Implement the metadata in both API and CLI. (#76)

* Roughly implement the /metadata in both API and CLI.

* Fix the arguments for metadata commands.

cromwell_tools/cli.py

@@ -41,6 +41,11 @@ def parser(arguments=None):
         help='release_hold help',
         description='Request Cromwell to release the hold on a workflow.',
     )
+    metadata = subparsers.add_parser(
+        'metadata',
+        help='metadata help',
+        description='Retrieve the workflow and call-level metadata for a specified workflow by UUID.',
+    )
     query = subparsers.add_parser(
         'query',
         help='query help',
@@ -53,7 +58,16 @@ def parser(arguments=None):
     )
 
     # cromwell url and authentication arguments apply to all sub-commands
-    cromwell_sub_commands = (submit, wait, status, abort, release_hold, query, health)
+    cromwell_sub_commands = (
+        submit,
+        wait,
+        status,
+        abort,
+        release_hold,
+        metadata,
+        query,
+        health,
+    )
     auth_args = {
         'url': 'The URL to the Cromwell server. e.g. "https://cromwell.server.org/"',
         'username': 'Cromwell username for HTTPBasicAuth.',
@@ -186,6 +200,31 @@ def add_auth_args(subcommand_parser):
         help='A Cromwell workflow UUID, which is the workflow identifier.',
     )
 
+    # metadata arguments
+    metadata.add_argument(
+        '--uuid',
+        required=True,
+        help='A Cromwell workflow UUID, which is the workflow identifier.',
+    )
+    # TODO: add a mutually exclusive group to make it fail early
+    metadata.add_argument(
+        '--includeKey',
+        nargs='+',
+        default=None,
+        help='When specified key(s) to include from the metadata. Matches any key starting with the value. May not be used with excludeKey.',
+    )
+    metadata.add_argument(
+        '--excludeKey',
+        nargs='+',
+        default=None,
+        help='When specified key(s) to exclude from the metadata. Matches any key starting with the value. May not be used with includeKey.',
+    )
+    metadata.add_argument(
+        '--expandSubWorkflows',
+        default=False,
+        help='When true, metadata for sub workflows will be fetched and inserted automatically in the metadata response.',
+    )
+
     # query arguments
     # TODO: implement CLI entry for query API.
 
@@ -200,6 +239,7 @@ def add_auth_args(subcommand_parser):
         'abort',
         'release_hold',
         'health',
+        'metadata',
     ):
         auth_arg_dict = {k: args.get(k) for k in auth_args.keys()}
         auth = CromwellAuth.harmonize_credentials(**auth_arg_dict)

cromwell_tools/cromwell_api.py

@@ -92,6 +92,67 @@ def abort(cls, uuid, auth, raise_for_status=False):
             cls._check_and_raise_status(response)
         return response
 
+    @classmethod
+    def metadata(
+        cls,
+        uuid,
+        auth,
+        includeKey=None,
+        excludeKey=None,
+        expandSubWorkflows=False,
+        raise_for_status=False,
+    ):
+        """Retrieve the workflow and call-level metadata for a specified workflow by UUID.
+
+        Args:
+            uuid (str): A Cromwell workflow UUID, which is the workflow identifier.
+            auth (cromwell_tools.cromwell_auth.CromwellAuth): The authentication class holding headers or auth
+                information to a Cromwell server.
+            includeKey (Optional[List]): When specified key(s) to include from the metadata. Matches any key
+                starting with the value. May not be used with excludeKey. (default None)
+            excludeKey (Optional[List]): When specified key(s) to exclude from the metadata. Matches any key
+                starting with the value. May not be used with includeKey. (default None)
+            expandSubWorkflows (Optional[bool]): When true, metadata for sub workflows will be fetched
+                and inserted automatically in the metadata response. (default False)
+            raise_for_status (Optional[bool]): Whether to check and raise for status based on the response. (default
+                False)
+
+        Raises:
+            requests.exceptions.HTTPError: This will be raised when raise_for_status is True and Cromwell returns
+                a response that satisfies 400 <= response.status_code < 600.
+
+        Returns:
+            requests.Response: HTTP response from Cromwell.
+        """
+
+        if excludeKey and includeKey:
+            raise ValueError('includeKey and excludeKey may not be specified together!')
+
+        params = {'expandSubWorkflows': json.dumps(expandSubWorkflows)}
+
+        if isinstance(excludeKey, str):
+            logger.info(f'Adding {excludeKey} to the request parameter list.')
+            params['excludeKey'] = [excludeKey]
+        elif isinstance(excludeKey, list) and len(excludeKey) >= 1:
+            params['excludeKey'] = excludeKey
+
+        if isinstance(includeKey, str):
+            logger.info(f'Adding {includeKey} to the request parameter list.')
+            params['includeKey'] = [includeKey]
+        elif isinstance(includeKey, list) and len(includeKey) >= 1:
+            params['includeKey'] = includeKey
+
+        response = requests.get(
+            url=auth.url + cls._metadata_endpoint.format(uuid=uuid),
+            auth=auth.auth,
+            headers=auth.header,
+            params=params,
+        )
+
+        if raise_for_status:
+            cls._check_and_raise_status(response)
+        return response
+
     @classmethod
     def status(cls, uuid, auth, raise_for_status=False):
         """Retrieves the current state for a workflow by UUID.

cromwell_tools/tests/test_cromwell_api.py

@@ -270,6 +270,29 @@ def _request_callback(request, context):
             with self.assertRaises(requests.exceptions.HTTPError):
                 CromwellAPI.release_hold(workflow_id, cromwell_auth).raise_for_status()
 
+    @requests_mock.mock()
+    def test_metadata_returns_200(self, mock_request):
+        workflow_id = '12345abcde'
+        test_include_key = 'workflow'
+
+        def _request_callback(request, context):
+            context.status_code = 200
+            context.headers['test'] = 'header'
+            return {'id': '12345abcde', 'actualWorkflowLanguageVersion': 'draft-2'}
+
+        for cromwell_auth in self.auth_options:
+            mock_request.get(
+                '{0}/api/workflows/v1/{1}/metadata?expandSubWorkflows=false&includeKey={2}'.format(
+                    cromwell_auth.url, workflow_id, test_include_key
+                ),
+                json=_request_callback,
+            )
+            result = CromwellAPI.metadata(
+                workflow_id, cromwell_auth, includeKey=test_include_key
+            )
+            self.assertEqual(result.status_code, 200)
+            self.assertEqual(result.json()['id'], workflow_id)
+
     @requests_mock.mock()
     def test_health_returns_200(self, mock_request):
         expected = {