/*
* (non-Javadoc)
* @see addressbook.model.PersistenceAccess#load()
*/
public void load() throws IOException {
// Read data from given file into DOM document
final FileInputStream in = new FileInputStream(dataFile);
Document document = null;
try {
document = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(in);
} catch (SAXException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ParserConfigurationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
in.close();
// Put document data in address book
// Get AddressBookAccess
Element ab = null;
if (document.getElementsByTagName("AddressBook").getLength() == 1) {
ab = (Element) document.getElementsByTagName("AddressBook").item(0);
} else {
// Parse error
throw new IOException("No single AddressBookAccess element found");
}
// Read and store entries
NodeList list = ab.getChildNodes();
for (int i = 0; i < list.getLength(); ++i) {
if (list.item(i).getNodeType() == Node.ELEMENT_NODE) {
Entry entry = new Entry();
Element el = (Element) list.item(i);
// Personal data
entry.setName(el.getAttribute("FirstName"), el.getAttribute("SurName"));
entry.setGender(
el.getAttribute("Gender").equalsIgnoreCase("M") ? Gender.Male : Gender.Female);
entry.setDateOfBirth(Entry.dateFormatter.parseDateTime(el.getAttribute("DateOfBirth")));
// Contact Information
if (el.getElementsByTagName("Contact").getLength() > 0) {
Element contactEl = (Element) el.getElementsByTagName("Contact").item(0);
if (contactEl.getAttribute("type").equalsIgnoreCase("phone")) {
entry.setContactPhoneNumber(Integer.parseInt(contactEl.getTextContent()));
} else if (contactEl.getAttribute("type").equalsIgnoreCase("email")) {
entry.setContactEmailAddress(contactEl.getTextContent());
}
}
try {
addEntry(entry);
} catch (SizeLimitReachedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
}
private void readCentralDirectoryEntry(final Map<ZipEntry, NameAndComment> noUTF8Flag)
throws IOException {
this.archive.readFully(this.CFH_BUF);
int off = 0;
final OffsetEntry offset = new OffsetEntry();
final Entry ze = new Entry(offset);
final int versionMadeBy = ZipShort.getValue(this.CFH_BUF, off);
off += 2;
ze.setPlatform(versionMadeBy >> 8 & 0xF);
off += 2;
final GeneralPurposeBit gpFlag = GeneralPurposeBit.parse(this.CFH_BUF, off);
final boolean hasUTF8Flag = gpFlag.usesUTF8ForNames();
final ZipEncoding entryEncoding =
hasUTF8Flag ? ZipEncodingHelper.UTF8_ZIP_ENCODING : this.zipEncoding;
ze.setGeneralPurposeBit(gpFlag);
off += 2;
ze.setMethod(ZipShort.getValue(this.CFH_BUF, off));
off += 2;
final long time = ZipUtil.dosToJavaTime(ZipLong.getValue(this.CFH_BUF, off));
ze.setTime(time);
off += 4;
ze.setCrc(ZipLong.getValue(this.CFH_BUF, off));
off += 4;
ze.setCompressedSize(ZipLong.getValue(this.CFH_BUF, off));
off += 4;
ze.setSize(ZipLong.getValue(this.CFH_BUF, off));
off += 4;
final int fileNameLen = ZipShort.getValue(this.CFH_BUF, off);
off += 2;
final int extraLen = ZipShort.getValue(this.CFH_BUF, off);
off += 2;
final int commentLen = ZipShort.getValue(this.CFH_BUF, off);
off += 2;
final int diskStart = ZipShort.getValue(this.CFH_BUF, off);
off += 2;
ze.setInternalAttributes(ZipShort.getValue(this.CFH_BUF, off));
off += 2;
ze.setExternalAttributes(ZipLong.getValue(this.CFH_BUF, off));
off += 4;
final byte[] fileName = new byte[fileNameLen];
this.archive.readFully(fileName);
ze.setName(entryEncoding.decode(fileName), fileName);
offset.headerOffset = ZipLong.getValue(this.CFH_BUF, off);
this.entries.add(ze);
final byte[] cdExtraData = new byte[extraLen];
this.archive.readFully(cdExtraData);
ze.setCentralDirectoryExtra(cdExtraData);
this.setSizesAndOffsetFromZip64Extra(ze, offset, diskStart);
final byte[] comment = new byte[commentLen];
this.archive.readFully(comment);
ze.setComment(entryEncoding.decode(comment));
if (!hasUTF8Flag && this.useUnicodeExtraFields) {
noUTF8Flag.put(ze, new NameAndComment(fileName, comment));
}
}
/**
* Save the current editor content to the given entry and write to disk.
