@Override
public boolean makeChange(BasePanel panel, BibtexDatabase secondary, NamedCompound undoEdit) {
panel.database().removeEntry(memEntry.getId());
undoEdit.addEdit(new UndoableRemoveEntry(panel.database(), memEntry, panel));
secondary.removeEntry(tmpEntry.getId());
return true;
}
/**
* Checks if the two entries represent the same publication.
*
* @param one BibtexEntry
* @param two BibtexEntry
* @return boolean
*/
public static boolean isDuplicate(BibtexEntry one, BibtexEntry two) {
// First check if they are of the same type - a necessary condition:
if (one.getType() != two.getType()) {
return false;
}
// The check if they have the same required fields:
String[] fields = one.getType().getRequiredFields().toArray(new String[0]);
double[] req;
if (fields == null) {
req = new double[] {0., 0.};
} else {
req = DuplicateCheck.compareFieldSet(fields, one, two);
}
if (Math.abs(req[0] - DuplicateCheck.duplicateThreshold) > DuplicateCheck.doubtRange) {
// Far from the threshold value, so we base our decision on the req. fields only
return req[0] >= DuplicateCheck.duplicateThreshold;
}
// Close to the threshold value, so we take a look at the optional fields, if any:
fields = one.getType().getOptionalFields().toArray(new String[0]);
if (fields != null) {
double[] opt = DuplicateCheck.compareFieldSet(fields, one, two);
double totValue =
((DuplicateCheck.reqWeight * req[0] * req[1]) + (opt[0] * opt[1]))
/ ((req[1] * DuplicateCheck.reqWeight) + opt[1]);
return totValue >= DuplicateCheck.duplicateThreshold;
}
return req[0] >= DuplicateCheck.duplicateThreshold;
}
@Test
@Ignore
public void testAddEntrysFromFiles() throws Exception {
ParserResult result =
BibtexParser.parse(new FileReader(ImportDataTest.UNLINKED_FILES_TEST_BIB));
BibtexDatabase database = result.getDatabase();
List<File> files = new ArrayList<File>();
files.add(ImportDataTest.FILE_NOT_IN_DATABASE);
files.add(ImportDataTest.NOT_EXISTING_PDF);
EntryFromFileCreatorManager manager = new EntryFromFileCreatorManager();
List<String> errors = manager.addEntrysFromFiles(files, database, null, true);
/** One file doesn't exist, so adding it as an entry should lead to an error message. */
Assert.assertEquals(1, errors.size());
boolean file1Found = false;
boolean file2Found = false;
for (BibtexEntry entry : database.getEntries()) {
String filesInfo = entry.getField("file");
if (filesInfo.contains(files.get(0).getName())) {
file1Found = true;
}
if (filesInfo.contains(files.get(1).getName())) {
file2Found = true;
}
}
Assert.assertTrue(file1Found);
Assert.assertFalse(file2Found);
}
private static void fixWrongFileEntries(BibtexEntry entry, NamedCompound ce) {
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
FileListEntry flEntry = flModel.getEntry(i);
String link = flEntry.getLink();
String description = flEntry.getDescription();
if ("".equals(link) && (!"".equals(description))) {
// link and description seem to be switched, quickly fix that
flEntry.setLink(flEntry.getDescription());
flEntry.setDescription("");
changed = true;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
private void doMakePathsRelative(BibtexEntry entry, NamedCompound ce) {
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
FileListEntry flEntry = flModel.getEntry(i);
String oldFileName = flEntry.getLink();
String newFileName =
FileUtil.shortenFileName(
new File(oldFileName), panel.metaData().getFileDirectory(Globals.FILE_FIELD))
.toString();
if (!oldFileName.equals(newFileName)) {
flEntry.setLink(newFileName);
changed = true;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
/**
* Format page numbers, separated either by commas or double-hyphens. Converts the range number
* format of the <code>pages</code> field to page_number--page_number.
*
* @see{PageNumbersFormatter}
*/
public void cleanup() {
final String field = "pages";
String value = entry.getField(field);
String newValue = BibtexFieldFormatters.PAGE_NUMBERS.format(value);
entry.setField(field, newValue);
}
/**
* Recursive method to include a tree of groups.
*
* @param cursor The current GroupTreeNode in the GroupsTree
* @param parentID The integer ID associated with the cursors's parent node
* @param currentID The integer value to associate with the cursor
* @param out The output (PrintStream or Connection) object to which the DML should be written.
* @param database_id Id of jabref database to which the group is part of
*/
private int populateEntryGroupsTable(
GroupTreeNode cursor, int parentID, int currentID, Object out, int database_id)
throws SQLException {
// if this group contains entries...
if (cursor.getGroup() instanceof ExplicitGroup) {
ExplicitGroup grp = (ExplicitGroup) cursor.getGroup();
for (BibtexEntry be : grp.getEntries()) {
SQLUtil.processQuery(
out,
"INSERT INTO entry_group (entries_id, groups_id) "
+ "VALUES ("
+ "(SELECT entries_id FROM entries WHERE jabref_eid="
+ '\''
+ be.getId()
+ "' AND database_id = "
+ database_id
+ "), "
+ "(SELECT groups_id FROM groups WHERE database_id="
+ '\''
+ database_id
+ "' AND parent_id="
+ '\''
+ parentID
+ "' AND label="
+ '\''
+ grp.getName()
+ "')"
+ ");");
}
}
// recurse on child nodes (depth-first traversal)
Object response =
SQLUtil.processQueryWithResults(
out,
"SELECT groups_id FROM groups WHERE label='"
+ cursor.getGroup().getName()
+ "' AND database_id='"
+ database_id
+ "' AND parent_id='"
+ parentID
+ "';");
// setting values to ID and myID to be used in case of textual SQL
// export
++currentID;
int myID = currentID;
if (response instanceof Statement) {
ResultSet rs = ((Statement) response).getResultSet();
rs.next();
myID = rs.getInt("groups_id");
}
for (Enumeration<GroupTreeNode> e = cursor.children(); e.hasMoreElements(); ) {
currentID = populateEntryGroupsTable(e.nextElement(), myID, currentID, out, database_id);
}
return currentID;
}
private static int compareSingleField(String field, BibtexEntry one, BibtexEntry two) {
String s1 = one.getField(field);
String s2 = two.getField(field);
if (s1 == null) {
if (s2 == null) {
return EMPTY_IN_BOTH;
}
return EMPTY_IN_ONE;
} else if (s2 == null) {
return EMPTY_IN_TWO;
}
if (field.equals("author") || field.equals("editor")) {
// Specific for name fields.
// Harmonise case:
String auth1 =
AuthorList.fixAuthor_lastNameOnlyCommas(s1, false).replaceAll(" and ", " ").toLowerCase();
String auth2 =
AuthorList.fixAuthor_lastNameOnlyCommas(s2, false).replaceAll(" and ", " ").toLowerCase();
double similarity = DuplicateCheck.correlateByWords(auth1, auth2, false);
if (similarity > 0.8) {
return EQUAL;
}
return NOT_EQUAL;
} else if (field.equals("pages")) {
// Pages can be given with a variety of delimiters, "-", "--", " - ", " -- ".
