Java Code Examples for org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity#ERROR

private ValidationResult verifyCodeInExpansion(ValueSet vs, String system, String code,
  String display) {
  ValueSetExpansionContainsComponent cc = findCode(vs.getExpansion().getContains(), code);
  if (cc == null) {
    return new ValidationResult(IssueSeverity.ERROR,
      "Unknown Code " + code + " in " + vs.getUrl());
  }
  if (display == null) {
    return new ValidationResult(
      new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
  }
  if (cc.hasDisplay()) {
    if (display.equalsIgnoreCase(cc.getDisplay())) {
      return new ValidationResult(
        new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
    }
    return new ValidationResult(IssueSeverity.WARNING,
      "Display Name for " + code + " must be '" + cc.getDisplay() + "'",
      new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
  }
  return null;
}
 

private ValidationResult loadFromCache(String fn) throws FileNotFoundException, IOException {
  if (fn == null) {
    return null;
  }
  if (!(new File(fn).exists())) {
    return null;
  }
  String cnt = TextFile.fileToString(fn);
  if (cnt.startsWith("!error: ")) {
    return new ValidationResult(IssueSeverity.ERROR, cnt.substring(8));
  } else if (cnt.startsWith("!warning: ")) {
    return new ValidationResult(IssueSeverity.ERROR, cnt.substring(10));
  } else {
    return new ValidationResult(new ConceptDefinitionComponent().setDisplay(cnt));
  }
}
 

private ValidationResult serverValidateCode(Parameters pin) {
Parameters pout = txServer.operateType(ValueSet.class, "validate-code", pin);
boolean ok = false;
String message = "No Message returned";
String display = null;
for (ParametersParameterComponent p : pout.getParameter()) {
  if (p.getName().equals("result"))
    ok = ((BooleanType) p.getValue()).getValue().booleanValue();
  else if (p.getName().equals("message"))
    message = ((StringType) p.getValue()).getValue();
  else if (p.getName().equals("display"))
    display = ((StringType) p.getValue()).getValue();
}
if (!ok)
  return new ValidationResult(IssueSeverity.ERROR, message);
else if (display != null)
  return new ValidationResult(new ConceptDefinitionComponent().setDisplay(display));
else
  return new ValidationResult(null);
}
 

private ValidationResult verifyCodeInCodeSystem(ValueSet vs, String system, String code, String display) {
  ConceptDefinitionComponent cc = findCodeInConcept(vs.getCodeSystem().getConcept(), code);
  if (cc == null)
    return new ValidationResult(IssueSeverity.ERROR, "Unknown Code "+code+" in "+vs.getCodeSystem().getSystem());
  if (display == null)
    return new ValidationResult(cc);
  CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
  if (cc.hasDisplay()) {
    b.append(cc.getDisplay());
    if (display.equalsIgnoreCase(cc.getDisplay()))
      return new ValidationResult(cc);
  }
  for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
    b.append(ds.getValue());
    if (display.equalsIgnoreCase(ds.getValue()))
      return new ValidationResult(cc);
  }
  return new ValidationResult(IssueSeverity.ERROR, "Display Name for "+code+" must be one of '"+b.toString()+"'");
}
 

public String getErrorCount() {
  int c = 0;
  for (ValidationMessage vm : messages)
    if (vm.getLevel() == IssueSeverity.ERROR)
      c++;
  return Integer.toString(c);
}
 

