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Add ieee-paper-reference-text.*#15069

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add-ieee-paper-reference-text
Feb 9, 2026
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Add ieee-paper-reference-text.*#15069
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add-ieee-paper-reference-text

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@koppor koppor commented Feb 9, 2026

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Example for #14085

Mandatory checks

  • I own the copyright of the code submitted and I license it under the MIT license
  • [/] I manually tested my changes in running JabRef (always required)
  • [/] I added JUnit tests for changes (if applicable)
  • [/] I added screenshots in the PR description (if change is visible to the user)
  • [/] I added a screenshot in the PR description showing a library with a single entry with me as author and as title the issue number.
  • [/] I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
  • [/] I checked the user documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

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Review Summary by Qodo

Add IEEE paper reference text example with bibliography

✨ Enhancement 🧪 Tests

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Walkthroughs

Description
• Add IEEE paper reference text example with 16 bibliography entries
• Create LaTeX source files for IEEE conference paper testing
• Include BibTeX database with chocolate health research articles
• Update existing IEEE paper LaTeX configuration and dependencies
Diagram
flowchart LR
  A["IEEE Test Resources"] --> B["LaTeX Sources"]
  A --> C["PDF Resources"]
  B --> D["ieee-paper-reference-text.tex"]
  B --> E["ieee-paper-reference-text.bib"]
  B --> F["latexmkrc Config"]
  B --> G["ieee-paper.tex Updates"]
  C --> H["README.md"]
Loading

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File Changes

1. jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib 🧪 Tests +238/-0

Add comprehensive BibTeX bibliography for IEEE paper

• Added 16 BibTeX article entries covering chocolate and cocoa health research
• Entries span from 1969 to 2024 with complete metadata (DOI, ISSN, pages, publishers)
• Includes JabRef-specific metadata like read status and grouping information
• Contains JabRef database configuration comments for proper file handling

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib


2. jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex 🧪 Tests +40/-0

Create IEEE paper LaTeX template with citations

• Created new IEEE conference paper LaTeX template with related work section
• Includes abstract, introduction, related work, contribution, and conclusion sections
• Related work section contains three citations from the bibliography
• Uses IEEEtran document class with proper author and title formatting

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex


3. jablib/src/test/latex/pdfs/IEEE/ieee-paper.tex ✨ Enhancement +1/-3

Update IEEE paper LaTeX package dependencies

• Replaced flushend package with pbalance for better column balancing
• Removed \atColsEnd{\vfil} command for cleaner document structure
• Maintains existing document structure and content

jablib/src/test/latex/pdfs/IEEE/ieee-paper.tex


View more (2)
4. jablib/src/test/latex/pdfs/IEEE/latexmkrc ⚙️ Configuration changes +2/-0

Add LaTeX build configuration file

• Added LaTeX build configuration file for automated PDF generation
• Configured PDF mode and BibTeX usage settings
• Enables proper compilation of LaTeX sources to PDF

jablib/src/test/latex/pdfs/IEEE/latexmkrc


5. jablib/src/test/resources/pdfs/IEEE/README.md 📝 Documentation +3/-0

Add IEEE PDF resources documentation

• Created documentation file explaining PDF source location
• Points users to LaTeX source files in jablib/src/test/latex/pdfs/IEEE

jablib/src/test/resources/pdfs/IEEE/README.md


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qodo-free-for-open-source-projects Bot commented Feb 9, 2026

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Code Review by Qodo

🐞 Bugs (4) 📘 Rule violations (0) 📎 Requirement gaps (2)

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Action required

1. Related work text tab missing 📎 Requirement gap ✓ Correctness
Description
• Compliance requires a UI tab explicitly titled Related work text with an input area for pasted
  text.
• This PR only adds LaTeX/BibTeX test fixtures and related documentation, and does not introduce any
  UI elements or input surface.
• As a result, users still have no place in the UI to paste related-work text to start the workflow.
Code

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[R24-29]

+\section{Related Work}
+
+% Text generated by https://app.scienceos.ai
+A study on the Colombian chocolate industry represents the first application of a social life cycle assessment (S-LCA) to cover both cocoa cultivation and chocolate manufacturing \cite{LunaOstos_2024}.
+A study on selective, hedonic deprivation found that restricting chocolate intake for two weeks increased state chocolate craving, but only in individuals who already had high trait chocolate craving~\cite{Richard_2017}.
+Research suggests that the health benefits of moderate cocoa or dark chocolate consumption, which include cardiovascular and cognitive advantages, likely outweigh the risks associated with its high energy density~\cite{Katz_2011}.
Evidence
PR Compliance ID 7 requires adding a Related work text UI tab for pasted input. The PR changes
shown are limited to test/fixture LaTeX resources and a small README describing those PDFs, with no
UI implementation present in the modified files.

