Add validator support for -check-references and -resolution-context
This commit is contained in:
Grahame Grieve
parent
99697351a0
commit
8ed34e2604
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@ -129,6 +129,22 @@ public class ManagedFileAccess {
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throw new IOException("Internal Error");
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}
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}
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public static File file(File root, String filepath) throws IOException {
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switch (accessPolicy) {
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case DIRECT:
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if (!inAllowedPaths(root.getAbsolutePath())) {
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throw new IOException("The path '"+root.getAbsolutePath()+"' cannot be accessed by policy");
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}
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return new File(root.getAbsolutePath(), filepath);
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case MANAGED:
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return accessor.file(Utilities.path(root.getAbsolutePath(), filepath));
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case PROHIBITED:
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throw new IOException("Access to files is not allowed by local security policy");
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default:
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throw new IOException("Internal Error");
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}
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}
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/**
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* Open a FileInputStream, conforming to local security policy
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**/
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@ -1184,4 +1184,5 @@ public class I18nConstants {
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public static final String CODESYSTEM_PROPERTY_BAD_INTERNAL_REFERENCE = "CODESYSTEM_PROPERTY_BAD_INTERNAL_REFERENCE";
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public static final String CODESYSTEM_PROPERTY_BAD_PROPERTY_CODE = "CODESYSTEM_PROPERTY_BAD_PROPERTY_CODE";
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public static final String CODESYSTEM_DUPLICATE_CODE = "CODESYSTEM_DUPLICATE_CODE";
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public static final String REFERENCE_RESOLUTION_FAILED = "REFERENCE_RESOLUTION_FAILED";
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}
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@ -343,7 +343,8 @@ public class BaseValidator implements IValidationContextResourceLoader, IMessagi
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protected boolean slicingHint(List<ValidationMessage> errors, String ruleDate, IssueType type, int line, int col, String path, boolean thePass, boolean isCritical, String msg, String html, String[] text) {
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if (!thePass && doingHints()) {
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addValidationMessage(errors, ruleDate, type, line, col, path, msg, IssueSeverity.INFORMATION, null).setSlicingHint(true).setSliceHtml(html, text).setCriticalSignpost(isCritical);
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addValidationMessage(errors, ruleDate, type, line, col, path, msg, IssueSeverity.INFORMATION, null)
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.setMessageId(I18nConstants.DETAILS_FOR__MATCHING_AGAINST_PROFILE_).setSlicingHint(true).setSliceHtml(html, text).setCriticalSignpost(isCritical);
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}
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return thePass;
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}
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@ -356,7 +357,8 @@ public class BaseValidator implements IValidationContextResourceLoader, IMessagi
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*/
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protected boolean slicingHint(List<ValidationMessage> errors, String ruleDate, IssueType type, int line, int col, String path, boolean thePass, boolean isCritical, String msg, String html, String[] text, List<ValidationMessage> sliceInfo, String id) {
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if (!thePass && doingHints()) {
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addValidationMessage(errors, ruleDate, type, line, col, path, msg, IssueSeverity.INFORMATION, id).setSlicingHint(true).setSliceHtml(html, text).setCriticalSignpost(isCritical).setSliceInfo(sliceInfo);
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addValidationMessage(errors, ruleDate, type, line, col, path, msg, IssueSeverity.INFORMATION, id)
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.setMessageId(I18nConstants.DETAILS_FOR__MATCHING_AGAINST_PROFILE_).setSlicingHint(true).setSliceHtml(html, text).setCriticalSignpost(isCritical).setSliceInfo(sliceInfo);
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}
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return thePass;
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}
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@ -35,8 +35,12 @@ import org.hl7.fhir.r5.context.ILoggingService;
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import org.hl7.fhir.r5.context.IWorkerContextManager;
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import org.hl7.fhir.r5.context.SimpleWorkerContext;
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import org.hl7.fhir.r5.context.SystemOutLoggingService;
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import org.hl7.fhir.r5.elementmodel.*;
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import org.hl7.fhir.r5.elementmodel.Element;
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import org.hl7.fhir.r5.elementmodel.Manager;
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import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r5.elementmodel.ObjectConverter;
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import org.hl7.fhir.r5.elementmodel.ParserBase;
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import org.hl7.fhir.r5.elementmodel.SHCParser;
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import org.hl7.fhir.r5.fhirpath.ExpressionNode;
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import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
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import org.hl7.fhir.r5.formats.FormatUtilities;
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@ -61,9 +65,9 @@ import org.hl7.fhir.r5.model.StructureMap;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.renderers.RendererFactory;
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import org.hl7.fhir.r5.renderers.utils.RenderingContext;
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import org.hl7.fhir.r5.renderers.utils.ResourceWrapper;
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import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
