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Rework AutoSetFileLinks #3368

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merged 14 commits into from
Oct 31, 2017
Merged

Rework AutoSetFileLinks #3368

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61fb09f
Rework AutoSetFileLinks
Siedlerchr Oct 28, 2017
d03f155
Only add first found file
Siedlerchr Oct 28, 2017
51fe583
Improve magic AutoFileLinking in entry editor by using same logic as …
Siedlerchr Oct 28, 2017
0a305fe
Don't use paths.get
Siedlerchr Oct 28, 2017
124bc37
add changelog entry
Siedlerchr Oct 28, 2017
8ab45cd
refactor
Siedlerchr Oct 29, 2017
8aed0d0
Use HashMap with BibEntry and LinkedFiles
Siedlerchr Oct 29, 2017
fd29758
improve optional code
Siedlerchr Oct 29, 2017
12f21bf
logging
Siedlerchr Oct 29, 2017
fff82ea
pass preferences to method
Siedlerchr Oct 29, 2017
1e16b17
Merge remote-tracking branch 'upstream/master' into autofilelink
Siedlerchr Oct 29, 2017
1948112
Merge remote-tracking branch 'upstream/master' into autofilelink
Siedlerchr Oct 29, 2017
229ce64
Return list of Linkedfiles and let caller handle bib entries
Siedlerchr Oct 30, 2017
05fa33f
Replace mocking of Jabrefs prefs with autolink prefs
Siedlerchr Oct 30, 2017
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68 changes: 68 additions & 0 deletions src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,68 @@
package org.jabref.gui.externalfiles;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;

import org.jabref.gui.externalfiletype.ExternalFileType;
import org.jabref.gui.externalfiletype.ExternalFileTypes;
import org.jabref.gui.externalfiletype.UnknownExternalFileType;
import org.jabref.logic.util.io.AutoLinkPreferences;
import org.jabref.logic.util.io.FileFinder;
import org.jabref.logic.util.io.FileFinders;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.LinkedFile;
import org.jabref.model.metadata.FileDirectoryPreferences;
import org.jabref.model.util.FileHelper;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

public class AutoSetFileLinksUtil {

private static final Log LOGGER = LogFactory.getLog(AutoSetLinks.class);

public List<LinkedFile> findassociatedNotLinkedFiles(BibEntry entry, BibDatabaseContext databaseContext, FileDirectoryPreferences fileDirPrefs, AutoLinkPreferences autoLinkPrefs, ExternalFileTypes externalFileTypes) {
List<LinkedFile> linkedFiles = new ArrayList<>();

List<Path> dirs = databaseContext.getFileDirectoriesAsPaths(fileDirPrefs);
List<String> extensions = externalFileTypes.getExternalFileTypeSelection().stream().map(ExternalFileType::getExtension).collect(Collectors.toList());

// Run the search operation:
FileFinder fileFinder = FileFinders.constructFromConfiguration(autoLinkPrefs);
List<Path> result = fileFinder.findAssociatedFiles(entry, dirs, extensions);

// Iterate over the entries:

for (Path foundFile : result) {
boolean existingSameFile = entry.getFiles().stream()
.map(file -> file.findIn(dirs))
.anyMatch(file -> {
try {
return file.isPresent() && Files.isSameFile(file.get(), foundFile);
} catch (IOException e) {
LOGGER.error("Problem with isSameFile", e);
}
return false;
});
if (!existingSameFile) {

Optional<ExternalFileType> type = FileHelper.getFileExtension(foundFile)
.map(externalFileTypes::getExternalFileTypeByExt)
.orElse(Optional.of(new UnknownExternalFileType("")));

String strType = type.isPresent() ? type.get().getName() : "";

LinkedFile linkedFile = new LinkedFile("", foundFile.toString(), strType);
linkedFiles.add(linkedFile);
}
}

return linkedFiles;
}
}
153 changes: 49 additions & 104 deletions src/main/java/org/jabref/gui/externalfiles/AutoSetLinks.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,10 @@
import java.awt.BorderLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;

import javax.swing.BorderFactory;
import javax.swing.JDialog;
Expand All @@ -24,19 +18,15 @@
import org.jabref.Globals;
import org.jabref.gui.externalfiletype.ExternalFileType;
import org.jabref.gui.externalfiletype.ExternalFileTypes;
import org.jabref.gui.externalfiletype.UnknownExternalFileType;
import org.jabref.gui.filelist.FileListEntry;
import org.jabref.gui.filelist.FileListTableModel;
import org.jabref.gui.undo.NamedCompound;
import org.jabref.gui.undo.UndoableFieldChange;
import org.jabref.gui.util.DefaultTaskExecutor;
import org.jabref.logic.l10n.Localization;
import org.jabref.logic.util.io.FileFinder;
import org.jabref.logic.util.io.FileFinders;
import org.jabref.logic.util.io.FileUtil;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.FieldName;
import org.jabref.model.util.FileHelper;
import org.jabref.model.entry.FileFieldWriter;
import org.jabref.model.entry.LinkedFile;

public class AutoSetLinks {

Expand All @@ -50,7 +40,7 @@ private AutoSetLinks() {
* @param databaseContext the database for which links are set
*/
public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext databaseContext) {
autoSetLinks(entries, null, null, null, databaseContext, null, null);
autoSetLinks(entries, null, null, databaseContext, null, null);
}

