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Fix downloading pdf produces html as extension #4965

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merged 5 commits into from
May 18, 2019
Merged

Fix downloading pdf produces html as extension #4965

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d3ce2e2
Fix downloading pdf produces html as extension
Siedlerchr May 11, 2019
888aa6f
Merge remote-tracking branch 'upstream/master' into fileURlfix
Siedlerchr May 17, 2019
bd016c1
add relativze if not an URL
Siedlerchr May 17, 2019
c21c0f8
Create Test for download pdf document
Siedlerchr May 17, 2019
adfa4a4
refactor and simply test
Siedlerchr May 18, 2019
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5 changes: 3 additions & 2 deletions src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import org.jabref.gui.BasePanel;
import org.jabref.gui.DialogService;
import org.jabref.gui.actions.SimpleCommand;
import org.jabref.gui.externalfiletype.ExternalFileTypes;
import org.jabref.gui.fieldeditors.LinkedFileViewModel;
import org.jabref.gui.fieldeditors.LinkedFilesEditorViewModel;
import org.jabref.gui.util.BackgroundTask;
Expand Down Expand Up @@ -136,15 +137,15 @@ private void addLinkedFileFromURL(URL url, BibEntry entry, Path targetDirectory)
basePanel.getBibDatabaseContext(),
Globals.TASK_EXECUTOR,
dialogService,
JabRefPreferences.getInstance());
JabRefPreferences.getInstance(), ExternalFileTypes.getInstance());

try {
URLDownload urlDownload = new URLDownload(newLinkedFile.getLink());
BackgroundTask<Path> downloadTask = onlineFile.prepareDownloadTask(targetDirectory, urlDownload);
downloadTask.onSuccess(destination -> {
LinkedFile downloadedFile = LinkedFilesEditorViewModel.fromFile(
destination,
basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(JabRefPreferences.getInstance().getFilePreferences()));
basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(JabRefPreferences.getInstance().getFilePreferences()), ExternalFileTypes.getInstance());
entry.addFile(downloadedFile);
dialogService.notify(Localization.lang("Finished downloading full text document for entry %0.",
entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));
Expand Down
13 changes: 8 additions & 5 deletions src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,13 +66,15 @@ public class LinkedFileViewModel extends AbstractViewModel {
private final FilePreferences filePreferences;
private final XmpPreferences xmpPreferences;
private final LinkedFileHandler linkedFileHandler;
private final ExternalFileTypes externalFileTypes;

public LinkedFileViewModel(LinkedFile linkedFile,
BibEntry entry,
BibDatabaseContext databaseContext,
TaskExecutor taskExecutor,
DialogService dialogService,
JabRefPreferences preferences) {
JabRefPreferences preferences,
ExternalFileTypes externalFileTypes) {

this.linkedFile = linkedFile;
this.filePreferences = preferences.getFilePreferences();
Expand All @@ -81,6 +83,7 @@ public LinkedFileViewModel(LinkedFile linkedFile,
this.entry = entry;
this.dialogService = dialogService;
this.taskExecutor = taskExecutor;
this.externalFileTypes = externalFileTypes;

xmpPreferences = preferences.getXMPPreferences();
downloadOngoing.bind(downloadProgress.greaterThanOrEqualTo(0).and(downloadProgress.lessThan(1)));
Expand Down Expand Up @@ -402,7 +405,7 @@ public void download() {
URLDownload urlDownload = new URLDownload(linkedFile.getLink());
BackgroundTask<Path> downloadTask = prepareDownloadTask(targetDirectory.get(), urlDownload);
downloadTask.onSuccess(destination -> {
LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences));
LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences), externalFileTypes);
linkedFile.setLink(newLinkedFile.getLink());
linkedFile.setFileType(newLinkedFile.getFileType());
});
Expand All @@ -420,7 +423,7 @@ public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownloa
String suggestedTypeName = suggestedType.map(ExternalFileType::getName).orElse("");
linkedFile.setFileType(suggestedTypeName);

String suggestedName = linkedFileHandler.getSuggestedFileName();
String suggestedName = linkedFileHandler.getSuggestedFileName(suggestedTypeName);
return targetDirectory.resolve(suggestedName);
})
.then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))
Expand All @@ -443,15 +446,15 @@ private Optional<ExternalFileType> inferFileTypeFromMimeType(URLDownload urlDown

if (mimeType != null) {
LOGGER.debug("MIME Type suggested: " + mimeType);
return ExternalFileTypes.getInstance().getExternalFileTypeByMimeType(mimeType);
return externalFileTypes.getExternalFileTypeByMimeType(mimeType);
} else {
return Optional.empty();
}
}

private Optional<ExternalFileType> inferFileTypeFromURL(String url) {
return URLUtil.getSuffix(url)
.flatMap(extension -> ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension));
.flatMap(extension -> externalFileTypes.getExternalFileTypeByExt(extension));
}