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import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
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import org.hl7.fhir.r5.renderers.utils.ResourceWrapper;
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import org.hl7.fhir.r5.utils.EOperationOutcome;
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import org.hl7.fhir.r5.utils.ToolingExtensions;
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import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
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@ -79,6 +83,7 @@ import org.hl7.fhir.r5.utils.validation.constants.CheckDisplayOption;
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import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
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import org.hl7.fhir.r5.utils.validation.constants.IdStatus;
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import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
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import org.hl7.fhir.utilities.ByteProvider;
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import org.hl7.fhir.utilities.FhirPublication;
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import org.hl7.fhir.utilities.IniFile;
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import org.hl7.fhir.utilities.SIDUtilities;
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@ -107,7 +112,6 @@ import org.hl7.fhir.validation.cli.utils.ValidationLevel;
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import org.hl7.fhir.validation.instance.InstanceValidator;
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import org.hl7.fhir.validation.instance.advisor.BasePolicyAdvisorForFullValidation;
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import org.hl7.fhir.validation.instance.utils.ValidationContext;
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import org.hl7.fhir.utilities.ByteProvider;
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import org.xml.sax.SAXException;
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import lombok.Getter;
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@ -59,6 +59,15 @@ public class CliContext {
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@SerializedName("assumeValidRestReferences")
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private
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boolean assumeValidRestReferences = false;
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@JsonProperty("checkReferences")
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@SerializedName("checkReferences")
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private
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boolean checkReferences = false;
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@JsonProperty("resolutionContext")
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@SerializedName("resolutionContext")
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private
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String resolutionContext = null;
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@JsonProperty("canDoNative")
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@SerializedName("canDoNative")
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private
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@ -381,6 +390,18 @@ public class CliContext {
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return this;
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}
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@SerializedName("resolutionContext")
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@JsonProperty("resolutionContext")
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public String getResolutionContext() {
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return resolutionContext;
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}
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@SerializedName("resolutionContext")
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@JsonProperty("resolutionContext")
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public CliContext setResolutionContext(String resolutionContext) {
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this.resolutionContext = resolutionContext;
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return this;
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}
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@SerializedName("langTransform")
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@JsonProperty("langTransform")
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@ -967,6 +988,19 @@ public class CliContext {
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return this;
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}
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@SerializedName("checkReferences")
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@JsonProperty("checkReferences")
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public boolean isCheckReferences() {
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return checkReferences;
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}
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@SerializedName("checkReferences")
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@JsonProperty("checkReferences")
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public CliContext setCheckReferences(boolean checkReferences) {
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this.checkReferences = checkReferences;
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return this;
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}
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@SerializedName("noInternalCaching")
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@JsonProperty("noInternalCaching")
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public boolean isNoInternalCaching() {
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@ -1150,6 +1184,7 @@ public class CliContext {
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recursive == that.recursive &&
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doDebug == that.doDebug &&
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assumeValidRestReferences == that.assumeValidRestReferences &&
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checkReferences == that.checkReferences &&
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canDoNative == that.canDoNative &&
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noInternalCaching == that.noInternalCaching &&
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noExtensibleBindingMessages == that.noExtensibleBindingMessages &&
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@ -1161,6 +1196,7 @@ public class CliContext {
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checkIPSCodes == that.checkIPSCodes &&
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Objects.equals(extensions, that.extensions) &&
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Objects.equals(map, that.map) &&
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Objects.equals(resolutionContext, that.resolutionContext) &&
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Objects.equals(htmlInMarkdownCheck, that.htmlInMarkdownCheck) &&