*
* @param entry entry object to save.
* @throws IOException
*/
public void saveEntry(final Entry entry) throws IOException {
if (entry == null) return;
entry.setName(nameField.getText());
entry.setComment(commentField.getText());
entry.setIcon(iconField.getText());
entry.setExec(execField.getText());
entry.setType(typeField.getText());
entry.setCategories(categoryField.getText());
entry.setTerminal(terminalBox.isSelected());
entry.setStartupNotify(startupNotifyBox.isSelected());
FileWriter writer = new FileWriter(entry.getFile());
writer.write(entry.toContentString());
writer.close();
JOptionPane.showMessageDialog(null, entry.getFile().getName() + " has been saved!");
}
/**
* Creates a new file in the config/upgrade folder. The new file is a concatenation of entries of
* all files contained in the config/schema folder.
*
* @param folder The folder containing the schema files.
* @param revision The revision number of the current binary version.
* @throws Exception If we cannot read the files contained in the folder where the schema files
* are supposed to be, or the file has errors.
*/
static void updateConfigUpgradeSchemaFile(final File folder, final String revision)
throws Exception {
// We need to upgrade the schema.ldif.<rev> file contained in the
// config/upgrade folder otherwise, we cannot enable the backend at
// server's start. We need to read all files contained in config/schema
// and add all attribute/object classes in this new super entry which
// will be read at start-up.
Entry theNewSchemaEntry = new LinkedHashMapEntry();
LDIFEntryReader reader = null;
LDIFEntryWriter writer = null;
try {
if (folder.isDirectory()) {
final FilenameFilter filter = new SchemaConfigManager.SchemaFileFilter();
for (final File f : folder.listFiles(filter)) {
logger.debug(LocalizableMessage.raw(String.format("Processing %s", f.getAbsolutePath())));
reader = new LDIFEntryReader(new FileInputStream(f));
try {
while (reader.hasNext()) {
final Entry entry = reader.readEntry();
theNewSchemaEntry.setName(entry.getName());
for (final Attribute at : entry.getAllAttributes()) {
theNewSchemaEntry.addAttribute(at);
}
}
} catch (Exception ex) {
throw new Exception(
"Error parsing existing schema file " + f.getName() + " - " + ex.getMessage(), ex);
}
}
// Creates a File object representing
// config/upgrade/schema.ldif.revision which the server creates
// the first time it starts if there are schema customizations.
final File destination =
new File(
configDirectory,
Installation.UPGRADE_PATH + File.separator + "schema.ldif." + revision);
// Checks if the parent exists (eg. embedded
// server doesn't seem to provide that folder)
File parentDirectory = destination.getParentFile();
if (!parentDirectory.exists()) {
logger.debug(
LocalizableMessage.raw(
String.format("Parent file of %s doesn't exist", destination.getPath())));
parentDirectory.mkdirs();
logger.debug(
LocalizableMessage.raw(
String.format("Parent directory %s created.", parentDirectory.getPath())));
}
if (!destination.exists()) {
destination.createNewFile();
}
logger.debug(
LocalizableMessage.raw(
String.format("Writing entries in %s.", destination.getAbsolutePath())));
writer = new LDIFEntryWriter(new FileOutputStream(destination));
writer.writeEntry(theNewSchemaEntry);
logger.debug(
LocalizableMessage.raw(
String.format(
"%s created and completed successfully.", destination.getAbsolutePath())));
}
} finally {
StaticUtils.close(reader, writer);
}
}
/**
* Updates the entry based on the field that is specified. Mainly created for use by the bulk
* import auto update
*
* @param entry entry to be updated
* @param plasmid should be set if updating strain with plasmid
* @param value value to be set
* @param field to set
* @return updated entry array containing both entry and plasmid. if plasmid is null only entry is
* returned
*/
public static Entry[] infoToEntryForField(
Entry entry, Entry plasmid, String value, EntryField field) {
switch (field) {
case PI:
{
entry.setPrincipalInvestigator(value);
if (plasmid != null) plasmid.setPrincipalInvestigator(value);
break;
}
case PI_EMAIL:
{
entry.setPrincipalInvestigatorEmail(value);
break;
}
