Example usage for javax.persistence EntityManager getTransaction

List of usage examples for javax.persistence EntityManager getTransaction

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Introduction

In this page you can find the example usage for javax.persistence EntityManager getTransaction.

Prototype

public EntityTransaction getTransaction();

Source Link

Document

Return the resource-level EntityTransaction object.

Usage

From source file:gov.osti.services.Metadata.java

/**
 * Perform SAVE workflow on indicated METADATA.
 *
 * @param json the JSON String containing the metadata to SAVE
 * @param file a FILE associated with this record if any
 * @param fileInfo the FILE disposition information if any
 * @param container a CONTAINER IMAGE associated with this record if any
 * @param containerInfo the CONTAINER IMAGE disposition of information if any
 * @return a Response containing the JSON of the saved record if successful,
 * or error information if not//from  w ww  . j a  v a 2  s.  c  o  m
 */
private Response doSave(String json, InputStream file, FormDataContentDisposition fileInfo,
        InputStream container, FormDataContentDisposition containerInfo) {
    EntityManager em = DoeServletContextListener.createEntityManager();
    Subject subject = SecurityUtils.getSubject();
    User user = (User) subject.getPrincipal();

    try {
        validateUploads(fileInfo, containerInfo);

        DOECodeMetadata md = DOECodeMetadata.parseJson(new StringReader(json));

        em.getTransaction().begin();

        performDataNormalization(md);

        md.setWorkflowStatus(Status.Saved); // default to this
        md.setOwner(user.getEmail()); // this User should OWN it
        md.setSiteOwnershipCode(user.getSiteId());

        store(em, md, user);

        // re-attach metadata to transaction in order to store any changes beyond this point
        md = em.find(DOECodeMetadata.class, md.getCodeId());

        // if there's a FILE associated here, store it
        if (null != file && null != fileInfo) {
            try {
                String fileName = writeFile(file, md.getCodeId(), fileInfo.getFileName(), FILE_UPLOADS);
                md.setFileName(fileName);
            } catch (IOException e) {
                log.error("File Upload Failed: " + e.getMessage());
                return ErrorResponse.internalServerError("File upload failed.").build();
            }
        }

        // if there's a CONTAINER IMAGE associated here, store it
        if (null != container && null != containerInfo) {
            try {
                String containerName = writeFile(container, md.getCodeId(), containerInfo.getFileName(),
                        CONTAINER_UPLOADS);
                md.setContainerName(containerName);
            } catch (IOException e) {
                log.error("Container Image Upload Failed: " + e.getMessage());
                return ErrorResponse.internalServerError("Container Image upload failed.").build();
            }
        }

        // we're done here
        em.getTransaction().commit();

        return Response.status(200)
                .entity(mapper.createObjectNode().putPOJO("metadata", md.toJson()).toString()).build();
    } catch (BadRequestException e) {
        return e.getResponse();
    } catch (NotFoundException e) {
        return ErrorResponse.notFound(e.getMessage()).build();
    } catch (IllegalAccessException e) {
        log.warn("Persistence Error:  Invalid update attempt from " + user.getEmail());
        log.warn("Message: " + e.getMessage());
        return ErrorResponse.forbidden("Unable to persist update for indicated record.").build();
    } catch (ValidationException e) {
        log.warn("Validation Error: " + e.getMessage());
        return ErrorResponse.badRequest(e.getMessage()).build();
    } catch (IOException | InvocationTargetException e) {
        if (em.getTransaction().isActive())
            em.getTransaction().rollback();

        log.warn("Persistence Error: " + e.getMessage());
        return ErrorResponse.internalServerError("Save IO Error: " + e.getMessage()).build();
    } finally {
        em.close();
    }
}

From source file:com.hiperf.common.ui.server.storage.impl.PersistenceHelper.java

@Override
public TransactionContext createTransactionalContext() {
    EntityManager em = getEntityManager();
    switch (this.type) {
    case LOCAL://from  w w w .ja v a  2 s.  c o  m
        return new TransactionContext(new LocalTransaction(em.getTransaction()), em);
    default:
        return new TransactionContext(tx, em);
    }
}

From source file:gov.osti.services.Metadata.java

/**
 * Perform ANNOUNCE workflow operation, optionally with associated file uploads.
 *
 * @param json String containing JSON of the Metadata to ANNOUNCE
 * @param file the FILE (if any) to attach to this metadata
 * @param fileInfo file disposition information if FILE present
 * @return a Response containing the JSON of the submitted record if successful, or
 * error information if not//from   www  .  j a va 2 s  .c  o  m
 */
private Response doAnnounce(String json, InputStream file, FormDataContentDisposition fileInfo,
        InputStream container, FormDataContentDisposition containerInfo) {
    EntityManager em = DoeServletContextListener.createEntityManager();
    Subject subject = SecurityUtils.getSubject();
    User user = (User) subject.getPrincipal();

    try {
        validateUploads(fileInfo, containerInfo);

        DOECodeMetadata md = DOECodeMetadata.parseJson(new StringReader(json));

        Long currentCodeId = md.getCodeId();
        boolean previouslySaved = false;
        if (currentCodeId != null) {
            DOECodeMetadata emd = em.find(DOECodeMetadata.class, currentCodeId);

            if (emd != null)
                previouslySaved = Status.Saved.equals(emd.getWorkflowStatus());
        }

        em.getTransaction().begin();

        performDataNormalization(md);

