Ecosyste.ms: Issues

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GitHub / titipata/pubmed_parser issues and pull requests

#162 - Extract all affiliations for each author

Pull Request - State: closed - Opened by ZhangWoW123 20 days ago

#161 - Syntax issues when parsing pubmed baseline xml

Issue - State: open - Opened by robinweisenburger 20 days ago
Labels: bug

#159 - Bug 158

Pull Request - State: open - Opened by nils-herrmann 24 days ago

#158 - Can't extract article title from nested XML file

Issue - State: open - Opened by ZhangWoW123 25 days ago - 9 comments
Labels: bug

#157 - Accomodate date-type in parse_date

Pull Request - State: closed - Opened by enjalot about 1 month ago

#155 - #154 Handle missing ppub and collection

Pull Request - State: closed - Opened by nils-herrmann 3 months ago

#154 - Error parsing date

Issue - State: closed - Opened by nils-herrmann 3 months ago
Labels: bug

#152 - [Bug report] No module find error

Issue - State: closed - Opened by jonghyunlee1993 3 months ago - 3 comments
Labels: bug

#151 - AttributeError: 'NoneType' object has no attribute 'getchildren'

Issue - State: open - Opened by qm-intel 3 months ago - 1 comment
Labels: bug

#149 - How to extract the figures' inline mentions from the artcile xml file?

Issue - State: open - Opened by qm-intel 3 months ago - 2 comments
Labels: question

#148 - It couldn't recognize the xml file I downloaded from pubmed

Issue - State: open - Opened by wildwhip 4 months ago - 6 comments
Labels: bug

#147 - Drop all_paragraph from parse_pubmed_paragraph()

Issue - State: closed - Opened by mattyding 4 months ago - 7 comments
Labels: enhancement

#146 - #144 Update action versions and implement checkout of fork for tests

Pull Request - State: closed - Opened by nils-herrmann 5 months ago - 1 comment

#145 - #144 Fix checks

Pull Request - State: closed - Opened by nils-herrmann 5 months ago

#144 - Fix GitHub workflows

Issue - State: closed - Opened by nils-herrmann 5 months ago - 4 comments
Labels: bug

#143 - #110 Parse text inside journal-title nodes.

Pull Request - State: closed - Opened by nils-herrmann 6 months ago

#142 - #119 Modify XPath to retreive tables and references.

Pull Request - State: closed - Opened by nils-herrmann 6 months ago

#141 - #112 Parse epub insed of mix of ppub and epub

Pull Request - State: closed - Opened by nils-herrmann 6 months ago - 2 comments

#140 - Handling of non-ASCII / unicode characters

Issue - State: open - Opened by Michael-E-Rose 6 months ago

#139 - #125 Create exception for empty figures and parse figure sub-points.

Pull Request - State: closed - Opened by nils-herrmann 7 months ago - 1 comment

#138 - Parse `pii` in the web parser

Pull Request - State: closed - Opened by nils-herrmann 7 months ago

#137 - Add `pii` to web parser

Pull Request - State: closed - Opened by nils-herrmann 7 months ago

#135 - Inconsistent PMID and DOI when using parse_xml_web for an XML file.

Issue - State: closed - Opened by JIBSN 7 months ago - 1 comment
Labels: bug

#134 - Parse VersionID and VersionDate

Issue - State: closed - Opened by Michael-E-Rose 8 months ago

#133 - Fix Medline parser tests

Issue - State: closed - Opened by nils-herrmann 8 months ago - 1 comment
Labels: bug

#132 - Up-to-date tests for Medline and PubMed OA parsers

Pull Request - State: closed - Opened by nils-herrmann 8 months ago

#131 - Update tests: Use current data

Issue - State: closed - Opened by nils-herrmann 9 months ago - 2 comments

#130 - #129 Parse language in parse_xml_web()

Pull Request - State: closed - Opened by nils-herrmann 9 months ago - 4 comments

#129 - Parse language in `parse_xml_web()`

Issue - State: closed - Opened by nils-herrmann 9 months ago - 1 comment

#128 - CALL FOR MAINTAINER/CONTRIBUTOR FOR PUBMED_PARSER

Issue - State: open - Opened by titipata about 1 year ago - 7 comments
Labels: enhancement

#127 - Bug report - XML citations from website

Issue - State: open - Opened by chungimungi about 1 year ago - 1 comment
Labels: bug

