galaxyproject / galaxyproject/planemo

planemo URL checking fails Error 401 on TravisCI for Nature

Open
#677 0 comments 0 reactions 0 assignees View on GitHub
question
Dominant language
Python
Stars
110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
13

Description

This is similar to #578 where some websites blocked our URL checks based on the user agent.

http://dx.doi.org/10.1038/nature06203 works in browser and when running planemo locally, but is failing from TravisCI using ``planemo shed_lint`` e.g. https://travis-ci.org/peterjc/pico_galaxy/jobs/235163218

```
$ planemo shed_lint --tools --fail_level error --ensure_metadata --urls -r ${TRAVIS_BUILD_DIR}
...
+Linting tool /home/travis/build/peterjc/pico_galaxy/tools/protein_analysis/tools/protein_analysis/rxlr_motifs.xml
Applying linter tests... CHECK
.. CHECK: 4 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 2 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.0.12].
.. CHECK: Tool defines a name [RXLR Motifs].
.. CHECK: Tool defines an id [rxlr_motifs].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Command uses deprecated 'interpreter' attribute.
.. INFO: Tool contains a command with interpreter of type [python].
Applying linter citations... CHECK
.. CHECK: Found 7 likely valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter tool_urls... FAIL
.. ERROR: HTTP Error 401 accessing http://dx.doi.org/10.1038/nature06203
.. INFO: URL OK http://dx.doi.org/10.7717/peerj.167
.. INFO: URL OK http://dx.doi.org/10.1105/tpc.107.051037
.. INFO: URL OK http://dx.doi.org/10.1371/journal.ppat.0020050
.. INFO: URL OK http://dx.doi.org/10.1101/gr.910003
.. INFO: URL OK http://dx.doi.org/10.1093/bioinformatics/14.9.755
.. INFO: URL OK http://dx.doi.org/10.1093/protein/10.1.1
.. INFO: URL OK http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
```

Run locally,

```
$ planemo lint --urls tools/protein_analysis/rxlr_motifs.xml
Linting tool /mnt/shared/users/pc40583/repositories/pico_galaxy/tools/protein_analysis/rxlr_motifs.xml
Applying linter tests... CHECK
.. CHECK: 4 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 2 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.0.12].
.. CHECK: Tool defines a name [RXLR Motifs].
.. CHECK: Tool defines an id [rxlr_motifs].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Command uses deprecated 'interpreter' attribute.
.. INFO: Tool contains a command with interpreter of type [python].
Applying linter citations... CHECK
.. CHECK: Found 7 likely valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter tool_urls... CHECK
.. INFO: URL OK http://dx.doi.org/10.7717/peerj.167
.. INFO: URL OK http://dx.doi.org/10.1038/nature06203
.. INFO: URL OK http://dx.doi.org/10.1105/tpc.107.051037
.. INFO: URL OK http://dx.doi.org/10.1371/journal.ppat.0020050
.. INFO: URL OK http://dx.doi.org/10.1101/gr.910003
.. INFO: URL OK http://dx.doi.org/10.1093/bioinformatics/14.9.755
.. INFO: URL OK http://dx.doi.org/10.1093/protein/10.1.1
.. INFO: URL OK http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
```

I have re-run the TravisCI job, and can try again in a few days just to rule out a transient failure, but I suspect Nature is blocking by IP address?

(I was going to add the ``--urls`` switch to my master branch, but in light of this will hold off)

Has anyone else seen this with journals on Nature?

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.