@JsonIgnore
public ManyMap<String, Attachment> getAttachmentMap() {
ManyMap<String, Attachment> map = new ManyMap<String, Attachment>();
if (attachments != null && !attachments.isEmpty()) {
for (Attachment attachment : attachments) {
map.putOne(attachment.getName(), attachment);
}
}
return map;
}
public SequencingAnalysis copy() {
SequencingAnalysis dst = new SequencingAnalysis();
dst.subject = subject == null ? null : subject.copy();
dst.date = date == null ? null : date.copy();
dst.name = name == null ? null : name.copy();
dst.genome = genome == null ? null : genome.copy(dst);
dst.file = new ArrayList<Attachment>();
for (Attachment i : file) dst.file.add(i.copy());
dst.inputLab = new ArrayList<ResourceReference>();
for (ResourceReference i : inputLab) dst.inputLab.add(i.copy());
dst.inputAnalysis = new ArrayList<ResourceReference>();
for (ResourceReference i : inputAnalysis) dst.inputAnalysis.add(i.copy());
return dst;
}
public RelatedPerson copy() {
RelatedPerson dst = new RelatedPerson();
dst.identifier = new ArrayList<Identifier>();
for (Identifier i : identifier) dst.identifier.add(i.copy());
dst.patient = patient == null ? null : patient.copy();
dst.relationship = relationship == null ? null : relationship.copy();
dst.name = name == null ? null : name.copy();
dst.telecom = new ArrayList<Contact>();
for (Contact i : telecom) dst.telecom.add(i.copy());
dst.gender = gender == null ? null : gender.copy();
dst.address = address == null ? null : address.copy();
dst.photo = new ArrayList<Attachment>();
for (Attachment i : photo) dst.photo.add(i.copy());
return dst;
}
/**
* 사용자 정보 수정
*
* @return
*/
@With(AnonymousCheckAction.class)
@Transactional
public static Result editUserInfo() {
Form<User> userForm = new Form<>(User.class).bindFromRequest("name", "email");
String newEmail = userForm.data().get("email");
String newName = userForm.data().get("name");
User user = UserApp.currentUser();
if (StringUtils.isEmpty(newEmail)) {
userForm.reject("email", "user.wrongEmail.alert");
} else {
if (!StringUtils.equals(user.email, newEmail) && User.isEmailExist(newEmail)) {
userForm.reject("email", "user.email.duplicate");
}
}
if (userForm.error("email") != null) {
flash(Constants.WARNING, userForm.error("email").message());
return badRequest(edit.render(userForm, user));
}
user.email = newEmail;
user.name = newName;
try {
Long avatarId = Long.valueOf(userForm.data().get("avatarId"));
if (avatarId != null) {
Attachment attachment = Attachment.find.byId(avatarId);
String primary = attachment.mimeType.split("/")[0].toLowerCase();
if (attachment.size > AVATAR_FILE_LIMIT_SIZE) {
userForm.reject("avatarId", "user.avatar.fileSizeAlert");
}
if (primary.equals("image")) {
Attachment.deleteAll(currentUser().avatarAsResource());
attachment.moveTo(currentUser().avatarAsResource());
}
}
} catch (NumberFormatException ignored) {
}
Email.deleteOtherInvalidEmails(user.email);
user.update();
return redirect(
routes.UserApp.userInfo(user.loginId, DEFAULT_GROUP, DAYS_AGO, DEFAULT_SELECTED_TAB));
}
// FIXME: Should also use events!
