Add http endpoints for JabMap

.jbang/JabSrvLauncher.java

@@ -12,6 +12,7 @@
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/cayw/SimpleJson.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/GlobalExceptionMapper.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/GsonFactory.java
+//SOURCES ../jabsrv/src/main/java/org/jabref/http/dto/LinkedPdfFileDTO.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/JabrefMediaType.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWResource.java
 //SOURCES ../jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWQueryParams.java

jabsrv/src/main/java/module-info.java

@@ -8,6 +8,7 @@
     opens org.jabref.http.server to org.glassfish.hk2.utilities, org.glassfish.hk2.locator;
     exports org.jabref.http.server.cayw;
     opens org.jabref.http.server.cayw to com.google.gson, org.glassfish.hk2.locator, org.glassfish.hk2.utilities;
+    opens org.jabref.http.dto to com.google.gson;
 
     requires javafx.base;
 

jabsrv/src/main/java/org/jabref/http/dto/LinkedPdfFileDTO.java

@@ -0,0 +1,28 @@
+package org.jabref.http.dto;
+
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
+
+public class LinkedPdfFileDTO {
+    private final String fileName;
+    private final String parentCitationKey;
+    private final String path;
+
+    public LinkedPdfFileDTO(BibEntry parentEntry, LinkedFile file) {
+        this.parentCitationKey = parentEntry.getCitationKey().orElse("N/A");
+        this.path = file.getLink();
+        this.fileName = path.substring(path.lastIndexOf('/') + 1);
+    }
+
+    public String getFileName() {
+        return fileName;
+    }
+
+    public String getParentCitationKey() {
+        return parentCitationKey;
+    }
+
+    public String getPath() {
+        return path;
+    }
+}

jabsrv/src/main/java/org/jabref/http/server/CORSFilter.java

@@ -9,13 +9,7 @@
 public class CORSFilter implements ContainerResponseFilter {
     @Override
     public void filter(ContainerRequestContext requestContext, ContainerResponseContext responseContext) {
-        String requestOrigin = requestContext.getHeaderString("Origin");
-        if (requestOrigin == null) {
-            // IntelliJ's rest client is calling
-            responseContext.getHeaders().add("Access-Control-Allow-Origin", "*");
-        } else if (requestOrigin.contains("://localhost")) {
-            responseContext.getHeaders().add("Access-Control-Allow-Origin", requestOrigin);
-        }
+        responseContext.getHeaders().add("Access-Control-Allow-Origin", "*");
         responseContext.getHeaders().add("Access-Control-Allow-Methods", "GET, POST, PUT, DELETE, OPTIONS");
         responseContext.getHeaders().add("Access-Control-Allow-Headers", "origin, content-type, accept");
         responseContext.getHeaders().add("Access-Control-Allow-Credentials", "false");

jabsrv/src/main/java/org/jabref/http/server/LibraryResource.java

@@ -3,25 +3,33 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.file.Files;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 
 import org.jabref.http.JabrefMediaType;
 import org.jabref.http.dto.BibEntryDTO;
+import org.jabref.http.dto.LinkedPdfFileDTO;
 import org.jabref.http.server.services.ContextsToServe;
 import org.jabref.http.server.services.FilesToServe;
 import org.jabref.http.server.services.ServerUtils;
 import org.jabref.logic.citationstyle.JabRefItemDataProvider;
 import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.LinkedFile;
+import org.jabref.model.entry.field.StandardField;
 
 import com.airhacks.afterburner.injection.Injector;
 import com.google.gson.Gson;
 import jakarta.inject.Inject;
+import jakarta.ws.rs.Consumes;
 import jakarta.ws.rs.GET;
 import jakarta.ws.rs.InternalServerErrorException;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.PUT;
 import jakarta.ws.rs.Path;
 import jakarta.ws.rs.PathParam;
 import jakarta.ws.rs.Produces;
@@ -48,18 +56,94 @@ public class LibraryResource {
     @Inject
     Gson gson;
 
