AI chatting functionality (#11430)

* Fix the code from code review * Fix from code review and create new AiChatTabWorking * Improve chat history storage code * More fix from code review * Remove obsolete parameter * Add JavaDoc comment * Fix checkstyle * Fix JavaDoc * Fix more checkstyle * More checkstyle fixes * Fix code changes * Improve the PR * Rework ADR-0031 to enable to use another option * Add many LOGGEr.trace statements * Change "message window" to "context window" * Fix compiler errors * Fix issue list index issue of langchain4j * Fix lint issue * Update 0031-store-chats-alongside-database.md * More tracing * Refine logging * Remove closing of AiChatLanguageModel (because it's not closable) * Use external package for OpenAI API connection * Provide a custom executor for RetrievalAugmentor * Fix shutdown issue (I hope) * Refactor classes * Change BibDatabaseChatHistoryFile * Revert BibDatabaseChatHistoryFile to old version because of langchain4j * Make round corners for chat messages * Refactor embeddings generation * Refactor embeddings generation * Refactor embeddings generation * Fix CHANGELOG.md * Remove jpro-mdfx * Add comment * Fix localizations * Fix checkstyle and remove OpenAI from PRIVACY.md * Remove unnecessary comments * Fix privacy notice UI * Introduce new ApiKeyMissingComponent * Thanks Tobiaz Diez for writing such a good EntryEditorTab class * Fix InAnYan/jabref issues * Merge `build.gradle` and `settings.gradle` from main branch * Update ADRs * Implement rethought ADR for chat history * Use OpenAI embedding model * Use Deep Java embedding model * Remove old langchain4j embedding models * Fix checkstyle errors * Fix checkstyle and remove old dependencies * Fixes from code review * Restructure * Fix checkstyle errors * Add API base URL parameter * Fix localization * Fix from code review + ADR * Something broken * Now MistralAI and Hugging Face work * Fix base URL for other LLM providers * Fix base URL for other LLM providers * Refactor MVStore usage * Load embedding model in background * Bump langchain4j version * Fix bug * Fix checkstyle and localization * Implement summarization * Fix checkstyle and localization * Improve PrivacyNoticeComponent * Fix from code review * Update localization * Wrap text * Add padding * Fix markdown * Use stuff algorithm * Add GPT-4o-mini * Make chat model editable * Update context window size and summarization * Fix checkstyle * Update PrivacyNoticeComponent.fxml * Update AI summary tab * Fix localization * Change order so that there is no diff * Reorrder dependencies * Add missing CHANGELOG.md entry * Refine ADR-0033 * Refine ADR0034 * Fix typos * Refine ADR-0036 * Fix ADR-0037 * Fix title case * Fix changes in module-info.java * Readd removed requires org.apache.httpcomponents.core5.httpcore5 * Revert change in JabRefGUI to avoid conflicts * Remove empty lines * Reorder entries in JabRef_en.properties * Simplify SummariesStorage (and add test) * Use region/endregion * Fix position of comment * Add comment why the event bus is needed * Do not show exception to the user - just that an error is occurred (saves %0 in localization) * Use "URL %0" without colon (consistency) * Fix typos * History has to be kept * Remove empty lines * Fix language (hopefully) * Compilefix * Simplify BibDatabaseChatHistoryManager * Fix from code review * Fix issue #103 * Rework embeddings cache clearing * Fix #99 and partially #101 * Partially fixing shutdown issues and UI progress monitor issue * Add "requires scala.library" and add "region:" / "endregion" * More grouping (move de.saxsys.mvvmfx.validation up) * Add alphabetical hint * Fix InAnYan#101 and InAnYan#106 * Discard changes to settings.gradle * Fix InAnYan#105 * Follow-up fix for InAnYan#103 * Follow-up fix for InAnYan#103 * Remove obsolete class * Partially fix InAnYan#98 * We do need dependencies to the AI providers, don't we? * Fix InAnYan#93 * Simplify code * Partially fix InAnYan#92 * Fix checkstyle and localization * Fix hyperlinks and text in ApiKeyMissingComponent * Fixes from code review * Fix InAnYan#120 * Remove "X% work