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Failing on valid XML #362

erasche opened this Issue Oct 31, 2015 · 0 comments


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erasche commented Oct 31, 2015

Error loading tool with path /home/hxr/work/tools-iuc/tools/ncbi_entrez_eutils/esearch.xml
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/planemo_ext/galaxy/tools/", line 39, in load_tool_elements_from_path
    tool_elements.append((file, loader.load_tool(file)))
TypeError: expected a character buffer object
Could not lint /home/hxr/work/tools-iuc/tools/ncbi_entrez_eutils/esearch.xml due to malformed xml.

The snippet in particular that triggered this was the following in the macros file:

<token name="@REFERENCES@"><![CDATA[]]></token>

@erasche erasche added the bug label Oct 31, 2015

erasche added a commit to galaxyproject/tools-iuc that referenced this issue Oct 31, 2015

Remove stdio
Empty CDATA is an issue. galaxyproject/planemo#362

jmchilton added a commit to jmchilton/galaxy that referenced this issue Nov 18, 2015

Fix macro bug with empty CDATA being None instead of ''.
Fixes galaxyproject/planemo#362 thanks for the report @erasche.

Test using the following command:

nosetests test/unit/tools/

@jmchilton jmchilton closed this in 541c7c3 Nov 18, 2015

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