+    /**
+     * At http://localhost:23119/libraries/{id}
+     *
+     * @param id The specified library
+     * @return specified library in JSON format
+     * @throws IOException
+     */
     @GET
     @Produces(MediaType.APPLICATION_JSON)
     public String getJson(@PathParam("id") String id) throws IOException {
         BibDatabaseContext databaseContext = getDatabaseContext(id);
         BibEntryTypesManager entryTypesManager = Injector.instantiateModelOrService(BibEntryTypesManager.class);
         List<BibEntryDTO> list = databaseContext.getDatabase().getEntries().stream()
-                                             .peek(bibEntry -> bibEntry.getSharedBibEntryData().setSharedID(Objects.hash(bibEntry)))
-                                             .map(entry -> new BibEntryDTO(entry, databaseContext.getMode(), preferences.getFieldPreferences(), entryTypesManager))
-                                             .toList();
+                                                .peek(bibEntry -> bibEntry.getSharedBibEntryData().setSharedID(Objects.hash(bibEntry)))
+                                                .map(entry -> new BibEntryDTO(entry, databaseContext.getMode(), preferences.getFieldPreferences(), entryTypesManager))
+                                                .toList();
         return gson.toJson(list);
     }
 
+    /**
+     * At http://localhost:23119/libraries/{id}/map <br><br>
+     *
+     * Looks for the .jmp file in the directory of the given library ({id}.bib file).
+     *
+     * @param id The given library
+     * @return A JSON String containing the mindmap data. If no {id}.jmp file was found, returns the standard mindmap
+     * @throws IOException
+     */
+    @GET
+    @Path("map")
+    @Produces(MediaType.APPLICATION_JSON)
+    public String getJabMapJson(@PathParam("id") String id) throws IOException {
+        boolean isDemo = "demo".equals(id);
+        java.nio.file.Path jabMapPath;
+        if (isDemo) {
+            jabMapPath = getJabMapDemoPath();
+        } else {
+            jabMapPath = getJabMapPath(id);
+        }
+        // if no file is found, return the default mindmap
+        if (!Files.exists(jabMapPath)) {
+            return """
+                    {
+                      "map": {
+                        "meta": {
+                          "name": "JabMap",
+                          "author": "JabMap",
+                          "version": "1.0"
+                        },
+                        "format": "node_tree",
+                        "data": {
+                          "id": "root",
+                          "topic": "JabMap",
+                          "expanded": true,
+                          "icons": [],
+                          "highlight": null,
+                          "type": "Text"
+                        }
+                      }
+                    }
+                    """;
+        }
+        return Files.readString(jabMapPath);
+    }
+
+    /**
+     * At http://localhost:23119/libraries/{id}/map <br><br>
+     *
+     * Saves the mindmap next to its associated library.
+     *
+     * @param id The given library
+     *
+     * @throws IOException
+     */
+    @PUT
+    @Path("map")
+    @Consumes(MediaType.APPLICATION_JSON)
+    public void updateJabMapJson(@PathParam("id") String id, String fileContent) throws IOException {
+        boolean isDemo = "demo".equals(id);
+        java.nio.file.Path targetPath;
+        if (isDemo) {
+            targetPath = getJabMapDemoPath();
+        } else {
+            targetPath = getJabMapPath(id);
+        }
+        Files.writeString(targetPath, fileContent);
+    }
+
     @GET
     @Produces(JabrefMediaType.JSON_CSL_ITEM)
     public String getClsItemJson(@PathParam("id") String id) throws IOException {
@@ -94,17 +178,165 @@ public Response getBibtex(@PathParam("id") String id) {
             throw new InternalServerErrorException("Could not read library " + library, e);
         }
         return Response.ok()
-                .header("Content-Disposition", "attachment; filename=\"" + library.getFileName() + "\"")
-                .entity(libraryAsString)
-                .build();
+                       .header("Content-Disposition", "attachment; filename=\"" + library.getFileName() + "\"")
+                       .entity(libraryAsString)
+                       .build();
+    }
+
+    private java.nio.file.Path getJabMapPath(String id) {
+        java.nio.file.Path libraryPath = ServerUtils.getLibraryPath(id, filesToServe, contextsToServe);
+        String newName = libraryPath.getFileName().toString().replaceFirst("\\.bib$", ".jmp");
+        return libraryPath.getParent().resolve(newName);
+    }
+
+    private java.nio.file.Path getJabMapDemoPath() {
+        java.nio.file.Path result = java.nio.file.Path.of(System.getProperty("java.io.tmpdir")).resolve("demo.jmp");
+        LOGGER.debug("Using temporary file for demo jmp: {}", result);
+        return result;
     }
 
