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update fhir net api version to 2.0.3 #97

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merged 4 commits into from
Mar 22, 2021
Merged

update fhir net api version to 2.0.3 #97

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29fbc6b
update fhir net api version to 2.0.3
hongyh13 Feb 22, 2021
eea0edc
fix bug
hongyh13 Feb 23, 2021
7b46f4a
unchange readme.md
hongyh13 Mar 9, 2021
b8ab003
Merge branch 'master' into personal/yanhon/update-fhir-net-api-203
hongyh13 Mar 17, 2021
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2 changes: 1 addition & 1 deletion Directory.Build.props
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@@ -1,7 +1,7 @@
<Project>

<PropertyGroup>
<Version>2.1.0</Version>
<Version>2.2.0</Version>
</PropertyGroup>

</Project>
4 changes: 2 additions & 2 deletions ...ir.Anonymizer.R4.Core.UnitTests/Microsoft.Health.Fhir.Anonymizer.R4.Core.UnitTests.csproj
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Expand Up @@ -7,8 +7,8 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="Hl7.Fhir.R4" Version="1.7.0" />
<PackageReference Include="Hl7.FhirPath" Version="1.7.0" />
<PackageReference Include="Hl7.Fhir.R4" Version="2.0.3" />
<PackageReference Include="Hl7.FhirPath" Version="2.0.3" />
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.2.0" />
<PackageReference Include="xunit" Version="2.4.0" />
<PackageReference Include="xunit.runner.visualstudio" Version="2.4.0" />
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4 changes: 2 additions & 2 deletions src/Microsoft.Health.Fhir.Anonymizer.R4.Core/Microsoft.Health.Fhir.Anonymizer.R4.Core.csproj
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Expand Up @@ -8,8 +8,8 @@

<ItemGroup>
<PackageReference Include="Ensure.That" Version="9.2.0" />
<PackageReference Include="Hl7.Fhir.R4" Version="1.7.0" />
<PackageReference Include="Hl7.FhirPath" Version="1.7.0" />
<PackageReference Include="Hl7.Fhir.R4" Version="2.0.3" />
<PackageReference Include="Hl7.FhirPath" Version="2.0.3" />
<PackageReference Include="MathNet.Numerics" Version="4.11.0" />
<PackageReference Include="Microsoft.Extensions.Logging" Version="3.1.2" />
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
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4 changes: 2 additions & 2 deletions ....Anonymizer.R4.FunctionalTests/Microsoft.Health.Fhir.Anonymizer.R4.FunctionalTests.csproj
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Expand Up @@ -7,8 +7,8 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="Hl7.Fhir.R4" Version="1.7.0" />
<PackageReference Include="Hl7.FhirPath" Version="1.7.0" />
<PackageReference Include="Hl7.Fhir.R4" Version="2.0.3" />
<PackageReference Include="Hl7.FhirPath" Version="2.0.3" />
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.2.0" />
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
<PackageReference Include="xunit" Version="2.4.0" />
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22 changes: 19 additions & 3 deletions src/Microsoft.Health.Fhir.Anonymizer.R4.FunctionalTests/VersionSpecificTests.cs
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Expand Up @@ -2,6 +2,7 @@
using System.Collections.Generic;
using System.IO;
using Hl7.FhirPath;
using Hl7.Fhir.ElementModel;
using Microsoft.Health.Fhir.Anonymizer.Core;
using Microsoft.Health.Fhir.Anonymizer.Core.Extensions;
using Xunit;
Expand Down Expand Up @@ -29,9 +30,14 @@ public static IEnumerable<object[]> GetR4OnlyResources()
yield return new object[] { "R4OnlyResource/ServiceRequest.json", "R4OnlyResource/ServiceRequest-target.json" };
}

public static IEnumerable<object[]> GetCommonResourcesWithStu3OnlyField()
public static IEnumerable<object[]> GetCommonResourcesWithStu3OnlyValue()
{
yield return new object[] { "Stu3OnlyResource/Claim-Stu3.json" };

}

public static IEnumerable<object[]> GetCommonResourcesWithStu3OnlyElement()
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{
yield return new object[] { "Stu3OnlyResource/Account-Stu3.json" };
yield return new object[] { "Stu3OnlyResource/Contract-Stu3.json" };
}
Expand Down Expand Up @@ -72,15 +78,25 @@ public void GivenCommonResourceWithR4OnlyField_WhenAnonymizing_AnonymizedJsonSho
}