private ValidationResult verifyCodeInCodeSystem(CodeSystem cs, String system, String code,
  String display) throws Exception {
  ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code);
  if (cc == null) {
    if (cs.getContent().equals(CodeSystem.CodeSystemContentMode.COMPLETE)) {
      return new ValidationResult(IssueSeverity.ERROR,
        "Unknown Code " + code + " in " + cs.getUrl());
    } else if (!cs.getContent().equals(CodeSystem.CodeSystemContentMode.NOTPRESENT)) {
      return new ValidationResult(IssueSeverity.WARNING,
        "Unknown Code " + code + " in partial code list of " + cs.getUrl());
    } else {
      return verifyCodeExternal(null,
        new Coding().setSystem(system).setCode(code).setDisplay(display), false);
    }
  }
  //
  //        return new ValidationResult(IssueSeverity.WARNING, "A definition was found for "+cs.getUrl()+", but it has no codes in the definition");
  //      return new ValidationResult(IssueSeverity.ERROR, "Unknown Code "+code+" in "+cs.getUrl());
  if (display == null) {
    return new ValidationResult(cc);
  }
  CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
  if (cc.hasDisplay()) {
    b.append(cc.getDisplay());
    if (display.equalsIgnoreCase(cc.getDisplay())) {
      return new ValidationResult(cc);
    }
  }
  for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
    b.append(ds.getValue());
    if (display.equalsIgnoreCase(ds.getValue())) {
      return new ValidationResult(cc);
    }
  }
  return new ValidationResult(IssueSeverity.WARNING,
    "Display Name for " + code + " must be one of '" + b.toString() + "'", cc);
}
 

private ValidationResult verifyCodeInternal(ValueSet vs, CodeableConcept code) throws Exception {
  for (Coding c : code.getCoding()) {
    ValidationResult res = verifyCodeInternal(vs, c.getSystem(), c.getCode(), c.getDisplay());
    if (res.isOk()) {
      return res;
    }
  }
  if (code.getCoding().isEmpty()) {
    return new ValidationResult(IssueSeverity.ERROR, "None code provided");
  } else {
    return new ValidationResult(IssueSeverity.ERROR,
      "None of the codes are in the specified value set");
  }
}
 

public void logError(int line, int col, String path, IssueType type, String message, IssueSeverity level) throws FHIRFormatError {
  if (policy == ValidationPolicy.EVERYTHING) {
    ValidationMessage msg = new ValidationMessage(Source.InstanceValidator, type, line, col, path, message, level);
    errors.add(msg);
  } else if (level == IssueSeverity.FATAL || (level == IssueSeverity.ERROR && policy == ValidationPolicy.QUICK))
    throw new FHIRFormatError(message+String.format(" at line %d col %d", line, col));
}
 

public String getErrorCount() {
  int c = 0;
  for (ValidationMessage vm : messages)
    if (vm.getLevel() == IssueSeverity.ERROR)
      c++;
  return Integer.toString(c);
}
 

public void logError(int line, int col, String path, IssueType type, String message, IssueSeverity level) throws FHIRFormatError {
  if (policy == ValidationPolicy.EVERYTHING) {
    ValidationMessage msg = new ValidationMessage(Source.InstanceValidator, type, line, col, path, message, level);
    errors.add(msg);
  } else if (level == IssueSeverity.FATAL || (level == IssueSeverity.ERROR && policy == ValidationPolicy.QUICK))
    throw new FHIRFormatError(message+String.format(" at line %d col %d", line, col));
}
 

public void logError(int line, int col, String path, IssueType type, String message, IssueSeverity level) throws FHIRFormatError {
  if (policy == ValidationPolicy.EVERYTHING) {
    ValidationMessage msg = new ValidationMessage(Source.InstanceValidator, type, line, col, path, message, level);
    errors.add(msg);
  } else if (level == IssueSeverity.FATAL || (level == IssueSeverity.ERROR && policy == ValidationPolicy.QUICK))
    throw new FHIRFormatError(message+String.format(" at line %d col %d", line, col));
}
 

private ValidationResult verifyCodeInternal(ValueSet vs, CodeableConcept code) throws FileNotFoundException, ETooCostly, IOException {
  for (Coding c : code.getCoding()) {
    ValidationResult res = verifyCodeInternal(vs, c.getSystem(), c.getCode(), c.getDisplay());
    if (res.isOk())
      return res;
  }
  if (code.getCoding().isEmpty())
    return new ValidationResult(IssueSeverity.ERROR, "None code provided");
  else
    return new ValidationResult(IssueSeverity.ERROR, "None of the codes are in the specified value set");
}
 

