Examples with ValueSetExpansionOutcome org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome used on opensource projects

Example 56 with ValueSetExpansionOutcome

use of org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class TerminologyCache method load.

private void load() throws FHIRException {
    for (String fn : new File(folder).list()) {
        if (fn.endsWith(".cache") && !fn.equals("validation.cache")) {
            try {
                // System.out.println("Load "+fn);
                String title = fn.substring(0, fn.lastIndexOf("."));
                NamedCache nc = new NamedCache();
                nc.name = title;
                caches.put(title, nc);
                System.out.print(" - load " + title + ".cache");
                String src = TextFile.fileToString(Utilities.path(folder, fn));
                if (src.startsWith("?"))
                    src = src.substring(1);
                int i = src.indexOf(ENTRY_MARKER);
                while (i > -1) {
                    String s = src.substring(0, i);
                    System.out.print(".");
                    src = src.substring(i + ENTRY_MARKER.length() + 1);
                    i = src.indexOf(ENTRY_MARKER);
                    if (!Utilities.noString(s)) {
                        int j = s.indexOf(BREAK);
                        String q = s.substring(0, j);
                        String p = s.substring(j + BREAK.length() + 1).trim();
                        CacheEntry ce = new CacheEntry();
                        ce.persistent = true;
                        ce.request = q;
                        boolean e = p.charAt(0) == 'e';
                        p = p.substring(3);
                        JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(p);
                        String error = loadJS(o.get("error"));
                        if (e) {
                            if (o.has("valueSet"))
                                ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
                            else
                                ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
                        } else {
                            IssueSeverity severity = o.get("severity") instanceof JsonNull ? null : IssueSeverity.fromCode(o.get("severity").getAsString());
                            String display = loadJS(o.get("display"));
                            ce.v = new ValidationResult(severity, error, new ConceptDefinitionComponent().setDisplay(display));
                        }
                        nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
                        nc.list.add(ce);
                    }
                }
                System.out.println("done");
            } catch (Exception e) {
                throw new FHIRException("Error loading " + fn + ": " + e.getMessage(), e);
            }
        }
    }
}

Example 57 with ValueSetExpansionOutcome

use of org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method handleByCache.

private ValidationResult handleByCache(ValueSet vs, Coding coding, boolean tryCache) {
    String cacheId = cacheId(coding);
    Map<String, ValidationResult> cache = validationCache.get(vs.getUrl());
    if (cache == null) {
        cache = new HashMap<String, IWorkerContext.ValidationResult>();
        validationCache.put(vs.getUrl(), cache);
    }
    if (cache.containsKey(cacheId))
        return cache.get(cacheId);
    if (!tryCache)
        return null;
    if (!cacheValidation)
        return null;
    if (failed.contains(vs.getUrl()))
        return null;
    ValueSetExpansionOutcome vse = expandVS(vs, true);
    if (vse.getValueset() == null || notcomplete(vse.getValueset())) {
        failed.add(vs.getUrl());
        return null;
    }
    ValidationResult res = validateCode(coding, vse.getValueset());
    cache.put(cacheId, res);
    return res;
}

Example 58 with ValueSetExpansionOutcome

use of org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class ValueSetExpansionCache method loadCache.

private void loadCache() throws FHIRFormatError, IOException {
    File[] files = new File(cacheFolder).listFiles();
    for (File f : files) {
        if (f.getName().endsWith(".xml")) {
            final FileInputStream is = new FileInputStream(f);
            try {
                Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
                if (r instanceof OperationOutcome) {
                    OperationOutcome oo = (OperationOutcome) r;
                    expansions.put(ToolingExtensions.getExtension(oo, VS_ID_EXT).getValue().toString(), new ValueSetExpansionOutcome(new XhtmlComposer(true, false).composePlainText(oo.getText().getDiv())));
                } else {
                    ValueSet vs = (ValueSet) r;
                    expansions.put(vs.getUrl(), new ValueSetExpansionOutcome(vs, null));
                }
            } finally {
                IOUtils.closeQuietly(is);
            }
        }
    }
}

Example 59 with ValueSetExpansionOutcome

use of org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome 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 60 with ValueSetExpansionOutcome

use of org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome in project org.hl7.fhir.core by hapifhir.

the class ProfileComparer method compareBindings.

