public void GivenANodesByNameRule_WhenProcess_AllNodesShouldBeProcessed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("nodesByName('city')", "nodesByName('city')", "", "redact", AnonymizerRuleType.FhirPathRule, "nodesByName('city')"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var organization = CreateTestOrganization();
var person = CreateTestPerson();
patient.Contained.Add(organization);
organization.Contained.Add(person);
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var personCity = patientNode.Select("Patient.contained[0].contained[0].address[0].city").FirstOrDefault();
var personCountry = patientNode.Select("Patient.contained[0].contained[0].address[0].country").First().Value.ToString();
var organizationCity = patientNode.Select("Patient.contained[0].address[0].city").FirstOrDefault();
var organizationCountry = patientNode.Select("Patient.contained[0].address[0].country").First().Value.ToString();
var patientCity = patientNode.Select("Patient.address[0].city").FirstOrDefault();
var patientCountry = patientNode.Select("Patient.address[0].country").First().Value.ToString();
Assert.Null(personCity);
Assert.Null(organizationCity);
Assert.Null(patientCity);
Assert.Equal("persontestcountry", personCountry);
Assert.Equal("OrgTestCountry", organizationCountry);
Assert.Equal("patienttestcountry1", patientCountry);
}
public void GivenANodesByTypeRule_WhenProcess_AllNodesShouldBeProcessed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("nodesByType('Address')", "nodesByType('Address')", "", "redact", AnonymizerRuleType.FhirPathRule, "nodesByType('Address')"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var org = CreateTestOrganization();
var person = CreateTestPerson();
patient.Contained.Add(org);
org.Contained.Add(person);
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var personAddress = patientNode.Select("Patient.contained[0].contained[0].address[0]").FirstOrDefault();
var patientAddress = patientNode.Select("Patient.address[0]").FirstOrDefault();
Assert.Null(personAddress);
Assert.Null(patientAddress);
}
public void GivenAFhirPathMatchContainedNode_WhenProcess_NodesInContainedShouldBeRedact()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Person.address.city", "address.city", "Person", "redact", AnonymizerRuleType.FhirPathRule, "Person.address"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var org = CreateTestOrganization();
var person = CreateTestPerson();
patient.Contained.Add(org);
org.Contained.Add(person);
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var personCity = patientNode.Select("Patient.contained[0].contained[0].address[0].city[0]").FirstOrDefault();
Assert.Null(personCity);
patient = patientNode.ToPoco <Patient>();
Assert.Single(patient.Meta.Security);
Assert.Contains(SecurityLabels.REDACT.Code, patient.Meta.Security.Select(s => s.Code));
Assert.Null(patient.Contained[0].Meta);
}
public void GivenABundleWith2RuleOfDifferentMethods_WhenProcess_SecurityTagShouldBeAddedCorrectly()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Patient.nodesByType('date')", "nodesByType('date')", "", "dateshift", AnonymizerRuleType.FhirPathRule, "Patient.nodesByType('date')"),
new AnonymizationFhirPathRule("Person.nodesByType('Address')", "nodesByType('Address')", "Person", "redact", AnonymizerRuleType.FhirPathRule, "Person.nodesByType('Address')"),
};
var person = CreateTestPerson();
var patient = CreateTestPatient();
var bundle = new Bundle();
bundle.AddResourceEntry(person, "http://example.org/fhir/Person/1");
bundle.AddResourceEntry(patient, "http://example.org/fhir/Patient/1");
var bundleNode = ElementNode.FromElement(bundle.ToTypedElement());
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
bundleNode.Accept(visitor);
bundleNode.RemoveEmptyNodes();
bundle = bundleNode.ToPoco <Bundle>();
Assert.Equal(2, bundle.Meta.Security.Count);
Assert.Contains(SecurityLabels.REDACT.Code, bundle.Meta.Security.Select(s => s.Code));
Assert.Contains(SecurityLabels.PERTURBED.Code, bundle.Meta.Security.Select(s => s.Code));
Resource resource = bundle.Entry[0].Resource;
Assert.Single(resource.Meta.Security);
Assert.Contains(SecurityLabels.REDACT.Code, resource.Meta.Security.Select(s => s.Code));
resource = bundle.Entry[1].Resource;
Assert.Single(resource.Meta.Security);
Assert.Contains(SecurityLabels.PERTURBED.Code, resource.Meta.Security.Select(s => s.Code));
}
