Examples with PatientIdentifier org.openmrs.PatientIdentifier used on opensource projects

Example 11 with PatientIdentifier

use of org.openmrs.PatientIdentifier in project openmrs-core by openmrs.

the class HibernatePatientDAOTest method getPatientIdentifiers_shouldGetByIdentifierType.

@Test
public void getPatientIdentifiers_shouldGetByIdentifierType() {
    List<PatientIdentifierType> identifierTypes = singletonList(new PatientIdentifierType(2));
    List<PatientIdentifier> identifiers = hibernatePatientDao.getPatientIdentifiers(null, identifierTypes, emptyList(), emptyList(), null);
    List<Integer> identifierIds = identifiers.stream().map(PatientIdentifier::getId).collect(Collectors.toList());
    Assert.assertEquals(2, identifiers.size());
    Assert.assertThat(identifierIds, hasItems(1, 3));
}

Example 12 with PatientIdentifier

use of org.openmrs.PatientIdentifier in project openmrs-core by openmrs.

the class HL7ServiceImpl method resolvePersonFromIdentifiers.

/**
 * @param identifiers CX identifier list from an identifier (either PID or NK1)
 * @return The internal id number of the Patient based on one of the given identifiers, or null
 *         if the patient is not found
 * @throws HL7Exception
 */
@Override
@Transactional(readOnly = true)
public Person resolvePersonFromIdentifiers(CX[] identifiers) throws HL7Exception {
    // give up if no identifiers exist
    if (identifiers.length < 1) {
        throw new HL7Exception("Missing patient identifier in PID segment");
    }
    // Take the first uniquely matching identifier
    for (CX identifier : identifiers) {
        String hl7PersonId = identifier.getIDNumber().getValue();
        // TODO if 1st component is blank, check 2nd and 3rd of assigning
        // authority
        String assigningAuthority = identifier.getAssigningAuthority().getNamespaceID().getValue();
        if (StringUtils.isNotBlank(assigningAuthority)) {
            // Assigning authority defined
            try {
                PatientIdentifierType pit = Context.getPatientService().getPatientIdentifierTypeByName(assigningAuthority);
                if (pit == null) {
                    // there is no matching PatientIdentifierType
                    if (assigningAuthority.equals(HL7Constants.HL7_AUTHORITY_UUID)) {
                        // the identifier is a UUID
                        Person p = Context.getPersonService().getPersonByUuid(hl7PersonId);
                        if (p != null) {
                            return p;
                        }
                        log.warn("Can't find person for UUID '" + hl7PersonId + "'");
                        // skip identifiers with unknown type
                        continue;
                    } else if (assigningAuthority.equals(HL7Constants.HL7_AUTHORITY_LOCAL)) {
                        // the ID is internal (local)
                        String idType = identifier.getIdentifierTypeCode().getValue();
                        try {
                            if (idType.equals(HL7Constants.HL7_ID_PERSON)) {
                                Integer pid = Integer.parseInt(hl7PersonId);
                                // patient_id == person_id, so just look for
                                // the person
                                Person p = Context.getPersonService().getPerson(pid);
                                if (p != null) {
                                    return p;
                                }
                            } else if (idType.equals(HL7Constants.HL7_ID_PATIENT)) {
                                Integer pid = Integer.parseInt(hl7PersonId);
                                // patient_id == person_id, so just look for
                                // the person
                                Patient p = Context.getPatientService().getPatient(pid);
                                if (p != null) {
                                    return p;
                                }
                            }
                        } catch (NumberFormatException e) {
                        }
                        log.warn("Can't find Local identifier of '" + hl7PersonId + "'");
                        // skip identifiers with unknown type
                        continue;
                    }
                    log.warn("Can't find PatientIdentifierType named '" + assigningAuthority + "'");
                    // skip identifiers with unknown type
                    continue;
                }
                List<PatientIdentifier> matchingIds = Context.getPatientService().getPatientIdentifiers(hl7PersonId, Collections.singletonList(pit), null, null, null);
                if (matchingIds == null || matchingIds.isEmpty()) {
                    // no matches
                    log.warn("NO matches found for " + hl7PersonId);
                    // try next identifier
                    continue;
                } else if (matchingIds.size() == 1) {
                    // unique match -- we're done
                    return matchingIds.get(0).getPatient();
                } else {
                    // ambiguous identifier
                    log.debug("Ambiguous identifier in PID. " + matchingIds.size() + " matches for identifier '" + hl7PersonId + "' of type '" + pit + "'");
                    // try next identifier
                    continue;
                }
            } catch (Exception e) {
                log.error("Error resolving patient identifier '" + hl7PersonId + "' for assigning authority '" + assigningAuthority + "'", e);
                continue;
            }
        } else {
            try {
                log.debug("CX contains ID '" + hl7PersonId + "' without assigning authority -- assuming patient.patient_id");
                return Context.getPatientService().getPatient(Integer.parseInt(hl7PersonId));
            } catch (NumberFormatException e) {
                log.warn("Invalid patient ID '" + hl7PersonId + "'");
            }
        }
    }
    return null;
}

