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gabrielaltay commited on
Commit
c2d7dc4
1 Parent(s): 5c08365

fix parsing imports

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Files changed (1) hide show
  1. cellfinder.py +6 -3
cellfinder.py CHANGED
@@ -31,6 +31,9 @@ import datasets
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  from .bigbiohub import kb_features
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  from .bigbiohub import BigBioConfig
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  from .bigbiohub import Tasks
 
 
 
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  _LANGUAGES = ['English']
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  _PUBMED = True
@@ -216,7 +219,7 @@ class CellFinderDataset(datasets.GeneratorBasedBuilder):
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  continue
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  # Read brat annotations for the given text file and convert example to the source format
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- brat_example = parsing.parse_brat_file(file)
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  source_example = self._to_source_example(file, brat_example)
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  yield source_example["document_id"], source_example
@@ -232,8 +235,8 @@ class CellFinderDataset(datasets.GeneratorBasedBuilder):
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  continue
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  # Read brat annotations for the given text file and convert example to the BigBio-KB format
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- brat_example = parsing.parse_brat_file(file)
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- kb_example = parsing.brat_parse_to_bigbio_kb(brat_example)
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  kb_example["id"] = kb_example["document_id"]
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  # Fix text type annotation for the converted example
 
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  from .bigbiohub import kb_features
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  from .bigbiohub import BigBioConfig
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  from .bigbiohub import Tasks
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+ from .bigbiohub import parse_brat_file
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+ from .bigbiohub import brat_parse_to_bigbio_kb
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+
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  _LANGUAGES = ['English']
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  _PUBMED = True
 
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  continue
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  # Read brat annotations for the given text file and convert example to the source format
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+ brat_example = parse_brat_file(file)
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  source_example = self._to_source_example(file, brat_example)
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  yield source_example["document_id"], source_example
 
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  continue
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  # Read brat annotations for the given text file and convert example to the BigBio-KB format
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+ brat_example = parse_brat_file(file)
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+ kb_example = brat_parse_to_bigbio_kb(brat_example)
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  kb_example["id"] = kb_example["document_id"]
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  # Fix text type annotation for the converted example