#126 - ValueError when attempting to parse OA XML

Issue - State: closed - Opened by mazzespazze about 1 year ago - 3 comments
Labels: bug

#125 - parse_pubmed_caption() failing on some papers

Issue - State: closed - Opened by oblodgett over 1 year ago
Labels: bug

#124 - Question: parsing error first line expecting '<' not found

Issue - State: closed - Opened by jjgreen12 over 1 year ago

#123 - question using pp.parese_medline

Issue - State: closed - Opened by scm1210 over 1 year ago - 2 comments
Labels: invalid

#122 - Question: Abstract with Mesh Tag

Issue - State: closed - Opened by shrimonmuke0202 over 1 year ago - 3 comments
Labels: question

#121 - Question for extracting text

Issue - State: closed - Opened by shrimonmuke0202 almost 2 years ago - 1 comment
Labels: question

#120 - turn parse_medline_xml into an iterator to save memory

Pull Request - State: closed - Opened by seandavi almost 2 years ago - 1 comment

#119 - parse_pubmed_table() and parse_pubmed_references() returning None

Issue - State: closed - Opened by octotus over 2 years ago - 1 comment
Labels: bug

#118 - Table parsing issues with parse_pubmed_table

Issue - State: closed - Opened by octotus over 2 years ago - 2 comments
Labels: duplicate

#117 - Add optional parsing of MeSH subheadings

Pull Request - State: closed - Opened by raypereda over 2 years ago - 8 comments

#116 - Fix Nonetype in article_meta

Pull Request - State: closed - Opened by titipata over 2 years ago

#115 - AttributeError: 'NoneType' object has no attribute 'find'

Issue - State: closed - Opened by JIBINJOHNV over 2 years ago - 2 comments

#114 - fix git install link

Pull Request - State: closed - Opened by grivaz over 2 years ago

#112 - physical & electronic publication dates can be mixed into erroneous dates

Issue - State: closed - Opened by ghost almost 3 years ago - 1 comment
Labels: bug

#111 - parse_pubmed_paragraph() function seems to miss some paragraphs sometimes.

Issue - State: open - Opened by zhao-zy15 almost 3 years ago
Labels: bug

#110 - PMC OA: tags in the <journal-title> field break parse_pubmed_xml

Issue - State: closed - Opened by ghost almost 3 years ago - 2 comments
Labels: bug

#109 - All of PubMed XML was updated to follow the MEDLINE XML format.

Issue - State: open - Opened by MattYoon almost 3 years ago
Labels: enhancement

#108 - bug correction for vernacular title extraction

Pull Request - State: closed - Opened by jtourille almost 3 years ago

#106 - add Language and VernacularTitle element extraction

Pull Request - State: closed - Opened by jtourille almost 3 years ago

#105 - Fix syntax error: `not in ""`.

Pull Request - State: closed - Opened by TiansuYu about 3 years ago - 2 comments

#104 - medline_parser has syntax error: `"is not" with a literal`

Issue - State: closed - Opened by TiansuYu about 3 years ago - 1 comment
Labels: bug

#103 - Example of processing in dask rather than pyspark

Issue - State: closed - Opened by charliejeynes about 3 years ago - 2 comments

#102 - fix pubmed_caption [UnboundLocalError: local variable 'graphic_ref' r…

Pull Request - State: closed - Opened by zyi103 about 3 years ago

#101 - Upload package on PyPI

Issue - State: closed - Opened by FrancescoCasalegno over 3 years ago - 3 comments

#100 - Added issue, page number, and firstname to medline_parse_xml()

Pull Request - State: closed - Opened by raypereda-gr over 3 years ago - 1 comment

#99 - Fix error using parse_pubmed_xml() on current pubmed XML file

Pull Request - State: closed - Opened by raypereda over 3 years ago - 1 comment

#98 - Fixing SyntaxError in issue #49

Pull Request - State: closed - Opened by zyi103 over 3 years ago

#97 - Extracting sections at a time rather than paragraphs

Issue - State: closed - Opened by krishxmatta over 3 years ago - 1 comment

#96 - Question about Original XML

Issue - State: closed - Opened by dsdoermann almost 4 years ago - 3 comments
Labels: question

#95 - Error using parse_pubmed_xml

Issue - State: open - Opened by sublimotion about 4 years ago - 5 comments
Labels: bug, help wanted