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Objects.equals(output, that.output) &&
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Objects.equals(outputSuffix, that.outputSuffix) &&
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@ -1206,7 +1242,7 @@ public class CliContext {
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@Override
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public int hashCode() {
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return Objects.hash(baseEngine, doNative, extensions, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching,
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return Objects.hash(baseEngine, doNative, extensions, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, checkReferences,canDoNative, noInternalCaching, resolutionContext,
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noExtensibleBindingMessages, noInvariants, displayWarnings, wantInvariantsInMessages, map, output, outputSuffix, htmlOutput, txServer, sv, txLog, txCache, mapLog, lang, srcLang, tgtLang, fhirpath, snomedCT,
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targetVer, packageName, igs, questionnaireMode, level, profiles, options, sources, inputs, mode, locale, locations, crumbTrails, showMessageIds, forPublication, showTimes, allowExampleUrls, outputStyle, jurisdiction, noUnicodeBiDiControlChars,
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watchMode, watchScanDelay, watchSettleTime, bestPracticeLevel, unknownCodeSystemsCauseErrors, noExperimentalContent, advisorFile, expansionParameters, format, htmlInMarkdownCheck, allowDoubleQuotesInFHIRPath, checkIPSCodes);
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@ -1222,6 +1258,7 @@ public class CliContext {
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", recursive=" + recursive +
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", doDebug=" + doDebug +
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", assumeValidRestReferences=" + assumeValidRestReferences +
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", checkReferences=" + checkReferences +
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", canDoNative=" + canDoNative +
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", noInternalCaching=" + noInternalCaching +
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", noExtensibleBindingMessages=" + noExtensibleBindingMessages +
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@ -1238,6 +1275,7 @@ public class CliContext {
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", txLog='" + txLog + '\'' +
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", txCache='" + txCache + '\'' +
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", mapLog='" + mapLog + '\'' +
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", resolutionContext='" + resolutionContext + '\'' +
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", lang='" + lang + '\'' +
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", srcLang='" + srcLang + '\'' +
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", tgtLang='" + tgtLang + '\'' +
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@ -1,9 +1,14 @@
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package org.hl7.fhir.validation.cli.services;
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import java.io.ByteArrayInputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.net.MalformedURLException;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.EnumSet;
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import java.util.HashMap;
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import java.util.HashSet;
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@ -12,12 +17,18 @@ import java.util.Locale;
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import java.util.Map;
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import java.util.Set;
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import javax.annotation.Nonnull;
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import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
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import org.hl7.fhir.exceptions.DefinitionException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.context.IWorkerContextManager;
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import org.hl7.fhir.r5.elementmodel.Element;
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import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
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import org.hl7.fhir.r5.elementmodel.Manager;
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import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r5.model.CanonicalResource;
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import org.hl7.fhir.r5.model.ElementDefinition;
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import org.hl7.fhir.r5.model.Resource;
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@ -28,17 +39,16 @@ import org.hl7.fhir.r5.utils.validation.IMessagingServices;
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import org.hl7.fhir.r5.utils.validation.IResourceValidator;
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import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor;
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import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
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import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.AdditionalBindingPurpose;
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import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.CodedContentValidationAction;
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import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.ElementValidationAction;
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import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.ResourceValidationAction;
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import org.hl7.fhir.r5.utils.validation.constants.BindingKind;
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import org.hl7.fhir.r5.utils.validation.constants.CodedContentValidationPolicy;
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import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
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import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
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import org.hl7.fhir.utilities.TextFile;
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import org.hl7.fhir.utilities.Utilities;
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import org.hl7.fhir.utilities.VersionUtilities;
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import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
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import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
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import org.hl7.fhir.utilities.http.HTTPResult;
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import org.hl7.fhir.utilities.http.ManagedWebAccess;
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import org.hl7.fhir.utilities.json.model.JsonObject;
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import org.hl7.fhir.utilities.json.parser.JsonParser;