private boolean compareBindings(ProfileComparison outcome, ElementDefinition subset, ElementDefinition superset, String path, ElementDefinition lDef, ElementDefinition rDef) throws FHIRFormatError {
    assert (lDef.hasBinding() || rDef.hasBinding());
    if (!lDef.hasBinding()) {
        subset.setBinding(rDef.getBinding());
        // technically, the super set is unbound, but that's not very useful - so we use the provided on as an example
        superset.setBinding(rDef.getBinding().copy());
        superset.getBinding().setStrength(BindingStrength.EXAMPLE);
        return true;
    }
    if (!rDef.hasBinding()) {
        subset.setBinding(lDef.getBinding());
        superset.setBinding(lDef.getBinding().copy());
        superset.getBinding().setStrength(BindingStrength.EXAMPLE);
        return true;
    }
    ElementDefinitionBindingComponent left = lDef.getBinding();
    ElementDefinitionBindingComponent right = rDef.getBinding();
    if (Base.compareDeep(left, right, false)) {
        subset.setBinding(left);
        superset.setBinding(right);
    }
    // superset:
    if (isPreferredOrExample(left) && isPreferredOrExample(right)) {
        if (right.getStrength() == BindingStrength.PREFERRED && left.getStrength() == BindingStrength.EXAMPLE && !Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
            outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Example/preferred bindings differ at " + path + " using binding from " + outcome.rightName(), ValidationMessage.IssueSeverity.INFORMATION));
            status(subset, ProfileUtilities.STATUS_HINT);
            subset.setBinding(right);
            superset.setBinding(unionBindings(superset, outcome, path, left, right));
        } else {
            if ((right.getStrength() != BindingStrength.EXAMPLE || left.getStrength() != BindingStrength.EXAMPLE) && !Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
                outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Example/preferred bindings differ at " + path + " using binding from " + outcome.leftName(), ValidationMessage.IssueSeverity.INFORMATION));
                status(subset, ProfileUtilities.STATUS_HINT);
            }
            subset.setBinding(left);
            superset.setBinding(unionBindings(superset, outcome, path, left, right));
        }
        return true;
    }
    // if either of them are extensible/required, then it wins
    if (isPreferredOrExample(left)) {
        subset.setBinding(right);
        superset.setBinding(unionBindings(superset, outcome, path, left, right));
        return true;
    }
    if (isPreferredOrExample(right)) {
        subset.setBinding(left);
        superset.setBinding(unionBindings(superset, outcome, path, left, right));
        return true;
    }
    // ok, both are extensible or required.
    ElementDefinitionBindingComponent subBinding = new ElementDefinitionBindingComponent();
    subset.setBinding(subBinding);
    ElementDefinitionBindingComponent superBinding = new ElementDefinitionBindingComponent();
    superset.setBinding(superBinding);
    subBinding.setDescription(mergeText(subset, outcome, path, "description", left.getDescription(), right.getDescription()));
    superBinding.setDescription(mergeText(subset, outcome, null, "description", left.getDescription(), right.getDescription()));
    if (left.getStrength() == BindingStrength.REQUIRED || right.getStrength() == BindingStrength.REQUIRED)
        subBinding.setStrength(BindingStrength.REQUIRED);
    else
        subBinding.setStrength(BindingStrength.EXTENSIBLE);
    if (left.getStrength() == BindingStrength.EXTENSIBLE || right.getStrength() == BindingStrength.EXTENSIBLE)
        superBinding.setStrength(BindingStrength.EXTENSIBLE);
    else
        superBinding.setStrength(BindingStrength.REQUIRED);
    if (Base.compareDeep(left.getValueSet(), right.getValueSet(), false)) {
        subBinding.setValueSet(left.getValueSet());
        superBinding.setValueSet(left.getValueSet());
        return true;
    } else if (!left.hasValueSet()) {
        outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "No left Value set at " + path, ValidationMessage.IssueSeverity.ERROR));
        return true;
    } else if (!right.hasValueSet()) {
        outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "No right Value set at " + path, ValidationMessage.IssueSeverity.ERROR));
        return true;
    } else {
        // ok, now we compare the value sets. This may be unresolvable.
        ValueSet lvs = resolveVS(outcome.left, left.getValueSet());
        ValueSet rvs = resolveVS(outcome.right, right.getValueSet());
        if (lvs == null) {
            outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Unable to resolve left value set " + left.getValueSet().toString() + " at " + path, ValidationMessage.IssueSeverity.ERROR));
            return true;
        } else if (rvs == null) {
            outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Unable to resolve right value set " + right.getValueSet().toString() + " at " + path, ValidationMessage.IssueSeverity.ERROR));
            return true;
        } else {
            // first, we'll try to do it by definition
            ValueSet cvs = intersectByDefinition(lvs, rvs);
            if (cvs == null) {
                // if that didn't work, we'll do it by expansion
                ValueSetExpansionOutcome le;
                ValueSetExpansionOutcome re;
                try {
                    le = context.expandVS(lvs, true, false);
                    re = context.expandVS(rvs, true, false);
                    if (!closed(le.getValueset()) || !closed(re.getValueset()))
                        throw new DefinitionException("unclosed value sets are not handled yet");
                    cvs = intersectByExpansion(lvs, rvs);
                    if (!cvs.getCompose().hasInclude()) {
                        outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "The value sets " + lvs.getUrl() + " and " + rvs.getUrl() + " do not intersect", ValidationMessage.IssueSeverity.ERROR));
                        status(subset, ProfileUtilities.STATUS_ERROR);
                        return false;
                    }
                } catch (Exception e) {
                    outcome.messages.add(new ValidationMessage(Source.ProfileComparer, ValidationMessage.IssueType.STRUCTURE, path, "Unable to expand or process value sets " + lvs.getUrl() + " and " + rvs.getUrl() + ": " + e.getMessage(), ValidationMessage.IssueSeverity.ERROR));
                    status(subset, ProfileUtilities.STATUS_ERROR);
                    return false;
                }
            }
            subBinding.setValueSet(new Reference().setReference("#" + addValueSet(cvs)));
            superBinding.setValueSet(new Reference().setReference("#" + addValueSet(unite(superset, outcome, path, lvs, rvs))));
        }
    }
    return false;
}