public void deleteAttachment(Attachment att) throws ProviderException {
if (m_provider == null) return;
m_provider.deleteAttachment(att);
m_engine.getSearchManager().pageRemoved(att);
m_engine.getReferenceManager().clearPageEntries(att.getName());
}
public DiagnosticReport copy() {
DiagnosticReport dst = new DiagnosticReport();
dst.status = status == null ? null : status.copy();
dst.issued = issued == null ? null : issued.copy();
dst.subject = subject == null ? null : subject.copy();
dst.performer = performer == null ? null : performer.copy();
dst.reportId = reportId == null ? null : reportId.copy();
dst.requestDetail = new ArrayList<DiagnosticReportRequestDetailComponent>();
for (DiagnosticReportRequestDetailComponent i : requestDetail)
dst.requestDetail.add(i.copy(dst));
dst.serviceCategory = serviceCategory == null ? null : serviceCategory.copy();
dst.diagnostic = diagnostic == null ? null : diagnostic.copy();
dst.results = results == null ? null : results.copy(dst);
dst.image = new ArrayList<ResourceReference>();
for (ResourceReference i : image) dst.image.add(i.copy());
dst.conclusion = conclusion == null ? null : conclusion.copy();
dst.codedDiagnosis = new ArrayList<CodeableConcept>();
for (CodeableConcept i : codedDiagnosis) dst.codedDiagnosis.add(i.copy());
dst.representation = new ArrayList<Attachment>();
for (Attachment i : representation) dst.representation.add(i.copy());
return dst;
}
public boolean isEmpty() {
return super.isEmpty()
&& (type == null || type.isEmpty())
&& (subtype == null || subtype.isEmpty())
&& (identifier == null || identifier.isEmpty())
&& (subject == null || subject.isEmpty())
&& (operator == null || operator.isEmpty())
&& (view == null || view.isEmpty())
&& (deviceName == null || deviceName.isEmpty())
&& (height == null || height.isEmpty())
&& (width == null || width.isEmpty())
&& (frames == null || frames.isEmpty())
&& (duration == null || duration.isEmpty())
&& (content == null || content.isEmpty());
}
/**
* Stores an attachment directly from a stream. If the attachment did not exist previously, this
* method will create it. If it did exist, it stores a new version.
*
* @param att Attachment to store this under.
* @param in InputStream from which the attachment contents will be read.
* @throws IOException If writing the attachment failed.
* @throws ProviderException If something else went wrong.
*/
public void storeAttachment(Attachment att, InputStream in)
throws IOException, ProviderException {
if (m_provider == null) {
return;
}
//
// Checks if the actual, real page exists without any modifications
// or aliases. We cannot store an attachment to a non-existant page.
//
if (!m_engine.getPageManager().pageExists(att.getParentName())) {
// the caller should catch the exception and use the exception text as an i18n key
throw new ProviderException("attach.parent.not.exist");
}
m_provider.putAttachmentData(att, in);
m_engine.getReferenceManager().updateReferences(att.getName(), new java.util.Vector());
WikiPage parent = new WikiPage(m_engine, att.getParentName());
m_engine.updateReferences(parent);
m_engine.getSearchManager().reindexPage(att);
}
/** New attachment insertion */
public Attachment updateAttachment(long noteId, Attachment attachment, SQLiteDatabase db) {
ContentValues valuesAttachments = new ContentValues();
valuesAttachments.put(
KEY_ATTACHMENT_ID,
attachment.getId() != null ? attachment.getId() : Calendar.getInstance().getTimeInMillis());
valuesAttachments.put(KEY_ATTACHMENT_NOTE_ID, noteId);
valuesAttachments.put(KEY_ATTACHMENT_URI, attachment.getUri().toString());
valuesAttachments.put(KEY_ATTACHMENT_MIME_TYPE, attachment.getMime_type());
valuesAttachments.put(KEY_ATTACHMENT_NAME, attachment.getName());
valuesAttachments.put(KEY_ATTACHMENT_SIZE, attachment.getSize());
valuesAttachments.put(KEY_ATTACHMENT_LENGTH, attachment.getLength());
