Examples with ValueSet org.hl7.fhir.r4.model.ValueSet used on opensource projects

Example 91 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project org.hl7.fhir.core by hapifhir.

the class ICD11Generator method processMMSEntity.

private void processMMSEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
    System.out.print(".");
    JsonObject entity = fetchJson(url(base, ref));
    cc.setId(tail(ref));
    if (entity.has("code") && !Utilities.noString(entity.get("code").getAsString())) {
        cc.setCode(entity.get("code").getAsString());
    } else if (entity.has("blockId") && !Utilities.noString(entity.get("blockId").getAsString())) {
        cc.setCode(entity.get("blockId").getAsString());
    } else {
        cc.setCode(cc.getId());
        cc.addProperty().setCode("abstract").setValue(new BooleanType(true));
    }
    if (entity.has("classKind") && !Utilities.noString(entity.get("classKind").getAsString()) && !"category".equals(entity.get("classKind").getAsString())) {
        cc.addProperty().setCode("kind").setValue(new CodeType(entity.get("classKind").getAsString()));
    }
    cc.setDisplay(readString(entity, "title"));
    StringBuilder defn = new StringBuilder();
    String d = readString(entity, "definition");
    if (d != null) {
        defn.append(d);
    }
    if (d == null && (entity.has("inclusion") || entity.has("exclusion"))) {
        defn.append(cc.getDisplay());
    }
    if (entity.has("inclusion")) {
        defn.append(". Includes: ");
        boolean first = true;
        for (JsonElement child : entity.getAsJsonArray("inclusion")) {
            if (first)
                first = false;
            else
                defn.append(", ");
            defn.append(readString((JsonObject) child, "label"));
        }
    }
    if (entity.has("exclusion")) {
        defn.append(". Excludes: ");
        boolean first = true;
        for (JsonElement child : entity.getAsJsonArray("exclusion")) {
            if (first)
                first = false;
            else
                defn.append(", ");
            JsonObject co = (JsonObject) child;
            String v = readString(co, "label");
            if (v != null) {
                defn.append(v);
                if (co.has("linearizationReference")) {
                    cc.addProperty().setValue(new Coding().setSystem("http://id.who.int/icd11/mms").setCode(tail(co.get("linearizationReference").getAsString())).setDisplay(v)).setCode("exclusion");
                }
            }
        }
    }
    cc.setDefinition(defn.toString());
    addDesignation(readString(entity, "longDefinition"), cc, "http://id.who.int/icd11/mms/designation", "longDefinition");
    addDesignation(readString(entity, "fullySpecifiedName"), cc, "http://snomed.info/sct", "900000000000003001");
    addProperty(readString(entity, "codingNote"), cc, "codingNote");
    if (entity.has("indexTerm")) {
        // }
        for (JsonElement child : entity.getAsJsonArray("indexTerm")) {
            processIndexTerm(cc, (JsonObject) child);
        }
    }
    if (entity.has("postcoordinationScale")) {
        for (JsonElement child : entity.getAsJsonArray("postcoordinationScale")) {
            JsonObject o = (JsonObject) child;
            String name = tail(o.get("axisName").getAsString());
            ConceptPropertyComponent prop = cc.addProperty();
            prop.setCode("postcoordinationScale");
            prop.setValue(new CodeType(name));
            ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/required", o.get("requiredPostcoordination").getAsBoolean());
            ToolingExtensions.addBooleanExtension(prop, "http://id.who.int/icd11/extensions/repeats", o.get("allowMultipleValues").getAsBoolean());
            if (o.has("scaleEntity")) {
                ToolingExtensions.addUriExtension(prop, "http://id.who.int/icd11/extensions/valueSet", buildValueSet(cs, cc.getCode(), name, o, dest));
            }
        }
    }
    if (entity.has("child")) {
        for (JsonElement child : entity.getAsJsonArray("child")) {
            processMMSEntity(cs, base, child.getAsString(), cc.addConcept(), dest);
        }
    }
}

Example 92 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method generateComposition.

private boolean generateComposition(XhtmlNode x, ValueSet vs, boolean header) {
    boolean hasExtensions = false;
    if (!vs.hasCodeSystem()) {
        if (header) {
            XhtmlNode h = x.addTag("h2");
            h.addText(vs.getName());
            XhtmlNode p = x.addTag("p");
            smartAddText(p, vs.getDescription());
            if (vs.hasCopyrightElement())
                generateCopyright(x, vs);
        }
        XhtmlNode p = x.addTag("p");
        p.addText("This value set includes codes from the following code systems:");
    } else {
        XhtmlNode p = x.addTag("p");
        p.addText("In addition, this value set includes codes from other code systems:");
    }
    XhtmlNode ul = x.addTag("ul");
    XhtmlNode li;
    for (UriType imp : vs.getCompose().getImport()) {
        li = ul.addTag("li");
        li.addText("Import all the codes that are contained in ");
        AddVsRef(imp.getValue(), li);
    }
    for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
        hasExtensions = genInclude(ul, inc, "Include") || hasExtensions;
    }
    for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
        hasExtensions = genInclude(ul, exc, "Exclude") || hasExtensions;
    }
    return hasExtensions;
}

Example 93 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method countMembership.

private Integer countMembership(ValueSet vs) {
    int count = 0;
    if (vs.hasExpansion())
        count = count + conceptCount(vs.getExpansion().getContains());
    else {
        if (vs.hasCodeSystem())
            count = count + countConcepts(vs.getCodeSystem().getConcept());
        if (vs.hasCompose()) {
            if (vs.getCompose().hasExclude()) {
                try {
                    ValueSetExpansionOutcome vse = context.expandVS(vs, true);
                    count = 0;
                    count += conceptCount(vse.getValueset().getExpansion().getContains());
                    return count;
                } catch (Exception e) {
                    return null;
                }
            }
            for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
                if (inc.hasFilter())
                    return null;
                if (!inc.hasConcept())
                    return null;
                count = count + inc.getConcept().size();
            }
        }
    }
    return count;
}

Example 94 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method expandVS.

@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk) {
    try {
        Map<String, String> params = new HashMap<String, String>();
        params.put("_limit", "10000");
        params.put("_incomplete", "true");
        params.put("profile", "http://www.healthintersections.com.au/fhir/expansion/no-details");
        ValueSet result = txServer.expandValueset(vs, null, params);
        return new ValueSetExpansionOutcome(result);
    } catch (Exception e) {
        return new ValueSetExpansionOutcome("Error expanding ValueSet \"" + vs.getUrl() + ": " + e.getMessage());
    }
}

Example 95 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method validateCode.

@Override
public ValidationResult validateCode(String system, String code, String display, ConceptSetComponent vsi) {
    try {
        ValueSet vs = new ValueSet().setUrl(Utilities.makeUuidUrn());
        vs.getCompose().addInclude(vsi);
        return verifyCodeExternal(vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
    } catch (Exception e) {
        return new ValidationResult(IssueSeverity.FATAL, "Error validating code \"" + code + "\" in system \"" + system + "\": " + e.getMessage());
    }
}