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iloveskittles82palukkukopporInAnYansubhramit
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Add http endpoints for JabMap (#13519)
Co-authored-by: Philip <[email protected]> Co-authored-by: Oliver Kopp <[email protected]> Co-authored-by: Ruslan <[email protected]> Co-authored-by: Subhramit Basu <[email protected]>
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-21
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7 files changed

+304
-21
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‎.jbang/JabSrvLauncher.java‎

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

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

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opens org.jabref.http.server to org.glassfish.hk2.utilities, org.glassfish.hk2.locator;
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exports org.jabref.http.server.cayw;
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opens org.jabref.http.server.cayw to com.google.gson, org.glassfish.hk2.locator, org.glassfish.hk2.utilities;
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opens org.jabref.http.dto to com.google.gson;
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requires javafx.base;
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‎jabsrv/src/main/java/org/jabref/http/dto/LinkedPdfFileDTO.java‎

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

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

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

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

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@@ -3,25 +3,33 @@
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import java.io.IOException;
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import java.io.InputStream;
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import java.nio.file.Files;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Objects;
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import org.jabref.http.JabrefMediaType;
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import org.jabref.http.dto.BibEntryDTO;
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import org.jabref.http.dto.LinkedPdfFileDTO;
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import org.jabref.http.server.services.ContextsToServe;
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import org.jabref.http.server.services.FilesToServe;
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import org.jabref.http.server.services.ServerUtils;
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import org.jabref.logic.citationstyle.JabRefItemDataProvider;
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import org.jabref.logic.preferences.CliPreferences;
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import org.jabref.model.database.BibDatabase;
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import org.jabref.model.database.BibDatabaseContext;
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import org.jabref.model.entry.BibEntry;
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import org.jabref.model.entry.BibEntryTypesManager;
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import org.jabref.model.entry.LinkedFile;
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import org.jabref.model.entry.field.StandardField;
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import com.airhacks.afterburner.injection.Injector;
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import com.google.gson.Gson;
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import jakarta.inject.Inject;
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import jakarta.ws.rs.Consumes;
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import jakarta.ws.rs.GET;
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import jakarta.ws.rs.InternalServerErrorException;
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import jakarta.ws.rs.NotFoundException;
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import jakarta.ws.rs.PUT;
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import jakarta.ws.rs.Path;
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import jakarta.ws.rs.PathParam;
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import jakarta.ws.rs.Produces;
@@ -48,18 +56,94 @@ public class LibraryResource {
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@Inject
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Gson gson;
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/**
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* At http://localhost:23119/libraries/{id}
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*
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* @param id The specified library
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* @return specified library in JSON format
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* @throws IOException
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*/
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@GET
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@Produces(MediaType.APPLICATION_JSON)
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public String getJson(@PathParam("id") String id) throws IOException {
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BibDatabaseContext databaseContext = getDatabaseContext(id);
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BibEntryTypesManager entryTypesManager = Injector.instantiateModelOrService(BibEntryTypesManager.class);
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List<BibEntryDTO> list = databaseContext.getDatabase().getEntries().stream()
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.peek(bibEntry -> bibEntry.getSharedBibEntryData().setSharedID(Objects.hash(bibEntry)))
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.map(entry -> new BibEntryDTO(entry, databaseContext.getMode(), preferences.getFieldPreferences(), entryTypesManager))
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.toList();
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.peek(bibEntry -> bibEntry.getSharedBibEntryData().setSharedID(Objects.hash(bibEntry)))
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.map(entry -> new BibEntryDTO(entry, databaseContext.getMode(), preferences.getFieldPreferences(), entryTypesManager))
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.toList();
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return gson.toJson(list);
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}
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/**
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* At http://localhost:23119/libraries/{id}/map <br><br>
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*
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* Looks for the .jmp file in the directory of the given library ({id}.bib file).
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*
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* @param id The given library
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* @return A JSON String containing the mindmap data. If no {id}.jmp file was found, returns the standard mindmap
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* @throws IOException
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*/
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@GET
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@Path("map")
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@Produces(MediaType.APPLICATION_JSON)
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public String getJabMapJson(@PathParam("id") String id) throws IOException {
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boolean isDemo = "demo".equals(id);
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java.nio.file.Path jabMapPath;
