Add ADR for preference for the compatiblity mode by pluto-han · Pull Request #16025 · JabRef/jabref

pluto-han · 2026-06-21T00:13:34Z

Related issues and pull requests

Related to #15869

PR Description

Add ADR for preference for the compatiblity mode. We decide not to use a preference.

AI usage

No

Checklist

I own the copyright of the code submitted and I license it under the MIT license
If AI tools were used, I disclosed them in the "AI usage" section and reviewed, understood, and take full ownership of all AI-generated code
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 can be understood by the average user (if change is visible to the user)
[/] I checked the user documentation for up to dateness and submitted a pull request to our user documentation repository

qodo-free-for-open-source-projects · 2026-06-21T00:14:16Z

PR Summary by Qodo

Add ADR: avoid preference for Zotero/JabRef compatibility mode
📝 Documentation 🕐 Less than 10 minutes

Description

• Add an ADR documenting whether Zotero compatibility mode needs a user preference.
• Decide to avoid a preference and rely on existing citation-js mapping fallback.
• Capture trade-offs (UX simplicity vs. risk of unawareness/information loss).

Diagram

graph TD
  A["Zotero reference marks"] --> B["JabRef citation converter"] --> C["BibLaTeX output"]
  B --> D["citation-js mapping (ADR 64)"]
  E["ADR 65: No preference"] --> F["No compat-mode preference UI"] --> B

High-Level Assessment

The PR’s approach is appropriate: capturing the rationale and trade-offs in a dedicated ADR is the right artifact for an architectural/UX decision, and the document clearly records why a preference is unnecessary given the citation-js fallback.

Files changed (1) +54 / -0

Documentation (1) +54 / -0

0065-use-preference-for-zotero-jabref-compatibility-or-not.mdAdd ADR 65 deciding against a compatibility-mode preference +54/-0

Add ADR 65 deciding against a compatibility-mode preference
• Introduces a new Architecture Decision Record evaluating whether Zotero/JabRef compatibility mode should be controlled by a user preference. Records the decision to avoid a preference and rely on citation-js mapping as a fallback, along with consequences and pros/cons.
docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md

qodo-free-for-open-source-projects · 2026-06-21T00:16:12Z

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📎 Requirement gaps (0) 🎨 UX issues (0) 🔗 Cross-repo conflicts (0) 📜 Skill insights (0)

1. nav_order format inconsistent ✓ Resolved 📘 Rule violation ⚙ Maintainability

Description

The new ADR uses nav_order: 65, which is inconsistent with the existing four-digit nav_order
style (e.g., 0063) used by other ADRs. This can reduce consistency and may affect
ordering/readability of Decision Records navigation.

Code

docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md[R1-4]
+---
+nav_order: 65
+parent: Decision Records
+---

Evidence
Compliance ID 7 requires preserving existing formatting/naming conventions. The new ADR sets
nav_order: 65 while an adjacent ADR uses nav_order: 0063, demonstrating a convention mismatch
introduced by this PR.
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Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative: AGENTS.md: Preserve Existing Formatting and Naming Conventions; Keep Code Small, Focused, and Non-Duplicative
docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md[1-4]
docs/decisions/0063-use-picocli-exceptionhandler.md[1-4]

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 ADR front-matter uses `nav_order: 65`, but existing ADRs use a four-digit style (e.g., `0063`). This is an inconsistency in documentation conventions and may impact ordering in the rendered docs.
## Issue Context
Other decision record files under `docs/decisions/` use `nav_order` with leading zeros.
## Fix Focus Areas
- docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md[1-4]

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

2. ~~Unlinked ADR reference~~ ✓ Resolved 🐞 Bug ⚙ Maintainability

Description

The new ADR references "ADR-64" as plain text instead of using the repository’s usual linked ADR
format, making it harder to navigate to/verify the referenced decision. This also diverges from the
4-digit ADR numbering pattern used elsewhere (e.g., ADR-0001).

Code

docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md[49]

+Since JabRef uses citation-js's mapping logic (see ADR-64) as fallback strategy, users do not need to manually enable a preference to recognize Zotero's reference mark. JabRef will convert the citation to BibLateX format when it reads Zotero's reference mark. Possible problems will be added in release page and user documentation.