public LinkedFile getFile() {
Expand Down
21 changes: 11 additions & 10 deletions src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,21 +48,22 @@ public class LinkedFilesEditorViewModel extends AbstractEditorViewModel {
private final BibDatabaseContext databaseContext;
private final TaskExecutor taskExecutor;
private final JabRefPreferences preferences;
private final ExternalFileTypes externalFileTypes = ExternalFileTypes.getInstance();

public LinkedFilesEditorViewModel(String fieldName, AutoCompleteSuggestionProvider<?> suggestionProvider,
DialogService dialogService,
BibDatabaseContext databaseContext,
TaskExecutor taskExecutor,
FieldCheckers fieldCheckers,
JabRefPreferences preferences) {

super(fieldName, suggestionProvider, fieldCheckers);

this.dialogService = dialogService;
this.databaseContext = databaseContext;
this.taskExecutor = taskExecutor;
this.preferences = preferences;


BindingsHelper.bindContentBidirectional(
files,
text,
Expand All @@ -86,9 +87,9 @@ private static String getStringRepresentation(List<LinkedFileViewModel> files) {
*
* TODO: Move this method to {@link LinkedFile} as soon as {@link CustomExternalFileType} lives in model.
*/
public static LinkedFile fromFile(Path file, List<Path> fileDirectories) {
public static LinkedFile fromFile(Path file, List<Path> fileDirectories, ExternalFileTypes externalFileTypesFile) {
String fileExtension = FileHelper.getFileExtension(file).orElse("");
ExternalFileType suggestedFileType = ExternalFileTypes.getInstance()
ExternalFileType suggestedFileType = externalFileTypesFile
.getExternalFileTypeByExt(fileExtension)
.orElse(new UnknownExternalFileType(fileExtension));
Path relativePath = FileUtil.relativize(file, fileDirectories);
Expand All @@ -98,8 +99,8 @@ public static LinkedFile fromFile(Path file, List<Path> fileDirectories) {
public LinkedFileViewModel fromFile(Path file) {
List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());

LinkedFile linkedFile = fromFile(file, fileDirectories);
return new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences);
LinkedFile linkedFile = fromFile(file, fileDirectories, externalFileTypes);
return new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes);

}

Expand All @@ -113,7 +114,7 @@ public BooleanProperty fulltextLookupInProgressProperty() {

private List<LinkedFileViewModel> parseToFileViewModel(String stringValue) {
return FileFieldParser.parse(stringValue).stream()
.map(linkedFile -> new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences))
.map(linkedFile -> new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes))
.collect(Collectors.toList());
}

Expand All @@ -135,8 +136,8 @@ public void addNewFile() {

List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
LinkedFile newLinkedFile = fromFile(newFile, fileDirectories);
files.add(new LinkedFileViewModel(newLinkedFile, entry, databaseContext, taskExecutor, dialogService, preferences));
LinkedFile newLinkedFile = fromFile(newFile, fileDirectories, externalFileTypes);
files.add(new LinkedFileViewModel(newLinkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes));
});
}

Expand All @@ -162,7 +163,7 @@ private List<LinkedFileViewModel> findAssociatedNotLinkedFiles(BibEntry entry) {
try {
List<LinkedFile> linkedFiles = util.findAssociatedNotLinkedFiles(entry);
for (LinkedFile linkedFile : linkedFiles) {
LinkedFileViewModel newLinkedFile = new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences);
LinkedFileViewModel newLinkedFile = new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes);
newLinkedFile.markAsAutomaticallyFound();
result.add(newLinkedFile);
}
Expand Down Expand Up @@ -205,7 +206,7 @@ public void addFromURL() {
}

private void addFromURL(URL url) {
LinkedFileViewModel onlineFile = new LinkedFileViewModel(new LinkedFile(url, ""), entry, databaseContext, taskExecutor, dialogService, preferences);
LinkedFileViewModel onlineFile = new LinkedFileViewModel(new LinkedFile(url, ""), entry, databaseContext, taskExecutor, dialogService, preferences, externalFileTypes);
files.add(onlineFile);
onlineFile.download();
}
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/jabref/gui/filelist/AttachFileAction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import org.jabref.gui.BasePanel;
import org.jabref.gui.DialogService;
import org.jabref.gui.actions.SimpleCommand;
import org.jabref.gui.externalfiletype.ExternalFileTypes;
import org.jabref.gui.fieldeditors.LinkedFilesEditorViewModel;
import org.jabref.gui.undo.UndoableFieldChange;
import org.jabref.gui.util.FileDialogConfiguration;
Expand Down Expand Up @@ -38,7 +39,7 @@ public void execute() {

dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {

LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile, panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()));
LinkedFile linkedFile = LinkedFilesEditorViewModel.fromFile(newFile, panel.getBibDatabaseContext().getFileDirectoriesAsPaths(Globals.prefs.getFilePreferences()), ExternalFileTypes.getInstance());

