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

Example 91 with ConceptSetComponent

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

the class ProfileComparer method unite.

private ValueSet unite(ElementDefinition ed, ProfileComparison outcome, String path, ValueSet lvs, ValueSet rvs) {
    ValueSet vs = new ValueSet();
    if (lvs.hasCompose()) {
        for (ConceptSetComponent inc : lvs.getCompose().getInclude()) vs.getCompose().getInclude().add(inc);
        if (lvs.getCompose().hasExclude()) {
            outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "The value sets " + lvs.getUrl() + " has exclude statements, and no union involving it can be correctly determined", ValidationMessage.IssueSeverity.ERROR));
            status(ed, ProfileUtilities.STATUS_ERROR);
        }
    }
    if (rvs.hasCompose()) {
        for (ConceptSetComponent inc : rvs.getCompose().getInclude()) if (!mergeIntoExisting(vs.getCompose().getInclude(), inc))
            vs.getCompose().getInclude().add(inc);
        if (rvs.getCompose().hasExclude()) {
            outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "The value sets " + lvs.getUrl() + " has exclude statements, and no union involving it can be correctly determined", ValidationMessage.IssueSeverity.ERROR));
            status(ed, ProfileUtilities.STATUS_ERROR);
        }
    }
    return vs;
}

Example 92 with ConceptSetComponent

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

the class TerminologyCache method generateExpandToken.

public CacheToken generateExpandToken(ValueSet vs, boolean heirarchical) {
    CacheToken ct = new CacheToken();
    ValueSet vsc = getVSEssense(vs);
    for (ConceptSetComponent inc : vs.getCompose().getInclude()) if (inc.hasSystem())
        ct.setName(getNameForSystem(inc.getSystem()));
    for (ConceptSetComponent inc : vs.getCompose().getExclude()) if (inc.hasSystem())
        ct.setName(getNameForSystem(inc.getSystem()));
    for (ValueSetExpansionContainsComponent inc : vs.getExpansion().getContains()) if (inc.hasSystem())
        ct.setName(getNameForSystem(inc.getSystem()));
    JsonParser json = new JsonParser();
    json.setOutputStyle(OutputStyle.PRETTY);
    try {
        ct.request = "{\"hierarchical\" : " + (heirarchical ? "true" : "false") + ", \"valueSet\" :" + json.composeString(vsc) + "}\r\n";
    } catch (IOException e) {
        throw new Error(e);
    }
    ct.key = String.valueOf(hashNWS(ct.request));
    return ct;
}

Example 93 with ConceptSetComponent

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

the class NarrativeGenerator method genInclude.

private boolean genInclude(XhtmlNode ul, ConceptSetComponent inc, String type) {
    boolean hasExtensions = false;
    XhtmlNode li;
    li = ul.addTag("li");
    ValueSet e = context.fetchCodeSystem(inc.getSystem());
    if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
        li.addText(type + " all codes defined in ");
        addCsRef(inc, li, e);
    } else {
        if (inc.getConcept().size() > 0) {
            li.addText(type + " these codes as defined in ");
            addCsRef(inc, li, e);
            XhtmlNode t = li.addTag("table");
            boolean hasComments = false;
            boolean hasDefinition = false;
            for (ConceptReferenceComponent c : inc.getConcept()) {
                hasComments = hasComments || ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_COMMENT);
                hasDefinition = hasDefinition || ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_DEFINITION);
            }
            if (hasComments || hasDefinition)
                hasExtensions = true;
            addTableHeaderRowStandard(t, false, true, hasDefinition, hasComments, false);
            for (ConceptReferenceComponent c : inc.getConcept()) {
                XhtmlNode tr = t.addTag("tr");
                tr.addTag("td").addText(c.getCode());
                ConceptDefinitionComponent cc = getConceptForCode(e, c.getCode(), inc.getSystem());
                XhtmlNode td = tr.addTag("td");
                if (!Utilities.noString(c.getDisplay()))
                    td.addText(c.getDisplay());
                else if (cc != null && !Utilities.noString(cc.getDisplay()))
                    td.addText(cc.getDisplay());
                td = tr.addTag("td");
                if (ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_DEFINITION))
                    smartAddText(td, ToolingExtensions.readStringExtension(c, ToolingExtensions.EXT_DEFINITION));
                else if (cc != null && !Utilities.noString(cc.getDefinition()))
                    smartAddText(td, cc.getDefinition());
                if (ExtensionHelper.hasExtension(c, ToolingExtensions.EXT_COMMENT)) {
                    smartAddText(tr.addTag("td"), "Note: " + ToolingExtensions.readStringExtension(c, ToolingExtensions.EXT_COMMENT));
                }
            }
        }
        boolean first = true;
        for (ConceptSetFilterComponent f : inc.getFilter()) {
            if (first) {
                li.addText(type + " codes from ");
                first = false;
            } else
                li.addText(" and ");
            addCsRef(inc, li, e);
            li.addText(" where " + f.getProperty() + " " + describe(f.getOp()) + " ");
            if (e != null && codeExistsInValueSet(e, f.getValue())) {
                XhtmlNode a = li.addTag("a");
                a.addText(f.getValue());
                a.setAttribute("href", prefix + getCsRef(e) + "#" + Utilities.nmtokenize(f.getValue()));
            } else
                li.addText(f.getValue());
            String disp = ToolingExtensions.getDisplayHint(f);
            if (disp != null)
                li.addText(" (" + disp + ")");
        }
    }
    return hasExtensions;
}

