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Elsevier prep.20240417 #103

Merged
merged 10 commits into from May 2, 2024
Merged

Elsevier prep.20240417 #103

merged 10 commits into from May 2, 2024

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seasidesparrow
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  • Unit test cleanup + additional tests
  • Adjustments to Elsevier parsing for mathml handling, nested author-group and affil handling

@seasidesparrow
Adds msup tag to allowed MathML in base.py
524b613 
 	modified:   adsingestp/parsers/base.py
@seasidesparrow
Uniform test output jsons (indent, sort_keys)
711ec36 
	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/crossref_10.1002_1521-3994.json
	modified:   tests/stubdata/output/crossref_10.1103_PhysRevD_64-117303.json
	modified:   tests/stubdata/output/crossref_10.1146_annurev.energy.25.1.441.json
	modified:   tests/stubdata/output/crossref_10.3137_a0410105.json
	modified:   tests/stubdata/output/crossref_10.3847_2041-8213.json
	modified:   tests/stubdata/output/crossref_book_10.1007-978-1-4614-3520-4.json
	modified:   tests/stubdata/output/crossref_book_10.1017-CBO9780511709265.json
	modified:   tests/stubdata/output/crossref_cn_10.1051=0004-6361=202243540.json
	modified:   tests/stubdata/output/crossref_cn_10.1088=1475-7516=2022=10=098.json
	modified:   tests/stubdata/output/crossref_cn_10.1093=mnras=stac2975.json
	modified:   tests/stubdata/output/crossref_cn_10.1093=pasj=psac053.json
	modified:   tests/stubdata/output/crossref_cn_10.3847=1538-4357=ac8c2f.json
	modified:   tests/stubdata/output/crossref_conf_10.1049-cp.2010.1342.json
	modified:   tests/stubdata/output/crossref_conf_10.1109-MWSYM.2013.6697399.json
	modified:   tests/stubdata/output/crossref_preprint_10.1002-essoar.10508651.1.json
	modified:   tests/stubdata/output/crossref_preprint_10.1002-essoar.10511074.2.json
	modified:   tests/stubdata/output/crossref_preprint_10.31223-X55K7G.json
	modified:   tests/stubdata/output/crossref_preprint_10.31223-X5FW25.json
	modified:   tests/stubdata/output/crossref_preprint_10.31223-X5WD2C.json
	modified:   tests/stubdata/output/datacite_schema3.1_example-full.json
	modified:   tests/stubdata/output/datacite_schema4.1_example-full.json
	modified:   tests/stubdata/output/datacite_schema4.1_example-software.json
	modified:   tests/stubdata/output/datacite_schema4_example-habanero-pdsdataset.json
	modified:   tests/stubdata/output/els_missing_keywords_tag.json
	modified:   tests/stubdata/output/jats_a+a_multiparagraph_abstract.json
	modified:   tests/stubdata/output/jats_a+a_subtitle.json
	modified:   tests/stubdata/output/jats_aip_aipc_2470_040010.json
	modified:   tests/stubdata/output/jats_aip_amjph_90_286.json
	modified:   tests/stubdata/output/jats_aj_158_4_139.json
	modified:   tests/stubdata/output/jats_aj_158_4_139_fulltext.json
	modified:   tests/stubdata/output/jats_aj_158_4_139_fulltext_tags.json
	modified:   tests/stubdata/output/jats_iop_aj_162_1.json
	modified:   tests/stubdata/output/jats_iop_ansnn_12_2_025001.json
	modified:   tests/stubdata/output/jats_iop_apj_923_1_47.json
	modified:   tests/stubdata/output/jats_iop_no_contribs.json
	modified:   tests/stubdata/output/jats_iop_no_orcid_tag.json
	modified:   tests/stubdata/output/jats_iop_preprint_in_record.json
	modified:   tests/stubdata/output/jats_mnras_493_1_141.json
	modified:   tests/stubdata/output/jats_phrvd_106_023001.json
	modified:   tests/stubdata/output/jats_pnas_1715554115.json
	modified:   tests/stubdata/output/jats_spie_opten_1.OE.62.4.048103.json
	modified:   tests/stubdata/output/jats_spie_opten_1.OE.62.4.066101.json
	modified:   tests/stubdata/output/jats_spie_spie_12.2690579.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_NatCo_s41467-023-40272-3.json
	modified:   tests/stubdata/output/jats_springer_Natur_s41598-023-38673-x.json
	modified:   tests/stubdata/output/jats_springer_ZaMP_s00033-023-02064-z.json
	modified:   tests/stubdata/output/wiley_jgra_12057.json
	modified:   tests/stubdata/output/wiley_jgra_57392.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
	modified:   tests/stubdata/output/zenodo_test.json
	modified:   tests/stubdata/output/zenodo_test2.json
	modified:   tests/stubdata/output/zenodo_test3.json
	modified:   tests/stubdata/output/zenodo_test4.json
@seasidesparrow
Added more mathml tags, updated unit test output
