cli: new flag for overriding workflow parameters

* Introducing new flag for `start` command to override workflow
  input parameters. Closes #200

Signed-off-by: Rokas Maciulaitis <rokas.maciulaitis@cern.ch>

docs/userguide.rst

@@ -96,6 +96,21 @@ so that a hard copy of the link target is uploaded to the cloud
 storage workspace. The link is not maintained throughout the
 workflow execution.
 
+Overriding default input parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you want to run a workflow with different input parameters than the ones in
+``reana.yaml``, you can do it by running `reana-client start` with flag ``-p``
+and specifying parameters that you want to override.
+
+Note that parameters passed with ``-p`` flag must exist in reana.yaml.
+Non-existing parameters will be skipped.
+
+.. code-block:: console
+
+   $ reana-client start -p myparam1=myval1 -p myparam2=myval2
+   workflow.1 has been started.
+
 Downloading outputs
 ~~~~~~~~~~~~~~~~~~~
 

reana_client/api/client.py

@@ -26,7 +26,7 @@ class Client(BaseAPIClient):
     def ping(self):
         """Health check REANA server."""
         try:
-            response, http_response = self._client.api.get_api_ping().result()
+            response, http_response = self._client.api.ping().result()
             if http_response.status_code == 200:
                 return response['message']
             else:
@@ -363,3 +363,30 @@ def upload_to_server(self, workflow, paths, access_token):
                         logging.debug(str(e))
                         logging.info("Something went wrong while uploading {}".
                                      format(fname))
+
+    def get_workflow_parameters(self, workflow, access_token):
+        """Get parameters of previously created workflow."""
+        try:
+            response, http_response = self.\
+                _client.api.get_workflow_parameters(
+                    workflow_id_or_name=workflow,
+                    access_token=access_token)\
+                .result()
+            if http_response.status_code == 200:
+                return response
+            else:
+                raise Exception(
+                    "Expected status code 200 but replied with "
+                    "{status_code}".format(
+                        status_code=http_response.status_code))
+
+        except HTTPError as e:
+            logging.debug(
+                'Workflow parameters could not be retrieved: '
+                '\nStatus: {}\nReason: {}\n'
+                'Message: {}'.format(e.response.status_code,
+                                     e.response.reason,
+                                     e.response.json()['message']))
+            raise Exception(e.response.json()['message'])
+        except Exception as e:
+            raise e

reana_client/cli/workflow.py

@@ -26,6 +26,11 @@
 from reana_client.cli.utils import add_access_token_options
 from reana_client.cli.files import upload_files
 
+from reana_client.cli.files import upload_files
+
+from reana_db.database import Session
+from reana_db.models import Workflow
+
 
 class _WorkflowStatus(Enum):
     created = 0
@@ -196,10 +201,11 @@ def workflow_create(ctx, file, name, skip_validation, access_token):
     help="""
     Start previously created workflow.
 
-    The workflow execution can be further influenced by setting operational
-    prameters using `-p` or `--parameter` option.  The option can be
-    repetitive. For example, to disable caching for the Serial workflow
-    engine, you can set ``-p CACHE=off``.
+    The workflow execution can be further influenced by setting input prameters
+    using `-p` or `--parameters` flag or by setting operational options using
+    `-o` or `--options`.  The input parameters and operational options can be
+    repetitive. For example, to disable caching for the Serial workflow engine,
+    you can set ``-o CACHE=off``.
     """)
 @click.option(
     '-w',
@@ -210,14 +216,22 @@ def workflow_create(ctx, file, name, skip_validation, access_token):
          'Overrides value of REANA_WORKON.')
 @add_access_token_options
 @click.option(
-    '-p', '--parameter',
+    '-p', '--parameter', 'parameters',
     multiple=True,
-    help='Optional operational parameters for the workflow execution. '
+    help='Additional input parameters to override '
+         'original ones from reana.yaml. '
+         'E.g. -p myparam1=myval1 -p myparam2=myval2.',
+)
+@click.option(
+    '-o', '--option', 'options',
+    multiple=True,
+    help='Additional operatioal options for the workflow execution. '
          'E.g. CACHE=off.',
 )
 @click.pass_context
 @with_api_client
-def workflow_start(ctx, workflow, access_token, parameter):  # noqa: D301
