Added reading and writing with JSON for save actions metadata by ZiadAbdElFatah · Pull Request #15159 · JabRef/jabref

ZiadAbdElFatah · 2026-02-19T10:10:46Z

Related issues and pull requests

PR Description

Added reading and writing of save actions metadata using JSON with unit tests.
Now, save actions metadata is written using the old format and the new JSON format, and also, the two formats can be read for save actions.

Checklist

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 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

ZiadAbdElFatah · 2026-02-19T10:15:57Z

I think now step 1 and step 2 here #10371 (comment) are complete, if so I will move to big part in the issue which is step 3 @koppor.

Write logic code to parse, read and write new JSON format.

I didn't find the proper place to put these logic code, maybe I should put them in MetaDataSerializer, >>MetaDataParser?

And I didn't find the old code to read @comment in this step now, maybe in BibtexDatabaseWriter?

The hole MetaDataParser can be "deleted" - and a new loading from JSON. I think, it is JSON -> DTO -> metadata. Maybe also directly from JSON to MetaData. -- "deleted" is not quite true, because JabRef should be able to read "old" files - and on version 7, the old metadata is not writtin any more. In version 6, both formats are read and written; with the new format taking predecdence)

koppor · 2026-02-19T10:26:01Z

think now step 1 and step 2 here #10371 (comment) are complete, if

I think its wrong. Because the testing needs to be redone. Based on the custom logic for each preference

ZiadAbdElFatah · 2026-02-19T14:19:59Z

Because the testing needs to be redone. Based on the custom logic for each preference

Correct me if I am wrong, I know that there will be many tests generated for this feature as mentioned here #10371 (comment)

There will be many unit tests for that.

But I think step 3 must be implemented first

Write logic code to parse, read and write new JSON format.

Then the unit tests will be generated for each preference.

koppor · 2026-02-20T10:35:46Z

But I think step 3 must be implemented first

Not for all at once. One after another. An easy one can be done here first to show all the impact.

Just reading and writing JSON is OK, but in the cutrent state it does not bring any value to the user.

If you feel unable to split down the work in small steps for yourself, maybe this is the wrong issue.

ZiadAbdElFatah · 2026-02-20T15:25:44Z

But I think step 3 must be implemented first

Not for all at once. One after another. An easy one can be done here first to show all the impact.

Just reading and writing JSON is OK, but in the cutrent state it does not bring any value to the user.

If you feel unable to split down the work in small steps for yourself, maybe this is the wrong issue.

I do already plan to finish one preference after another, logic, and unit tests for each one.
But I just wanted to make sure that this requested change https://github.com/JabRef/jabref/pull/12145/changes#r1944599873 is addressed. I will start working on one soon to get it reviewed.

ZiadAbdElFatah · 2026-02-23T20:29:49Z

I added writing and reading for JSON to save actions metadata.
Would you prefer to open a single PR for every metadata or all metadata in one PR @koppor?

koppor · 2026-02-24T07:53:00Z

I added writing and reading for JSON to save actions metadata.
Would you prefer to open a single PR for every metadata or all metadata in one PR @koppor?

What is not clear at

Not for all at once. One after another. An easy one can be done here first to show all the impact.

You need to be clear when writing "all". "all" matches "Not for all" in my comment.... Same letters!!

qodo-free-for-open-source-projects · 2026-02-24T11:22:11Z

Review Summary by Qodo

Add JSON serialization for save actions metadata

✨ Enhancement

Walkthroughs

Description

• Add JSON format support for save actions metadata
• Implement bidirectional reading/writing of save actions
• Maintain backward compatibility with legacy format
• Add comprehensive unit tests for JSON parsing

Diagram

flowchart LR
  A["BibDatabaseWriter"] -->|"serialize to JSON"| B["Save Actions JSON"]
  C["BibtexParser"] -->|"parse from JSON"| B
  B -->|"read/write"| D["MetaData"]
  E["Legacy Format"] -->|"backward compatible"| D

File Changes

1. jablib/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java ✨ Enhancement +49/-0

Add JSON serialization for save actions

• Added JSON serialization for save actions metadata
• Implemented serializeSaveActionsToJson() method to convert FieldFormatterCleanupActions to
 JSON format
• Implemented writeMetaDataJson() method to write metadata in new JSON format alongside legacy
 format
• Added imports for Gson, JsonObject, JsonArray, and LinkedHashMap

jablib/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java

2. jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java ✨ Enhancement +43/-0