private void checkOutcomes(List<ValidationMessage> errors, JsonObject focus) {
  JsonObject output = focus.getAsJsonObject("output");
  int ec = 0;
  int wc = 0;
  int hc = 0;
  List<String> errLocs = new ArrayList<>();
  for (ValidationMessage vm : errors) {
    if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) {
      ec++;
      if (PRINT_OUTPUT_TO_CONSOLE) {
        System.out.println(vm.getDisplay());
      }
      errLocs.add(vm.getLocation());
    }
    if (vm.getLevel() == IssueSeverity.WARNING) {
      wc++;
      if (PRINT_OUTPUT_TO_CONSOLE) {
        System.out.println(vm.getDisplay());
      }
    }
    if (vm.getLevel() == IssueSeverity.INFORMATION) {
      hc++;
      if (PRINT_OUTPUT_TO_CONSOLE) {
        System.out.println(vm.getDisplay());
      }
    }
  }
  Assertions.assertEquals(output.get("errorCount").getAsInt(), ec, "Expected " + Integer.toString(output.get("errorCount").getAsInt()) + " errors, but found " + Integer.toString(ec) + ".");
  if (output.has("warningCount"))
    Assertions.assertEquals(output.get("warningCount").getAsInt(), wc, "Expected " + Integer.toString(output.get("warningCount").getAsInt()) + " warnings, but found " + Integer.toString(wc) + ".");
  if (output.has("infoCount"))
    Assertions.assertEquals(output.get("infoCount").getAsInt(), hc, "Expected " + Integer.toString(output.get("infoCount").getAsInt()) + " hints, but found " + Integer.toString(hc) + ".");
}
 

private static IssueSeverity mapSeverity(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity severity) {
  switch (severity) {
  case ERROR: return IssueSeverity.ERROR;
  case FATAL: return IssueSeverity.FATAL;
  case INFORMATION: return IssueSeverity.INFORMATION;
  case WARNING: return IssueSeverity.WARNING;
  default: return null;
  }
}
 

public void logError(int line, int col, String path, IssueType type, String message, IssueSeverity level) throws FHIRFormatError {
  if (policy == ValidationPolicy.EVERYTHING) {
    ValidationMessage msg = new ValidationMessage(Source.InstanceValidator, type, line, col, path, message, level);
    errors.add(msg);
  } else if (level == IssueSeverity.FATAL || (level == IssueSeverity.ERROR && policy == ValidationPolicy.QUICK))
    throw new FHIRFormatError(message+String.format(" at line %d col %d", line, col));
}
 

private static IssueSeverity mapSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity severity) {
  switch (severity) {
  case ERROR: return IssueSeverity.ERROR;
  case FATAL: return IssueSeverity.FATAL;
  case INFORMATION: return IssueSeverity.INFORMATION;
  case WARNING: return IssueSeverity.WARNING;
  default: return null;
  }
}
 

public boolean hasErrors() {
  for (ValidationMessage vm : messages) {
    if (vm.getLevel() == IssueSeverity.ERROR) {
      return true;
    }
  }
  return false;
}
 

@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem,
    String theCode, String theDisplay, String theValueSetUrl) {
  IssueSeverity severity = IssueSeverity.WARNING;
  String message = "Unsupported CodeSystem";

  if (isCodeSystemSupported(theContext, theCodeSystem)) {
    severity = IssueSeverity.ERROR;
    message = "Code not found";

    CodeSystem cs = codeSystemMap.get(theCodeSystem);
    for (ConceptDefinitionComponent def : cs.getConcept()) {
      if (def.getCode().equals(theCode)) {
        if (def.getDisplay() != null && theDisplay != null) {
          if (def.getDisplay().equals(theDisplay)) {
            severity = IssueSeverity.INFORMATION;
            message = "Validated Successfully";
          } else {
            severity = IssueSeverity.WARNING;
            message = "Validated Code; Display mismatch";
          }
        } else {
          severity = IssueSeverity.WARNING;
          message = "Validated Code; No display";
        }
      }
    }
  }