+def workflow_start(ctx, workflow, access_token,
+                   parameters, options):  # noqa: D301
     """Start previously created workflow."""
     logging.debug('command: {}'.format(ctx.command_path.replace(" ", ".")))
     for p in ctx.params:
@@ -229,10 +243,33 @@ def workflow_start(ctx, workflow, access_token, parameter):  # noqa: D301
                         fg='red'), err=True)
         sys.exit(1)
 
-    parsed_parameters = {'parameters':
-                         dict(p.split('=') for p in parameter)}
+    parsed_parameters = {'input_parameters':
+                         dict(p.split('=') for p in parameters)}
+    parsed_parameters['operational_options'] = \
+        dict(p.split('=') for p in options)
 
     if workflow:
+        if parameters:
+            try:
+                response =  \
+                    ctx.obj.client.get_workflow_parameters(workflow,
+                                                           access_token)
+                parsed_input_parameters =  \
+                    dict(parsed_parameters['input_parameters'])
+                for parameter in parsed_input_parameters.keys():
+                    if parameter not in response['parameters']:
+                        click.echo(
+                            click.style('Given parameter - {0}, is not in '
+                                        'reana.yaml'.format(parameter),
+                                        fg='red'),
+                            err=True)
+                        del parsed_parameters['input_parameters'][parameter]
+            except Exception as e:
+                click.echo(
+                    click.style('Could not apply given input parameters: '
+                                '{0} \n{1}'.format(parameters, str(e))),
+                    err=True)
+
         try:
             logging.info('Connecting to {0}'.format(ctx.obj.client.server_url))
             response = ctx.obj.client.start_workflow(workflow,
@@ -510,7 +547,7 @@ def workflow_validate(ctx, file):
 @click.option(
     '-p', '--parameter',
     multiple=True,
-    help='Optional operational parameters for the workflow execution. '
+    help='Optional operational options for the workflow execution. '
          'E.g. CACHE=off.',
 )
 @add_access_token_options

reana_client/utils.py

@@ -102,7 +102,7 @@ def load_reana_spec(filepath, skip_validation=False):
                 get('specification')
             kwargs['parameters'] = \
                 reana_yaml.get('inputs', {}).get('parameters', {})
-
+            kwargs['original'] = True
         reana_yaml['workflow']['specification'] = load_workflow_spec(
             reana_yaml['workflow']['type'],
             reana_yaml['workflow'].get('file'),

setup.py

@@ -28,7 +28,7 @@
     'pytest-cache>=1.0',
     'pytest-cov>=1.8.0',
     'pytest-pep8>=1.0.6',
-    'pytest-reana>=0.4.0,<0.5.0',
+    'pytest-reana>=v0.5.0.dev20181119'
 ]
 
 extras_require = {
@@ -54,7 +54,7 @@
     'click>=7,<8',
     'cwltool==1.0.20180912090223',
     'pyOpenSSL==17.5.0',  # FIXME remove once yadage-schemas solves deps.
-    'reana-commons>=0.4.0,<0.5.0',
+    'reana-commons>=0.5.0.dev20181116,<0.6.0',
     'rfc3987==1.3.7',  # FIXME remove once yadage-schemas solves deps.
     'strict-rfc3339==0.7',  # FIXME remove once yadage-schemas solves deps.
     'tablib>=0.12.1,<0.13',

tests/test_cli_workflows.py

@@ -232,3 +232,29 @@ def test_run(workflow_start_mock,
     assert workflow_create_mock.called is True
     assert upload_file_mock.called is True
     assert workflow_start_mock.called is True
+
+
+def test_workflow_input_parameters(mock_base_api_client):
+    """Test if not existing input parameters from CLI are applied."""
+    status_code = 200
+    response = {'id': 'd9304bdf-0d19-45d9-ae87-d5fd18059193',
+                'name': 'workflow.19',
+                'parameters': {'helloworld': 'code/helloworld.py',
+                               'inputfile': 'data/names.txt',
+                               'outputfile': 'results/greetings.txt',
+                               'sleeptime': 2}}
+    env = {'REANA_SERVER_URL': 'localhost'}
+    mocked_api_client = mock_base_api_client(status_code,
+                                             response,
+                                             'reana-server')
+    parameter = "Debug"
+    expected_message = '{0}, is not in reana.yaml'.format(parameter)
+    config = Config(mocked_api_client)
+    reana_token = '000000'
+    runner = CliRunner(env=env)
+    result = runner.invoke(
+        cli,
+        ['start', '-at', reana_token, '-w workflow.19',
+         '-p {0}=True'.format(parameter)],
+        obj=config)
+    assert expected_message in result.output