Add JSON deserialization for save actions

• Added JSON parsing capability for save actions metadata
• Implemented parseCommentToJson() method to extract JSON from comments
• Implemented parseSaveActionsFromJson() method to deserialize JSON to
 FieldFormatterCleanupActions
• Added field to store parsed JSON metadata and integrate it into parser result
• Added imports for Gson, JsonObject, JsonElement, and StringJoiner

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

3. jablib/src/main/java/org/jabref/model/metadata/MetaData.java ✨ Enhancement +1/-0

Add JSON metadata format flag constant
• Added new constant META_FLAG_V1 for JSON metadata format identifier
• Maintains existing META_FLAG for backward compatibility with legacy format
jablib/src/main/java/org/jabref/model/metadata/MetaData.java

View more (2)

4. jablib/src/test/java/org/jabref/logic/exporter/BibDatabaseWriterTest.java 🧪 Tests +21/-4

Update save actions test for dual format

• Updated writeSaveActions() test to verify both legacy and JSON formats are written
• Test now validates that save actions are written in both old format and new JSON format
• Verifies correct JSON structure with proper indentation and field ordering

jablib/src/test/java/org/jabref/logic/exporter/BibDatabaseWriterTest.java

5. jablib/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java 🧪 Tests +43/-0

Add JSON parsing tests for save actions

• Added integrationTestSaveActionsJson() test to verify JSON parsing of save actions
• Added parseCommentToJson() unit test to validate JSON extraction from comments
• Tests verify correct deserialization of JSON metadata into FieldFormatterCleanupActions

jablib/src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java

qodo-free-for-open-source-projects · 2026-02-24T11:22:12Z

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (1) 📎 Requirement gaps (0)

1. parseCommentToJson uncaught JsonSyntaxException 📘 Rule violation ≡ Correctness

Description

JSON metadata parsing uses gson.fromJson(...) without handling malformed JSON, which can throw a
runtime exception and abort import. This violates the requirement for robust, contextual error
handling during parsing of external file content.

Code

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[R423-427]

+    Optional<JsonObject> parseCommentToJson(String comment) {
+        Gson gson = new Gson();
+        String content = comment.substring(MetaData.META_FLAG_V1.length());
+        return Optional.ofNullable(gson.fromJson(content, JsonObject.class));
+    }

Evidence
The checklist requires handling potential failure points with meaningful context rather than
allowing crashes. The new parseCommentToJson method directly parses untrusted comment content via
Gson without any try/catch or parserResult error reporting, so malformed JSON can propagate as an
unchecked exception.
Rule 3: Generic: Robust Error Handling and Edge Case Management
AGENTS.md
jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[423-427]

Agent prompt

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

## Issue description
`parseCommentToJson` parses JSON from untrusted file content using `gson.fromJson` without handling malformed JSON, which can throw a runtime exception and crash parsing.
## Issue Context
This is part of BibTeX import logic; invalid/malformed metadata comments should not abort import and should instead be reported as a parser exception/warning with location/context.
## Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[415-427]

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

2. JSON meta duplicated on save 🐞 Bug ≡ Correctness

Description

META_FLAG_V1 (@Comment JSON) is parsed but not removed from the raw text buffer, so it can be stored
in the first entry’s parsed serialization and later written back verbatim. Since the writer also
always emits JSON metadata, saving can duplicate the JSON metadata block in the output file.

Code

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[R418-420]

+        } else if (comment.startsWith(MetaData.META_FLAG_V1)) {
+            parsedJsonMetaData = parseCommentToJson(comment);
+        }

Evidence
Legacy metadata comments are explicitly dropped from the preserved text buffer via
dumpTextReadSoFarToString(), but the new JSON metadata branch does not. The preserved text
(including comments) is later attached to the first entry’s parsedSerialization/commentsBeforeEntry.
When saving without reformatting and the entry is unchanged, BibEntryWriter writes
parsedSerialization verbatim; additionally, BibDatabaseWriter always writes JSON metadata via
writeMetaDataJson, leading to duplicated JSON blocks (one before the first entry, one in the
metadata section).
jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[372-421]
jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[335-360]
jablib/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java[68-74]
jablib/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java[275-327]