// We do a replace to harmonize these to a simple "-":
// After this, a simple test for equality should be enough:
s1 = s1.replaceAll("[- ]+", "-");
s2 = s2.replaceAll("[- ]+", "-");
if (s1.equals(s2)) {
return EQUAL;
}
return NOT_EQUAL;
} else if (field.equals("journal")) {
// We do not attempt to harmonize abbreviation state of the journal names,
// but we remove periods from the names in case they are abbreviated with
// and without dots:
s1 = s1.replaceAll("\\.", "").toLowerCase();
s2 = s2.replaceAll("\\.", "").toLowerCase();
double similarity = DuplicateCheck.correlateByWords(s1, s2, true);
if (similarity > 0.8) {
return EQUAL;
}
return NOT_EQUAL;
} else {
s1 = s1.toLowerCase();
s2 = s2.toLowerCase();
double similarity = DuplicateCheck.correlateByWords(s1, s2, false);
if (similarity > 0.8) {
return EQUAL;
}
return NOT_EQUAL;
}
}
/**
* Converts the text in 1st, 2nd, ... to real superscripts by wrapping in \textsuperscript{st},
* ...
*/
private static void doCleanUpSuperscripts(BibtexEntry entry, NamedCompound ce) {
for (String name : entry.getFieldNames()) {
String oldValue = entry.getField(name);
// run formatter
String newValue = BibtexFieldFormatters.SUPERSCRIPTS.format(oldValue);
// undo action
if (!oldValue.equals(newValue)) {
entry.setField(name, newValue);
ce.addEdit(new UndoableFieldChange(entry, name, oldValue, newValue));
}
}
}
/** Converts HTML code to LaTeX code */
private static void doConvertHTML(BibtexEntry entry, NamedCompound ce) {
final String field = "title";
String oldValue = entry.getField(field);
if (oldValue == null) {
return;
}
final HTMLConverter htmlConverter = new HTMLConverter();
String newValue = htmlConverter.format(oldValue);
if (!oldValue.equals(newValue)) {
entry.setField(field, newValue);
ce.addEdit(new UndoableFieldChange(entry, field, oldValue, newValue));
}
}
/** Converts Unicode characters to LaTeX code */
private static void doConvertUnicode(BibtexEntry entry, NamedCompound ce) {
final String[] fields = {"title", "author", "abstract"};
for (String field : fields) {
String oldValue = entry.getField(field);
if (oldValue == null) {
return;
}
final HTMLConverter htmlConverter = new HTMLConverter();
String newValue = htmlConverter.formatUnicode(oldValue);
if (!oldValue.equals(newValue)) {
entry.setField(field, newValue);
ce.addEdit(new UndoableFieldChange(entry, field, oldValue, newValue));
}
}
}
@Override
public void redo() {
super.redo();
// Redo the change.
try {
if (newValue != null) {
entry.setField(field, newValue);
} else {
entry.clearField(field);
}
} catch (IllegalArgumentException ex) {
LOGGER.info("Cannot perform redo", ex);
}
}
@Override
public void undo() {
super.undo();
// Revert the change.
try {
if (oldValue != null) {
entry.setField(field, oldValue);
} else {
entry.clearField(field);
}
// this is the only exception explicitly thrown here
} catch (IllegalArgumentException ex) {
LOGGER.info("Cannot perform undo", ex);
}
}
/** Runs the field formatter on the entry and records the change. */
private static void doFieldFormatterCleanup(
BibtexEntry entry, FieldFormatterCleanup cleaner, NamedCompound ce) {
String oldValue = entry.getField(cleaner.getField());
if (oldValue == null) {
return;
}
// run formatter
cleaner.cleanup(entry);
String newValue = entry.getField(cleaner.getField());
// undo action
if (!oldValue.equals(newValue)) {
ce.addEdit(new UndoableFieldChange(entry, cleaner.getField(), oldValue, newValue));
}
}
private static void doCleanUpMonth(BibtexEntry entry, NamedCompound ce) {
// implementation based on patch 3470076 by Mathias Walter
String oldValue = entry.getField("month");
if (oldValue == null) {
return;
}
String newValue = oldValue;
MonthUtil.Month month = MonthUtil.getMonth(oldValue);
if (month.isValid()) {
newValue = month.bibtexFormat;
}
if (!oldValue.equals(newValue)) {
entry.setField("month", newValue);
ce.addEdit(new UndoableFieldChange(entry, "month", oldValue, newValue));
}
}
public static double compareEntriesStrictly(BibtexEntry one, BibtexEntry two) {
HashSet<String> allFields = new HashSet<>();
allFields.addAll(one.getFieldNames());
allFields.addAll(two.getFieldNames());
int score = 0;
for (String field : allFields) {
Object en = one.getField(field);
Object to = two.getField(field);
if (((en != null) && (to != null) && en.equals(to)) || ((en == null) && (to == null))) {
score++;
}
}
if (score == allFields.size()) {
return 1.01; // Just to make sure we can
// use score>1 without
// trouble.
}
return (double) score / allFields.size();
}
@Override
public Object getColumnValue(BibtexEntry entry, int column) {
if (column < PAD) {
Object o;
switch (column) {
case FILE_COL:
o = entry.getField(Globals.FILE_FIELD);
if (o != null) {
FileListTableModel model = new FileListTableModel();
model.setContent((String) o);
fileLabel.setToolTipText(model.getToolTipHTMLRepresentation());
if (model.getRowCount() > 0) {
fileLabel.setIcon(model.getEntry(0).getType().getIcon());
}
return fileLabel;
} else {
return null;
}
case URL_COL:
o = entry.getField("url");
if (o != null) {
urlLabel.setToolTipText((String) o);
return urlLabel;
} else {
return null;
}
default:
return null;
}
} else {
String field = fields[column - PAD];
if (field.equals("author") || field.equals("editor")) {
// For name fields, tap into a MainTableFormat instance and use
// the same name formatting as is used in the entry table:
if (frame.basePanel() != null) {
return frame.basePanel().tableFormat.formatName(entry.getField(field));
}
}
return entry.getField(field);
}
}
@Override
public void mouseClicked(MouseEvent e) {
if (e.isPopupTrigger()) {
processPopupTrigger(e);
return;
}
// if (e.)
final int col = entryTable.columnAtPoint(e.getPoint());
final int row = entryTable.rowAtPoint(e.getPoint());
if (col < PAD) {
BibtexEntry entry = sortedEntries.get(row);
BasePanel p = entryHome.get(entry);
switch (col) {
case FILE_COL:
Object o = entry.getField(Globals.FILE_FIELD);
if (o != null) {
FileListTableModel tableModel = new FileListTableModel();
tableModel.setContent((String) o);
if (tableModel.getRowCount() == 0) {
return;
}
FileListEntry fl = tableModel.getEntry(0);
(new ExternalFileMenuItem(
frame, entry, "", fl.getLink(), null, p.metaData(), fl.getType()))
.actionPerformed(null);
}
break;
case URL_COL:
Object link = entry.getField("url");
try {
if (link != null) {
JabRefDesktop.openExternalViewer(p.metaData(), (String) link, "url");
}
} catch (IOException ex) {
ex.printStackTrace();
}
break;
}
}
}
/**
* If the user has signalled the opening of a context menu, the event gets redirected to this
* method. Here we open a file link menu if the user is pointing at a file link icon. Otherwise
* a general context menu should be shown.
