qiime2 / galaxy-tools

Official QIIME 2 tools for Galaxy
BSD 3-Clause "New" or "Revised" License
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BUG: fix improperly escaped quotes #22

Closed ebolyen closed 1 year ago

ebolyen commented 1 year ago

Turns out planemo won't escape double quotes in the shed.yml file correctly, generating bad XML like this:

<repositories description="Galaxy suite for QIIME 2 plugin: "qiime2 alignment". Plugin for generating and manipulating alignments.">  <repository owner="q2d2" name="qiime2__alignment__mafft" />
  <repository owner="q2d2" name="qiime2__alignment__mafft_add" />
  <repository owner="q2d2" name="qiime2__alignment__mask" />
</repositories>

Hopefully that's the reason for:

 Could not update suite_qiime2__alignment
Unexpected HTTP status code: 500: {"err_msg": "Exception attempting to parse /srv/toolshed-repos/test/007/repo_7351/repository_dependencies.xml: attributes construct error, line 1, column 62 (repository_dependencies.xml, line 1)"}
ebolyen commented 1 year ago

Found another, this time with an ampersand:

<repositories description="Galaxy suite for QIIME 2 plugin: 'demux'. Plugin for demultiplexing & viewing sequence quality.">  <repository owner="q2d2" name="qiime2__demux__emp_paired" />
  <repository owner="q2d2" name="qiime2__demux__emp_single" />
  <repository owner="q2d2" name="qiime2__demux__filter_samples" />
  <repository owner="q2d2" name="qiime2__demux__subsample_paired" />
  <repository owner="q2d2" name="qiime2__demux__subsample_single" />
  <repository owner="q2d2" name="qiime2__demux__summarize" />
</repositories>