public <T> T putWor(
String url,
String resourcePath,
Object object,
Class<T> responseClass,
Map<String, Object> queryParams,
String worToken) {
WebTarget target = client.target("https://" + url).path(resourcePath);
if (queryParams != null) {
for (Map.Entry<String, Object> entry : queryParams.entrySet()) {
target = target.queryParam(entry.getKey(), entry.getValue());
}
}
Invocation.Builder invocationBuilder = target.request(MediaType.APPLICATION_JSON_TYPE);
setHeaders(invocationBuilder, worToken);
Response putResponse =
invocationBuilder.put(Entity.entity(object, MediaType.APPLICATION_JSON_TYPE));
if (putResponse.getStatus() != Response.Status.OK.getStatusCode()) {
Logger.error(
"PUT call to "
+ url
+ "/"
+ resourcePath
+ " returned status of "
+ putResponse.getStatus());
return null;
}
if (responseClass != null
&& putResponse.hasEntity()
&& putResponse.getStatus() == Response.Status.OK.getStatusCode())
return putResponse.readEntity(responseClass);
return null;
}
public PartData retrieveEntryDetails(String userId, String id) {
try {
Entry entry = getEntry(id);
if (entry == null) return null;
return retrieveEntryDetails(userId, entry);
} catch (Exception e) {
Logger.error(e);
return null;
}
}
public boolean deleteTraceSequence(String userId, long entryId, long traceId) {
Entry entry = dao.get(entryId);
if (entry == null) return false;
TraceSequenceDAO traceSequenceDAO = DAOFactory.getTraceSequenceDAO();
TraceSequence traceSequence = traceSequenceDAO.get(traceId);
if (traceSequence == null || !canEdit(userId, traceSequence.getDepositor(), entry))
return false;
try {
new SequenceAnalysisController().removeTraceSequence(traceSequence);
} catch (Exception e) {
Logger.error(e);
return false;
}
return true;
}
private static Entry infoToSeedForField(Entry entry, String value, EntryField field) {
if (!entry.getRecordType().equalsIgnoreCase(EntryType.ARABIDOPSIS.toString())) return entry;
ArabidopsisSeed seed = (ArabidopsisSeed) entry;
switch (field) {
case HOMOZYGOSITY:
seed.setHomozygosity(value);
return seed;
case ECOTYPE:
seed.setEcotype(value);
return seed;
case HARVEST_DATE:
if (value != null && !value.isEmpty()) {
try {
Date date = SimpleDateFormat.getDateInstance(DateFormat.SHORT).parse(value);
seed.setHarvestDate(date);
} catch (ParseException ia) {
Logger.error(ia);
}
}
return seed;
case GENERATION:
seed.setGeneration(Generation.fromString(value));
return seed;
case SENT_TO_ABRC:
seed.setSentToABRC("yes".equalsIgnoreCase(value) || "true".equalsIgnoreCase(value));
return seed;
case PLANT_TYPE:
seed.setPlantType(PlantType.fromString(value));
return seed;
case PARENTS:
seed.setParents(value);
return seed;
default:
return seed;
}
}
@Override
public Key getKey(final String keyId) {
try {
// find file named by keyId in the directory
final File keyFile = new File(directory, keyId);
// collect all lines in the file to a buffer
final StringBuilder encoded = new StringBuilder();
try (final FileReader reader = new FileReader(keyFile);
final BufferedReader buffered = new BufferedReader(reader); ) {
String line;
while ((line = buffered.readLine()) != null) {
encoded.append(line);
}
// after reading all lines, decode value into a Key object
return HmacSignatureFactory.decodeKey(encoded.toString());
}
} catch (final Throwable t) {
Logger.error("Failed to load rest-auth key " + keyId);
}
return null;
}
public <T> T put(String url, String resourcePath, Object object, Class<T> responseClass) {
WebTarget target = client.target("https://" + url).path(resourcePath);
Invocation.Builder invocationBuilder = target.request(MediaType.APPLICATION_JSON_TYPE);
Response putResponse =
invocationBuilder.put(Entity.entity(object, MediaType.APPLICATION_JSON_TYPE));
if (putResponse.getStatus() != Response.Status.OK.getStatusCode()) {
