Always extract all affiliations for each author (close #160)

pubmed_parser/medline_parser.py

@@ -424,11 +424,14 @@ def parse_author_affiliation(medline):
                 else:
                     identifier = ""
                 if author.find("AffiliationInfo/Affiliation") is not None:
-                    affiliation = author.find("AffiliationInfo/Affiliation").text or ""
-                    affiliation = affiliation.replace(
-                        "For a full list of the authors' affiliations please see the Acknowledgements section.",
-                        "",
-                    )
+                    affiliation = list(chain(*([c.text] for c in author.findall("AffiliationInfo/Affiliation")))) or []
+                    affiliation = [
+                        c.replace(
+                            "For a full list of the authors' affiliations please see the Acknowledgements section.",
+                            "",
+                        ) for c in affiliation
+                    ]
+                    affiliation = "|".join(affiliation)
                 else:
                     affiliation = ""
                 authors.append(

tests/test_medline_parser.py

@@ -34,7 +34,7 @@ def test_affiliations():
     """This is a test for the affiliations field."""
     affiliations_36400559 = 'Department of Neurological Surgery, The Ohio State Wexner Medical Center, 410 West 10th Street, Columbus, OH 43210, USA; The Ohio State University College of Medicine, 370 West 9th street, Columbus, OH 43210, USA.;Department of Neurological Surgery, The Ohio State Wexner Medical Center, 410 West 10th Street, Columbus, OH 43210, USA.;Department of Neurological Surgery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.;Department of Neurological Surgery, The Ohio State Wexner Medical Center, 410 West 10th Street, Columbus, OH 43210, USA; Department of Neurological Surgery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA. Electronic address: [email protected].'
     assert article_36400559['affiliations'] == affiliations_36400559
-    affiliations_28786991 = 'Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.;Centers for Disease Control and Prevention, Division of Tuberculosis Elimination, Atlanta, Georgia, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.'
+    affiliations_28786991 = 'Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.|Global Health Sciences, University of California, San Francisco, San Francisco, California, United States of America.|The Consortium for the Assessment of Prevention Economics (CAPE), University of California, San Francisco, San Francisco, California, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.|The Consortium for the Assessment of Prevention Economics (CAPE), University of California, San Francisco, San Francisco, California, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.|The Consortium for the Assessment of Prevention Economics (CAPE), University of California, San Francisco, San Francisco, California, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.|Global Health Sciences, University of California, San Francisco, San Francisco, California, United States of America.|The Consortium for the Assessment of Prevention Economics (CAPE), University of California, San Francisco, San Francisco, California, United States of America.;Centers for Disease Control and Prevention, Division of Tuberculosis Elimination, Atlanta, Georgia, United States of America.;Phillip R. Lee Institute for Health Policy Studies, University of California, San Francisco, San Francisco, California, United States of America.|Global Health Sciences, University of California, San Francisco, San Francisco, California, United States of America.|The Consortium for the Assessment of Prevention Economics (CAPE), University of California, San Francisco, San Francisco, California, United States of America.'
     assert article_28786991['affiliations'] == affiliations_28786991