done" messages * Fix InAnYan#114 * Partially fix InAnYan#113 * Partially fix InAnYan#110 * Fix InAnYan#110 * Fix InAnYan#111 * Improve embedding model downloading notifications * Fix InAnYan#124 * Fix InAnYan#122 * Fix wrong context window size when expert settings customization is turned off * Attempt to fix InAnYan#95 * Finally fix InAnYan#105 * Fix InAnYan#108 * Attempt to fix InAnYan#98 * Fix for InAnYan#104 * Fix for InAnYan#98 * Fix for InAnYan#95 (comment) * Fix for InAnYan#98 (comment) * Fix for InAnYan#126 * Fix for InAnYan#115 * Fix for InAnYan#113 * Fix for InAnYan#91 * Fix for InAnYan#121 * Fix for InAnYan#112 and InAnYan#116 * Fix for InAnYan#125 * Fixes from commit comments * Fix for InAnYan#115 * Fix for InAnYan#120 * Fix for InAnYan#132 * Fix for InAnYan#132 * Fix for InAnYan#104 * Fix for InAnYan#118 * Fix for InAnYan#114 * Fix for InAnYan#104 * Store error messages in chat history * Make error be a ChatMessageComponent * Implement delete messages InAnYan#136 * Fix for InAnYan#118 * Fix for InAnYan#92 * Fix checkstyle and localization. And refactoring * Fix for InAnYan#92 * Fix for InAnYan#139 * Show "Delete message" button only when necessary * Fix for InAnYan#83 * Update src/main/java/org/jabref/logic/ai/AiService.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * Update src/main/java/org/jabref/logic/ai/chathistory/BibDatabaseChatHistoryManager.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * Update src/main/java/org/jabref/logic/ai/AiService.java Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * Update src/main/java/org/jabref/gui/Base.css Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * Update src/main/java/org/jabref/gui/Base.css Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> * Fix from code review * Partial fix for InAnYan#125 * Update colors for error message * Fix for InAnYan#145 and InAnYan#142 * Make progress for embedding model download * Fix checkstyle and localization * Add workaround to get FileHistoryMenuTest running again * Small fixes * Revert "Small fixes" This reverts commit 85382a1. * Introduce AiApiKeyProvider * Fix IDE setup instructions * Do not load API keys on startup * Rely on keystore encryption * Prevent mulitple rebuilds when muliple preferences are updated * Fix localization to be more provider independent * Fix method names * Add poor man's solution to notify of API key changes * Reduce calls to key store (and fix key saving) * Fix for InAnYan#148 and partially InAnYan#146 * Revert "Fix for InAnYan#148 and partially InAnYan#146" This reverts commit 5fa3bb5. * Fix for scrolling down when deleting a message * Sort EmbeddingModel enum variants * Fix GenerateSummaryTask progress indication * Fix dark mode * Add notice for embedding models size --------- Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
JabRef · Aug 14, 2024 · 8a0edc2 · 8a0edc2
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diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
@@ -35,7 +35,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest, buildjet-4vcpu-ubuntu-2204-arm]
+        os: [ubuntu-latest, windows-latest, macos-latest, buildjet-8vcpu-ubuntu-2204-arm]
         jdk: [22]
         javafx: [23]
         include:
@@ -45,7 +45,7 @@ jobs:
           - os: windows-latest
             displayName: windows
             archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
-          - os: buildjet-4vcpu-ubuntu-2204-arm
+          - os: buildjet-8vcpu-ubuntu-2204-arm
             displayName: "linux-arm"
             archivePortable: "tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux-arm64.tar.gz && rm -R build/distribution/JabRef"
           - os: macos-latest
@@ -78,7 +78,7 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install pigz and cache (linux)
-        if: (matrix.os == 'ubuntu-latest') || (matrix.os == 'buildjet-4vcpu-ubuntu-2204-arm')
+        if: (matrix.os == 'ubuntu-latest') || (matrix.os == 'buildjet-8vcpu-ubuntu-2204-arm')
         uses: awalsh128/cache-apt-pkgs-action@master
         with:
           packages: pigz
@@ -115,7 +115,7 @@ jobs:
 
