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sra_to_isatab_batch_convert from the develop branch does not work #568

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tbrittoborges opened this issue Aug 28, 2024 · 0 comments
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@tbrittoborges
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I am testing the functionality from sra_to_isatab_batch_convert:

from isatools.net import sra2isatab

DEFAULT_SAXON_EXECUTABLE = '../saxon9he.jar'

zipped_bytes = sra2isatab.sra_to_isatab_batch_convert("ERP005654", DEFAULT_SAXON_EXECUTABLE)

Which outputs:

>> 2024-08-28 13:49:46,368 [INFO]: sra2isatab.py(sra_to_isatab_batch_convert:106) >> This function uses The Saxon XSLT XQuery Processor from Saxonica Limited (http://www.saxonica.com/)
>> 2024-08-28 13:49:46,371 [INFO]: sra2isatab.py(sra_to_isatab_batch_convert:114) >> Destination dir is: [/var/folders/jf/chyv7rv55y73v_zyt1zh_7c40000gn/T/tmpjconbek4](https://file+.vscode-resource.vscode-cdn.net/var/folders/jf/chyv7rv55y73v_zyt1zh_7c40000gn/T/tmpjconbek4)
Syntax error at char 177 near {...IMENT')]/following-sibling:...} in expression in xsl:variable/@select on line 39 column 233 of extract-studies-rice.xsl:
  XPST0003: expected ")", found "<eof>"
Syntax error at char 64 near {....uk/ena/browser/api/xml/', ...} in expression in xsl:value-of/@select on line 43 column 106 of extract-studies-rice.xsl:
  XPST0003: expected ")", found "<eof>"
Errors were reported during stylesheet compilation
>> 2024-08-28 13:49:47,175 [INFO]: sra2isatab.py(sra_to_isatab_batch_convert:130) >> Subprocess Saxon exited with code: 2

Accordingly, the resulting zipped_bytes is empty: len(zipped_bytes.getvalue()) returns 0.
The saxon9he.jar, which is missing from the develop branch, was downloaded from the master
wget https://github.com/ISA-tools/isa-api/raw/develop/isatools/net/resources/saxon9/s axon9he.jar. I tested several other datasets, with the same error. I was using the develop branch, as the master does not with more recent software versions.
Any tips to get this working?

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