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import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
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@ -47,8 +57,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
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import org.hl7.fhir.validation.cli.utils.Common;
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import org.hl7.fhir.validation.instance.advisor.BasePolicyAdvisorForFullValidation;
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import javax.annotation.Nonnull;
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public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IValidationPolicyAdvisor, IWorkerContextManager.ICanonicalResourceLocator {
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@ -60,6 +68,9 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
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private Map<String, String> pidList = new HashMap<>();
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private Map<String, NpmPackage> pidMap = new HashMap<>();
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private IValidationPolicyAdvisor policyAdvisor;
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private String resolutionContext;
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private Map<String, String> knownFiles = new HashMap<>();
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public StandAloneValidatorFetcher(FilesystemPackageCacheManager pcm, IWorkerContext context, IPackageInstaller installer) {
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this.pcm = pcm;
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@ -69,8 +80,98 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
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}
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@Override
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public Element fetch(IResourceValidator validator, Object appContext, String url) throws FHIRException {
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throw new FHIRException("The URL '" + url + "' is not known to the FHIR validator, and has not been provided as part of the setup / parameters");
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public Element fetch(IResourceValidator validator, Object appContext, String url) throws FHIRException, IOException {
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if (!Utilities.isAbsoluteUrl(url) && Utilities.startsWithInList(resolutionContext, "http:", "https:")) {
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url = Utilities.pathURL(resolutionContext, url);
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}
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if (Utilities.isAbsoluteUrl(url)) {
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HTTPResult cnt = null;
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try {
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cnt = ManagedWebAccess.get(Arrays.asList("web"), url, "application/json");
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cnt.checkThrowException();
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} catch (Exception e) {
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cnt = ManagedWebAccess.get(Arrays.asList("web"), url, "application/fhir+xml");
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cnt.checkThrowException();
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}
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if (cnt.getContentType() != null && cnt.getContentType().contains("xml")) {
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return Manager.parse(context, new ByteArrayInputStream(cnt.getContent()), FhirFormat.XML).get(0).getElement();
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} else {
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return Manager.parse(context, new ByteArrayInputStream(cnt.getContent()), FhirFormat.JSON).get(0).getElement();
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}
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} else if (resolutionContext == null) {
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throw new FHIRException("The URL '" + url + "' is not known to the FHIR validator, and a resolution context has not been provided as part of the setup / parameters");
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} else if (resolutionContext.startsWith("file:")) {
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File rc = ManagedFileAccess.file(resolutionContext.substring(5));
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if (!rc.exists()) {
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throw new FHIRException("The URL '" + url + "' is not known to the FHIR validator, and a resolution context has not been provided as part of the setup / parameters");
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}
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// first we look for the file by several different patterns
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File tgt = ManagedFileAccess.file(rc, url);
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if (tgt.exists()) {
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return see(tgt, loadFile(tgt));
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}
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tgt = ManagedFileAccess.file(rc, url+".json");
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if (tgt.exists()) {
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return see(tgt, loadFile(tgt));
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}
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tgt = ManagedFileAccess.file(rc, url+".xml");
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if (tgt.exists()) {
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return see(tgt, loadFile(tgt));
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}
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String[] p = url.split("\\/");
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if (p.length != 2) {
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throw new FHIRException("The URL '" + url + "' was not understood - expecting type/id");
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}
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if (knownFiles.containsKey(p[0]+"/"+p[1])) {
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tgt = ManagedFileAccess.file(knownFiles.get(p[0]+"/"+p[1]));
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return loadFile(tgt);
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}
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tgt = ManagedFileAccess.file(rc, p[0]+"-"+p[1]+".json");
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if (tgt.exists()) {
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return see(tgt, loadFile(tgt));
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}
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tgt = ManagedFileAccess.file(rc, p[0]+"-"+p[1]+".xml");
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if (tgt.exists()) {
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return see(tgt, loadFile(tgt));
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}
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// didn't find it? now scan...