       # JavaFX
       - name: Download and extract JavaFX ${{ matrix.javafx }}
-        if: (matrix.os != 'buildjet-4vcpu-ubuntu-2204-arm')
+        if: (matrix.os != 'buildjet-8vcpu-ubuntu-2204-arm')
         shell: bash
         run: |
           cd javafx
@@ -127,7 +127,7 @@ jobs:
               EXTRACT="tar xzf *.tar.gz"
               EXT="tar.gz"
               ;;
-            "buildjet-4vcpu-ubuntu-2204-arm")
+            "buildjet-8vcpu-ubuntu-2204-arm")
               OS="linux"
               EXTRACT="tar xzf *.tar.gz"
               EXT="tar.gz"
@@ -163,19 +163,19 @@ jobs:
           $EXTRACT
           rm *.$EXT
       - name: 'Set JavaFX ${{ matrix.javafx }} (linux, Windows)'
-        if: (matrix.os != 'macos-latest') && (matrix.os != 'buildjet-4vcpu-ubuntu-2204-arm')
+        if: (matrix.os != 'macos-latest') && (matrix.os != 'buildjet-8vcpu-ubuntu-2204-arm')
         run: |
           sed -i '/javafx {/{n;s#version = ".*"#sdk = "javafx/javafx-sdk-${{ matrix.javafx }}"#}' build.gradle
           sed -i "s#jlink {#jlink { addExtraModulePath 'javafx/javafx-jmods-${{ matrix.javafx }}'#" build.gradle
           cat build.gradle
       - name: 'Set JavaFX ${{ matrix.javafx }} (macOS)'
-        if: (matrix.os == 'macos-latest') && (matrix.os != 'buildjet-4vcpu-ubuntu-2204-arm')
+        if: (matrix.os == 'macos-latest') && (matrix.os != 'buildjet-8vcpu-ubuntu-2204-arm')
         run: |
           sed -i '.bak' -e '/javafx {/{n' -e 's#version = ".*"#sdk = "javafx/javafx-sdk-${{ matrix.javafx }}"#;}' build.gradle
           sed -i '.bak' -e "s#jlink {#jlink { addExtraModulePath 'javafx/javafx-jmods-${{ matrix.javafx }}'#" build.gradle
           cat build.gradle
       - name: 'Set JavaFX ${{ matrix.javafx }} (linux-arm)'
-        if: (matrix.os == 'buildjet-4vcpu-ubuntu-2204-arm')
+        if: (matrix.os == 'buildjet-8vcpu-ubuntu-2204-arm')
         # No JavaFX EA build for ARM at https://jdk.java.net/javafx23/, therefore using Maven Central artifact
         run: |
           curl -s "https://search.maven.org/solrsearch/select?q=g:org.openjfx+AND+a:javafx&rows=10&core=gav" > /tmp/versions.json

