Introduces test http server

.gitattributes

@@ -12,6 +12,8 @@ gradlew text eol=lf
 
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol
+# Exception: The files used for the http server test - they should have linux line endings
+src/test/resources/org/jabref/http/server/*.bib text eol=lf
 
 # Citavi needs to be LF line ending
 # This overwrites the setting of "*.bib"

build.gradle

@@ -179,6 +179,8 @@ dependencies {
     implementation "org.tinylog:tinylog-api:2.6.1"
     implementation "org.tinylog:slf4j-tinylog:2.6.1"
     implementation "org.tinylog:tinylog-impl:2.6.1"
+    // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
+    implementation 'org.slf4j:jul-to-slf4j:2.0.7'
 
     implementation 'de.undercouch:citeproc-java:3.0.0-beta.2'
 
@@ -199,6 +201,24 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
+    // JAX-RS implemented by Jersey
+    // API
+    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.1.0'
+    // Implementation of the API
+    implementation 'org.glassfish.jersey.core:jersey-server:3.1.1'
+    // injection framework
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.1'
+    implementation 'org.glassfish.hk2:hk2-api:2.6.1'
+    // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
+    // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
+    // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
+    // HTTP server
+    // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.1'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.1'
+    // Allow objects "magically" to be mapped to JSON using GSON
+    // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
+
     testImplementation 'io.github.classgraph:classgraph:4.8.157'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.9.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.9.2'

docs/decisions/0027-http-return-bibtex-string.md

@@ -0,0 +1,53 @@
+---
+nav_order: 27
+parent: Decision Records
+---
+<!-- we need to disable MD025, because we use the different heading "ADR Template" in the homepage (see above) than it is foreseen in the template -->
+<!-- markdownlint-disable-next-line MD025 -->
+# Return BibTeX string and CSL Item JSON in the API
+
+## Context and Problem Statement
+
+In the context of an http server, when a http client `GETs` a JSON data structure containing BibTeX data, which format should that have?
+
+## Considered Options
+
+* Offer both, BibTeX string and CSL JSON
+* Return BibTeX as is as string
+* Convert BibTeX to JSON
+
+## Decision Outcome
+
+Chosen option: "Offer both, BibTeX string and CSL JSON", because there are many browser libraries out there being able to parse BibTeX. Thus, we don't need to convert it.
+
+## Pros and Cons of the Options
+
+### Offer both, BibTeX string and CSL JSON
+
+- Good, because this follows "Backend for Frontend"
+- Good, because Word Addin works seamless with the data provided (and does not need another dependency)
+- Good, because other clients can work with BibTeX data
+- Bad, because two serializations have to be kept
+
+### Return BibTeX as is as string
+
+- Good, because we don't need to think about any conversion
+- Bad, because it is unclear how to ship BibTeX data where the entry is dependent on
+- Bad, because client needs add additional parsing logic
+
+### Convert BibTeX to JSON
+
+More thought has to be done when converting to JSON.
+There seems to be a JSON format from [@citation-js/plugin-bibtex](https://www.npmjs.com/package/@citation-js/plugin-bibtex).
+We could do an additional self-made JSON format, but this increases the number of available JSON serializations for BibTeX.
+
+- Good, because it could flatten BibTeX data (example: `author = first # " and " # second`)
+- Bad, because conversion is difficult in BibTeX special cases. For instance, if Strings are used (example: `author = first # " and " # second`) and one doesn't want to flatten ("normalize") this.
+
+## More Information
+
+Existing JavaScript BibTeX libraries:
+
+* [bibtex-js](https://github.com/digitalheir/bibtex-js)
+* [bibtexParseJS](https://github.com/ORCID/bibtexParseJs)
+* [@citation-js/plugin-bibtex](https://www.npmjs.com/package/@citation-js/plugin-bibtex)

src/main/java/module-info.java

@@ -15,6 +15,9 @@
     requires afterburner.fx;
     requires com.jfoenix;
     requires de.saxsys.mvvmfx;
+    requires reactfx;
+    requires de.saxsys.mvvmfx.validation;
+    requires org.fxmisc.flowless;
 
     requires org.kordamp.ikonli.core;
     requires org.kordamp.ikonli.javafx;
@@ -38,6 +41,7 @@
 
     // Logging
     requires org.slf4j;
+    requires jul.to.slf4j;
     requires org.tinylog.api;
     requires org.tinylog.api.slf4j;
     requires org.tinylog.impl;
@@ -46,47 +50,58 @@
     with org.jabref.gui.logging.GuiWriter,
          org.jabref.gui.logging.ApplicationInsightsWriter;
 
-    // Preferences and XML
     requires java.prefs;
+
+    // Annotations (@PostConstruct)
+    requires jakarta.annotation;
+    requires jakarta.inject;
+
+    // http server and client exchange
+    requires java.net.http;
+    requires jakarta.ws.rs;
+    requires grizzly.framework;
+
+    // data mapping
     requires jakarta.xml.bind;
+    requires jdk.xml.dom;
+    requires com.google.gson;
+    requires com.fasterxml.jackson.databind;
+    requires com.fasterxml.jackson.dataformat.yaml;
+    requires com.fasterxml.jackson.datatype.jsr310;
     // needs to be loaded here as it's otherwise not found at runtime
     requires org.glassfish.jaxb.runtime;
-    requires jdk.xml.dom;
 
