planemo URL checking fails Error 401 on TravisCI for Nature #677
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?