*
* @param e The triggering mouse event.
*/
public void processPopupTrigger(MouseEvent e) {
BibtexEntry entry = sortedEntries.get(entryTable.rowAtPoint(e.getPoint()));
BasePanel p = entryHome.get(entry);
int col = entryTable.columnAtPoint(e.getPoint());
JPopupMenu menu = new JPopupMenu();
int count = 0;
if (col == FILE_COL) {
// We use a FileListTableModel to parse the field content:
Object o = entry.getField(Globals.FILE_FIELD);
FileListTableModel fileList = new FileListTableModel();
fileList.setContent((String) o);
// If there are one or more links, open the first one:
for (int i = 0; i < fileList.getRowCount(); i++) {
FileListEntry flEntry = fileList.getEntry(i);
String description = flEntry.getDescription();
if ((description == null) || (description.trim().isEmpty())) {
description = flEntry.getLink();
}
menu.add(
new ExternalFileMenuItem(
p.frame(),
entry,
description,
flEntry.getLink(),
flEntry.getType().getIcon(),
p.metaData(),
flEntry.getType()));
count++;
}
}
if (count > 0) {
menu.show(entryTable, e.getX(), e.getY());
}
}
/**
* Generates the DML required to populate the entries table with jabref data and writes it to the
* output PrintStream.
*
* @param database_id ID of Jabref database related to the entries to be exported This information
* can be gathered using getDatabaseIDByPath(metaData, out)
* @param entries The BibtexEntries to export
* @param out The output (PrintStream or Connection) object to which the DML should be written.
*/
private void populateEntriesTable(int database_id, List<BibtexEntry> entries, Object out)
throws SQLException {
String query;
String val;
String insert =
"INSERT INTO entries (jabref_eid, entry_types_id, cite_key, "
+ fieldStr
+ ", database_id) VALUES (";
for (BibtexEntry entry : entries) {
query =
insert
+ '\''
+ entry.getId()
+ '\''
+ ", (SELECT entry_types_id FROM entry_types WHERE label='"
+ entry.getType().getName().toLowerCase()
+ "'), '"
+ entry.getCiteKey()
+ '\'';
for (int i = 0; i < SQLUtil.getAllFields().size(); i++) {
query = query + ", ";
val = entry.getField(SQLUtil.getAllFields().get(i));
if (val != null) {
val = val.replace("\\", "\\\\");
val = val.replace("\"", "\\\"");
val = val.replace("\'", "''");
val = val.replace("`", "\\`");
query = query + '\'' + val + '\'';
} else {
query = query + "NULL";
}
}
query = query + ", '" + database_id + "');";
SQLUtil.processQuery(out, query);
}
}
/** Update the merged BibtexEntry with source and preview panel everytime something is changed */
private void updateAll() {
if (!doneBuilding) {
// If we've not done adding everything, do not do anything...
return;
}
// Check if the type is changed
if (!identical[0]) {
if (rb[0][0].isSelected()) {
mergedEntry.setType(one.getType());
} else {
mergedEntry.setType(two.getType());
}
}
// Check all fields
for (int i = 0; i < joint.size(); i++) {
if (!identical[i + 1]) {
if (rb[0][i + 1].isSelected()) {
mergedEntry.setField(jointStrings[i], one.getField(jointStrings[i]));
} else if (rb[2][i + 1].isSelected()) {
mergedEntry.setField(jointStrings[i], two.getField(jointStrings[i]));
} else {
mergedEntry.setField(jointStrings[i], null);
}
}
}
// Update the PreviewPanel
pp.setEntry(mergedEntry);
// Update the Bibtex source view
StringWriter sw = new StringWriter();
try {
new BibtexEntryWriter(new LatexFieldFormatter(), false).write(mergedEntry, sw);
} catch (IOException ex) {
LOGGER.error("Error in entry" + ": " + ex.getMessage(), ex);
}
jta.setText(sw.getBuffer().toString());
jta.setCaretPosition(0);
}
/**
* Tries to find a fulltext URL for a given BibTex entry.
*
* <p>Currently only uses the DOI if found.
*
* @param entry The Bibtex entry
* @return The fulltext PDF URL Optional, if found, or an empty Optional if not found.
* @throws NullPointerException if no BibTex entry is given
* @throws java.io.IOException
*/
public Optional<URL> findFullText(BibtexEntry entry) throws IOException {
Objects.requireNonNull(entry);
Optional<URL> pdfLink = Optional.empty();
// DOI search
Optional<DOI> doi = DOI.build(entry.getField("doi"));
if (doi.isPresent()) {
String source = String.format(SOURCE, doi.get().getDOI());
// Retrieve PDF link
Document html = Jsoup.connect(source).ignoreHttpErrors(true).get();
Element link = html.select(".pdf-high-res a").first();
if (link != null) {
LOGGER.info("Fulltext PDF found @ ACS.");
pdfLink = Optional.of(new URL(source.replaceFirst("/abs/", "/pdf/")));
}
}
return pdfLink;
}
/**
* Removes the http://... for each DOI Moves DOIs from URL and NOTE filed to DOI field
*
* @param ce
*/
private static void doCleanUpDOI(BibtexEntry bes, NamedCompound ce) {
// fields to check
String[] fields = {"note", "url", "ee"};
// First check if the Doi Field is empty
if (bes.getField("doi") != null) {
String doiFieldValue = bes.getField("doi");
Optional<DOI> doi = DOI.build(doiFieldValue);
if (doi.isPresent()) {
String newValue = doi.get().getDOI();
if (!doiFieldValue.equals(newValue)) {
ce.addEdit(new UndoableFieldChange(bes, "doi", doiFieldValue, newValue));
bes.setField("doi", newValue);
}
// Doi field seems to contain Doi
// -> cleanup note, url, ee field
for (String field : fields) {
DOI.build(bes.getField((field))).ifPresent(unused -> removeFieldValue(bes, field, ce));
}
}
} else {
// As the Doi field is empty we now check if note, url, or ee field contains a Doi
for (String field : fields) {
Optional<DOI> doi = DOI.build(bes.getField(field));
if (doi.isPresent()) {
// update Doi
String oldValue = bes.getField("doi");
String newValue = doi.get().getDOI();
ce.addEdit(new UndoableFieldChange(bes, "doi", oldValue, newValue));
bes.setField("doi", newValue);
removeFieldValue(bes, field, ce);
}
}
}
}
private void doRenamePDFs(BibtexEntry entry, NamedCompound ce) {
// Extract the path
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
String realOldFilename = flModel.getEntry(i).getLink();
if (cleanUpRenamePDFonlyRelativePaths.isSelected()
&& (new File(realOldFilename).isAbsolute())) {
continue;
}
String newFilename = Util.getLinkedFileName(panel.database(), entry);
// String oldFilename = bes.getField(GUIGlobals.FILE_FIELD); // would have to be stored for
// undoing purposes
// Add extension to newFilename
newFilename = newFilename + "." + flModel.getEntry(i).getType().getExtension();
// get new Filename with path
// Create new Path based on old Path and new filename
File expandedOldFile =
FileUtil.expandFilename(
realOldFilename, panel.metaData().getFileDirectory(Globals.FILE_FIELD));
if (expandedOldFile.getParent() == null) {
// something went wrong. Just skip this entry
continue;
}
String newPath =
expandedOldFile
.getParent()
.concat(System.getProperty("file.separator"))
.concat(newFilename);
if (new File(newPath).exists()) {
// we do not overwrite files
// TODO: we could check here if the newPath file is linked with the current entry. And if
// not, we could add a link
continue;
}
// do rename
boolean renameSuccessful = FileUtil.renameFile(expandedOldFile.toString(), newPath);
if (renameSuccessful) {
changed = true;
// Change the path for this entry
String description = flModel.getEntry(i).getDescription();
ExternalFileType type = flModel.getEntry(i).getType();
flModel.removeEntry(i);
// we cannot use "newPath" to generate a FileListEntry as newPath is absolute, but we want
// to keep relative paths whenever possible
File parent = (new File(realOldFilename)).getParentFile();
String newFileEntryFileName;
if (parent == null) {
newFileEntryFileName = newFilename;
} else {
newFileEntryFileName =
parent.toString().concat(System.getProperty("file.separator")).concat(newFilename);
}
flModel.addEntry(i, new FileListEntry(description, newFileEntryFileName, type));
} else {
unsuccessfulRenames++;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
// we put an undo of the field content here
// the file is not being renamed back, which leads to inconsistencies
// if we put a null undo object here, the change by "doMakePathsRelative" would overwrite the
// field value nevertheless.
