@Test(groups = {PERSISTENCE, INTEGRATION})
@SpecAssertions({
@SpecAssertion(section = PASSIVATION_CAPABLE_DEPENDENCY_EE, id = "db"),
@SpecAssertion(section = PASSIVATION_CAPABLE_DEPENDENCY_EE, id = "dc")
})
public void testPersistenceUnitAndContext() throws IOException, ClassNotFoundException {
Profile profile = getContextualReference(Profile.class);
assertNotNull(profile);
assertNotNull(profile.getEntityManager());
assertTrue(profile.getEntityManager().isOpen());
assertNotNull(profile.getEntityManagerFactory());
assertTrue(profile.getEntityManagerFactory().isOpen());
String profileId = profile.getId();
byte[] serializedProfile = passivate(profile);
Profile profileCopy = (Profile) activate(serializedProfile);
assertEquals(profileCopy.getId(), profileId);
assertNotNull(profileCopy.getEntityManager());
assertTrue(profileCopy.getEntityManager().isOpen());
assertNotNull(profileCopy.getEntityManagerFactory());
assertTrue(profileCopy.getEntityManagerFactory().isOpen());
}
@POST
@Path("/profile")
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
public Response addProfile(Profile profile) {
// http://localhost:8080/CitoServer/rest/profileService/add
if (profile.getId() > 0) {
dao.updateProfile(mapper.mapToDb(profile));
} else {
int id = dao.addProfile(mapper.mapToDb(profile));
profile.setId(id);
}
ReturnId returnId = new ReturnId(profile.getId());
return Response.status(200).entity(returnId).build();
}
public static void updateActiveProfilesValue(
final NewLiferayPluginProjectOp op, final ElementList<Profile> profiles) {
final StringBuilder sb = new StringBuilder();
if (profiles.size() > 0) {
for (Profile profile : profiles) {
if (!profile.getId().empty()) {
sb.append(profile.getId().content());
sb.append(',');
}
}
}
// remove trailing ','
op.setActiveProfilesValue(sb.toString().replaceAll("(.*),$", "$1"));
}
private void createNotification(
Profile profile, UGCAudit currentAudit, Map<String, Profile> actionOwnersCache) {
if (currentAudit.getProfileId() != null
&& !currentAudit.getProfileId().equalsIgnoreCase("anonymous")) {
Notification notification = new Notification();
// ACTION of the current JOB
notification.setAction(profile.getSubscriptions().getAction());
notification.setCreatedDate(new Date());
notification.setRow(currentAudit.getRow());
// FORMAT of the current JOB
notification.setFormat(profile.getSubscriptions().getFormat());
// FORMAT of the current JOB
notification.setFrequency(profile.getSubscriptions().getFrequency());
notification.setSubscriberUsername(profile.getUserName());
notification.setSubscriberEmail(profile.getEmail());
notification.setSubscriberId(profile.getId());
notification.setTransmitedStatus(TransmittedStatus.PENDING);
notification.setEvent(
createEvent(currentAudit, getActionAuditOwner(actionOwnersCache, currentAudit)));
this.notificationRepository.save(notification);
}
}
public void write(Profile profile) {
com.aerospike.client.Key key = new com.aerospike.client.Key("test", "demo", profile.getId());
Bin bin1 = new Bin("bin1", profile.toJSon());
// Bin bin2 = new Bin("bin2", "value2");
// console.info("Put: namespace=%s set=%s key=%s bin1=%s value1=%s bin2=%s value2=%s",
// key.namespace, key.setName, key.userKey, bin1.name, bin1.value, bin2.name,
// bin2.value);
client.put(null, key, bin1);
}
public void awrite(Profile profile) {
com.aerospike.client.Key key = new com.aerospike.client.Key("test", "demo", profile.getId());
Bin bin1 = new Bin("bin1", profile.toJSon());
aclient.put(
null,
new WriteListener() {
@Override
public void onSuccess(Key key) {}
@Override
public void onFailure(AerospikeException e) {}
},
key,
bin1);
}
private Profile getActionAuditOwner(
Map<String, Profile> actionOwnersCache, UGCAudit currentAudit) {
Profile p = actionOwnersCache.get(currentAudit.getProfileId());
if (p == null) {
Profile currentProfile =
this.profileRepository.findOne(new ObjectId(currentAudit.getProfileId()));
p = new Profile();
if (currentProfile != null) {
p.setUserName(currentProfile.getUserName());
p.setTenantName(currentProfile.getTenantName());
p.setEmail(currentProfile.getEmail());
p.setId(currentProfile.getId());
}
actionOwnersCache.put(currentAudit.getProfileId(), p);
}
return p;
}
/**
* Adds information about defined profile.
*
* @param pomDescriptor The descriptor for the current POM.
* @param model The Maven Model.
* @param scannerContext The scanner context.
