Fix sanitizer from SemiBin #7366
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i had to change nameing of the softlink a bit to remove the file extension which was in the name. Now |
tools/semibin/macros.xml
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| #for $e in $mode.multi_fasta.input_fasta | ||
| #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) | ||
| #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier)) | ||
| #set $final_identifier = '_'.join($identifier.split('_')[:-1]) |
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This is not a good idea. If people have collection element identifiers containing any sanitized character or an underscore this will remove part of the identifier. Users should remove file extensions during collection creation.
I guess you had some problems in the test due to the file extensions. Then its better to adapt test assumptions.
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The problem in thr test was a code error because of the new naming of the file. The code tried to run to find something with S1 but since the name of the file was S1_fasta it could not find it. So therefor i dont know how to fix beside of deleteing the test which should not be the point.
Do you might have any idea for this because i didnt thought about your point. I can also add a check to see if there is any file extension left of so cut it out?
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I guess S1 is somewhere hardcoded in the test data files. This then need to be changed.
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After some work it should be fine now. I had to add extra files just for the one test case where the naming of the file was a problem.
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You should be able to merge it now. The fix is also implemented in my other PR!
| #if $e.ext.endswith(".gz") | ||
| gunzip -c '$e' > '${final_identifier}.fasta' && | ||
| gunzip -c '$e' > '${identifier}.fasta' && | ||
| #else | ||
| ln -s '$e' '${final_identifier}.fasta' && | ||
| ln -s '$e' '${identifier}.fasta' && | ||
| #end if |
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| #if $e.ext.endswith(".gz") | |
| gunzip -c '$e' > '${final_identifier}.fasta' && | |
| gunzip -c '$e' > '${identifier}.fasta' && | |
| #else | |
| ln -s '$e' '${final_identifier}.fasta' && | |
| ln -s '$e' '${identifier}.fasta' && | |
| #end if | |
| ln -s '$e' '${identifier}.${e.ext}' && |
semibin should be able to unzip itself: https://github.com/BigDataBiology/SemiBin/blob/886913b48814cc0cd426ee46ec20d22cee875bf5/SemiBin/fasta.py#L23
also we should allow fasta.bz2 in the formats of the input parameter (macros input-fasta-single and input-fasta-multiple). But this probably also requires changes in other tools?
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Will change it later today :)
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