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if (isDemo) {
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jabMapPath = getJabMapDemoPath();
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} else {
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jabMapPath = getJabMapPath(id);
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}
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// if no file is found, return the default mindmap
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if (!Files.exists(jabMapPath)) {
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return """
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{
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"map": {
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"meta": {
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"name": "JabMap",
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"author": "JabMap",
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"version": "1.0"
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},
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"format": "node_tree",
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"data": {
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"id": "root",
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"topic": "JabMap",
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"expanded": true,
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"icons": [],
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"highlight": null,
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"type": "Text"
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}
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}
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}
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""";
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}
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return Files.readString(jabMapPath);
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}
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/**
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* At http://localhost:23119/libraries/{id}/map <br><br>
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*
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* Saves the mindmap next to its associated library.
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*
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* @param id The given library
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*
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* @throws IOException
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*/
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@PUT
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@Path("map")
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@Consumes(MediaType.APPLICATION_JSON)
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public void updateJabMapJson(@PathParam("id") String id, String fileContent) throws IOException {
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boolean isDemo = "demo".equals(id);
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java.nio.file.Path targetPath;
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if (isDemo) {
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targetPath = getJabMapDemoPath();
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} else {
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targetPath = getJabMapPath(id);
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}
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Files.writeString(targetPath, fileContent);
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}
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@GET
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@Produces(JabrefMediaType.JSON_CSL_ITEM)
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public String getClsItemJson(@PathParam("id") String id) throws IOException {
@@ -94,17 +178,165 @@ public Response getBibtex(@PathParam("id") String id) {
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throw new InternalServerErrorException("Could not read library " + library, e);
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}
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return Response.ok()
97-
.header("Content-Disposition", "attachment; filename=\"" + library.getFileName() + "\"")
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.entity(libraryAsString)
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.build();
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.header("Content-Disposition", "attachment; filename=\"" + library.getFileName() + "\"")
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.entity(libraryAsString)
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.build();
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}
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private java.nio.file.Path getJabMapPath(String id) {
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java.nio.file.Path libraryPath = ServerUtils.getLibraryPath(id, filesToServe, contextsToServe);
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String newName = libraryPath.getFileName().toString().replaceFirst("\\.bib$", ".jmp");
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return libraryPath.getParent().resolve(newName);
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}
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private java.nio.file.Path getJabMapDemoPath() {
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java.nio.file.Path result = java.nio.file.Path.of(System.getProperty("java.io.tmpdir")).resolve("demo.jmp");
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LOGGER.debug("Using temporary file for demo jmp: {}", result);
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return result;
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}
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102-
/// @param id - also "demo" for the Chocolate.bib file
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/**
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* @param id - also "demo" for the Chocolate.bib file
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*/
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private BibDatabaseContext getDatabaseContext(String id) throws IOException {
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return ServerUtils.getBibDatabaseContext(id, filesToServe, contextsToServe, preferences.getImportFormatPreferences());
105203
}
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107-
/// @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)
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/**
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* At http://localhost:23119/libraries/{id}/entries/{entryId} <br><br>
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*
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* Combines attributes of a given BibEntry into a basic entry preview for as plain text.
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*
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* @param id The name of the library
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* @param entryId The CitationKey of the BibEntry
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* @return a basic entry preview as plain text
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* @throws IOException
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* @throws NotFoundException
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*/
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@GET
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@Path("entries/{entryId}")
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@Produces(MediaType.TEXT_PLAIN + ";charset=UTF-8")