-    // Annotations (@PostConstruct)
-    requires jakarta.annotation;
+    // dependency injection using HK2
+    requires org.glassfish.hk2.api;
 
     // Microsoft application insights
     requires applicationinsights.core;
     requires applicationinsights.logging.log4j2;
 
-    // Libre Office
-    requires org.libreoffice.uno;
-
-    // Other modules
-    requires com.google.common;
-    requires jakarta.inject;
-    requires reactfx;
-    requires commons.cli;
-    requires com.github.tomtung.latex2unicode;
-    requires fastparse;
-    requires jbibtex;
-    requires citeproc.java;
-    requires de.saxsys.mvvmfx.validation;
-    requires com.google.gson;
+    // http clients
     requires unirest.java;
     requires org.apache.httpcomponents.httpclient;
     requires org.jsoup;
-    requires org.apache.commons.csv;
-    requires io.github.javadiffutils;
-    requires java.string.similarity;
+
+    // SQL databases
     requires ojdbc10;
     requires org.postgresql.jdbc;
     requires org.mariadb.jdbc;
     uses org.mariadb.jdbc.credential.CredentialPlugin;
+
+    // Apache Commons and other (similar) helper libraries
+    requires commons.cli;
+    requires org.apache.commons.csv;
     requires org.apache.commons.lang3;
-    requires org.antlr.antlr4.runtime;
-    requires org.fxmisc.flowless;
+    requires com.google.common;
+    requires io.github.javadiffutils;
+    requires java.string.similarity;
+
+    requires com.github.tomtung.latex2unicode;
+    requires fastparse;
+
+    requires jbibtex;
+    requires citeproc.java;
 
     requires pdfbox;
     requires xmpbox;
@@ -95,26 +110,27 @@
     requires flexmark;
     requires flexmark.util.ast;
     requires flexmark.util.data;
-    requires com.h2database.mvstore;
 
     // fulltext search
     requires org.apache.lucene.core;
     // In case the version is updated, please also adapt SearchFieldConstants#VERSION to the newly used version
     uses org.apache.lucene.codecs.lucene94.Lucene94Codec;
-
     requires org.apache.lucene.queryparser;
     uses org.apache.lucene.queryparser.classic.MultiFieldQueryParser;
     requires org.apache.lucene.analysis.common;
     requires org.apache.lucene.highlighter;
 
-    requires com.fasterxml.jackson.databind;
-    requires com.fasterxml.jackson.dataformat.yaml;
-    requires com.fasterxml.jackson.datatype.jsr310;
     requires net.harawata.appdirs;
     requires com.sun.jna;
     requires com.sun.jna.platform;
 
     requires org.eclipse.jgit;
     uses org.eclipse.jgit.transport.SshSessionFactory;
     uses org.eclipse.jgit.lib.GpgSigner;
+
+    // other libraries
+    requires com.h2database.mvstore;
+    requires org.antlr.antlr4.runtime;
+    requires org.libreoffice.uno;
+
 }

src/main/java/org/jabref/cli/Launcher.java

@@ -33,6 +33,7 @@
 import org.apache.commons.cli.ParseException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.slf4j.bridge.SLF4JBridgeHandler;
 import org.tinylog.configuration.Configuration;
 
 /**
@@ -47,6 +48,7 @@ public class Launcher {
     private static String[] ARGUMENTS;
 
     public static void main(String[] args) {
+        routeLoggingToSlf4J();
         ARGUMENTS = args;
         addLogToDisk();
         try {
@@ -85,6 +87,11 @@ public static void main(String[] args) {
         }
     }
 
+    private static void routeLoggingToSlf4J() {
+        SLF4JBridgeHandler.removeHandlersForRootLogger();
+        SLF4JBridgeHandler.install();
+    }
+
     /**
      * This needs to be called as early as possible. After the first log write, it
      * is not possible to alter
@@ -93,10 +100,10 @@ public static void main(String[] args) {
     private static void addLogToDisk() {
         Path directory = Path.of(AppDirsFactory.getInstance()
                                                .getUserDataDir(
-                OS.APP_DIR_APP_NAME,
-                "logs",
-                OS.APP_DIR_APP_AUTHOR))
-                .resolve(new BuildInfo().version.toString());
+                                                       OS.APP_DIR_APP_NAME,
+                                                       "logs",
+                                                       OS.APP_DIR_APP_AUTHOR))
+                             .resolve(new BuildInfo().version.toString());
         try {
             Files.createDirectories(directory);
         } catch (IOException e) {
@@ -187,9 +194,9 @@ private static void clearOldSearchIndices() {
                         && !path.equals(currentIndexPath)) {
                     LOGGER.info("Deleting out-of-date fulltext search index at {}.", path);
                     Files.walk(path)
-                            .sorted(Comparator.reverseOrder())
-                            .map(Path::toFile)
-                            .forEach(File::delete);
+                         .sorted(Comparator.reverseOrder())
+                         .map(Path::toFile)
+                         .forEach(File::delete);
                 }
             }
         } catch (IOException e) {

src/main/java/org/jabref/gui/preferences/network/NetworkTabViewModel.java

@@ -376,7 +376,7 @@ public void addCertificateFile() {
                 .build();
 
