Examples with ListResource org.hl7.fhir.r5.model.ListResource used on opensource projects

Example 11 with ListResource

use of org.hl7.fhir.r5.model.ListResource in project integration-adaptor-111 by nhsconnect.

the class ListMapperTest method shouldMapList.

@Test
public void shouldMapList() {
    ListResource listResource = listMapper.mapList(clinicalDocument, encounter, resourcesCreated, deviceRef);
    assertThat(listResource.getStatus()).isEqualTo(CURRENT);
    assertThat(listResource.getTitle()).isEqualTo("111 Report List");
    assertThat(listResource.getMode()).isEqualTo(WORKING);
    Coding orderByCode = listResource.getOrderedBy().getCodingFirstRep();
    assertThat(orderByCode.getSystem()).isEqualTo("http://hl7.org/fhir/list-order");
    assertThat(orderByCode.getCode()).isEqualTo("event-date");
    assertThat(orderByCode.getDisplay()).isEqualTo("Sorted by Event Date");
    Coding code = listResource.getCode().getCodingFirstRep();
    assertThat(code.getSystem()).isEqualTo("http://snomed.info/sct");
    assertThat(code.getCode()).isEqualTo("225390008");
    assertThat(code.getDisplay()).isEqualTo("Triage");
    assertThat(listResource.getEntry().size()).isEqualTo(1);
    assertThat(listResource.getIdElement().getValue()).isEqualTo(RANDOM_UUID);
    assertThat(deviceRef).isEqualTo(listResource.getSource());
    assertThat(listResource.getDateElement().getValue()).isEqualTo(DateUtil.parse(effectiveTime.getValue()).getValue());
}

Example 12 with ListResource

use of org.hl7.fhir.r5.model.ListResource in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processAllergyProblemAct.

protected void processAllergyProblemAct(ListResource list, Element concern) throws Exception {
    cda.checkTemplateId(concern, "2.16.840.1.113883.10.20.22.4.30");
    // Allergy Problem Act - this is a concern - we treat the concern as information about it's place in the list
    checkNoNegationOrNullFlavor(concern, "Allergy Problem Act");
    checkNoSubject(concern, "Allergy Problem Act");
    // SHALL contain exactly one [1..1] Allergy - intolerance Observation
    for (Element entry : cda.getChildren(concern, "entryRelationship")) {
        Element obs = cda.getChild(entry, "observation");
        cda.checkTemplateId(obs, "2.16.840.1.113883.10.20.22.4.7");
        checkNoNegationOrNullFlavor(obs, "Allergy - intolerance Observation");
        checkNoSubject(obs, "Allergy Problem Act");
        AllergyIntolerance ai = new AllergyIntolerance();
        ListEntryComponent item = addItemToList(list, ai);
        // SHALL contain at least one [1..*] id (CONF:7472).
        for (Element e : cda.getChildren(concern, "id")) ai.getIdentifier().add(convert.makeIdentifierFromII(e));
        // SHALL contain exactly one [1..1] statusCode, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.80.68 HITSPProblemStatus DYNAMIC (CONF:7485)
        // the status code is about the concern (e.g. the entry in the list)
        // possible values: active, suspended, aborted, completed, with an effective time
        String s = cda.getStatus(concern);
        item.setFlag(Factory.newCodeableConcept(s, "http://hl7.org/fhir/v3/ActStatus", s));
        if (// only on this condition?
        s.equals("aborted"))
            item.setDeleted(true);
        // SHALL contain exactly one [1..1] effectiveTime (CONF:7498)
