Examples with Type model.Type used on opensource projects

Example 6 with Type

use of model.Type 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 7 with Type

use of model.Type in project uPMT by coco35700.

the class Main method createBasicSchema.

/**
 * Creates a basic scheme as a default
 * should be improved if desired
 */
private void createBasicSchema() {
    Type s = new Schema((_langBundle.getString("default_scheme")));
    Type general = new Folder(_langBundle.getString("general"));
    Type autre = new Folder(_langBundle.getString("other"));
    Type visuel = new Category(_langBundle.getString("visual"));
    Type image = new Property(_langBundle.getString("picture"));
    Type sensoriel = new Category(_langBundle.getString("sensory"));
    Type emotionnel = new Category(_langBundle.getString("emotional"));
    Type sonore = new Category(_langBundle.getString("acoustic"));
    visuel.addType(image);
    general.addType(visuel);
    general.addType(sensoriel);
    general.addType(emotionnel);
    general.addType(sonore);
    s.addType(general);
    s.addType(autre);
    this.BasicSchema = (Schema) s;
}

Example 8 with Type

use of model.Type in project uPMT by coco35700.

the class Main method writeMoment.

/**
 * Recursive method used to recursively transform a Moment and its sub Moments into CSV compatible DATAZ
 */
private void writeMoment(DescriptionInterview ent, MomentExperience m, PrintWriter writer, String hierarchy) {
    LinkedList<String> classes = new LinkedList<String>();
    for (Type t : m.getTypes()) {
        for (Type prop : t.getTypes()) {
            Property p = (Property) prop;
            classes.add(format(t.getName()) + "," + format(p.getName()) + "," + format(p.getValue()));
        }
    }
    if (!classes.isEmpty()) {
        for (String s : classes) {
            writer.println(format(ent.getName()) + ",\"" + hierarchy + "\"" + "," + format(m.getName()) + "," + format(m.getDescripteme()) + "," + format(m.getColor()) + "," + format(m.getDuration()) + "," + s);
        }
    } else {
        writer.println(format(ent.getName()) + ",\"" + hierarchy + "\"" + "," + format(m.getName()) + "," + format(m.getDescripteme()) + "," + format(m.getColor()) + "," + format(m.getDuration()) + ",\"\",\"\",\"\"");
    }
    for (int i = 0; i < m.getSubMoments().size(); i++) {
        MomentExperience sub = m.getSubMoments().get(i);
        writeMoment(ent, sub, writer, hierarchy + "." + (i + 1));
    }
}

Example 9 with Type

use of model.Type in project uPMT by coco35700.

the class TypeClassRepresentationController method RemoveProperty.

public void RemoveProperty(Property p) {
    for (Type t : this.classe.getTypes()) {
        if (t.getName().equals(p.getName())) {
            this.classe.getTypes().remove(t);
            // System.out.println("TESTEST "+t.hashCode()+ " , "+t);
            stack.push((Property) t);
            break;
        }
    }
    for (Node n : this.properties.getChildren()) {
        TypePropertyRepresentation tpr = (TypePropertyRepresentation) n;
        if (tpr.getProperty().getName().equals(p.getName())) {
            this.properties.getChildren().remove(n);
            break;
        }
    }
}

Example 10 with Type

use of model.Type in project uPMT by coco35700.

the class TypeClassRepresentationController method updateVue.

@Override
public void updateVue(Observable obs, Object value) {
    // TODO Auto-generated method stub
    if (obs.getClass().equals(RenameClassSchemeController.class)) {
        renameClass((String) value);
    }
    if (obs.getClass().equals(ChangeColorClassSchemeController.class)) {
        setColor((String) value);
    }
    if (obs.getClass().equals(AddPropertySchemeController.class)) {
        Property n = new Property(((Property) value).getName());
        boolean contain = false;
        for (Type t : classe.getTypes()) {
            if (t.getName().equals(n.getName())) {
                contain = true;
                break;
            }
        }
        if (!this.classe.getTypes().contains(n)) {
            addProperty((Property) n);
        } else {
        // System.out.println("AH BAH VOILA !!!!!");
        }
    }
    if (obs.getClass().equals(RemovePropertySchemeController.class)) {
        Property toRemove = (Property) value;
        // System.out.println("Remove dans TypeClassRpzCtrl "+toRemove.getName());
        RemoveProperty(toRemove);
    }
    if (obs.getClass().equals(AddPropertySchemeWithValueController.class)) {
        addProperty(stack.pop());
    }
    if (obs.getClass().equals(RemoveClassSchemeController.class)) {
        // System.out.println("DELETINGCLASS");
        moment.removeTypeClassRep(this);
    }
    if (obs.getClass().equals(AddClassSchemeController.class)) {
        // System.out.println("REPUTINGCLASS");
        moment.putPreviousClassRep();
    }
}