public void GivenAPatientWithOnlyId_WhenProcess_NodeShouldBeRedact()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Patient.id", "id", "Patient", "redact", AnonymizerRuleType.FhirPathRule, "Patient.id"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = new Patient();
patient.Id = "Test";
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var patientId = patientNode.Select("Patient.id").FirstOrDefault();
Assert.Null(patientId);
patient = patientNode.ToPoco <Patient>();
Assert.Single(patient.Meta.Security);
Assert.Contains(SecurityLabels.REDACT.Code, patient.Meta.Security.Select(s => s.Code));
}
public void GivenAnEncryptRule_WhenProcess_NodeShouldBeEncrypted()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Patient.address", "address", "Patient", "encrypt", AnonymizerRuleType.FhirPathRule, "Patient.address"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var patientCity = patientNode.Select("Patient.address[0].city").FirstOrDefault();
var key = Encoding.UTF8.GetBytes("1234567890123456");
var plainValue = EncryptUtility.DecryptTextFromBase64WithAes(patientCity.Value.ToString(), key);
Assert.Equal("patienttestcity1", plainValue);
patient = patientNode.ToPoco <Patient>();
Assert.Single(patient.Meta.Security);
Assert.Contains(SecurityLabels.MASKED.Code, patient.Meta.Security.Select(s => s.Code));
}
public void GivenARedactRuleAndThenAPerturbRule_WhenProcess_NodeShouldBeRedacted()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Observation.referenceRange.low.value", "referenceRange.low.value", "Observation", "redact", AnonymizerRuleType.FhirPathRule, "Observation.referenceRange.low.value"),
new AnonymizationFhirPathRule("Observation.referenceRange.low", "referenceRange.low", "Observation", "perturb", AnonymizerRuleType.FhirPathRule, "Observation.referenceRange.low",
new Dictionary <string, object> {
{ "span", "2" }
}),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var observation = CreateTestObservation();
var observationNode = ElementNode.FromElement(observation.ToTypedElement());
observationNode.Accept(visitor);
var lowNode = observationNode.Select("Observation.referenceRange.low");
var perturbedValue = lowNode.Children("value").First().Value;
Assert.Null(perturbedValue);
observation = observationNode.ToPoco <Observation>();
Assert.Contains(SecurityLabels.REDACT.Code, observation.Meta.Security.Select(s => s.Code));
Assert.DoesNotContain(SecurityLabels.PERTURBED.Code, observation.Meta.Security.Select(s => s.Code));
}
public void GivenAPerturbRule_WhenProcess_NodeShouldBePerturbed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Observation.referenceRange.low", "referenceRange.low", "Observation", "perturb", AnonymizerRuleType.FhirPathRule, "Observation.referenceRange.low",
new Dictionary <string, object> {
{ "span", 4 }
}),
new AnonymizationFhirPathRule("Observation.referenceRange.high.value", "referenceRange.high.value", "Observation", "perturb", AnonymizerRuleType.FhirPathRule, "Observation.referenceRange.high.value",
new Dictionary <string, object> {
{ "span", 0.2 }, { "rangeType", "proportional" }
})
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var observation = CreateTestObservation();
var observationNode = ElementNode.FromElement(observation.ToTypedElement());
observationNode.Accept(visitor);
observationNode.RemoveEmptyNodes();
var lowNode = observationNode.Select("Observation.referenceRange.low");
var perturbedValue = decimal.Parse(lowNode.Children("value").First().Value.ToString());
Assert.InRange(perturbedValue, 8, 12);
var highNode = observationNode.Select("Observation.referenceRange.high");
perturbedValue = decimal.Parse(highNode.Children("value").First().Value.ToString());
Assert.InRange(perturbedValue, 90, 110);
observation = observationNode.ToPoco <Observation>();
Assert.Contains(SecurityLabels.PERTURBED.Code, observation.Meta.Security.Select(s => s.Code));
}
private IEnumerable <ITypedElement> GetMatchNodes(AnonymizationFhirPathRule rule, ITypedElement node)
{
var typeMatch = AnonymizationFhirPathRule.TypeRuleRegex.Match(rule.Path);
var nameMatch = AnonymizationFhirPathRule.NameRuleRegex.Match(rule.Path);
if (typeMatch.Success)
{
return(GetMatchNodesFromLookUp(_typeToNodeLookUp, typeMatch.Groups["type"].Value, typeMatch.Groups["expression"].Value));
}
if (nameMatch.Success)
{
return(GetMatchNodesFromLookUp(_nameToNodeLookUp, nameMatch.Groups["name"].Value, nameMatch.Groups["expression"].Value));
}
/*
* Special case handling:
* Senario: FHIR path only contains resourceType: Patient, Resource.