Example 13 with PatientIdentifier

use of org.openmrs.PatientIdentifier in project openmrs-core by openmrs.

the class HL7ServiceImpl method createPersonFromNK1.

/**
 * @see org.openmrs.hl7.HL7Service#createPersonFromNK1(ca.uhn.hl7v2.model.v25.segment.NK1)
 */
@Override
public Person createPersonFromNK1(NK1 nk1) throws HL7Exception {
    // NOTE: following block (with minor modifications) stolen from
    // ADTA28Handler
    // TODO: generalize this for use with both PID and NK1 segments
    Person person = new Person();
    // UUID
    CX[] identifiers = nk1.getNextOfKinAssociatedPartySIdentifiers();
    String uuid = getUuidFromIdentifiers(identifiers);
    if (Context.getPersonService().getPersonByUuid(uuid) != null) {
        throw new HL7Exception("Non-unique UUID '" + uuid + "' for new person");
    }
    person.setUuid(uuid);
    // Patient Identifiers
    List<PatientIdentifier> goodIdentifiers = new ArrayList<>();
    for (CX id : identifiers) {
        String assigningAuthority = id.getAssigningAuthority().getNamespaceID().getValue();
        String hl7PatientId = id.getIDNumber().getValue();
        log.debug("identifier has id=" + hl7PatientId + " assigningAuthority=" + assigningAuthority);
        if (assigningAuthority != null && assigningAuthority.length() > 0) {
            try {
                PatientIdentifierType pit = Context.getPatientService().getPatientIdentifierTypeByName(assigningAuthority);
                if (pit == null) {
                    if (!"UUID".equals(assigningAuthority)) {
                        log.warn("Can't find PatientIdentifierType named '" + assigningAuthority + "'");
                    }
                    // skip identifiers with unknown type
                    continue;
                }
                PatientIdentifier pi = new PatientIdentifier();
                pi.setIdentifierType(pit);
                pi.setIdentifier(hl7PatientId);
                // Get default location
                Location location = Context.getLocationService().getDefaultLocation();
                if (location == null) {
                    throw new HL7Exception("Cannot find default location");
                }
                pi.setLocation(location);
                try {
                    PatientIdentifierValidator.validateIdentifier(pi);
                    goodIdentifiers.add(pi);
                } catch (PatientIdentifierException ex) {
                    log.warn("Patient identifier in NK1 is invalid: " + pi, ex);
                }
            } catch (Exception e) {
                log.error("Uncaught error parsing/creating patient identifier '" + hl7PatientId + "' for assigning authority '" + assigningAuthority + "'", e);
            }
        } else {
            log.debug("NK1 contains identifier with no assigning authority");
            continue;
        }
    }
    if (!goodIdentifiers.isEmpty()) {
        // If we have one identifier, set it as the preferred to make the validator happy.
        if (goodIdentifiers.size() == 1) {
            goodIdentifiers.get(0).setPreferred(true);
        }
        // cast the person as a Patient and add identifiers
        person = new Patient(person);
        ((Patient) person).addIdentifiers(goodIdentifiers);
    }
    // Person names
    for (XPN patientNameX : nk1.getNKName()) {
        PersonName name = new PersonName();
        name.setFamilyName(patientNameX.getFamilyName().getSurname().getValue());
        name.setGivenName(patientNameX.getGivenName().getValue());
        name.setMiddleName(patientNameX.getSecondAndFurtherGivenNamesOrInitialsThereof().getValue());
        person.addName(name);
    }
    // Gender (checks for null, but not for 'M' or 'F')
    String gender = nk1.getAdministrativeSex().getValue();
    if (gender == null) {
        throw new HL7Exception("Missing gender in an NK1 segment");
    }
    gender = gender.toUpperCase();
    if (!OpenmrsConstants.GENDER().containsKey(gender)) {
        throw new HL7Exception("Unrecognized gender: " + gender);
    }
    person.setGender(gender);
    // Date of Birth
    TS dateOfBirth = nk1.getDateTimeOfBirth();
    if (dateOfBirth == null || dateOfBirth.getTime() == null || dateOfBirth.getTime().getValue() == null) {
        throw new HL7Exception("Missing birth date in an NK1 segment");
    }
    person.setBirthdate(HL7Util.parseHL7Timestamp(dateOfBirth.getTime().getValue()));
    // Estimated birthdate?
    ID precisionTemp = dateOfBirth.getDegreeOfPrecision();
    if (precisionTemp != null && precisionTemp.getValue() != null) {
        String precision = precisionTemp.getValue().toUpperCase();
        log.debug("The birthdate is estimated: " + precision);
        if ("Y".equals(precision) || "L".equals(precision)) {
            person.setBirthdateEstimated(true);
        }
    }
    // save the new person or patient
    if (person instanceof Patient) {
        Context.getPatientService().savePatient((Patient) person);
    } else {
        Context.getPersonService().savePerson(person);
    }
    return person;
}