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public String getPlainRepresentation(@PathParam("id") String id, @PathParam("entryId") String entryId) throws IOException {
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BibDatabaseContext databaseContext = getDatabaseContext(id);
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List<BibEntry> entriesByCitationKey = databaseContext.getDatabase().getEntriesByCitationKey(entryId);
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if (entriesByCitationKey.isEmpty()) {
223+
throw new NotFoundException("Entry with citation key '" + entryId + "' not found in library " + id);
224+
}
225+
if (entriesByCitationKey.size() > 1) {
226+
LOGGER.warn("Multiple entries found with citation key '{}'. Using the first one.", entryId);
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}
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// TODO: Currently, the preview preferences are in GUI package, which is not accessible here.
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// build the preview
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BibEntry entry = entriesByCitationKey.getFirst();
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String author = entry.getField(StandardField.AUTHOR).orElse("(N/A)");
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String title = entry.getField(StandardField.TITLE).orElse("(N/A)");
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String journal = entry.getField(StandardField.JOURNAL).orElse("(N/A)");
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String volume = entry.getField(StandardField.VOLUME).orElse("(N/A)");
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String number = entry.getField(StandardField.NUMBER).orElse("(N/A)");
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String pages = entry.getField(StandardField.PAGES).orElse("(N/A)");
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String releaseDate = entry.getField(StandardField.DATE).orElse("(N/A)");
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// the only difference to the HTML version of this method is the format of the output:
242+
String preview =
243+
"Author: " + author
244+
+ "\nTitle: " + title
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+ "\nJournal: " + journal
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+ "\nVolume: " + volume
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+ "\nNumber: " + number
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+ "\nPages: " + pages
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+ "\nReleased on: " + releaseDate;
250+
251+
return preview;
252+
}
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/**
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* At http://localhost:23119/libraries/{id}/entries/{entryId} <br><br>
256+
*
257+
* Combines attributes of a given BibEntry into a basic entry preview for as HTML text.
258+
*
259+
* @param id The name of the library
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* @param entryId The CitationKey of the BibEntry
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* @return a basic entry preview as HTML text
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* @throws IOException
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*/
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@GET
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@Path("entries/{entryId}")
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@Produces(MediaType.TEXT_HTML + ";charset=UTF-8")
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public String getHTMLRepresentation(@PathParam("id") String id, @PathParam("entryId") String entryId) throws IOException {
268+
List<BibEntry> entriesByCitationKey = getDatabaseContext(id).getDatabase().getEntriesByCitationKey(entryId);
269+
if (entriesByCitationKey.isEmpty()) {
270+
throw new NotFoundException("Entry with citation key '" + entryId + "' not found in library " + id);
271+
}
272+
if (entriesByCitationKey.size() > 1) {
273+
LOGGER.warn("Multiple entries found with citation key '{}'. Using the first one.", entryId);
274+
}
275+
276+
// TODO: Currently, the preview preferences are in GUI package, which is not accessible here.
277+
// build the preview
278+
BibEntry entry = entriesByCitationKey.getFirst();
279+
280+
String author = entry.getField(StandardField.AUTHOR).orElse("(N/A)");
281+
String title = entry.getField(StandardField.TITLE).orElse("(N/A)");
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String journal = entry.getField(StandardField.JOURNAL).orElse("(N/A)");
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String volume = entry.getField(StandardField.VOLUME).orElse("(N/A)");
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String number = entry.getField(StandardField.NUMBER).orElse("(N/A)");
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String pages = entry.getField(StandardField.PAGES).orElse("(N/A)");
286+
String releaseDate = entry.getField(StandardField.DATE).orElse("(N/A)");
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288+
// the only difference to the plain text version of this method is the format of the output:
289+
String preview =
290+
"<strong>Author:</strong> " + author + "<br>" +
291+
"<strong>Title:</strong> " + title + "<br>" +
292+
"<strong>Journal:</strong> " + journal + "<br>" +
293+
"<strong>Volume:</strong> " + volume + "<br>" +
294+
"<strong>Number:</strong> " + number + "<br>" +
295+
"<strong>Pages:</strong> " + pages + "<br>" +
296+
"<strong>Released on:</strong> " + releaseDate;
297+
298+
return preview;
299+
}
300+
301+
/**
302+
* At http://localhost:23119/libraries/{id}/entries/pdffiles <br><br>
303+
*
304+
* Loops through all entries in the specified library and adds attached files of type "PDF" to
305+
* a list and JSON serialises it.
306+
*/
307+
@GET
308+
@Path("entries/pdffiles")
309+
@Produces(MediaType.APPLICATION_JSON + ";charset=UTF-8")
310+
public String getPDFFilesAsList(@PathParam("id") String id) throws IOException {
311+
// get a list of all entries in library (specified by "id")
312+
BibDatabaseContext databaseContext = getDatabaseContext(id);
313+
List<LinkedPdfFileDTO> response = new ArrayList<>();
314+
List<BibEntry> entries = databaseContext.getDatabase().getEntries();
315+
if (entries.isEmpty()) {
316+
throw new NotFoundException("No entries found for library: " + id);
317+
}
318+
319+
// loop through all entries to extract pdfs and paths
320+
for (BibEntry entry : entries) {
321+
List<LinkedFile> pathsToFiles = entry.getFiles();
322+
if (!pathsToFiles.isEmpty()) {
323+
for (LinkedFile file : pathsToFiles) {
324+
// ignore all non pdf files and online references
325+
if (!"PDF".equals(file.getFileType()) || LinkedFile.isOnlineLink(file.getLink())) {
326+
continue;
327+
}
328+
// add file to response body
329+
LinkedPdfFileDTO localPdfFile = new LinkedPdfFileDTO(entry, file);
330+
response.add(localPdfFile);
331+
}
332+
}
333+
}
334+
return gson.toJson(response);
335+
}
336+
337+
/**
338+
* @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)
339+
*/
108340
private @Nullable InputStream getChocolateBibAsStream() {
109341
return BibDatabase.class.getResourceAsStream("/Chocolate.bib");
110342
}

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

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@@ -94,6 +94,7 @@ private HttpServer startServer(ServiceLocator serviceLocator, URI uri) {
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9595
// see https://stackoverflow.com/a/33794265/873282
9696
final ResourceConfig resourceConfig = new ResourceConfig();
97+
resourceConfig.property("jersey.config.server.wadl.disableWadl", true);
9798
// TODO: Add SSL
9899
resourceConfig.register(RootResource.class);
99100
resourceConfig.register(LibrariesResource.class);

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