galaxyproject / galaxyproject/galaxy

Failure to parse job_conf.xml if id and tags attributes are identical

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friendliness/intermediate kind/bug
Dominant language
Python
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Avg merge
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Merged PRs (30d)
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Description

The following XML code block is valid but causes a parsing error:

```

trackster

```

The exception doesn't mention what is wrong and reports:

```
Exception: Problem parsing the XML in file /galaxy_dist/config/job_conf.xml, please correct the indicated portion of the file and restart Galaxy.'tuple' object has no attribute 'append'
```

The problem is fixed if id= and tags= are set to different values.

From @Unode on [trello](https://trello.com/c/1uSmezQu/2430-failure-to-parse-job-conf-xml-if-id-and-tags-attributes-are-identical).

@erasche confirmed this bug today, simply adding `tags="local"` to the `sample_basic` reproduces it.

Contributor guide

Open the contributing guide

Research direction

Start with config/job_conf.xml and the sample_basic configuration, reproducing the failure with identical id and tags attributes. Trace the job configuration parser to identify why this valid XML produces the tuple append error. Done means the example parses successfully and the parser reports a useful error for genuinely invalid configuration.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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