Fix/12832 pubmed url import #12839
Fix/12832 pubmed url import #12839
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i'll adjust the needed files for the tests tmrw. |
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I don't understand the failing OpenRewrite test. Can you help me out? @koppor |
Execute ./gradlew rewriteRun and check the diff. Does that work in your side? |
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| @TechReport{, | |||
| doi = {10.1016/j.cpr.2005.02.002}, | |||
| pmid = {22664220}, | |||
| location-id = {https://pubmed.ncbi.nlm.nih.gov/22664220/ [pii]}, | |||
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Simply using 'url' doesn't work because of the 'LID' in the corresponding .txt file. I couldn't find a better solution for this, so maybe it could have just been left out, but this also works.
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should i remove it? @koppor
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It seems like the suffix can be stripped somehow?
Maybe @ryan-carpenter has an idea for this
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I think there might be some misunderstanding. We want the URL of the PubMed record, which is not included in the AID or LID field and does not belong there. Those contain identifiers and locations from the publisher.
Valid URLs can be formed from the PMID and/or PMCID fields (two different URLs), regardless of the data in AID and LID. I'm not sure what the best standard bibtex field is for this. Other databases use the url field, which I think is non-standard.
The suffix [pii] is not important to keep after the PII data is parsed into the correct fields. It's the same as DOI. You don't need to keep [DOI] after moving the data into the doi field.
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how about now? @koppor @Siedlerchr
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@trag-bot didn't find any issues in the code! ✅✨ |
Closes #12832
Description
This PR ensures that when importing from PubMed, the PubMed URL is automatically added to the
URLfield if it is missing.PMID) from the article metadata.URLfield is found, constructs a PubMed URL usinghttps://pubmed.ncbi.nlm.nih.gov/{PMID}/.URLentry is not overwritten.articleIdListonly once.Before:
After:
Mandatory checks
CHANGELOG.mddescribed in a way that is understandable for the average user (if change is visible to the user)