From d5580b393eedcc9cfb2b8d35e254e5cc0e3b4121 Mon Sep 17 00:00:00 2001 From: Thomas Eidens Date: Wed, 4 Oct 2023 21:27:08 +0200 Subject: [PATCH] Improved handling of empty/short affiliations --- mecadoi/crossref/peer_review.py | 46 +++--- scripts/unittest.sh | 2 +- tests/resources/expected/no-institution.xml | 115 ++++++++++++++ tests/resources/expected/no-institution.yml | 34 +++++ .../688_1_merged_1608565201.pdf | Bin 0 -> 3016 bytes .../Article Tracked Changes.doc | Bin 0 -> 30208 bytes .../meca/no-institution/Article-1.doc | Bin 0 -> 30208 bytes .../resources/meca/no-institution/Article.doc | Bin 0 -> 30208 bytes .../resources/meca/no-institution/article.xml | 137 +++++++++++++++++ .../meca/no-institution/decision.pdf | Bin 0 -> 4459 bytes .../meca/no-institution/manifest.xml | 43 ++++++ .../resources/meca/no-institution/reviews.xml | 119 +++++++++++++++ .../meca/no-institution/transfer.xml | 57 +++++++ tests/test_article.py | 141 +++++++++++++----- tests/test_batch.py | 6 +- tests/test_cli.py | 2 +- tests/test_generate_peer_review_deposition.py | 1 + tests/test_meca.py | 117 +++++++++++++++ 18 files changed, 762 insertions(+), 58 deletions(-) create mode 100644 tests/resources/expected/no-institution.xml create mode 100644 tests/resources/expected/no-institution.yml create mode 100644 tests/resources/meca/no-institution/688_1_merged_1608565201.pdf create mode 100644 tests/resources/meca/no-institution/Article Tracked Changes.doc create mode 100644 tests/resources/meca/no-institution/Article-1.doc create mode 100644 tests/resources/meca/no-institution/Article.doc create mode 100644 tests/resources/meca/no-institution/article.xml create mode 100644 tests/resources/meca/no-institution/decision.pdf create mode 100644 tests/resources/meca/no-institution/manifest.xml create mode 100644 tests/resources/meca/no-institution/reviews.xml create mode 100644 tests/resources/meca/no-institution/transfer.xml diff --git a/mecadoi/crossref/peer_review.py b/mecadoi/crossref/peer_review.py index 91360ba..e056e82 100644 --- a/mecadoi/crossref/peer_review.py +++ b/mecadoi/crossref/peer_review.py @@ -27,7 +27,7 @@ DoiBatch, DoiData, Head, - Institution, + Institution as CrossrefInstitution, InterWorkRelation, Orcid, PeerReview, @@ -37,7 +37,7 @@ ReviewDate, Titles, ) -from mecadoi.model import Author +from mecadoi.model import Author, Institution as MecadoiInstitution def generate_peer_review_deposition(articles: List[Article]) -> str: @@ -119,7 +119,7 @@ def generate_reviews(article: Article) -> Generator[PeerReview, None, None]: month=review.publication_date.month, day=review.publication_date.day, ), - institution=Institution(institution_name=INSTITUTION_NAME), + institution=CrossrefInstitution(institution_name=INSTITUTION_NAME), running_number=str(running_number), program=Program(related_item=[is_review_of_relation]), doi_data=DoiData( @@ -149,7 +149,7 @@ def generate_reviews(article: Article) -> Generator[PeerReview, None, None]: month=review.publication_date.month, day=review.publication_date.day, ), - institution=Institution(institution_name=INSTITUTION_NAME), + institution=CrossrefInstitution(institution_name=INSTITUTION_NAME), running_number="Author Reply", program=Program( related_item=[is_review_of_relation] @@ -171,6 +171,30 @@ def generate_reviews(article: Article) -> Generator[PeerReview, None, None]: ) +def create_institution(institution: MecadoiInstitution) -> CrossrefInstitution: + city = ( + institution.city + if institution.city and len(institution.city) > 1 + else None + ) + country = ( + institution.country + if institution.country and len(institution.country) > 1 + else None + ) + place = ( + f"{city}, {country}" if city and country + else city if city + else country if country + else None + ) + return CrossrefInstitution( + institution_name=institution.name, + institution_department=institution.department, + institution_place=place, + ) + + def create_contributors(authors: List[Author]) -> Contributors: contributors = Contributors( person_name=[ @@ -182,19 +206,7 @@ def create_contributors(authors: List[Author]) -> Contributors: affiliations=( Affiliations( institution=[ - Institution( - institution_name=institution.name, - institution_department=institution.department, - institution_place=( - f"{institution.city}, {institution.country}" - if