Example 94 with ConceptSetComponent

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

the class BaseWorkerContext method expandVS.

public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk, Parameters p) {
    if (p == null) {
        throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
    }
    if (vs.hasExpansion()) {
        return new ValueSetExpansionOutcome(vs.copy());
    }
    if (!vs.hasUrl()) {
        throw new Error(formatMessage(I18nConstants.NO_VALUE_SET_IN_URL));
    }
    for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
        codeSystemsUsed.add(inc.getSystem());
    }
    for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
        codeSystemsUsed.add(inc.getSystem());
    }
    CacheToken cacheToken = txCache.generateExpandToken(vs, heirarchical);
    ValueSetExpansionOutcome res;
    if (cacheOk) {
        res = txCache.getExpansion(cacheToken);
        if (res != null) {
            return res;
        }
    }
    p.setParameter("includeDefinition", false);
    p.setParameter("excludeNested", !heirarchical);
    if (incompleteOk) {
        p.setParameter("incomplete-ok", true);
    }
    List<String> allErrors = new ArrayList<>();
    // ok, first we try to expand locally
    ValueSetExpanderSimple vse = new ValueSetExpanderSimple(this);
    try {
        res = vse.expand(vs, p);
        allErrors.addAll(vse.getAllErrors());
        if (res.getValueset() != null) {
            if (!res.getValueset().hasUrl()) {
                throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET));
            }
            txCache.cacheExpansion(cacheToken, res, TerminologyCache.TRANSIENT);
            return res;
        }
    } catch (Exception e) {
        allErrors.addAll(vse.getAllErrors());
        e.printStackTrace();
    }
    // if that failed, we try to expand on the server
    if (addDependentResources(p, vs)) {
        p.addParameter().setName("cache-id").setValue(new StringType(cacheId));
    }
    if (noTerminologyServer) {
        return new ValueSetExpansionOutcome(formatMessage(I18nConstants.ERROR_EXPANDING_VALUESET_RUNNING_WITHOUT_TERMINOLOGY_SERVICES), TerminologyServiceErrorClass.NOSERVICE, allErrors);
    }
    Map<String, String> params = new HashMap<String, String>();
    params.put("_limit", Integer.toString(expandCodesLimit));
    params.put("_incomplete", "true");
    tlog("$expand on " + txCache.summary(vs));
    try {
        ValueSet result = txClient.expandValueset(vs, p, params);
        if (!result.hasUrl()) {
            result.setUrl(vs.getUrl());
        }
        if (!result.hasUrl()) {
            throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET_2));
        }
        res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());
    } catch (Exception e) {
        res = new ValueSetExpansionOutcome(e.getMessage() == null ? e.getClass().getName() : e.getMessage(), TerminologyServiceErrorClass.UNKNOWN, allErrors).setTxLink(txLog == null ? null : txLog.getLastId());
    }
    txCache.cacheExpansion(cacheToken, res, TerminologyCache.PERMANENT);
    return res;
}

Example 95 with ConceptSetComponent

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

the class OIDBasedValueSetImporter method getInclude.

protected ConceptSetComponent getInclude(ValueSet vs, String url, String csver) {
    for (ConceptSetComponent t : vs.getCompose().getInclude()) {
        if (csver == null) {
            if (t.getSystem().equals(url) && !t.hasVersion()) {
                return t;
            }
        } else {
            if (t.getSystem().equals(url) && t.hasVersion() && t.getVersion().equals(csver)) {
                return t;
            }
        }
    }
    ConceptSetComponent c = vs.getCompose().addInclude();
    c.setSystem(url);
    c.setVersion(csver);
    return c;
}