Logger.error(
"PUT call to "
+ url
+ "/"
+ resourcePath
+ " returned status of "
+ putResponse.getStatus());
return null;
}
if (responseClass != null
&& putResponse.hasEntity()
&& putResponse.getStatus() == Response.Status.OK.getStatusCode())
return putResponse.readEntity(responseClass);
return null;
}
/**
* Moves the specified list of entries to the deleted folder
*
* @param userId unique identifier for user making the request. Must have write access privileges
* on the entries in the list
* @param list unique identifiers for entries
* @return true or false if operation succeeds on all listed entries or not
*/
public boolean moveEntriesToTrash(String userId, ArrayList<PartData> list) {
List<Entry> toTrash = new LinkedList<>();
for (PartData data : list) {
Entry entry = dao.get(data.getId());
if (entry == null || !authorization.canWriteThoroughCheck(userId, entry)) return false;
toTrash.add(entry);
}
// add to bin
try {
for (Entry entry : toTrash) {
entry.setVisibility(Visibility.DELETED.getValue());
dao.update(entry);
}
} catch (DAOException de) {
Logger.error(de);
return false;
}
return true;
}
protected static Entry setSeedFields(ArabidopsisSeedData seedData, Entry entry) {
ArabidopsisSeed seed = (ArabidopsisSeed) entry;
if (seedData == null) return entry;
if (seedData.getHomozygosity() != null) seed.setHomozygosity(seedData.getHomozygosity());
if (StringUtils.isNotEmpty(seedData.getHarvestDate())) {
DateFormat format = new SimpleDateFormat("MM/dd/YYYY");
try {
Date date = format.parse(seedData.getHarvestDate());
seed.setHarvestDate(date);
} catch (ParseException e) {
Logger.error("Could not parse date " + seedData.getHarvestDate());
return null;
}
}
String ecoType = seedData.getEcotype() == null ? "" : seedData.getEcotype();
seed.setEcotype(ecoType);
String parents = seedData.getSeedParents() == null ? "" : seedData.getSeedParents();
seed.setParents(parents);
if (seedData.getGeneration() != null) {
Generation generation = Generation.fromString(seedData.getGeneration().name());
seed.setGeneration(generation);
} else {
seed.setGeneration(Generation.UNKNOWN);
}
if (seedData.getPlantType() != null) {
PlantType plantType = PlantType.fromString(seedData.getPlantType().name());
seed.setPlantType(plantType);
} else {
seed.setPlantType(PlantType.NULL);
}
seed.setSentToABRC(seedData.isSentToAbrc());
return entry;
}
// uploads trace sequence file and builds or rebuilds alignment
private boolean parseTraceSequence(String userId, Entry entry, String fileName, byte[] bytes) {
DNASequence dnaSequence = sequenceAnalysisController.parse(bytes);
if (dnaSequence == null || dnaSequence.getSequence() == null) {
String errMsg =
("Could not parse \"" + fileName + "\". Only Fasta, GenBank & ABI files are supported.");
Logger.error(errMsg);
return false;
}
TraceSequence traceSequence =
sequenceAnalysisController.uploadTraceSequence(
entry,
fileName,
userId,
dnaSequence.getSequence().toLowerCase(),
new ByteArrayInputStream(bytes));
if (traceSequence == null) return false;
Sequence sequence = DAOFactory.getSequenceDAO().getByEntry(entry);
if (sequence == null) return true;
sequenceAnalysisController.buildOrRebuildAlignment(traceSequence, sequence);
return true;
}
public boolean addTraceSequence(String userId, long partId, File file, String uploadFileName) {
Entry entry = dao.get(partId);
if (entry == null) return false;
authorization.expectRead(userId, entry);
FileInputStream inputStream;
try {
inputStream = new FileInputStream(file);
} catch (FileNotFoundException e) {
Logger.error(e);
return false;
}
if (uploadFileName.toLowerCase().endsWith(".zip")) {
try (ZipInputStream zis = new ZipInputStream(inputStream)) {
ZipEntry zipEntry;
while (true) {
zipEntry = zis.getNextEntry();
