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b/tests/pipeline/test_deduce.py |
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import docdeid as dd |
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from deduce.person import Person |
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text = ( |
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"betreft: Jan Jansen, bsn 111222333, patnr 000334433. De patient J. Jansen is 64 " |
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"jaar oud en woonachtig in Utrecht. Hij werd op 10 oktober 2018 door arts " |
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"Peter de Visser ontslagen van de kliniek van het UMCU. Voor nazorg kan hij " |
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"worden bereikt via j.JNSEN.123@gmail.com of (06)12345678." |
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) |
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class TestDeduce: |
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def test_annotate(self, model): |
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metadata = {"patient": Person(first_names=["Jan"], surname="Jansen")} |
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doc = model.deidentify(text, metadata=metadata) |
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expected_annotations = dd.AnnotationSet( |
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[ |
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dd.Annotation( |
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text="(06)12345678", |
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start_char=272, |
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end_char=284, |
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tag="telefoonnummer", |
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), |
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dd.Annotation(text="111222333", start_char=25, end_char=34, tag="bsn"), |
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dd.Annotation( |
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text="Peter de Visser", start_char=153, end_char=168, tag="persoon" |
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), |
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dd.Annotation( |
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text="j.JNSEN.123@gmail.com", |
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start_char=247, |
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end_char=268, |
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tag="emailadres", |
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), |
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dd.Annotation( |
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text="J. Jansen", start_char=64, end_char=73, tag="patient" |
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), |
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dd.Annotation( |
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text="Jan Jansen", start_char=9, end_char=19, tag="patient" |
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), |
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dd.Annotation( |
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text="10 oktober 2018", start_char=127, end_char=142, tag="datum" |
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), |
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dd.Annotation(text="64", start_char=77, end_char=79, tag="leeftijd"), |
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dd.Annotation(text="000334433", start_char=42, end_char=51, tag="id"), |
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dd.Annotation( |
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text="Utrecht", start_char=106, end_char=113, tag="locatie" |
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), |
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dd.Annotation( |
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text="UMCU", start_char=202, end_char=206, tag="ziekenhuis" |
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), |
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] |
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) |
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assert doc.annotations == set(expected_annotations) |
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def test_deidentify(self, model): |
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metadata = {"patient": Person(first_names=["Jan"], surname="Jansen")} |
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doc = model.deidentify(text, metadata=metadata) |
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expected_deidentified = ( |
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"betreft: [PATIENT], bsn [BSN-1], patnr [ID-1]. De patient [PATIENT] is " |
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"[LEEFTIJD-1] jaar oud en woonachtig in [LOCATIE-1]. Hij werd op " |
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"[DATUM-1] door arts [PERSOON-1] ontslagen van de kliniek van het " |
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"[ZIEKENHUIS-1]. Voor nazorg kan hij worden bereikt via [EMAILADRES-1] " |
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"of [TELEFOONNUMMER-1]." |
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) |
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assert doc.deidentified_text == expected_deidentified |
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def test_annotate_intext(self, model): |
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metadata = {"patient": Person(first_names=["Jan"], surname="Jansen")} |
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doc = model.deidentify(text, metadata=metadata) |
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expected_intext_annotated = ( |
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"betreft: <PATIENT>Jan Jansen</PATIENT>, bsn <BSN>111222333</BSN>, " |
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"patnr <ID>000334433</ID>. De patient <PATIENT>J. Jansen</PATIENT> is " |
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"<LEEFTIJD>64</LEEFTIJD> jaar oud en woonachtig in <LOCATIE>Utrecht" |
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"</LOCATIE>. Hij werd op <DATUM>10 oktober 2018</DATUM> door arts " |
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"<PERSOON>Peter de Visser</PERSOON> ontslagen van de kliniek van het " |
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"<ZIEKENHUIS>UMCU</ZIEKENHUIS>. Voor nazorg kan hij worden bereikt " |
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"via <EMAILADRES>j.JNSEN.123@gmail.com</EMAILADRES> of " |
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"<TELEFOONNUMMER>(06)12345678</TELEFOONNUMMER>." |
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) |
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assert dd.utils.annotate_intext(doc) == expected_intext_annotated |