/**
Expand All @@ -64,12 +54,7 @@ public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext datab
* @param entries A collection of BibEntry objects to find links for.
* @param ce A NamedCompound to add UndoEdit elements to.
* @param changedEntries MODIFIED, optional. A Set of BibEntry objects to which all modified entries is added.
* This is used for status output and debugging
* @param singleTableModel UGLY HACK. The table model to insert links into. Already existing links are not
* duplicated or removed. This parameter has to be null if entries.count() != 1. The hack has been
* introduced as a bibtexentry does not (yet) support the function getListTableModel() and the
* FileListEntryEditor editor holds an instance of that table model and does not reconstruct it after the
* search has succeeded.

* @param databaseContext The database providing the relevant file directory, if any.
* @param callback An ActionListener that is notified (on the event dispatch thread) when the search is finished.
* The ActionEvent has id=0 if no new links were added, and id=1 if one or more links were added. This
Expand All @@ -79,7 +64,7 @@ public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext datab
* @return the thread performing the automatically setting
*/
public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCompound ce,
final Set<BibEntry> changedEntries, final FileListTableModel singleTableModel,
final Set<BibEntry> changedEntries,
final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
final Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
if (diag != null) {
Expand All @@ -95,97 +80,58 @@ public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCom
diag.setLocationRelativeTo(diag.getParent());
}

Runnable r = new Runnable() {

@Override
public void run() {
// determine directories to search in
final List<Path> dirs = databaseContext.getFileDirectoriesAsPaths(Globals.prefs.getFileDirectoryPreferences());

// determine extensions
final List<String> extensions = types.stream().map(ExternalFileType::getExtension).collect(Collectors.toList());

// Run the search operation:
FileFinder fileFinder = FileFinders.constructFromConfiguration(Globals.prefs.getAutoLinkPreferences());
Map<BibEntry, List<Path>> result = fileFinder.findAssociatedFiles(entries, dirs, extensions);

boolean foundAny = false;
// Iterate over the entries:
for (Entry<BibEntry, List<Path>> entryFilePair : result.entrySet()) {
FileListTableModel tableModel;
Optional<String> oldVal = entryFilePair.getKey().getField(FieldName.FILE);
if (singleTableModel == null) {
tableModel = new FileListTableModel();
oldVal.ifPresent(tableModel::setContent);
} else {
assert entries.size() == 1;
tableModel = singleTableModel;
Runnable r = () -> {
boolean foundAny = false;
AutoSetFileLinksUtil util = new AutoSetFileLinksUtil();

for (BibEntry entry : entries) {

List<LinkedFile> linkedFiles = util.findassociatedNotLinkedFiles(entry, databaseContext, Globals.prefs.getFileDirectoryPreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());

if (ce != null) {
for (LinkedFile linkedFile : linkedFiles) {
// store undo information
String newVal = FileFieldWriter.getStringRepresentation(linkedFile);

String oldVal = entry.getField(FieldName.FILE).orElse(null);

UndoableFieldChange fieldChange = new UndoableFieldChange(entry, FieldName.FILE, oldVal, newVal);
ce.addEdit(fieldChange);

DefaultTaskExecutor.runInJavaFXThread(() -> {
entry.addFile(linkedFile);
});
foundAny = true;
}
List<Path> files = entryFilePair.getValue();
for (Path file : files) {
file = FileUtil.shortenFileName(file, dirs);
boolean alreadyHas = false;

for (int j = 0; j < tableModel.getRowCount(); j++) {
FileListEntry existingEntry = tableModel.getEntry(j);
if (Paths.get(existingEntry.getLink()).equals(file)) {
alreadyHas = true;
foundAny = true;
break;
}
}
if (!alreadyHas) {
foundAny = true;
Optional<ExternalFileType> type = FileHelper.getFileExtension(file)
.map(extension -> ExternalFileTypes.getInstance().getExternalFileTypeByExt(extension))
.orElse(Optional.of(new UnknownExternalFileType("")));
FileListEntry flEntry = new FileListEntry("", file.toString(), type);
tableModel.addEntry(tableModel.getRowCount(), flEntry);

String newVal = tableModel.getStringRepresentation();
if (newVal.isEmpty()) {
newVal = null;
}
if (ce != null) {
// store undo information
UndoableFieldChange change = new UndoableFieldChange(entryFilePair.getKey(),
FieldName.FILE, oldVal.orElse(null), newVal);
ce.addEdit(change);
}
// hack: if table model is given, do NOT modify entry
if (singleTableModel == null) {
entryFilePair.getKey().setField(FieldName.FILE, newVal);
}
if (changedEntries != null) {
changedEntries.add(entryFilePair.getKey());
}
}

if (changedEntries != null) {
changedEntries.add(entry);
}
}

// handle callbacks and dialog
// FIXME: The ID signals if action was successful :/
final int id = foundAny ? 1 : 0;
SwingUtilities.invokeLater(new Runnable() {