* Sample AnonymizationFhirPathRule: { "path": "Patient", "method": "keep" }
*
* Current FHIR path lib do not support navigate such ResourceType FHIR path from resource in bundle.
* Example: navigate with FHIR path "Patient" from "Bundle.entry[0].resource[0]" is not support
*/
return(rule.IsResourceTypeRule ? new List <ITypedElement> {
node
} : node.Select(rule.Expression).ToList());
}
public void GivenAKeepRuleAndThenANodesByTypeRule_WhenProcess_NodesShouldBeProcessedCorrectly()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Person.address.country", "Person.address.country", "Person", "keep", AnonymizerRuleType.FhirPathRule, "Person.address.country"),
new AnonymizationFhirPathRule("nodesByType('Address')", "nodesByType('Address')", "", "redact", AnonymizerRuleType.FhirPathRule, "nodesByType('Address')"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var person = CreateTestPerson();
patient.Contained.Add(person);
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var patientAddress = patientNode.Select("Patient.address[0]").FirstOrDefault();
var personAddress = patientNode.Select("Patient.contained[0].address[0]").FirstOrDefault();
var personCity = patientNode.Select("Patient.contained[0].address[0].city").FirstOrDefault();
var personCountry = patientNode.Select("Patient.contained[0].address[0].country").First().Value.ToString();
Assert.Null(patientAddress);
Assert.NotNull(personAddress);
Assert.Null(personCity);
Assert.Equal("persontestcountry", personCountry);
}
public void GivenANodesByTypeRuleWithResourceType_WhenProcess_OnlyNodesInSpecificResourceTypeShouldBeProcessed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Person.nodesByType('Address')", "nodesByType('Address')", "Person", "redact", AnonymizerRuleType.FhirPathRule, "Person.nodesByType('Address')"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var org = CreateTestOrganization();
var person = CreateTestPerson();
patient.Contained.Add(org);
org.Contained.Add(person);
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var personAddress = patientNode.Select("Patient.contained[0].contained[0].address[0]").FirstOrDefault();
string patientCity = patientNode.Select("Patient.address[0].city").First().Value.ToString();
string patientCountry = patientNode.Select("Patient.address[0].country").First().Value.ToString();
Assert.Equal("patienttestcity1", patientCity);
Assert.Equal("patienttestcountry1", patientCountry);
Assert.Null(personAddress);
}
public AnonymizerConfigurationManager(AnonymizerConfiguration configuration)
{
_validator.Validate(configuration);
configuration.GenerateDefaultParametersIfNotConfigured();
_configuration = configuration;
FhirPathRules = _configuration.FhirPathRules.Select(entry => AnonymizationFhirPathRule.CreateAnonymizationFhirPathRule(entry)).ToArray();
}
public void GivenAFhirPath_WhenCreatePathRule_FhirRuleShouldBeCreateCorrectly(Dictionary <string, object> config, string expectResourceType, string expectExpression, string expectPath, string expectMethod)
{
var rule = AnonymizationFhirPathRule.CreateAnonymizationFhirPathRule(config);
Assert.Equal(expectPath, rule.Path);
Assert.Equal(expectMethod, rule.Method);
Assert.Equal(expectResourceType, rule.ResourceType);
Assert.Equal(expectExpression, rule.Expression);
}
private void LogProcessResult(ElementNode node, AnonymizationFhirPathRule rule, ProcessResult resultOnRule)
{
if (_logger.IsEnabled(LogLevel.Debug))
{
string resourceId = node.GetNodeId();
foreach (var processRecord in resultOnRule.ProcessRecords)
{
foreach (var matchNode in processRecord.Value)
{
_logger.LogDebug($"[{resourceId}]: Rule '{rule.Path}' matches '{matchNode.Location}' and perform operation '{processRecord.Key}'");
}
}
}
}
public void GivenAFhirPathMatchBundleEntryNode_WhenProcess_NodesInBundleShouldBeRedact()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Person.address.city", "address.city", "Person", "redact", AnonymizerRuleType.FhirPathRule, "Person.address"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var person = CreateTestPerson();
var bundle = new Bundle();
bundle.AddResourceEntry(person, "http://example.org/fhir/Person/1");
var bundleNode = ElementNode.FromElement(bundle.ToTypedElement());
bundleNode.Accept(visitor);
bundleNode.RemoveEmptyNodes();
var personCity = bundleNode.Select("Bundle.entry[0].resource[0].address[0].city[0]").FirstOrDefault();
