Merge 17.09. #5227
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Merge 17.09. #5227
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[17.09] Small deployer doc fixes.
before checking whether stderr and exit code combination should result in a failed job. This should fix galaxyproject#5214.
…led outputs. I like this better for three reasons: - Since usually it is scripts producing this JSON - we have the most control at that point for determining the failure and we don't have to deal with an artificial dependency between the tool's stdio and the output. - At some point we could potentially allow some datasets to be ok now even though the job fails. - It is a cleaner interface at the Python level between job finish and output collection IMO (no need for isinstance checking).
…to_stderr Let ToolProvidedMetadata interface more directly decide if it has failed outputs.
…n_tools_write_to_stderr [17.09] Fail job if tools that use galaxy.json write to stderr
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jmchilton
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test/base/populators.py
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| run = run_response.json() | ||
| assert run_response.status_code == 200, run | ||
| job = run["jobs"][0] | ||
| self.wait_for_job(job["id"], timeout=timeout) | ||
| self.wait_for_history(history_id, assert_ok=True, timeout=timeout) | ||
| self.wait_for_history(history_id, assert_ok=assert_ok) |
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And that isn't right - the PR was a good choice.
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nsoranzo
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nsoranzo
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test/base/populators.py
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| @@ -145,15 +145,15 @@ def new_dataset_request(self, history_id, content=None, wait=False, **kwds): | |||
| payload = self.upload_payload(history_id, content=content, **kwds) | |||
| run_response = self.tools_post(payload) | |||
| if wait: | |||
| self.wait_for_tool_run(history_id, run_response) | |||
| self.wait_for_tool_run(history_id, run_response, kwds.get('assert_ok', True)) | |||
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That should be assert_ok=kwds.get('assert_ok', True)
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Tricky merge of #5217 - I'd like to see the API tests pass.