db.insertWithOnConflict(
TABLE_ATTACHMENTS, KEY_ATTACHMENT_ID, valuesAttachments, SQLiteDatabase.CONFLICT_REPLACE);
return attachment;
}
public Media copy() {
Media dst = new Media();
copyValues(dst);
dst.type = type == null ? null : type.copy();
dst.subtype = subtype == null ? null : subtype.copy();
if (identifier != null) {
dst.identifier = new ArrayList<Identifier>();
for (Identifier i : identifier) dst.identifier.add(i.copy());
}
;
dst.subject = subject == null ? null : subject.copy();
dst.operator = operator == null ? null : operator.copy();
dst.view = view == null ? null : view.copy();
dst.deviceName = deviceName == null ? null : deviceName.copy();
dst.height = height == null ? null : height.copy();
dst.width = width == null ? null : width.copy();
dst.frames = frames == null ? null : frames.copy();
dst.duration = duration == null ? null : duration.copy();
dst.content = content == null ? null : content.copy();
return dst;
}
public GVFVariant copy() {
GVFVariant dst = new GVFVariant();
dst.subject = subject == null ? null : subject.copy(dst);
dst.meta = meta == null ? null : meta.copy();
dst.sourceFile = sourceFile == null ? null : sourceFile.copy();
dst.seqid = seqid == null ? null : seqid.copy();
dst.source = source == null ? null : source.copy();
dst.type = type == null ? null : type.copy();
dst.start = start == null ? null : start.copy();
dst.end = end == null ? null : end.copy();
dst.score = score == null ? null : score.copy();
dst.strand = strand == null ? null : strand.copy();
dst.featureId = featureId == null ? null : featureId.copy();
dst.alias = alias == null ? null : alias.copy();
dst.dbxref = dbxref == null ? null : dbxref.copy(dst);
dst.variantSeq = new ArrayList<String_>();
for (String_ i : variantSeq) dst.variantSeq.add(i.copy());
dst.referenceSeq = referenceSeq == null ? null : referenceSeq.copy();
dst.variantFreq = new ArrayList<Decimal>();
for (Decimal i : variantFreq) dst.variantFreq.add(i.copy());
dst.variantEffect = new ArrayList<GVFVariantVariantEffectComponent>();
for (GVFVariantVariantEffectComponent i : variantEffect) dst.variantEffect.add(i.copy(dst));
dst.startRange = startRange == null ? null : startRange.copy(dst);
dst.endRange = endRange == null ? null : endRange.copy(dst);
dst.variantCodon = new ArrayList<String_>();
for (String_ i : variantCodon) dst.variantCodon.add(i.copy());
dst.referenceCodon = referenceCodon == null ? null : referenceCodon.copy();
dst.variantAA = new ArrayList<String_>();
for (String_ i : variantAA) dst.variantAA.add(i.copy());
dst.referenceAA = new ArrayList<String_>();
for (String_ i : referenceAA) dst.referenceAA.add(i.copy());
dst.breakpointDetail = breakpointDetail == null ? null : breakpointDetail.copy(dst);
dst.sequenceContext = sequenceContext == null ? null : sequenceContext.copy(dst);
dst.individual = new ArrayList<String_>();
for (String_ i : individual) dst.individual.add(i.copy());
dst.sample = new ArrayList<GVFVariantSampleComponent>();
for (GVFVariantSampleComponent i : sample) dst.sample.add(i.copy(dst));
return dst;
}
public void testAddRemoveAttachment() throws Exception {
Map vars = new HashMap();
vars.put("users", users);
vars.put("groups", groups);
vars.put("now", new Date());
String str =
"(with (new Task()) { priority = 55, taskData = (with( new TaskData()) { createdOn = now, activationTime = now}), ";
str += "deadlines = new Deadlines(),";
str += "delegation = new Delegation(),";
str += "peopleAssignments = new PeopleAssignments(),";
str += "names = [ new I18NText( 'en-UK', 'This is my task name')] })";
Task task = (Task) eval(new StringReader(str), vars);
client.addTask(task, null);
long taskId = task.getId();
Attachment attachment = new Attachment();
Date attachedAt = new Date(System.currentTimeMillis());
attachment.setAttachedAt(attachedAt);
attachment.setAttachedBy(users.get("luke"));
