Examples with ConceptSetComponent org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent used on opensource projects

Example 96 with ConceptSetComponent

use of org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method getIncSummary.

private String getIncSummary(ConceptSetComponent cc) {
    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
    for (UriType vs : cc.getValueSet()) {
        b.append(vs.asStringValue());
    }
    String vsd = b.length() > 0 ? " where the codes are in the value sets (" + b.toString() + ")" : "";
    String system = cc.getSystem();
    if (cc.hasConcept()) {
        return Integer.toString(cc.getConcept().size()) + " codes from " + system + vsd;
    }
    if (cc.hasFilter()) {
        String s = "";
        for (ConceptSetFilterComponent f : cc.getFilter()) {
            if (!Utilities.noString(s)) {
                s = s + " & ";
            }
            s = s + f.getProperty() + " " + f.getOp().toCode() + " " + f.getValue();
        }
        return "from " + system + " where " + s + vsd;
    }
    return "All codes from " + system + vsd;
}

Example 97 with ConceptSetComponent

use of org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent 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();
        vs.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());
    }
}

Example 98 with ConceptSetComponent

use of org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method doInternalIncludeCodes.

public void doInternalIncludeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> imports, CodeSystem cs) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
    if (cs == null) {
        if (context.isNoTerminologyServer())
            throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
        else
            throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
    }
    cs.checkNoModifiers("Code System", "expanding");
    if (cs.getContent() != CodeSystemContentMode.COMPLETE)
        throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
    if (cs.hasVersion())
        if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
            params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
    if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
        // special case - add all the code system
        for (ConceptDefinitionComponent def : cs.getConcept()) {
            addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null);
        }
    }
    if (!inc.getConcept().isEmpty()) {
        canBeHeirarchy = false;
        for (ConceptReferenceComponent c : inc.getConcept()) {
            c.checkNoModifiers("Code in Code System", "expanding");
            addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
        }
    }
    if (inc.getFilter().size() > 1) {
        // which will bt the case if we get around to supporting this
        canBeHeirarchy = false;
        // need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
        throw new TerminologyServiceException("Multiple filters not handled yet");
    }
    if (inc.getFilter().size() == 1) {
        ConceptSetFilterComponent fc = inc.getFilter().get(0);
        if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
            // special: all codes in the target code system under the value
            ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
            if (def == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null);
        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
            // special: all codes in the target code system that are not under the value
            ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
            if (defEx == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            for (ConceptDefinitionComponent def : cs.getConcept()) {
                addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx);
            }
        } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
            // special: all codes in the target code system under the value
            ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
            if (def == null)
                throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
            for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null);
        } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
            // gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
            canBeHeirarchy = false;
            ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
            if (def != null) {
                if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
                    if (def.getDisplay().contains(fc.getValue())) {
                        addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), imports);
                    }
                }
            }
        } else
            throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
    }
}

Example 99 with ConceptSetComponent

use of org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method handleCompose.

private void handleCompose(ValueSetComposeComponent compose, List<ValueSetExpansionParameterComponent> params, Parameters expParams, String ctxt) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
    compose.checkNoModifiers("ValueSet.compose", "expanding");
    // Exclude comes first because we build up a map of things to exclude
    for (ConceptSetComponent inc : compose.getExclude()) excludeCodes(inc, params, ctxt);
    canBeHeirarchy = !expParams.getParameterBool("excludeNested") && excludeKeys.isEmpty() && excludeSystems.isEmpty();
    boolean first = true;
    for (ConceptSetComponent inc : compose.getInclude()) {
        if (first == true)
            first = false;
        else
            canBeHeirarchy = false;
        includeCodes(inc, params, expParams, canBeHeirarchy);
    }
}

Example 100 with ConceptSetComponent

use of org.hl7.fhir.r4b.model.ValueSet.ConceptSetComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetUtilities method markStatus.

public static void markStatus(ValueSet vs, String wg, StandardsStatus status, String pckage, String fmm, IWorkerContext context, String normativeVersion) throws FHIRException {
    if (vs.hasUserData("external.url"))
        return;
    if (wg != null) {
        if (!ToolingExtensions.hasExtension(vs, ToolingExtensions.EXT_WORKGROUP) || (!Utilities.existsInList(ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_WORKGROUP), "fhir", "vocab") && Utilities.existsInList(wg, "fhir", "vocab"))) {
            ToolingExtensions.setCodeExtension(vs, ToolingExtensions.EXT_WORKGROUP, wg);
        }
    }
    if (status != null) {
        StandardsStatus ss = ToolingExtensions.getStandardsStatus(vs);
        if (ss == null || ss.isLowerThan(status))
            ToolingExtensions.setStandardsStatus(vs, status, normativeVersion);
        if (pckage != null) {
            if (!vs.hasUserData("ballot.package"))
                vs.setUserData("ballot.package", pckage);
            else if (!pckage.equals(vs.getUserString("ballot.package")))
                if (!"infrastructure".equals(vs.getUserString("ballot.package")))
                    System.out.println("Value Set " + vs.getUrl() + ": ownership clash " + pckage + " vs " + vs.getUserString("ballot.package"));
        }
        if (status == StandardsStatus.NORMATIVE) {
            vs.setExperimental(false);
            vs.setStatus(PublicationStatus.ACTIVE);
        }
    }
    if (fmm != null) {
        String sfmm = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_FMM_LEVEL);
        if (Utilities.noString(sfmm) || Integer.parseInt(sfmm) < Integer.parseInt(fmm))
            ToolingExtensions.setIntegerExtension(vs, ToolingExtensions.EXT_FMM_LEVEL, Integer.parseInt(fmm));
    }
    if (vs.hasUserData("cs"))
        CodeSystemUtilities.markStatus((CodeSystem) vs.getUserData("cs"), wg, status, pckage, fmm, normativeVersion);
    else if (status == StandardsStatus.NORMATIVE && context != null) {
        for (ConceptSetComponent csc : vs.getCompose().getInclude()) {
            if (csc.hasSystem()) {
                CodeSystem cs = context.fetchCodeSystem(csc.getSystem());
                if (cs != null) {
                    CodeSystemUtilities.markStatus(cs, wg, status, pckage, fmm, normativeVersion);
                }
            }
        }
    }
}