        Period p = convert.makePeriodFromIVL(cda.getChild(concern, "effectiveTime"));
        item.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/list-period", p, false));
        if (p.getEnd() != null)
            item.setDate(p.getEnd());
        else
            item.setDate(p.getStart());
        // SHALL contain at least one [1..*] id (CONF:7382)
        for (Element e : cda.getChildren(obs, "id")) ai.getIdentifier().add(convert.makeIdentifierFromII(e));
        // SHALL contain exactly one [1..1] effectiveTime (CONF:7387)
        ai.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/allergyintolerance-period", convert.makePeriodFromIVL(cda.getChild(obs, "effectiveTime")), false));
        // SHALL contain exactly one [1..1] value with @xsi:type="CD" (CONF:7390)
        CodeableConcept type = convert.makeCodeableConceptFromCD(cda.getChild(obs, "value"));
        // This value SHALL contain @code, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.3221.6.2 Allergy/Adverse Event Type
        String ss = type.getCoding().get(0).getCode();
        if (ss.equals("416098002") || ss.equals("414285001"))
            ai.setType(AllergyIntoleranceType.ALLERGY);
        else if (ss.equals("59037007") || ss.equals("235719002"))
            ai.setType(AllergyIntoleranceType.INTOLERANCE);
        ai.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/allergy-category", type, false));
        // SHOULD contain zero or one [0..1] participant (CONF:7402) such that it
        // ......This playingEntity SHALL contain exactly one [1..1] code
        ai.setCode(convert.makeCodeableConceptFromCD(cda.getDescendent(obs, "participant/participantRole/playingEntity/code")));
        // SHOULD contain zero or more [0..*] entryRelationship (CONF:7447) such that it SHALL contain exactly one [1..1] Reaction Observation (templateId:2.16.840.1.113883.10.20.22.4.9) (CONF:7450).
        for (Element e : cda.getChildren(obs, "entryRelationship")) {
            Element child = cda.getChild(e, "observation");
            if (cda.hasTemplateId(child, "2.16.840.1.113883.10.20.22.4.28") && ai.getClinicalStatus() == null) {
                // SHALL contain exactly one [1..1] value with @xsi:type="CE", where the @code SHALL be selected from ValueSet Problem Status Value Set 2.16.840.1.113883.3.88.12.80.68 DYNAMIC (CONF:7322).
                // 55561003  SNOMED CT  Active
                // 73425007  SNOMED CT  Inactive
                // 413322009  SNOMED CT  Resolved
                String sc = cda.getChild(child, "value").getAttribute("code");
                if (sc.equals("55561003")) {
                    ai.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
                    ai.setVerificationStatus(AllergyIntoleranceVerificationStatus.CONFIRMED);
                } else
                    ai.setClinicalStatus(AllergyIntoleranceClinicalStatus.RESOLVED);
            } else if (cda.hasTemplateId(child, "2.16.840.1.113883.10.20.22.4.9")) {
                ai.getReaction().add(processAdverseReactionObservation(child));
            }
        }
        // SHOULD contain zero or one [0..1] entryRelationship (CONF:9961) such that it SHALL contain exactly one [1..1] Severity Observation (templateId:2.16.840.1.113883.10.20.22.4.8) (CONF:9963).
        ai.setCriticality(readCriticality(cda.getSeverity(obs)));
    }
}