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
+- We added an AI-based chat for entries with linked PDF files. [#11430](https://github.com/JabRef/jabref/pull/11430)
+- We added an AI-based summarization possibility for entries with linked PDF files. [#11430](https://github.com/JabRef/jabref/pull/11430)
 - We added support for selecting and using CSL Styles in JabRef's OpenOffice/LibreOffice integration for inserting bibliographic and in-text citations into a document. [#2146](https://github.com/JabRef/jabref/issues/2146), [#8893](https://github.com/JabRef/jabref/issues/8893)
 - We added Tools > New library based on references in PDF file... to create a new library based on the references section in a PDF file. [#11522](https://github.com/JabRef/jabref/pull/11522)
 - When converting the references section of a paper (PDF file), more than the last page is treated. [#11522](https://github.com/JabRef/jabref/pull/11522)

diff --git a/build.gradle b/build.gradle
@@ -45,6 +45,7 @@ version = project.findProperty('projVersion') ?: '100.0.0'
 java {
     sourceCompatibility = JavaVersion.VERSION_21
     targetCompatibility = JavaVersion.VERSION_21
+
     // Workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
     // Should be removed as soon as Gradle 7.0.1 is released ( https://github.com/gradle/gradle/issues/16922#issuecomment-828217060 )
     modularity.inferModulePath.set(false)
@@ -125,6 +126,8 @@ repositories {
     maven { url 'https://s01.oss.sonatype.org/content/repositories/snapshots/' }
     maven { url 'https://jitpack.io' }
     maven { url 'https://oss.sonatype.org/content/groups/public' }
+
+    // Required for one.jpro.jproutils:tree-showing
     maven { url 'https://sandec.jfrog.io/artifactory/repo' }
 }
 
@@ -238,12 +241,17 @@ dependencies {
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
         exclude group: 'org.apache.commons.commons-logging'
+        exclude module: 'kotlin-stdlib-jdk8'
+        exclude group: 'com.squareup.retrofit2'
         exclude group: 'org.openjfx'
         exclude group: 'org.apache.logging.log4j'
         exclude group: 'tech.units'
     }
     // Required by gemsfx
     implementation 'tech.units:indriya:2.2'
+    implementation ('com.squareup.retrofit2:retrofit:2.11.0') {
+        exclude group: 'com.squareup.okhttp3'
+    }
 
     implementation 'org.controlsfx:controlsfx:11.2.1'
 
@@ -315,6 +323,25 @@ dependencies {
     // YAML formatting
     implementation 'org.yaml:snakeyaml:2.2'
 
+    // AI
+    implementation 'dev.langchain4j:langchain4j:0.33.0'
+    // Even though we use jvm-openai for LLM connection, we still need this package for tokenization.
+    implementation('dev.langchain4j:langchain4j-open-ai:0.33.0') {
+        exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
+    }
+    implementation('dev.langchain4j:langchain4j-mistral-ai:0.33.0')
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.33.0')
+    implementation 'ai.djl:api:0.29.0'
+    implementation 'ai.djl.pytorch:pytorch-model-zoo:0.29.0'
+    implementation 'ai.djl.huggingface:tokenizers:0.29.0'
+    implementation 'io.github.stefanbratanov:jvm-openai:0.9.3'
+    // openai depends on okhttp, which needs kotlin - see https://github.com/square/okhttp/issues/5299 for details
+    implementation ('com.squareup.okhttp3:okhttp:4.12.0') {
+        exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
+    }
+    // GemxFX also (transitively) depends on kotlin
+    implementation 'org.jetbrains.kotlin:kotlin-stdlib-jdk8:1.9.24'
+
     implementation 'commons-io:commons-io:2.16.1'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.174'
@@ -455,8 +482,8 @@ compileJava {
     options.generatedSourceOutputDirectory.set(file("src-gen/main/java"))
 
     moduleOptions {
-        // TODO: Remove access to internal api
         addExports = [
+                // TODO: Remove access to internal api
                 'javafx.controls/com.sun.javafx.scene.control' : 'org.jabref',
                 'org.controlsfx.controls/impl.org.controlsfx.skin' : 'org.jabref'
         ]
@@ -470,10 +497,10 @@ run {
         application.applicationDefaultJvmArgs = []
     }
 