        // set the OWNER
        md.setOwner(user.getEmail());
        // set the WORKFLOW STATUS
        md.setWorkflowStatus(Status.Announced);
        // set the SITE
        md.setSiteOwnershipCode(user.getSiteId());
        // if there is NO DOI set, get one
        if (StringUtils.isEmpty(md.getDoi())) {
            DoiReservation reservation = getReservedDoi();
            if (null == reservation)
                throw new IOException("DOI reservation failure.");
            // set it
            md.setDoi(reservation.getReservedDoi());
        }

        // persist this to the database
        store(em, md, user);

        // re-attach metadata to transaction in order to store any changes beyond this point
        md = em.find(DOECodeMetadata.class, md.getCodeId());

        // if there's a FILE associated here, store it
        String fullFileName = "";
        if (null != file && null != fileInfo) {
            try {
                fullFileName = writeFile(file, md.getCodeId(), fileInfo.getFileName(), FILE_UPLOADS);
                md.setFileName(fullFileName);
            } catch (IOException e) {
                log.error("File Upload Failed: " + e.getMessage());
                return ErrorResponse.internalServerError("File upload failed.").build();
            }
        }

        // if there's a CONTAINER IMAGE associated here, store it
        String fullContainerName = "";
        if (null != container && null != containerInfo) {
            try {
                fullContainerName = writeFile(container, md.getCodeId(), containerInfo.getFileName(),
                        CONTAINER_UPLOADS);
                md.setContainerName(fullContainerName);
            } catch (IOException e) {
                log.error("Container Image Upload Failed: " + e.getMessage());
                return ErrorResponse.internalServerError("Container Image upload failed.").build();
            }
        }

        // check validations
        List<String> errors = validateAnnounce(md);
        if (!errors.isEmpty()) {
            return ErrorResponse.badRequest(errors).build();
        }

        // create OSTI Hosted project, as needed
        try {
            // process local GitLab, if needed
            processOSTIGitLab(md);
        } catch (Exception e) {
            log.error("OSTI GitLab failure: " + e.getMessage());
            return ErrorResponse.internalServerError("Unable to create OSTI Hosted project: " + e.getMessage())
                    .build();
        }

        // send this file upload along to archiver if configured
        try {
            // if no file/container, but previously Saved with a file/container, we need to attach to those streams and send to Archiver
            if (previouslySaved) {
                if (null == file && !StringUtils.isBlank(md.getFileName())) {
                    java.nio.file.Path destination = Paths.get(FILE_UPLOADS, String.valueOf(md.getCodeId()),
                            md.getFileName());
                    fullFileName = destination.toString();
                    file = Files.newInputStream(destination);
                }
                if (null == container && !StringUtils.isBlank(md.getContainerName())) {
                    java.nio.file.Path destination = Paths.get(CONTAINER_UPLOADS,
                            String.valueOf(md.getCodeId()), md.getContainerName());
                    fullContainerName = destination.toString();
                    container = Files.newInputStream(destination);
                }
            }

            // if a FILE or CONTAINER was sent, create a File Object from it
            File archiveFile = (null == file) ? null : new File(fullFileName);
            File archiveContainer = null; //(null==container) ? null : new File(fullContainerName);
            if (DOECodeMetadata.Accessibility.CO.equals(md.getAccessibility()))
                // if CO project type, no need to archive the repo because it is local GitLab
                sendToArchiver(md.getCodeId(), null, archiveFile, archiveContainer);
            else
                sendToArchiver(md.getCodeId(), md.getRepositoryLink(), archiveFile, archiveContainer);
        } catch (IOException e) {
            log.error("Archiver call failure: " + e.getMessage());
            return ErrorResponse.internalServerError("Unable to archive project.").build();
        }

        // send any updates to DataCite as well (if RELEASE DATE is set)
        if (StringUtils.isNotEmpty(md.getDoi()) && null != md.getReleaseDate()) {
            try {
                DataCite.register(md);
            } catch (IOException e) {
                // if DataCite registration failed, say why
                log.warn("DataCite ERROR: " + e.getMessage());
                return ErrorResponse.internalServerError(
                        "The DOI registration service is currently unavailable, please try to submit your record later. If the issue persists, please contact doecode@osti.gov.")
                        .build();
            }
        }
        // store the snapshot copy of Metadata in SPECIAL STATUS
        MetadataSnapshot snapshot = new MetadataSnapshot();
        snapshot.getSnapshotKey().setCodeId(md.getCodeId());
        snapshot.getSnapshotKey().setSnapshotStatus(md.getWorkflowStatus());
        snapshot.setDoi(md.getDoi());
        snapshot.setDoiIsMinted(md.getReleaseDate() != null);
        snapshot.setJson(md.toJson().toString());

        em.merge(snapshot);

        // if we make it this far, go ahead and commit the transaction
        em.getTransaction().commit();

        // send NOTIFICATION if configured
        sendStatusNotification(md);

        // and we're happy
        return Response.ok().entity(mapper.createObjectNode().putPOJO("metadata", md.toJson()).toString())
                .build();
    } catch (BadRequestException e) {
        return e.getResponse();
    } catch (NotFoundException e) {
        return ErrorResponse.notFound(e.getMessage()).build();
    } catch (IllegalAccessException e) {
        log.warn("Persistence Error: Invalid owner update attempt: " + user.getEmail());
        log.warn("Message: " + e.getMessage());
        return ErrorResponse.forbidden("Invalid Access: Unable to edit indicated record.").build();
    } catch (ValidationException e) {
        log.warn("Validation Error: " + e.getMessage());
        return ErrorResponse.badRequest(e.getMessage()).build();
    } catch (IOException | InvocationTargetException e) {
        if (em.getTransaction().isActive())
            em.getTransaction().rollback();

        log.warn("Persistence Error: " + e.getMessage());
        return ErrorResponse.internalServerError("IO Error announcing record.").build();
    } finally {
        em.close();
    }
}