Example 13 with ListResource

use of org.hl7.fhir.r5.model.ListResource in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processProcedure.

protected void processProcedure(ListResource list, Element procedure, ProcedureType type) throws Exception {
    switch(type) {
        case Procedure:
            cda.checkTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.14");
            break;
        case Observation:
            cda.checkTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.13");
            break;
        case Act:
            cda.checkTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.12");
    }
    checkNoNegationOrNullFlavor(procedure, "Procedure (" + type + ")");
    checkNoSubject(procedure, "Procedure (" + type + ")");
    Procedure p = new Procedure();
    addItemToList(list, p);
    // moodCode is either INT or EVN. INT is not handled yet. INT is deprecated anyway
    if (procedure.getAttribute("moodCode").equals("INT"))
        p.getModifierExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-planned", Factory.newBoolean(true), false));
    // SHALL contain at least one [1..*] id (CONF:7655).
    for (Element e : cda.getChildren(procedure, "id")) p.getIdentifier().add(convert.makeIdentifierFromII(e));
    // SHALL contain exactly one [1..1] code (CONF:7656).
    // This code @code in a procedure activity SHOULD be selected from LOINC or SNOMED CT and MAY be selected from CPT-4, ICD9 Procedures, ICD10 Procedures
    p.setCode(convert.makeCodeableConceptFromCD(cda.getChild(procedure, "code")));
    // SHALL contain exactly one [1..1] statusCode/@code, which SHALL be selected from ValueSet 2.16.840.1.113883.11.20.9.22 ProcedureAct
    // completed | active | aborted | cancelled - not in FHIR
    p.getModifierExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-status", Factory.newCode(cda.getStatus(procedure)), false));
    // SHOULD contain zero or one [0..1] effectiveTime (CONF:7662).
    p.setPerformed(convert.makePeriodFromIVL(cda.getChild(procedure, "effectiveTime")));
    // MAY contain zero or one [0..1] priorityCode/@code, which SHALL be selected from ValueSet 2.16.840.1.113883.1.11.16866 ActPriority DYNAMIC (CONF:7668)
    p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-priority", convert.makeCodeableConceptFromCD(cda.getChild(procedure, "priorityCode")), false));
    // MAY contain zero or one [0..1] methodCode (CONF:7670).
    p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-method", convert.makeCodeableConceptFromCD(cda.getChild(procedure, "methodCode")), false));
    if (type == ProcedureType.Observation) {
    // for Procedure-Observation:
    // 9.	SHALL contain exactly one [1..1] value (CONF:16846).
    // don't know what this is. It's not the actual result of the procedure (that goes in results "This section records ... procedure observations"), and there seems to be no value. The example as <value xsi:type="CD"/> which is not valid
    // so we ignore this for now
    }
    // SHOULD contain zero or more [0..*] targetSiteCode/@code, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.3221.8.9 Body site DYNAMIC (CONF:7683).
    for (Element e : cda.getChildren(procedure, "targetSiteCode")) p.addBodySite(convert.makeCodeableConceptFromCD(e));
    // SHOULD contain zero or more [0..*] performer (CONF:7718) such that it
    for (Element e : cda.getChildren(procedure, "performer")) {
        ProcedurePerformerComponent pp = new ProcedurePerformerComponent();
        p.getPerformer().add(pp);
        pp.setActor(makeReferenceToPractitionerForAssignedEntity(e, p));
    }
    for (Element participant : cda.getChildren(procedure, "participant")) {
        Element participantRole = cda.getlastChild(participant);
        if (type == ProcedureType.Procedure && cda.hasTemplateId(participantRole, "2.16.840.1.113883.10.20.22.4.37")) {
            // MAY contain zero or more [0..*] participant (CONF:7751) such that it  SHALL contain exactly one [1..1] @typeCode="DEV" Device
            // implanted devices
            p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/implanted-devices", Factory.makeReference(processDevice(participantRole, p)), false));
        } else if (cda.hasTemplateId(participantRole, "2.16.840.1.113883.10.20.22.4.32")) {
            // MAY contain zero or more [0..*] participant (CONF:7765) such that it SHALL contain exactly one [1..1] Service Delivery Location (templateId:2.16.840.1.113883.10.20.22.4.32) (CONF:7767)
            p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/location", Factory.makeReference(processSDLocation(participantRole, p)), false));
        }
    }
    for (Element e : cda.getChildren(procedure, "entryRelationship")) {
        Element a = /* act*/
        cda.getlastChild(e);
        if (a.getLocalName().equals("encounter")) {
        // MAY contain zero or more [0..*] entryRelationship (CONF:7768) such that it SHALL contain exactly one encounter which SHALL contain exactly one [1..1] id (CONF:7773).
        // todo - and process as a full encounter while we're at it
        } else if (cda.hasTemplateId(a, "2.16.840.1.113883.10.20.22.4.20")) {
            // MAY contain zero or one [0..1] entryRelationship (CONF:7775) such that it SHALL contain exactly one [1..1] Instructions (templateId:2.16.840.1.113883.10.20.22.4.20) (CONF:7778).
            // had code for type, plus text for instructions
            Extension n = Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-instructions", null, true);
            n.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-instructions-type", convert.makeCodeableConceptFromCD(cda.getChild(a, "code")), false));
            n.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-instructions-text", convert.makeStringFromED(cda.getChild(a, "text")), false));
            p.getExtension().add(n);
        } else if (cda.hasTemplateId(a, "2.16.840.1.113883.10.20.22.4.19")) {
            // MAY contain zero or more [0..*] entryRelationship (CONF:7779) such that it SHALL contain exactly one [1..1] Indication (templateId:2.16.840.1.113883.10.20.22.4.19) (CONF:7781).
            p.addReasonCode(processIndication(a));
        } else if (cda.hasTemplateId(cda.getlastChild(e), "2.16.840.1.113883.10.20.22.4.16")) {
        // MAY contain zero or one [0..1] entryRelationship (CONF:7886) such that it SHALL contain exactly one [1..1] Medication Activity (templateId:2.16.840.1.113883.10.20.22.4.16) (CONF:7888).
        // todo
        }
    }
}

Example 14 with ListResource

use of org.hl7.fhir.r5.model.ListResource in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processSocialObservation.

protected void processSocialObservation(ListResource list, Element so, SocialHistoryType type) throws Exception {
    Observation obs = new Observation();
    addItemToList(list, obs);
    switch(type) {
        case SocialHistory:
            cda.checkTemplateId(so, "2.16.840.1.113883.10.20.22.4.38");
            // SHALL contain exactly one [1..1] code (CONF:8558/).
            obs.setCode(convert.makeCodeableConceptFromCD(cda.getChild(so, "code")));
            break;
        case Pregnancy:
            cda.checkTemplateId(so, "2.16.840.1.113883.10.20.15.3.8");
            // SHALL contain exactly one [1..1] code (CONF:8558/), which SHALL be an assertion
            obs.setCode(Factory.newCodeableConcept("11449-6", "http://loinc.org", "Pregnancy Status"));
            break;
        case SmokingStatus:
            cda.checkTemplateId(so, "2.16.840.1.113883.10.20.22.4.78");
            // SHALL contain exactly one [1..1] code (CONF:8558/), which SHALL be an assertion
            obs.setCode(Factory.newCodeableConcept("72166-2", "http://loinc.org", "Tobacco Smoking Status"));
            break;
        case TobaccoUse:
            cda.checkTemplateId(so, "2.16.840.1.113883.10.20.22.4.12");
            // SHALL contain exactly one [1..1] code (CONF:8558/), which SHALL be an assertion
            obs.setCode(Factory.newCodeableConcept("11367-0", "http://loinc.org", "History of Tobacco Use"));
    }
    // SHALL contain at least one [1..*] id (8551).
    for (Element e : cda.getChildren(so, "id")) obs.getIdentifier().add(convert.makeIdentifierFromII(e));
    // SHALL contain exactly one [1..1] statusCode (CONF:8553/455/14809).
    // a.	This statusCode SHALL contain exactly one [1..1] @code="completed" Completed (CodeSystem: ActStatus 2.16.840.1.113883.5.14 STATIC) (CONF:19117).
    obs.setStatus(ObservationStatus.FINAL);
    // SHOULD contain zero or one [0..1] effectiveTime (CONF:2018/14814).
    // for smoking status/tobacco: low only. in R2, this is just value. So we treat low only as just a value
    Element et = cda.getChild(so, "effectiveTime");
    if (et != null) {
        if (cda.getChild(et, "low") != null)
            obs.setEffective(convert.makeDateTimeFromTS(cda.getChild(et, "low")));
        else
            obs.setEffective(convert.makeDateTimeFromIVL(et));
    }
    // a.	Observation/value can be any data type.
    for (Element e : cda.getChildren(so, "value")) if (obs.getValue() == null) {
        // special case for pregnancy:
        if (type == SocialHistoryType.Pregnancy && "true".equals(e.getAttribute("negationInd"))) {
            obs.setValue(Factory.newCodeableConcept("60001007", "http://snomed.info/sct", "Not pregnant"));
        } else {
            // negationInd is not described. but it might well be used. For now, we blow up
            checkNoNegation(so, "Social Observation (" + type + ")");
            if (so.hasAttribute("nullFlavor"))
                obs.setValue(convert.makeCodeableConceptFromNullFlavor(so.getAttribute("nullFlavor")));
            else if (e.hasAttribute("nullFlavor") && !"OTH".equals(e.getAttribute("nullFlavor")))
                obs.setValue(convert.makeCodeableConceptFromNullFlavor(e.getAttribute("nullFlavor")));
            else
                obs.setValue(convert.makeTypeFromANY(e));
        }
    } else
        throw new Exception("too many values on Social Observation");
    if (type == SocialHistoryType.Pregnancy) {
        for (Element e : cda.getChildren(so, "entyRelationship")) {
            Element dd = cda.getChild(e, "observation");
            checkNoNegationOrNullFlavor(dd, "Estimated Date of Delivery");
            // MAY contain zero or one [0..1] entryRelationship (CONF:458) such that it
            // SHALL contain exactly one [1..1] @typeCode="REFR" Refers to (CodeSystem: HL7ActRelationshipType 2.16.840.1.113883.5.1002 STATIC) (CONF:459).
            // SHALL contain exactly one [1..1] Estimated Date of Delivery (templateId:2.16.840.1.113883.10.20.15.3.1) (CONF:15584).
            Observation co = new Observation();
            String id = nextRef();
            co.setId(id);
            obs.getContained().add(co);
            ObservationRelatedComponent or = new ObservationRelatedComponent();
            obs.getRelated().add(or);
            or.setType(ObservationRelationshipType.HASMEMBER);
            or.setTarget(Factory.makeReference("#" + id));
            co.setCode(Factory.newCodeableConcept("11778-8", "http://loinc.org", "Delivery date Estimated"));
            // not legal, see gForge http://gforge.hl7.org/gf/project/fhir/tracker/?action=TrackerItemEdit&tracker_item_id=3125&start=0
            co.setValue(convert.makeDateTimeFromTS(cda.getChild(dd, "value")));
        }
    }
}