attachment.setName("file1.txt");
attachment.setAccessType(AccessType.Inline);
attachment.setContentType("txt");
byte[] bytes = "Ths is my attachment text1".getBytes();
Content content = new Content();
content.setContent(bytes);
client.addAttachment(taskId, attachment, content);
Task task1 = client.getTask(taskId);
// For local clients this will be the same.. that's why is commented
// assertNotSame(task, task1);
// assertFalse(task.equals(task1));
List<Attachment> attachments1 = task1.getTaskData().getAttachments();
assertEquals(1, attachments1.size());
Attachment returnedAttachment = attachments1.get(0);
assertEquals(attachedAt, returnedAttachment.getAttachedAt());
assertEquals(users.get("luke"), returnedAttachment.getAttachedBy());
assertEquals(AccessType.Inline, returnedAttachment.getAccessType());
assertEquals("txt", returnedAttachment.getContentType());
assertEquals("file1.txt", returnedAttachment.getName());
assertEquals(bytes.length, returnedAttachment.getSize());
assertEquals((long) attachment.getId(), (long) returnedAttachment.getId());
assertEquals((long) content.getId(), (long) returnedAttachment.getAttachmentContentId());
// Make the same as the returned tasks, so we can test equals
task.getTaskData().setAttachments(attachments1);
task.getTaskData().setStatus(Status.Created);
assertEquals(task, task1);
content = client.getContent(returnedAttachment.getAttachmentContentId());
assertEquals("Ths is my attachment text1", new String(content.getContent()));
// test we can have multiple attachments
attachment = new Attachment();
attachedAt = new Date(System.currentTimeMillis());
attachment.setAttachedAt(attachedAt);
attachment.setAttachedBy(users.get("tony"));
attachment.setName("file2.txt");
attachment.setAccessType(AccessType.Inline);
attachment.setContentType("txt");
bytes = "Ths is my attachment text2".getBytes();
content = new Content();
content.setContent(bytes);
client.addAttachment(taskId, attachment, content);
task1 = client.getTask(taskId);
// In local clients this will be the same object and we are reusing the tests
// assertNotSame(task, task1);
// assertFalse(task.equals(task1));
List<Attachment> attachments2 = task1.getTaskData().getAttachments();
assertEquals(2, attachments2.size());
content = client.getContent(content.getId());
assertEquals("Ths is my attachment text2", new String(content.getContent()));
// make two collections the same and compare
attachment.setSize(26);
attachment.setAttachmentContentId(content.getId());
attachments1.add(attachment);
assertTrue(CollectionUtils.equals(attachments2, attachments1));
client.deleteAttachment(taskId, attachment.getId(), content.getId());
task1 = client.getTask(taskId);
attachments2 = task1.getTaskData().getAttachments();
assertEquals(1, attachments2.size());
assertEquals("file1.txt", attachments2.get(0).getName());
}
@Override
public String attachVolume(String instanceId, String volumeId, String deviceName) {
IaasProvider iaasInfo = getIaasProvider();
ComputeServiceContext context = iaasInfo.getComputeService().getContext();
String region = ComputeServiceBuilderUtil.extractRegion(iaasInfo);
String zone = ComputeServiceBuilderUtil.extractZone(iaasInfo);
String device = deviceName == null ? "/dev/sdh" : deviceName;
if (region == null || zone == null) {
log.fatal(
"Cannot attach the volume [id]: "
+ volumeId
+ " in the [region] : "
+ region
+ ", [zone] : "
+ zone
+ " of Iaas : "
+ iaasInfo);
return null;
}
ElasticBlockStoreApi blockStoreApi =
context.unwrapApi(AWSEC2Api.class).getElasticBlockStoreApiForRegion(region).get();
Volume.Status volumeStatus = this.getVolumeStatus(blockStoreApi, region, volumeId);
if (log.isDebugEnabled()) {
log.debug("Volume " + volumeId + " is in state " + volumeStatus);
}
while (volumeStatus != Volume.Status.AVAILABLE) {
try {
// TODO Use a proper mechanism to wait till volume becomes available.
