Examples with TS ca.uhn.hl7v2.model.v25.datatype.TS used on opensource projects

Example 1 with TS

use of ca.uhn.hl7v2.model.v25.datatype.TS in project streamsx.health by IBMStreams.

the class ObxToSplMapper method messageToModel.

@SuppressWarnings("unchecked")
public <T> Iterable<T> messageToModel(Message message) {
    ArrayList<Observation> observations = new ArrayList<Observation>();
    if (message instanceof ORU_R01) {
        ORU_R01 oruMsg = (ORU_R01) message;
        String obxTs = "";
        String obxLocation = "";
        String sendingApp = "";
        String sendingFacility = "";
        try {
            MSH msh = oruMsg.getMSH();
            sendingApp = msh.getSendingApplication().encode();
            sendingFacility = msh.getSendingFacility().encode();
            List<ORU_R01_PATIENT_RESULT> patient_RESULTAll = ((ORU_R01) message).getPATIENT_RESULTAll();
            for (ORU_R01_PATIENT_RESULT result : patient_RESULTAll) {
                ORU_R01_ORDER_OBSERVATION order_OBSERVATION = result.getORDER_OBSERVATION();
                OBR obr = order_OBSERVATION.getOBR();
                DTM ts = obr.getObservationDateTime();
                obxTs = ts.getValue();
                ORU_R01_PATIENT patient = result.getPATIENT();
                ORU_R01_VISIT visit = patient.getVISIT();
                PL location = visit.getPV1().getAssignedPatientLocation();
                obxLocation = location.encode();
                List<ORU_R01_OBSERVATION> observationAll = order_OBSERVATION.getOBSERVATIONAll();
                for (ORU_R01_OBSERVATION oru_R01_OBSERVATION : observationAll) {
                    parseOBX(observations, obxTs, obxLocation, oru_R01_OBSERVATION.getOBX(), sendingApp, sendingFacility);
                }
            }
        } catch (HL7Exception e) {
            if (TRACE.isDebugEnabled())
                TRACE.log(TraceLevel.WARN, e);
        }
        try {
            OBR obr = (OBR) oruMsg.get("OBR");
            DTM ts = obr.getObservationDateTime();
            obxTs = ts.getValue();
            Structure tmp = oruMsg.get("PV1");
            if (tmp != null) {
                PV1 pv1 = (PV1) tmp;
                PL location = pv1.getAssignedPatientLocation();
                obxLocation = location.encode();
            }
            Structure[] structures = oruMsg.getAll("OBX");
            for (Structure structure : structures) {
                parseOBX(observations, obxTs, obxLocation, (OBX) structure, sendingApp, sendingFacility);
            }
        } catch (HL7Exception e) {
            if (TRACE.isDebugEnabled())
                TRACE.log(TraceLevel.WARN, e);
        }
    }
    return (Iterable<T>) observations;
}

Example 2 with TS

use of ca.uhn.hl7v2.model.v25.datatype.TS in project openmrs-core by openmrs.

the class ORUR01Handler method getDatetime.

/**
 * Return a java date object for the given TS
 *
 * @param ts TS to parse
 * @return date object or null
 * @throws HL7Exception
 */
private Date getDatetime(TS ts) throws HL7Exception {
    Date datetime = null;
    DTM value = ts.getTime();
    if (value.getYear() == 0 || value.getValue() == null) {
        return null;
    }
    try {
        datetime = getDate(value.getYear(), value.getMonth(), value.getDay(), value.getHour(), value.getMinute(), value.getSecond());
    } catch (DataTypeException e) {
    }
    return datetime;
}

Example 3 with TS

use of ca.uhn.hl7v2.model.v25.datatype.TS 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 4 with TS

use of ca.uhn.hl7v2.model.v25.datatype.TS in project openmrs-core by openmrs.

the class ORUR01Handler method parseObs.

