toil also support CWL v1.1 and v1.2

Author: mr-c

wes_service/arvados_wes.py

@@ -85,7 +85,9 @@ def GetServiceInfo(self):
             ["arvados-cwl-runner", "--version"], stderr=subprocess.PIPE
         ).communicate()
         return {
-            "workflow_type_versions": {"CWL": {"workflow_type_version": ["v1.0", "v1.1", "v1.2"]}},
+            "workflow_type_versions": {
+                "CWL": {"workflow_type_version": ["v1.0", "v1.1", "v1.2"]}
+            },
             "supported_wes_versions": ["0.3.0", "1.0.0"],
             "supported_filesystem_protocols": ["http", "https", "keep"],
             "workflow_engine_versions": {"arvados-cwl-runner": str(stderr)},

wes_service/toil_wes.py

@@ -121,7 +121,12 @@ def call_cmd(self, cmd, cwd):
             f.write(str(cmd))
         stdout = open(self.outfile, "w")
         stderr = open(self.errfile, "w")
-        logging.info("Calling: %s, with outfile: %s and errfile: %s", (" ".join(cmd)), self.outfile, self.errfile)
+        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
         )
@@ -208,10 +213,10 @@ def run(self, request, tempdir, opts):
         wftype = request["workflow_type"].lower().strip()
         version = request["workflow_type_version"]
 
-        if version != "v1.0" and wftype == "cwl":
+        if wftype == "cwl" and version not in ("v1.0", "v1.1", "v1.2"):
             raise RuntimeError(
                 'workflow_type "cwl" requires '
-                '"workflow_type_version" to be "v1.0": ' + str(version)
+                '"workflow_type_version" to be "v1.[012]": ' + str(version)
             )
         if version != "2.7" and wftype == "py":
             raise RuntimeError(
@@ -274,7 +279,12 @@ def getstate(self):
                     logging.info("Workflow " + self.run_id + ": EXECUTOR_ERROR")
                     open(self.staterrorfile, "a").close()
                     return "EXECUTOR_ERROR", 255
-        if subprocess.run(["toil", "status", "--failIfNotComplete", self.jobstorefile]).returncode == 0:
+        if (
+            subprocess.run(
+                ["toil", "status", "--failIfNotComplete", self.jobstorefile]
+            ).returncode
+            == 0
+        ):
             completed = True
         if completed:
             logging.info("Workflow " + self.run_id + ": COMPLETE")
@@ -296,7 +306,7 @@ class ToilBackend(WESBackend):
     def GetServiceInfo(self):
         return {
             "workflow_type_versions": {
-                "CWL": {"workflow_type_version": ["v1.0"]},
+                "CWL": {"workflow_type_version": ["v1.0", "v1.1", "v1.2"]},
                 "WDL": {"workflow_type_version": ["draft-2"]},
                 "PY": {"workflow_type_version": ["2.7"]},
             },