[25.0] Directory converters: fix for flat zip files #20857
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| <option value="directory">directory</option> | ||
| <option value="zarr">zarr</option> | ||
| <option value="ome_zarr">ome_zarr</option> | ||
| <option value="lexicmap_index">lexicmap_index</option> |
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Wondering why the tar2directory converter does not have this parameter. Should I add it?
Edit: Or should the tar2directory converter be replaced by this tool?
EditEdit: Ahh it already is.
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Hrm, Timeout for the test? Worked with Edit: Guess this was the galaxy-tool-util problem with conda |
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Setting this to draft until this is tested: galaxyproject/tools-iuc#7106 (comment) |
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Instead of 4679231 one might modify the extract method .. but I was afraid of the fallout. |
bernt-matthias
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| <datatype extension='qiime2.tabular' type="galaxy.datatypes.qiime2:QIIME2Metadata" display_in_upload="true"/> | ||
| <datatype extension="zip" type="galaxy.datatypes.binary:CompressedZipArchive" display_in_upload="true"> | ||
| <converter file="archive_to_directory.xml" target_datatype="directory" /> | ||
| <converter file="archive_to_directory.xml" target_datatype="lexicmap_index"/> |
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This doesn't really make sense to me, that means every zip file is also a lexicmap_index.
| <!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; --> | ||
| <requirements> | ||
| <requirement type="package" version="23.2.1">galaxy-util</requirement> | ||
| <requirement type="package" version="25.0.2">galaxy-util</requirement> |
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Is this the fix you're referring to in https://github.com/galaxyproject/tools-iuc/pull/7257/files#r2323290063 ?
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The fix is in the command block.
The bump is essentially a backport of #20834
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I tried to cleanup the PR and removed all the lexicmap stuff
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The command block doesn't look right to me, if the input was flat files or directories it either shouldn't be needed or there is a fix necessary in CompressedFile.
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https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/compression_utils.py#L257-L259 that seems like it would be a problem, and is rather unpredictable.
with conda I get
```
Traceback (most recent call last):
File "<string>", line 1, in <module>
from galaxy.util.compression_utils import CompressedFile; CompressedFile('/tmp/tmp3v2nuot4/files/a/9/7/dataset_a97aebb4-46f7-47a9-b418-11ff1deeed74.dat').extract('.')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/berntm/miniforge3/envs/[email protected]/lib/python3.13/site-packages/galaxy/util/compression_utils.py", line 29, in <module>
from .checkers import (
...<2 lines>...
)
File "/home/berntm/miniforge3/envs/[email protected]/lib/python3.13/site-packages/galaxy/util/checkers.py", line 20, in <module>
from galaxy.util.image_util import image_type
File "/home/berntm/miniforge3/envs/[email protected]/lib/python3.13/site-packages/galaxy/util/image_util.py", line 3, in <module>
import imghdr
ModuleNotFoundError: No module named 'imghdr'
```
zip files whose content is in a single top dir is correctly extracted. but if the content is contained in the zip's root the extract method will [add another level (the dataset name)](https://github.com/galaxyproject/galaxy/blob/af2d24082c52cbf8709561044f2082758aec6ff3/lib/galaxy/util/compression_utils.py#L256).
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Closing in favor of: #20929 |
2 participants
Was wondering converters should be added automatically for subclassed datatypes?
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