/**
 * Creates the Obs pojo from the OBX message
 *
 * @param encounter The Encounter object this Obs is a member of
 * @param obx The hl7 obx message
 * @param obr The parent hl7 or message
 * @param uid unique string for this message for any error reporting purposes
 * @return Obs pojo with all values filled in
 * @throws HL7Exception if there is a parsing exception
 * @throws ProposingConceptException if the answer to this obs is a proposed concept
 * @should add comments to an observation from NTE segments
 * @should add multiple comments for an observation as one comment
 * @should add comments to an observation group
 */
private Obs parseObs(Encounter encounter, OBX obx, OBR obr, String uid) throws HL7Exception, ProposingConceptException {
    if (log.isDebugEnabled()) {
        log.debug("parsing observation: " + obx);
    }
    Varies[] values = obx.getObservationValue();
    // bail out if no values were found
    if (values == null || values.length < 1) {
        return null;
    }
    String hl7Datatype = values[0].getName();
    if (log.isDebugEnabled()) {
        log.debug("  datatype = " + hl7Datatype);
    }
    Concept concept = getConcept(obx.getObservationIdentifier(), uid);
    if (log.isDebugEnabled()) {
        log.debug("  concept = " + concept.getConceptId());
    }
    ConceptName conceptName = getConceptName(obx.getObservationIdentifier());
    if (log.isDebugEnabled()) {
        log.debug("  concept-name = " + conceptName);
    }
    Date datetime = getDatetime(obx);
    if (log.isDebugEnabled()) {
        log.debug("  timestamp = " + datetime);
    }
    if (datetime == null) {
        datetime = encounter.getEncounterDatetime();
    }
    Obs obs = new Obs();
    obs.setPerson(encounter.getPatient());
    obs.setConcept(concept);
    obs.setEncounter(encounter);
    obs.setObsDatetime(datetime);
    obs.setLocation(encounter.getLocation());
    obs.setCreator(encounter.getCreator());
    obs.setDateCreated(encounter.getDateCreated());
    // set comments if there are any
    StringBuilder comments = new StringBuilder();
    ORU_R01_OBSERVATION parent = (ORU_R01_OBSERVATION) obx.getParent();
    // iterate over all OBX NTEs
    for (int i = 0; i < parent.getNTEReps(); i++) {
        for (FT obxComment : parent.getNTE(i).getComment()) {
            if (comments.length() > 0) {
                comments.append(" ");
            }
            comments = comments.append(obxComment.getValue());
        }
    }
    // only set comments if there are any
    if (StringUtils.hasText(comments.toString())) {
        obs.setComment(comments.toString());
    }
    Type obx5 = values[0].getData();
    if ("NM".equals(hl7Datatype)) {
        String value = ((NM) obx5).getValue();
        if (value == null || value.length() == 0) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        } else if ("0".equals(value) || "1".equals(value)) {
            concept = concept.hydrate(concept.getConceptId().toString());
            obs.setConcept(concept);
            if (concept.getDatatype().isBoolean()) {
                obs.setValueBoolean("1".equals(value));
            } else if (concept.getDatatype().isNumeric()) {
                try {
                    obs.setValueNumeric(Double.valueOf(value));
                } catch (NumberFormatException e) {
                    throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.notnumericConcept", new Object[] { value, concept.getConceptId(), conceptName.getName(), uid }, null), e);
                }
            } else if (concept.getDatatype().isCoded()) {
                Concept answer = "1".equals(value) ? Context.getConceptService().getTrueConcept() : Context.getConceptService().getFalseConcept();
                boolean isValidAnswer = false;
                Collection<ConceptAnswer> conceptAnswers = concept.getAnswers();
                if (conceptAnswers != null && !conceptAnswers.isEmpty()) {
                    for (ConceptAnswer conceptAnswer : conceptAnswers) {
                        if (conceptAnswer.getAnswerConcept().getId().equals(answer.getId())) {
                            obs.setValueCoded(answer);
                            isValidAnswer = true;
                            break;
                        }
                    }
                }
                // answer the boolean answer concept was't found
                if (!isValidAnswer) {
                    throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.invalidAnswer", new Object[] { answer.toString(), uid }, null));
                }
            } else {
                // throw this exception to make sure that the handler doesn't silently ignore bad hl7 message
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.CannotSetBoolean", new Object[] { obs.getConcept().getConceptId() }, null));
            }
        } else {
            try {
