Test logs errors

Author: Peter Amstutz

test/test_integration.py

@@ -8,6 +8,7 @@
 import shutil
 import logging
 import sys
+import requests
 
 pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))  # noqa
 sys.path.insert(0, pkg_root)  # noqa
@@ -60,7 +61,7 @@ def test_dockstore_md5sum(self):
                                           json_input=self.cwl_json_input,
                                           workflow_attachment=self.cwl_attachments)
         state = self.wait_for_finish(run_id)
-        assert state == "COMPLETE"
+        self.check_complete(run_id)
         self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + str(outfile_path))
 
     def test_local_md5sum(self):
@@ -69,7 +70,7 @@ def test_local_md5sum(self):
                                                json_input=self.cwl_json_input,
                                                workflow_attachment=self.cwl_attachments)
         state = self.wait_for_finish(run_id)
-        assert state == "COMPLETE"
+        self.check_complete(run_id)
         self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + str(outfile_path))
 
     def test_run_attachments(self):
@@ -79,7 +80,7 @@ def test_run_attachments(self):
                                                workflow_attachment=self.cwl_attachments)
         get_response = self.client.get_run_log(run_id)["request"]
         state = self.wait_for_finish(run_id)
-        assert state == "COMPLETE"
+        self.check_complete(run_id)
         self.assertTrue(check_for_file(outfile_path), 'Output file was not found: ' + get_response["workflow_attachment"])
         attachment_tool_path = get_response["workflow_attachment"][7:] + "/dockstore-tool-md5sum.cwl"
         self.assertTrue(check_for_file(attachment_tool_path), 'Attachment file was not found: ' + get_response["workflow_attachment"])
@@ -137,6 +138,14 @@ def wait_for_finish(self, run_id, seconds=120):
             r = self.client.get_run_status(run_id)
         return r["state"]
 
+    def check_complete(self, run_id):
+        s = self.client.get_run_log(run_id)
+        if s["state"] != "COMPLETE":
+            logging.info(str(s["run_log"]["stderr"]))
+            if str(s["run_log"]["stderr"]).startswith("http"):
+                logs = requests.get(s["run_log"]["stderr"], headers=auth).text
+                logging.info("Run log:\n" + logs)
+        assert s["state"] == "COMPLETE"
 
 def get_server_pids():
     try:

wes_client/util.py

@@ -241,7 +241,7 @@ def cancel(self, run_id):
         :return: The body of the delete result as a dictionary.
         """
         postresult = requests.post("%s://%s/ga4gh/wes/v1/runs/%s/cancel" % (self.proto, self.host, run_id),
-                                     headers=self.auth)
+                                   headers=self.auth)
         return wes_reponse(postresult)
 
     def get_run_log(self, run_id):