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
/** Converts to BibLatex format */
public static void convertToBiblatex(BibtexEntry entry, NamedCompound ce) {
for (Map.Entry<String, String> alias : EntryConverter.FIELD_ALIASES_TEX_TO_LTX.entrySet()) {
String oldFieldName = alias.getKey();
String newFieldName = alias.getValue();
String oldValue = entry.getField(oldFieldName);
String newValue = entry.getField(newFieldName);
if ((oldValue != null) && (!oldValue.isEmpty()) && (newValue == null)) {
// There is content in the old field and no value in the new, so just copy
entry.setField(newFieldName, oldValue);
ce.addEdit(new UndoableFieldChange(entry, newFieldName, null, oldValue));
entry.setField(oldFieldName, null);
ce.addEdit(new UndoableFieldChange(entry, oldFieldName, oldValue, null));
}
}
// Dates: create date out of year and month, save it and delete old fields
if ((entry.getField("date") == null) || (entry.getField("date").isEmpty())) {
String newDate = entry.getFieldOrAlias("date");
String oldYear = entry.getField("year");
String oldMonth = entry.getField("month");
entry.setField("date", newDate);
entry.setField("year", null);
entry.setField("month", null);
ce.addEdit(new UndoableFieldChange(entry, "date", null, newDate));
ce.addEdit(new UndoableFieldChange(entry, "year", oldYear, null));
ce.addEdit(new UndoableFieldChange(entry, "month", oldMonth, null));
}
}
private static void removeFieldValue(
BibtexEntry entry, String fieldName, NamedCompound compound) {
String origValue = entry.getField(fieldName);
compound.addEdit(new UndoableFieldChange(entry, fieldName, origValue, null));
entry.setField(fieldName, null);
}
/** Main function for building the merge entry JPanel */
private void initialize() {
joint = new TreeSet<>(one.getFieldNames());
joint.addAll(two.getFieldNames());
// Remove field starting with __
TreeSet<String> toberemoved = new TreeSet<>();
for (String field : joint) {
if (field.startsWith("__")) {
toberemoved.add(field);
}
}
for (String field : toberemoved) {
joint.remove(field);
}
// Create storage arrays
rb = new JRadioButton[3][joint.size() + 1];
ButtonGroup[] rbg = new ButtonGroup[joint.size() + 1];
identical = new Boolean[joint.size() + 1];
jointStrings = new String[joint.size()];
// Create main layout
String colSpecMain =
"left:pref, 5px, center:3cm:grow, 5px, center:pref, 3px, center:pref, 3px, center:pref, 5px, center:3cm:grow";
String colSpecMerge =
"left:pref, 5px, fill:3cm:grow, 5px, center:pref, 3px, center:pref, 3px, center:pref, 5px, fill:3cm:grow";
String rowSpec = "pref, pref, 10px, fill:5cm:grow, 10px, pref, 10px, fill:3cm:grow";
StringBuilder rowBuilder = new StringBuilder("");
for (int i = 0; i < joint.size(); i++) {
rowBuilder.append("pref, ");
}
rowBuilder.append("pref");
FormLayout mainLayout = new FormLayout(colSpecMain, rowSpec);
FormLayout mergeLayout = new FormLayout(colSpecMerge, rowBuilder.toString());
mainPanel.setLayout(mainLayout);
mergePanel.setLayout(mergeLayout);
JLabel label = new JLabel(Localization.lang("Use"));
Font font = label.getFont();
label.setFont(font.deriveFont(font.getStyle() | Font.BOLD));
mainPanel.add(label, cc.xyw(4, 1, 7, "center, bottom"));
// Set headings
JLabel headingLabels[] = new JLabel[6];
for (int i = 0; i < 6; i++) {
headingLabels[i] = new JLabel(columnHeadings[i]);
font = headingLabels[i].getFont();
headingLabels[i].setFont(font.deriveFont(font.getStyle() | Font.BOLD));
mainPanel.add(headingLabels[i], cc.xy(1 + (i * 2), 2));
}
mainPanel.add(new JSeparator(), cc.xyw(1, 3, 11));
// Start with entry type
EntryType type1 = one.getType();
EntryType type2 = two.getType();
mergedEntry.setType(type1);
label = new JLabel(Localization.lang("Entry type"));
font = label.getFont();
label.setFont(font.deriveFont(font.getStyle() | Font.BOLD));
mergePanel.add(label, cc.xy(1, 1));
JTextArea type1ta = new JTextArea(type1.getName());
type1ta.setEditable(false);
mergePanel.add(type1ta, cc.xy(3, 1));
if (type1.compareTo(type2) != 0) {
identical[0] = false;
rbg[0] = new ButtonGroup();
for (int k = 0; k < 3; k += 2) {
rb[k][0] = new JRadioButton();
rbg[0].add(rb[k][0]);
mergePanel.add(rb[k][0], cc.xy(5 + (k * 2), 1));
rb[k][0].addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
updateAll();
}
});
}
rb[0][0].setSelected(true);
} else {
identical[0] = true;
}
JTextArea type2ta = new JTextArea(type2.getName());
type2ta.setEditable(false);
mergePanel.add(type2ta, cc.xy(11, 1));
// For all fields in joint add a row and possibly radio buttons
int row = 2;
int maxLabelWidth = -1;
int tmpLabelWidth = 0;
for (String field : joint) {
jointStrings[row - 2] = field;
label = new JLabel(CaseChangers.UPPER_FIRST.format(field));
font = label.getFont();
label.setFont(font.deriveFont(font.getStyle() | Font.BOLD));
mergePanel.add(label, cc.xy(1, row));
String string1 = one.getField(field);
String string2 = two.getField(field);
identical[row - 1] = false;
if ((string1 != null) && (string2 != null)) {
if (string1.equals(string2)) {
identical[row - 1] = true;
}
}
tmpLabelWidth = label.getPreferredSize().width;
if (tmpLabelWidth > maxLabelWidth) {
maxLabelWidth = tmpLabelWidth;
}
if ("abstract".equals(field) || "review".equals(field)) {
// Treat the abstract and review fields special
JTextArea tf = new JTextArea();
tf.setLineWrap(true);
tf.setEditable(false);
JScrollPane jsptf = new JScrollPane(tf);
mergeLayout.setRowSpec(row, RowSpec.decode("center:2cm:grow"));
mergePanel.add(jsptf, cc.xy(3, row, "f, f"));
tf.setText(string1);
