fix for recent Toil

Author: mr-c

test/test_integration.py

@@ -88,7 +88,9 @@ def test_local_md5sum(self):
         )
 
     # See https://ga4gh.github.io/workflow-execution-service-schemas/docs/#operation/GetRunLog
-    @pytest.mark.skip("workflow_attachment is not part of WES spec for the log.request body")
+    @pytest.mark.skip(
+        "workflow_attachment is not part of WES spec for the log.request body"
+    )
     def test_run_attachments(self):
         """LOCAL md5sum cwl to the wes-service server, check for attachments."""
         outfile_path, run_id = self.run_md5sum(
@@ -257,21 +259,6 @@ def test_local_wdl(self):
                 "Output file was not found: " + str(outfile_path),
             )
 
-    def test_dockstore_md5sum(self):
-        # TODO: currently not working after update on Sept. 22, 2019
-        # see: https://github.com/common-workflow-language/workflow-service/issues/73
-        pass
-
-    def test_local_md5sum(self):
-        # TODO: currently not working after update on Sept. 22, 2019
-        # see: https://github.com/common-workflow-language/workflow-service/issues/73
-        pass
-
-    def test_run_attachments(self):
-        # TODO: currently not working after update on Sept. 22, 2019
-        # see: https://github.com/common-workflow-language/workflow-service/issues/73
-        pass
-
 
 @pytest.mark.skipif(
     not os.environ.get("ARVADOS_API_TOKEN"), reason="Arvados not configured"

wes_service/toil_wes.py

@@ -121,7 +121,7 @@ def call_cmd(self, cmd, cwd):
             f.write(str(cmd))
         stdout = open(self.outfile, "w")
         stderr = open(self.errfile, "w")
-        logging.info("Calling: " + " ".join(cmd))
+        logging.info("Calling: %s, with outfile: %s and errfile: %s", (" ".join(cmd)), self.outfile, self.errfile)
         process = subprocess.Popen(
             cmd, stdout=stdout, stderr=stderr, close_fds=True, cwd=cwd
         )
@@ -267,18 +267,15 @@ def getstate(self):
             logging.info("Workflow " + self.run_id + ": INITIALIZING")
             return "INITIALIZING", -1
 
-        # TODO: Query with "toil status"
         completed = False
         with open(self.errfile) as f:
             for line in f:
                 if "Traceback (most recent call last)" in line:
                     logging.info("Workflow " + self.run_id + ": EXECUTOR_ERROR")
                     open(self.staterrorfile, "a").close()
                     return "EXECUTOR_ERROR", 255
-                # run can complete successfully but fail to upload outputs to cloud buckets
-                # so save the completed status and make sure there was no error elsewhere
-                if "Finished toil run successfully." in line:
-                    completed = True
+        if subprocess.run(["toil", "status", "--failIfNotComplete", self.jobstorefile]).returncode == 0:
+            completed = True
         if completed:
             logging.info("Workflow " + self.run_id + ": COMPLETE")
             open(self.statcompletefile, "a").close()