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add Cleanup for copying over physcial review article id as the page n… #7025

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merged 11 commits into from
Oct 20, 2020
Merged

add Cleanup for copying over physcial review article id as the page n… #7025

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c9b5284
add Cleanup for copying over physcial review article id as the page n…
tmrd993 Oct 18, 2020
3856f25
remove PageFieldCleanup, add private methods to DoiFetcher
tmrd993 Oct 19, 2020
342cacb
remove comment from DoiFetcherTest
tmrd993 Oct 19, 2020
e69989a
replace regex with substring and string comparison
tmrd993 Oct 19, 2020
1779e42
fix checkstyle issues
tmrd993 Oct 19, 2020
3704269
fix checkstyle issues
tmrd993 Oct 19, 2020
1853df7
add regex to check aps doi format
tmrd993 Oct 20, 2020
983962f
move suffix pattern to private static field
tmrd993 Oct 20, 2020
a1fe707
add changelog entry
tmrd993 Oct 20, 2020
593c86d
add issue link to changelog entry
tmrd993 Oct 20, 2020
a1fdf3e
Merge branch 'master' into add-cleanup-for-replacing-page-number-with…
tmrd993 Oct 20, 2020
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34 changes: 34 additions & 0 deletions src/main/java/org/jabref/logic/cleanup/PageFieldCleanup.java
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@@ -0,0 +1,34 @@
package org.jabref.logic.cleanup;

import java.util.ArrayList;
import java.util.List;
import java.util.Optional;

import org.jabref.model.FieldChange;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.StandardField;

/**
* adds the article ID of a journal as the page count, but only if the page field is empty
*/
public class PageFieldCleanup implements CleanupJob {
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Since this is only used for the DOI fetcher, I would suggest to add this functionality as a private class method in DoiFetcher instead of a new class.


@Override
public List<FieldChange> cleanup(BibEntry entry) {
List<FieldChange> changes = new ArrayList<>();
Optional<String> doiAsString = entry.getField(StandardField.DOI);

if (doiAsString.isPresent() && !entry.hasField(StandardField.PAGES)) {
String articleId = new String();
int index = doiAsString.get().length() - 1;
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I would simply use a substring with lastIndexOf(.) to the the part after the last dot.
https://docs.oracle.com/en/java/javase/14/docs/api/java.base/java/lang/String.html#lastIndexOf(java.lang.String)

while (Character.isDigit(doiAsString.get().charAt(index))) {
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Since this issue only concerns articles from Physical Review, I would suggest to use a regex based on the format outlined in #7019 (comment). In particular, make sure it only applies to doi's to Physical Review, and not all dois ending on some number.

articleId = doiAsString.get().charAt(index--) + articleId;
}
entry.setField(StandardField.PAGES, articleId);
FieldChange change = new FieldChange(entry, StandardField.PAGES, "", articleId);
changes.add(change);
}

return changes;
}
}
2 changes: 2 additions & 0 deletions src/main/java/org/jabref/logic/importer/fetcher/DoiFetcher.java
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Expand Up @@ -7,6 +7,7 @@
import java.util.Optional;

import org.jabref.logic.cleanup.FieldFormatterCleanup;
import org.jabref.logic.cleanup.PageFieldCleanup;
import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
import org.jabref.logic.formatter.bibtexfields.NormalizePagesFormatter;
import org.jabref.logic.help.HelpFile;
Expand Down Expand Up @@ -89,6 +90,7 @@ public Optional<BibEntry> performSearchById(String identifier) throws FetcherExc
}

private void doPostCleanup(BibEntry entry) {
new PageFieldCleanup().cleanup(entry);
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This is not a good idea to put it here, because it would be called for every type of DOI, and the APS are only a very specific subset.
I would suggest adding it as a CleanupPreset Step:
https://github.com/JabRef/jabref/blob/1b35f8cb0040fdfb515974e78532598f07e11af2/src/main/java/org/jabref/logic/cleanup/CleanupPreset.java

and also adding it to the Cleanup Dialog maybe as Move article id to pages? (APS).

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I do think it's the right place, the DOI fetcher is not returning the right/full information, so we improve this here. Of course, you are right and the extraction should only be applied for DOI's from APS (see my comment above).

new FieldFormatterCleanup(StandardField.PAGES, new NormalizePagesFormatter()).cleanup(entry);
new FieldFormatterCleanup(StandardField.URL, new ClearFormatter()).cleanup(entry);
}
Expand Down