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

Example 91 with ConceptSetComponent

use of org.hl7.fhir.r4b.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.r4b.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.r4b.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.r4b.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.r4b.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;
}