-    // TODO: Remove access to internal api
     moduleOptions {
         // On a change here, also adapt "application > applicationDefaultJvmArgs"
         addExports = [
+                // TODO: Remove access to internal api
                 'javafx.base/com.sun.javafx.event' : 'org.jabref.merged.module',
                 'javafx.controls/com.sun.javafx.scene.control' : 'org.jabref',
 

diff --git a/docs/decisions/0032-store-chats-in-local-user-folder.md b/docs/decisions/0032-store-chats-in-local-user-folder.md
@@ -0,0 +1,66 @@
+---
+nav_order: 0032
+parent: Decision Records
+---
+# Store Chats Alongside Database
+
+## Context and Problem Statement
+
+Chats with AI should be stored somewhere. But where and how?
+
+## Considered Options
+
+* Inside `.bib` file
+* In local user folder
+* Alongside `.bib` file
+
+## Decision Drivers
+
+* Should work when shared with OneDrive, Dropbox or similar asynchronous services
+* Should work on network drives
+* Should be "easy" for users to follow
+* Should be the same in a shared and non-shared setting (e.g., if Dropbox is used or not should make a difference)
+
+## Decision Outcome
+
+Chosen option: "In local user folder", because
+it's very hard to work with a shared library, if two users will work
+simultaneously on one library, then AI chats file will be absolutely arbitrary
+and unmergable.
+
+## Pros and Cons of the Options
+
+### Inside `.bib` file
+
+* Good, because we already have a machinery for managing the fields and other information of BIB entries
+* Good, because chats are stored inside one file, and if the `.bib` file is moved, the chat history is preserved
+* Bad, because there may be lots of chats and messages and `.bib` file become too cluttered and too big which slows down the processing of `.bib` file
+* Bad, because if user shares a `.bib` file, they will also share chat messages, but chats are not ideal, so user may not
+  want to share them
+
+### In local user folder
+
+One can use `%APPDATA%`, where JabRef stores the Lucene index and other information.
+See `org.jabref.gui.desktop.os.NativeDesktop#getFulltextIndexBaseDirectory` for use in JabRef and
+<https://github.com/harawata/appdirs> for general information.
+
+Concrete example for backup folder: `C:\Users\${username}\AppData\Local\org.jabref\jabref\backups`.
+Example filename: `4a070cf3--Chocolate.bib--2024-03-25--14.20.12.bak`.
+
+* Good, because `.bib` file is kept clean
+* Good, because chat messages are saved locally
+* Neutral, because may be a little harder to implement
+* Bad, because chat messages cannot be easily shared
+* Bad, because when path of a `.bib` file is changed, the chats are lost
+
+### Alongside `.bib` file
+
+* Good, because simple implementation
+* Good, because, the user can send the chats file alongside the `.bib` file if they want to share the chats. If users do not want
+  to share the messages, then they can omit the chats file
+* Good, because `.bib` files is kept clean
+* Bad, because user may not expect that a new file will be created alongside their `.bib` (or other LaTeX-related) files
+* Bad, because, it may be not convenient to share both files (`.bib` file and chats file) in order to share chat history.
+* Bad, because if `.bib` files are edited externally (meaning, not inside the JabRef), then chats file will not be updated correspondingly
+* Bad, because if user moves `.bib` file, they should move the chats file too
+* Bad, because if two persons work in parallel using a OneDrive share, the file is overwritten or a conflict file is generated. ([Dropbox "conflicted copy"](https://help.dropbox.com/en-en/organize/conflicted-copy))
diff --git a/docs/decisions/0033-store-chats-in-mvstore.md b/docs/decisions/0033-store-chats-in-mvstore.md
@@ -0,0 +1,53 @@
+---
+nav_order: 0033
+parent: Decision Records
+---
+
+# Store Chats in MVStore
+
+## Context and Problem Statement
+
+This is a follow-up to [ADR-031](0032-store-chats-in-local-user-folder).
+
+The chats with AI should be saved on exit from JabRef and retrieved on launch. We need to decide the format of
