Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 059b0437f725732f97900366c3af48e6c19ed816 https://github.com/galaxyproject/galaxy/commit/059b0437f725732f97900366c3af4... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/base/populators.py Log Message: ----------- Improve error logging for API-based testing. ``` ====================================================================== FAIL: test_recover_mapping_in_subworkflow (api.test_workflows.WorkflowsApiTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/api/test_workflows.py", line 1467, in test_recover_mapping_in_subworkflow """, history_id=history_id, wait=True) File "/Users/john/workspace/galaxy/test/api/test_workflows.py", line 251, in _run_jobs self.workflow_populator.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=assert_ok) File "/Users/john/workspace/galaxy/test/base/populators.py", line 445, in wait_for_workflow self.wait_for_invocation(workflow_id, invocation_id, timeout=timeout) File "/Users/john/workspace/galaxy/test/base/populators.py", line 440, in wait_for_invocation return wait_on_state(lambda: self._get(url), desc="workflow invocation state", timeout=timeout) File "/Users/john/workspace/galaxy/test/base/populators.py", line 810, in wait_on_state raise TimeoutAssertionError("%s Current response containing state [%s]." % (e.message, response.json())) TimeoutAssertionError: Timed out after 60.25 seconds waiting on workflow invocation state. Current response containing state [{u'inputs': {u'0': {u'src': u'hda', u'id': u'adb5f5c93f827949', u'uuid': u'de3d999f-d993-447f-a7c4-0389a358034f'}}, u'update_time': u'2018-03-14T15:58:08.615444', u'uuid': u'7b0fc935-27a0-11e8-b255-784f435ea615', u'outputs': {}, u'history_id': u'adb5f5c93f827949', u'workflow_id': u'529fd61ab1c6cc36', u'output_collections': {}, u'state': u'ready', u'steps': [{u'workflow_step_label': u'outer_input', u'update_time': u'2018-03-14T15:58:05.629190', u'job_id': None, u'state': u'scheduled', u'workflow_step_uuid': u'afafbeb3-c3d8-49c8-ae21-5add12558c90', u'order_index': 0, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'cb6e11b662890a90', u'id': u'adb5f5c93f827949'}, {u'workflow_step_label': u'first_cat', u'update_time': u'2018-03-14T15:58:06.015192', u'job_id': u'529fd61ab1c6cc36', u'state': u'scheduled', u'workflow_step_uuid': u'6a 5b3ac3-bacf-4e97-bcca-57ea8d8161dd', u'order_index': 1, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'cb227cec8ca83994', u'id': u'529fd61ab1c6cc36'}, {u'workflow_step_label': u'nested_workflow', u'update_time': u'2018-03-14T15:58:06.770332', u'job_id': None, u'state': u'scheduled', u'workflow_step_uuid': u'55640d5d-5e8d-490f-9d68-736f66b1b65a', u'order_index': 2, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'f3f73e481f432006', u'id': u'd9abeb98649a6a7e'}, {u'workflow_step_label': u'second_cat', u'update_time': u'2018-03-14T15:58:06.770643', u'job_id': None, u'state': u'new', u'workflow_step_uuid': u'67beb950-271c-46f4-aca0-42dbe59c6d57', u'order_index': 3, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'2234cb1fd1df4331', u'id': u'cb6e11b662890a90'}], u'model_class': u'WorkflowInvocation', u'id': u'adb5f5c93f827949'}]. -------------------- >> begin captured stdout << --------------------- Executing git --work-tree test-data-cache/ad1daf4e1504da1acd42c088c6f49be6 --git-dir test-data-cache/ad1daf4e1504da1acd42c088c6f49be6/.git fetch && git --work-tree test-data-cache/ad1daf4e1504da1acd42c088c6f49be6 --git-dir test-data-cache/ad1daf4e1504da1acd42c088c6f49be6/.git merge origin/master Problem in history with id adb5f5c93f827949 - summary of history's datasets and jobs below. -------------------------------------- | 1 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 65 lines | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -</td></tr><tr><td>chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +</td></tr><tr><td>chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -</td></tr><tr><td>chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +</td></tr><tr><td>chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - Concatenate datasets on data 1 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 65 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -</td></tr><tr><td>chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +</td></tr><tr><td>chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -</td></tr><tr><td>chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +</td></tr><tr><td>chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 3 - Select random lines on data 2 (HID - NAME) | Dataset State: | running | Dataset Blurb: | queued | Dataset Info: | None | Peek: | None | Dataset Job Standard Output: | None | Dataset Job Standard Error: | None | -------------------------------------- | 4 - lines (HID - NAME) | Dataset Collection: {u'hid': 4, u'history_content_type': u'dataset_collection', u'populated_state_message': None, u'name': u'lines', u'populated': False, u'deleted': False, u'job_source_type': u'Job', u'history_id': u'adb5f5c93f827949', u'tags': [], u'element_count': None, u'job_source_id': u'f3f73e481f432006', u'visible': True, u'elements': [], u'collection_type': u'list', u'url': u'/api/histories/adb5f5c93f827949/contents/dataset_collections/adb5f5c93f827949', u'model_class': u'HistoryDatasetCollectionAssociation', u'type': u'collection', u'id': u'adb5f5c93f827949', u'populated_state': u'new'} | -------------------------------------- | Job d9abeb98649a6a7e | State: | running | Update Time: | 2018-03-14T15:58:09.483449 | Create Time: | 2018-03-14T15:58:06.139665 | -------------------------------------- | Job 529fd61ab1c6cc36 | State: | ok | Update Time: | 2018-03-14T15:58:08.633359 | Create Time: | 2018-03-14T15:58:05.706745 | -------------------------------------- | Job f3f73e481f432006 | State: | new | Update Time: | 2018-03-14T15:58:06.559809 | Create Time: | 2018-03-14T15:58:06.559799 | -------------------------------------- | Job adb5f5c93f827949 | State: | ok | Update Time: | 2018-03-14T15:58:04.602106 | Create Time: | 2018-03-14T15:58:00.368911 | -------------------------------------- ``` Commit: 0f3259c4b1f91b20965214d144b6705c802146ee https://github.com/galaxyproject/galaxy/commit/0f3259c4b1f91b20965214d144b67... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/base/populators.py Log Message: ----------- Merge pull request #5697 from jmchilton/api_test_logging Improve error logging for API-based testing. Compare: https://github.com/galaxyproject/galaxy/compare/2ace504daea6...0f3259c4b1f9