Example 14 with PatientIdentifier

use of org.openmrs.PatientIdentifier in project openmrs-core by openmrs.

the class MigrationHelper method importRelationships.

/**
 * Takes a list of Strings of the format RELATIONSHIP:<user last name>,<user first
 * name>,<relationship type name>,<patient identifier type name>,<identifier> so if user hfraser
 * if the cardiologist of the patient with patient_id 8039 in PIH's old emr, then:
 * RELATIONSHIP:hfraser,Cardiologist,HIV-EMRV1,8039 (the "RELATIONSHIP:" is not actually
 * necessary. Anything before and including the first : will be dropped If autoCreateUsers is
 * true, and no user exists with the given username, one will be created. If autoAddRole is
 * true, then whenever a user is auto-created, if a role exists with the same name as
 * relationshipType.name, then the user will be added to that role
 */
public static int importRelationships(Collection<String> relationships, boolean autoCreateUsers, boolean autoAddRole) {
    PatientService ps = Context.getPatientService();
    UserService us = Context.getUserService();
    PersonService personService = Context.getPersonService();
    List<Relationship> relsToAdd = new ArrayList<>();
    Random rand = new Random();
    for (String s : relationships) {
        if (s.contains(":")) {
            s = s.substring(s.indexOf(":") + 1);
        }
        String[] ss = s.split(",");
        if (ss.length < 5) {
            throw new IllegalArgumentException("The line '" + s + "' is in the wrong format");
        }
        String userLastName = ss[0];
        String userFirstName = ss[1];
        String username = (userFirstName + userLastName).replaceAll(" ", "");
        String relationshipType = ss[2];
        String identifierType = ss[3];
        String identifier = ss[4];
        User user = null;
        {
            // first try looking for non-voided users
            List<User> users = us.getUsersByName(userFirstName, userLastName, false);
            if (users.size() == 1) {
                user = users.get(0);
            } else if (users.size() > 1) {
                throw new IllegalArgumentException("Found " + users.size() + " users named '" + userLastName + ", " + userFirstName + "'");
            }
        }
        if (user == null) {
            // next try looking for voided users
            List<User> users = us.getUsersByName(userFirstName, userLastName, false);
            if (users.size() == 1) {
                user = users.get(0);
            } else if (users.size() > 1) {
                throw new IllegalArgumentException("Found " + users.size() + " voided users named '" + userLastName + ", " + userFirstName + "'");
            }
        }
        if (user == null && autoCreateUsers) {
            user = new User();
            user.setPerson(new Person());
            PersonName pn = new PersonName(userFirstName, "", userLastName);
            user.addName(pn);
