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softwareRef
Tried to parse a single file KA1_GB1_01_10465.mzML, got the following traceback:
KA1_GB1_01_10465.mzML
raceback (most recent call last): File "/home/althonos/Code/mzml2isa/mzml2isa/mzml.py", line 267, in cvParam_loop soft_ref = get_parent(e, self.tree).attrib['softwareRef'] File "src/lxml/lxml.etree.pyx", line 2467, in lxml.etree._Attrib.__getitem__ (src/lxml/lxml.etree.c:70679) KeyError: 'softwareRef' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/python3.6/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/usr/lib/python3.6/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/althonos/Code/mzml2isa/mzml2isa/__main__.py", line 5, in <module> parsing.main() File "/home/althonos/Code/mzml2isa/mzml2isa/parsing.py", line 224, in main jobs=args.jobs, template_directory=args.template_dir, OUT_dir=args.OUT_path File "/home/althonos/Code/mzml2isa/mzml2isa/parsing.py", line 158, in convert metalist = [_parse_file([mzml_file, ontology, parser, pbar]) for mzml_file in sorted(mzml_files, key=str)] File "/home/althonos/Code/mzml2isa/mzml2isa/parsing.py", line 158, in <listcomp> metalist = [_parse_file([mzml_file, ontology, parser, pbar]) for mzml_file in sorted(mzml_files, key=str)] File "/home/althonos/Code/mzml2isa/mzml2isa/utils.py", line 245, in new_func return func(*args[0]) File "/home/althonos/Code/mzml2isa/mzml2isa/parsing.py", line 77, in _parse_file meta = parser(filepath, ontology).meta File "/home/althonos/Code/mzml2isa/mzml2isa/mzml.py", line 146, in __init__ self.extract_meta(terms, xpaths_meta) File "/home/althonos/Code/mzml2isa/mzml2isa/mzml.py", line 195, in extract_meta self.cvParam_loop(elements, location_name, terms) File "/home/althonos/Code/mzml2isa/mzml2isa/mzml.py", line 269, in cvParam_loop soft_ref = get_parent(get_parent(e, self.tree), self.tree).attrib['softwareRef'] File "src/lxml/lxml.etree.pyx", line 2467, in lxml.etree._Attrib.__getitem__ (src/lxml/lxml.etree.c:70679) KeyError: 'softwareRef'
It seems the file was converted from mzXML before hand as suggested from the sourceFile tag.
mzXML
sourceFile
The text was updated successfully, but these errors were encountered:
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Tried to parse a single file
KA1_GB1_01_10465.mzML
, got the following traceback:It seems the file was converted from
mzXML
before hand as suggested from thesourceFile
tag.The text was updated successfully, but these errors were encountered: