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@pvanheus
Created Jun 2, 2022
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Error parsing file /tmp/tmpv_mpl4ub/job_working_directory/000/1/registry.xml
Traceback (most recent call last):
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/util/__init__.py", line 275, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1876, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1902, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "/tmp/tmpv_mpl4ub/job_working_directory/000/1/registry.xml", line 4
lxml.etree.XMLSyntaxError: Extra content at the end of the document, line 4, column 116786
Traceback (most recent call last):
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/tools/data_fetch.py", line 606, in <module>
main()
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/tools/data_fetch.py", line 49, in main
registry.load_datatypes(root_dir=args.galaxy_root, config=args.datatypes_registry)
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/datatypes/registry.py", line 135, in load_datatypes
tree = galaxy.util.parse_xml(config)
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/util/__init__.py", line 275, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1876, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1902, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "/tmp/tmpv_mpl4ub/job_working_directory/000/1/registry.xml", line 4
lxml.etree.XMLSyntaxError: Extra content at the end of the document, line 4, column 116786
Galaxy job runner generated the following standard error:
Error parsing file /tmp/tmpv_mpl4ub/job_working_directory/000/1/registry.xml
Traceback (most recent call last):
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/util/__init__.py", line 275, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1876, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1902, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "/tmp/tmpv_mpl4ub/job_working_directory/000/1/registry.xml", line 4
lxml.etree.XMLSyntaxError: Extra content at the end of the document, line 4, column 116786
Traceback (most recent call last):
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/tools/data_fetch.py", line 606, in <module>
main()
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/tools/data_fetch.py", line 49, in main
registry.load_datatypes(root_dir=args.galaxy_root, config=args.datatypes_registry)
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/datatypes/registry.py", line 135, in load_datatypes
tree = galaxy.util.parse_xml(config)
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/util/__init__.py", line 275, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1876, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1902, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "/tmp/tmpv_mpl4ub/job_working_directory/000/1/registry.xml", line 4
lxml.etree.XMLSyntaxError: Extra content at the end of the document, line 4, column 116786
ERROR:galaxy.util:Error parsing file metadata/registry.xml
Traceback (most recent call last):
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/util/__init__.py", line 275, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1876, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1902, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "metadata/registry.xml", line 4
lxml.etree.XMLSyntaxError: Extra content at the end of the document, line 4, column 116786
Traceback (most recent call last):
File "metadata/set.py", line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/metadata/set_metadata.py", line 122, in set_metadata
set_metadata_portable()
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/metadata/set_metadata.py", line 157, in set_metadata_portable
datatypes_registry = validate_and_load_datatypes_config(datatypes_config)
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/metadata/set_metadata.py", line 467, in validate_and_load_datatypes_config
datatypes_registry.load_datatypes(
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/datatypes/registry.py", line 135, in load_datatypes
tree = galaxy.util.parse_xml(config)
File "/home/pvh/Documents/code/SANBI/pvh-forks/galaxy/lib/galaxy/util/__init__.py", line 275, in parse_xml
tree = etree.parse(fname, parser=parser)
File "src/lxml/etree.pyx", line 3536, in lxml.etree.parse
File "src/lxml/parser.pxi", line 1876, in lxml.etree._parseDocument
File "src/lxml/parser.pxi", line 1902, in lxml.etree._parseDocumentFromURL
File "src/lxml/parser.pxi", line 1805, in lxml.etree._parseDocFromFile
File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
File "metadata/registry.xml", line 4
lxml.etree.XMLSyntaxError: Extra content at the end of the document, line 4, column 116786
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