case FUNDING_SOURCE:
{
entry.setFundingSource(value);
if (plasmid != null) plasmid.setFundingSource(value);
break;
}
case IP:
entry.setIntellectualProperty(value);
if (plasmid != null) plasmid.setIntellectualProperty(value);
break;
case BIO_SAFETY_LEVEL:
Integer level = BioSafetyOption.intValue(value);
if (level == null) {
if (value.contains("1")) level = 1;
else if (value.contains("2")) level = 2;
else break;
}
entry.setBioSafetyLevel(level);
if (plasmid != null) {
plasmid.setBioSafetyLevel(level);
}
break;
case NAME:
entry.setName(value);
break;
case ALIAS:
entry.setAlias(value);
break;
case KEYWORDS:
entry.setKeywords(value);
break;
case SUMMARY:
entry.setShortDescription(value);
break;
case NOTES:
entry.setLongDescription(value);
break;
case REFERENCES:
entry.setReferences(value);
break;
case LINKS:
HashSet<Link> links = new HashSet<>();
Link link = new Link();
link.setLink(value);
link.setEntry(entry);
links.add(link);
entry.setLinks(links);
break;
case STATUS:
entry.setStatus(value);
if (plasmid != null) plasmid.setStatus(value);
break;
case SELECTION_MARKERS:
HashSet<SelectionMarker> markers = new HashSet<>();
SelectionMarker marker = new SelectionMarker(value, entry);
markers.add(marker);
entry.setSelectionMarkers(markers);
break;
case PARENTAL_STRAIN:
case GENOTYPE_OR_PHENOTYPE:
case PLASMIDS:
entry = infoToStrainForField(entry, value, field);
break;
case BACKBONE:
case ORIGIN_OF_REPLICATION:
case CIRCULAR:
case PROMOTERS:
case REPLICATES_IN:
entry = infoToPlasmidForField(entry, value, field);
break;
case HOMOZYGOSITY:
case ECOTYPE:
case HARVEST_DATE:
case GENERATION:
case SENT_TO_ABRC:
case PLANT_TYPE:
case PARENTS:
entry = infoToSeedForField(entry, value, field);
break;
default:
break;
}
if (plasmid == null) return new Entry[] {entry};
return new Entry[] {entry, plasmid};
}
private static Entry setCommon(Entry entry, PartData info) {
if (entry == null || info == null) return null;
if (info.getName() != null) entry.setName(info.getName());
if (info.getSelectionMarkers() != null) {
Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
entry.setSelectionMarkers(markers);
}
if (info.getReferences() != null) entry.setReferences(info.getReferences());
if (StringUtils.isBlank(entry.getPartNumber())) entry.setPartNumber(info.getPartId());
Date currentTime = new Date();
if (entry.getCreationTime() == null) entry.setCreationTime(currentTime);
entry.setModificationTime(currentTime);
if (info.getOwnerEmail() != null) {
entry.setOwnerEmail(info.getOwnerEmail());
}
if (info.getOwner() != null) entry.setOwner(info.getOwner());
if (info.getCreatorEmail() != null) {
entry.setCreatorEmail(info.getCreatorEmail());
}
if (info.getCreator() != null) entry.setCreator(info.getCreator());
if (info.getStatus() == null) {
if (StringUtils.isBlank(entry.getStatus())) entry.setStatus("");
} else entry.setStatus(info.getStatus());
if (info.getAlias() != null) entry.setAlias(info.getAlias());
if (info.getBioSafetyLevel() == null) {
if (entry.getBioSafetyLevel() == null) entry.setBioSafetyLevel(0);
} else entry.setBioSafetyLevel(info.getBioSafetyLevel());
if (info.getShortDescription() != null) entry.setShortDescription(info.getShortDescription());
if (info.getLongDescription() != null) entry.setLongDescription(info.getLongDescription());
if (info.getIntellectualProperty() != null)
entry.setIntellectualProperty(info.getIntellectualProperty());
Set<Link> links = getLinks(info.getLinks(), entry);
entry.setLinks(links);
Visibility visibility = info.getVisibility();
if (visibility != null) entry.setVisibility(visibility.getValue());
// checking for null instead of blank since it could be cleared
if (info.getFundingSource() != null) entry.setFundingSource(info.getFundingSource());
if (info.getPrincipalInvestigator() != null)
entry.setPrincipalInvestigator(info.getPrincipalInvestigator());
if (info.getPrincipalInvestigatorEmail() != null)
entry.setPrincipalInvestigatorEmail(info.getPrincipalInvestigatorEmail());
if (info.getKeywords() != null) entry.setKeywords(info.getKeywords());
// parameters
List<Parameter> parameters = getParameters(info.getCustomFields(), entry);
entry.setParameters(parameters);
return entry;
}