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for (File f : ManagedFileAccess.listFiles(rc)) {
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if (isPossibleMatch(f, p[0], p[1])) {
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Element e = see(f, loadFile(f));
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if (p[0].equals(e.fhirType()) && p[1].equals(e.getIdBase())) {
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return e;
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}
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}
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}
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return null;
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} else {
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throw new FHIRException("The resolution context '"+resolutionContext+"' was not understood");
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}
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}
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private Element see(File f, Element e) {
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knownFiles.put(e.fhirType()+"/"+e.getIdBase(), f.getAbsolutePath());
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return e;
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}
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private boolean isPossibleMatch(File f, String rt, String id) throws FileNotFoundException, IOException {
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String src = TextFile.fileToString(f);
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if (f.getName().endsWith(".xml")) {
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return src.contains("<"+rt) && src.contains("\""+id+"\"");
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} else {
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return src.contains("\""+rt+"\"") && src.contains("\""+id+"\"");
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}
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}
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private Element loadFile(File tgt) throws FHIRFormatError, DefinitionException, FHIRException, FileNotFoundException, IOException {
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if (tgt.getName().endsWith(".xml")) {
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return Manager.parse(context, new FileInputStream(tgt), FhirFormat.XML).get(0).getElement();
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} else {
|
||||
return Manager.parse(context, new FileInputStream(tgt), FhirFormat.JSON).get(0).getElement();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -78,7 +179,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
|
|||
Object appContext,
|
||||
String path,
|
||||
String url) {
|
||||
return ReferenceValidationPolicy.IGNORE;
|
||||
return policyAdvisor.policyForReference(validator, appContext, path, url);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -344,6 +445,14 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
|
|||
return policyAdvisor.getReferencePolicy();
|
||||
}
|
||||
|
||||
public void setReferencePolicy(ReferenceValidationPolicy policy) {
|
||||
if (policyAdvisor instanceof BasePolicyAdvisorForFullValidation) {
|
||||
((BasePolicyAdvisorForFullValidation) policyAdvisor).setRefpol(policy);
|
||||
} else {
|
||||
throw new Error("Cannot set reference policy on a "+policy.getClass().getName());
|
||||
}
|
||||
}
|
||||
|
||||
public IValidationPolicyAdvisor getPolicyAdvisor() {
|
||||
return policyAdvisor;
|
||||
}
|
||||
|
|
@ -353,4 +462,12 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
|
|||
return this;
|
||||
}
|
||||
|
||||
public String getResolutionContext() {
|
||||
return resolutionContext;
|
||||
}
|
||||
|
||||
public void setResolutionContext(String resolutionContext) {
|
||||
this.resolutionContext = resolutionContext;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -636,6 +636,12 @@ public class ValidationService {
|
|||
validationEngine.setFetcher(fetcher);
|
||||
validationEngine.getContext().setLocator(fetcher);
|
||||
validationEngine.setPolicyAdvisor(fetcher);
|
||||
if (cliContext.isCheckReferences()) {
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
} else {
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.IGNORE);
|
||||
}
|
||||
fetcher.setResolutionContext(cliContext.getResolutionContext());
|
||||
} else {
|
||||
DisabledValidationPolicyAdvisor fetcher = new DisabledValidationPolicyAdvisor();
|
||||