Provide a UI tab named "Related work text" for input
jablib/src/test/resources/pdfs/IEEE/README.md[1-3]
jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[24-29]


2. No parsing/update workflow 📎 Requirement gap ✓ Correctness
Description
• Compliance requires that pasted related-work text is parsed to identify citations, look
  up/create/update matching library entries, extract descriptive snippets, and write them into
  comments-{username} using the specified [{citation-key}]:  prefix and append behavior.
• This PR adds only example LaTeX/BibTeX sources and build configuration for generating PDFs, but
  does not add any implementation that performs parsing, entry lookup/update, snippet extraction, or
  comment-field writing.
• Therefore, the end-to-end knowledge-harvesting behavior described by the checklist is not
  implemented by this change set.
Code

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[R24-35]

+\section{Related Work}
+
+% Text generated by https://app.scienceos.ai
+A study on the Colombian chocolate industry represents the first application of a social life cycle assessment (S-LCA) to cover both cocoa cultivation and chocolate manufacturing \cite{LunaOstos_2024}.
+A study on selective, hedonic deprivation found that restricting chocolate intake for two weeks increased state chocolate craving, but only in individuals who already had high trait chocolate craving~\cite{Richard_2017}.
+Research suggests that the health benefits of moderate cocoa or dark chocolate consumption, which include cardiovascular and cognitive advantages, likely outweigh the risks associated with its high energy density~\cite{Katz_2011}.
+
+\section{Contribution}
+\lipsum[4]
+
+\section{Conclusion and Outlook}
+\lipsum[3]
Evidence
PR Compliance IDs 8-13 define required behavior (parse pasted text, update library entries, extract
descriptions, write/append to comments-{username} with the required prefix, and focus on knowledge
harvesting). The PR modifications shown are limited to LaTeX/BibTeX fixtures and latexmkrc, and do
not include any code that implements these behaviors.

Parse pasted related-work text to identify cited references
Lookup identified references and create or update library entries
Extract descriptive text snippets about each referenced paper from the pasted text
Write extracted descriptive text into per-user comment field using required prefix format
Append to existing comments-{username} content with an empty line separator
Feature behavior targets knowledge harvesting from PDF text (not citation relations)
jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[24-35]
jablib/src/test/latex/pdfs/IEEE/latexmkrc[1-2]


3. CI missing pbalance package 🐞 Bug ⛯ Reliability
Description
ieee-paper.tex now depends on \usepackage{pbalance}, but the CI TeX Live installation is
  driven by jablib/src/test/latex/Texlivefile, which does not list pbalance.
• The LaTeX GitHub Action compiles jablib/src/test/latex/pdfs/IEEE/ieee-paper with pdflatex;
  missing pbalance.sty will fail the workflow and block merges.
Code

jablib/src/test/latex/pdfs/IEEE/ieee-paper.tex[5]

+\usepackage{pbalance}
Evidence
The modified IEEE test document imports pbalance. CI installs TeX Live packages strictly from
Texlivefile and then compiles ieee-paper.tex in that directory; since pbalance is not present
in Texlivefile, compilation is likely to fail due to a missing style file.

jablib/src/test/latex/pdfs/IEEE/ieee-paper.tex[1-6]
jablib/src/test/latex/Texlivefile[1-20]
.github/workflows/latex.yml[31-48]
.github/workflows/latex.yml[91-100]

Agent prompt
The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The LaTeX CI job compiles the IEEE test document which now imports `pbalance`, but the TeX Live packages installed in CI are pinned by `jablib/src/test/latex/Texlivefile` and currently don’t include `pbalance`. This likely breaks the LaTeX workflow with a missing `pbalance.sty` error.
### Issue Context
CI installs TeX Live packages from `jablib/src/test/latex/Texlivefile` and then runs `pdflatex` in `jablib/src/test/latex/pdfs/IEEE`.
### Fix Focus Areas
- jablib/src/test/latex/Texlivefile[1-40]
- jablib/src/test/latex/pdfs/IEEE/ieee-paper.tex[1-6]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools



Remediation recommended

4. New doc not compiled in CI 🐞 Bug ⛯ Reliability
Description
• The PR adds a new LaTeX document ieee-paper-reference-text.tex, but the LaTeX CI workflow only
  compiles ieee-paper in the IEEE directory.
• This means the new source can silently drift/break (packages/bibliography/compilation errors)
  without any CI signal.
Code

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[R1-5]

+\documentclass[conference,a4paper,english]{IEEEtran}[2015/08/26]
+
+\usepackage{lipsum}
+\usepackage{hyperref}
+\usepackage{pbalance}
Evidence
The new .tex file exists in the IEEE LaTeX sources directory, but the LaTeX workflow matrix lists
only tex: ieee-paper for that directory, so the new document is never built or validated in CI.