From source file:mil.navy.med.dzreg.dao.RegistriesManagerDAO.java

/**
 * Register a new registry profile.//from   www .  jav  a2  s.  c  o  m
 * @param profile
 * @return
 * @throws Exception
 */
public AckType register(PersonRegistryProfileType profile) {

    EntityManager em = null;
    PersistentServiceFactory psf = null;
    StringBuffer exceptionMsg = new StringBuffer();

    AckType ack = new AckType();
    ack.setResponseCode(_APPLICATION_ERROR);

    if (profile != null && profile.getPerson() != null && profile.getRegistry() != null
            && !profile.getRegistry().isEmpty() && profile.getDataSource() != null) {
        //------------------------------------------------------------------------
        // Registry type must be valid.
        //------------------------------------------------------------------------
        Map<Integer, DzType> toBeRegisterDzTypes = Collections.synchronizedMap(new HashMap<Integer, DzType>());
        for (RegistryType r : profile.getRegistry()) {
            try {
                DzType dzType = this.validRegistryType(r);
                if (dzType != null) {
                    toBeRegisterDzTypes.put(Integer.valueOf(dzType.getDztypeId()), dzType);
                } else {
                    exceptionMsg.append("Invalid/Unknown registy type specified - " + r.getRegistryId() + ";");
                }
            } catch (Exception ex) {
                exceptionMsg.append(ex.getMessage() + ";");
            }
        }

        //----------------------------------------------------------------------
        // Person info must have following elements:
        //   1. Identifer
        //   2. Name
        //   3. Date of birth
        //   4. Data Source
        //----------------------------------------------------------------------
        PersonType person = profile.getPerson();

        if (person.getName() == null || person.getName().isEmpty()
                || (person.getDataSource() == null && profile.getDataSource() == null)) {
            ack.setDetectedIssueText("Missing required metadata (person identifier or name or data source);");
            return ack;
        }

        //------------------------------------------------------------------------
        // Check to see if this person already registered.
        //------------------------------------------------------------------------
        DzPatients registeredPatient = null;

        try {
            registeredPatient = validPerson(person);
        } catch (javax.persistence.NoResultException nre) {
        } catch (Exception ex) {
            ack.setDetectedIssueText("Failed to register patient - " + ex.getMessage());
            return ack;
        }

        try {
            psf = PersistentServiceFactory.getInstance(REGISTRY_MANAGER_PU);
            em = psf.getEntityManager();

            em.getTransaction().begin();

            // Get the date today using Calendar object.
            Calendar cal = Calendar.getInstance();
            Timestamp today = new Timestamp(cal.getTimeInMillis());

            //----------------------------------------------------------------------
            // If yes, only need to add a record to table DZ_REG for each new
            // registry type.
            //----------------------------------------------------------------------
            if (registeredPatient != null) {
                // remove any registry type (from request) that is already assigned to
                // this person
                Collection<DzReg> registries = registeredPatient.getDzRegCollection();
                for (DzReg r : registries) {
                    Integer intDzTypeId = Integer.valueOf(r.getDzType().getDztypeId());
                    if (toBeRegisterDzTypes.containsKey(intDzTypeId)) {
                        toBeRegisterDzTypes.remove(intDzTypeId);

                        log.debug("Already registered in Registry " + intDzTypeId + "!");
                        exceptionMsg.append("Already registered in Registry " + intDzTypeId + ";");
                    }
                }

                // what we have left is new registry type to be add to person registry
                // profile
                Collection<DzType> toBeRegisterColl = toBeRegisterDzTypes.values();
                for (DzType d : toBeRegisterColl) {
                    // only need to add a record to table DZ_REG
                    DzRegPK pk = new DzRegPK(person.getId(), d.getDztypeId());
                    DzReg newDzreg = new DzReg();
                    newDzreg.setDzRegPK(pk);
                    newDzreg.setActive(_ACTIVE);
                    newDzreg.setDataSource(person.getDataSource());
                    newDzreg.setRegisteredDt(today);
                    newDzreg.setInsertedDt(today);

                    em.persist(newDzreg);
                }
            } //----------------------------------------------------------------------
              // If no, need to insert a new record in DZ_PATIENTS table and a new
              // record in table DZ_REG for each new registry type.
              //----------------------------------------------------------------------
            else {
                DzPatients newDzPatient = map(person);
                newDzPatient.setInsertedDt(today);
                newDzPatient.setUpdatedDt(today);
                if (person.getDataSource() == null) {
                    if (profile.getDataSource() != null) {
                        newDzPatient.setDataSource(profile.getDataSource());
                    } else {
                        // cannot insert record
                        throw new Exception("Missing required metadata (data source);");
                    }
                } else {
                    newDzPatient.setDataSource(profile.getDataSource());
                }