Thread.sleep(1000);
volumeStatus = this.getVolumeStatus(blockStoreApi, region, volumeId);
if (log.isDebugEnabled()) {
log.debug(
"Volume " + volumeId + " is still NOT in AVAILABLE. Current State=" + volumeStatus);
}
} catch (InterruptedException e) {
// Ignoring the exception
}
}
if (log.isDebugEnabled()) {
log.debug("Volume " + volumeId + " became AVAILABLE");
}
Attachment attachment =
blockStoreApi.attachVolumeInRegion(region, volumeId, instanceId, device);
if (attachment == null) {
log.fatal(
"Volume [id]: "
+ volumeId
+ " attachment for instance [id]: "
+ instanceId
+ " was unsuccessful. [region] : "
+ region
+ ", [zone] : "
+ zone
+ " of Iaas : "
+ iaasInfo);
return null;
}
log.info(
"Volume [id]: "
+ volumeId
+ " attachment for instance [id]: "
+ instanceId
+ " was successful [status]: "
+ attachment.getStatus().value()
+ ". [region] : "
+ region
+ ", [zone] : "
+ zone
+ " of Iaas : "
+ iaasInfo);
return attachment.getStatus().value();
}
// Inserting or updating single note
public Note updateNote(Note note, boolean updateLastModification) {
SQLiteDatabase db = getDatabase(true);
String content;
if (note.isLocked()) {
content = Security.encrypt(note.getContent(), prefs.getString(Constants.PREF_PASSWORD, ""));
} else {
content = note.getContent();
}
// To ensure note and attachments insertions are atomical and boost performances transaction are
// used
db.beginTransaction();
ContentValues values = new ContentValues();
values.put(KEY_TITLE, note.getTitle());
values.put(KEY_CONTENT, content);
values.put(
KEY_CREATION,
note.getCreation() != null ? note.getCreation() : Calendar.getInstance().getTimeInMillis());
values.put(
KEY_LAST_MODIFICATION,
updateLastModification
? Calendar.getInstance().getTimeInMillis()
: (note.getLastModification() != null
? note.getLastModification()
: Calendar.getInstance().getTimeInMillis()));
values.put(KEY_ARCHIVED, note.isArchived());
values.put(KEY_TRASHED, note.isTrashed());
values.put(KEY_REMINDER, note.getAlarm());
values.put(KEY_REMINDER_FIRED, note.isReminderFired());
values.put(KEY_RECURRENCE_RULE, note.getRecurrenceRule());
values.put(KEY_LATITUDE, note.getLatitude());
values.put(KEY_LONGITUDE, note.getLongitude());
values.put(KEY_ADDRESS, note.getAddress());
values.put(KEY_CATEGORY, note.getCategory() != null ? note.getCategory().getId() : null);
boolean locked = note.isLocked() != null ? note.isLocked() : false;
values.put(KEY_LOCKED, locked);
boolean checklist = note.isChecklist() != null ? note.isChecklist() : false;
values.put(KEY_CHECKLIST, checklist);
db.insertWithOnConflict(TABLE_NOTES, KEY_ID, values, SQLiteDatabase.CONFLICT_REPLACE);
Log.d(Constants.TAG, "Updated note titled '" + note.getTitle() + "'");
// Updating attachments
List<Attachment> deletedAttachments = note.getAttachmentsListOld();
for (Attachment attachment : note.getAttachmentsList()) {
updateAttachment(
note.get_id() != null ? note.get_id() : values.getAsLong(KEY_CREATION), attachment, db);
deletedAttachments.remove(attachment);
}
// Remove from database deleted attachments
for (Attachment attachmentDeleted : deletedAttachments) {
db.delete(