institution.city and institution.country - else institution.city - if institution.city - else institution.country - if institution.country - else None - ), - ) + create_institution(institution) for institution in author.institutions ] ) diff --git a/scripts/unittest.sh b/scripts/unittest.sh index 063e28c..d16af7b 100755 --- a/scripts/unittest.sh +++ b/scripts/unittest.sh @@ -3,4 +3,4 @@ # If any command fails, exit immediately with that command's exit status set -eo pipefail -ENV_FILE=.env.ci python -m unittest \ No newline at end of file +ENV_FILE=.env.ci python -m unittest $@ diff --git a/tests/resources/expected/no-institution.xml b/tests/resources/expected/no-institution.xml new file mode 100644 index 0000000..1caac8b --- /dev/null +++ b/tests/resources/expected/no-institution.xml @@ -0,0 +1,115 @@ + + + 0000 + 0 + + EMBO + eidens@embl.de + + EMBO + + + + + + + + Peer Review #1 of An article with a single revision round. + + + 10 + 20 + 2020 + + + Review Commons + + 1 + + + 10.1101/single-revision-round.123.456.7890 + + + + 10.15252/rc.2020123456 + https://eeb.embo.org/doi/10.1101/single-revision-round.123.456.7890#rev0-rr1 + + + + + + + + Peer Review #2 of An article with a single revision round. + + + 10 + 20 + 2020 + + + Review Commons + + 2 + + + 10.1101/single-revision-round.123.456.7890 + + + + 10.15252/rc.2020123456 + https://eeb.embo.org/doi/10.1101/single-revision-round.123.456.7890#rev0-rr2 + + + + + + Jane + Doe + + + / + + + https://orcid.org/0000-0012-3456-7890 + + + John + Doe + + + / + + + + + + Author Reply to Peer Reviews of An article with a single revision round. + + + 10 + 20 + 2020 + + + Review Commons + + Author Reply + + + 10.1101/single-revision-round.123.456.7890 + + + 10.15252/rc.2020123456 + + + 10.15252/rc.2020123456 + + + + 10.15252/rc.2020123456 + https://eeb.embo.org/doi/10.1101/single-revision-round.123.456.7890#rev0-ar + + + + \ No newline at end of file diff --git a/tests/resources/expected/no-institution.yml b/tests/resources/expected/no-institution.yml new file mode 100644 index 0000000..b59bffa --- /dev/null +++ b/tests/resources/expected/no-institution.yml @@ -0,0 +1,34 @@ +doi: 10.1101/single-revision-round.123.456.7890 +review_process: +- author_reply: + authors: + - affiliation: / + given_name: Jane + is_corresponding_author: true + orcid: + id: https://orcid.org/0000-0012-3456-7890 + is_authenticated: true + surname: Doe + - affiliation: / + given_name: John + is_corresponding_author: false + orcid: null + surname: Doe + doi: 10.15252/rc.2020123456 + publication_date: 2020-10-20 00:00:00 + text: {} + reviews: + - authors: [] + doi: 10.15252/rc.2020123456 + publication_date: 2020-10-20 00:00:00 + text: + Estimated time to Complete Revisions (Required): Cannot tell / Not applicable + Significance (Required): Lorem ipsum dolor sit amet. + - authors: [] + doi: 10.15252/rc.2020123456 + publication_date: 2020-10-20 00:00:00 + text: + Estimated time to Complete Revisions (Required): Between 3 and 6 months + Evidence, reproducibility and clarity (Required): 'Summary: this is a test' + Significance (Required): 'Signification: also a test' +title: An article with a single revision round. diff --git a/tests/resources/meca/no-institution/688_1_merged_1608565201.pdf b/tests/resources/meca/no-institution/688_1_merged_1608565201.pdf new file mode 100644 index 0000000000000000000000000000000000000000..7cb1aa187932502ab1f3ea9d9b9b68ceab7b82bd GIT binary patch literal 3016 zcmc&$32YQq7#^*1tX4qoF3MxV+h4e-_-&OEBjC>bG1Q|68@?DcA;mW24hJ&iD)*DG&p(dGyMA(kta#c@` 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+ + + reviewcommonstest + + Review Commons - TEST + + + 2575-1077 + 2575-1077 + + + 10.12345/single-revision-round.1234567890 + single-revision-round-2020-1234 + + + Research Article + + + + An article with a single revision round. + + + + https://orcid.org/0000-0012-3456-7890 + + Doe + Jane + Dr. + + janedoe@example.com + + + + + + Doe + John + + johndoe@example.com + + + + + / + None + / + / + / + + + / + None + / + / + + + + + + Corresponding Author: + Jane Doe, Medicinal Chemistry, EMBL + + +

Author contributions: J.D. conceptualization; J.D. data curation.

