Merge pull request #69 from common-workflow-language/form-params

Handle form parameters in POST that are not attachments
common-workflow-language · Feb 11, 2019 · 65571a4 · 65571a4
2 parents 22c2d18 + b236857
commit 65571a4
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Showing 4 changed files with 21 additions and 9 deletions.
diff --git a/setup.py b/setup.py
@@ -26,15 +26,15 @@
           'future',
           'connexion==1.4.2',
           'ruamel.yaml >= 0.12.4, <= 0.15.77',
-          'cwlref-runner==1.0',
-          'schema-salad >= 3.0, < 3.1',
+          'schema-salad',
           'subprocess32==3.5.2'
                         ],
       entry_points={
           'console_scripts': ["wes-server=wes_service.wes_service_main:main",
                               "wes-client=wes_client.wes_client_main:main"]
                     },
       extras_require={
+          "cwltool": ['cwlref-runner'],
           "arvados": ["arvados-cwl-runner"
                       ],
           "toil": ["toil[all]==3.18.0"

diff --git a/test/test_integration.py b/test/test_integration.py
@@ -9,6 +9,7 @@
 import logging
 import sys
 import requests
+import pytest
 
 pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))  # noqa
 sys.path.insert(0, pkg_root)  # noqa
@@ -180,6 +181,7 @@ def setUp(self):
         self.wes_server_process = subprocess.Popen(
             ['python', os.path.abspath('wes_service/wes_service_main.py'),
              '--backend=wes_service.cwl_runner',
+             '--opt', 'runner=cwltool',
              '--port=8080',
              '--debug'])
         time.sleep(5)
@@ -209,6 +211,7 @@ def test_local_wdl(self):
             self.assertTrue(self.check_for_file(outfile_path), 'Output file was not found: ' + str(outfile_path))
 
 
+@pytest.mark.skipif(not os.environ.get("ARVADOS_API_TOKEN"), reason="Arvados not configured")
 class ArvadosTest(IntegrationTest):
     """Test using arvados-cwl-runner."""
 

diff --git a/wes_service/arvados_wes.py b/wes_service/arvados_wes.py
@@ -129,7 +129,7 @@ def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
         })
 
         try:
-            with tempfile.NamedTemporaryFile(dir=tempdir, suffix=".json") as inputtemp:
+            with tempfile.NamedTemporaryFile("wt", dir=tempdir, suffix=".json") as inputtemp:
                 json.dump(workflow_params, inputtemp)
                 inputtemp.flush()
 
@@ -163,7 +163,7 @@ def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
                 if proc.returncode != 0:
                     api.container_requests().update(uuid=cr_uuid, body={"priority": 0}).execute()
 
-                self.log_for_run(cr_uuid, stderrdata, env['ARVADOS_API_TOKEN'])
+                self.log_for_run(cr_uuid, stderrdata.decode("utf-8"), env['ARVADOS_API_TOKEN'])
 
             if tempdir:
                 shutil.rmtree(tempdir)
@@ -212,7 +212,8 @@ def RunWorkflow(self, **args):
                                                                   tempdir)).start()
 
         except Exception as e:
-            self.log_for_run(cr["uuid"], str(e))
+            logging.exception("Error")
+            self.log_for_run(cr["uuid"], "An exception ocurred while handling your request: " + str(e))
             cr = api.container_requests().update(uuid=cr["uuid"],
                                                  body={"container_request":
                                                        {"priority": 0}}).execute()

diff --git a/wes_service/util.py b/wes_service/util.py
@@ -68,10 +68,18 @@ def collect_attachments(self, run_id=None):
                     body[k] = json.loads(content.decode("utf-8"))
                 else:
                     body[k] = v.read().decode()
+        for k, ls in iterlists(connexion.request.form):
+            for v in ls:
+                if k in ("workflow_params", "tags", "workflow_engine_parameters"):
+                    body[k] = json.loads(v)
+                else:
+                    body[k] = v
 
-        if ":" not in body["workflow_url"]:
-            body["workflow_url"] = "file://%s" % os.path.join(tempdir, secure_filename(body["workflow_url"]))
-
-        self.log_for_run(run_id, "Using workflow_url '%s'" % body.get("workflow_url"))
+        if "workflow_url" in body:
+            if ":" not in body["workflow_url"]:
+                body["workflow_url"] = "file://%s" % os.path.join(tempdir, secure_filename(body["workflow_url"]))
+            self.log_for_run(run_id, "Using workflow_url '%s'" % body.get("workflow_url"))
+        else:
+            raise Exception("Missing 'workflow_url' in submission")
 
         return tempdir, body