validationEngine.setPolicyAdvisor(fetcher);
|
||||
|
|
|
|||
|
|
@ -38,6 +38,8 @@ public class Params {
|
|||
public static final String QUESTIONNAIRE = "-questionnaire";
|
||||
public static final String NATIVE = "-native";
|
||||
public static final String ASSUME_VALID_REST_REF = "-assumeValidRestReferences";
|
||||
public static final String CHECK_REFERENCES = "-check-references";
|
||||
public static final String RESOLUTION_CONTEXT = "-resolution-context";
|
||||
public static final String DEBUG = "-debug";
|
||||
public static final String SCT = "-sct";
|
||||
public static final String RECURSE = "-recurse";
|
||||
|
|
@ -273,6 +275,10 @@ public class Params {
|
|||
cliContext.setDoNative(true);
|
||||
} else if (args[i].equals(ASSUME_VALID_REST_REF)) {
|
||||
cliContext.setAssumeValidRestReferences(true);
|
||||
} else if (args[i].equals(CHECK_REFERENCES)) {
|
||||
cliContext.setCheckReferences(true);
|
||||
} else if (args[i].equals(RESOLUTION_CONTEXT)) {
|
||||
cliContext.setResolutionContext(args[++i]);
|
||||
} else if (args[i].equals(DEBUG)) {
|
||||
cliContext.setDoDebug(true);
|
||||
} else if (args[i].equals(SCT)) {
|
||||
|
|
|
|||
|
|
@ -2023,21 +2023,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
return ok;
|
||||
}
|
||||
|
||||
private Set<String> getUnknownSystems(ValidationResult vr) {
|
||||
if (vr == null) {
|
||||
return null;
|
||||
}
|
||||
if (vr.getUnknownSystems() != null && !vr.getUnknownSystems().isEmpty()) {
|
||||
return vr.getUnknownSystems();
|
||||
}
|
||||
if (vr.getSystem() != null) {
|
||||
Set<String> set = new HashSet<String>();
|
||||
set.add(vr.getSystem());
|
||||
return set;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
private boolean convertCDACodeToCodeableConcept(List<ValidationMessage> errors, String path, Element element, StructureDefinition logical, CodeableConcept cc) {
|
||||
boolean ok = true;
|
||||
cc.setText(element.getNamedChildValue("originalText", false));
|
||||
|
|
@ -2525,7 +2510,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
boolean ok = false;
|
||||
CommaSeparatedStringBuilder contexts = new CommaSeparatedStringBuilder();
|
||||
List<String> plist = new ArrayList<>();
|
||||
plist.add(stripIndexes(stack.getLiteralPath()));
|
||||
plist.add(stripIndexes(stripRefs(stack.getLiteralPath())));
|
||||
for (String s : stack.getLogicalPaths()) {
|
||||
String p = stripIndexes(s);
|
||||
// all extensions are always allowed in ElementDefinition.example.value, and in fixed and pattern values. TODO: determine the logical paths from the path stated in the element definition....
|
||||
|
|
@ -2683,6 +2668,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
}
|
||||
}
|
||||
|
||||
private String stripRefs(String literalPath) {
|
||||
if (literalPath.contains(".resolve().ofType(")) {
|
||||
String s = literalPath.substring(literalPath.lastIndexOf(".resolve().")+18);
|
||||
int i = s.indexOf(")");
|
||||
s = s.substring(0, i)+s.substring(i+1);
|
||||
return s;
|
||||
} else {
|
||||
return literalPath;
|
||||
}
|
||||
}
|
||||
|
||||
private boolean containsAny(Set<String> set, List<String> list) {
|
||||
for (String p : list) {
|
||||
if (set.contains(p)) {
|
||||
|
|
@ -4182,9 +4178,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
} else {
|
||||
try {
|
||||
ext = fetcher.fetch(this, valContext.getAppContext(), ref);
|
||||
} catch (IOException e) {
|
||||
} catch (Exception e) {
|
||||
if (STACK_TRACE) e.printStackTrace();
|
||||
throw new FHIRException(e);
|
||||
ext = null;
|
||||
|
||||
// it's probably an error, but here we're just giving the user information about why resolution failed
|
||||
hint(errors, NO_RULE_DATE, IssueType.INFORMATIONAL, element.line(), element.col(), path,
|
||||
false, I18nConstants.REFERENCE_RESOLUTION_FAILED, ref, e.getClass().getName(), e.getMessage());
|
||||
|
||||
}
|
||||
if (ext != null) {
|
||||
setParents(ext);
|
||||
|
|
|
|||
|
|
@ -39,6 +39,14 @@ public class BasePolicyAdvisorForFullValidation implements IValidationPolicyAdvi
|
|||
this.refpol = refpol;
|
||||
}
|
||||
|
||||
public ReferenceValidationPolicy getRefpol() {
|
||||
return refpol;
|
||||
}
|
||||
|
||||
public void setRefpol(ReferenceValidationPolicy refpol) {
|
||||
this.refpol = refpol;
|
||||
}
|
||||
|
||||
@Override
|
||||
public ReferenceValidationPolicy policyForReference(IResourceValidator validator, Object appContext, String path, String url) {
|
||||
return refpol;
|
||||
|
|
|
|||
|
|
@ -64,7 +64,12 @@ public class NodeStack {
|
|||
this.context = context;
|
||||
ids = new HashMap<>();
|
||||
this.element = element;