+ + + + + 1234-5678.single-revision-round-2020-1234 + + + 12 + 12 + 2020 + + + + + 2020 + + +

This article has a single revision round and thus in ...

+ + + test + test1 + test2 + + + + + EMBO + http://dx.doi.org/10.12345/asdf1234567890 + + + + + + + dual_publication + 0 + + + human_subjects + 0 + + + animal_subjects + 0 + + + Rebuttal Submitted to Hypothes.is + Yes + + + Pre-existing BioRxiv Preprint + Yes + + + Pre-existing BioRxiv Preprint DOI + 10.1101/single-revision-round.123.456.7890 + + + BioRxiv Preprint Submitted on Author's Behalf + Yes + + + Acknowledgment of Policy on Original Data + EJ + + + + +
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15 + 07 + 2019 + + + 26 + 07 + 2019 + + + 25 + 07 + 2019 + + + + + + redacted + + + + + + + + + <b>Significance:</b> + Significance (Required) + + + + Lorem ipsum dolor sit amet. + + + + + <b>How much time do you estimate the authors will need to complete the suggested revisions:</b> + Estimated time to Complete Revisions (Required) + (Decision Recommendation) + + + Cannot tell / Not applicable + + + + + + + + 16 + 07 + 2019 + + + 26 + 07 + 2019 + + + 21 + 12 + 2020 + + + + + + redacted + redacted + redacted + + redacted + + + redacted + + + + + <b>Evidence, reproducibility and clarity:</b> + Evidence, reproducibility and clarity (Required) + + + + Summary: this is a test + + + + + <b>Significance:</b> + Significance (Required) + + + + Signification: also a test + + + + + <b>How much time do you estimate the authors will need to complete the suggested revisions:</b> + Estimated time to Complete Revisions (Required) + (Decision Recommendation) + + + Between 3 and 6 months + + + + + + diff --git a/tests/resources/meca/no-institution/transfer.xml b/tests/resources/meca/no-institution/transfer.xml new file mode 100644 index 0000000..ab5b8f8 --- /dev/null +++ b/tests/resources/meca/no-institution/transfer.xml @@ -0,0 +1,57 @@ + + + + + + eJournalPress + + + Support + eJournalPress + + + + + + + Review Commons - TEST + reviewcommonstest + + + + + + + + + + + + + + + + + + + + + + + + eLife Test + elifetest + + + + + + + + + + + + + + diff --git a/tests/test_article.py b/tests/test_article.py index 5997b86..9297e81 100644 --- a/tests/test_article.py +++ b/tests/test_article.py @@ -133,9 +133,9 @@ def assertArticlesEqual( ] ARTICLES = { - "no-author-reply": Article( - doi="10.1101/no-author-reply.123.456.7890", - title="An article without author reply.", + "multiple-revision-rounds": Article( + doi="10.1101/multiple-revision-rounds.123.456.7890", + title="An article with multiple revision rounds.", review_process=[ RevisionRound( reviews=[ @@ -143,7 +143,7 @@ def assertArticlesEqual( authors=[], text={ "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Significance (Required)": "Consectetur adipiscing elit.", + "Significance (Required)": "Lorem ipsum dolor sit amet.", }, doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, publication_date=PUBLICATION_DATE, @@ -152,7 +152,7 @@ def assertArticlesEqual( authors=[], text={ "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Significance (Required)": "Sed do eiusmod tempor incididunt ut labore et dolore.", + "Significance (Required)": "Consectetur adipiscing elit.", }, doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, publication_date=PUBLICATION_DATE, @@ -161,13 +161,47 @@ def assertArticlesEqual( authors=[], text={ "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Significance (Required)": "Cras adipiscing enim eu turpis egestas pretium aenean.", + "Significance (Required)": "Sed do eiusmod tempor incididunt ut labore.", }, doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, publication_date=PUBLICATION_DATE, ), ], - author_reply=None, + author_reply=AuthorReply( + authors=[ + Author( + given_name="Jane", + surname="Doe", + orcid=None, + is_corresponding_author=True, + institutions=[ + Institution( + name="EMBL", + department="Medicinal Chemistry", + city="Heidelberg", + country="Germany", + ) + ], + ), + Author( + given_name="John", + surname="Doe", + orcid=None, + is_corresponding_author=False, + institutions=[ + Institution( + name="EMBL", + department="Medicinal Chemistry", + city="Heidelberg", + country="Germany", + ) + ], + ), + ], + text={}, + doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, + publication_date=PUBLICATION_DATE, + ), ), RevisionRound( reviews=[ @@ -186,9 +220,9 @@ def assertArticlesEqual( ), ], ), - "multiple-revision-rounds": Article( - doi="10.1101/multiple-revision-rounds.123.456.7890", - title="An article with multiple revision rounds.", + "no-author-reply": Article( + doi="10.1101/no-author-reply.123.456.7890", + title="An article without author reply.", review_process=[ RevisionRound( reviews=[ @@ -196,7 +230,7 @@ def assertArticlesEqual( authors=[], text={ "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Significance (Required)": "Lorem ipsum dolor sit amet.", + "Significance (Required)": "Consectetur adipiscing elit.", }, doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, publication_date=PUBLICATION_DATE, @@ -205,7 +239,7 @@ def assertArticlesEqual( authors=[], text={ "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Significance (Required)": "Consectetur adipiscing elit.", + "Significance (Required)": "Sed do eiusmod tempor incididunt ut labore et dolore.", }, doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, publication_date=PUBLICATION_DATE, @@ -214,7 +248,52 @@ def assertArticlesEqual( authors=[], text={ "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Significance (Required)": "Sed do eiusmod tempor incididunt ut labore.", + "Significance (Required)": "Cras adipiscing enim eu turpis egestas pretium aenean.", + }, + doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, + publication_date=PUBLICATION_DATE, + ), + ], + author_reply=None, + ), + RevisionRound( + reviews=[ + Review( + authors=[], + text={ + "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", + "Evidence, reproducibility and clarity (Required)": "This is sample of evidence answer", + "Significance (Required)": "This is a sample of significance", + }, + doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, + publication_date=PUBLICATION_DATE, + ), + ], + author_reply=None, + ), + ], + ), + "no-institution": Article( + doi="10.1101/single-revision-round.123.456.7890", + title="An article with a single revision round.", + review_process=[ + RevisionRound( + reviews=[ + Review( + authors=[], + text={ + "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", + "Significance (Required)": "Lorem ipsum dolor sit amet.", + }, + doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, + publication_date=PUBLICATION_DATE, + ), + Review( + authors=[], + text={ + "Estimated time to Complete Revisions (Required)": "Between 3 and 6 months", + "Evidence, reproducibility and clarity (Required)": "Summary: this is a test", + "Significance (Required)": "Signification: also a test", }, doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, publication_date=PUBLICATION_DATE, @@ -225,14 +304,17 @@ def assertArticlesEqual( Author( given_name="Jane", surname="Doe", - orcid=None, + orcid=Orcid( + id="https://orcid.org/0000-0012-3456-7890", + is_authenticated=True, + ), is_corresponding_author=True, institutions=[ Institution( - name="EMBL", - department="Medicinal Chemistry", - city="Heidelberg", - country="Germany", + name="/", + department=None, + city="/", + country="/", ) ], ), @@ -243,10 +325,10 @@ def assertArticlesEqual( is_corresponding_author=False, institutions=[ Institution( - name="EMBL", - department="Medicinal Chemistry", - city="Heidelberg", - country="Germany", + name="/", + department=None, + city="/", + country=None, ) ], ), @@ -256,21 +338,6 @@ def assertArticlesEqual( publication_date=PUBLICATION_DATE, ), ), - RevisionRound( - reviews=[ - Review( - authors=[], - text={ - "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", - "Evidence, reproducibility and clarity (Required)": "This is sample of evidence answer", - "Significance (Required)": "This is a sample of significance", - }, - doi=DOI_FOR_REVIEWS_AND_AUTHOR_REPLIES, - publication_date=PUBLICATION_DATE, - ), - ], - author_reply=None, - ), ], ), "single-revision-round": Article( diff --git a/tests/test_batch.py b/tests/test_batch.py index 9a1a680..1f20bb8 100644 --- a/tests/test_batch.py +++ b/tests/test_batch.py @@ -35,6 +35,7 @@ def setUp(self) -> None: ParsedFile.Valid: [ "multiple-revision-rounds", "no-author-reply", + "no-institution", "single-revision-round", ], } @@ -111,6 +112,7 @@ def setUp(self) -> None: input_files = [ "multiple-revision-rounds", "no-author-reply", + # "no-institution", "single-revision-round", ] parsed_files = [ @@ -234,7 +236,7 @@ def test_depositing_parsed_files( expected_deposition_attempts, actual_deposition_attempts ) self.assertEqual(self.expected_articles, actual_articles) - self.assertEqual(3, len(deposit_file_mock.mock_calls)) + self.assertEqual(len(self.parsed_files), len(deposit_file_mock.mock_calls)) self.assert_deposition_attempts_in_db(expected_deposition_attempts) def test_deposition_fails( @@ -257,7 +259,7 @@ def test_deposition_fails( ) self.assertEqual([], actual_articles) self.assert_deposition_attempts_in_db(expected_deposition_attempts) - self.assertEqual(3, len(deposit_file_mock.mock_calls)) + self.assertEqual(len(self.parsed_files), len(deposit_file_mock.mock_calls)) @patch( "mecadoi.batch.generate_peer_review_deposition", side_effect=Exception("Boom!") diff --git a/tests/test_cli.py b/tests/test_cli.py index 9d18e75..e56be48 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -172,7 +172,7 @@ def test_batch_deposit( self.assert_deposition_attempts_in_db(self.expected_deposition_attempts()) self.assert_articles_in_output_dir(actual_output["id"], self.expected_articles) - self.assertEqual(3, len(deposit_file_mock.mock_calls)) + self.assertEqual(len(self.parsed_files), len(deposit_file_mock.mock_calls)) def test_batch_deposit_retry( self, diff --git a/tests/test_generate_peer_review_deposition.py b/tests/test_generate_peer_review_deposition.py index ad40e0e..1e2bd9f 100644 --- a/tests/test_generate_peer_review_deposition.py +++ b/tests/test_generate_peer_review_deposition.py @@ -11,6 +11,7 @@ def setUp(self) -> None: self.fixtures = [ "multiple-revision-rounds", "no-author-reply", + "no-institution", "single-revision-round", ] self.publication_date = datetime(2020, 10, 10) diff --git a/tests/test_meca.py b/tests/test_meca.py index 28e45a4..c833048 100644 --- a/tests/test_meca.py +++ b/tests/test_meca.py @@ -45,6 +45,123 @@ def assertArticlesEqual( MANUSCRIPTS = { + "no-institution": Manuscript( + authors=[ + Author( + given_name="Jane", + surname="Doe", + orcid=Orcid( + id="https://orcid.org/0000-0012-3456-7890", is_authenticated=True + ), + is_corresponding_author=True, + institutions=[ + Institution( + name="/", + department=None, + city="/", + country="/", + ) + ], + ), + Author( + given_name="John", + surname="Doe", + orcid=None, + is_corresponding_author=False, + institutions=[ + Institution( + name="/", + department=None, + city="/", + country=None, + ) + ], + ), + ], + text={ + "abstract": "This article has a single revision round and thus in ...", + }, + doi="10.12345/single-revision-round.1234567890", + preprint_doi="10.1101/single-revision-round.123.456.7890", + journal="Review Commons - TEST", + review_process=[ + RevisionRound( + revision_id="0", + reviews=[ + Review( + authors=[ + Author( + given_name="", + surname="redacted", + orcid=None, + is_corresponding_author=False, + institutions=[], + ), + ], + text={ + "Estimated time to Complete Revisions (Required)": "Cannot tell / Not applicable", + "Significance (Required)": "Lorem ipsum dolor sit amet.", + }, + running_number="1", + ), + Review( + authors=[ + Author( + given_name="redacted", + surname="redacted", + orcid=None, + is_corresponding_author=False, + institutions=[], + ), + ], + text={ + "Estimated time to Complete Revisions (Required)": "Between 3 and 6 months", + "Evidence, reproducibility and clarity (Required)": "Summary: this is a test", + "Significance (Required)": "Signification: also a test", + }, + running_number="2", + ), + ], + author_reply=AuthorReply( + authors=[ + Author( + given_name="Jane", + surname="Doe", + orcid=Orcid( + id="https://orcid.org/0000-0012-3456-7890", + is_authenticated=True, + ), + is_corresponding_author=True, + institutions=[ + Institution( + name="/", + department=None, + city="/", + country="/", + ) + ], + ), + Author( + given_name="John", + surname="Doe", + orcid=None, + is_corresponding_author=False, + institutions=[ + Institution( + name="/", + department=None, + city="/", + country=None, + ) + ], + ), + ], + text={}, + ), + ), + ], + title="An article with a single revision round.", + ), "no-reviews": Manuscript( authors=[ Author(