Examples with ValidationResult org.hl7.fhir.r5.context.IWorkerContext.ValidationResult used on opensource projects

Example 56 with ValidationResult

use of org.hl7.fhir.r5.context.IWorkerContext.ValidationResult in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method validateCode.

@Override
public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
    CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
    ValidationResult res = txCache.getValidation(cacheToken);
    if (res != null)
        return res;
    // ok, first we try to validate locally
    try {
        ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this);
        res = vsc.validateCode(code);
        txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
        return res;
    } catch (Exception e) {
    }
    // if that failed, we try to validate on the server
    if (noTerminologyServer)
        return new ValidationResult(IssueSeverity.ERROR, "Error validating code: running without terminology services", TerminologyServiceErrorClass.NOSERVICE);
    tlog("$validate " + txCache.summary(code) + " for " + txCache.summary(vs));
    try {
        Parameters pIn = new Parameters();
        pIn.addParameter().setName("codeableConcept").setValue(code);
        if (options != null)
            setTerminologyOptions(options, pIn);
        res = validateOnServer(vs, pIn);
    } catch (Exception e) {
        res = new ValidationResult(IssueSeverity.ERROR, e.getMessage() == null ? e.getClass().getName() : e.getMessage()).setTxLink(txLog.getLastId());
    }
    txCache.cacheValidation(cacheToken, res, TerminologyCache.PERMANENT);
    return res;
}

Example 57 with ValidationResult

use of org.hl7.fhir.r5.context.IWorkerContext.ValidationResult in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilities method describeCoded.

private Piece describeCoded(HierarchicalTableGenerator gen, Type fixed) {
    if (fixed instanceof Coding) {
        Coding c = (Coding) fixed;
        ValidationResult vr = context.validateCode(terminologyServiceOptions, c.getSystem(), c.getCode(), c.getDisplay());
        if (vr.getDisplay() != null)
            return gen.new Piece(null, " (" + vr.getDisplay() + ")", null).addStyle("color: darkgreen");
    } else if (fixed instanceof CodeableConcept) {
        CodeableConcept cc = (CodeableConcept) fixed;
        for (Coding c : cc.getCoding()) {
            ValidationResult vr = context.validateCode(terminologyServiceOptions, c.getSystem(), c.getCode(), c.getDisplay());
            if (vr.getDisplay() != null)
                return gen.new Piece(null, " (" + vr.getDisplay() + ")", null).addStyle("color: darkgreen");
        }
    }
    return null;
}

Example 58 with ValidationResult

use of org.hl7.fhir.r5.context.IWorkerContext.ValidationResult 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 59 with ValidationResult

use of org.hl7.fhir.r5.context.IWorkerContext.ValidationResult in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method checkCode.