-    /// @param id - also "demo" for the Chocolate.bib file
+    /**
+     * @param id - also "demo" for the Chocolate.bib file
+     */
     private BibDatabaseContext getDatabaseContext(String id) throws IOException {
         return ServerUtils.getBibDatabaseContext(id, filesToServe, contextsToServe, preferences.getImportFormatPreferences());
     }
 
-    /// @return a stream to the Chocolate.bib file in the classpath (is null only if the file was moved or there are issues with the classpath)
+    /**
+     * At http://localhost:23119/libraries/{id}/entries/{entryId} <br><br>
+     *
+     * Combines attributes of a given BibEntry into a basic entry preview for as plain text.
+     *
+     * @param id The name of the library
+     * @param entryId The CitationKey of the BibEntry
+     * @return a basic entry preview as plain text
+     * @throws IOException
+     * @throws NotFoundException
+     */
+    @GET
+    @Path("entries/{entryId}")
+    @Produces(MediaType.TEXT_PLAIN + ";charset=UTF-8")
+    public String getPlainRepresentation(@PathParam("id") String id, @PathParam("entryId") String entryId) throws IOException {
+        BibDatabaseContext databaseContext = getDatabaseContext(id);
+        List<BibEntry> entriesByCitationKey = databaseContext.getDatabase().getEntriesByCitationKey(entryId);
+        if (entriesByCitationKey.isEmpty()) {
+            throw new NotFoundException("Entry with citation key '" + entryId + "' not found in library " + id);
+        }
+        if (entriesByCitationKey.size() > 1) {
+            LOGGER.warn("Multiple entries found with citation key '{}'. Using the first one.", entryId);
+        }
+
+        // TODO: Currently, the preview preferences are in GUI package, which is not accessible here.
+        // build the preview
+        BibEntry entry = entriesByCitationKey.getFirst();
+
+        String author = entry.getField(StandardField.AUTHOR).orElse("(N/A)");
+        String title = entry.getField(StandardField.TITLE).orElse("(N/A)");
+        String journal = entry.getField(StandardField.JOURNAL).orElse("(N/A)");
+        String volume = entry.getField(StandardField.VOLUME).orElse("(N/A)");
+        String number = entry.getField(StandardField.NUMBER).orElse("(N/A)");
+        String pages = entry.getField(StandardField.PAGES).orElse("(N/A)");
+        String releaseDate = entry.getField(StandardField.DATE).orElse("(N/A)");
+
+        // the only difference to the HTML version of this method is the format of the output:
+        String preview =
+                "Author: " + author
+                        + "\nTitle: " + title
+                        + "\nJournal: " + journal
+                        + "\nVolume: " + volume
+                        + "\nNumber: " + number
+                        + "\nPages: " + pages
+                        + "\nReleased on: " + releaseDate;
+
+        return preview;
+    }
+
+    /**
+     * At http://localhost:23119/libraries/{id}/entries/{entryId} <br><br>
+     *
+     * Combines attributes of a given BibEntry into a basic entry preview for as HTML text.
+     *
+     * @param id The name of the library
+     * @param entryId The CitationKey of the BibEntry
+     * @return a basic entry preview as HTML text
+     * @throws IOException
+     */
+    @GET
+    @Path("entries/{entryId}")
+    @Produces(MediaType.TEXT_HTML + ";charset=UTF-8")
+    public String getHTMLRepresentation(@PathParam("id") String id, @PathParam("entryId") String entryId) throws IOException {
+        List<BibEntry> entriesByCitationKey = getDatabaseContext(id).getDatabase().getEntriesByCitationKey(entryId);
+        if (entriesByCitationKey.isEmpty()) {
+            throw new NotFoundException("Entry with citation key '" + entryId + "' not found in library " + id);
+        }
+        if (entriesByCitationKey.size() > 1) {