|
||||
literalPath = refPath + "->" + element.getName();
|
||||
int i = element.getName().indexOf(".");
|
||||
if (i == -1) {
|
||||
literalPath = refPath+".resolve().ofType(" + element.getName()+")";
|
||||
} else {
|
||||
literalPath = refPath+".resolve().ofType(" + element.getName().substring(0, i)+")"+element.getName().substring(i);
|
||||
}
|
||||
workingLang = validationLanguage;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -3,21 +3,30 @@ package org.hl7.fhir.validation.tests;
|
|||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r5.test.utils.TestingUtilities;
|
||||
import org.hl7.fhir.r5.utils.OperationOutcomeUtilities;
|
||||
import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
|
||||
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
|
||||
import org.hl7.fhir.utilities.FhirPublication;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
|
||||
import org.hl7.fhir.utilities.settings.FhirSettings;
|
||||
import org.hl7.fhir.utilities.tests.CacheVerificationLogger;
|
||||
import org.hl7.fhir.validation.IgLoader;
|
||||
import org.hl7.fhir.validation.ValidationEngine;
|
||||
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher;
|
||||
import org.hl7.fhir.validation.tests.utilities.TestUtilities;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.DisplayName;
|
||||
|
|
@ -285,4 +294,149 @@ public class ValidationEngineTests {
|
|||
System.out.println("Finished");
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testResolveRelativeFileValid() throws Exception {
|
||||
String folder = setupFolder();
|
||||
try {
|
||||
ValidationEngine ve = TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, FhirPublication.R4, "4.0.1");
|
||||
StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(ve.getPcm(), ve.getContext(), ve);
|
||||
ve.setFetcher(fetcher);
|
||||
ve.getContext().setLocator(fetcher);
|
||||
ve.setPolicyAdvisor(fetcher);
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
fetcher.setResolutionContext("file:"+folder);
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "relative-url-valid.json"), null);
|
||||
Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op,
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
|
||||
"Observation null warning/invariant: Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)"));
|
||||
} finally {
|
||||
Utilities.clearDirectory(folder);
|
||||
ManagedFileAccess.file(folder).delete();
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testResolveRelativeFileInvalid() throws Exception {
|
||||
String folder = setupFolder();
|
||||
try {
|
||||
ValidationEngine ve = TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, FhirPublication.R4, "4.0.1");
|
||||
StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(ve.getPcm(), ve.getContext(), ve);
|
||||
ve.setFetcher(fetcher);
|
||||
ve.getContext().setLocator(fetcher);
|
||||
ve.setPolicyAdvisor(fetcher);
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
fetcher.setResolutionContext("file:"+folder);
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "relative-url-invalid.json"), null);
|
||||
Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op,
|
||||
"Observation.subject null error/structure: Unable to find a profile match for Patient/example-newborn among choices: http://hl7.org/fhir/test/StructureDefinition/PatientRule\n"+
|
||||
"Observation.subject null information/structure: Details for Patient/example-newborn matching against profile http://hl7.org/fhir/test/StructureDefinition/PatientRule|0.1.0\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
|
||||
"Observation null warning/invariant: Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)"));
|
||||
} finally {
|
||||
Utilities.clearDirectory(folder);
|
||||
ManagedFileAccess.file(folder).delete();
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testResolveRelativeFileError() throws Exception {
|
||||
String folder = setupFolder();
|
||||
try {
|
||||
ValidationEngine ve = TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, FhirPublication.R4, "4.0.1");
|
||||
StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(ve.getPcm(), ve.getContext(), ve);
|
||||
ve.setFetcher(fetcher);
|
||||
ve.getContext().setLocator(fetcher);
|
||||
ve.setPolicyAdvisor(fetcher);
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
fetcher.setResolutionContext("file:"+folder);
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "relative-url-error.json"), null);
|
||||
Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op,
|
||||
