Fix PushToPreferences reset and import by calixtus · Pull Request #15395 · JabRef/jabref

calixtus · 2026-03-23T16:46:27Z

Related issues and pull requests

Follow-up to #14410

PR Description

Qodo:
• Removed redundant defaultFontSize property from WorkspacePreferences
• Refactored PushToApplicationPreferences to use factory pattern with getDefault() and setAll() methods
• Consolidated push application path constants into a single Map for maintainability
• Fixed preference import/export to properly restore PushToApplicationPreferences state
• Moved ImportFormatPreferences and LayoutFormatterPreferences to interface defaults
• Removed duplicate VSCode application entry in push applications list

Steps to test

Open File > Preferences
Clear or import preference

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

…ferences

calixtus · 2026-03-23T21:37:57Z

Checkstyle fails because of checkstyle/checkstyle#19342 / checkstyle/checkstyle#17052

qodo-free-for-open-source-projects · 2026-03-26T21:51:07Z

Review Summary by Qodo

Refactor preferences handling and fix PushToApplicationPreferences reset/import

🐞 Bug fix ✨ Enhancement

Walkthroughs

Description

• Removed redundant defaultFontSize property from WorkspacePreferences
• Refactored PushToApplicationPreferences to use factory pattern with getDefault() and setAll()
  methods
• Consolidated push application path constants into a single Map for maintainability
• Fixed preference import/export to properly restore PushToApplicationPreferences state
• Moved ImportFormatPreferences and LayoutFormatterPreferences to interface defaults
• Removed duplicate VSCode application entry in push applications list

Diagram

flowchart LR
  A["PushToApplicationPreferences"] -->|"getDefault()"| B["Default Instance"]
  A -->|"setAll()"| C["Copy State"]
  D["JabRefCliPreferences"] -->|"getPushToApplicationPreferencesFromBackingStore()"| E["Load from Storage"]
  F["Import/Export"] -->|"restore"| A
  G["WorkspacePreferences"] -->|"removed defaultFontSize"| H["Simplified"]

File Changes

1. jabgui/src/main/java/org/jabref/gui/WorkspacePreferences.java 🐞 Bug fix +0/-9

Removed redundant defaultFontSize property

jabgui/src/main/java/org/jabref/gui/WorkspacePreferences.java

2. jabgui/src/main/java/org/jabref/gui/preferences/JabRefGuiPreferences.java 🐞 Bug fix +0/-1

Removed defaultFontSize from workspace preferences loading

jabgui/src/main/java/org/jabref/gui/preferences/JabRefGuiPreferences.java

3. jabgui/src/main/java/org/jabref/gui/preferences/external/ExternalTabViewModel.java ✨ Enhancement +12/-14

Simplified PushToApplicationPreferences initialization with factory pattern

jabgui/src/main/java/org/jabref/gui/preferences/external/ExternalTabViewModel.java

View more (8)

4. jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplication.java Formatting +4/-1

Reformatted method signature for readability

jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplication.java

5. jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplicationSettings.java ✨ Enhancement +2/-8

Simplified storeSettings to directly modify command paths map

jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplicationSettings.java

6. jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplications.java 🐞 Bug fix +1/-2

Removed duplicate VSCode application entry

jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplications.java

7. jabgui/src/main/java/org/jabref/gui/theme/ThemeManager.java ✨ Enhancement +3/-2

Updated font size logic to use default factory method

jabgui/src/main/java/org/jabref/gui/theme/ThemeManager.java

8. jablib/src/main/java/org/jabref/logic/preferences/CliPreferences.java ✨ Enhancement +18/-4

Moved ImportFormatPreferences and LayoutFormatterPreferences to defaults

jablib/src/main/java/org/jabref/logic/preferences/CliPreferences.java

9. jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java ✨ Enhancement +90/-137

Refactored PushToApplicationPreferences initialization and storage logic

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java

10. jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java ✨ Enhancement +38/-10

Added factory pattern and setAll method for state management

jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java

11. jabgui/src/main/resources/org/jabref/gui/preferences/external/ExternalTab.fxml Formatting +1/-1

Removed editable attribute from SearchableComboBox

jabgui/src/main/resources/org/jabref/gui/preferences/external/ExternalTab.fxml

qodo-free-for-open-source-projects · 2026-03-26T21:51:08Z

Code Review by Qodo

🐞 Bugs (3) 📘 Rule violations (2) 📎 Requirement gaps (0) 📐 Spec deviations (0)

1. getCommandPaths() mutated directly 📘 Rule violation ⛯ Reliability ⭐ New

Description

GuiPushToApplicationSettings.storeSettings() mutates the map returned by the preferences getter
via put(...) instead of creating a mutable copy and setting it back. This can break if the
returned map is immutable or shared, violating the rule to defensively copy before modifying
preference-returned collections.