@Override
public void run() {
if (diag != null) {
diag.dispose();
}
if (callback != null) {
callback.actionPerformed(new ActionEvent(this, id, ""));
}
}
});
}

final int id = foundAny ? 1 : 0;
SwingUtilities.invokeLater(() -> {

if (diag != null) {
diag.dispose();
}
if (callback != null) {
callback.actionPerformed(new ActionEvent(AutoSetLinks.class, id, ""));
}

});

};

SwingUtilities.invokeLater(() -> {
// show dialog which will be hidden when the task is done
if (diag != null) {
diag.setVisible(true);
}
});

return r;
}

Expand All @@ -194,8 +140,7 @@ public void run() {
* of external file types. The entry itself is not modified. The entry's bibtex key must have been set.
*
* @param entry The BibEntry to find links for.
* @param singleTableModel The table model to insert links into. Already existing links are not duplicated or
* removed.

* @param databaseContext The database providing the relevant file directory, if any.
* @param callback An ActionListener that is notified (on the event dispatch thread) when the search is finished.
* The ActionEvent has id=0 if no new links were added, and id=1 if one or more links were added. This
Expand All @@ -206,9 +151,9 @@ public void run() {
* parameter can be null, which means that no progress update will be shown.
* @return the runnable able to perform the automatically setting
*/
public static Runnable autoSetLinks(final BibEntry entry, final FileListTableModel singleTableModel,
public static Runnable autoSetLinks(final BibEntry entry,
final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
return autoSetLinks(Collections.singletonList(entry), null, null, singleTableModel, databaseContext, callback,
return autoSetLinks(Collections.singletonList(entry), null, null, databaseContext, callback,
diag);
}

Expand Down
25 changes: 15 additions & 10 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 @@ -2,6 +2,7 @@

import java.io.IOException;
import java.net.URL;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
Expand All @@ -14,6 +15,7 @@
import org.jabref.Globals;
import org.jabref.gui.BasePanel;
import org.jabref.gui.undo.UndoableFieldChange;
import org.jabref.gui.util.DefaultTaskExecutor;
import org.jabref.gui.worker.AbstractWorker;
import org.jabref.logic.importer.FulltextFetchers;
import org.jabref.logic.l10n.Localization;
Expand Down Expand Up @@ -81,9 +83,9 @@ public void update() {
BibEntry entry = download.getValue();
Optional<URL> result = download.getKey();
if (result.isPresent()) {
List<String> dirs = basePanel.getBibDatabaseContext()
.getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
if (dirs.isEmpty()) {
Optional<Path> dir = basePanel.getBibDatabaseContext().getFirstExistingFileDir(Globals.prefs.getFileDirectoryPreferences());

if (!dir.isPresent()) {
JOptionPane.showMessageDialog(basePanel.frame(),
Localization.lang("Main file directory not set!") + " " + Localization.lang("Preferences")
+ " -> " + Localization.lang("File"),
Expand All @@ -94,13 +96,16 @@ public void update() {
basePanel.getBibDatabaseContext(), entry);
try {
def.download(result.get(), file -> {
Optional<FieldChange> fieldChange = entry.addFile(file);
if (fieldChange.isPresent()) {
UndoableFieldChange edit = new UndoableFieldChange(entry, FieldName.FILE,
entry.getField(FieldName.FILE).orElse(null), fieldChange.get().getNewValue());
basePanel.getUndoManager().addEdit(edit);
basePanel.markBaseChanged();
}
DefaultTaskExecutor.runInJavaFXThread(() -> {
Optional<FieldChange> fieldChange = entry.addFile(file);
if (fieldChange.isPresent()) {
UndoableFieldChange edit = new UndoableFieldChange(entry, FieldName.FILE,
entry.getField(FieldName.FILE).orElse(null), fieldChange.get().getNewValue());
basePanel.getUndoManager().addEdit(edit);
basePanel.markBaseChanged();
}
});

});
} catch (IOException e) {
LOGGER.warn("Problem downloading file", e);
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/jabref/gui/externalfiles/SynchronizeFileField.java
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ public void run() {
List<BibEntry> entries = new ArrayList<>(sel);

// Start the automatically setting process:
Runnable r = AutoSetLinks.autoSetLinks(entries, ce, changedEntries, null, panel.getBibDatabaseContext(), null, null);
Runnable r = AutoSetLinks.autoSetLinks(entries, ce, changedEntries, panel.getBibDatabaseContext(), null, null);
JabRefExecutorService.INSTANCE.executeAndWait(r);
}
progress += sel.size() * weightAutoSet;
Expand Down
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