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Entrez error: Failed to find tag 'AssemblyStatusSort' #202

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HadrienG opened this issue May 3, 2021 · 0 comments
Closed

Entrez error: Failed to find tag 'AssemblyStatusSort' #202

HadrienG opened this issue May 3, 2021 · 0 comments
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@HadrienG
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HadrienG commented May 3, 2021

Happens on some machines:

INFO:iss.app:Starting iss generate
INFO:iss.app:Using kde ErrorModel
INFO:iss.download:Searching for bacteria to download
Traceback (most recent call last):
  File "/lustre2/scratch/shahab/conda/iss/bin/iss", line 10, in <module>
    sys.exit(main())
  File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/iss/app.py", line 608, in main
    args.func(args)
  File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/iss/app.py", line 99, in generate_reads
    g, n, args.output + '_ncbi_genomes.fasta')
  File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/iss/download.py", line 51, in ncbi
    id=ident))["DocumentSummarySet"]["DocumentSummary"][0]
  File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/Bio/Entrez/__init__.py", line 508, in read
    record = handler.read(handle)
  File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/Bio/Entrez/Parser.py", line 304, in read
    self.parser.ParseFile(handle)
  File "/home/conda/feedstock_root/build_artifacts/python_1613748395163/work/Modules/pyexpat.c", line 417, in StartElement
  File "/lustre2/scratch/shahab/conda/iss/lib/python3.7/site-packages/Bio/Entrez/Parser.py", line 581, in startElementHandler
    raise ValidationError(tag)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'AssemblyStatusSort' in the DTD. To skip all tags that are not represented in the DTD, please call Bio.Entrez.read or Bio.Entrez.parse with validate=False.

can probably be fixed adding validate=False to the Entrez.read calls

@HadrienG HadrienG self-assigned this May 3, 2021
@HadrienG HadrienG added the bug label May 3, 2021
HadrienG added a commit that referenced this issue May 3, 2021
HadrienG added a commit that referenced this issue May 5, 2021
@HadrienG HadrienG closed this as completed May 5, 2021
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