                obs.setValueNumeric(Double.valueOf(value));
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.notnumericConcept", new Object[] { value, concept.getConceptId(), conceptName.getName(), uid }, null), e);
            }
        }
    } else if ("CWE".equals(hl7Datatype)) {
        log.debug("  CWE observation");
        CWE value = (CWE) obx5;
        String valueIdentifier = value.getIdentifier().getValue();
        log.debug("    value id = " + valueIdentifier);
        String valueName = value.getText().getValue();
        log.debug("    value name = " + valueName);
        if (isConceptProposal(valueIdentifier)) {
            if (log.isDebugEnabled()) {
                log.debug("Proposing concept");
            }
            throw new ProposingConceptException(concept, valueName);
        } else {
            log.debug("    not proposal");
            try {
                Concept valueConcept = getConcept(value, uid);
                obs.setValueCoded(valueConcept);
                if (HL7Constants.HL7_LOCAL_DRUG.equals(value.getNameOfAlternateCodingSystem().getValue())) {
                    Drug valueDrug = new Drug();
                    valueDrug.setDrugId(Integer.valueOf(value.getAlternateIdentifier().getValue()));
                    obs.setValueDrug(valueDrug);
                } else {
                    ConceptName valueConceptName = getConceptName(value);
                    if (valueConceptName != null) {
                        if (log.isDebugEnabled()) {
                            log.debug("    value concept-name-id = " + valueConceptName.getConceptNameId());
                            log.debug("    value concept-name = " + valueConceptName.getName());
                        }
                        obs.setValueCodedName(valueConceptName);
                    }
                }
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.InvalidConceptId", new Object[] { valueIdentifier, valueName }, null));
            }
        }
        if (log.isDebugEnabled()) {
            log.debug("  Done with CWE");
        }
    } else if ("CE".equals(hl7Datatype)) {
        CE value = (CE) obx5;
        String valueIdentifier = value.getIdentifier().getValue();
        String valueName = value.getText().getValue();
        if (isConceptProposal(valueIdentifier)) {
            throw new ProposingConceptException(concept, valueName);
        } else {
            try {
                obs.setValueCoded(getConcept(value, uid));
                obs.setValueCodedName(getConceptName(value));
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.InvalidConceptId", new Object[] { valueIdentifier, valueName }, null));
            }
        }
    } else if ("DT".equals(hl7Datatype)) {
        DT value = (DT) obx5;
        if (value != null) {
            Date valueDate = getDate(value.getYear(), value.getMonth(), value.getDay(), 0, 0, 0);
            obs.setValueDatetime(valueDate);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("TS".equals(hl7Datatype)) {
        DTM value = ((TS) obx5).getTime();
        if (value != null) {
            Date valueDate = getDate(value.getYear(), value.getMonth(), value.getDay(), value.getHour(), value.getMinute(), value.getSecond());
            obs.setValueDatetime(valueDate);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("TM".equals(hl7Datatype)) {
        TM value = (TM) obx5;
        if (value != null) {
            Date valueTime = getDate(0, 0, 0, value.getHour(), value.getMinute(), value.getSecond());
            obs.setValueDatetime(valueTime);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("ST".equals(hl7Datatype)) {
        ST value = (ST) obx5;
        if (value == null || value.getValue() == null || value.getValue().trim().length() == 0) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
        obs.setValueText(value.getValue());
    } else if ("ED".equals(hl7Datatype)) {
        ED value = (ED) obx5;
        if (value == null || value.getData() == null || !StringUtils.hasText(value.getData().getValue())) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
        // we need to hydrate the concept so that the EncounterSaveHandler
        // doesn't fail since it needs to check if it is a concept numeric
        Concept c = Context.getConceptService().getConcept(obs.getConcept().getConceptId());
        obs.setConcept(c);
        String title = null;
        if (obs.getValueCodedName() != null) {
            title = obs.getValueCodedName().getName();
        }
        if (!StringUtils.hasText(title)) {
            title = c.getName().getName();
        }
        obs.setComplexData(new ComplexData(title, value.getData().getValue()));
    } else {
        // do we need to support BIT just in case it slips thru?
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.UpsupportedObsType", new Object[] { hl7Datatype }, null));
    }
    return obs;
}