tf.setCaretPosition(0);
} else {
JTextArea tf = new JTextArea(string1);
mergePanel.add(tf, cc.xy(3, row));
tf.setCaretPosition(0);
tf.setEditable(false);
}
// Add radio buttons if the two entries do not have identical fields
if (!identical[row - 1]) {
rbg[row - 1] = new ButtonGroup();
for (int k = 0; k < 3; k++) {
rb[k][row - 1] = new JRadioButton();
rbg[row - 1].add(rb[k][row - 1]);
mergePanel.add(rb[k][row - 1], cc.xy(5 + (k * 2), row));
rb[k][row - 1].addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
updateAll();
}
});
}
if (string1 != null) {
mergedEntry.setField(field, string1);
rb[0][row - 1].setSelected(true);
if (string2 == null) {
rb[2][row - 1].setEnabled(false);
}
} else {
rb[0][row - 1].setEnabled(false);
mergedEntry.setField(field, string2);
rb[2][row - 1].setSelected(true);
}
} else {
mergedEntry.setField(field, string1);
}
if ("abstract".equals(field) || "review".equals(field)) {
// Again, treat abstract and review special
JTextArea tf = new JTextArea();
tf.setLineWrap(true);
tf.setEditable(false);
JScrollPane jsptf = new JScrollPane(tf);
mergePanel.add(jsptf, cc.xy(11, row, "f, f"));
tf.setText(string2);
tf.setCaretPosition(0);
} else {
JTextArea tf = new JTextArea(string2);
mergePanel.add(tf, cc.xy(11, row));
tf.setCaretPosition(0);
tf.setEditable(false);
}
row++;
}
JScrollPane scrollPane =
new JScrollPane(
mergePanel,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
scrollPane.setBorder(BorderFactory.createEmptyBorder());
mainPanel.add(scrollPane, cc.xyw(1, 4, 11));
mainPanel.add(new JSeparator(), cc.xyw(1, 5, 11));
// Synchronize column widths
String rbAlign[] = {"right", "center", "left"};
mainLayout.setColumnSpec(1, ColumnSpec.decode(Integer.toString(maxLabelWidth) + "px"));
Integer maxRBWidth = -1;
Integer tmpRBWidth;
for (int k = 0; k < 3; k++) {
tmpRBWidth = headingLabels[k + 2].getPreferredSize().width;
if (tmpRBWidth > maxRBWidth) {
maxRBWidth = tmpRBWidth;
}
}
for (int k = 0; k < 3; k++) {
mergeLayout.setColumnSpec(
5 + (k * 2), ColumnSpec.decode(rbAlign[k] + ":" + maxRBWidth + "px"));
}
// Setup a PreviewPanel and a Bibtex source box for the merged entry
label = new JLabel(Localization.lang("Merged entry"));
font = label.getFont();
label.setFont(font.deriveFont(font.getStyle() | Font.BOLD));
mainPanel.add(label, cc.xyw(1, 6, 6));
String layoutString = Globals.prefs.get(JabRefPreferences.PREVIEW_0);
pp = new PreviewPanel(null, mergedEntry, null, new MetaData(), layoutString);
// JScrollPane jsppp = new JScrollPane(pp, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
// JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
mainPanel.add(pp, cc.xyw(1, 8, 6));
label = new JLabel(Localization.lang("Merged BibTeX source code"));
font = label.getFont();
label.setFont(font.deriveFont(font.getStyle() | Font.BOLD));
mainPanel.add(label, cc.xyw(8, 6, 4));
jta = new JTextArea();
jta.setLineWrap(true);
JScrollPane jspta = new JScrollPane(jta);
mainPanel.add(jspta, cc.xyw(8, 8, 4));
jta.setEditable(false);
StringWriter sw = new StringWriter();
try {
new BibtexEntryWriter(new LatexFieldFormatter(), false).write(mergedEntry, sw);
} catch (IOException ex) {
LOGGER.error("Error in entry" + ": " + ex.getMessage(), ex);
}
jta.setText(sw.getBuffer().toString());
jta.setCaretPosition(0);
// Add some margin around the layout
mainLayout.appendRow(RowSpec.decode("10px"));
mainLayout.appendColumn(ColumnSpec.decode("10px"));
mainLayout.insertRow(1, RowSpec.decode("10px"));
mainLayout.insertColumn(1, ColumnSpec.decode("10px"));
if (mainPanel.getHeight() > DIM.height) {
mainPanel.setSize(new Dimension(mergePanel.getWidth(), DIM.height));
}
if (mainPanel.getWidth() > DIM.width) {
mainPanel.setSize(new Dimension(DIM.width, mergePanel.getHeight()));
}
// Everything done, allow any action to actually update the merged entry
doneBuilding = true;
// Show what we've got
mainPanel.setVisible(true);
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
@Override
public void run() {
scrollPane.getVerticalScrollBar().setValue(0);
}
});
}
/** Parse the entries in the source, and return a List of BibtexEntry objects. */
@Override
public List<BibtexEntry> importEntries(InputStream stream, OutputPrinter status)
throws IOException {
ArrayList<BibtexEntry> bibItems = new ArrayList<BibtexEntry>();
BufferedReader in = new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));
String line;
HashMap<String, String> hm = new HashMap<String, String>();
HashMap<String, StringBuffer> lines = new HashMap<String, StringBuffer>();
StringBuffer previousLine = null;
while ((line = in.readLine()) != null) {
if (line.isEmpty()) {
continue; // ignore empty lines, e.g. at file
}
// end
// entry delimiter -> item complete
if (line.equals("------")) {
String[] type = new String[2];
String[] pages = new String[2];
String country = null;
String address = null;
String titleST = null;
String titleTI = null;
Vector<String> comments = new Vector<String>();
// add item
for (Map.Entry<String, StringBuffer> entry : lines.entrySet()) {
if (entry.getKey().equals("AU")) {
hm.put("author", entry.getValue().toString());
} else if (entry.getKey().equals("TI")) {
titleTI = entry.getValue().toString();
} else if (entry.getKey().equals("ST")) {
titleST = entry.getValue().toString();
} else if (entry.getKey().equals("YP")) {
hm.put("year", entry.getValue().toString());
} else if (entry.getKey().equals("VL")) {
hm.put("volume", entry.getValue().toString());
} else if (entry.getKey().equals("NB")) {