*/
private void addProfiles(
MavenPomDescriptor pomDescriptor, Model model, ScannerContext scannerContext) {
List<Profile> profiles = model.getProfiles();
Store store = scannerContext.getStore();
for (Profile profile : profiles) {
MavenProfileDescriptor mavenProfileDescriptor = store.create(MavenProfileDescriptor.class);
pomDescriptor.getProfiles().add(mavenProfileDescriptor);
mavenProfileDescriptor.setId(profile.getId());
addProperties(mavenProfileDescriptor, profile.getProperties(), store);
addModules(mavenProfileDescriptor, profile.getModules(), store);
addPlugins(mavenProfileDescriptor, profile.getBuild(), scannerContext);
addManagedPlugins(mavenProfileDescriptor, profile.getBuild(), scannerContext);
addManagedDependencies(
mavenProfileDescriptor,
profile.getDependencyManagement(),
scannerContext,
ProfileManagesDependencyDescriptor.class);
addProfileDependencies(mavenProfileDescriptor, profile.getDependencies(), scannerContext);
addActivation(mavenProfileDescriptor, profile.getActivation(), store);
}
}
@Override
public View getView(int position, View convertView, ViewGroup parent) {
// 特定の行(position)のデータを得る
Profile item = (Profile) getItem(position);
// convertViewは使い回しされている可能性があるのでnullの時だけ新しく作る
if (null == convertView) {
convertView = layoutInflater_.inflate(R.layout.profilerow, null);
}
// 奇数行
if (position % 2 == 0) {
convertView.setBackgroundColor(Color.parseColor("#FFE0C0"));
}
// 偶数行
else {
convertView.setBackgroundColor(Color.parseColor("#FFEABF"));
}
// CustomDataのデータをViewの各Widgetにセットする
// ID
TextView textView_id;
textView_id = (TextView) convertView.findViewById(R.id.id);
textView_id.setText(item.getId());
// 会社名
TextView textView_company;
textView_company = (TextView) convertView.findViewById(R.id.company);
textView_company.setText(item.getCompany());
// 役職
TextView textView_yakushoku;
textView_yakushoku = (TextView) convertView.findViewById(R.id.yakushoku);
textView_yakushoku.setText(item.getYakushoku());
// 名前
TextView textView_name;
textView_name = (TextView) convertView.findViewById(R.id.name);
textView_name.setText(item.getName());
// メールアドレス
TextView textView_mail;
textView_mail = (TextView) convertView.findViewById(R.id.mail);
textView_mail.setText(item.getMail());
// 電話番号
TextView textView_phone;
textView_phone = (TextView) convertView.findViewById(R.id.phone);
textView_phone.setText(item.getPhone());
// 20161008 yasui add start
// よみがな
TextView textView_nameKana;
textView_nameKana = (TextView) convertView.findViewById(R.id.nameKana);
textView_nameKana.setText(item.getNameKana());
// 性別
TextView textView_sex;
textView_sex = (TextView) convertView.findViewById(R.id.sex);
textView_sex.setText(Integer.toString(item.getSex()));
// メモ
TextView textView_memo;
textView_memo = (TextView) convertView.findViewById(R.id.memo);
textView_memo.setText(item.getMemo());
// 20161008 yasui add end
return convertView;
}
private void computeCorrelations() {
log.info("Filling repository with most correlated profiles");
List<String> referenceProfile;
for (AssayType assayType : AssayType.values()) {
referenceProfile = getReferenceProfile(assayType);
List<Profile> profiles = profileRepository.findByAssayType(assayType);
String[] profileNames = new String[profiles.size()];
double[][] distanceMatrix = new double[profiles.size()][profiles.size()];
int i = 0;
for (Profile profileA : profiles) {
profileNames[i] = profileA.getId().toString();
Double maxPearson = Double.MIN_VALUE;
Profile maxProfile = profileA;
int j = 0;
for (Profile profileB : profiles) {
if (profileA.equals(profileB)) {
distanceMatrix[i][j] = 0;
j++;
continue;
}
double[] vectorA = profileA.getVector();
double[] vectorB = profileB.getVector();
PearsonsCorrelation pearson = new PearsonsCorrelation();
Double pearsonCorrelation = pearson.correlation(vectorA, vectorB);
if (pearsonCorrelation >= maxPearson) {
maxPearson = pearsonCorrelation;
maxProfile = profileB;
}
double[] profileAasDouble = UtilsTransform.intArrayToDouble(profileA.getColors());
double[] profileBasDouble = UtilsTransform.intArrayToDouble(profileB.getColors());
Double pearsonOfColors = pearson.correlation(profileAasDouble, profileBasDouble);
distanceMatrix[i][j] = pearsonOfColors;
j++;
}
profileA.setCorrelatedVector(maxProfile.getListWrapper());
SortedSet<StringDouble> positivePeptides =
UtilsStatistics.influentialPeptides(
profileA.getVector(), maxProfile.getVector(), referenceProfile, true);
profileA.setPositivePeptides(UtilsTransform.SortedSetToHTML(positivePeptides, false));
DecimalFormat df = new DecimalFormat("0.0000");
String peptideCorrelation = " <br/><br/><b style=\"color: #23527c;\">%s</b>";
profileA.setPositiveCorrelation(
maxProfile.toString() + String.format(peptideCorrelation, df.format(maxPearson)));
profileRepository.save(profileA);
i++;
}
}
}