if (zipEntry != null) {
if (!zipEntry.isDirectory() && !zipEntry.getName().startsWith("__MACOSX")) {
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
int c;
while ((c = zis.read()) != -1) {
byteArrayOutputStream.write(c);
}
boolean parsed =
parseTraceSequence(
userId, entry, zipEntry.getName(), byteArrayOutputStream.toByteArray());
if (!parsed) {
String errMsg =
("Could not parse \""
+ zipEntry.getName()
+ "\". Only Fasta, GenBank & ABI files are supported.");
Logger.error(errMsg);
return false;
}
}
} else {
break;
}
}
} catch (IOException e) {
String errMsg = ("Could not parse zip file.");
Logger.error(errMsg);
return false;
}
} else {
try {
boolean parsed =
parseTraceSequence(userId, entry, uploadFileName, IOUtils.toByteArray(inputStream));
if (!parsed) {
String errMsg =
("Could not parse \""
+ uploadFileName
+ "\". Only Fasta, GenBank & ABI files are supported.");
Logger.error(errMsg);
return false;
}
} catch (IOException e) {
Logger.error(e);
return false;
}
}
return true;
}
protected PartData retrieveEntryDetails(String userId, Entry entry) {
// user must be able to read if not public entry
if (!permissionsController.isPubliclyVisible(entry)) authorization.expectRead(userId, entry);
PartData partData = ModelToInfoFactory.getInfo(entry);
if (partData == null) return null;
boolean hasSequence = sequenceDAO.hasSequence(entry.getId());
partData.setHasSequence(hasSequence);
boolean hasOriginalSequence = sequenceDAO.hasOriginalSequence(entry.getId());
partData.setHasOriginalSequence(hasOriginalSequence);
// permissions
partData.setCanEdit(authorization.canWriteThoroughCheck(userId, entry));
partData.setPublicRead(permissionsController.isPubliclyVisible(entry));
// create audit event if not owner
// todo : remote access check
if (userId != null
&& authorization.getOwner(entry) != null
&& !authorization.getOwner(entry).equalsIgnoreCase(userId)) {
try {
Audit audit = new Audit();
audit.setAction(AuditType.READ.getAbbrev());
audit.setEntry(entry);
audit.setUserId(userId);
audit.setLocalUser(true);
audit.setTime(new Date(System.currentTimeMillis()));
auditDAO.create(audit);
} catch (Exception e) {
Logger.error(e);
}
}
// retrieve more information about linked entries if any (default only contains id)
if (partData.getLinkedParts() != null) {
ArrayList<PartData> newLinks = new ArrayList<>();
for (PartData link : partData.getLinkedParts()) {
Entry linkedEntry = dao.get(link.getId());
if (!authorization.canRead(userId, linkedEntry)) continue;
link = ModelToInfoFactory.createTipView(linkedEntry);
Sequence sequence = sequenceDAO.getByEntry(linkedEntry);
if (sequence != null) {
link.setBasePairCount(sequence.getSequence().length());
link.setFeatureCount(sequence.getSequenceFeatures().size());
}
newLinks.add(link);
}
partData.getLinkedParts().clear();
partData.getLinkedParts().addAll(newLinks);
}
// check if there is a parent available
List<Entry> parents = dao.getParents(entry.getId());
if (parents == null) return partData;
for (Entry parent : parents) {
if (!authorization.canRead(userId, parent)) continue;
if (parent.getVisibility() != Visibility.OK.getValue()
&& !authorization.canWriteThoroughCheck(userId, entry)) continue;
EntryType type = EntryType.nameToType(parent.getRecordType());
PartData parentData = new PartData(type);
parentData.setId(parent.getId());
parentData.setName(parent.getName());
parentData.setVisibility(Visibility.valueToEnum(parent.getVisibility()));
partData.getParents().add(parentData);
}
return partData;
}
/**
* Used to log user actions
*
* @param userId unique user identifier
* @param message log message
*/
protected void log(final String userId, final String message) {
final String who = (userId == null) ? "Unknown" : userId;
Logger.info(who + ": " + message);
}