Export for academicpages 12727#15262
Merged
Siedlerchr merged 37 commits intoMar 16, 2026
Merged
Conversation
Contributor
Review Summary by QodoAdd academicpages export format for JabRef
WalkthroughsDescription• Implements new academicpages Jekyll template export format • Generates individual Markdown files with YAML front matter per entry • Automatically copies attached PDFs and creates .bib files • Sorts entries by type and generates IEEE-style citations Diagramflowchart LR
BibEntry["BibEntry"] -->|"extract metadata"| Markdown["Markdown File<br/>with YAML Front Matter"]
BibEntry -->|"copy PDF"| FilesDir["files/ directory"]
BibEntry -->|"generate .bib"| BibFile[".bib file"]
Markdown --> PublicationsDir["_publications/<br/>directory"]
FilesDir --> OutputDir["Output Directory"]
BibFile --> OutputDir
PublicationsDir --> OutputDir
File Changes1. jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java
|
Contributor
Code Review by Qodo
1. paperurl missing without PDF
|
Comment on lines
+184
to
+188
| buildVenue(entry).ifPresent(venue -> | ||
| sb.append("venue: '").append(escapeSingleQuotes(removeLatexEscapes(venue))).append("'\n")); | ||
| copyPdfAndGetUrl(entry, outputDir, key, fileDirForDatabase).ifPresent(paperUrl -> | ||
| sb.append("paperurl: '/files/").append(paperUrl).append("'\n")); | ||
| writeBibFile(entry, outputDir, key).ifPresent(bibUrl -> |
Contributor
There was a problem hiding this comment.
1. paperurl missing without pdf 📎 Requirement gap ✓ Correctness
The exporter only writes paperurl when a PDF attachment is found, and otherwise omits the key entirely instead of falling back to DOI/URL. This can produce AcademicPages-incompatible front matter missing required fields and broken links.
Agent Prompt
## Issue description
The exporter currently writes `paperurl` only when it can copy a PDF attachment; if no PDF is attached (or attachment cannot be resolved), the `paperurl` YAML key is omitted entirely and there is no fallback to DOI/URL.
## Issue Context
AcademicPages front matter requires `paperurl` and the mapping requires choosing it from a copied adjacent attachment when available, otherwise falling back to DOI/URL.
## Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java[184-190]
- jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java[206-228]
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+246
to
+255
| /// Generates a citation string from the entry using citation style IEEE | ||
| private String buildCitation(BibEntry entry, BibDatabaseContext databaseContext) { | ||
| BibDatabaseContext context = new BibDatabaseContext(new BibDatabase(List.of(entry))); | ||
| context.setMode(databaseContext.getMode()); | ||
| String style = CSLStyleLoader.getDefaultStyle().getSource(); | ||
| return CitationStyleGenerator.generateBibliography( | ||
| List.of(entry), style, CitationStyleOutputFormat.TEXT, context, entryTypesManager) | ||
| .getFirst() | ||
| .trim(); | ||
| } |
Contributor
There was a problem hiding this comment.
3. Citation not preview-based 📎 Requirement gap ✓ Correctness
The exporter generates citation via CSL default style bibliography generation rather than using JabRef’s preview rendering (or an approved short alternative). This can cause citation output to differ from JabRef preview expectations.
Agent Prompt
## Issue description
The `citation` YAML value is currently produced via CSL default bibliography generation rather than the JabRef preview renderer required by compliance.
## Issue Context
AcademicPages export is expected to produce citations consistent with JabRef preview output.
## Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java[246-255]
- jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java[171-198]
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
Comment on lines
+251
to
+254
| return CitationStyleGenerator.generateBibliography( | ||
| List.of(entry), style, CitationStyleOutputFormat.TEXT, context, entryTypesManager) | ||
| .getFirst() | ||
| .trim(); |
Contributor
There was a problem hiding this comment.
4. Unsafe .getfirst() usage 📘 Rule violation ⛯ Reliability
buildCitation calls .getFirst() on the generated bibliography list without checking whether it is empty. If bibliography generation returns an empty list for any entry, export can crash at runtime.
Agent Prompt
## Issue description
The exporter uses `.getFirst()` on a list returned by citation generation without checking that the list contains an element.
## Issue Context
If citation generation fails or returns no entries for certain BibTeX data, export should not crash.
## Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java[246-255]
ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools
This comment has been minimized.
This comment has been minimized.
koppor
previously requested changes
Mar 3, 2026
koppor
left a comment
Member
There was a problem hiding this comment.
