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SiedlerchrSiedlerchr
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Merge remote-tracking branch 'upstream/main'
* upstream/main: Add http endpoints for JabMap (#13519)
2 parents cb77f24 + 25ae95d commit 6772596

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+304
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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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@@ -8,6 +8,7 @@
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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;
1010
opens org.jabref.http.server.cayw to com.google.gson, org.glassfish.hk2.locator, org.glassfish.hk2.utilities;
11+
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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@@ -0,0 +1,28 @@
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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 {
7+
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();
14+
this.fileName = path.substring(path.lastIndexOf('/') + 1);
15+
}
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public String getFileName() {
18+
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()
57-
.peek(bibEntry -> bibEntry.getSharedBibEntryData().setSharedID(Objects.hash(bibEntry)))
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.map(entry -> new BibEntryDTO(entry, databaseContext.getMode(), preferences.getFieldPreferences(), entryTypesManager))
59-
.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);
6176
}
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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")
89+
@Produces(MediaType.APPLICATION_JSON)
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public String getJabMapJson(@PathParam("id") String id) throws IOException {
91+
boolean isDemo = "demo".equals(id);
92+
java.nio.file.Path jabMapPath;
93+
if (isDemo) {
94+
jabMapPath = getJabMapDemoPath();
95+
} else {
96+
jabMapPath = getJabMapPath(id);
97+
}
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// if no file is found, return the default mindmap
99+
if (!Files.exists(jabMapPath)) {
100+
return """
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{
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"map": {
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"meta": {
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"name": "JabMap",
105+
"author": "JabMap",
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"version": "1.0"
107+
},
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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,
115+
"type": "Text"
116+
}
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}
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}
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""";
120+
}
121+
return Files.readString(jabMapPath);
122+
}
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/**
125+
* 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
134+
@Path("map")
135+
@Consumes(MediaType.APPLICATION_JSON)
136+
public void updateJabMapJson(@PathParam("id") String id, String fileContent) throws IOException {
137+
boolean isDemo = "demo".equals(id);
138+
java.nio.file.Path targetPath;
139+
if (isDemo) {
140+
targetPath = getJabMapDemoPath();
141+
} else {
142+
targetPath = getJabMapPath(id);
143+
}
144+
Files.writeString(targetPath, fileContent);
145+
}
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63147
@GET
64148
@Produces(JabrefMediaType.JSON_CSL_ITEM)
65149
public String getClsItemJson(@PathParam("id") String id) throws IOException {
@@ -94,17 +178,165 @@ public Response getBibtex(@PathParam("id") String id) {
94178
throw new InternalServerErrorException("Could not read library " + library, e);
95179
}
96180
return Response.ok()
97-
.header("Content-Disposition", "attachment; filename=\"" + library.getFileName() + "\"")
98-
.entity(libraryAsString)
99-
.build();
181+
.header("Content-Disposition", "attachment; filename=\"" + library.getFileName() + "\"")
182+
.entity(libraryAsString)
183+
.build();
184+
}
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186+
private java.nio.file.Path getJabMapPath(String id) {
187+
java.nio.file.Path libraryPath = ServerUtils.getLibraryPath(id, filesToServe, contextsToServe);
188+
String newName = libraryPath.getFileName().toString().replaceFirst("\\.bib$", ".jmp");
189+
return libraryPath.getParent().resolve(newName);
190+
}
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192+
private java.nio.file.Path getJabMapDemoPath() {
193+
java.nio.file.Path result = java.nio.file.Path.of(System.getProperty("java.io.tmpdir")).resolve("demo.jmp");
194+
LOGGER.debug("Using temporary file for demo jmp: {}", result);
195+
return result;
100196
}
101197

102-
/// @param id - also "demo" for the Chocolate.bib file
198+
/**
199+
* @param id - also "demo" for the Chocolate.bib file
200+
*/
103201
private BibDatabaseContext getDatabaseContext(String id) throws IOException {
104202
return ServerUtils.getBibDatabaseContext(id, filesToServe, contextsToServe, preferences.getImportFormatPreferences());
105203
}
106204

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)
205+
/**
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* At http://localhost:23119/libraries/{id}/entries/{entryId} <br><br>
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*
208+
* Combines attributes of a given BibEntry into a basic entry preview for as plain text.
209+
*
210+
* @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
213+
* @throws IOException
214+
* @throws NotFoundException
215+
*/
216+
@GET
217+
@Path("entries/{entryId}")
218+
@Produces(MediaType.TEXT_PLAIN + ";charset=UTF-8")
219+
public String getPlainRepresentation(@PathParam("id") String id, @PathParam("entryId") String entryId) throws IOException {
220+
BibDatabaseContext databaseContext = getDatabaseContext(id);
221+
List<BibEntry> entriesByCitationKey = databaseContext.getDatabase().getEntriesByCitationKey(entryId);
222+
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);
227+
}
228+
229+
// TODO: Currently, the preview preferences are in GUI package, which is not accessible here.
230+
// build the preview
231+
BibEntry entry = entriesByCitationKey.getFirst();
232+
233+
String author = entry.getField(StandardField.AUTHOR).orElse("(N/A)");
234+
String title = entry.getField(StandardField.TITLE).orElse("(N/A)");
235+
String journal = entry.getField(StandardField.JOURNAL).orElse("(N/A)");
236+
String volume = entry.getField(StandardField.VOLUME).orElse("(N/A)");
237+
String number = entry.getField(StandardField.NUMBER).orElse("(N/A)");
238+
String pages = entry.getField(StandardField.PAGES).orElse("(N/A)");
239+
String releaseDate = entry.getField(StandardField.DATE).orElse("(N/A)");
240+
241+
// 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
245+
+ "\nJournal: " + journal
246+
+ "\nVolume: " + volume
247+
+ "\nNumber: " + number
248+
+ "\nPages: " + pages
249+
+ "\nReleased on: " + releaseDate;
250+
251+
return preview;
252+
}
253+
254+
/**
255+
* 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
260+
* @param entryId The CitationKey of the BibEntry
261+
* @return a basic entry preview as HTML text
262+
* @throws IOException
263+
*/
264+
@GET
265+
@Path("entries/{entryId}")
266+
@Produces(MediaType.TEXT_HTML + ";charset=UTF-8")
267+
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)");
282+
String journal = entry.getField(StandardField.JOURNAL).orElse("(N/A)");
283+
String volume = entry.getField(StandardField.VOLUME).orElse("(N/A)");
284+
String number = entry.getField(StandardField.NUMBER).orElse("(N/A)");
285+
String pages = entry.getField(StandardField.PAGES).orElse("(N/A)");
286+
String releaseDate = entry.getField(StandardField.DATE).orElse("(N/A)");
287+
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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Original file line numberDiff line numberDiff line change
@@ -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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