Agent prompt

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

## Issue description
`META_FLAG_V1` JSON metadata comments are parsed but not removed from the parser’s preserved text buffer. This can cause the JSON `@Comment{jabref-meta-0.1.0 ...}` block to be stored as “user comments before the first entry” and later written back verbatim, while `BibDatabaseWriter` also writes a fresh JSON metadata block — resulting in duplicated JSON metadata after saving.
### Issue Context
Legacy JabRef metadata comments call `dumpTextReadSoFarToString()` to ensure metadata comments are rewritten by JabRef and not kept verbatim in the file. The JSON metadata branch should follow the same strategy.
### Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[372-421]
- jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[335-360]
- jablib/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java[68-74]
### Suggested approach
1. In the `comment.startsWith(MetaData.META_FLAG_V1)` branch, after parsing (and/or even on parse failure, consistent with how entrytype comments are treated), call `dumpTextReadSoFarToString()` so the comment is not retained as user text.
2. Consider adding a regression test that:
- Parses a file containing only the JSON metadata comment + an entry.
- Saves with `shouldReformatFile() == false` and the entry unchanged.
- Asserts the output contains only one JSON metadata block (not one before the entry plus one in the metadata section).

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

qodo-free-for-open-source-projects · 2026-02-24T11:29:24Z

+    Optional<JsonObject> parseCommentToJson(String comment) {
+        Gson gson = new Gson();
+        String content = comment.substring(MetaData.META_FLAG_V1.length());
+        return Optional.ofNullable(gson.fromJson(content, JsonObject.class));
+    }


1. parsecommenttojson uncaught jsonsyntaxexception 📘 Rule violation ⛯ Reliability

JSON metadata parsing uses gson.fromJson(...) without handling malformed JSON, which can throw a runtime exception and abort import. This violates the requirement for robust, contextual error handling during parsing of external file content.

Agent Prompt

## Issue description `parseCommentToJson` parses JSON from untrusted file content using `gson.fromJson` without handling malformed JSON, which can throw a runtime exception and crash parsing. ## Issue Context This is part of BibTeX import logic; invalid/malformed metadata comments should not abort import and should instead be reported as a parser exception/warning with location/context. ## Fix Focus Areas - jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[415-427]

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

qodo-free-for-open-source-projects · 2026-02-24T11:29:24Z

+        } else if (comment.startsWith(MetaData.META_FLAG_V1)) {
+            parsedJsonMetaData = parseCommentToJson(comment);
+        }


2. Json meta duplicated on save 🐞 Bug ✓ Correctness

META_FLAG_V1 (@Comment JSON) is parsed but not removed from the raw text buffer, so it can be stored in the first entry’s parsed serialization and later written back verbatim. Since the writer also always emits JSON metadata, saving can duplicate the JSON metadata block in the output file.

Agent Prompt

### Issue description `META_FLAG_V1` JSON metadata comments are parsed but not removed from the parser’s preserved text buffer. This can cause the JSON `@Comment{jabref-meta-0.1.0 ...}` block to be stored as “user comments before the first entry” and later written back verbatim, while `BibDatabaseWriter` also writes a fresh JSON metadata block — resulting in duplicated JSON metadata after saving. ### Issue Context Legacy JabRef metadata comments call `dumpTextReadSoFarToString()` to ensure metadata comments are rewritten by JabRef and not kept verbatim in the file. The JSON metadata branch should follow the same strategy. ### Fix Focus Areas - jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[372-421] - jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java[335-360] - jablib/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java[68-74] ### Suggested approach 1. In the `comment.startsWith(MetaData.META_FLAG_V1)` branch, after parsing (and/or even on parse failure, consistent with how entrytype comments are treated), call `dumpTextReadSoFarToString()` so the comment is not retained as user text. 2. Consider adding a regression test that: - Parses a file containing only the JSON metadata comment + an entry. - Saves with `shouldReformatFile() == false` and the entry unchanged. - Asserts the output contains only one JSON metadata block (not one before the entry plus one in the metadata section).

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

ZiadAbdElFatah · 2026-02-25T13:28:53Z

I won't be able to continue working on the rest of the metadata until this one is reviewed, to be able to make the best out of the rest of the metadata. Also, I think there will be merge conflicts if I try to work on other metadata before this one is merged.

koppor

Wrong architecture.