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(certPath -> SSLCertificate.fromPath(certPath).ifPresent(sslCertificate -> {
-            if (!trustStoreManager.isCertificateExist(formatCustomAlias(sslCertificate.getSHA256Thumbprint()))) {
+            if (!trustStoreManager.certificateExists(formatCustomAlias(sslCertificate.getSHA256Thumbprint()))) {
                 customCertificateListProperty.add(CustomCertificateViewModel.fromSSLCertificate(sslCertificate)
                                                                             .setPath(certPath.toAbsolutePath().toString()));
             } else {

src/main/java/org/jabref/http/MediaType.java

@@ -0,0 +1,6 @@
+package org.jabref.http;
+
+public class MediaType {
+    public static final String BIBTEX = "application/x-bibtex";
+    public static final String JSON_CSL_ITEM = "application/x-bibtex-library-csl+json";
+}

src/main/java/org/jabref/http/dto/BibEntryDTO.java

@@ -0,0 +1,71 @@
+package org.jabref.http.dto;
+
+import java.io.IOException;
+import java.io.StringWriter;
+
+import org.jabref.logic.bibtex.BibEntryWriter;
+import org.jabref.logic.bibtex.FieldWriter;
+import org.jabref.logic.bibtex.FieldWriterPreferences;
+import org.jabref.logic.exporter.BibWriter;
+import org.jabref.model.database.BibDatabaseMode;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.SharedBibEntryData;
+
+import com.google.common.base.MoreObjects;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * The data transfer object (DTO) for an BibEntry
+ *
+ * @param sharingMetadata the data used for sharing
+ * @param userComments the comments before the BibTeX entry
+ * @param citationKey the citation key (duplicated from BibEntry to ease processing by the client)
+ * @param bibtex the BibEntry as BibTeX string (see ADR-0027 for more information, why we don't use a HashMap / JSON)
+ */
+public record BibEntryDTO(SharedBibEntryData sharingMetadata, String userComments, String citationKey, String bibtex) implements Comparable<BibEntryDTO> {
+
+    public static final Logger LOGGER = LoggerFactory.getLogger(BibEntryDTO.class);
+
+    public BibEntryDTO(BibEntry bibEntry, BibDatabaseMode bibDatabaseMode, FieldWriterPreferences fieldWriterPreferences, BibEntryTypesManager bibEntryTypesManager) {
+        this(bibEntry.getSharedBibEntryData(),
+                bibEntry.getUserComments(),
+                bibEntry.getCitationKey().orElse(""),
+                convertToString(bibEntry, bibDatabaseMode, fieldWriterPreferences, bibEntryTypesManager)
+        );
+    }
+
+    private static String convertToString(BibEntry entry, BibDatabaseMode bibDatabaseMode, FieldWriterPreferences fieldWriterPreferences, BibEntryTypesManager bibEntryTypesManager) {
+        StringWriter rawEntry = new StringWriter();
+        BibWriter bibWriter = new BibWriter(rawEntry, "\n");
+        BibEntryWriter bibtexEntryWriter = new BibEntryWriter(new FieldWriter(fieldWriterPreferences), bibEntryTypesManager);
+        try {
+            bibtexEntryWriter.write(entry, bibWriter, bibDatabaseMode);
+        } catch (IOException e) {
+            LOGGER.warn("Problem creating BibTeX entry.", e);
+            return "error";
+        }
+        return rawEntry.toString();
+    }
+
+    @Override
+    public int compareTo(BibEntryDTO o) {
+        int sharingComparison = sharingMetadata.compareTo(o.sharingMetadata);
+        if (sharingComparison != 0) {
+            return sharingComparison;
+        }
+        LOGGER.error("Comparing equal DTOs");
+        return 0;
+    }
+
+    @Override
+    public String toString() {
+        return MoreObjects.toStringHelper(this)
+                          .add("sharingMetadata", sharingMetadata)
+                          .add("userComments", userComments)
+                          .add("citationkey", citationKey)
+                          .add("bibtex", bibtex)
+                          .toString();
+    }
+}

src/main/java/org/jabref/http/dto/GsonFactory.java

@@ -0,0 +1,18 @@
+package org.jabref.http.dto;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import org.glassfish.hk2.api.Factory;
+
+public class GsonFactory implements Factory<Gson> {
+    @Override
+    public Gson provide() {
+        return new GsonBuilder()
+                .setPrettyPrinting()
+                .create();
+    }
+
+    @Override
+    public void dispose(Gson instance) {
+    }
+}