                Collection<DzType> dzTypes = toBeRegisterDzTypes.values();
                Collection<DzReg> newDzregList = new ArrayList<DzReg>(dzTypes.size());
                for (DzType dzType : dzTypes) {
                    DzRegPK pk = new DzRegPK(person.getId(), dzType.getDztypeId());
                    DzReg newDzreg = new DzReg();
                    newDzreg.setDzRegPK(pk);
                    newDzreg.setActive(_ACTIVE);
                    newDzreg.setRegisteredDt(today);
                    newDzreg.setInsertedDt(today);

                    if (person.getDataSource() == null) {
                        newDzreg.setDataSource(profile.getDataSource());
                    } else {
                        newDzreg.setDataSource(person.getDataSource());
                    }

                    newDzregList.add(newDzreg);
                }

                newDzPatient.setDzRegCollection(newDzregList);
                em.persist(newDzPatient);
            }

            em.getTransaction().commit();

            ack.setResponseCode(_OK);
            ack.setDetectedIssueText(exceptionMsg.toString());

            return ack;
        } catch (Exception ex) {
            ex.printStackTrace();
            em.getTransaction().rollback();
            log.error("Failed to create new records in table DZ_PATIENTS/DZ_REG for profile=" + profile);

            ack.setDetectedIssueText(
                    "Failed to register patient " + profile.getPerson().getId() + "-" + ex.getMessage());
            return ack;
        } finally {
            em.close();
        }
    } else {
        ack.setDetectedIssueText("Invalid registry profile");
        return ack;
    }
}

From source file:com.gigglinggnus.controllers.StudentMakeAppointmentController.java

/**
 *
 * @param request servlet request//  w ww.ja va  2 s.  c o m
 * @param response servlet response
 * @throws ServletException if a servlet-specific error occurs
 * @throws IOException if an I/O error occurs
 */
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {
    EntityManager em = (EntityManager) request.getSession().getAttribute("em");

    String msg = request.getParameter("msg");
    User user = (User) (request.getSession().getAttribute("user"));
    Clock clk = (Clock) (request.getSession().getAttribute("clock"));

    if (msg.equals("lookup_student")) {
        String studId = request.getParameter("studentId");
        List<Exam> exams = user.getRegistrableExams();
        JSONObject json = new JSONObject();
        json.put("students_idNumber", studId);
        json.put("firstName", user.getFirstName());
        json.put("lastName", user.getLastName());
        JSONArray jExams = new JSONArray();
        for (Exam exam : exams) {
            JSONObject elem = new JSONObject();

            String examId = exam.getExamId();
            String termId = exam.getTerm().getTermId();
            String start = exam.getInterval().getStart().atZone(ZoneId.systemDefault()).toLocalDate()
                    .toString();
            String end = exam.getInterval().getEnd().atZone(ZoneId.systemDefault()).toLocalDate().toString();
            elem.put("examId", examId);
            elem.put("termId", termId);
            if (exam instanceof CourseExam) {
                String courseId = ((CourseExam) exam).getCourse().getCourseId();
                elem.put("courseId", courseId);
                elem.put("examType", "Course");
            } else {
                elem.put("courseId", "N/A");
                elem.put("examType", "AdHoc");
            }
            elem.put("start", start);
            elem.put("end", end);
            jExams.put(elem);
        }
        json.put("exams", jExams);
        response.getWriter().write(json.toString());
    } else if (msg.equals("exam_available_timeslots")) {
        String examId = request.getParameter("examId");
        String dateStr = request.getParameter("date");
        Exam exam = em.find(Exam.class, examId);
        LocalDate apptDate = LocalDate.parse(dateStr);
        List<LocalTime> timeslots = exam.getTimeslotsForDay(apptDate);

        JSONObject json = new JSONObject();
        json.put("examId", examId);
        JSONArray jTimeSlots = new JSONArray();
        for (LocalTime timeslot : timeslots) {
            String start = timeslot.toString();
            String end = timeslot.plus(exam.getDuration()).toString();
            JSONObject elem = new JSONObject();
            elem.put("start", start);
            elem.put("end", end);
            jTimeSlots.put(elem);
        }
        json.put("timeSlots", jTimeSlots);
        response.getWriter().write(json.toString());
    } else if (msg.equals("submit-appointment")) {
        String studId = request.getParameter("studentId");
        String examId = request.getParameter("examId");
        String stDate = request.getParameter("examDate");
        String stTime = request.getParameter("startTime") + ":00";
        String stSeat = request.getParameter("seatType");

        Exam exam = em.find(Exam.class, examId);
        LocalDate lDate = LocalDate.parse(stDate);
        LocalTime lTime = LocalTime.parse(stTime);
        Instant inst = ZonedDateTime.of(lDate, lTime, ZoneId.systemDefault()).toInstant();
        JSONObject json = new JSONObject();
        try {
            em.getTransaction().begin();
            user.makeAppointment(exam, inst, clk);
            em.getTransaction().commit();
            json.put("success", "Appointment Made!");
            response.getWriter().write(json.toString());
        } catch (Exception e) {
            em.getTransaction().rollback();
            json.put("error", e.toString());
            response.getWriter().write(json.toString());
        }
    } else {
        JSONObject json = new JSONObject();
        json.put("error", msg);
        response.getWriter().write(json.toString());
    }
}