Separate the convertes

We also miss some data models - and model convertion

Look for "Data Transfer Object" implementation pattern in the net.

koppor · 2026-03-16T10:49:01Z

+                + ";}" + OS.NEWLINE
+                + OS.NEWLINE
+                + "@Comment{jabref-meta-0.1.0" + OS.NEWLINE
+                + "{" + OS.NEWLINE
+                + "  \"saveActions\": {" + OS.NEWLINE
+                + "    \"state\": true," + OS.NEWLINE
+                + "    \"title\": [" + OS.NEWLINE
+                + "      \"lower_case\"" + OS.NEWLINE
+                + "    ]," + OS.NEWLINE
+                + "    \"journal\": [" + OS.NEWLINE
+                + "      \"title_case\"" + OS.NEWLINE
+                + "    ]," + OS.NEWLINE
+                + "    \"day\": [" + OS.NEWLINE
+                + "      \"upper_case\"" + OS.NEWLINE
+                + "    ]" + OS.NEWLINE
+                + "  }" + OS.NEWLINE
+                + "}" + OS.NEWLINE
+                + "}" + OS.NEWLINE;
+


Why no """ `?

I thought it would be better to follow the old style.

koppor · 2026-03-16T10:51:35Z

+        writeMetaDataJson(metaData);
+    }
+
+    private JsonObject serializeSaveActionsToJson(FieldFormatterCleanupActions saveActions) {


Wrong place

See preferences how JabRef handles - see org.jabref.logic.preferences.JabRefCliPreferences and the sub preferences

It is a no go to create a monster class BibDatabaseWriter.

testlens-app · 2026-03-25T20:44:57Z

✅ All tests passed ✅

🏷️ Commit: 7b1c83a
▶️ Tests: 10205 executed
⚪️ Checks: 50/50 completed

Learn more about TestLens at testlens.app.

ZiadAbdElFatah · 2026-03-25T22:29:38Z

Wrong architecture.

Separate the convertes

We also miss some data models - and model convertion

Look for "Data Transfer Object" implementation pattern in the net.

Thanks for providing the correct pattern I studied it well and made the changes.

I removed the @ADR because there were 4 failing checks because of it, I don't know really if removing it is right or not but all the checks now pass, but if removing it is wrong I will restore it again.

calixtus · 2026-04-17T20:10:48Z

Please put the ADR annotations back in.
Was fixed in a recent PR by koppor.

) Bumps org.libreoffice:libreoffice from 24.8.4 to 25.2.7. --- updated-dependencies: - dependency-name: org.libreoffice:libreoffice dependency-version: 25.2.7 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

ZiadAbdElFatah · 2026-04-18T03:28:41Z

Please put the ADR annotations back in. Was fixed in a recent PR by koppor.

I updated the branch and added the ADR annotations back in, but the same checks still fail.

calixtus · 2026-04-18T04:25:19Z

Will be fixed when #15559 is merged

Added unit test for parsing JSON

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Merge branch 'JabRef:main' into fix-for-issue-10371

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ZiadAbdElFatah added 2 commits February 23, 2026 22:24

Merge branch 'main' into fix-for-issue-10371

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Added reading and writing using JSON for save actions

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ZiadAbdElFatah changed the title ~~Added parsing metadata using JSON with a unit test~~ Added reading and writing with JSON for save actions metadata Feb 24, 2026

Merge branch 'main' into fix-for-issue-10371

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ZiadAbdElFatah marked this pull request as ready for review February 24, 2026 11:21

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ZiadAbdElFatah mentioned this pull request Feb 25, 2026

Allow keeping empty field in MultiMergeEntries dialog #15014

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jabref-meta storage in bib file should be improved (by switching to embedded JSON) #10371

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Merge branch 'JabRef:main' into fix-for-issue-10371

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Merge branch 'main' into fix-for-issue-10371

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ZiadAbdElFatah added 2 commits March 25, 2026 21:47

Used the """ for the test strings

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Refactored the architecture to DTO and added converters

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Solved failing check

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Solved failing check

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ZiadAbdElFatah requested a review from koppor March 25, 2026 22:31

ZiadAbdElFatah and others added 3 commits April 18, 2026 05:14

Merge branch 'main' into fix-for-issue-10371

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Added the ADR annotation back

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ZiadAbdElFatah and others added 2 commits April 20, 2026 08:13

Merge branch 'main' into fix-for-issue-10371

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Merge branch 'main' into fix-for-issue-10371

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