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[1-8]
.github/workflows/latex.yml[41-48]

Agent prompt
The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
A new LaTeX source file was added under `jablib/src/test/latex/pdfs/IEEE`, but CI does not compile it. This reduces test-asset reproducibility and allows silent breakage.
### Issue Context
The LaTeX workflow is matrix-driven and currently only compiles `ieee-paper` in the IEEE directory.
### Fix Focus Areas
- .github/workflows/latex.yml[39-82]
- jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[1-40]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools


5. BibLaTeX .bib with BibTeX 🐞 Bug ✓ Correctness
Description
ieee-paper-reference-text.tex uses a BibTeX-style bibliography (\bibliographystyle{IEEEtran} +
  \bibliography{...}), but its .bib declares databaseType:biblatex and uses BibLaTeX field names
  like date and journaltitle.
• If/when compiled with BibTeX/IEEEtran.bst, those fields will be ignored, silently producing
  incomplete/incorrect bibliography output (hurting reproducibility and making it hard to match the
  intended PDF/text extraction).
Code

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib[R1-5]

+@Article{Corti_2009,
+  author       = {Corti, Roberto and Flammer, Andreas J. and Hollenberg, Norman K. and Lüscher, Thomas F.},
+  date         = {2009-03},
+  journaltitle = {Circulation},
+  title        = {Cocoa and Cardiovascular Health},
Evidence
The .tex explicitly uses IEEEtran.bst (BibTeX workflow). The corresponding .bib is
BibLaTeX-oriented (declares biblatex database type and uses biblatex fields). The existing IEEE
example .bib uses BibTeX fields (year, journal), demonstrating the expected format for the
BibTeX-based pipeline in this directory/CI.

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[37-40]
jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib[1-6]
jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib[220-223]
jablib/src/test/latex/pdfs/IEEE/ieee-paper.bib[1-10]
.github/workflows/latex.yml[43-47]

Agent prompt
The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
`ieee-paper-reference-text.tex` uses a BibTeX/IEEEtran.bst workflow, but `ieee-paper-reference-text.bib` is BibLaTeX-oriented (fields like `date`/`journaltitle`, and metadata `databaseType:biblatex`). This will silently drop key metadata when compiling with BibTeX.
### Issue Context
The existing IEEE example in the same directory (`ieee-paper.bib`) uses BibTeX fields (`year`, `journal`). CI also uses `bibtex` as the bibengine for the IEEE directory.
### Fix Focus Areas
- jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[37-40]
- jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib[1-40]
- jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.bib[220-223]
- jablib/src/test/latex/pdfs/IEEE/ieee-paper.bib[1-51]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools


6. AI-generated text marker 🐞 Bug ⛯ Reliability
Description
• The new LaTeX source explicitly states “Text generated by https://app.scienceos.ai”. The project’s
  contribution guidelines state it does not accept fully AI-generated contributions and requires human
  ownership/responsibility.
• Leaving this marker in committed sources can raise compliance concerns and may trigger maintainer
  rejection unless the contributor can demonstrate human authorship/responsibility and discloses AI
  usage appropriately.
Code

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[R26-29]

+% Text generated by https://app.scienceos.ai
+A study on the Colombian chocolate industry represents the first application of a social life cycle assessment (S-LCA) to cover both cocoa cultivation and chocolate manufacturing \cite{LunaOstos_2024}.
+A study on selective, hedonic deprivation found that restricting chocolate intake for two weeks increased state chocolate craving, but only in individuals who already had high trait chocolate craving~\cite{Richard_2017}.
+Research suggests that the health benefits of moderate cocoa or dark chocolate consumption, which include cardiovascular and cognitive advantages, likely outweigh the risks associated with its high energy density~\cite{Katz_2011}.
Evidence
The added .tex file contains an explicit attribution that the prose was generated by an AI tool.
The repository contribution policy warns against fully/largely AI-generated contributions and
requires human responsibility and appropriate disclosure, making this a potential compliance issue.

jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[24-30]
CONTRIBUTING.md[165-169]
AI_USAGE_POLICY.md[10-12]

Agent prompt
The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The new LaTeX test source includes an explicit note that the text was generated by an AI tool. The project’s AI policy requires human ownership/responsibility and may reject largely AI-generated contributions.
### Issue Context
This is test/document source material, but it is still part of the repository and subject to contribution policies.
### Fix Focus Areas
- jablib/src/test/latex/pdfs/IEEE/ieee-paper-reference-text.tex[24-30]
- CONTRIBUTING.md[165-182]
- AI_USAGE_POLICY.md[1-36]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools


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Comment on lines +24 to +29
\section{Related Work}

% Text generated by https://app.scienceos.ai
A study on the Colombian chocolate industry represents the first application of a social life cycle assessment (S-LCA) to cover both cocoa cultivation and chocolate manufacturing \cite{LunaOstos_2024}.
A study on selective, hedonic deprivation found that restricting chocolate intake for two weeks increased state chocolate craving, but only in individuals who already had high trait chocolate craving~\cite{Richard_2017}.
Research suggests that the health benefits of moderate cocoa or dark chocolate consumption, which include cardiovascular and cognitive advantages, likely outweigh the risks associated with its high energy density~\cite{Katz_2011}.

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Action required

1. related work text tab missing 📎 Requirement gap ✓ Correctness

• Compliance requires a UI tab explicitly titled Related work text with an input area for pasted
  text.
• This PR only adds LaTeX/BibTeX test fixtures and related documentation, and does not introduce any
  UI elements or input surface.
• As a result, users still have no place in the UI to paste related-work text to start the workflow.

Comment on lines +24 to +35
\section{Related Work}

% Text generated by https://app.scienceos.ai
A study on the Colombian chocolate industry represents the first application of a social life cycle assessment (S-LCA) to cover both cocoa cultivation and chocolate manufacturing \cite{LunaOstos_2024}.
A study on selective, hedonic deprivation found that restricting chocolate intake for two weeks increased state chocolate craving, but only in individuals who already had high trait chocolate craving~\cite{Richard_2017}.
Research suggests that the health benefits of moderate cocoa or dark chocolate consumption, which include cardiovascular and cognitive advantages, likely outweigh the risks associated with its high energy density~\cite{Katz_2011}.

\section{Contribution}
\lipsum[4]

\section{Conclusion and Outlook}
\lipsum[3]

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Choose a reason for hiding this comment

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Action required

2. No parsing/update workflow 📎 Requirement gap ✓ Correctness

• Compliance requires that pasted related-work text is parsed to identify citations, look
  up/create/update matching library entries, extract descriptive snippets, and write them into
  comments-{username} using the specified [{citation-key}]:  prefix and append behavior.
• This PR adds only example LaTeX/BibTeX sources and build configuration for generating PDFs, but
  does not add any implementation that performs parsing, entry lookup/update, snippet extraction, or
  comment-field writing.
• Therefore, the end-to-end knowledge-harvesting behavior described by the checklist is not
  implemented by this change set.

\usepackage{lipsum}
\usepackage{hyperref}
\usepackage{flushend}
\usepackage{pbalance}

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Action required

3. Ci missing pbalance package 🐞 Bug ⛯ Reliability

ieee-paper.tex now depends on \usepackage{pbalance}, but the CI TeX Live installation is
  driven by jablib/src/test/latex/Texlivefile, which does not list pbalance.
• The LaTeX GitHub Action compiles jablib/src/test/latex/pdfs/IEEE/ieee-paper with pdflatex;
  missing pbalance.sty will fail the workflow and block merges.
Agent Prompt
### Issue description
The LaTeX CI job compiles the IEEE test document which now imports `pbalance`, but the TeX Live packages installed in CI are pinned by `jablib/src/test/latex/Texlivefile` and currently don’t include `pbalance`. This likely breaks the LaTeX workflow with a missing `pbalance.sty` error.

### Issue Context
CI installs TeX Live packages from `jablib/src/test/latex/Texlivefile` and then runs `pdflatex` in `jablib/src/test/latex/pdfs/IEEE`.

### Fix Focus Areas
- jablib/src/test/latex/Texlivefile[1-40]
- jablib/src/test/latex/pdfs/IEEE/ieee-paper.tex[1-6]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

Siedlerchr
Siedlerchr previously approved these changes Feb 9, 2026
@koppor koppor enabled auto-merge February 9, 2026 10:30
@koppor koppor added the automerge PR is tagged with that label will be merged if workflows are green label Feb 9, 2026
@koppor koppor disabled auto-merge February 9, 2026 10:37
@koppor koppor merged commit bd77352 into main Feb 9, 2026
70 of 75 checks passed
@koppor koppor deleted the add-ieee-paper-reference-text branch February 9, 2026 10:37
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3 participants