  ValueSet vs = fetchValueSet(theContext, theValueSetUrl);
  if (vs != null && vs.hasCompose() && vs.getCompose().hasExclude()) {
    for (ConceptSetComponent exclude : vs.getCompose().getExclude()) {
      if (exclude.getSystem().equals(theCodeSystem) && exclude.hasConcept()) {
        for (ConceptReferenceComponent concept : exclude.getConcept()) {
          if (concept.getCode().equals(theCode)) {
            severity = IssueSeverity.ERROR;
            message += "; Code Excluded from ValueSet";
          }
        }
      }
    }
  }

  return new CodeValidationResult(severity, message);
}
 

private ValidationResult serverValidateCode(Parameters pin, boolean doCache) throws Exception {
  if (noTerminologyServer) {
    return new ValidationResult(null, null, TerminologyServiceErrorClass.NOSERVICE);
  }
  String cacheName = doCache ? generateCacheName(pin) : null;
  ValidationResult res = loadFromCache(cacheName);
  if (res != null) {
    return res;
  }
  tlog("Terminology Server: $validate-code " + describeValidationParameters(pin));
  for (ParametersParameterComponent pp : pin.getParameter()) {
    if (pp.getName().equals("profile")) {
      throw new Error("Can only specify profile in the context");
    }
  }
  if (expProfile == null) {
    throw new Exception("No ExpansionProfile provided");
  }
  pin.addParameter().setName("profile").setResource(expProfile);

  Parameters pout = txServer.operateType(ValueSet.class, "validate-code", pin);
  boolean ok = false;
  String message = "No Message returned";
  String display = null;
  TerminologyServiceErrorClass err = TerminologyServiceErrorClass.UNKNOWN;
  for (ParametersParameterComponent p : pout.getParameter()) {
    if (p.getName().equals("result")) {
      ok = ((BooleanType) p.getValue()).getValue().booleanValue();
    } else if (p.getName().equals("message")) {
      message = ((StringType) p.getValue()).getValue();
    } else if (p.getName().equals("display")) {
      display = ((StringType) p.getValue()).getValue();
    } else if (p.getName().equals("cause")) {
      try {
        IssueType it = IssueType.fromCode(((StringType) p.getValue()).getValue());
        if (it == IssueType.UNKNOWN) {
          err = TerminologyServiceErrorClass.UNKNOWN;
        } else if (it == IssueType.NOTSUPPORTED) {
          err = TerminologyServiceErrorClass.VALUESET_UNSUPPORTED;
        }
      } catch (FHIRException e) {
      }
    }
  }
  if (!ok) {
    res = new ValidationResult(IssueSeverity.ERROR, message, err);
  } else if (display != null) {
    res = new ValidationResult(new ConceptDefinitionComponent().setDisplay(display));
  } else {
    res = new ValidationResult(new ConceptDefinitionComponent());
  }
  saveToCache(res, cacheName);
  return res;
}
 

@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem,
    String theCode, String theDisplay, String theValueSetUrl) {
  IssueSeverity severity = IssueSeverity.WARNING;
  String message = "Unsupported CodeSystem";

  if (isCodeSystemSupported(theContext, theCodeSystem)) {
    severity = IssueSeverity.ERROR;
    message = "Code not found";

    CodeSystem cs = codeSystemMap.get(theCodeSystem);
    for (ConceptDefinitionComponent def : cs.getConcept()) {
      if (def.getCode().equals(theCode)) {
        if (def.getDisplay() != null && theDisplay != null) {
          if (def.getDisplay().equals(theDisplay)) {
            severity = IssueSeverity.INFORMATION;
            message = "Validated Successfully";
          } else {
            severity = IssueSeverity.WARNING;
            message = "Validated Code; Display mismatch";
          }
        } else {
          severity = IssueSeverity.WARNING;
          message = "Validated Code; No display";
        }
      }
    }
  }

  ValueSet vs = fetchValueSet(theContext, theValueSetUrl);
  if (vs != null && vs.hasCompose() && vs.getCompose().hasExclude()) {
    for (ConceptSetComponent exclude : vs.getCompose().getExclude()) {
      if (exclude.getSystem().equals(theCodeSystem) && exclude.hasConcept()) {
        for (ConceptReferenceComponent concept : exclude.getConcept()) {
          if (concept.getCode().equals(theCode)) {
            severity = IssueSeverity.ERROR;
            message += "; Code Excluded from ValueSet";
          }
        }
      }
    }
  }

  return new CodeValidationResult(severity, message);
}