Good first step. Still many JabRef tooling (BbiEntry.getFieldOrAlias, FileUtil, FileUniqueness) unknown. Also unknown that SnakeYaml exists and used in JabRef. -- I commented inside.
|
|
||
| private static final String COLLECTION = "publications"; | ||
|
|
||
| private static final Comparator<BibEntry> ENTRY_TYPE_ORDER = Comparator.comparingInt( |
|
|
||
| /// Exports a JabRef library to the <a href="https://academicpages.github.io">academicpages</a> Jekyll template format. | ||
| /// Each {@link BibEntry} is written to a separate Markdown file in the given output directory. | ||
| /// The file name follows the pattern {@code YYYY-MM-DD-citationkey.md}. |
Member
There was a problem hiding this comment.
Use Markdown
Suggested change
| /// The file name follows the pattern {@code YYYY-MM-DD-citationkey.md}. | |
| /// The file name follows the pattern `YYYY-MM-DD-citationkey.md`. |
|
|
||
| import org.jspecify.annotations.NonNull; | ||
|
|
||
| /// Exports a JabRef library to the <a href="https://academicpages.github.io">academicpages</a> Jekyll template format. |
Member
There was a problem hiding this comment.
Use Markdown. Links are different in Markdown.
| } | ||
|
|
||
| /// Builds the full Markdown file content: YAML front matter + abstract body | ||
| private String buildContent(BibEntry entry, Path outputDir, BibDatabaseContext databaseContext, List<Path> fileDirForDatabase) { |
Member
There was a problem hiding this comment.
Note: This method is the main reason why this is NOT a good first or second issue.
| } | ||
|
|
||
| /// Removes common LaTeX escape sequences for use in plain text contexts | ||
| private String removeLatexEscapes(String value) { |
Member
There was a problem hiding this comment.
No - Use org.jabref.model.entry.BibEntry#getFieldOrAliasLatexFree when reading field content
Comment on lines
+201
to
+202
| return entry.getField(StandardField.JOURNAL) | ||
| .or(() -> entry.getField(StandardField.JOURNALTITLE)) |
Member
There was a problem hiding this comment.
Combine in getFieldOrAliasLatexFree
| public void export(@NonNull BibDatabaseContext databaseContext, | ||
| @NonNull Path outputFile, | ||
| @NonNull List<BibEntry> entries, | ||
| List<Path> fileDirForDatabase, |
Member
There was a problem hiding this comment.
OMG - this parameter is wrong - it should be removed.
The constructor should get FilePreferences and store it.
Here, org.jabref.model.database.BibDatabaseContext#getFileDirectories should be used.
However, this might be too complex for now (because other classes also need to be rewritten) --> follow-up.
| assertTrue(Files.exists(generated)); | ||
|
|
||
| String content = Files.readString(generated); | ||
| assertTrue(content.contains("title: \"A Great Paper\"")); |
Member
There was a problem hiding this comment.
Please test a complete export - not with "contains".
You can have multi line java string constants with """
You can replace placeholders before checking. Maybe {test-temp-dir} could be such a placeholder
…porter.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
This comment has been minimized.
This comment has been minimized.
subhramit
reviewed
Mar 3, 2026
Comment on lines
+39
to
+50
| entry -> switch (entry.getType().getName()) { | ||
| case "book" -> | ||
| 0; | ||
| case "article" -> | ||
| 1; | ||
| case "incollection" -> | ||
| 2; | ||
| case "inproceedings" -> | ||
| 3; | ||
| default -> | ||
| 4; | ||
| } |
Member
There was a problem hiding this comment.
Is there a possibility of more entry types being supported here in future? In that case, 0 should go to default to ensure a better backward compatibility practice.
subhramit
reviewed
Mar 3, 2026
| private String buildDate(BibEntry entry) { | ||
| String year = entry.getField(StandardField.YEAR) | ||
| .or(() -> entry.getField(StandardField.DATE) | ||
| .map(date -> date.length() >= 4 ? date.substring(0, 4) : date)) |
Member
There was a problem hiding this comment.
This may need a bit of an explanation in a comment. Just document an example.
subhramit
reviewed
Mar 3, 2026
| return year + "-" + month + "-01"; | ||
| } | ||
|
|
||
| /// Normalizes a BibTeX month value to a two-digit string |
Member
There was a problem hiding this comment.
Use org.jabref.model.entry.Month
subhramit
reviewed
Mar 3, 2026
Comment on lines
+117
to
+169
| private String normalizeMonth(String month) { | ||
| return switch (month.toLowerCase(Locale.ROOT).trim()) { | ||
| case "1", | ||
| "jan", | ||
| "january" -> | ||
| "01"; | ||
| case "2", | ||
| "feb", | ||
| "february" -> | ||
| "02"; | ||
| case "3", | ||
| "mar", | ||
| "march" -> | ||
| "03"; | ||
| case "4", | ||
| "apr", | ||
| "april" -> | ||
| "04"; | ||
| case "5", | ||
| "may" -> | ||
| "05"; | ||
| case "6", | ||
| "jun", | ||
| "june" -> | ||
| "06"; | ||
| case "7", | ||
| "jul", | ||
| "july" -> | ||
| "07"; | ||
| case "8", | ||
| "aug", | ||
| "august" -> | ||
| "08"; | ||
| case "9", | ||
| "sep", | ||
| "september" -> | ||
| "09"; | ||
| case "10", | ||
| "oct", | ||
| "october" -> | ||
| "10"; | ||
| case "11", | ||
| "nov", | ||
| "november" -> | ||
| "11"; | ||
| case "12", | ||
| "dec", | ||
| "december" -> | ||
| "12"; | ||
| default -> | ||
| "01"; | ||
| }; | ||
| } |
Member
There was a problem hiding this comment.
This should then become just:
Suggested change
| private String normalizeMonth(String month) { | |
| return switch (month.toLowerCase(Locale.ROOT).trim()) { | |
| case "1", | |
| "jan", | |
| "january" -> | |
| "01"; | |
| case "2", | |
| "feb", | |
| "february" -> | |
| "02"; | |
| case "3", | |
| "mar", | |
| "march" -> | |
| "03"; | |
| case "4", | |
| "apr", | |
| "april" -> | |
| "04"; | |
| case "5", | |
| "may" -> | |
| "05"; | |
| case "6", | |
| "jun", | |
| "june" -> | |
| "06"; | |
| case "7", | |
| "jul", | |
| "july" -> | |
| "07"; | |
| case "8", | |
| "aug", | |
| "august" -> | |
| "08"; | |
| case "9", | |
| "sep", | |
| "september" -> | |
| "09"; | |
| case "10", | |
| "oct", | |
| "october" -> | |
| "10"; | |
| case "11", | |
| "nov", | |
| "november" -> | |
| "11"; | |
| case "12", | |
| "dec", | |
| "december" -> | |
| "12"; | |
| default -> | |
| "01"; | |
| }; | |
| } | |
| private String normalizeMonth(String month) { | |
| return Month.parse(month) | |
| .map(Month::getTwoDigitNumber) | |
| .orElse("01"); | |
| } |
(check the indentation)
subhramit
reviewed
Mar 3, 2026
| } | ||
|
|
||
| /// Builds the full Markdown file content: YAML front matter + abstract body | ||
| private String buildContent(BibEntry entry, Path outputDir, BibDatabaseContext databaseContext, List<Path> fileDirForDatabase) { |
Member
There was a problem hiding this comment.
Name all of these "build" methods to something more precise as they sound like void methods.
I can think of "buildAndGetContent" but open to better ideas.
subhramit
reviewed
Mar 3, 2026
| return sb.toString(); | ||
| } | ||
|
|
||
| private Optional<String> buildVenue(BibEntry entry) { |
subhramit
reviewed
Mar 3, 2026
| } | ||
|
|
||
| /// Generates a citation string from the entry using citation style IEEE | ||
| private String buildCitation(BibEntry entry, BibDatabaseContext databaseContext) { |
…5/jabref into export-for-academicpages-12727
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
This comment has been minimized.
Siedlerchr
previously approved these changes
Mar 16, 2026
This comment has been minimized.
This comment has been minimized.
Siedlerchr
previously approved these changes
Mar 16, 2026
calixtus
reviewed
Mar 16, 2026
✅ All tests passed ✅🏷️ Commit: 7f44514 Learn more about TestLens at testlens.app. |
Siedlerchr
approved these changes
Mar 16, 2026
faneeshh
pushed a commit
to faneeshh/jabref
that referenced
this pull request
Mar 16, 2026
* Add new export format for academicpages * exporting JabRef libraries to academicpages format * includes various test cases to validate the export functionality * Add AcademicPagesExporter for enhanced export functionality * Update jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * methods for unique file name generation and enhanced date handling using TemporalAccessor * improve YAML output validation and test coverage for different entry types. Updated expected output format and added assertions for citation and file generation. * renamed methods for file name generation, content building, and venue resolution to better reflect their functionality * Add space to 12727 description * created new layout files for various academic publication types including articles, books, incollections, and inproceedings. Each layout includes fields for title, collection, excerpt, and venue. * adding mock for LayoutFormatterPreferences and updating expected YAML output format * integrate layout preferences and enhance file management * include layout preferences in constructor * Update CHANGELOG * Restore formatDate back to be clean and more readable * Refactor layout handling in AcademicPagesExporter to use TemplateExporter constants for layout prefix and extension. * Reorder the final varialbe * restore some missed files * Update academic layout files to categorize entries as 'manuscripts' and 'conferences' where applicable * improve entry type ordering and enhance date handling. Introduced a map for entry type priority and updated date resolution to return an Optional, ensuring cleaner permalink generation. * Remove test for missing month defaulting to January and add new test to verify that missing date omits date and permalink in exported files * Update CHANGELOG.md * use entrytype --------- Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> Co-authored-by: Christoph <siedlerkiller@gmail.com>
AnvitaPrasad
pushed a commit
to AnvitaPrasad/jabref
that referenced
this pull request
Mar 18, 2026
* Add new export format for academicpages * exporting JabRef libraries to academicpages format * includes various test cases to validate the export functionality * Add AcademicPagesExporter for enhanced export functionality * Update jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * methods for unique file name generation and enhanced date handling using TemporalAccessor * improve YAML output validation and test coverage for different entry types. Updated expected output format and added assertions for citation and file generation. * renamed methods for file name generation, content building, and venue resolution to better reflect their functionality * Add space to 12727 description * created new layout files for various academic publication types including articles, books, incollections, and inproceedings. Each layout includes fields for title, collection, excerpt, and venue. * adding mock for LayoutFormatterPreferences and updating expected YAML output format * integrate layout preferences and enhance file management * include layout preferences in constructor * Update CHANGELOG * Restore formatDate back to be clean and more readable * Refactor layout handling in AcademicPagesExporter to use TemplateExporter constants for layout prefix and extension. * Reorder the final varialbe * restore some missed files * Update academic layout files to categorize entries as 'manuscripts' and 'conferences' where applicable * improve entry type ordering and enhance date handling. Introduced a map for entry type priority and updated date resolution to return an Optional, ensuring cleaner permalink generation. * Remove test for missing month defaulting to January and add new test to verify that missing date omits date and permalink in exported files * Update CHANGELOG.md * use entrytype --------- Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> Co-authored-by: Christoph <siedlerkiller@gmail.com>
FynnianB
pushed a commit
to FynnianB/jabref
that referenced
this pull request
Mar 19, 2026
* Add new export format for academicpages * exporting JabRef libraries to academicpages format * includes various test cases to validate the export functionality * Add AcademicPagesExporter for enhanced export functionality * Update jablib/src/main/java/org/jabref/logic/exporter/AcademicPagesExporter.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * methods for unique file name generation and enhanced date handling using TemporalAccessor * improve YAML output validation and test coverage for different entry types. Updated expected output format and added assertions for citation and file generation. * renamed methods for file name generation, content building, and venue resolution to better reflect their functionality * Add space to 12727 description * created new layout files for various academic publication types including articles, books, incollections, and inproceedings. Each layout includes fields for title, collection, excerpt, and venue. * adding mock for LayoutFormatterPreferences and updating expected YAML output format * integrate layout preferences and enhance file management * include layout preferences in constructor * Update CHANGELOG * Restore formatDate back to be clean and more readable * Refactor layout handling in AcademicPagesExporter to use TemplateExporter constants for layout prefix and extension. * Reorder the final varialbe * restore some missed files * Update academic layout files to categorize entries as 'manuscripts' and 'conferences' where applicable * improve entry type ordering and enhance date handling. Introduced a map for entry type priority and updated date resolution to return an Optional, ensuring cleaner permalink generation. * Remove test for missing month defaulting to January and add new test to verify that missing date omits date and permalink in exported files * Update CHANGELOG.md * use entrytype --------- Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> Co-authored-by: Christoph <siedlerkiller@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
5 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Related issues and pull requests
Closes #12727
PR Description
Implements an exporter for the academicpages.
The exporter generates one Markdown file per entry with YAML front matter (title, venue, date, IEEE citation, category) and copies attached PDFs
Steps to test
1- Open library .bib
2- Select some entries
3- Click File -> Export -> Export selected entries
3- Choose Academic Pages (*.md), type a folder name, click Save, output folder contains:
Checklist
CHANGELOG.mdin a way that can be understood by the average user (if change is visible to the user)