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.

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

Failing on valid XML #362

Closed
erasche opened this Issue Oct 31, 2015 · 0 comments

Comments

Projects
None yet
1 participant
@erasche
Copy link
Member

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/loader_directory.py", 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/test_tool_loader.py
```

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment