Examples with ValueSetExpansionOutcome org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome used on opensource projects

Example 46 with ValueSetExpansionOutcome

use of org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method doServerIncludeCodes.

private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, ValueSetExpansionComponent exp, List<ValueSet> imports, Parameters expParams, List<Extension> extensions) throws FHIRException {
    ValueSetExpansionOutcome vso = context.expandVS(inc, heirarchical);
    if (vso.getError() != null) {
        throw failTSE("Unable to expand imported value set: " + vso.getError());
    }
    ValueSet vs = vso.getValueset();
    if (vs.hasVersion()) {
        if (!existsInParams(exp.getParameter(), "version", new UriType(vs.getUrl() + "|" + vs.getVersion()))) {
            exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
        }
    }
    for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
        if (!existsInParams(exp.getParameter(), p.getName(), p.getValue())) {
            exp.getParameter().add(p);
        }
    }
    for (Extension ex : vs.getExpansion().getExtension()) {
        if (Utilities.existsInList(ex.getUrl(), ToolingExtensions.EXT_EXP_TOOCOSTLY, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed")) {
            if (!hasExtension(extensions, ex.getUrl())) {
                extensions.add(ex);
            }
        }
    }
    for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
        addCodeAndDescendents(cc, null, expParams, imports);
    }
}

Example 47 with ValueSetExpansionOutcome

use of org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpanderSimple method excludeCodes.

private void excludeCodes(ConceptSetComponent exc, List<ValueSetExpansionParameterComponent> params, String ctxt) throws FHIRException {
    exc.checkNoModifiers("Compose.exclude", "expanding");
    if (exc.hasSystem() && exc.getConcept().size() == 0 && exc.getFilter().size() == 0) {
        excludeSystems.add(exc.getSystem());
    }
    if (exc.hasValueSet())
        throw fail("Processing Value set references in exclude is not yet done in " + ctxt);
    // importValueSet(imp.getValue(), params, expParams);
    CodeSystem cs = context.fetchCodeSystem(exc.getSystem());
    if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem())) {
        ValueSetExpansionOutcome vse = context.expandVS(exc, false);
        ValueSet valueset = vse.getValueset();
        if (valueset == null)
            throw failTSE("Error Expanding ValueSet: " + vse.getError());
        excludeCodes(valueset.getExpansion(), params);
        return;
    }
    for (ConceptReferenceComponent c : exc.getConcept()) {
        excludeCode(exc.getSystem(), c.getCode());
    }
    if (exc.getFilter().size() > 0)
        throw fail("not done yet - multiple filters");
}

Example 48 with ValueSetExpansionOutcome

use of org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class ValueSetRenderer method countMembership.

private Integer countMembership(ValueSet vs) {
    int count = 0;
    if (vs.hasExpansion())
        count = count + conceptCount(vs.getExpansion().getContains());
    else {
        if (vs.hasCompose()) {
            if (vs.getCompose().hasExclude()) {
                try {
                    ValueSetExpansionOutcome vse = getContext().getWorker().expandVS(vs, true, false);
                    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 49 with ValueSetExpansionOutcome

use of org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class StructureMapUtilities method buildCoding.

private Coding buildCoding(String uri, String code) throws FHIRException {
    // if we can get this as a valueSet, we will
    String system = null;
    String display = null;
    String version = null;
    ValueSet vs = Utilities.noString(uri) ? null : worker.fetchResourceWithException(ValueSet.class, uri);
    if (vs != null) {
        ValueSetExpansionOutcome vse = worker.expandVS(vs, true, false);
        if (vse.getError() != null)
            throw new FHIRException(vse.getError());
        CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
        for (ValueSetExpansionContainsComponent t : vse.getValueset().getExpansion().getContains()) {
            if (t.hasCode())
                b.append(t.getCode());
            if (code.equals(t.getCode()) && t.hasSystem()) {
                system = t.getSystem();
                version = t.getVersion();
                display = t.getDisplay();
                break;
            }
            if (code.equalsIgnoreCase(t.getDisplay()) && t.hasSystem()) {
                system = t.getSystem();
                version = t.getVersion();
                display = t.getDisplay();
                break;
            }
        }
        if (system == null)
            throw new FHIRException("The code '" + code + "' is not in the value set '" + uri + "' (valid codes: " + b.toString() + "; also checked displays)");
    } else {
        system = uri;
    }
    ValidationResult vr = worker.validateCode(terminologyServiceOptions.setVersionFlexible(true), system, version, code, null);
    if (vr != null && vr.getDisplay() != null)
        display = vr.getDisplay();
    return new Coding().setSystem(system).setCode(code).setDisplay(display);
}

Example 50 with ValueSetExpansionOutcome

use of org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project kindling by HL7.

the class MarkDownPreProcessor method process.

public static String process(Definitions definitions, BuildWorkerContext workerContext, List<ValidationMessage> validationErrors, String text, String location, String prefix) throws Exception {
    if (Utilities.noString(text))
        return "";
    text = text.replace("||", "\r\n\r\n");
    while (text.contains("[[[")) {
        String left = text.substring(0, text.indexOf("[[["));
        if (text.indexOf("]]]") < 0)
            throw new Error(location + ": Missing closing ]]] in markdown text: " + text);
        String linkText = text.substring(text.indexOf("[[[") + 3, text.indexOf("]]]"));
        String right = text.substring(text.indexOf("]]]") + 3);
        if (linkText.startsWith("valueset:")) {
            String vsid = linkText.substring(9);
            ValueSet vs = workerContext.fetchResource(ValueSet.class, "http://hl7.org/fhir/ValueSet/" + vsid);
            ValueSetExpansionOutcome exp = workerContext.expandVS(vs, true, false);
            if (exp.getValueset() != null)
                text = left + presentExpansion(exp.getValueset().getExpansion().getContains(), workerContext) + right;
            else
                text = left + "[" + vs.getName() + "](" + vs.getUserData("path") + ")" + right;
        } else {
            String url = "";
            String[] parts = linkText.split("\\#");
            if (parts[0].contains("/StructureDefinition/")) {
                StructureDefinition ed = workerContext.getExtensionStructure(null, parts[0]);
                if (ed == null)
                    throw new Error(location + ": Unable to find extension " + parts[0]);
                url = ed.getUserString("path");
                if (url == null && ed.hasUserData("filename")) {
                    url = ed.getUserData("filename") + ".html";
                }
                if (url == null) {
                    System.out.println("Broken link for " + ed.getUrl());
                }
            }
            if (Utilities.noString(url)) {
                String[] paths = parts[0].split("\\.");
                StructureDefinition p = new ProfileUtilities(workerContext, null, null).getProfile(null, paths[0]);
                if (p != null) {
                    String suffix = (paths.length > 1) ? "-definitions.html#" + parts[0] : ".html";
                    if (p.getUserData("filename") == null)
                        url = paths[0].toLowerCase() + suffix;
                    else
                        url = p.getUserData("filename") + suffix;
                } else if (definitions.hasResource(linkText)) {
                    url = linkText.toLowerCase() + ".html#";
                } else if (definitions.hasResource(paths[0])) {
                    url = paths[0].toLowerCase() + "-definitions.html#" + linkText;
                } else if (definitions.hasElementDefn(linkText)) {
                    url = definitions.getSrcFile(linkText) + ".html#" + linkText;
                } else if (definitions.hasPrimitiveType(linkText)) {
                    url = "datatypes.html#" + linkText;
                } else if (definitions.getPageTitles().containsKey(linkText)) {
                    url = definitions.getPageTitles().get(linkText);
                } else if (definitions.getLogicalModel(linkText.toLowerCase()) != null) {
                    url = definitions.getLogicalModel(linkText.toLowerCase()).getId() + ".html";
                } else if (validationErrors != null) {
                    validationErrors.add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, -1, -1, location, "Unresolved logical URL '" + linkText + "'", IssueSeverity.WARNING));
                // throw new Exception("Unresolved logical URL "+url);
                } else
                    url = "??";
            }
            text = left + "[" + linkText + "](" + url + ")" + right;
        }
    }
    // 1. if prefix <> "", then check whether we need to insert the prefix
    if (!Utilities.noString(prefix)) {
        int i = text.length() - 3;
        while (i > 0) {
            if (text.substring(i, i + 2).equals("](")) {
                if (!text.substring(i, i + 7).equals("](http:")) {
                    // && !text.substring(i, i+8).equals("](https:"));
                    text = text.substring(0, i) + "](" + prefix + text.substring(i + 2);
                }
            }
            i--;
        }
    }
    return text;
}