Code

jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplicationSettings.java[79]
+        preferences.getCommandPaths().put(application.getDisplayName(), path.getText());

Evidence
PR Compliance ID 30 forbids mutating collections returned by preference getters without copying to a
mutable collection first. The new code writes into preferences.getCommandPaths() directly using
put(...).
jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplicationSettings.java[76-80]
Best Practice: Learned patterns

Agent prompt

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

## Issue description
`GuiPushToApplicationSettings.storeSettings()` directly mutates the map returned by `preferences.getCommandPaths()`. Per compliance, preference-returned collections should be treated as potentially immutable/shared and must be copied before modification.

## Issue Context
The previous implementation created a new `HashMap<>(preferences.getCommandPaths())`, updated it, then stored it back. The new implementation uses `put` on the getter result.

## Fix Focus Areas
- jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplicationSettings.java[76-80]

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2. Optional.get() in switch 📘 Rule violation ⛯ Reliability

Description

New code calls Optional.get() without proving presence, which can throw NoSuchElementException
when the key is unknown/corrupt. This risks crashes during preference persistence and violates the
safe-access requirement.

Code

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[R1107-1115]

+    private void storePushToApplicationPath(Map<String, String> commandPair) {
+        commandPair.forEach((key, value) -> {
+            // is only for the preferences and therefore is okay to throw NoSuchElementException
+            switch (PushApplications.getApplicationByDisplayName(key).get()) {
+                case PushApplications.EMACS ->
+                        put(PUSH_EMACS_PATH, value);
+                case PushApplications.LYX ->
+                        put(PUSH_LYXPIPE, value);
+                case PushApplications.TEXMAKER ->

Evidence
PR Compliance ID 32 forbids unsafe Optional access such as Optional.get() without proven presence.
The added code uses PushApplications.getApplicationByDisplayName(key).get() inside
storePushToApplicationPath, which can throw if the Optional is empty.
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1107-1115]
Best Practice: Learned patterns

Agent prompt

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

## Issue description
`storePushToApplicationPath` calls `Optional.get()` on the result of `PushApplications.getApplicationByDisplayName(key)` without guaranteeing the Optional is present, which can throw `NoSuchElementException`.
## Issue Context
This method processes preference keys/values and may encounter unexpected/unknown keys (e.g., corrupted prefs, future values, manual edits). Compliance requires safe Optional access.
## Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1107-1131]
Suggested direction:
- Replace `.get()` with `ifPresent(...)` (ignore unknown keys) or `orElseThrow(...)` with a clear, handled exception path (if unknown keys should be treated as errors), or provide a safe default mapping.

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

3. Import refresh no-op 🐞 Bug ✓ Correctness

Description

JabRefCliPreferences#importPreferences copies each cached preference object onto itself
(setAll(getX())), so values imported into the Java Preferences backing store are never loaded into
the in-memory preferences objects.

Code

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[R1044-1045]
+        getProxyPreferences().setAll(getProxyPreferences());
+        getPushToApplicationPreferences().setAll(getPushToApplicationPreferences());

Evidence
After importing into the backing store, the code performs setAll(getProxyPreferences()) and
setAll(getPushToApplicationPreferences()), which are self-assignments and therefore cannot reflect
newly imported backing-store values. Both getProxyPreferences() and
getPushToApplicationPreferences() cache instances, so without re-reading from the backing store,
imported values won't apply.
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1037-1046]
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1337-1343]
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1080-1086]

Agent prompt

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

## Issue description
`importPreferences` imports into the Java Preferences backing store, but then performs self-assignments (`setAll(getX())`), so imported values are never applied.
### Issue Context
Both proxy and push-to-application preferences are cached in fields and only initialized once.
### Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1037-1046]
- jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1080-1105]
- jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1337-1374]
### Implementation notes
After `importPreferencesToBackingStore(path)`, rebuild fresh objects from the backing store and then `setAll` onto the cached instances, using the *current* values as defaults for missing keys. For example:
- `ProxyPreferences merged = getProxyPreferencesFromBackingStore(getProxyPreferences()); getProxyPreferences().setAll(merged);`
- `PushToApplicationPreferences merged = getPushToApplicationPreferencesFromBackingStore(getPushToApplicationPreferences()); getPushToApplicationPreferences().setAll(merged);`
(Ensure the push defaults-merging uses correct default map keys; see the separate finding.)

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

View more (2)

4. Push paths not persisted 🐞 Bug ⛯ Reliability

Description

JabRefCliPreferences listens to command-path changes using a property ChangeListener on the
MapProperty, but PushToApplicationPreferences updates the map via clear/putAll, which does not fire
a property change; thus storePushToApplicationPath is never invoked and changes are not written to
PREFS_NODE.