hm.put("number", entry.getValue().toString());
} else if (entry.getKey().equals("PS")) {
pages[0] = entry.getValue().toString();
} else if (entry.getKey().equals("PE")) {
pages[1] = entry.getValue().toString();
} else if (entry.getKey().equals("KW")) {
hm.put("keywords", entry.getValue().toString());
} else if (entry.getKey().equals("RT")) {
type[0] = entry.getValue().toString();
} else if (entry.getKey().equals("SB")) {
comments.add("Subject: " + entry.getValue());
} else if (entry.getKey().equals("SA")) {
comments.add("Secondary Authors: " + entry.getValue());
} else if (entry.getKey().equals("NT")) {
hm.put("note", entry.getValue().toString());
} else if (entry.getKey().equals("PB")) {
hm.put("publisher", entry.getValue().toString());
} else if (entry.getKey().equals("TA")) {
comments.add("Tertiary Authors: " + entry.getValue());
} else if (entry.getKey().equals("TT")) {
comments.add("Tertiary Title: " + entry.getValue());
} else if (entry.getKey().equals("ED")) {
hm.put("edition", entry.getValue().toString());
} else if (entry.getKey().equals("TW")) {
type[1] = entry.getValue().toString();
} else if (entry.getKey().equals("QA")) {
comments.add("Quaternary Authors: " + entry.getValue());
} else if (entry.getKey().equals("QT")) {
comments.add("Quaternary Title: " + entry.getValue());
} else if (entry.getKey().equals("IS")) {
hm.put("isbn", entry.getValue().toString());
} else if (entry.getKey().equals("AB")) {
hm.put("abstract", entry.getValue().toString());
} else if (entry.getKey().equals("AD")) {
address = entry.getValue().toString();
} else if (entry.getKey().equals("LG")) {
hm.put("language", entry.getValue().toString());
} else if (entry.getKey().equals("CO")) {
country = entry.getValue().toString();
} else if (entry.getKey().equals("UR") || entry.getKey().equals("AT")) {
String s = entry.getValue().toString().trim();
hm.put(
s.startsWith("http://") || s.startsWith("ftp://") ? "url" : "pdf",
entry.getValue().toString());
} else if (entry.getKey().equals("C1")) {
comments.add("Custom1: " + entry.getValue());
} else if (entry.getKey().equals("C2")) {
comments.add("Custom2: " + entry.getValue());
} else if (entry.getKey().equals("C3")) {
comments.add("Custom3: " + entry.getValue());
} else if (entry.getKey().equals("C4")) {
comments.add("Custom4: " + entry.getValue());
} else if (entry.getKey().equals("C5")) {
comments.add("Custom5: " + entry.getValue());
} else if (entry.getKey().equals("C6")) {
comments.add("Custom6: " + entry.getValue());
} else if (entry.getKey().equals("DE")) {
hm.put("annote", entry.getValue().toString());
} else if (entry.getKey().equals("CA")) {
comments.add("Categories: " + entry.getValue());
} else if (entry.getKey().equals("TH")) {
comments.add("Short Title: " + entry.getValue());
} else if (entry.getKey().equals("SE")) {
hm.put("chapter", entry.getValue().toString());
// else if (entry.getKey().equals("AC"))
// hm.put("",entry.getValue().toString());
// else if (entry.getKey().equals("LP"))
// hm.put("",entry.getValue().toString());
}
}
String bibtexType = "misc";
// to find type, first check TW, then RT
for (int i = 1; i >= 0 && bibtexType.equals("misc"); --i) {
if (type[i] == null) {
continue;
}
type[i] = type[i].toLowerCase();
if (type[i].contains("article")) {
bibtexType = "article";
} else if (type[i].contains("journal")) {
bibtexType = "article";
} else if (type[i].contains("book section")) {
bibtexType = "inbook";
} else if (type[i].contains("book")) {
bibtexType = "book";
} else if (type[i].contains("conference")) {
bibtexType = "inproceedings";
} else if (type[i].contains("proceedings")) {
bibtexType = "inproceedings";
} else if (type[i].contains("report")) {
bibtexType = "techreport";
} else if (type[i].contains("thesis") && type[i].contains("master")) {
bibtexType = "mastersthesis";
} else if (type[i].contains("thesis")) {
bibtexType = "phdthesis";
}
}
// depending on bibtexType, decide where to place the titleRT and
// titleTI
if (bibtexType.equals("article")) {
if (titleST != null) {
hm.put("journal", titleST);
}
if (titleTI != null) {
hm.put("title", titleTI);
}
} else if (bibtexType.equals("inbook")) {
if (titleST != null) {
hm.put("booktitle", titleST);
}
if (titleTI != null) {
hm.put("title", titleTI);
}
} else {
if (titleST != null) {
hm.put("booktitle", titleST); // should not
}
// happen, I
// think
if (titleTI != null) {
hm.put("title", titleTI);
}
}
// concatenate pages
if (pages[0] != null || pages[1] != null) {
hm.put(
"pages",
(pages[0] != null ? pages[0] : "") + (pages[1] != null ? "--" + pages[1] : ""));
}
// concatenate address and country
if (address != null) {
hm.put("address", address + (country != null ? ", " + country : ""));
}
if (!comments.isEmpty()) { // set comment if present
StringBuilder s = new StringBuilder();
for (int i = 0; i < comments.size(); ++i) {
s.append(i > 0 ? "; " : "").append(comments.elementAt(i));
}
hm.put("comment", s.toString());
}
BibtexEntry b =
new BibtexEntry(DEFAULT_BIBTEXENTRY_ID, BibtexEntryTypes.getEntryType(bibtexType));
b.setField(hm);
bibItems.add(b);
hm.clear();
lines.clear();
previousLine = null;
continue;
}
// new key
if (line.startsWith("--") && line.length() >= 7 && line.substring(4, 7).equals("-- ")) {
lines.put(line.substring(2, 4), previousLine = new StringBuffer(line.substring(7)));
continue;
}
// continuation (folding) of previous line
if (previousLine == null) {
return null;
}
previousLine.append(line.trim());
}
return bibItems;
}
@Override
