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add test showing error during import job preparion
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the following Traceback can be found in the logs (the test itself is not
executed)

```
Traceback (most recent call last):
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 291, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1254, in prepare
    ) = tool_evaluator.build()
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 566, in build
    global_tool_logs(self._build_config_files, config_file, "Building Config Files")
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
    raise e
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
    return func()
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 633, in _build_config_files
    self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template)
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 756, in __write_workdir_file
    value = fill_template(content, context=context, python_template_version=self.tool.python_template_version)
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
    raise first_exception or e
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
    return unicodify(t, log_exception=False)
  File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
    value = str(value)
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.10/site-packages/Cheetah/Template.py", line 1053, in __unicode__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1705952649_1165519_57877.py", line 119, in respond
  File "cheetah_DynamicallyCompiledCheetahTemplate_1705952649_1165519_57877.py", line 102, in stringify
  File "cheetah_DynamicallyCompiledCheetahTemplate_1705952649_1165519_57877.py", line 113, in stringify
AttributeError: 'TreeDict' object has no attribute 'is_collection'
```
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bernt-matthias committed Jan 22, 2024
1 parent 65e4952 commit 8125f49
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Showing 3 changed files with 33 additions and 3 deletions.
36 changes: 33 additions & 3 deletions tools/suite_qiime2_core__tools/qiime2_core__tools__import.xml
Original file line number Diff line number Diff line change
Expand Up @@ -969,7 +969,7 @@ write(json.dumps(inputs))
<option value="individual">Associate individual files</option>
</param>
<when value="collection">
<param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
<param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
<option value="no">No, use element identifiers as is</option>
Expand Down Expand Up @@ -1146,7 +1146,7 @@ write(json.dumps(inputs))
<option value="individual">Associate individual files</option>
</param>
<when value="collection">
<param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
<param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\.fastq\.gz"/>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
<option value="no">No, use element identifiers as is</option>
Expand Down Expand Up @@ -1177,7 +1177,7 @@ write(json.dumps(inputs))
<option value="individual">Associate individual files</option>
</param>
<when value="collection">
<param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
<param name="elementss" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz"/>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
<option value="no">No, use element identifiers as is</option>
Expand Down Expand Up @@ -1657,6 +1657,36 @@ write(json.dumps(inputs))
<outputs>
<data name="imported_data" format="qza" from_work_dir="imported_data.qza"/>
</outputs>
<tests>
<test>
<conditional name="import_root">
<param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>
<conditional name="__q2galaxy__GUI__cond__format__">
<param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/>
<section name="import_sequences">
<conditional name="__q2galaxy__GUI__cond__sequences__">
<param name="__q2galaxy__GUI__select__picker__" value="collection"/>
<param name="elementss">
<collection type="list">
<element name="YY_S49_R1_001.fastq,gz" ftype="tabular" value="YY/YY_S49_R1_001.fastq.gz" />
<element name="YY_S49_R2_001.fastq.gz" ftype="tabular" value="YY/YY_S49_R2_001.fastq.gz" />
</collection>
</param>
<conditional name="__q2galaxy__GUI__cond__add_ext__">
<param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>
<param name="ext" label="fastq.gz"/>
</conditional>
</conditional>
</section>
</conditional>
</conditional>
<output name="imported_data">
<assert_contents>
<has_size min="1"/>
</assert_contents>
</output>
</test>
</tests>
<help>
QIIME 2: tools import
=====================
Expand Down
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