TABLE_ATTACHMENTS,
KEY_ATTACHMENT_ID + " = ?",
new String[] {String.valueOf(attachmentDeleted.getId())});
}
db.setTransactionSuccessful();
db.endTransaction();
// Fill the note with correct data before returning it
note.setCreation(
note.getCreation() != null ? note.getCreation() : values.getAsLong(KEY_CREATION));
note.setLastModification(values.getAsLong(KEY_LAST_MODIFICATION));
return note;
}
/** Retrieves statistics data based on app usage */
public Stats getStats() {
Stats mStats = new Stats();
// Categories
mStats.setCategories(getCategories().size());
// Everything about notes and their text stats
int notesActive = 0,
notesArchived = 0,
notesTrashed = 0,
reminders = 0,
remindersFuture = 0,
checklists = 0,
notesMasked = 0,
tags = 0,
locations = 0;
int totalWords = 0, totalChars = 0, maxWords = 0, maxChars = 0, avgWords = 0, avgChars = 0;
int words, chars;
List<Note> notes = getAllNotes(false);
for (Note note : notes) {
if (note.isTrashed()) {
notesTrashed++;
} else if (note.isArchived()) {
notesArchived++;
} else {
notesActive++;
}
if (note.getAlarm() != null && Long.parseLong(note.getAlarm()) > 0) {
if (Long.parseLong(note.getAlarm()) > Calendar.getInstance().getTimeInMillis()) {
remindersFuture++;
} else {
reminders++;
}
}
if (note.isChecklist()) {
checklists++;
}
if (note.isLocked()) {
notesMasked++;
}
tags += TagsHelper.retrieveTags(note).size();
if (note.getLongitude() != null && note.getLongitude() != 0) {
locations++;
}
words = getWords(note);
chars = getChars(note);
if (words > maxWords) {
maxWords = words;
}
if (chars > maxChars) {
maxChars = chars;
}
totalWords += words;
totalChars += chars;
}
mStats.setNotesActive(notesActive);
mStats.setNotesArchived(notesArchived);
mStats.setNotesTrashed(notesTrashed);
mStats.setReminders(reminders);
mStats.setRemindersFutures(remindersFuture);
mStats.setNotesChecklist(checklists);
mStats.setNotesMasked(notesMasked);
mStats.setTags(tags);
mStats.setLocation(locations);
avgWords = totalWords / (notes.size() != 0 ? notes.size() : 1);
avgChars = totalChars / (notes.size() != 0 ? notes.size() : 1);
mStats.setWords(totalWords);
mStats.setWordsMax(maxWords);
mStats.setWordsAvg(avgWords);
mStats.setChars(totalChars);
mStats.setCharsMax(maxChars);
mStats.setCharsAvg(avgChars);
// Everything about attachments
int attachmentsAll = 0, images = 0, videos = 0, audioRecordings = 0, sketches = 0, files = 0;
List<Attachment> attachments = getAllAttachments();
for (Attachment attachment : attachments) {
if (Constants.MIME_TYPE_IMAGE.equals(attachment.getMime_type())) {
images++;
} else if (Constants.MIME_TYPE_VIDEO.equals(attachment.getMime_type())) {
videos++;
} else if (Constants.MIME_TYPE_AUDIO.equals(attachment.getMime_type())) {
audioRecordings++;
} else if (Constants.MIME_TYPE_SKETCH.equals(attachment.getMime_type())) {
sketches++;
} else if (Constants.MIME_TYPE_FILES.equals(attachment.getMime_type())) {
files++;
}
}
mStats.setAttachments(attachmentsAll);
mStats.setImages(images);
mStats.setVideos(videos);
mStats.setAudioRecordings(audioRecordings);
mStats.setSketches(sketches);
mStats.setFiles(files);
return mStats;
}