Evidence
The new ADR contains a plain-text reference to ADR-64, while existing ADRs use markdown links for
ADR cross-references, so the new reference is inconsistent and non-navigable.
docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md[49-49]
docs/decisions/0006-only-translated-strings-in-language-file.md[47-50]

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 ADR text uses an unlinked reference ("ADR-64"), which breaks the typical cross-ADR linking pattern and reduces navigability.
## Issue Context
Other ADRs use markdown links for related decisions (e.g., `Related to [ADR-0001](0001-use-crowdin-for-translations.md)`).
## Fix Focus Areas
- docs/decisions/0065-use-preference-for-zotero-jabref-compatibility-or-not.md[49-49]
## Suggested fix
Replace `ADR-64` with a markdown link using the standard ADR formatting (e.g., `see [ADR-0064](0064-...)` or adjust to the correct existing ADR number/file name if different).

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

pluto-han · 2026-06-21T00:17:55Z

Waiting for #15907 to be merged

koppor · 2026-06-21T04:42:09Z

+parent: Decision Records
+---
+
+# Do we need a preference for the compatibility mode?


The title is the solution, not the question.

Same for the filename.

Do we need to refine the template? https://github.com/adr/madr/blob/develop/template/adr-template.md - I was thinking that "found solution" together with "and" was a strong hint.

koppor · 2026-06-21T04:43:31Z

+## Considered Options
+
+* Use a preference for the compatibility mode.
+* Do not use a preference.


Maybe

Suggested change

* Do not use a preference.

* Transparent handling of Zotero reference marks.

koppor · 2026-06-21T04:44:02Z

+* Good, because JabRef reads and converts Zotero's reference mark automatically, which does not disturb users.
+* Good, because user does not need to enable anything to use this feature.
+* Good, because it avoids the risk Zotero's reference mark being ignored if user forgets to enable the compatibility mode.
+* Bad, because user may not be aware of the problems it may bring, such as information loss, unless they read the release page or user documentation.


I don't get "information loss". A concrete case should be written down here.

updated. I moved the concrete case to "option description"

koppor · 2026-06-21T04:45:25Z

+
+## Context and Problem Statement
+
+JabRef is implementing compatibility with Zotero's reference marks. Apart from JabRef's own reference mark, JabRef should also support Zotero's reference mark.


There should be more context

Is it about postrgres and JabGui? No, it is about the LibreOffice integration - please state this.

Will JabRef's reference marks be supported as deprecated or full support?

What for new docments., will these be Zotero or JabRef style?

koppor · 2026-06-25T16:27:18Z

+
+## Context and Problem Statement
+
+JabRef is implementing compatibility with Zotero reference marks in the LibreOffice integration. Apart from JabRef's own reference mark, JabRef should also support Zotero's reference mark. Zotero reference marks are supported as an additional input format so that JabRef can read citations created by Zotero. For documents connected to JabRef, JabRef continues to write its own reference mark format.


Hyperlink Zotero Reference Marks (zotero) and Libre Office Integration (jabref docu)

koppor · 2026-06-25T16:28:40Z

+
+* Users should be disturbed as little as possible.
+* Users should be warned about the possible problems.
+* Users should be able to use this feature with as few steps as possible.


Remove "the"- or do have a concrete and complete(!) list of the problems?

koppor · 2026-06-25T16:29:02Z

+
+## Considered Options
+
+* Use a preference for the compatibility mode.


No dot at the end (or at both)

I think a push is missing?

Updated. I modified #Decision Drivers but forgot #Considered Options 😅

koppor · 2026-06-25T16:29:49Z

+
+## Decision Outcome
+
+Chosen option: "Do not use a preference", because JabRef already uses citation-js's mapping logic as the fallback strategy. Adding a preference is unnecessary. It also brings some additional benefits, such as not disturbing users when connecting to a document.


Deep link to the class. Use GitHub permanent link.

koppor · 2026-06-25T16:30:53Z

+
+Since JabRef uses citation-js's mapping logic (see ADR-64) as fallback strategy, users do not need to manually enable a preference to recognize Zotero's reference mark. JabRef will convert the citation to BibLaTeX format when it reads Zotero's reference mark. Possible problems will be documented in release page and user documentation. For example, CSL item type `map` is converted to `Misc`, and the CSL field `Scale` is lost during the conversion. JabRef maps CSL item types and fields into BibLaTeX ones, but the field mapping for each CSL type may be incomplete.
+
+* Good, because JabRef reads and converts Zotero's reference mark automatically, which does not disturb users.


Convert???? Does JabRef destroy the marks?? No more opening with Zotero plugin???

