Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Example citations not resolving as expected #166

Closed
slochower opened this issue Mar 7, 2019 · 6 comments
Closed

Example citations not resolving as expected #166

slochower opened this issue Mar 7, 2019 · 6 comments

Comments

@slochower
Copy link
Collaborator

slochower commented Mar 7, 2019 •
edited
Loading

I just tried the recommended citation in the manuscript (unlike source code, there doesn't seem to be a way to link and directly embed Markdown lines in an Issue) and received an error for both citations.

manubot cite --render --format=markdown \
  --csl=https://github.com/citation-style-language/styles/raw/master/peerj.csl \
  pmid:29618526 doi:10.1038/550143a

I am using the latest GitHub commit of manubot (81394c0):

Thu Mar 07 13:25:44 warthog:~
$ pip install --upgrade git+https://github.com/manubot/manubot@81394c0
[...]
Installing collected packages: isbnlib, jsonref, ratelimiter, manubot
  Found existing installation: manubot 0.0.0
    Uninstalling manubot-0.0.0:
      Successfully uninstalled manubot-0.0.0
Successfully installed isbnlib-3.9.6 jsonref-0.2 manubot-0.2.3 ratelimiter-1.2.0.post0
You are using pip version 18.0, however version 19.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.                                                       

Thu Mar 07 13:26:13 warthog:~
$ manubot cite --render --format=markdown   --csl=https://github.com/citation-style-language/styles/raw/master/peerj.csl   pmid:29618526 doi:10.1038/550143a
## ERROR
Error fetching metadata for doi:10.1038/550143a.
Invalid response from https://data.crossref.org/10.1038%2F550143a:

## ERROR
citation_to_citeproc for doi:10.1038/550143a failed due to a JSONDecodeError:
Expecting value: line 1 column 1 (char 0)
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. 2018. Opportunities and obstacles for deep learning in biology and medicine. *Journal of the Royal Society, Interface* 15. DOI: [10.1098/rsif.2017.0387](https://doi.org/10.1098/rsif.2017.0387).
## CRITICAL
Failure: exiting with code 1 due to logged errors
@slochower
Copy link
Collaborator Author

If I re-run the exact same command, there's a little more from Crossref:

$ manubot cite --render --format=markdown   --csl=https://github.com/citation-style-language/styles/raw/master/peerj.csl   pmid:29618526 doi:10.1038/550143a
## ERROR
Error fetching metadata for doi:10.1038/550143a.
Invalid response from https://data.crossref.org/10.1038%2F550143a:
<html><body><h1>503 Service Unavailable</h1>
No server is available to handle this request.
</body></html>

## ERROR
citation_to_citeproc for doi:10.1038/550143a failed due to a JSONDecodeError:
Expecting value: line 1 column 1 (char 0)
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. 2018. Opportunities and obstacles for deep learning in biology and medicine. *Journal of the Royal Society, Interface* 15. DOI: [10.1098/rsif.2017.0387](https://doi.org/10.1098/rsif.2017.0387).
## CRITICAL
Failure: exiting with code 1 due to logged errors

@dhimmel
Copy link
Contributor

dhimmel commented Mar 7, 2019

It almost certainly a temperamental error upstream like a server outage that should resolve without us doing anything.

Currently, it looks like the Crossref infrastructure is experiencing issues, as attempting to query https://api.crossref.org/works/10.1038/550143a is very slow for me (but does work, as does the manubot cite command).

@agitter
Copy link
Collaborator

agitter commented Mar 7, 2019

The example manubot command worked for me now. @slochower is it back up for you as well?

@slochower
Copy link
Collaborator Author

Indeed, it did just work for me.

@agitter
Copy link
Collaborator

agitter commented Mar 8, 2019

Should we close this and attribute it to an intermittent upstream problem?

@slochower
Copy link
Collaborator Author

Yes, that's fair. I think it's a great thing we cache the references, otherwise this issue would be more troubling.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@dhimmel @agitter @slochower