public List<BibtexEntry> importEntries(InputStream in, OutputPrinter status) throws IOException {
final ArrayList<BibtexEntry> res = new ArrayList<BibtexEntry>(1);
PDDocument document;
try {
document = PDDocument.load(in);
} catch (IOException e) {
LOGGER.error("Could not load document", e);
return res;
}
try {
if (document.isEncrypted()) {
LOGGER.error(Localization.lang("Encrypted documents are not supported"));
// return res;
}
PDFTextStripper stripper = new PDFTextStripper();
stripper.setStartPage(1);
stripper.setEndPage(1);
stripper.setSortByPosition(true);
stripper.setParagraphEnd(System.lineSeparator());
StringWriter writer = new StringWriter();
stripper.writeText(document, writer);
String textResult = writer.toString();
String doi = new DOI(textResult).getDOI();
if (doi.length() < textResult.length()) {
// A Doi was found in the text
// We do NO parsing of the text, but use the Doi fetcher
ImportInspector i =
new ImportInspector() {
@Override
public void toFront() {}
@Override
public void setProgress(int current, int max) {}
@Override
public void addEntry(BibtexEntry entry) {
// add the entry to the result object
res.add(entry);
}
};
PdfContentImporter.doiToBibTeXFetcher.processQuery(doi, i, status);
if (!res.isEmpty()) {
// if something has been found, return the result
return res;
} else {
// otherwise, we just parse the PDF
}
}
String author;
String editor = null;
String institution = null;
String abstractT = null;
String keywords = null;
String title;
String conference = null;
String DOI = null;
String series = null;
String volume = null;
String number = null;
String pages = null;
// year is a class variable as the method extractYear() uses it;
String publisher = null;
BibtexEntryType type = BibtexEntryTypes.INPROCEEDINGS;
final String lineBreak = System.lineSeparator();
split = textResult.split(lineBreak);
// idea: split[] contains the different lines
// blocks are separated by empty lines
// treat each block
// or do special treatment at authors (which are not broken)
// therefore, we do a line-based and not a block-based splitting
// i points to the current line
// curString (mostly) contains the current block
// the different lines are joined into one and thereby separated by " "
proceedToNextNonEmptyLine();
if (i >= split.length) {
// PDF could not be parsed or is empty
// return empty list
return res;
}
curString = split[i];
i = i + 1;
if (curString.length() > 4) {
// special case: possibly conference as first line on the page
extractYear();
if (curString.contains("Conference")) {
fillCurStringWithNonEmptyLines();
conference = curString;
curString = "";
} else {
// e.g. Copyright (c) 1998 by the Genetics Society of America
// future work: get year using RegEx
String lower = curString.toLowerCase();
if (lower.contains("copyright")) {
fillCurStringWithNonEmptyLines();
publisher = curString;
curString = "";
}
}
}
// start: title
fillCurStringWithNonEmptyLines();
title = streamlineTitle(curString);
curString = "";
// i points to the next non-empty line
// after title: authors
author = null;
while (i < split.length && !split[i].equals("")) {
// author names are unlikely to be split among different lines
// treat them line by line
curString = streamlineNames(split[i]);
if (author == null) {
author = curString;
} else {
if (curString.equals("")) {
// if split[i] is "and" then "" is returned by streamlineNames -> do nothing
} else {
author = author.concat(" and ").concat(curString);
}
}
i++;
}
curString = "";
i++;
// then, abstract and keywords follow
while (i < split.length) {
curString = split[i];
if (curString.length() >= "Abstract".length()
&& curString.substring(0, "Abstract".length()).equalsIgnoreCase("Abstract")) {
if (curString.length() == "Abstract".length()) {
// only word "abstract" found -- skip line
curString = "";
} else {
curString = curString.substring("Abstract".length() + 1).trim().concat(lineBreak);
}
i++;
// fillCurStringWithNonEmptyLines() cannot be used as that uses " " as line separator
// whereas we need linebreak as separator
while (i < split.length && !split[i].equals("")) {
curString = curString.concat(split[i]).concat(lineBreak);
i++;
}
abstractT = curString;
i++;
} else if (curString.length() >= "Keywords".length()
&& curString.substring(0, "Keywords".length()).equalsIgnoreCase("Keywords")) {
if (curString.length() == "Keywords".length()) {
// only word "Keywords" found -- skip line
curString = "";
} else {
curString = curString.substring("Keywords".length() + 1).trim();
}
i++;
fillCurStringWithNonEmptyLines();
keywords = removeNonLettersAtEnd(curString);
} else {
String lower = curString.toLowerCase();
int pos = lower.indexOf("technical");
if (pos >= 0) {
type = BibtexEntryTypes.TECHREPORT;
pos = curString.trim().lastIndexOf(' ');
if (pos >= 0) {
// assumption: last character of curString is NOT ' '
// otherwise pos+1 leads to an out-of-bounds exception
number = curString.substring(pos + 1);
}
}
i++;
proceedToNextNonEmptyLine();
}
}
i = split.length - 1;
// last block: DOI, detailed information
// sometimes, this information is in the third last block etc...
// therefore, read until the beginning of the file
while (i >= 0) {
readLastBlock();
// i now points to the block before or is -1
// curString contains the last block, separated by " "
extractYear();
int pos = curString.indexOf("(Eds.)");
if (pos >= 0 && publisher == null) {
// looks like a Springer last line
// e.g: A. Persson and J. Stirna (Eds.): PoEM 2009, LNBIP 39, pp. 161-175, 2009.