No, should be "map" instead of "convert"

koppor · 2026-07-03T23:22:35Z

+
+## Decision Outcome
+
+Chosen option: "Do not use a preference", because JabRef already uses [citation-js's mapping logic](https://github.com/JabRef/jabref/blob/07e475dcf8e2f00447667ebd1814a09176293948/jablib/src/main/java/org/jabref/logic/openoffice/CSLItemTypeDefinitions.java#L23-L84) as the fallback strategy. Adding a preference is unnecessary. It also brings some additional benefits, such as not disturbing users when connecting to a document.


"Do not use a preference" is not listed as optoin, maybe you meant " Use transparent Handling of Zotero Reference Marks"

(I would not capitalize "Handling")

refernce to the adr is missing

"Do not use a preference" is not listed as optoin, maybe you meant " Use transparent Handling of Zotero Reference Marks"

(I would not capitalize "Handling")

Updated

koppor · 2026-07-03T23:23:38Z

+* Good, because JabRef reads and maps Zotero's reference mark automatically, which does not disturb users.
+* Good, because user does not need to enable anything to use this feature.
+* Good, because it avoids the risk Zotero's reference mark being ignored if user forgets to enable the compatibility mode.
+* Bad, because user may not be aware of the problems it may bring (information loss), unless they read the release page or user documentation.


no need to really copy and paste from below, you can just write in plain text or use other words.

Information loss is not clear at this point, but it should, the sections should (more or less) self contained.

Updated. Thank you for the advice!

koppor · 2026-07-03T23:23:52Z

+
+### Use transparent Handling of Zotero Reference Marks
+
+Since JabRef uses [citation-js's mapping logic](https://github.com/JabRef/jabref/blob/07e475dcf8e2f00447667ebd1814a09176293948/jablib/src/main/java/org/jabref/logic/openoffice/CSLItemTypeDefinitions.java#L23-L84) (see ADR-64) as fallback strategy, users do not need to manually enable a preference to recognize Zotero's reference mark. JabRef will map the citation to BibLaTeX format when it reads Zotero's reference mark. Possible problems will be documented in release page and user documentation. For example, CSL item type `map` is mapped to `Misc`, and the CSL field `Scale` is lost during the conversion. JabRef maps CSL item types and fields into BibLaTeX ones, but the field mapping for each CSL type may be incomplete.


ADR can be linked as file (now)

Add ADR

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Update filename and option

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Add more content to Context and Problem Statement

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Delete dots at the end

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do not use "convert"

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Add more information in section consequences

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1384b8b

	* Do not use a preference.
	* Transparent handling of Zotero reference marks.


		## Context and Problem Statement

		JabRef is implementing compatibility with Zotero's reference marks. Apart from JabRef's own reference mark, JabRef should also support Zotero's reference mark.


		## Considered Options

		* Use a preference for the compatibility mode.


		## Decision Outcome

		Chosen option: "Do not use a preference", because JabRef already uses citation-js's mapping logic as the fallback strategy. Adding a preference is unnecessary. It also brings some additional benefits, such as not disturbing users when connecting to a document.


		Since JabRef uses citation-js's mapping logic (see ADR-64) as fallback strategy, users do not need to manually enable a preference to recognize Zotero's reference mark. JabRef will convert the citation to BibLaTeX format when it reads Zotero's reference mark. Possible problems will be documented in release page and user documentation. For example, CSL item type `map` is converted to `Misc`, and the CSL field `Scale` is lost during the conversion. JabRef maps CSL item types and fields into BibLaTeX ones, but the field mapping for each CSL type may be incomplete.

		* Good, because JabRef reads and converts Zotero's reference mark automatically, which does not disturb users.


		### Use transparent Handling of Zotero Reference Marks

		Since JabRef uses [citation-js's mapping logic](https://github.com/JabRef/jabref/blob/07e475dcf8e2f00447667ebd1814a09176293948/jablib/src/main/java/org/jabref/logic/openoffice/CSLItemTypeDefinitions.java#L23-L84) (see ADR-64) as fallback strategy, users do not need to manually enable a preference to recognize Zotero's reference mark. JabRef will map the citation to BibLaTeX format when it reads Zotero's reference mark. Possible problems will be documented in release page and user documentation. For example, CSL item type `map` is mapped to `Misc`, and the CSL field `Scale` is lost during the conversion. JabRef maps CSL item types and fields into BibLaTeX ones, but the field mapping for each CSL type may be incomplete.

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