v0.16.26 (#137)

Enabled deep copy of objects with a given prefix when cloning a workspace (closes #131).

For workflow submissions, enabled running non-data model configs by making entity name optional in the CLI, and not including entity name and type in the API payload when they have not been set.

Specifics:
api.py
* added copyFilesWithPrefix parameter to clone_workspace
* create_submission no longer includes entity name and type in its payload when they are not set

fiss.py
* added copyFilesWithPrefix parameter to space_clone
* config_start no longer requires entity to be set

Co-authored-by: M. Morgan Taylor <[email protected]>

changelog.txt

@@ -3,6 +3,12 @@ Change Log for FISSFC: the (Fi)recloud (S)ervice (S)elector
 =======================================================================
 Terms used below:  HL = high level interface, LL = low level interface
 
+v0.16.26 - LL: added copyFilesWithPrefix parameter to clone_workspace,
+           create_submission no longer includes entity name and type in its
+           payload when they are not set; HL: added copyFilesWithPrefix 
+           parameter to space_clone, config_start no longer requires entity to
+           be set in order to enable running non-data model configs.
+
 v0.16.25 - HL: multiple enhancements to mop; only delete unreferenced files
            generated by workflows, ignore more files generated by the execution
            engine (e.g. rc, script, stdout, stderr), report file sizes, allow

firecloud/__about__.py

@@ -1,2 +1,2 @@
 # Package version
-__version__ = "0.16.25"
+__version__ = "0.16.26"

firecloud/api.py

@@ -1034,7 +1034,7 @@ def list_submissions(namespace, workspace):
     return __get(uri)
 
 def create_submission(wnamespace, workspace, cnamespace, config,
-                      entity, etype, expression=None, use_callcache=True):
+                      entity=None, etype=None, expression=None, use_callcache=True):
     """Submit job in FireCloud workspace.
 
     Args:
@@ -1058,11 +1058,15 @@ def create_submission(wnamespace, workspace, cnamespace, config,
     body = {
         "methodConfigurationNamespace" : cnamespace,
         "methodConfigurationName" : config,
-         "entityType" : etype,
-         "entityName" : entity,
          "useCallCache" : use_callcache
     }
 
+    if etype:
+        body['entityType'] = etype
+
+    if entity:
+        body['entityName'] = entity
+
     if expression:
         body['expression'] = expression
 
@@ -1246,7 +1250,7 @@ def update_workspace_acl(namespace, workspace, acl_updates, invite_users_not_fou
     return __SESSION.patch(uri, headers=headers, data=json.dumps(acl_updates))
 
 def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
-                    authorizationDomain=""):
+                    authorizationDomain="", copyFilesWithPrefix=None):
     """Clone a FireCloud workspace.
 
     A clone is a shallow copy of a FireCloud workspace, enabling
@@ -1258,6 +1262,7 @@ def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
         to_namespace (str):  project to which target workspace belongs
         to_workspace (str): Target workspace's name
         authorizationDomain: (str) required authorization domains
+        copyFilesWithPrefix: (str) prefix of bucket objects to copy to the destination workspace
 
     Swagger:
         https://api.firecloud.org/#!/Workspaces/cloneWorkspace
@@ -1277,6 +1282,9 @@ def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
         "attributes": dict(),
         "authorizationDomain": authDomain,
     }
+
+    if copyFilesWithPrefix is not None:
+        body["copyFilesWithPrefix"] = copyFilesWithPrefix
 
     uri = "workspaces/{0}/{1}/clone".format(from_namespace, from_workspace)
     return __post(uri, json=body)

firecloud/fiss.py

@@ -147,7 +147,7 @@ def space_clone(args):
         return 1
 
     r = fapi.clone_workspace(args.project, args.workspace, args.to_project,
-                                                            args.to_workspace)
+                             args.to_workspace, args.copyFilesWithPrefix)
     fapi._check_response_code(r, 201)
 
     if fcconfig.verbosity:
@@ -567,6 +567,10 @@ def config_start(args):
         args.namespace = fcconfig.method_ns
     if not args.namespace:
         raise RuntimeError("namespace not provided, or configured by default")
+
+    # If no entity name is given, unset entity_type
+    if args.entity is None:
+        args.entity_type = None
 
     r = fapi.create_submission(args.project, args.workspace,args.namespace,
                             args.config, args.entity, args.entity_type,
@@ -2100,6 +2104,8 @@ def main(argv=None):
                  'be different from the workspace being cloned'
     subp = subparsers.add_parser('space_clone', description=clone_desc,
                                  parents=[workspace_parent, dest_space_parent])
+    subp.add_argument('-f', '--copyFilesWithPrefix', help='Specify a prefix ' +
+                      'of bucket objects to copy to the destination workspace')
     subp.set_defaults(func=space_clone)
 
     # Import data into a workspace
@@ -2495,12 +2501,14 @@ def main(argv=None):
     # Invoke a method configuration
     subp = subparsers.add_parser('config_start',
         description='Start running workflow in a given space',
-        parents=[workspace_parent, conf_parent, entity_parent])
+        parents=[workspace_parent, conf_parent])
+    subp.add_argument('-e', '--entity', help="Entity name (required if " +
+                      "executing on an entity)")
     # Duplicate entity type here since we want sample_set to be default
     subp.add_argument('-t', '--entity-type', default='sample_set',
                       choices=etype_choices,
-                      help='Entity type to assign null values, if attribute ' +
-                           'is missing. Default: %(default)s')
+                      help='Entity type of specified entity. Not used if no ' +
+                      'entity is named. Default: %(default)s')
     expr_help = "(optional) Entity expression to use when entity type " \
                 "doesn't match the method configuration." \
                 "Example: 'this.samples'"