Examples with Section org.hl7.fhir.utilities.turtle.Turtle.Section used on opensource projects

Example 61 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method processAllergiesSection.

private void processAllergiesSection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
    scanSection("Allergies", section);
    ListResource list = new ListResource();
    list.setId(context.getBaseId() + "-list-allergies");
    list.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/list-daf-dafallergylist");
    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.setDateElement(context.getNow());
    list.setSource(context.getAuthorRef());
    list.setMode(ListMode.SNAPSHOT);
    buildNarrative(list, cda.getChild(section, "text"));
    int i = 0;
    for (Element c : cda.getChildren(section, "entry")) {
        // allergy problem act
        Element apa = cda.getChild(c, "act");
        AllergyIntolerance ai = new AllergyIntolerance();
        ai.setId(context.getBaseId() + "-allergy-" + i);
        ai.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/allergyintolerance-daf-dafallergyintolerance");
        i++;
        ai.setPatient(context.getSubjectRef());
        ai.setAssertedDateElement(convert.makeDateTimeFromTS(cda.getChild(cda.getChild(apa, "effectiveTime"), "low")));
        boolean found = false;
        for (Element e : cda.getChildren(apa, "id")) {
            Identifier id = convert.makeIdentifierFromII(e);
            ai.getIdentifier().add(id);
        }
        if (!found) {
            list.addEntry().setItem(new Reference().setReference("AllergyIntolerance/" + ai.getId()));
            // allergy observation
            Element ao = cda.getChild(cda.getChild(apa, "entryRelationship"), "observation");
            if (!cda.getChild(ao, "value").getAttribute("code").equals("419511003"))
                throw new Error("unexpected code");
            // nothing....
            // no allergy status observation
            List<Element> reactions = cda.getChildren(ao, "entryRelationship");
            Element pe = cda.getChild(cda.getChild(cda.getChild(ao, "participant"), "participantRole"), "playingEntity");
            Element pec = cda.getChild(pe, "code");
            if (pec == null || !Utilities.noString(pec.getAttribute("nullFlavor"))) {
                String n = cda.getChild(pe, "name").getTextContent();
                // if (n.contains("No Known Drug Allergies") && reactions.isEmpty())
                // ai.setSubstance(new CodeableConcept().setText(n)); // todo: what do with this?
                // else
                ai.setCode(new CodeableConcept().setText(n));
            } else
                ai.setCode(inspectCode(convert.makeCodeableConceptFromCD(pec), null));
            recordAllergyCode(ai.getCode());
            if (!reactions.isEmpty()) {
                AllergyIntoleranceReactionComponent aie = ai.addReaction();
                for (Element er : reactions) {
                    Element ro = cda.getChild(er, "observation");
                    aie.addManifestation(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(ro, "value")), null));
                }
            }
            saveResource(ai);
        }
    }
    saveResource(list);
}

Example 62 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method processImmunizationsSection.

private void processImmunizationsSection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
    scanSection("Immunizations", section);
    ListResource list = new ListResource();
    list.setId(context.getBaseId() + "-list-immunizations");
    list.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/list-daf-dafimmunizationlist");
    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");
        Immunization imm = new Immunization();
        imm.setId(context.getBaseId() + "-immunization-" + i);
        imm.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/immunization-daf-dafimmunization");
        i++;
        imm.setPatient(context.getSubjectRef());
        imm.setEncounter(new Reference().setReference("Encounter/" + context.getEncounter().getId()));
        imm.setNotGiven("true".equals(sa.getAttribute("negationInd")));
        imm.setStatus(convertImmunizationStatus(cda.getChild(sa, "statusCode")));
        boolean found = false;
        for (Element e : cda.getChildren(sa, "id")) {
            Identifier id = convert.makeIdentifierFromII(e);
            imm.getIdentifier().add(id);
        }
        if (!found) {
            list.addEntry().setItem(new Reference().setReference("Immunization/" + imm.getId()));
            imm.setDateElement(convert.makeDateTimeFromTS(cda.getChild(cda.getChild(sa, "effectiveTime"), "low")));
            if (imm.getNotGiven()) {
                Element reason = cda.getChild(cda.getChildByAttribute(sa, "entryRelationship", "typeCode", "RSON"), "observation");
                imm.setExplanation(new ImmunizationExplanationComponent());
                imm.getExplanation().addReasonNotGiven(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(reason, "code")), null));
            }
            Element mm = cda.getChild(cda.getChild(cda.getChild(sa, "consumable"), "manufacturedProduct"), "manufacturedMaterial");
            imm.setVaccineCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(mm, "code")), null));
            imm.setRoute(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(sa, "routeCode")), null));
            if (cda.getChild(mm, "lotNumberText") != null)
                imm.setLotNumber(cda.getChild(mm, "lotNumberText").getTextContent());
            Element mr = cda.getChild(cda.getChild(cda.getChild(sa, "consumable"), "manufacturedProduct"), "manufacturerOrganization");
            if (mr != null)
                imm.setManufacturer(new Reference().setDisplay(cda.getChild(mr, "name").getTextContent()));
            // the problem with this is that you can't have just a dose sequence number
            // Element subject = cda.getChild(cda.getChildByAttribute(sa, "entryRelationship", "typeCode", "SUBJ"), "observation");
            // if (subject != null)
            // imm.addVaccinationProtocol().setDoseSequence(Integer.parseInt(cda.getChild(subject, "value").getAttribute("value")));
            boolean hasprf = false;
            for (Element e : cda.getChildren(sa, "performer")) {
                if (imm.hasPractitioner())
                    throw new Error("additional performer discovered");
                Practitioner p = processPerformer(cda, convert, context, e, "assignedEntity", "assignedPerson");
                Reference ref = new Reference().setReference("Practitioner/" + p.getId()).setDisplay(p.getUserString("display"));
                imm.addPractitioner().setActor(ref).setRole(new org.hl7.fhir.dstu3.model.CodeableConcept().addCoding(new Coding().setSystem("http://hl7.org/fhir/v2/0443").setCode("AP")));
                hasprf = true;
            }
            imm.setPrimarySource(hasprf);
            saveResource(imm);
        }
    }
    saveResource(list);
}

