Multiple bugfixes and changes by seasidesparrow · Pull Request #178 · adsabs/ADSIngestParser

seasidesparrow · 2025-07-16T17:16:23Z

Adds support for name prefixes (e.g. Dr.) and suffixes (e.g. Jr.) [Fixes JATS and other parsers need to capture <prefix> and <suffix> from contributor names #177]
Fixes bug to catch and suppress malformed ORCiDs in publisher XML [Fixes JATS parser fails with uncaught exception when author ORCID is malformed #174]
Adds additional XML sources to output loadFormat in place of OtherXML
Date handling improvements
Collab handling improvements

commit b9ef70f Merge: 3bdd018 dbe6c27 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Wed May 7 07:20:52 2025 -0400 Merge branch 'main' of github.com:adsabs/ADSIngestParser into add_formats.20250225 commit 3bdd018 Merge: 5a81acc f0a2725 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Wed Apr 30 12:23:08 2025 -0400 Merge branch 'main' of github.com:adsabs/ADSIngestParser into add_formats.20250225 commit 5a81acc Merge: 0863f5a db1b3f6 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Fri Mar 7 10:27:22 2025 -0500 Merge branch 'main' of github.com:adsabs/ADSIngestParser into add_formats.20250225 commit 0863f5a Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Tue Feb 25 13:30:43 2025 -0500 Modified output formats modified: adsingestp/parsers/base.py modified: adsingestp/parsers/copernicus.py modified: adsingestp/parsers/elsevier.py modified: adsingestp/parsers/ieee.py modified: adsingestp/parsers/wiley.py modified: adsingestp/parsers/base.py modified: adsingestp/parsers/copernicus.py modified: adsingestp/parsers/elsevier.py modified: adsingestp/parsers/ieee.py modified: adsingestp/parsers/wiley.py

commit 6082397 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Wed Jul 16 10:29:20 2025 -0400 test for malformed orcid fix + pre-commit modified: adsingestp/parsers/base.py deleted: adsingestp/parsers/bits.py modified: adsingestp/parsers/jats.py new file: tests/stubdata/input/jats_iop_malformed_orcid.xml modified: tests/stubdata/input/jats_sage_epubppub_date.xml new file: tests/stubdata/output/jats_iop_malformed_orcid.json modified: tests/test_jats.py commit 0fbf136 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Wed Jul 16 09:58:38 2025 -0400 ignore malformed orcids modified: adsingestp/parsers/jats.py commit fbfa826 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Wed Jul 16 09:04:02 2025 -0400 updated jats tests for prefix/suffix mod modified: adsingestp/parsers/jats.py new file: tests/stubdata/input/jats_sci_fix_collab_duplication.xml modified: tests/stubdata/output/jats_pnas_1715554115.json new file: tests/stubdata/output/jats_sci_fix_collab_duplication.json modified: tests/stubdata/output/jats_springer_EPJC_s10052-023-11699-1.json modified: tests/stubdata/output/jats_springer_EPJC_s10052-023-11733-2.json modified: tests/stubdata/output/jats_springer_jhep_2022_05_05.json modified: tests/test_jats.py commit 1c2d6b1 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Tue Jul 15 12:52:15 2025 -0400 fix for "epub-ppub" pubdate modified: adsingestp/parsers/jats.py renamed: jats_aps_fix_collab_failure.xml -> tests/stubdata/input/jats_aps_fix_collab_failure.xml new file: tests/stubdata/input/jats_sage_epubppub_date.xml renamed: jats_aps_fix_collab_failure.json -> tests/stubdata/output/jats_aps_fix_collab_failure.json new file: tests/stubdata/output/jats_sage_epubppub_date.json modified: tests/test_jats.py commit b9f14c8 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Tue Jul 15 10:12:46 2025 -0400 fix for "epub-ppub" date-type modified: adsingestp/parsers/jats.py new file: jats_aps_fix_collab_failure.json new file: jats_aps_fix_collab_failure.xml commit 5c997ad Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Wed Jun 11 15:24:39 2025 -0400 ignore alternative names tagged as "western" modified: adsingestp/parsers/jats.py new file: tests/stubdata/input/ieee_jats_omit_western_name_alternatives.xml new file: tests/stubdata/output/ieee_jats_omit_western_name_alternatives.json modified: tests/test_jats.py commit 0ac41ce Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Tue Jun 10 13:07:13 2025 -0400 otherDate is an array of dicts, take the zeroth modified: adsingestp/parsers/base.py commit 65a7015 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Tue Jun 10 12:56:37 2025 -0400 bugfix modified: adsingestp/parsers/base.py commit ea04803 Author: Matthew Templeton <matthew.templeton@cfa.harvard.edu> Date: Tue Jun 10 12:52:00 2025 -0400 otherDate can also provide the pubyear modified: adsingestp/parsers/base.py modified: adsingestp/parsers/base.py modified: adsingestp/parsers/jats.py new file: tests/stubdata/input/ieee_jats_omit_western_name_alternatives.xml new file: tests/stubdata/input/jats_aps_fix_collab_failure.xml new file: tests/stubdata/input/jats_iop_malformed_orcid.xml new file: tests/stubdata/input/jats_sage_epubppub_date.xml new file: tests/stubdata/input/jats_sci_fix_collab_duplication.xml new file: tests/stubdata/output/ieee_jats_omit_western_name_alternatives.json new file: tests/stubdata/output/jats_aps_fix_collab_failure.json new file: tests/stubdata/output/jats_iop_malformed_orcid.json modified: tests/stubdata/output/jats_pnas_1715554115.json new file: tests/stubdata/output/jats_sage_epubppub_date.json new file: tests/stubdata/output/jats_sci_fix_collab_duplication.json modified: tests/stubdata/output/jats_springer_EPJC_s10052-023-11699-1.json modified: tests/stubdata/output/jats_springer_EPJC_s10052-023-11733-2.json modified: tests/stubdata/output/jats_springer_jhep_2022_05_05.json modified: tests/test_jats.py