From source file:de.egore911.opengate.services.PilotService.java

@POST
@Path("/register")
@Produces("application/json")
@Documentation("Register a new pilot. This will at first verify the login and email are "
        + "unique and the email is valid. After this it will register the pilot and send "
        + "and email to him to verify the address. The 'verify' will finalize the registration. "
        + "This method returns a JSON object containing a status field, i.e. {status: 'failed', "
        + "details: '...'} in case of an error and {status: 'ok', id: ...}. If an internal "
        + "error occured an HTTP 500 will be sent.")
public Response performRegister(@FormParam("login") String login, @FormParam("email") String email,
        @FormParam("faction_id") @Documentation("ID of the faction this pilot will be working for") long factionId) {
    JSONObject jsonObject = new JSONObject();
    EntityManager em = EntityManagerFilter.getEntityManager();
    Number n = (Number) em
            .createQuery("select count(pilot.key) from Pilot pilot " + "where pilot.login = (:login)")
            .setParameter("login", login).getSingleResult();
    if (n.intValue() > 0) {
        try {/*from   w ww.  j a va 2 s . co  m*/
            StatusHelper.failed(jsonObject, "Duplicate login");
            return Response.ok(jsonObject.toString()).build();
        } catch (JSONException e) {
            LOG.log(Level.SEVERE, e.getMessage(), e);
            return Response.status(Status.INTERNAL_SERVER_ERROR).build();
        }
    }

    n = (Number) em.createQuery("select count(pilot.key) from Pilot pilot " + "where pilot.email = (:email)")
            .setParameter("email", email).getSingleResult();
    if (n.intValue() > 0) {
        try {
            StatusHelper.failed(jsonObject, "Duplicate email");
            return Response.ok(jsonObject.toString()).build();
        } catch (JSONException e) {
            LOG.log(Level.SEVERE, e.getMessage(), e);
            return Response.status(Status.INTERNAL_SERVER_ERROR).build();
        }
    }

    InternetAddress recipient;
    try {
        recipient = new InternetAddress(email, login);
    } catch (UnsupportedEncodingException e1) {
        try {
            StatusHelper.failed(jsonObject, "Invalid email");
            return Response.ok(jsonObject.toString()).build();
        } catch (JSONException e) {
            LOG.log(Level.SEVERE, e.getMessage(), e);
            return Response.status(Status.INTERNAL_SERVER_ERROR).build();
        }
    }

    Faction faction;
    try {
        faction = em.find(Faction.class, factionId);
    } catch (NoResultException e) {
        try {
            StatusHelper.failed(jsonObject, "Invalid faction");
            return Response.ok(jsonObject.toString()).build();
        } catch (JSONException e1) {
            LOG.log(Level.SEVERE, e.getMessage(), e1);
            return Response.status(Status.INTERNAL_SERVER_ERROR).build();
        }
    }

    Vessel vessel;
    try {
        vessel = (Vessel) em
                .createQuery("select vessel from Vessel vessel " + "where vessel.faction = :faction "
                        + "order by vessel.techLevel asc")
                .setParameter("faction", faction).setMaxResults(1).getSingleResult();
        // TODO assign initical equipment as well
    } catch (NoResultException e) {
        try {
            StatusHelper.failed(jsonObject, "Faction has no vessel");
            return Response.ok(jsonObject.toString()).build();
        } catch (JSONException e1) {
            LOG.log(Level.SEVERE, e.getMessage(), e1);
            return Response.status(Status.INTERNAL_SERVER_ERROR).build();
        }
    }

    String passwordHash;
    String password = randomText();
    try {
        passwordHash = hashPassword(password);
    } catch (NoSuchAlgorithmException e) {
        LOG.log(Level.SEVERE, e.getMessage(), e);
        return Response.status(Status.INTERNAL_SERVER_ERROR).build();
    }

    em.getTransaction().begin();
    try {
        Pilot pilot = new Pilot();
        pilot.setLogin(login);
        pilot.setCreated(new Date());
        pilot.setPasswordHash(passwordHash);
        pilot.setEmail(email);
        pilot.setFaction(faction);
        pilot.setVessel(vessel);
        pilot.setVerificationCode(randomText());
        em.persist(pilot);
        em.getTransaction().commit();
        try {
            // send e-mail to registered user containing the new password

            Properties props = new Properties();
            Session session = Session.getDefaultInstance(props, null);

            String msgBody = "Welcome to opengate!\n\nSomeone, propably you, registered the user "
                    + pilot.getLogin()
                    + " with your e-mail adress. The following credentials can be used for your account:\n"
                    + "  login : " + pilot.getLogin() + "\n" + "  password : " + password + "\n\n"
                    + "To log into the game you need to verify your account using the following link: http://opengate-meta.appspot.com/services/pilot/verify/"
                    + pilot.getLogin() + "?verification=" + pilot.getVerificationCode();

            try {
                Message msg = new MimeMessage(session);
                msg.setFrom(new InternetAddress("egore911@gmail.com", "Opengate administration"));
                msg.addRecipient(Message.RecipientType.TO, recipient);
                msg.setSubject("Your Example.com account has been activated");
                msg.setText(msgBody);
                Transport.send(msg);

            } catch (AddressException e) {
                LOG.log(Level.SEVERE, e.getMessage(), e);
                return Response.status(Status.INTERNAL_SERVER_ERROR).build();
            } catch (MessagingException e) {
                LOG.log(Level.SEVERE, e.getMessage(), e);
                return Response.status(Status.INTERNAL_SERVER_ERROR).build();
            } catch (UnsupportedEncodingException e) {
                LOG.log(Level.SEVERE, e.getMessage(), e);
                return Response.status(Status.INTERNAL_SERVER_ERROR).build();
            }