LinkedFileEditDialogView dialog = new LinkedFileEditDialogView(linkedFile);

Expand Down
13 changes: 8 additions & 5 deletions src/main/java/org/jabref/gui/filelist/LinkedFilesEditDialogViewModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -76,9 +76,9 @@ public void openBrowseDialog() {
String fileName = Paths.get(fileText).getFileName().toString();

FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
.withInitialDirectory(workingDir)
.withInitialFileName(fileName)
.build();
.withInitialDirectory(workingDir)
.withInitialFileName(fileName)
.build();

dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(path -> {
// Store the directory for next time:
Expand All @@ -92,8 +92,11 @@ public void openBrowseDialog() {
public void setValues(LinkedFile linkedFile) {
description.set(linkedFile.getDescription());

Path linkPath = Paths.get(linkedFile.getLink());
link.set(relativize(linkPath));
if (linkedFile.isOnlineLink()) {
link.setValue(linkedFile.getLink()); //Might be an URL
} else {
link.setValue(relativize(Paths.get(linkedFile.getLink())));
}

selectedExternalFileType.setValue(null);

Expand Down
5 changes: 3 additions & 2 deletions src/main/java/org/jabref/gui/maintable/MainTableColumnFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ class MainTableColumnFactory {
private final CellFactory cellFactory;
private final UndoManager undoManager;
private final DialogService dialogService;


public MainTableColumnFactory(BibDatabaseContext database, ColumnPreferences preferences, ExternalFileTypes externalFileTypes, UndoManager undoManager, DialogService dialogService) {
this.database = Objects.requireNonNull(database);
Expand Down Expand Up @@ -264,7 +265,7 @@ private TableColumn<BibEntryTableViewModel, List<LinkedFile>> createFileColumn()
.withOnMouseClickedEvent((entry, linkedFiles) -> event -> {
if ((event.getButton() == MouseButton.PRIMARY) && (linkedFiles.size() == 1)) {
// Only one linked file -> open directly
LinkedFileViewModel linkedFileViewModel = new LinkedFileViewModel(linkedFiles.get(0), entry.getEntry(), database, Globals.TASK_EXECUTOR, dialogService, Globals.prefs);
LinkedFileViewModel linkedFileViewModel = new LinkedFileViewModel(linkedFiles.get(0), entry.getEntry(), database, Globals.TASK_EXECUTOR, dialogService, Globals.prefs, externalFileTypes);
linkedFileViewModel.open();
}
})
Expand All @@ -287,7 +288,7 @@ private ContextMenu createFileMenu(BibEntryTableViewModel entry, List<LinkedFile
ContextMenu contextMenu = new ContextMenu();

for (LinkedFile linkedFile : linkedFiles) {
LinkedFileViewModel linkedFileViewModel = new LinkedFileViewModel(linkedFile, entry.getEntry(), database, Globals.TASK_EXECUTOR, dialogService, Globals.prefs);
LinkedFileViewModel linkedFileViewModel = new LinkedFileViewModel(linkedFile, entry.getEntry(), database, Globals.TASK_EXECUTOR, dialogService, Globals.prefs, externalFileTypes);

MenuItem menuItem = new MenuItem(linkedFileViewModel.getDescriptionAndLink(), linkedFileViewModel.getTypeIcon().getGraphicNode());
menuItem.setOnAction(event -> linkedFileViewModel.open());
Expand Down
12 changes: 9 additions & 3 deletions src/main/java/org/jabref/logic/externalfiles/LinkedFileHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import org.slf4j.LoggerFactory;

public class LinkedFileHandler {

private static final Logger LOGGER = LoggerFactory.getLogger(LinkedFileHandler.class);

private final BibDatabaseContext databaseContext;
Expand Down Expand Up @@ -84,7 +85,7 @@ public boolean renameToName(String targetFileName) throws IOException {

String expandedOldFilePath = oldFile.get().toString();
boolean pathsDifferOnlyByCase = newPath.toString().equalsIgnoreCase(expandedOldFilePath)
&& !newPath.toString().equals(expandedOldFilePath);
&& !newPath.toString().equals(expandedOldFilePath);

if (Files.exists(newPath) && !pathsDifferOnlyByCase) {
// We do not overwrite files
Expand Down Expand Up @@ -113,9 +114,14 @@ private String relativize(Path path) {
public String getSuggestedFileName() {
String oldFileName = fileEntry.getLink();

String extension = FileHelper.getFileExtension(oldFileName).orElse(fileEntry.getFileType());
return getSuggestedFileName(extension);
}

public String getSuggestedFileName(String extension) {
String targetFileName = FileUtil.createFileNameFromPattern(databaseContext.getDatabase(), entry, filePreferences.getFileNamePattern()).trim()
+ '.'
+ FileHelper.getFileExtension(oldFileName).orElse(fileEntry.getFileType());
+ '.'
+ extension;

// Only create valid file names
return FileUtil.getValidFileName(targetFileName);
Expand Down
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