            user.setUsername(username);
            // Generate a temporary password: 8-12 random characters
            String pass;
            {
                int length = rand.nextInt(4) + 8;
                char[] password = new char[length];
                for (int x = 0; x < length; x++) {
                    int randDecimalAsciiVal = rand.nextInt(93) + 33;
                    password[x] = (char) randDecimalAsciiVal;
                }
                pass = new String(password);
            }
            if (autoAddRole) {
                Role role = us.getRole(relationshipType);
                if (role != null) {
                    user.addRole(role);
                }
            }
            us.createUser(user, pass);
        }
        if (user == null) {
            throw new IllegalArgumentException("Can't find user '" + userLastName + ", " + userFirstName + "'");
        }
        Person person = personService.getPerson(user.getUserId());
        RelationshipType relationship = personService.getRelationshipTypeByName(relationshipType);
        PatientIdentifierType pit = ps.getPatientIdentifierTypeByName(identifierType);
        List<PatientIdentifier> found = ps.getPatientIdentifiers(identifier, Collections.singletonList(pit), null, null, null);
        if (found.size() != 1) {
            throw new IllegalArgumentException("Found " + found.size() + " patients with identifier '" + identifier + "' of type " + identifierType);
        }
        Person relative = personService.getPerson(found.get(0).getPatient().getPatientId());
        Relationship rel = new Relationship();
        rel.setPersonA(person);
        rel.setRelationshipType(relationship);
        rel.setPersonB(relative);
        relsToAdd.add(rel);
    }
    int addedSoFar = 0;
    for (Relationship rel : relsToAdd) {
        personService.saveRelationship(rel);
        ++addedSoFar;
    }
    return addedSoFar;
}

Example 15 with PatientIdentifier

use of org.openmrs.PatientIdentifier in project openmrs-core by openmrs.

the class PatientServiceTest method isIdentifierInUseByAnotherPatient_shouldReturnTrueIfInUseForALocationAndIdTypeUniquenessIsSetToLocation.

/**
 * @see PatientService#isIdentifierInUseByAnotherPatient(PatientIdentifier)
 */
@Test
public void isIdentifierInUseByAnotherPatient_shouldReturnTrueIfInUseForALocationAndIdTypeUniquenessIsSetToLocation() throws Exception {
    PatientIdentifier duplicateId = patientService.getPatientIdentifier(1);
    Assert.assertNotNull(duplicateId.getLocation());
    PatientIdentifierType idType = duplicateId.getIdentifierType();
    idType.setUniquenessBehavior(UniquenessBehavior.LOCATION);
    patientService.savePatientIdentifierType(idType);
    PatientIdentifier pi = new PatientIdentifier(duplicateId.getIdentifier(), idType, duplicateId.getLocation());
    Assert.assertTrue(patientService.isIdentifierInUseByAnotherPatient(pi));
}