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Use github instead of NCBI for problematic data manager test FASTA. #5007

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merged 1 commit into from Nov 16, 2017

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@jmchilton
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commented Nov 14, 2017

Seems to be failing many of the integration tool runs I've seen today. I've seen a couple different errors:

|  File "/tmp/tmpVp6xM0/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 312, in download_from_ncbi
|  return get_stream_reader(urlopen(url), tmp_dir)
|  File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen
|  return opener.open(url, data, timeout)
|  File "/usr/lib/python2.7/urllib2.py", line 435, in open
|  response = meth(req, response)
|  File "/usr/lib/python2.7/urllib2.py", line 548, in http_response
|  'http', request, response, code, msg, hdrs)
|  File "/usr/lib/python2.7/urllib2.py", line 473, in error
|  return self._call_chain(*args)
|  File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain
|  result = func(*args)
|  File "/usr/lib/python2.7/urllib2.py", line 556, in http_error_default
|  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)

and

Timed out after 60.25 seconds waiting on state.
-------------------- >> begin captured stdout << ---------------------
Problem in history with id adb5f5c93f827949 - summary of datasets below.
--------------------------------------
| 1 - Create DBKey and Reference Genome (HID - NAME)
| Dataset State:
|  queued
| Dataset Blurb:
|  queued
| Dataset Info:
|  None
| Peek:
|  None
| Dataset Job Standard Output:
|  None
| Dataset Job Standard Error:
|  None
|
--------------------------------------
Use github instead of NCBI for problematic data manager test FASTA.
Seems to be failing many of the integration tool runs I've seen today. I've seen a couple different errors:

```
|  File "/tmp/tmpVp6xM0/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 312, in download_from_ncbi
|  return get_stream_reader(urlopen(url), tmp_dir)
|  File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen
|  return opener.open(url, data, timeout)
|  File "/usr/lib/python2.7/urllib2.py", line 435, in open
|  response = meth(req, response)
|  File "/usr/lib/python2.7/urllib2.py", line 548, in http_response
|  'http', request, response, code, msg, hdrs)
|  File "/usr/lib/python2.7/urllib2.py", line 473, in error
|  return self._call_chain(*args)
|  File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain
|  result = func(*args)
|  File "/usr/lib/python2.7/urllib2.py", line 556, in http_error_default
|  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
```

and

```
Timed out after 60.25 seconds waiting on state.
-------------------- >> begin captured stdout << ---------------------
Problem in history with id adb5f5c93f827949 - summary of datasets below.
--------------------------------------
| 1 - Create DBKey and Reference Genome (HID - NAME)
| Dataset State:
|  queued
| Dataset Blurb:
|  queued
| Dataset Info:
|  None
| Peek:
|  None
| Dataset Job Standard Output:
|  None
| Dataset Job Standard Error:
|  None
|
--------------------------------------
```
@mvdbeek
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Hmm, I would have guessed that github would be more robust. Let's see how this will do.

@jmchilton

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commented Nov 15, 2017

I don't know what is more robust - but I will say if Github is down the tests won't get this far so at least our errors are ... in sync. If there are still problems though I'll re-organize the test to try the other method if the first fails.

@natefoo natefoo merged commit 36dc156 into galaxyproject:dev Nov 16, 2017

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