            StatusHelper.ok(jsonObject);
            jsonObject.put("id", pilot.getKey().getId());
            jsonObject.put("vessel_id", pilot.getVessel().getKey().getId());
            // TODO properly wrap the vessel and its equipment/cargo
            return Response.ok(jsonObject.toString()).build();
        } catch (JSONException e) {
            LOG.log(Level.SEVERE, e.getMessage(), e);
            return Response.status(Status.INTERNAL_SERVER_ERROR).build();
        }
    } catch (NoResultException e) {
        return Response.status(Status.FORBIDDEN).build();
    } finally {
        if (em.getTransaction().isActive()) {
            em.getTransaction().rollback();
        }
    }
}

From source file:com.gigglinggnus.controllers.AdminMakeAppointmentController.java

/**
 *
 * @param request servlet request//from w w w  .j  a  v a  2 s .com
 * @param response servlet response
 * @throws ServletException if a servlet-specific error occurs
 * @throws IOException if an I/O error occurs
 */
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {
    EntityManager em = (EntityManager) request.getSession().getAttribute("em");

    String msg = request.getParameter("msg");
    User user = (User) (request.getSession().getAttribute("user"));
    Clock clk = (Clock) (request.getSession().getAttribute("clock"));

    if (msg.equals("lookup_student")) {
        String studId = request.getParameter("studentId");
        User student = em.find(User.class, studId);
        List<Exam> exams = student.getRegistrableExams();
        JSONObject json = new JSONObject();
        json.put("students_idNumber", studId);
        json.put("firstName", student.getFirstName());
        json.put("lastName", student.getLastName());
        JSONArray jExams = new JSONArray();
        for (Exam exam : exams) {
            JSONObject elem = new JSONObject();

            String examId = exam.getExamId();
            String termId = exam.getTerm().getTermId();
            String start = exam.getInterval().getStart().atZone(ZoneId.systemDefault()).toLocalDate()
                    .toString();
            String end = exam.getInterval().getEnd().atZone(ZoneId.systemDefault()).toLocalDate().toString();
            elem.put("examId", examId);
            elem.put("termId", termId);
            if (exam instanceof CourseExam) {
                String courseId = ((CourseExam) exam).getCourse().getCourseId();
                elem.put("courseId", courseId);
                elem.put("examType", "Course");
            } else {
                elem.put("courseId", "N/A");
                elem.put("examType", "AdHoc");
            }
            elem.put("start", start);
            elem.put("end", end);
            jExams.put(elem);
        }
        json.put("exams", jExams);
        response.getWriter().write(json.toString());
    } else if (msg.equals("exam_available_timeslots")) {
        String examId = request.getParameter("examId");
        String dateStr = request.getParameter("date");
        Exam exam = em.find(Exam.class, examId);
        LocalDate apptDate = LocalDate.parse(dateStr);
        List<LocalTime> timeslots = exam.getTimeslotsForDay(apptDate);

        JSONObject json = new JSONObject();
        json.put("examId", examId);
        JSONArray jTimeSlots = new JSONArray();
        for (LocalTime timeslot : timeslots) {
            String start = timeslot.toString();
            String end = timeslot.plus(exam.getDuration()).toString();
            JSONObject elem = new JSONObject();
            elem.put("start", start);
            elem.put("end", end);
            jTimeSlots.put(elem);
        }
        json.put("timeSlots", jTimeSlots);
        response.getWriter().write(json.toString());
    } else if (msg.equals("submit-appointment")) {
        String studId = request.getParameter("studentId");
        String examId = request.getParameter("examId");
        String stDate = request.getParameter("examDate");
        String stTime = request.getParameter("startTime") + ":00";
        String stSeat = request.getParameter("seatType");

        User student = em.find(User.class, studId);
        Exam exam = em.find(Exam.class, examId);
        LocalDate lDate = LocalDate.parse(stDate);
        LocalTime lTime = LocalTime.parse(stTime);
        Instant inst = ZonedDateTime.of(lDate, lTime, ZoneId.systemDefault()).toInstant();
        JSONObject json = new JSONObject();
        try {
            em.getTransaction().begin();
            if (stSeat.equals("normal")) {
                user.makeAppointment(student, Seating.NORMAL, exam, inst, clk);
                em.getTransaction().commit();
                json.put("success", "Appointment Made!");
                response.getWriter().write(json.toString());
            } else if (stSeat.equals("setaside")) {
                user.makeAppointment(student, Seating.SETASIDE, exam, inst, clk);
                em.getTransaction().commit();
                json.put("success", "Appointment Made!");
                response.getWriter().write(json.toString());
            } else {
                em.getTransaction().rollback();
                json.put("error", "invalid choice of seating");
                response.getWriter().write(json.toString());
            }
        } catch (Exception e) {
            em.getTransaction().rollback();
            json.put("error", e.toString());
            response.getWriter().write(json.toString());
        }
    } else {
        JSONObject json = new JSONObject();
        json.put("error", msg);
        response.getWriter().write(json.toString());
    }
}

From source file:gov.osti.services.Metadata.java

/**
 * APPROVE endpoint; sends the Metadata of a targeted project to Index.
 *
 * Will return a FORBIDDEN response if the OWNER logged in does not match
 * the record's OWNER.//from   w  ww .  java2s. com
 *
 * @param codeId the CODE ID of the record to APPROVE.
 * @return a Response containing the JSON of the approved record if successful, or
 * error information if not
 * @throws InternalServerErrorException on JSON parsing or other IO errors
 */
@GET
@Path("/approve/{codeId}")
@Produces(MediaType.APPLICATION_JSON)
@RequiresAuthentication
@RequiresRoles("OSTI")
public Response approve(@PathParam("codeId") Long codeId) {
    EntityManager em = DoeServletContextListener.createEntityManager();
    Subject subject = SecurityUtils.getSubject();
    User user = (User) subject.getPrincipal();

    try {
        DOECodeMetadata md = em.find(DOECodeMetadata.class, codeId);

        if (null == md)
            return ErrorResponse.notFound("Code ID not on file.").build();