Example 63 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method convert.

private void convert(String sourceFolder, String filename, Coding clss) throws IOException {
    if (new File(Utilities.path(sourceFolder, filename)).length() == 0)
        return;
    CDAUtilities cda;
    try {
        System.out.println("Process " + Utilities.path(sourceFolder, filename));
        cda = new CDAUtilities(new FileInputStream(Utilities.path(sourceFolder, filename)));
        zipJ = new ZipGenerator(Utilities.path(destFolder, "json/doc", Utilities.changeFileExt(filename, ".json.zip")));
        zipX = new ZipGenerator(Utilities.path(destFolder, "xml/doc", Utilities.changeFileExt(filename, ".xml.zip")));
        Element doc = cda.getElement();
        Convert convert = new Convert(cda, ucumSvc, "-0400");
        convert.setGenerateMissingExtensions(true);
        Context context = new Context();
        context.setBaseId(Utilities.changeFileExt(filename, ""));
        context.setEncClass(clss);
        makeSubject(cda, convert, doc, context, context.getBaseId() + "-patient");
        makeAuthor(cda, convert, doc, context, context.getBaseId() + "-author");
        makeEncounter(cda, convert, doc, context, context.getBaseId() + "-encounter");
        Element body = cda.getDescendent(doc, "component/structuredBody");
        for (Element c : cda.getChildren(body, "component")) {
            processSection(cda, convert, context, cda.getChild(c, "section"));
        }
        oids.addAll(convert.getOids());
        saveResource(context.getEncounter());
        makeBinary(sourceFolder, filename, context);
        makeDocumentReference(cda, convert, doc, context);
        zipJ.close();
        zipX.close();
    } catch (Exception e) {
        throw new Error("Unable to process " + Utilities.path(sourceFolder, filename) + ": " + e.getMessage(), e);
    }
}

Example 64 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processSocialHistorySection.

protected SectionComponent processSocialHistorySection(Element section) throws Exception {
    ListResource list = new ListResource();
    for (Element entry : cda.getChildren(section, "entry")) {
        Element observation = cda.getlastChild(entry);
        if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.22.4.38")) {
            processSocialObservation(list, observation, SocialHistoryType.SocialHistory);
        } else if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.15.3.8")) {
            processSocialObservation(list, observation, SocialHistoryType.Pregnancy);
        } else if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.22.4.78")) {
            processSocialObservation(list, observation, SocialHistoryType.SmokingStatus);
        } else if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.22.4.85")) {
            processSocialObservation(list, observation, SocialHistoryType.TobaccoUse);
        } else
            throw new Exception("Unhandled Section template ids: " + cda.showTemplateIds(observation));
    }
    // todo: text
    SectionComponent s = new Composition.SectionComponent();
    s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
    // todo: check subject
    s.addEntry(Factory.makeReference(addReference(list, "Procedures", makeUUIDReference())));
    return s;
}

Example 65 with Section

use of org.hl7.fhir.utilities.turtle.Turtle.Section in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processProceduresSection.

protected SectionComponent processProceduresSection(Element section) throws Exception {
    ListResource list = new ListResource();
    for (Element entry : cda.getChildren(section, "entry")) {
        Element procedure = cda.getlastChild(entry);
        if (cda.hasTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.14")) {
            processProcedure(list, procedure, ProcedureType.Procedure);
        } else if (cda.hasTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.13")) {
            processProcedure(list, procedure, ProcedureType.Observation);
        } else if (cda.hasTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.12")) {
            processProcedure(list, procedure, ProcedureType.Act);
        } else
            throw new Exception("Unhandled Section template ids: " + cda.showTemplateIds(procedure));
    }
    // todo: text
    SectionComponent s = new Composition.SectionComponent();
    s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
    // todo: check subject
    s.addEntry(Factory.makeReference(addReference(list, "Procedures", makeUUIDReference())));
    return s;
}