f7fa30a 
 	modified:   adsingestp/parsers/base.py
 	modified:   tests/stubdata/output/els_detag_example_2.json
 	modified:   tests/stubdata/output/jats_springer_EPJC_s10052-023-11699-1.json
 	modified:   tests/stubdata/output/jats_springer_JHEP_JHEP07_2023_200.json
 	modified:   tests/stubdata/output/jats_springer_ZaMP_s00033-023-02064-z.json
 	modified:   tests/test_elsevier.py
@seasidesparrow
Adding untested cases to tests with stubdata
03fb9ba 
 	new file:   tests/stubdata/output/jats_aps_phrvd_100_052015.json
 	new file:   tests/stubdata/output/jats_aps_phrvx_12_021031.json
 	new file:   tests/stubdata/output/jats_edp_aa_661_70.json
 	new file:   tests/stubdata/output/jats_edp_jnwpu_40_96.json
 	new file:   tests/stubdata/output/jats_iop_jinst_17_05_P05009.json
 	new file:   tests/stubdata/output/jats_nature_natsd_12_7375.json
 	new file:   tests/stubdata/output/jats_pnas_119_2201344119.json
 	new file:   tests/stubdata/output/jats_springer_cldy_84_1543.json
 	new file:   tests/stubdata/output/jats_springer_jhep_2022_05_05.json
 	new file:   tests/stubdata/output/mdpi_climate-11-00147.json
 	new file:   tests/stubdata/output/mdpi_galaxies-11-00090.json
 	new file:   tests/stubdata/output/mdpi_symmetry-15-00939.json
 	new file:   tests/stubdata/output/mdpi_universe-08-00651.json
 	new file:   tests/stubdata/output/nlm_tf_gapfd_116_38.json
 	modified:   tests/test_elsevier.py
 	modified:   tests/test_jats.py
@seasidesparrow
Removing commented-out logging blocks from tests
4f6e7bc 
 	modified:   tests/test_datacite.py
 	modified:   tests/test_wiley.py
@seasidesparrow
Fix for elsevier with nested author groups
918b718 
 	modified:   adsingestp/parsers/elsevier.py
 	new file:   tests/stubdata/input/els_phlb_compound_affil.xml
 	new file:   tests/stubdata/output/els_phlb_compound_affil.json
 	modified:   tests/test_elsevier.py
@seasidesparrow
Affs need to have all sources, not one or the other
8e8759e 
 	modified:   adsingestp/parsers/elsevier.py
@seasidesparrow
Mod correctly captures affils for other test cases
db22840 
 	modified:   adsingestp/parsers/elsevier.py
 	modified:   tests/stubdata/input/els_phlb_compound_affil.xml
 	modified:   tests/stubdata/output/els_book_review.json
 	modified:   tests/stubdata/output/els_phlb_compound_affil.json
 	modified:   tests/stubdata/output/els_simple_article_3.json
 	modified:   tests/stubdata/output/els_simple_article_4.json
@seasidesparrow
Case of coverDisplayDate of "month1-month2 year"
a27c5a7 
 	modified:   adsingestp/parsers/elsevier.py
 	new file:   tests/stubdata/input/els_odd_cover_date.xml
 	new file:   tests/stubdata/output/els_odd_cover_date.json
 	modified:   tests/test_elsevier.py
@seasidesparrow
Fix linter issue
06d2394 
 	modified:   tests/stubdata/input/els_odd_cover_date.xml
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Codecov Report

Attention: Patch coverage is 88.23529% with 10 lines in your changes are missing coverage. Please review.

Project coverage is 90.58%. Comparing base (ca0a121) to head (06d2394).
Report is 1 commits behind head on main.

Files Patch % Lines
adsingestp/parsers/elsevier.py 88.23% 10 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #103      +/-   ##
==========================================
+ Coverage   90.44%   90.58%   +0.13%     
==========================================
  Files          25       25              
  Lines        2627     2687      +60     
==========================================
+ Hits         2376     2434      +58     
- Misses        251      253       +2

☔ View full report in Codecov by Sentry.
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mugdhapolimera
mugdhapolimera approved these changes May 2, 2024
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Everything looks good to me!

@mugdhapolimera
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Feel free to merge at your convenience

@seasidesparrow seasidesparrow merged commit ed5f9a1 into adsabs:main May 2, 2024
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@seasidesparrow seasidesparrow deleted the elsevier_prep.20240417 branch May 3, 2024 16:44
@seasidesparrow seasidesparrow mentioned this pull request May 3, 2024
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@mugdhapolimera mugdhapolimera mugdhapolimera approved these changes

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