publisher = "Springer";
editor = streamlineNames(curString.substring(0, pos - 1));
curString =
curString.substring(
pos
+ "(Eds.)".length()
+ 2); // +2 because of ":" after (Eds.) and the subsequent space
String[] springerSplit = curString.split(", ");
if (springerSplit.length >= 4) {
conference = springerSplit[0];
String seriesData = springerSplit[1];
int lastSpace = seriesData.lastIndexOf(' ');
series = seriesData.substring(0, lastSpace);
volume = seriesData.substring(lastSpace + 1);
pages = springerSplit[2].substring(4);
if (springerSplit[3].length() >= 4) {
year = springerSplit[3].substring(0, 4);
}
}
} else {
if (DOI == null) {
pos = curString.indexOf("DOI");
if (pos < 0) {
pos = curString.indexOf("doi");
}
if (pos >= 0) {
pos += 3;
char delimiter = curString.charAt(pos);
if (delimiter == ':' || delimiter == ' ') {
pos++;
}
int nextSpace = curString.indexOf(' ', pos);
if (nextSpace > 0) {
DOI = curString.substring(pos, nextSpace);
} else {
DOI = curString.substring(pos);
}
}
}
if (publisher == null && curString.contains("IEEE")) {
// IEEE has the conference things at the end
publisher = "IEEE";
// year is extracted by extractYear
// otherwise, we could it determine as follows:
// String yearStr = curString.substring(curString.length()-4);
// if (isYear(yearStr)) {
// year = yearStr;
// }
if (conference == null) {
pos = curString.indexOf('$');
if (pos > 0) {
// we found the price
// before the price, the ISSN is stated
// skip that
pos -= 2;
while (pos >= 0 && curString.charAt(pos) != ' ') {
pos--;
}
if (pos > 0) {
conference = curString.substring(0, pos);
}
}
}
}
// String lower = curString.toLowerCase();
// if (institution == null) {
//
// }
}
}
BibtexEntry entry = new BibtexEntry();
entry.setType(type);
if (author != null) {
entry.setField("author", author);
}
if (editor != null) {
entry.setField("editor", editor);
}
if (institution != null) {
entry.setField("institution", institution);
}
if (abstractT != null) {
entry.setField("abstract", abstractT);
}
if (keywords != null) {
entry.setField("keywords", keywords);
}
if (title != null) {
entry.setField("title", title);
}
if (conference != null) {
entry.setField("booktitle", conference);
}
if (DOI != null) {
entry.setField("doi", DOI);
}
if (series != null) {
entry.setField("series", series);
}
if (volume != null) {
entry.setField("volume", volume);
}
if (number != null) {
entry.setField("number", number);
}
if (pages != null) {
entry.setField("pages", pages);
}
if (year != null) {
entry.setField("year", year);
}
if (publisher != null) {
entry.setField("publisher", publisher);
}
entry.setField("review", textResult);
res.add(entry);
} catch (NoClassDefFoundError e) {
if (e.getMessage().equals("org/bouncycastle/jce/provider/BouncyCastleProvider")) {
status.showMessage(
Localization.lang(
"Java Bouncy Castle library not found. Please download and install it. For more information see http://www.bouncycastle.org/."));
} else {
LOGGER.error("Could not find class", e);
}
} finally {
document.close();
}
return res;
}
/** Parse the entries in the source, and return a List of BibtexEntry objects. */
@Override
public List<BibtexEntry> importEntries(InputStream stream, OutputPrinter status)
throws IOException {
if (stream == null) {
throw new IOException("No stream given.");
}
ArrayList<BibtexEntry> bibitems = new ArrayList<BibtexEntry>();
StringBuilder sb = new StringBuilder();
BufferedReader in = new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));
// Pattern fieldPattern = Pattern.compile("^AU |^TI |^SO |^DT |^C1 |^AB
// |^ID |^BP |^PY |^SE |^PY |^VL |^IS ");
String str;
while ((str = in.readLine()) != null) {
if (str.length() < 3) {
continue;
}
// begining of a new item
if (str.substring(0, 3).equals("PT ")) {
sb.append("::").append(str);
} else {
String beg = str.substring(0, 3).trim();
// I could have used the fieldPattern regular expression instead
// however this seems to be
// quick and dirty and it works!
if (beg.length() == 2) {
sb.append(" ## "); // mark the begining of each field
sb.append(str);
} else {
sb.append("EOLEOL"); // mark the end of each line
sb.append(str.trim()); // remove the initial spaces
}
}
}
String[] entries = sb.toString().split("::");
HashMap<String, String> hm = new HashMap<String, String>();
// skip the first entry as it is either empty or has document header
for (String entry : entries) {
String[] fields = entry.split(" ## ");
if (fields.length == 0) {
fields = entry.split("\n");
}
String Type = "";
String PT = "";
String pages = "";
hm.clear();
for (String field : fields) {
// empty field don't do anything
if (field.length() <= 2) {
continue;
}
String beg = field.substring(0, 2);
String value = field.substring(3);
if (value.startsWith(" - ")) {
value = value.substring(3);
}
value = value.trim();
if (beg.equals("PT")) {
if (value.startsWith("J")) {
PT = "article";
} else {
PT = value;
}
Type = "article"; // make all of them PT?
} else if (beg.equals("TY")) {
if ("JOUR".equals(value)) {
Type = "article";
} else if ("CONF".equals(value)) {
Type = "inproceedings";
}
} else if (beg.equals("JO")) {
hm.put("booktitle", value);
} else if (beg.equals("AU")) {
String author = IsiImporter.isiAuthorsConvert(value.replaceAll("EOLEOL", " and "));
// if there is already someone there then append with "and"
if (hm.get("author") != null) {
author = hm.get("author") + " and " + author;
}
hm.put("author", author);
} else if (beg.equals("TI")) {
hm.put("title", value.replaceAll("EOLEOL", " "));
} else if (beg.equals("SO") || beg.equals("JA")) {
hm.put("journal", value.replaceAll("EOLEOL", " "));
} else if (beg.equals("ID") || beg.equals("KW")) {
value = value.replaceAll("EOLEOL", " ");
String existingKeywords = hm.get("keywords");
if (existingKeywords != null && !existingKeywords.contains(value)) {
existingKeywords += ", " + value;
} else {
existingKeywords = value;
}
hm.put("keywords", existingKeywords);
} else if (beg.equals("AB")) {
hm.put("abstract", value.replaceAll("EOLEOL", " "));
} else if (beg.equals("BP") || beg.equals("BR") || beg.equals("SP")) {
pages = value;
} else if (beg.equals("EP")) {
int detpos = value.indexOf(' ');
// tweak for IEEE Explore
if (detpos != -1 && !value.substring(0, detpos).trim().isEmpty()) {
value = value.substring(0, detpos);
}
pages = pages + "--" + value;
} else if (beg.equals("PS")) {
pages = IsiImporter.parsePages(value);
} else if (beg.equals("AR")) {
pages = value;
} else if (beg.equals("IS")) {
hm.put("number", value);
} else if (beg.equals("PY")) {
hm.put("year", value);
} else if (beg.equals("VL")) {
hm.put("volume", value);
} else if (beg.equals("PU")) {
hm.put("publisher", value);
} else if (beg.equals("DI")) {
hm.put("doi", value);
} else if (beg.equals("PD")) {
String month = IsiImporter.parseMonth(value);
if (month != null) {
hm.put("month", month);
}
} else if (beg.equals("DT")) {
Type = value;
if (Type.equals("Review")) {
Type = "article"; // set "Review" in Note/Comment?
} else if (Type.startsWith("Article")
|| Type.startsWith("Journal")
|| PT.equals("article")) {
Type = "article";
} else {
Type = "misc";
}
} else if (beg.equals("CR")) {
hm.put("CitedReferences", value.replaceAll("EOLEOL", " ; ").trim());
} else {
// Preserve all other entries except
if (beg.equals("ER") || beg.equals("EF") || beg.equals("VR") || beg.equals("FN")) {
continue;
}
hm.put(beg, value);
}
}
if (!"".equals(pages)) {
hm.put("pages", pages);
}
// Skip empty entries
if (hm.isEmpty()) {
continue;
}
BibtexEntry b = new BibtexEntry(DEFAULT_BIBTEXENTRY_ID, BibtexEntryTypes.getEntryType(Type));
// id assumes an existing database so don't
// Remove empty fields:
ArrayList<Object> toRemove = new ArrayList<Object>();
for (String key : hm.keySet()) {
String content = hm.get(key);
if (content == null || content.trim().isEmpty()) {
toRemove.add(key);
}
}
for (Object aToRemove : toRemove) {
hm.remove(aToRemove);
}
// Polish entries
IsiImporter.processSubSup(hm);
IsiImporter.processCapitalization(hm);
b.setField(hm);
bibitems.add(b);
}
return bibitems;
}