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Honor user-selected keyword delimiter in MedlinePlainImporter.java #11413

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ryan-carpenter opened this issue Jun 22, 2024 · 2 comments · Fixed by #11414
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Honor user-selected keyword delimiter in MedlinePlainImporter.java #11413

ryan-carpenter opened this issue Jun 22, 2024 · 2 comments · Fixed by #11414
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[outdated] type: bug Confirmed bugs or reports that are very likely to be bugs

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@ryan-carpenter
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Is your suggestion for improvement related to a problem? Please describe.
Jabref inserts commas between keywords imported from PubMed files, even if the user has specified another delimiter in File > Preferences > Entries. This is a problem with PubMed files, because Medline's subject headings (MeSH terms) include commas that should not be interpreted as delimiters.

Describe the solution you'd like
If the user has specified a non-default delimiter in settings and has designated the keywords field as one of the affected fields, then the importer should apply the specified delimiter instead of always using commas as the delimiter.

Additional context
See examples and additional description here: https://discourse.jabref.org/t/preserve-pubmed-subject-headings-on-import/4362/2. That discussion is about improving the usability of imported keywords. This GitHub issue only concerns the incorrect parsing of keywords due to the presence of commas in the source data.

This problem does not apply to PubMed records retrieved through JabRef's Web Search functionality. In this case, Jabref applies the user-specified delimiter, allowing correct parsing of the imported keywords.

https://github.com/JabRef/jabref/blob/af73e4e78985eefa7d0fb94c472a99a00c323d8d/src/main/java/org/jabref/logic/importer/fileformat/MedlinePlainImporter.java#L185C5-L192C1

@Siedlerchr Siedlerchr added the [outdated] type: bug Confirmed bugs or reports that are very likely to be bugs label Jun 22, 2024
@github-project-automation github-project-automation bot moved this to Normal priority in Prioritization Jun 22, 2024
Siedlerchr added a commit that referenced this issue Jun 22, 2024
adjust code with intellij suggestions

Fixes #11413
@Siedlerchr
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Thanks for creating that issue, I was about to create one based on your reporting as well :)
It was just a quick fix: (includes the importer module issues fixes as well)
https://builds.jabref.org/pull/11414/merge

@ryan-carpenter
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It was just a quick fix: (includes the importer module issues fixes as well) https://builds.jabref.org/pull/11414/merge

Ah, but what an improvement! Thanks.

github-merge-queue bot pushed a commit that referenced this issue Jun 24, 2024
* Fix dependendency issues with commons logging

update gemfx
update unirest to 4.x

* try again with logging module stuff

* remove commons logging from merged module agian

* fix transitive circular dep stuff

* cleanup , fix urls

* remove imports

* reset config

* fix keyword separator not respected in Medline importer

adjust code with intellij suggestions

Fixes #11413
@github-project-automation github-project-automation bot moved this from Normal priority to Done in Prioritization Jun 24, 2024
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