#94 - copyedits to README.md

Pull Request - State: closed - Opened by Daniel-Mietchen about 4 years ago - 1 comment

#93 - some copyedits to CONTRIBUTING.md

Pull Request - State: closed - Opened by Daniel-Mietchen about 4 years ago - 1 comment

#92 - Fix: Improved serialzation

Pull Request - State: closed - Opened by JovanVeljanoski about 4 years ago

#91 - ModuleNotFoundError: No module named 'pubmed_parser'

Issue - State: closed - Opened by alonasorochynska over 4 years ago - 3 comments
Labels: invalid

#90 - [pubmed oa] Parse conflict of interest statements

Pull Request - State: closed - Opened by simonwoerpel over 4 years ago - 10 comments

#89 - Fix subjects xpath in parse_pubmed_xml. Fixes #87

Pull Request - State: closed - Opened by thomascpan over 4 years ago

#88 - Fix subjects xpath in parse_pubmed_xml. Fixes #76

Pull Request - State: closed - Opened by thomascpan over 4 years ago

#87 - parse_pubmed_xml does not return "subjects"

Issue - State: closed - Opened by thomascpan over 4 years ago
Labels: bug

#86 - Reference fixes

Pull Request - State: closed - Opened by kthyng almost 5 years ago - 1 comment

#85 - Fix for one final pmid.text.strip().

Pull Request - State: closed - Opened by patrusso2 almost 5 years ago - 1 comment

#84 - Minor edits - JOSS pre-publication

Pull Request - State: closed - Opened by majensen almost 5 years ago - 2 comments

#83 - Handle field.text being None

Pull Request - State: closed - Opened by patrusso2 almost 5 years ago - 1 comment

#82 - Missing details in API docs

Issue - State: closed - Opened by tleonardi almost 5 years ago - 1 comment

#81 - Fixed in-text citation to Tang et al.

Pull Request - State: closed - Opened by tleonardi almost 5 years ago - 1 comment

#80 - Create test function for Pubmed Parser

Issue - State: closed - Opened by titipata almost 5 years ago - 3 comments
Labels: enhancement, feature request

#79 - Contributing guidelines are missing

Issue - State: closed - Opened by tleonardi almost 5 years ago - 3 comments

#78 - Various changes/fixes

Pull Request - State: closed - Opened by tleonardi almost 5 years ago - 2 comments

#77 - JOSS paper text

Issue - State: closed - Opened by tleonardi almost 5 years ago - 2 comments

#76 - Missing dependencies

Issue - State: closed - Opened by tleonardi almost 5 years ago - 1 comment
Labels: bug

#75 - SyntaxWarning raised during import

Issue - State: closed - Opened by tleonardi almost 5 years ago - 2 comments
Labels: bug

#74 - Question about downloading PubMed OA figures

Issue - State: closed - Opened by pidugusundeep almost 5 years ago - 6 comments
Labels: enhancement

#73 - fixed bugs where methods were being called on NoneType objects

Pull Request - State: closed - Opened by nicford almost 5 years ago - 1 comment

#72 - Add community guideline

Issue - State: closed - Opened by titipata almost 5 years ago - 1 comment
Labels: enhancement

#71 - JOSS submission

Pull Request - State: closed - Opened by titipata almost 5 years ago

#70 - Update README, place holder for JOSS submission

Pull Request - State: closed - Opened by titipata almost 5 years ago - 1 comment

#69 - Allow parsing DOI/PMID from PubmedData/ArticleIdList

Pull Request - State: closed - Opened by titipata about 5 years ago

#68 - Parsing DOI Medline XML

Issue - State: closed - Opened by sakrifor about 5 years ago - 7 comments
Labels: enhancement, help wanted

#67 - change parse_name_df to parse_affil_df

Pull Request - State: closed - Opened by tanganyao about 5 years ago

#66 - XMLSyntaxError

Issue - State: closed - Opened by musiccccc over 5 years ago

#65 - pip3 install wget

Issue - State: closed - Opened by 0BN0 over 5 years ago - 2 comments

#64 - medline xml equivalent for "parse_pubmed_references"?

Issue - State: closed - Opened by huminpurin over 5 years ago - 10 comments
Labels: enhancement

#63 - Revert paragraphs xpath change

Pull Request - State: closed - Opened by kjhenner almost 6 years ago