cli: passing operational options to cwl

* Allows passing operational options for CWL enggine.
  Connects github.com/reanahub/reana-workflow-engine-cwl/issues/69

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

reana_client/cli/workflow.py

@@ -22,7 +22,10 @@
 from reana_client.config import ERROR_MESSAGES, reana_yaml_default_file_path
 from reana_client.decorators import with_api_client
 from reana_client.utils import (get_workflow_name_and_run_number, is_uuid_v4,
-                                load_reana_spec, workflow_uuid_or_name)
+                                load_reana_spec, workflow_uuid_or_name,
+                                validate_cwl_operational_options,
+                                validate_serial_operational_options,
+                                validate_input_parameters)
 from reana_client.cli.utils import add_access_token_options
 from reana_client.cli.files import upload_files
 
@@ -234,7 +237,8 @@ def workflow_create(ctx, file, name, skip_validation, access_token):
     '-o', '--option', 'options',
     multiple=True,
     help='Additional operatioal options for the workflow execution. '
-         'E.g. CACHE=off.',
+         'E.g. CACHE=off. (workflow engine - serial) '
+         'E.g. --debug (workflow engine - cwl)',
 )
 @click.pass_context
 @with_api_client
@@ -250,28 +254,26 @@ def workflow_start(ctx, workflow, access_token,
             click.style(ERROR_MESSAGES['missing_access_token'],
                         fg='red'), err=True)
         sys.exit(1)
-
     parsed_parameters = {'input_parameters':
                          dict(p.split('=') for p in parameters)}
-    parsed_parameters['operational_options'] = \
-        dict(p.split('=') for p in options)
-
+    parsed_parameters['operational_options'] = ' '.join(options).split()
     if workflow:
-        if parameters:
+        if parameters or options:
             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]
+                if response['type'] == 'cwl':
+                    validate_cwl_operational_options(
+                        parsed_parameters['operational_options'])
+                if response['type'] == 'serial':
+                    parsed_parameters['operational_options'] = \
+                        validate_serial_operational_options(
+                            parsed_parameters['operational_options'])
+                parsed_parameters['input_parameters'] = \
+                    validate_input_parameters(
+                        parsed_parameters['input_parameters'],
+                        response['parameters'])
             except Exception as e:
                 click.echo(
                     click.style('Could not apply given input parameters: '

reana_client/utils.py

@@ -10,6 +10,7 @@
 import json
 import logging
 import os
+import subprocess
 import sys
 from uuid import UUID
 
@@ -108,12 +109,10 @@ def load_reana_spec(filepath, skip_validation=False):
             reana_yaml['workflow'].get('file'),
             **kwargs
         )
-
         if reana_yaml['workflow']['type'] == 'cwl' and \
                 'inputs' in reana_yaml:
             with open(reana_yaml['inputs']['parameters']['input']) as f:
                 reana_yaml['inputs']['parameters']['input'] = yaml.load(f)
-
         return reana_yaml
     except IOError as e:
         logging.info(
@@ -215,3 +214,46 @@ def get_workflow_root():
                 workflow_root = parent_dir
     workflow_root += '/'
     return workflow_root
+
+
+def validate_cwl_operational_options(operational_options):
+    """Validate cwl operational options."""
+    forbidden_args = ['--debug', '--tmpdir-prefix', '--tmp-outdir-prefix'
+                      '--default-container', '--outdir']
+    for option in operational_options:
+        if option in forbidden_args:
+            click.echo('Operational option {0} are not allowed. \n'
+                       .format(operational_options), err=True)
+            sys.exit(1)
+    cmd = 'cwltool --version {0}'.format(' '.join(operational_options))
+    try:
+        subprocess.check_call(cmd, shell=True)
+    except subprocess.CalledProcessError as err:
+        click.echo('Operational options {0} are not valid. \n'
+                   '{1}'.format(operational_options, err), err=True)
+        sys.exit(1)
+
+
+def validate_serial_operational_options(operational_options):
+    """Return validated serial operational options."""
+    try:
+        operational_options = {'input_parameters':
+                               dict(p.split('=') for p in operational_options)}
+    except Exception as err:
+        click.echo('Operational options {0} are not valid. \n'
+                   '{1}'.format(operational_options, err), err=True)
+        sys.exit(1)
+
+
+def validate_input_parameters(live_parameters, original_parameters):
+    """Return validated input parameters."""
+    parsed_input_parameters = dict(live_parameters)
+    for parameter in parsed_input_parameters.keys():
+        if parameter not in original_parameters:
+            click.echo(
+                click.style('Given parameter - {0}, is not in '
+                            'reana.yaml'.format(parameter),
+                            fg='red'),
+                err=True)
+            del live_parameters[parameter]
+    return live_parameters

setup.py

@@ -52,7 +52,7 @@
 
 install_requires = [
     'click>=7,<8',
-    'cwltool==1.0.20180912090223',
+    'cwltool==1.0.20181118133959',
     'pyOpenSSL==17.5.0',  # FIXME remove once yadage-schemas solves deps.
     'reana-commons>=0.5.0.dev20181204,<0.6.0',
     'rfc3987==1.3.7',  # FIXME remove once yadage-schemas solves deps.

tests/test_cli_workflows.py

@@ -239,6 +239,7 @@ def test_workflow_input_parameters(mock_base_api_client):
     status_code = 200
     response = {'id': 'd9304bdf-0d19-45d9-ae87-d5fd18059193',
                 'name': 'workflow.19',
+                'type': 'serial',
                 'parameters': {'helloworld': 'code/helloworld.py',
                                'inputfile': 'data/names.txt',
                                'outputfile': 'results/greetings.txt',