Assert.Null(personCity);
}
public void Given2ConflictRules_WhenProcess_SecondRuleShouldBeIgnored()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Patient", "Patient", "Patient", "keep", AnonymizerRuleType.FhirPathRule, "Patient"),
new AnonymizationFhirPathRule("Patient.address", "address", "Patient", "redact", AnonymizerRuleType.FhirPathRule, "Patient.address"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
string patientCity = patientNode.Select("Patient.address[0].city").First().Value.ToString();
string patientCountry = patientNode.Select("Patient.address[0].country").First().Value.ToString();
Assert.Equal("patienttestcity1", patientCity);
Assert.Equal("patienttestcountry1", patientCountry);
patient = patientNode.ToPoco <Patient>();
Assert.Null(patient.Meta);
}
public void GivenARuleForAll_WhenProcess_AllTypeNodesShouldBeProcessed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Resource", "Resource", "Resource", "redact", AnonymizerRuleType.FhirPathRule, "Resource"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var patientAddress = patientNode.Select("Patient.address[0]").FirstOrDefault();
Assert.Null(patientAddress);
patient = patientNode.ToPoco <Patient>();
Assert.Single(patient.Meta.Security);
Assert.Contains(SecurityLabels.REDACT.Code, patient.Meta.Security.Select(s => s.Code));
}
public void GivenACryptoHashRule_WhenProcess_NodeShouldBeHashed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Patient.address", "address", "Patient", "cryptoHash", AnonymizerRuleType.FhirPathRule, "Patient.address"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var patientAddress = patientNode.Select("Patient.address[0].city").FirstOrDefault();
Assert.Equal("c4321653de997f3029d2efa38dd4baa6c9c2f6bd67b8a52be789f157f8b286ce", patientAddress.Value.ToString());
patient = patientNode.ToPoco <Patient>();
Assert.Single(patient.Meta.Security);
Assert.Contains(SecurityLabels.CRYTOHASH.Code, patient.Meta.Security.Select(s => s.Code));
}
public void GivenANodesByTypeRuleWithExpressionFunction_WhenProcess_OnlyNodesMatchSpecificExpressionFunctionShouldBeProcessed()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("nodesByType('Address').where(city='patienttestcity1').city", "nodesByType('Address').where(city='patienttestcity1').city", "", "redact", AnonymizerRuleType.FhirPathRule, "nodesByType('Address').where(city='patienttestcity1').city"),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
var patientAddress = patientNode.Select("Patient.address[0]").FirstOrDefault();
var patientCity = patientNode.Select("Patient.address[0].city").FirstOrDefault();
var patientCountry = patientNode.Select("Patient.address[0].country").First().Value.ToString();
Assert.NotNull(patientAddress);
Assert.Null(patientCity);
Assert.Equal("patienttestcountry1", patientCountry);
}
public void GivenAComplexSubstituteRule_WhenProcess_NodeShouldBeSubstituted()
{
AnonymizationFhirPathRule[] rules = new AnonymizationFhirPathRule[]
{
new AnonymizationFhirPathRule("Patient.address", "address", "Patient", "substitute", AnonymizerRuleType.FhirPathRule, "Patient.address",
new Dictionary <string, object> {
{ "replaceWith", "{ \"city\": \"ExampleCity2020\" }" }
}),
};
AnonymizationVisitor visitor = new AnonymizationVisitor(rules, CreateTestProcessors());
var patient = CreateTestPatient();
var patientNode = ElementNode.FromElement(patient.ToTypedElement());
var patientCity = patientNode.Select("Patient.address[0].city").FirstOrDefault();
Assert.Equal("patienttestcity1", patientCity.Value.ToString());
var patientCountry = patientNode.Select("Patient.address[0].country").FirstOrDefault();
Assert.Equal("patienttestcountry1", patientCountry.Value.ToString());
patientNode.Accept(visitor);
patientNode.RemoveEmptyNodes();
patientCity = patientNode.Select("Patient.address[0].city").FirstOrDefault();
Assert.Equal("ExampleCity2020", patientCity.Value.ToString());
patientCountry = patientNode.Select("Patient.address[0].country").FirstOrDefault();
Assert.Null(patientCountry);
var patientCity2 = patientNode.Select("Patient.contact[0].address[0].city").FirstOrDefault();
Assert.Equal("patienttestcity2", patientCity2.Value.ToString());
patient = patientNode.ToPoco <Patient>();
Assert.Single(patient.Meta.Security);
Assert.Contains(SecurityLabels.SUBSTITUTED.Code, patient.Meta.Security.Select(s => s.Code));
}