// public API
private boolean checkCode(List<ValidationMessage> errors, Element element, String path, String code, String system, String version, String display, boolean checkDisplay, NodeStack stack) throws TerminologyServiceException {
    long t = System.nanoTime();
    boolean ss = context.supportsSystem(system);
    timeTracker.tx(t, "ss " + system);
    if (ss) {
        t = System.nanoTime();
        ValidationResult s = checkCodeOnServer(stack, code, system, version, display, checkDisplay);
        timeTracker.tx(t, "vc " + system + "#" + code + " '" + display + "'");
        if (s == null)
            return true;
        if (s.isOk()) {
            if (s.getMessage() != null)
                txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, I18nConstants.TERMINOLOGY_PASSTHROUGH_TX_MESSAGE, s.getMessage(), system, code);
            return true;
        }
        if (s.getErrorClass() != null && s.getErrorClass().isInfrastructure())
            txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
        else if (s.getSeverity() == IssueSeverity.INFORMATION)
            txHint(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
        else if (s.getSeverity() == IssueSeverity.WARNING)
            txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage());
        else
            return txRule(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, I18nConstants.TERMINOLOGY_PASSTHROUGH_TX_MESSAGE, s.getMessage(), system, code);
        return true;
    } else if (system.startsWith("http://build.fhir.org") || system.startsWith("https://build.fhir.org")) {
        rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_WRONG_BUILD, system, suggestSystemForBuild(system));
        return false;
    } else if (system.startsWith("http://hl7.org/fhir") || system.startsWith("https://hl7.org/fhir") || system.startsWith("http://www.hl7.org/fhir") || system.startsWith("https://www.hl7.org/fhir")) {
        if (SIDUtilities.isknownCodeSystem(system)) {
            // else don't check these (for now)
            return true;
        } else if (system.startsWith("http://hl7.org/fhir/test")) {
            // we don't validate these
            return true;
        } else if (system.endsWith(".html")) {
            rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_WRONG_HTML, system, suggestSystemForPage(system));
            return false;
        } else {
            CodeSystem cs = getCodeSystem(system);
            if (rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs != null, I18nConstants.TERMINOLOGY_TX_SYSTEM_UNKNOWN, system)) {
                ConceptDefinitionComponent def = getCodeDefinition(cs, code);
                if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, def != null, I18nConstants.TERMINOLOGY_TX_CODE_UNKNOWN, system, code))
                    return warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, display == null || display.equals(def.getDisplay()), I18nConstants.TERMINOLOGY_TX_DISPLAY_WRONG, def.getDisplay());
            }
            return false;
        }
    } else if (context.isNoTerminologyServer() && Utilities.existsInList(system, "http://loinc.org", "http://unitsofmeasure.org", "http://hl7.org/fhir/sid/icd-9-cm", "http://snomed.info/sct", "http://www.nlm.nih.gov/research/umls/rxnorm")) {
        // no checks in this case
        return true;
    } else if (startsWithButIsNot(system, "http://snomed.info/sct", "http://loinc.org", "http://unitsofmeasure.org", "http://www.nlm.nih.gov/research/umls/rxnorm")) {
        rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_INVALID, system);
        return false;
    } else {
        try {
            if (context.fetchResourceWithException(ValueSet.class, system) != null) {
                rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_VALUESET, system);
            // Lloyd: This error used to prohibit checking for downstream issues, but there are some cases where that checking needs to occur.  Please talk to me before changing the code back.
            }
            boolean done = false;
            if (system.startsWith("https:") && system.length() > 7) {
                String ns = "http:" + system.substring(6);
                CodeSystem cs = getCodeSystem(ns);
                if (cs != null || Utilities.existsInList(system, "https://loinc.org", "https://unitsofmeasure.org", "https://snomed.info/sct", "https://www.nlm.nih.gov/research/umls/rxnorm")) {
                    rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_SYSTEM_HTTPS, system);
                    done = true;
                }
            }
            hint(errors, IssueType.UNKNOWN, element.line(), element.col(), path, done, I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system);
            return true;
        } catch (Exception e) {
            return true;
        }
    }
}

Example 60 with ValidationResult

use of org.hl7.fhir.r5.context.IWorkerContext.ValidationResult in project org.hl7.fhir.core by hapifhir.

the class InstanceValidator method checkTerminologyCodeableConcept.