        // make sure this is Submitted or Announced
        if (!DOECodeMetadata.Status.Submitted.equals(md.getWorkflowStatus())
                && !DOECodeMetadata.Status.Announced.equals(md.getWorkflowStatus()))
            return ErrorResponse.badRequest("Metadata is not in the Submitted/Announced workflow state.")
                    .build();

        // move Approved Container to downloadable path
        try {
            approveContainerUpload(md);
        } catch (IOException e) {
            log.error("Container move failure: " + e.getMessage());
            return ErrorResponse.internalServerError(e.getMessage()).build();
        }

        // if approving announced, send this to OSTI
        if (DOECodeMetadata.Status.Announced.equals(md.getWorkflowStatus())) {
            sendToOsti(em, md);
        }

        em.getTransaction().begin();
        // set the WORKFLOW STATUS
        md.setWorkflowStatus(Status.Approved);

        // persist this to the database, as validations should already be complete at this stage.
        store(em, md, user);

        // prior to updating snapshot, gather RI List for backfilling
        List<RelatedIdentifier> previousRiList = getPreviousRiList(em, md);

        // store the snapshot copy of Metadata
        MetadataSnapshot snapshot = new MetadataSnapshot();
        snapshot.getSnapshotKey().setCodeId(md.getCodeId());
        snapshot.getSnapshotKey().setSnapshotStatus(md.getWorkflowStatus());
        snapshot.setDoi(md.getDoi());
        snapshot.setDoiIsMinted(md.getReleaseDate() != null);
        snapshot.setJson(md.toJson().toString());

        em.merge(snapshot);

        // perform RI backfilling
        backfillProjects(em, md, previousRiList);

        // if we make it this far, go ahead and commit the transaction
        em.getTransaction().commit();

        // send it to the indexer
        sendToIndex(em, md);

        // send APPROVAL NOTIFICATION to OWNER
        sendApprovalNotification(md);
        sendPOCNotification(md);

        // and we're happy
        return Response.status(Response.Status.OK)
                .entity(mapper.createObjectNode().putPOJO("metadata", md.toJson()).toString()).build();
    } catch (BadRequestException e) {
        return e.getResponse();
    } catch (NotFoundException e) {
        return ErrorResponse.status(Response.Status.NOT_FOUND, e.getMessage()).build();
    } catch (IllegalAccessException e) {
        log.warn("Persistence Error: Invalid owner update attempt: " + user.getEmail());
        log.warn("Message: " + e.getMessage());
        return ErrorResponse
                .status(Response.Status.FORBIDDEN, "Invalid Access:  Unable to edit indicated record.").build();
    } catch (IOException | InvocationTargetException e) {
        if (em.getTransaction().isActive())
            em.getTransaction().rollback();

        log.warn("Persistence Error: " + e.getMessage());
        return ErrorResponse
                .status(Response.Status.INTERNAL_SERVER_ERROR, "IO Error approving record: " + e.getMessage())
                .build();
    } finally {
        em.close();
    }
}

From source file:gov.osti.services.Metadata.java

/**
 * Handle SUBMIT workflow logic./*from   www.j  av a 2  s.c  om*/
 *
 * @param json JSON String containing the METADATA object to SUBMIT
 * @param file (optional) a FILE associated with this METADATA
 * @param fileInfo (optional) the FILE disposition information, if any
 * @param container (optional) a CONTAINER IMAGE associated with this METADATA
 * @param containerInfo (optional) the CONTAINER IMAGE disposition information, if any
 * @return an appropriate Response object to the caller
 */
private Response doSubmit(String json, InputStream file, FormDataContentDisposition fileInfo,
        InputStream container, FormDataContentDisposition containerInfo) {
    EntityManager em = DoeServletContextListener.createEntityManager();
    Subject subject = SecurityUtils.getSubject();
    User user = (User) subject.getPrincipal();

    try {
        validateUploads(fileInfo, containerInfo);

        DOECodeMetadata md = DOECodeMetadata.parseJson(new StringReader(json));

        Long currentCodeId = md.getCodeId();
        boolean previouslySaved = false;
        if (currentCodeId != null) {
            DOECodeMetadata emd = em.find(DOECodeMetadata.class, currentCodeId);

            if (emd != null)
                previouslySaved = Status.Saved.equals(emd.getWorkflowStatus());
        }

        // lookup Announced Snapshot status
        TypedQuery<MetadataSnapshot> querySnapshot = em
                .createNamedQuery("MetadataSnapshot.findByCodeIdAndStatus", MetadataSnapshot.class)
                .setParameter("codeId", currentCodeId).setParameter("status", DOECodeMetadata.Status.Announced);

        List<MetadataSnapshot> results = querySnapshot.setMaxResults(1).getResultList();
        if (results.size() > 0) {
            log.error("Cannot Submit, Previously Announced: " + currentCodeId);
            return ErrorResponse.internalServerError(
                    "This record was previously Announced to E-Link, if you need to update the metadata, please change your endpoint to \"/announce.\"")
                    .build();
        }

        em.getTransaction().begin();

        performDataNormalization(md);

