Merge pull request #114 from broadinstitute/wdl_retrieve

New WDL extraction capabilities

Author: noblem

changelog.txt

@@ -3,6 +3,11 @@ Change Log for FISSFC: the (Fi)recloud (S)ervice (S)elector
 =======================================================================
 Terms used below:  HL = high level interface, LL = low level interface
 
+v0.16.20 - Updated LL command get_repository_method with documentation link and
+           new parameter wdl_only; new HL commands config_wdl and meth_wdl
+           use the updated LL command to retrieve WDL from the workspace config
+           and method repository respectively.
+
 v0.16.19 - Added config_diff HL command, HL command mop updated to work in
            Python 3 and fail with proper error message when workspace bucket is
            inaccessible.

firecloud/__about__.py

@@ -1,2 +1,2 @@
 # Package version
-__version__ = "0.16.19"
+__version__ = "0.16.20"

firecloud/api.py

@@ -753,18 +753,21 @@ def get_repository_config(namespace, config, snapshot_id):
     uri = "configurations/{0}/{1}/{2}".format(namespace, config, snapshot_id)
     return __get(uri)
 
-def get_repository_method(namespace, method, snapshot_id):
+def get_repository_method(namespace, method, snapshot_id, wdl_only=False):
     """Get a method definition from the method repository.
 
     Args:
         namespace (str): Methods namespace
         method (str): method name
         version (int): snapshot_id of the method
+        wdl_only (bool): Exclude metadata
 
     Swagger:
-        UNDOCUMENTED
+        https://api.firecloud.org/#!/Method_Repository/get_api_methods_namespace_name_snapshotId
     """
-    uri = "methods/{0}/{1}/{2}".format(namespace, method, snapshot_id)
+    uri = "methods/{0}/{1}/{2}?onlyPayload={3}".format(namespace, method,
+                                                       snapshot_id,
+                                                       str(wdl_only).lower())
     return __get(uri)
 
 def update_repository_method(namespace, method, synopsis, wdl, doc=None,

firecloud/fiss.py

@@ -418,6 +418,14 @@ def meth_delete(args):
         print("Method %s removed from project %s" % (args.method,args.namespace))
     return 0
 
+@fiss_cmd
+def meth_wdl(args):
+    ''' Retrieve WDL for given version of a repository method'''
+    r = fapi.get_repository_method(args.namespace, args.method,
+                                   args.snapshot_id, True)
+    fapi._check_response_code(r, 200)
+    return r.text
+
 @fiss_cmd
 def meth_acl(args):
     ''' Retrieve access control list for given version of a repository method'''
@@ -565,6 +573,20 @@ def config_get(args):
     return json.dumps(r.json(), indent=4, separators=(',', ': '),
                       sort_keys=True, ensure_ascii=False)
 
+@fiss_cmd
+def config_wdl(args):
+    """ Retrieve the WDL for a method config in a workspace, send stdout """
+    r = fapi.get_workspace_config(args.project, args.workspace,
+                                  args.namespace, args.config)
+    fapi._check_response_code(r, 200)
+    
+    method = r.json()["methodRepoMethod"]
+    args.namespace   = method["methodNamespace"]
+    args.method      = method["methodName"]
+    args.snapshot_id = method["methodVersion"]
+    
+    return meth_wdl(args)
+
 @fiss_cmd
 def config_diff(args):
     """Compare method configuration definitions across workspaces. Ignores
@@ -2046,6 +2068,12 @@ def main(argv=None):
         description='Redact method from the methods repository',
         parents=[meth_parent, snapshot_parent])
     subp.set_defaults(func=meth_delete)
+    
+    # Retreive the WDL of a method
+    subp = subparsers.add_parser('meth_wdl',
+        description='Retrieve the WDL of a method',
+        parents=[meth_parent, snapshot_parent])
+    subp.set_defaults(func=meth_wdl)
 
     # Access control list operations (upon methods)
     # Get ACL
@@ -2102,6 +2130,15 @@ def main(argv=None):
                       help=proj_help, required=proj_required)
     subp.set_defaults(func=config_get)
 
+    subp = subparsers.add_parser('config_wdl',
+        description='Retrieve method configuration WDL',
+        parents=[conf_parent])
+    subp.add_argument('-w', '--workspace', help='Workspace name',
+                      default=fcconfig.workspace, required=workspace_required)
+    subp.add_argument('-p', '--project', default=fcconfig.project,
+                      help=proj_help, required=proj_required)
+    subp.set_defaults(func=config_wdl)
+    
     subp = subparsers.add_parser('config_diff',
         description='Compare method configuration definitions across workspaces',
         parents=[conf_parent])