Example 5 with TS

use of ca.uhn.hl7v2.model.v25.datatype.TS in project openmrs-core by openmrs.

the class ADTA28Handler method createPatient.

// Create a new patient when this patient doesn't exist in the database
private Patient createPatient(PID pid, String creatorName) throws HL7Exception {
    Patient patient = new Patient();
    // Try to use the specified username as the creator
    User creator = Context.getUserService().getUserByUsername(creatorName);
    if (creator != null) {
        patient.setCreator(creator);
    }
    // Create all patient identifiers specified in the message
    // Copied code from resolvePatientId() in HL7ServiceImpl.java
    CX[] idList = pid.getPatientIdentifierList();
    if (idList == null || idList.length < 1) {
        throw new HL7Exception("Missing patient identifier in PID segment");
    }
    List<PatientIdentifier> goodIdentifiers = new ArrayList<>();
    for (CX id : idList) {
        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) {
                    log.warn("Can't find PatientIdentifierType named '" + assigningAuthority + "'");
                    // skip identifiers with unknown type
                    continue;
                }
                PatientIdentifier pi = new PatientIdentifier();
                if (creator != null) {
                    pi.setCreator(creator);
                }
                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 PID is invalid: " + pi, ex);
                }
            } catch (Exception e) {
                log.error("Uncaught error parsing/creating patient identifier '" + hl7PatientId + "' for assigning authority '" + assigningAuthority + "'", e);
            }
        } else {
            log.error("PID contains identifier with no assigning authority");
            continue;
        }
    }
    if (goodIdentifiers.isEmpty()) {
        throw new HL7Exception("PID segment has no recognizable patient identifiers.");
    }
    patient.addIdentifiers(goodIdentifiers);
    // Extract patient name from the message
    XPN patientNameX = pid.getPatientName(0);
    if (patientNameX == null) {
        throw new HL7Exception("Missing patient name in the PID segment");
    }
    // Patient name
    PersonName name = new PersonName();
    name.setFamilyName(patientNameX.getFamilyName().getSurname().getValue());
    name.setGivenName(patientNameX.getGivenName().getValue());
    name.setMiddleName(patientNameX.getSecondAndFurtherGivenNamesOrInitialsThereof().getValue());
    if (creator != null) {
        name.setCreator(creator);
    }
    patient.addName(name);
    // Gender (checks for null, but not for 'M' or 'F')
    String gender = pid.getAdministrativeSex().getValue();
    if (gender == null) {
        throw new HL7Exception("Missing gender in the PID segment");
    }
    gender = gender.toUpperCase();
    if (!OpenmrsConstants.GENDER().containsKey(gender)) {
        throw new HL7Exception("Unrecognized gender: " + gender);
    }
    patient.setGender(gender);
    // Date of Birth
    TS dateOfBirth = pid.getDateTimeOfBirth();
    if (dateOfBirth == null || dateOfBirth.getTime() == null || dateOfBirth.getTime().getValue() == null) {
        throw new HL7Exception("Missing birth date in the PID segment");
    }
    patient.setBirthdate(tsToDate(dateOfBirth));
    // 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)) {
            patient.setBirthdateEstimated(true);
        }
    }
    return patient;
}