"Observation.subject null error/structure: Unable to resolve resource with reference 'patient/example-newborn-x'\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
|
||||
"Observation null warning/invariant: Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)"));
|
||||
} finally {
|
||||
Utilities.clearDirectory(folder);
|
||||
ManagedFileAccess.file(folder).delete();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testResolveAbsoluteValid() throws Exception {
|
||||
ValidationEngine ve = TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, FhirPublication.R4, "4.0.1");
|
||||
StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(ve.getPcm(), ve.getContext(), ve);
|
||||
ve.setFetcher(fetcher);
|
||||
ve.getContext().setLocator(fetcher);
|
||||
ve.setPolicyAdvisor(fetcher);
|
||||
ve.setShowMessagesFromReferences(true);
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "absolute-url-valid.json"), null);
|
||||
Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op,
|
||||
"Observation.subject.resolve().ofType(Patient).managingOrganization null error/structure: Unable to resolve resource with reference 'Organization/1'\n"+
|
||||
"Observation.subject.resolve().ofType(Patient).managingOrganization null information/informational: Fetching 'Organization/1' failed. System details: org.hl7.fhir.exceptions.FHIRException: The URL 'Organization/1' is not known to the FHIR validator, and a resolution context has not been provided as part of the setup / parameters\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
|
||||
"Observation null warning/invariant: Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testResolveAbsoluteInvalid() throws Exception {
|
||||
ValidationEngine ve = TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, FhirPublication.R4, "4.0.1");
|
||||
StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(ve.getPcm(), ve.getContext(), ve);
|
||||
ve.setFetcher(fetcher);
|
||||
ve.getContext().setLocator(fetcher);
|
||||
ve.setPolicyAdvisor(fetcher);
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "absolute-url-invalid.json"), null);
|
||||
Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op,
|
||||
"Observation.subject null error/structure: Unable to find a profile match for https://hl7.org/fhir/R4/patient-example-newborn.json among choices: http://hl7.org/fhir/test/StructureDefinition/PatientRule\n"+
|
||||
"Observation.subject null information/structure: Details for https://hl7.org/fhir/R4/patient-example-newborn.json matching against profile http://hl7.org/fhir/test/StructureDefinition/PatientRule|0.1.0\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
|
||||
"Observation null warning/invariant: Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testResolveAbsoluteError() throws Exception {
|
||||
ValidationEngine ve = TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, FhirPublication.R4, "4.0.1");
|
||||
StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(ve.getPcm(), ve.getContext(), ve);
|
||||
ve.setFetcher(fetcher);
|
||||
ve.getContext().setLocator(fetcher);
|
||||
ve.setPolicyAdvisor(fetcher);
|
||||
fetcher.setReferencePolicy(ReferenceValidationPolicy.CHECK_VALID);
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
|
||||
ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
|
||||
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "absolute-url-error.json"), null);
|
||||
Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op,
|
||||
"Observation.subject null error/structure: Unable to resolve resource with reference 'http://hl7x.org/fhir/R4/Patient/Patient/example-newborn'\n"+
|
||||
"Observation.subject null information/informational: Fetching 'http://hl7x.org/fhir/R4/Patient/Patient/example-newborn' failed. System details: java.net.UnknownHostException: hl7x.org\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
|
||||
"Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
|
||||
"Observation null warning/invariant: Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)"));
|
||||
}
|
||||
|
||||
private String setupFolder() throws IOException {
|
||||
String now = new SimpleDateFormat("yyyymmddhhMMss").format(new Date());
|
||||
String folder = Utilities.path("[tmp]", "validator-resolution", now);
|
||||
Utilities.createDirectory(folder);
|
||||
for (String s : Utilities.strings("Organization-first.xml", "Patient-example-newborn.json", "patient-example.json")) {
|
||||
TextFile.bytesToFile( TestingUtilities.loadTestResourceBytes("validator", "resolution", s), Utilities.path(folder, s));
|
||||
}
|
||||
return folder;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue