titipata pubmed_parser issues

titipata / pubmed_parser

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

http://titipata.github.io/pubmed_parser/

MIT License

559 stars 164 forks source link

issues

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#144 Update action versions and implement checkout of fork for tests

#146 nils-herrmann closed 2 weeks ago
1
#144 Fix checks

#145 nils-herrmann closed 3 weeks ago
0
Fix GitHub workflows

#144 nils-herrmann opened 3 weeks ago
3
#110 Parse text inside journal-title nodes.

#143 nils-herrmann closed 1 month ago
0
#119 Modify XPath to retreive tables and references.

#142 nils-herrmann closed 1 month ago
0
#112 Parse epub insed of mix of ppub and epub

#141 nils-herrmann opened 1 month ago
2
Handling of non-ASCII / unicode characters

#140 Michael-E-Rose opened 1 month ago
0
#125 Create exception for empty figures and parse figure sub-points.

#139 nils-herrmann closed 1 month ago
1
Parse `pii` in the web parser

#138 nils-herrmann closed 2 months ago
0
Add `pii` to web parser

#137 nils-herrmann closed 2 months ago
0
#135 Fix: Use doi from`ELocationID` insted of `ArticleIdList\\ArticleId`

#136 nils-herrmann closed 2 months ago
0
Inconsistent PMID and DOI when using parse_xml_web for an XML file.

#135 JIBSN closed 2 months ago
1
Parse VersionID and VersionDate

#134 Michael-E-Rose opened 3 months ago
0
Fix Medline parser tests

#133 nils-herrmann opened 3 months ago
0
Up-to-date tests for Medline and PubMed OA parsers

#132 nils-herrmann closed 2 months ago
0
Update tests: Use current data

#131 nils-herrmann opened 3 months ago
0
#129 Parse language in parse_xml_web()

#130 nils-herrmann closed 4 months ago
4
Parse language in `parse_xml_web()`

#129 nils-herrmann closed 4 months ago
1
CALL FOR MAINTAINER/CONTRIBUTOR FOR PUBMED_PARSER

#128 titipata opened 8 months ago
7
Bug report - XML citations from website

#127 chungimungi opened 8 months ago
1
ValueError when attempting to parse OA XML

#126 mazzespazze closed 4 months ago
3
parse_pubmed_caption() failing on some papers

#125 oblodgett closed 1 month ago
0
Question: parsing error first line expecting '<' not found

#124 jjgreen12 closed 1 year ago
0
question using pp.parese_medline

#123 scm1210 closed 1 month ago
2
Question: Abstract with Mesh Tag

#122 shrimonmuke0202 closed 1 month ago
3
Question for extracting text

#121 shrimonmuke0202 closed 4 months ago
1
turn parse_medline_xml into an iterator to save memory

#120 seandavi closed 1 year ago
1
parse_pubmed_table() and parse_pubmed_references() returning None

#119 octotus closed 1 month ago
1
Table parsing issues with parse_pubmed_table

#118 octotus closed 1 month ago
2
Add optional parsing of MeSH subheadings

#117 raypereda closed 2 years ago
8
Fix Nonetype in article_meta

#116 titipata closed 2 years ago
0
AttributeError: 'NoneType' object has no attribute 'find'

#115 JIBINJOHNV closed 2 years ago
2
fix git install link

#114 grivaz closed 2 years ago
0
Error: parse_medline_xml() is unable to parse the file even though the provided path is correct

#113 srishti-git1110 closed 2 years ago
11
physical & electronic publication dates can be mixed into erroneous dates

#112 ghost opened 2 years ago
1
parse_pubmed_paragraph() function seems to miss some paragraphs sometimes.

#111 zhao-zy15 opened 2 years ago
0
PMC OA: tags in the <journal-title> field break parse_pubmed_xml

#110 ghost closed 1 month ago
2
All of PubMed XML was updated to follow the MEDLINE XML format.

#109 MattYoon opened 2 years ago
0
bug correction for vernacular title extraction

#108 jtourille closed 2 years ago
0
Is there a reason why PubMed/MEDLINE extracted list elements are joined with ";" instead of keeping them as lists ?

#107 jtourille closed 1 month ago
2
add Language and VernacularTitle element extraction

#106 jtourille closed 2 years ago
0
Fix syntax error: `not in ""`.

#105 TiansuYu closed 2 years ago
2
medline_parser has syntax error: `"is not" with a literal`

#104 TiansuYu closed 2 years ago
1
Example of processing in dask rather than pyspark

#103 charliejeynes closed 2 years ago
2
fix pubmed_caption [UnboundLocalError: local variable 'graphic_ref' r…

#102 jimzijun closed 2 years ago
0
Upload package on PyPI

#101 FrancescoCasalegno closed 2 years ago
3
Added issue, page number, and firstname to medline_parse_xml()

#100 raypereda-gr closed 3 years ago
1
Fix error using parse_pubmed_xml() on current pubmed XML file

#99 raypereda closed 3 years ago
1
Fixing SyntaxError in issue #49

#98 jimzijun closed 3 years ago
0
Extracting sections at a time rather than paragraphs

#97 krishmatta closed 3 years ago
1