        // set the ownership and workflow status
        md.setOwner(user.getEmail());
        md.setWorkflowStatus(Status.Submitted);
        md.setSiteOwnershipCode(user.getSiteId());

        // store it
        store(em, md, user);

        // re-attach metadata to transaction in order to store any changes beyond this point
        md = em.find(DOECodeMetadata.class, md.getCodeId());

        // if there's a FILE associated here, store it
        String fullFileName = "";
        if (null != file && null != fileInfo) {
            try {
                fullFileName = writeFile(file, md.getCodeId(), fileInfo.getFileName(), FILE_UPLOADS);
                md.setFileName(fullFileName);
            } catch (IOException e) {
                log.error("File Upload Failed: " + e.getMessage());
                return ErrorResponse.internalServerError("File upload failed.").build();
            }
        }

        // if there's a CONTAINER IMAGE associated here, store it
        String fullContainerName = "";
        if (null != container && null != containerInfo) {
            try {
                fullContainerName = writeFile(container, md.getCodeId(), containerInfo.getFileName(),
                        CONTAINER_UPLOADS);
                md.setContainerName(fullContainerName);
            } catch (IOException e) {
                log.error("Container Image Upload Failed: " + e.getMessage());
                return ErrorResponse.internalServerError("Container Image upload failed.").build();
            }
        }

        // check validations for Submitted workflow
        List<String> errors = validateSubmit(md);
        if (!errors.isEmpty()) {
            // generate a JSONAPI errors object
            return ErrorResponse.badRequest(errors).build();
        }

        // create OSTI Hosted project, as needed
        try {
            // process local GitLab, if needed
            processOSTIGitLab(md);
        } catch (Exception e) {
            log.error("OSTI GitLab failure: " + e.getMessage());
            return ErrorResponse.internalServerError("Unable to create OSTI Hosted project: " + e.getMessage())
                    .build();
        }

        // send this file upload along to archiver if configured
        try {
            // if no file/container, but previously Saved with a file/container, we need to attach to those streams and send to Archiver
            if (previouslySaved) {
                if (null == file && !StringUtils.isBlank(md.getFileName())) {
                    java.nio.file.Path destination = Paths.get(FILE_UPLOADS, String.valueOf(md.getCodeId()),
                            md.getFileName());
                    fullFileName = destination.toString();
                    file = Files.newInputStream(destination);
                }
                if (null == container && !StringUtils.isBlank(md.getContainerName())) {
                    java.nio.file.Path destination = Paths.get(CONTAINER_UPLOADS,
                            String.valueOf(md.getCodeId()), md.getContainerName());
                    fullContainerName = destination.toString();
                    container = Files.newInputStream(destination);
                }
            }

            // if a FILE or CONTAINER was sent, create a File Object from it
            File archiveFile = (null == file) ? null : new File(fullFileName);
            File archiveContainer = null; //(null==container) ? null : new File(fullContainerName);
            if (DOECodeMetadata.Accessibility.CO.equals(md.getAccessibility()))
                // if CO project type, no need to archive the repo because it is local GitLab
                sendToArchiver(md.getCodeId(), null, archiveFile, archiveContainer);
            else
                sendToArchiver(md.getCodeId(), md.getRepositoryLink(), archiveFile, archiveContainer);
        } catch (IOException e) {
            log.error("Archiver call failure: " + e.getMessage());
            return ErrorResponse.internalServerError("Unable to archive project.").build();
        }

        // send to DataCite if needed (and there is a RELEASE DATE set)
        if (null != md.getDoi() && null != md.getReleaseDate()) {
            try {
                DataCite.register(md);
            } catch (IOException e) {
                // tell why the DataCite registration failed
                log.warn("DataCite ERROR: " + e.getMessage());
                return ErrorResponse.internalServerError(
                        "The DOI registration service is currently unavailable, please try to submit your record later. If the issue persists, please contact doecode@osti.gov.")
                        .build();
            }
        }

        // store the snapshot copy of Metadata
        MetadataSnapshot snapshot = new MetadataSnapshot();
        snapshot.getSnapshotKey().setCodeId(md.getCodeId());
        snapshot.getSnapshotKey().setSnapshotStatus(md.getWorkflowStatus());
        snapshot.setDoi(md.getDoi());
        snapshot.setDoiIsMinted(md.getReleaseDate() != null);
        snapshot.setJson(md.toJson().toString());

        em.merge(snapshot);

        // commit it
        em.getTransaction().commit();

        // send NOTIFICATION if configured to do so
        sendStatusNotification(md);

        // we are done here
        return Response.ok().entity(mapper.createObjectNode().putPOJO("metadata", md.toJson()).toString())
                .build();
    } catch (BadRequestException e) {
        return e.getResponse();
    } catch (NotFoundException e) {
        return ErrorResponse.notFound(e.getMessage()).build();
    } catch (IllegalAccessException e) {
        log.warn("Persistence Error: Unable to update record, invalid owner: " + user.getEmail());
        log.warn("Message: " + e.getMessage());
        return ErrorResponse.forbidden("Logged in User is not allowed to modify this record.").build();
    } catch (ValidationException e) {
        log.warn("Validation Error: " + e.getMessage());
        return ErrorResponse.badRequest(e.getMessage()).build();
    } catch (IOException | InvocationTargetException e) {
        if (em.getTransaction().isActive())
            em.getTransaction().rollback();

        log.warn("Persistence Error Submitting: " + e.getMessage());
        return ErrorResponse.internalServerError("Persistence error submitting record.").build();
    } finally {
        em.close();
    }
}