {
-                "from": {"name": from_id, "workspace": from_ws},
-                "to": {"name": to_id, "workspace": to_ws},
-            }
-            return wclient.copy_object(params)
+        _from = self.process_workspace_identifiers(from_id, from_ws)
+        _to = self.process_workspace_identifiers(to_id, to_ws)
 
-        pass
+        return KBaseObjectInfo(self.ws_client.copy_object({"from": _from, "to": _to}))
 
     def get_workspace_info(self, ws_id_or_name):
         if type(ws_id_or_name) == str: