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duecredit on nipype #72

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alexsavio opened this issue May 3, 2016 · 2 comments
Closed

duecredit on nipype #72

alexsavio opened this issue May 3, 2016 · 2 comments

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@alexsavio
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Hi @yarikoptic,

I am adding references on nipype (nipy/nipype#1466).

When I try to add the Zenodo DOI I don't see any difference in the report. After some attempts I decided to remove the mod_nipype.py injections file from duecredit and I get this warning:

2016-05-03 16:23:21,072 [WARNING] Failed to obtain bibtex from doi.org, retrying... (io.py:54)
160503-16:23:21,72 duecredit WARNING:
     Failed to obtain bibtex from doi.org, retrying...
2016-05-03 16:23:21,573 [WARNING] DueCredit internal failure while running <function DueSwitch._dump_collector_summary at 0x7f114a0dbd90>: ValueError('Query http://dx.doi.org/10.5281/zenodo.50186 for BibTeX for a DOI 10.5281/zenodo.50186 (wrong doi?) has failed. Response code 406. ',). Please report to developers at https://github.com/duecredit/duecredit/issues (utils.py:76)
160503-16:23:21,573 duecredit.utils WARNING:
     DueCredit internal failure while running <function DueSwitch._dump_collector_summary at 0x7f114a0dbd90>: ValueError('Query http://dx.doi.org/10.5281/zenodo.50186 for BibTeX for a DOI 10.5281/zenodo.50186 (wrong doi?) has failed. Response code 406. ',). Please report to developers at https://github.com/duecredit/duecredit/issues

Is there any other alternative? How can I fix it?

Many thanks.

Best,
Alex
@mvdoc
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mvdoc commented May 3, 2016

Thanks for the report. For some reason (that I'm yet to understand) any request we send to dx.doi.org to get a bibtex entry doesn't work with any zenodo doi. We'll have to figure out a workaround to get a more stable doi importer.

@alexsavio in the meanwhile, I think the easiest way is to enter a bibtex entry instead of a doi entry with BibTeX() instead of Doi().

This was referenced May 3, 2016
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@alexsavio
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Thanks @mvdoc!

@mvdoc mvdoc mentioned this issue May 4, 2016
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yarikoptic added a commit that referenced this issue May 11, 2016
@yarikoptic
Merge tag '0.5.0' into debian
b8ac998 
**Fixed bugs:**

- test\_noincorrect\_import\_if\_no\_lxml fails on my laptop \(and on travis\) [\#84](#84)
- zenodo and "unofficial" bibtex entry types [\#77](#77)

**Closed issues:**

- duecredit on nipype [\#72](#72)

**Merged pull requests:**

- BF: workaround for zenodo bibtex entries imported with import\_doi [\#85](#85) ([mvdoc](https://github.com/mvdoc))
- enable testing under python 3.5 on travis [\#79](#79) ([yarikoptic](https://github.com/yarikoptic))
- ENH: appveyor configuration \(based on shablona's\) based on mix of conda and pip [\#70](#70) ([yarikoptic](https://github.com/yarikoptic))

* tag '0.5.0': (38 commits)
  BF(TST): apparently StrictVersion might remove the trailing .0
  DOC: automatically generated CHANGELOG
  BF: convert @DaTa to @misc, ; to and, for zenodo dois
  Disable testing on python3.x on windows -- has difficulty installing lxml (no wheels yet)
  BF(temp skip test on windows): just skip on windows that test attempting to test with "absent" lxml
  BF: group operations correcly for appending "b" mode in with_tempfile
  Revert "enable again interactive session"
  ENH: skip the same failing test on appveyor + move _test_external up
  BF/ENH: no unqualified exec() invocations -- use custom env dicts
  enable again interactive session
  DOC: minor, just to push new commit in hope to please appveyor
  BF(khe khe): skip test on travis which can't troubleshoot out
  BF: do not use Popen.poll but .communicate (to avoid getting stuck under heavy output)
  BF: explicitely encode when writing to console using preferred encoding
  ENH: also disable "catch all exceptions" upon DUECREDIT_DEBUG env variable
  Actually we need to install all [tests] requirements as well to use it within tox etc
  disable interactive appveyor for now
  ENH: adding vcr cassette for the online test so we could avoid pestering the service
  BF: open pickle file in binary mode
  ENH: tox all py3 envs
  ...
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@alexsavio @mvdoc