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b/tests/surrogates/test_rewrite_dataset.py |
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import argparse |
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import filecmp |
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import glob |
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from os.path import basename, dirname, join |
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import pytest |
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from deidentify.base import Annotation |
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from deidentify.surrogates import rewrite_dataset |
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def test_apply_surrogates(): |
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text = 'ccc cc ccc c c ccc cccccc cccc' |
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annotations = [ |
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Annotation('ccc', start=0, end=3, tag='A'), |
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Annotation('cc', start=4, end=6, tag='A'), |
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Annotation('ccc', start=15, end=18, tag='B') |
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] |
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surrogates = ['a', 'dd', 'bbbbb'] |
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surrogate_doc = rewrite_dataset.apply_surrogates(text, annotations, surrogates) |
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assert surrogate_doc.text == 'a dd ccc c c bbbbb cccccc cccc' |
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assert surrogate_doc.annotations == [ |
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Annotation('a', start=0, end=1, tag='A'), |
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Annotation('dd', start=2, end=4, tag='A'), |
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Annotation('bbbbb', start=13, end=18, tag='B') |
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] |
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assert surrogate_doc.annotations_without_surrogates == [] |
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def test_apply_surrogates_no_annotations(): |
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surrogate_doc = rewrite_dataset.apply_surrogates('ccc cc ccc', annotations=[], surrogates=[]) |
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assert surrogate_doc.text == 'ccc cc ccc' |
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assert surrogate_doc.annotations == [] |
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assert surrogate_doc.annotations_without_surrogates == [] |
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def test_apply_surrogates_errors_raise(): |
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text = 'ccc cc ccc' |
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annotations = [ |
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Annotation('ccc', start=0, end=3, tag='A'), |
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Annotation('cc', start=4, end=6, tag='A'), |
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Annotation('ccc', start=7, end=10, tag='B') |
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] |
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surrogates = ['a', None, 'b'] |
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with pytest.raises(ValueError): |
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rewrite_dataset.apply_surrogates(text, annotations, surrogates) |
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with pytest.raises(ValueError): |
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rewrite_dataset.apply_surrogates(text, annotations, surrogates, errors='raise') |
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def test_apply_surrogates_errors_ignore(): |
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text = 'ccc cc ccc' |
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annotations = [ |
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Annotation('ccc', start=0, end=3, tag='A'), |
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Annotation('cc', start=4, end=6, tag='A'), |
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Annotation('ccc', start=7, end=10, tag='B') |
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] |
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surrogates = ['a', None, 'b'] |
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surrogate_doc = rewrite_dataset.apply_surrogates(text, annotations, surrogates, errors='ignore') |
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assert surrogate_doc.text == 'a cc b' |
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assert surrogate_doc.annotations == [ |
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Annotation('a', start=0, end=1, tag='A'), |
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Annotation('cc', start=2, end=4, tag='A'), |
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Annotation('b', start=5, end=6, tag='B') |
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] |
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assert surrogate_doc.annotations_without_surrogates == [ |
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Annotation('cc', start=4, end=6, tag='A'), |
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] |
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def test_apply_surrogates_errors_coerce(): |
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text = 'ccc cc ccc' |
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annotations = [ |
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Annotation('ccc', start=0, end=3, tag='A'), |
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Annotation('cc', start=4, end=6, tag='A'), |
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Annotation('ccc', start=7, end=10, tag='B') |
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] |
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surrogates = ['a', None, 'b'] |
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surrogate_doc = rewrite_dataset.apply_surrogates(text, annotations, surrogates, errors='coerce') |
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assert surrogate_doc.text == 'a [A] b' |
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assert surrogate_doc.annotations == [ |
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Annotation('a', start=0, end=1, tag='A'), |
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Annotation('[A]', start=2, end=5, tag='A'), |
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Annotation('b', start=6, end=7, tag='B') |
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] |
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assert surrogate_doc.annotations_without_surrogates == [ |
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Annotation('cc', start=4, end=6, tag='A'), |
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] |
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def test_main(tmpdir): |
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args = argparse.Namespace( |
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surrogate_table=join(dirname(__file__), 'data/annotations-rewrite-table.csv'), |
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data_path=join(dirname(__file__), 'data/original'), |
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output_path=tmpdir |
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) |
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ann_files = glob.glob(join(dirname(__file__), 'data/rewritten/*.ann')) |
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txt_files = glob.glob(join(dirname(__file__), 'data/rewritten/*.txt')) |
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to_compare = ann_files + txt_files |
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to_compare = [basename(f) for f in to_compare] |
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rewrite_dataset.main(args) |
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for file in to_compare: |
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expected = join(dirname(__file__), 'data/rewritten/', file) |
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actual = join(tmpdir, file) |
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assert filecmp.cmp(expected, actual) |