Code

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1088]
+        pushToApplicationPreferences.getCommandPaths().addListener((_, _, newValue) -> storePushToApplicationPath(newValue));

Evidence
The listener registered is a 3-arg ChangeListener on the MapProperty, which only triggers when the
property value (map reference) is replaced. However, PushToApplicationPreferences#setCommandPaths
and #setAll mutate the existing observable map via clear()+putAll(), so no property change occurs
and persistence via storePushToApplicationPath is skipped.
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1085-1092]
jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java[61-68]
jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java[82-89]
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1107-1131]

Agent prompt

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

## Issue description
Push-to-application command path updates are not persisted because the code registers a ChangeListener on the MapProperty instead of a MapChangeListener for map content mutations.
### Issue Context
`PushToApplicationPreferences#setCommandPaths` and `setAll` mutate the existing observable map (clear/putAll) without replacing the MapProperty value.
### Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1087-1092]
- jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java[61-89]
### Implementation notes
Replace the current listener with a `MapChangeListener` (or `InvalidationListener`) observing map content changes. For example:
- `pushToApplicationPreferences.getCommandPaths().addListener((MapChangeListener<String,String>) change -> storePushToApplicationPath(pushToApplicationPreferences.getCommandPaths()));`
Alternatively, change `setCommandPaths` to replace the property value (set a new observable map) so a ChangeListener would fire—but the MapChangeListener approach is the most direct.

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5. Push defaults lookup broken 🐞 Bug ✓ Correctness

Description

readPushToApplicationPath uses preference-key constants (e.g., PUSH_EMACS_PATH) to look up defaults
in a map that is keyed by application display names, so it falls back to empty strings and loses
OS-detected defaults.

Code

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[R1139-1147]

+        commands.put(PushApplications.EMACS.getDisplayName(), get(PUSH_EMACS_PATH, defaults.getOrDefault(PUSH_EMACS_PATH, "")));
+        commands.put(PushApplications.LYX.getDisplayName(), get(PUSH_LYXPIPE, defaults.getOrDefault(PUSH_LYXPIPE, "")));
+        commands.put(PushApplications.TEXMAKER.getDisplayName(), get(PUSH_TEXMAKER_PATH, defaults.getOrDefault(PUSH_TEXMAKER_PATH, "")));
+        commands.put(PushApplications.TEXSTUDIO.getDisplayName(), get(PUSH_TEXSTUDIO_PATH, defaults.getOrDefault(PUSH_TEXSTUDIO_PATH, "")));
+        commands.put(PushApplications.TEXWORKS.getDisplayName(), get(PUSH_TEXWORKS_PATH, defaults.getOrDefault(PUSH_TEXWORKS_PATH, "")));
+        commands.put(PushApplications.VIM.getDisplayName(), get(PUSH_VIM, defaults.getOrDefault(PUSH_VIM, "")));
+        commands.put(PushApplications.WIN_EDT.getDisplayName(), get(PUSH_WINEDT_PATH, defaults.getOrDefault(PUSH_WINEDT_PATH, "")));
+        commands.put(PushApplications.SUBLIME_TEXT.getDisplayName(), get(PUSH_SUBLIME_TEXT_PATH, defaults.getOrDefault(PUSH_SUBLIME_TEXT_PATH, "")));
+        commands.put(PushApplications.VSCODE.getDisplayName(), get(PUSH_VSCODE_PATH, defaults.getOrDefault(PUSH_VSCODE_PATH, "")));

Evidence
PushToApplicationPreferences.getDefault() builds its commandPaths map keyed by
PushApplications.*.getDisplayName() (e.g., "Emacs"), but readPushToApplicationPath tries to read
defaults from that map using keys like "emacsPath" (PUSH_EMACS_PATH). As a result,
defaults.getOrDefault(PUSH_EMACS_PATH, "") always misses and returns "", discarding the intended
OS.detectProgramPath defaults.
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1136-1148]
jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java[37-55]
jablib/src/main/java/org/jabref/logic/push/PushApplications.java[7-16]
jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[415-427]

Agent prompt

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

## Issue description
`readPushToApplicationPath` reads defaults from a `commandPaths` map keyed by application display names, but uses preference-key constants for lookup, so it always falls back to empty strings.
### Issue Context
`PushToApplicationPreferences.getDefault().getCommandPaths()` is keyed by `PushApplications.*.getDisplayName()`.
### Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java[1139-1147]
- jablib/src/main/java/org/jabref/logic/push/PushToApplicationPreferences.java[37-55]
### Implementation notes
Change default lookups to use display-name keys, e.g.
- `get(PUSH_EMACS_PATH, defaults.getOrDefault(PushApplications.EMACS.getDisplayName(), ""))`
Repeat for each application entry. This preserves existing preference storage keys (PUSH_* constants) while correctly sourcing default values from the defaults command-path map.

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

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testlens-app · 2026-03-26T21:51:12Z

✅ All tests passed ✅

🏷️ Commit: 40b18aa
▶️ Tests: 10203 executed
⚪️ Checks: 94/94 completed

Learn more about TestLens at testlens.app.

calixtus · 2026-03-26T22:08:07Z

            <Label text="%Application to push entries to"/>
            <SearchableComboBox fx:id="pushToApplicationCombo"
-                                prefWidth="200.0" GridPane.columnIndex="1"  editable="false"/>
+                                prefWidth="200.0" GridPane.columnIndex="1"/>


default behaviour

…o fix-group-icons * 'fix-group-icons' of github.com:geovani-rocha/jabref: (26 commits) chore(deps): update dependency org.apache.logging.log4j:log4j-to-slf4j to v2.25.4 (JabRef#15436) chore(deps): update jackson monorepo to v3.1.1 (JabRef#15435) Fix PushToPreferences reset and import (JabRef#15395) Add fulltext fetcher for Wiley via their TDM API (JabRef#15388) Embed in-text nature in reference marks for CSL citations (JabRef#15381) Chore(deps): Bump com.gradleup.shadow:shadow-gradle-plugin (JabRef#15430) Fix not on fx thread exceptions for cleanup and cite key generator (JabRef#15424) Revert "Update gradle to nightly of 2026-03-23 (JabRef#15372)" feat: add benchmarks for Lucene fulltext search and linked file indexing, including setup and teardown of the index. (JabRef#15385) Chore(deps): Bump org.openrewrite.recipe:rewrite-recipe-bom (JabRef#15418) Add claude gitignore (JabRef#15413) Fix group filter icon in side pane (JabRef#15408) Add new prs_link feature Chore(deps): Bump org.glassfish.hk2:hk2-api in /versions (JabRef#15422) Chore(deps): Bump org.openrewrite.rewrite from 7.28.2 to 7.29.0 (JabRef#15419) Chore(deps): Bump jablib/src/main/resources/csl-styles (JabRef#15417) Fix for inconsistent "hide tab bar" behavior (JabRef#15409) Update dependency org.glassfish.hk2:hk2-utils to v4 (JabRef#15407) Persist file notifications (JabRef#15403) Update dependency org.glassfish.hk2:hk2-locator to v4 (JabRef#15405) ...

* Initial cleanups * Adapt PushToApplicationPreferences * Fix artifact * Cleanup in WorkspacePreferences * Fix import * Fix and simplify Map of command paths * Fix duplicate VSCode application * Stylistic changes * Fix empty strings in prefs * Fix resetting of application settings * Fix checkstyle --------- Co-authored-by: Carl Christian Snethlage <calixtus@users.noreply.github.com>

calixtus added 5 commits March 16, 2026 20:13

Initial cleanups

f2fabb2

Adapt PushToApplicationPreferences

048bacc

Merge remote-tracking branch 'upstream/main' into cli_prefs_pushtopre…

ba4e977

…ferences

Fix artifact

be937bf

Cleanup in WorkspacePreferences

2bde4e1

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calixtus added dev: code-quality Issues related to code or architecture decisions component: preferences status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers labels Mar 23, 2026

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calixtus changed the title ~~Cli prefs pushtopreferences~~ Fix PushToPreferences reset and import Mar 23, 2026

Fix import

cbe39a8

calixtus marked this pull request as draft March 23, 2026 19:48

calixtus removed the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Mar 23, 2026

Fix and simplify Map of command paths

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calixtus added 4 commits March 26, 2026 15:02

Fix duplicate VSCode application

bd2fce5

Stylistic changes

2370ad5

Fix empty strings in prefs

f0722d0

Fix resetting of application settings

f45fb15

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Fix checkstyle

81b839d

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calixtus added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Mar 26, 2026

Merge branch 'main' into cli_prefs_pushtopreferences

40b18aa

calixtus marked this pull request as ready for review March 26, 2026 21:50

calixtus enabled auto-merge March 26, 2026 21:50

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Comment thread jabgui/src/main/java/org/jabref/gui/push/GuiPushToApplicationSettings.java

calixtus commented Mar 26, 2026

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subhramit approved these changes Mar 27, 2026

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calixtus added this pull request to the merge queue Mar 27, 2026

github-actions Bot added the status: to-be-merged PRs which are accepted and should go into the merge-queue. label Mar 27, 2026

Merged via the queue into main with commit 5772d68 Mar 27, 2026
94 of 95 checks passed

calixtus deleted the cli_prefs_pushtopreferences branch March 27, 2026 21:21

pluto-han mentioned this pull request Mar 28, 2026

Fix: Unable to remove multiline property from field #15242

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calixtus mentioned this pull request Apr 6, 2026

Reset and Import for abbreviation prefs and small fixes #15503

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Fix PushToPreferences reset and import#15395

Fix PushToPreferences reset and import#15395
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✅ All tests passed ✅

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