Merge branch 'release_18.09' into dev

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -341,7 +341,7 @@ def search(self, trans, payload, **kwd):
                 jobs.append(job)
         return [self.encode_all_ids(trans, single_job.to_dict('element'), True) for single_job in jobs]
 
-    @expose_api
+    @expose_api_anonymous
     def error(self, trans, id, **kwd):
         """
         error( trans, id )
@@ -364,10 +364,17 @@ def error(self, trans, id, **kwd):
         # Get job
         job = self.__get_job(trans, id)
         tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version) or None
+        email = kwd.get('email')
+        if not email and not trans.anonymous:
+            email = trans.user.email
         messages = trans.app.error_reports.default_error_plugin.submit_report(
-            dataset, job, tool, user_submission=True, user=trans.user,
-            email=kwd.get('email', trans.user.email),
-            message=kwd.get('message', None)
+            dataset=dataset,
+            job=job,
+            tool=tool,
+            user_submission=True,
+            user=trans.user,
+            email=email,
+            message=kwd.get('message')
         )
 
         return {'messages': messages}

test/api/test_jobs.py

@@ -4,7 +4,7 @@
 import time
 from operator import itemgetter
 
-from requests import put
+import requests
 
 from base import api  # noqa: I100,I202
 from base.api_asserts import assert_status_code_is_ok  # noqa: I100
@@ -141,6 +141,35 @@ def test_show_security(self, history_id):
         show_jobs_response = self._get("jobs/%s" % job_id, admin=True)
         self._assert_has_keys(show_jobs_response.json(), "command_line", "external_id")
 
+    @skip_without_tool('detect_errors_aggressive')
+    def test_report_error(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.run_tool_payload(
+                tool_id='detect_errors_aggressive',
+                inputs={'error_bool': 'true'},
+                history_id=history_id,
+            )
+            run_response = self._post("tools", data=payload).json()
+            job_id = run_response['jobs'][0]["id"]
+            dataset_id = run_response['outputs'][0]['id']
+            response = self._post('jobs/%s/error' % job_id,
+                                  data={'dataset_id': dataset_id})
+            assert response.status_code == 200
+
+    @skip_without_tool('detect_errors_aggressive')
+    def test_report_error_anon(self):
+        # Need to get a cookie and use that for anonymous tool runs
+        cookies = requests.get(self.galaxy_interactor.api_url.rsplit('/api', 1)[0]).cookies
+        payload = json.dumps({"tool_id": "detect_errors_aggressive",
+                              "inputs": {"error_bool": "true"}})
+        run_response = requests.post("%s/tools" % self.galaxy_interactor.api_url, data=payload, cookies=cookies).json()
+        job_id = run_response['jobs'][0]["id"]
+        dataset_id = run_response['outputs'][0]['id']
+        response = requests.post('%s/jobs/%s/error' % (self.galaxy_interactor.api_url, job_id),
+                                 params={'email': 'someone@domain.com', 'dataset_id': dataset_id},
+                                 cookies=cookies)
+        assert response.status_code == 200
+
     @uses_test_history(require_new=True)
     def test_deleting_output_keep_running_until_all_deleted(self, history_id):
         job_state, outputs = self._setup_running_two_output_job(history_id, 120)
@@ -275,7 +304,7 @@ def job_state():
 
     def _raw_update_history_item(self, history_id, item_id, data):
         update_url = self._api_url("histories/%s/contents/%s" % (history_id, item_id), use_key=True)
-        update_response = put(update_url, json=data)
+        update_response = requests.put(update_url, json=data)
         assert_status_code_is_ok(update_response)
         return update_response
 

test/unit/tools/test_toolbox.py

@@ -212,19 +212,38 @@ def test_tool_reload_for_broken_tool(self):
         tool_path = tool.config_file
         with open(tool.config_file, 'w') as out:
             out.write('certainly not a valid tool')
-        time.sleep(1.5)
-        tool = self.app.toolbox.get_tool("test_tool")
-        assert tool is not None
-        assert tool.version == "1.0"
-        assert tool.tool_errors == 'Current on-disk tool is not valid'
+
+        def check_tool_errors():
+            tool = self.app.toolbox.get_tool("test_tool")
+            assert tool is not None
+            assert tool.version == "1.0"
+            assert tool.tool_errors == 'Current on-disk tool is not valid'
+
+        self._try_until_no_errors(check_tool_errors)
+
         # Tool is still loaded, lets restore it with a new version
         self._init_tool(filename="simple_tool.xml", version="2.0")
-        time.sleep(1.5)
-        tool = self.app.toolbox.get_tool("test_tool")
-        assert tool is not None
-        assert tool.version == "2.0"
-        assert tool.tool_errors is None
-        assert tool_path == tool.config_file
+
+        def check_no_tool_errors():
+            tool = self.app.toolbox.get_tool("test_tool")
+            assert tool is not None
+            assert tool.version == "2.0"
+            assert tool.tool_errors is None
+            assert tool_path == tool.config_file, "config file"
+
+        self._try_until_no_errors(check_no_tool_errors)
+
+    def _try_until_no_errors(self, f):
+        e = None
+        for i in range(30):
+            try:
+                f()
+                return
+            except AssertionError as error:
+                e = error
+                time.sleep(.25)
+
+        raise e
 
     def test_enforce_tool_profile(self):
         self._init_tool(filename="old_tool.xml", version="1.0", profile="17.01", tool_id="test_old_tool_profile")