private boolean checkTerminologyCodeableConcept(List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, NodeStack stack, StructureDefinition logical) {
    boolean res = true;
    if (!noTerminologyChecks && theElementCntext != null && theElementCntext.hasBinding()) {
        ElementDefinitionBindingComponent binding = theElementCntext.getBinding();
        if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, I18nConstants.TERMINOLOGY_TX_BINDING_MISSING, path)) {
            if (binding.hasValueSet()) {
                ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl());
                if (valueset == null) {
                    CodeSystem cs = context.fetchCodeSystem(binding.getValueSet());
                    if (rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs == null, I18nConstants.TERMINOLOGY_TX_VALUESET_NOTFOUND_CS, describeReference(binding.getValueSet()))) {
                        warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, I18nConstants.TERMINOLOGY_TX_VALUESET_NOTFOUND, describeReference(binding.getValueSet()));
                    }
                } else {
                    try {
                        CodeableConcept cc = convertToCodeableConcept(element, logical);
                        if (!cc.hasCoding()) {
                            if (binding.getStrength() == BindingStrength.REQUIRED)
                                rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl());
                            else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
                                if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))
                                    rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CODE_VALUESETMAX, describeReference(ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")), valueset.getUrl());
                                else
                                    warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CODE_VALUESET_EXT, describeValueSet(binding.getValueSet()));
                            }
                        } else {
                            long t = System.nanoTime();
                            // Check whether the codes are appropriate for the type of binding we have
                            boolean bindingsOk = true;
                            if (binding.getStrength() != BindingStrength.EXAMPLE) {
                                if (binding.getStrength() == BindingStrength.REQUIRED) {
                                    removeTrackedMessagesForLocation(errors, element, path);
                                }
                                boolean atLeastOneSystemIsSupported = false;
                                for (Coding nextCoding : cc.getCoding()) {
                                    String nextSystem = nextCoding.getSystem();
                                    if (isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) {
                                        atLeastOneSystemIsSupported = true;
                                        break;
                                    }
                                }
                                if (!atLeastOneSystemIsSupported && binding.getStrength() == BindingStrength.EXAMPLE) {
                                // ignore this since we can't validate but it doesn't matter..
                                } else {
                                    // we're going to validate the codings directly
                                    ValidationResult vr = checkCodeOnServer(stack, valueset, cc, false);
                                    if (!vr.isOk()) {
                                        bindingsOk = false;
                                        if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) {
                                            if (binding.getStrength() == BindingStrength.REQUIRED)
                                                txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CONFIRM_1_CC, describeReference(binding.getValueSet()), vr.getErrorClass().toString());
                                            else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
                                                if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))
                                                    checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack);
                                                else if (!noExtensibleWarnings)
                                                    txWarningForLaterRemoval(element, errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CONFIRM_2_CC, describeReference(binding.getValueSet()), vr.getErrorClass().toString());
                                            } else if (binding.getStrength() == BindingStrength.PREFERRED) {
                                                if (baseOnly) {
                                                    txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CONFIRM_3_CC, describeReference(binding.getValueSet()), vr.getErrorClass().toString());
                                                }
                                            }
                                        } else {
                                            if (binding.getStrength() == BindingStrength.REQUIRED)
                                                txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_1_CC, describeValueSet(binding.getValueSet()), ccSummary(cc));
                                            else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
                                                if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))
                                                    checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack);
                                                if (!noExtensibleWarnings)
                                                    txWarningForLaterRemoval(element, errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_2_CC, describeValueSet(binding.getValueSet()), ccSummary(cc));
                                            } else if (binding.getStrength() == BindingStrength.PREFERRED) {
                                                if (baseOnly) {
                                                    txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_3_CC, describeValueSet(binding.getValueSet()), ccSummary(cc));
                                                }
                                            }
                                        }
                                    } else if (vr.getMessage() != null) {
                                        res = false;
                                        txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage());
                                    } else {
                                        res = false;
                                    }
                                }
                                // to validate, we'll validate that the codes actually exist
                                if (bindingsOk) {
                                    for (Coding nextCoding : cc.getCoding()) {
                                        String nextCode = nextCoding.getCode();
                                        String nextSystem = nextCoding.getSystem();
                                        String nextVersion = nextCoding.getVersion();
                                        if (isNotBlank(nextCode) && isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) {
                                            ValidationResult vr = checkCodeOnServer(stack, nextCode, nextSystem, nextVersion, null, false);
                                            if (!vr.isOk()) {
                                                txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CODE_NOTVALID, nextCode, nextSystem);
                                            }
                                        }
                                    }
                                }
                                timeTracker.tx(t, DataRenderer.display(context, cc));
                            }
                        }
                    } catch (Exception e) {
                        if (STACK_TRACE)
                            e.printStackTrace();
                        warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_ERROR_CODEABLECONCEPT, e.getMessage());
                    }
                    // special case: if the logical model has both CodeableConcept and Coding mappings, we'll also check the first coding.
                    if (getMapping("http://hl7.org/fhir/terminology-pattern", logical, logical.getSnapshot().getElementFirstRep()).contains("Coding")) {
                        checkTerminologyCoding(errors, path, element, profile, theElementCntext, true, true, stack, logical);
                    }
                }
            } else if (binding.hasValueSet()) {
                hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_BINDING_CANTCHECK);
            } else if (!noBindingMsgSuppressed) {
                hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_BINDING_NOSOURCE, path);
            }
        }
    }
    return res;
}