Example 15 with ListResource

use of org.hl7.fhir.r5.model.ListResource in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method processMedicationsSection.

private void processMedicationsSection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
    scanSection("Medications", section);
    ListResource list = new ListResource();
    list.setId(context.getBaseId() + "-list-medications");
    list.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/list-daf-dafmedicationlist");
    list.setSubject(context.getSubjectRef());
    list.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")), null));
    list.setTitle(cda.getChild(section, "title").getTextContent());
    list.setStatus(ListStatus.CURRENT);
    list.setMode(ListMode.SNAPSHOT);
    list.setDateElement(context.getNow());
    list.setSource(context.getAuthorRef());
    buildNarrative(list, cda.getChild(section, "text"));
    int i = 0;
    for (Element c : cda.getChildren(section, "entry")) {
        // allergy problem act
        Element sa = cda.getChild(c, "substanceAdministration");
        MedicationStatement ms = new MedicationStatement();
        ms.setId(context.getBaseId() + "-medication-" + i);
        ms.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/medicationstatement-daf-dafmedicationstatement");
        i++;
        ms.setSubject(context.getSubjectRef());
        boolean found = false;
        for (Element e : cda.getChildren(sa, "id")) {
            Identifier id = convert.makeIdentifierFromII(e);
            ms.getIdentifier().add(id);
        }
        if (!found) {
            ms.setStatus(MedicationStatementStatus.COMPLETED);
            list.addEntry().setItem(new Reference().setReference("MedicationStatement/" + ms.getId()));
            // allergy observation
            Element mm = cda.getChild(cda.getChild(cda.getChild(sa, "consumable"), "manufacturedProduct"), "manufacturedMaterial");
            ms.setMedication(new Reference().setReference("#med"));
            Medication med = new Medication();
            med.setId("med");
            med.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(mm, "code")), null));
            ms.getContained().add(med);
            Dosage dosage = ms.addDosage();
            // allergy observation
            Element qty = cda.getChild(sa, "doseQuantity");
            try {
                if (cda.getChild(qty, "low") != null) {
                    // todo: this is not correct?
                    dosage.getExtension().add(new Extension().setUrl("http://healthintersections.com.au/fhir/extensions/medication-statement-range").setValue(convert.makeRangeFromIVLPQ(qty)));
                } else {
                    dosage.setDose(convert.makeQuantityFromPQ(qty));
                }
            } catch (Exception e) {
                System.out.println("  invalid dose quantity '" + qty.getAttribute("value") + " " + qty.getAttribute("unit") + "' (" + e.getClass().getName() + ") in " + context.getBaseId());
            }
            dosage.setRoute(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(sa, "routeCode")), null));
            Type t = convert.makeSomethingFromGTS(cda.getChildren(sa, "effectiveTime"));
            if (t instanceof Timing) {
                dosage.setTiming((Timing) t);
                if (dosage.getTiming().hasRepeat() && dosage.getTiming().getRepeat().hasBounds())
                    ms.setEffective(dosage.getTiming().getRepeat().getBounds());
            } else if (t instanceof Period)
                ms.setEffective(t);
            else
                throw new Exception("Undecided how to handle " + t.getClass().getName());
            for (Element e : cda.getChildren(sa, "author")) {
                if (ms.hasInformationSource())
                    throw new Error("additional author discovered");
                Practitioner p = processPerformer(cda, convert, context, e, "assignedAuthor", "assignedPerson");
                Reference ref = new Reference().setReference("Practitioner/" + p.getId()).setDisplay(p.getUserString("display"));
                ms.setInformationSource(ref);
                ms.setDateAssertedElement(convert.makeDateTimeFromTS(cda.getChild(e, "time")));
            }
            saveResource(ms);
        }
    }
    saveResource(list);
}