+            LOGGER.warn("Multiple entries found with citation key '{}'. Using the first one.", entryId);
+        }
+
+        // TODO: Currently, the preview preferences are in GUI package, which is not accessible here.
+        // build the preview
+        BibEntry entry = entriesByCitationKey.getFirst();
+
+        String author = entry.getField(StandardField.AUTHOR).orElse("(N/A)");
+        String title = entry.getField(StandardField.TITLE).orElse("(N/A)");
+        String journal = entry.getField(StandardField.JOURNAL).orElse("(N/A)");
+        String volume = entry.getField(StandardField.VOLUME).orElse("(N/A)");
+        String number = entry.getField(StandardField.NUMBER).orElse("(N/A)");
+        String pages = entry.getField(StandardField.PAGES).orElse("(N/A)");
+        String releaseDate = entry.getField(StandardField.DATE).orElse("(N/A)");
+
+        // the only difference to the plain text version of this method is the format of the output:
+        String preview =
+                "<strong>Author:</strong> " + author + "<br>" +
+                        "<strong>Title:</strong> " + title + "<br>" +
+                        "<strong>Journal:</strong> " + journal + "<br>" +
+                        "<strong>Volume:</strong> " + volume + "<br>" +
+                        "<strong>Number:</strong> " + number + "<br>" +
+                        "<strong>Pages:</strong> " + pages + "<br>" +
+                        "<strong>Released on:</strong> " + releaseDate;
+
+        return preview;
+    }
+
+    /**
+     * At http://localhost:23119/libraries/{id}/entries/pdffiles <br><br>
+     *
+     * Loops through all entries in the specified library and adds attached files of type "PDF" to
+     * a list and JSON serialises it.
+     */
+    @GET
+    @Path("entries/pdffiles")
+    @Produces(MediaType.APPLICATION_JSON + ";charset=UTF-8")
+    public String getPDFFilesAsList(@PathParam("id") String id) throws IOException {
+        // get a list of all entries in library (specified by "id")
+        BibDatabaseContext databaseContext = getDatabaseContext(id);
+        List<LinkedPdfFileDTO> response = new ArrayList<>();
+        List<BibEntry> entries = databaseContext.getDatabase().getEntries();
+        if (entries.isEmpty()) {
+            throw new NotFoundException("No entries found for library: " + id);
+        }
+
+        // loop through all entries to extract pdfs and paths
+        for (BibEntry entry : entries) {
+            List<LinkedFile> pathsToFiles = entry.getFiles();
+            if (!pathsToFiles.isEmpty()) {
+                for (LinkedFile file : pathsToFiles) {
+                    // ignore all non pdf files and online references
+                    if (!"PDF".equals(file.getFileType()) || LinkedFile.isOnlineLink(file.getLink())) {
+                        continue;
+                    }
+                    // add file to response body
+                    LinkedPdfFileDTO localPdfFile = new LinkedPdfFileDTO(entry, file);
+                    response.add(localPdfFile);
+                }
+            }
+        }
+        return gson.toJson(response);
+    }
+
+    /**
+     * @return a stream to the Chocolate.bib file in the classpath (is null only if the file was moved or there are issues with the classpath)
+     */
     private @Nullable InputStream getChocolateBibAsStream() {
         return BibDatabase.class.getResourceAsStream("/Chocolate.bib");
     }

jabsrv/src/main/java/org/jabref/http/server/Server.java

@@ -94,6 +94,7 @@ private HttpServer startServer(ServiceLocator serviceLocator, URI uri) {
 
         // see https://stackoverflow.com/a/33794265/873282
         final ResourceConfig resourceConfig = new ResourceConfig();
+        resourceConfig.property("jersey.config.server.wadl.disableWadl", true);
         // TODO: Add SSL
         resourceConfig.register(RootResource.class);
         resourceConfig.register(LibrariesResource.class);