modified: adsingestp/parsers/base.py modified: tests/stubdata/input/jats_iop_malformed_orcid.xml

modified: tests/stubdata/output/copernicus_ESSD_essd-15-3075-2023.json modified: tests/stubdata/output/copernicus_GeChr_gchron-5-323-2023.json modified: tests/stubdata/output/copernicus_ISPAn_isprs-annals-X-M-1-2023-237-2023.json modified: tests/stubdata/output/copernicus_ISPAr_isprs-archives-XLVIII-M-2-2023-721-2023.json modified: tests/stubdata/output/copernicus_wes-8-1625-2023.json modified: tests/stubdata/output/els_abstract_author_1.json modified: tests/stubdata/output/els_apss_586_152807.json modified: tests/stubdata/output/els_book_chapter.json modified: tests/stubdata/output/els_book_review.json modified: tests/stubdata/output/els_converted_article.json modified: tests/stubdata/output/els_detag_example_1.json modified: tests/stubdata/output/els_detag_example_2.json modified: tests/stubdata/output/els_icar_382_115019.json modified: tests/stubdata/output/els_list.json modified: tests/stubdata/output/els_missing_keywords_tag.json modified: tests/stubdata/output/els_mononym.json modified: tests/stubdata/output/els_odd_cover_date.json modified: tests/stubdata/output/els_other_ref.json modified: tests/stubdata/output/els_phlb_compound_affil.json modified: tests/stubdata/output/els_roman_num_1.json modified: tests/stubdata/output/els_roman_num_2.json modified: tests/stubdata/output/els_simple_article_1.json modified: tests/stubdata/output/els_simple_article_2.json modified: tests/stubdata/output/els_simple_article_3.json modified: tests/stubdata/output/els_simple_article_4.json modified: tests/stubdata/output/els_simple_article_5.json modified: tests/stubdata/output/els_tex_title_1.json modified: tests/stubdata/output/ieee_example_1.json modified: tests/stubdata/output/ieee_example_2.json modified: tests/stubdata/output/wiley_jgra_12057.json modified: tests/stubdata/output/wiley_jgra_57392.json modified: tests/stubdata/output/wiley_jgra_58674.json modified: tests/stubdata/output/wiley_missing_open_attr.json modified: tests/stubdata/output/wiley_subsup_1.json modified: tests/stubdata/output/wiley_subsup_2.json modified: tests/stubdata/output/wiley_swe_21103.json modified: tests/stubdata/output/wiley_swe_461.json modified: tests/stubdata/output/wiley_swe_539.json

codecov-commenter · 2025-07-16T17:18:08Z

Codecov Report

Attention: Patch coverage is 96.77419% with 1 line in your changes missing coverage. Please review.

Project coverage is 91.47%. Comparing base (dbe6c27) to head (7f1b0b9).

Files with missing lines	Patch %	Lines
adsingestp/parsers/jats.py	96.15%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #178      +/-   ##
==========================================
+ Coverage   91.45%   91.47%   +0.01%     
==========================================
  Files          27       27              
  Lines        3206     3224      +18     
==========================================
+ Hits         2932     2949      +17     
- Misses        274      275       +1

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seasidesparrow added 4 commits July 16, 2025 12:30

pre-commit updates

9210343

modified: adsingestp/parsers/base.py modified: tests/stubdata/input/jats_iop_malformed_orcid.xml

ehenneken self-requested a review July 17, 2025 14:25

ehenneken approved these changes Jul 17, 2025

View reviewed changes

seasidesparrow merged commit 6770d18 into adsabs:main Jul 17, 2025
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seasidesparrow deleted the multi_20250716 branch July 21, 2025 11:28

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Multiple bugfixes and changes#178

Multiple bugfixes and changes#178
seasidesparrow merged 4 commits intoadsabs:mainfrom
seasidesparrow:multi_20250716

seasidesparrow commented Jul 16, 2025

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seasidesparrow commented Jul 16, 2025

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