+the serialized messages.
+
+## Decision Drivers
+
+* Easy to implement and maintain
+* Memory-efficient (because JabRef is said to consume much memory)
+
+## Considered Options
+
+* JSON
+* MVStore
+* Custom format
+
+## Decision Outcome
+
+Chosen option: "MVStore", because it is simple and memory-efficient.
+
+## Pros and Cons of the Options
+
+### JSON
+
+* Good, because allows for easy storing and loading of chats
+* Good, because cross-platform
+* Good, because widely used and accepted, so there are lots of libraries for JSON format
+* Good, because it is even possible to reuse the chats file for other purposes
+* Good, because has potential for being mergeable by external tooling
+* Bad, because too verbose (meaning the file size could be much smaller)
+
+### MVStore
+
+* Good, because automatic loading and saving to disk
+* Good, because memory-efficient
+* Bad, because does not support mutable values in maps.
+* Bad, because the order of messages need to be "hand-crafted" (e.g., by mapping from an Integer to the concrete message), since [MVStore does not support storing list which update](https://github.com/koppor/mvstore-mwe/pull/1).
+* Bad, because it stores data as key-values, but not as a custom data type (like tables in RDBMS)
+
+### Custom format
+
+* Good, because we have the full control
+* Bad, because involves writing our own language and parser
+* Bad, because we need to implement optimizations found in databases on our own (storing some data in RAM, other on disk)
diff --git a/docs/decisions/0034-use-citation-key-for-grouping-chat-messages.md b/docs/decisions/0034-use-citation-key-for-grouping-chat-messages.md
@@ -0,0 +1,69 @@
+---
+nav_order: 0034
+parent: Decision Records
+---
+
+# Use Citation Key for Grouping Chat Messages
+
+## Context and Problem Statement
+
+Because we store chat messages not inside a BIB entry in `.bib` filecc, the chats file is represented as a map to
+BIB entry and a list of messages. We need to specify the key of this map. Turns out, it is not that easy.
+
+## Decision Drivers
+
+* The key should exist for every BIB entry
+* The key should be unique along other BIB entries in one library file
+* The key should not change at run-time, between launches of JabRef, and should be cross-platform (most important)
+
+## Considered Options
+
+* `BibEntry` Java object
+* `BibEntry`'s `id`
+* `BibEntry`'s Citation key
+* `BibEntry`'s `ShareId`
+
+## Decision Outcome
+
+Chosen option: "`BibEntry`'s Citation key", because this is the only choice that complains to the third point in Decision Drivers.
+
+### Positive Consequences
+
+* Easy to implement
+* Cross-platform
+
+### Negative Consequences
+
+* If the citation key is changed externally, then the chats file becomes out-of-sync
+* Additional user interaction in order to make the citation key complain the first and second points of Decision Drivers
+
+## Pros and Cons of the Options
+
+### `BibEntry` Java object
+
+Very bad, because it works only at run-time and is not stable.
+
+### `BibEntry`'s `id`
+
+JabRef stores a unique identifier for each `BibEntry`.
+This identifier is created on each load of a library (and not stored permanently).
+
+Very bad, for the same reasons as `BibEntry` Java object.
+
+### `BibEntry`'s Citation key
+
+* Good, because it is cross-platform, stable (meaning stays the same across launches of JabRef)
+* Bad, because it is not guaranteed that citation key exists on `BibEntry`, and that it is unique across other
+`BibEntriy`'s' in the library
+
+### `BibEntry`'s `ShareId`
+
+[ADR-0027](0027-synchronization.md) describes the procedure of synchronization of a Bib(La)TeX library with a server.
+Thereby, also local and remote entries need to be kept consistent.
+The solution chosen there is that the **server** creates a UUID for each entry.
+
+This approach cannot be used here, because there is no server running which we can ask for an UUID of an entry.
+
+## More Information
+
+Refer to [issue #160](https://github.com/JabRef/jabref/issues/160) in JabRef main repository