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

@@ -193,6 +193,9 @@ dependencies {
     implementation "org.tinylog:slf4j-tinylog:2.6.2"
     implementation "org.tinylog:tinylog-impl:2.6.2"
 
+    // 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'
 
     // jakarta.activation is already dependency of glassfish
@@ -213,6 +216,23 @@ dependencies {
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
     implementation group: 'org.jooq', name: 'jool', version: '0.9.15'
+    // 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-hk2:3.1.3'
+    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:3.1.3'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.3'
+    // 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:4.8.162'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.0'
@@ -372,6 +392,12 @@ run {
                 'javafx.graphics/javafx.scene' : 'org.controlsfx.controls'
         ]
     }
+
+    if (project.hasProperty('component')){
+        if (component == 'httpserver'){
+            main = 'org.jabref.http.server.Server'
+        }
+    }
 }
 
 javadoc {
@@ -410,7 +436,7 @@ testlogger {
     showSkipped false
 }
 
-task databaseTest(type: Test) {
+tasks.register('databaseTest', Test) {
     useJUnitPlatform {
         includeTags 'DatabaseTest'
     }
@@ -422,7 +448,7 @@ task databaseTest(type: Test) {
     }
 }
 
-task fetcherTest(type: Test) {
+tasks.register('fetcherTest', Test) {
     useJUnitPlatform {
         includeTags 'FetcherTest'
     }
@@ -434,7 +460,7 @@ task fetcherTest(type: Test) {
     }
 }
 
-task guiTest(type: Test) {
+tasks.register('guiTest', Test) {
     useJUnitPlatform {
         includeTags 'GUITest'
     }
@@ -447,7 +473,7 @@ task guiTest(type: Test) {
 }
 
 // Test result tasks
-task copyTestResources(type: Copy) {
+tasks.register('copyTestResources', Copy) {
     from "${projectDir}/src/test/resources"
     into "${buildDir}/classes/test"
 }
@@ -457,11 +483,13 @@ tasks.withType(Test) {
     reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
 }
 
-task jacocoPrepare() {
+tasks.register('jacocoPrepare') {
     doFirst {
         // Ignore failures of tests
-        tasks.withType(Test) {
-            ignoreFailures = true
+        tasks.withType(Test).tap {
+            configureEach {
+                ignoreFailures = true
+            }
         }
     }
 }
@@ -519,7 +547,7 @@ modernizer {
 }
 
 // Release tasks
-task deleteInstallerTemp(type: Delete) {
+tasks.register('deleteInstallerTemp', Delete) {
     delete "$buildDir/installer"
 }
 

docs/code-howtos/http-server.md

@@ -0,0 +1,67 @@
+---
+parent: Code Howtos
+---
+# HTTP Server
+
+## Get SSL Working
+
+(Based on <https://stackoverflow.com/a/57511038/873282>)
+
+Howto for Windows - other operating systems work similar:
+
+1. As admin `choco install mkcert`
+2. As admin: `mkcert -install`
+3. `cd %APPDATA%\..\local\org.jabref\jabref\ssl`
+4. `mkcert -pkcs12 jabref.desktop jabref localhost 127.0.0.1 ::1`
+5. Rename the file to `server.p12`
+
+Note: If you do not do this, you get following error message:
+
+    Could not find server key store C:\Users\USERNAME\AppData\Local\org.jabref\jabref\ssl\server.p12.
+
+## Start http server
+
+The class starting the server is `org.jabref.http.server.Server`.
+
+Test files to server can be passed as arguments.
+If no files are passed, the last opened files are served.
+If that list is also empty, the file `src/main/resources/org/jabref/http/server/http-server-demo.bib` is served.
+
+### Starting with gradle
+
+Does not work.
+
+Current try:
+
+    ./gradlew run -Pcomment=httpserver
+
+However, there are with `ForkJoin` (discussion at https://discuss.gradle.org/t/is-it-ok-to-use-collection-parallelstream-or-other-potentially-multi-threaded-code-within-gradle-plugin-code/28003)
+
+Gradle output:
+
+```
+> Task :run
+2023-04-22 11:30:59 [main] org.jabref.http.server.Server.main()
+DEBUG: Libraries served: [C:\git-repositories\jabref-all\jabref\src\main\resources\org\jabref\http\server\http-server-demo.bib]
+2023-04-22 11:30:59 [main] org.jabref.http.server.Server.startServer()
+DEBUG: Starting server...
+<============-> 92% EXECUTING [2m 27s]
+> :run
+```
+
+IntelliJ output, if `org.jabref.http.server.Server#main` is executed:
+
+```
+DEBUG: Starting server...
+2023-04-22 11:44:59 [ForkJoinPool.commonPool-worker-1] org.glassfish.grizzly.http.server.NetworkListener.start()
+INFO: Started listener bound to [localhost:6051]
+2023-04-22 11:44:59 [ForkJoinPool.commonPool-worker-1] org.glassfish.grizzly.http.server.HttpServer.start()
+INFO: [HttpServer] Started.
+2023-04-22 11:44:59 [ForkJoinPool.commonPool-worker-1] org.jabref.http.server.Server.lambda$startServer$4()
+DEBUG: Server started.
+```
+
+## Developing with IntelliJ
+
+IntelliJ Ultimate offers a Markdown-based http-client. One has to open the file `src/test/java/org/jabref/testutils/interactive/http/rest-api.http`.
+Then, there are play buttons appearing for interacting with the server.

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)

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md

@@ -61,6 +61,8 @@ Then double click inside the cell "Compilation options" and enter following para
 ```text
 --add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref
 --add-exports=org.controlsfx.controls/impl.org.controlsfx.skin=org.jabref
+--add-reads org.jabref=org.fxmisc.flowless
+--add-reads org.jabref=org.apache.commons.csv
 ```
 
 Press <kbd>Enter</kbd> to have the value really stored.

src/main/java/module-info.java

@@ -16,6 +16,8 @@
     requires com.dlsc.gemsfx;
     uses com.dlsc.gemsfx.TagsField;
     requires de.saxsys.mvvmfx;
+    requires reactfx;
+    requires org.fxmisc.flowless;
 
     requires org.kordamp.ikonli.core;
     requires org.kordamp.ikonli.javafx;
@@ -39,6 +41,7 @@
 
     // Logging
     requires org.slf4j;
+    requires jul.to.slf4j;
     requires org.tinylog.api;
     requires org.tinylog.api.slf4j;
     requires org.tinylog.impl;
@@ -49,45 +52,57 @@
 
     // 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 org.apache.pdfbox;
     requires org.apache.xmpbox;
@@ -113,14 +128,17 @@
     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 org.antlr.antlr4.runtime;
+    requires org.libreoffice.uno;
+    requires de.saxsys.mvvmfx.validation;
+
 }

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

@@ -31,6 +31,7 @@
 import org.apache.commons.cli.ParseException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.slf4j.bridge.SLF4JBridgeHandler;
 import org.tinylog.configuration.Configuration;
 
 /**
@@ -46,6 +47,7 @@ public class Launcher {
     private static boolean isDebugEnabled;
 
     public static void main(String[] args) {
+        routeLoggingToSlf4J();
         ARGUMENTS = args;
 
         // We must configure logging as soon as possible, which is why we cannot wait for the usual
@@ -103,6 +105,11 @@ 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