[Theory]
[MemberData(nameof(GetCommonResourcesWithStu3OnlyField))]
public void GivenCommonResourceWithStu3OnlyField_WhenAnonymizing_ExceptionShouldBeThrown(string testFile)
[MemberData(nameof(GetCommonResourcesWithStu3OnlyValue))]
public void GivenCommonResourceWithStu3OnlyValue_WhenAnonymizing_ExceptionShouldBeThrown(string testFile)
{
AnonymizerEngine engine = new AnonymizerEngine("r4-configuration-sample.json");
string testContent = File.ReadAllText(ResourceTestsFile(testFile));

Assert.Throws<FormatException>(() => engine.AnonymizeJson(testContent));
}

[Theory]
[MemberData(nameof(GetCommonResourcesWithStu3OnlyElement))]
public void GivenCommonResourceWithStu3OnlyElement_WhenAnonymizing_ExceptionShouldBeThrown(string testFile)
{
AnonymizerEngine engine = new AnonymizerEngine("r4-configuration-sample.json");
string testContent = File.ReadAllText(ResourceTestsFile(testFile));

Assert.Throws<StructuralTypeException>(() => engine.AnonymizeJson(testContent));
}

private string ResourceTestsFile(string fileName)
{
return Path.Combine("TestResources", fileName);
Expand Down
2 changes: 1 addition & 1 deletion ....Health.Fhir.Anonymizer.Shared.Core.UnitTests/Extensions/FhirPathSymbolExtensionsTests.cs
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Expand Up @@ -55,7 +55,7 @@ public void GivenListOfPrimitiveElementNodes_WhenGetDecendantsByType_AllNodesSho
FhirBoolean boolean = new FhirBoolean();
FhirString fhirString = new FhirString();

var nodes = new Primitive[] { date, instant, boolean, fhirString }.Select(n => ElementNode.FromElement(n.ToTypedElement()));
var nodes = new PrimitiveType[] { date, instant, boolean, fhirString }.Select(n => ElementNode.FromElement(n.ToTypedElement()));

var results = FhirPathSymbolExtensions.NodesByType(nodes, "string").Select(n => n.Location);
Assert.Single(results);
Expand Down
67 changes: 47 additions & 20 deletions ...osoft.Health.Fhir.Anonymizer.Shared.Core.UnitTests/Processors/GeneralizeProcessorTests.cs
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Expand Up @@ -24,24 +24,24 @@ public static IEnumerable<object[]> GetEmptyNodesToGeneralize()

public static IEnumerable<object[]> GetIntegerNodesToGeneralizeWithRangeMapping()
{
yield return new object[] { new Integer(5), (long)20 };
yield return new object[] { new Integer(20), (long)40 };
yield return new object[] { new Integer(43), (long)60 };
yield return new object[] { new Integer(78), (long)80 };
yield return new object[] { new Integer(5), 20 };
yield return new object[] { new Integer(20), 40 };
yield return new object[] { new Integer(43), 60 };
yield return new object[] { new Integer(78), 80 };
yield return new object[] { new Integer(110), null, "Redact"};
yield return new object[] { new Integer(110), 110, "Keep" };
}

public static IEnumerable<object[]> GetIntegerNodesToGeneralizeWithApproximate()
{
yield return new object[] { new Integer(5), (long)-10 };
yield return new object[] { new Integer(20), (long)10 };
yield return new object[] { new Integer(43), (long)30 };
yield return new object[] { new Integer(78), (long)60 };
yield return new object[] { new Integer(5), -10 };
yield return new object[] { new Integer(20), 10 };
yield return new object[] { new Integer(43), 30 };
yield return new object[] { new Integer(78), 60 };
yield return new object[] { new Integer(110), null, "Redact" };
yield return new object[] { new Integer(110), 110, "Keep" };
yield return new object[] { new PositiveInt(24), (long)10 };
yield return new object[] { new UnsignedInt(24), (long)10 };
yield return new object[] { new PositiveInt(24), 10 };
yield return new object[] { new UnsignedInt(24), 10 };
}

public static IEnumerable<object[]> GetStringNodesToGeneralizeWithValueSet()
Expand All @@ -67,11 +67,14 @@ public static IEnumerable<object[]> GetDateNodesToGeneralizeWithRangeMapping()
yield return new object[] { new Date("1990-01-01"), "1990" };
yield return new object[] { new Date("2000-01-01"), null, "Redact" };
yield return new object[] { new Date("1990"), "1990", "Redact" };
yield return new object[] { new Date("2000"), null, "Redact" };
yield return new object[] { new Date("2010"), "2010-01-01", "Redact" };
yield return new object[] { new Date("2010-01-01"), null, "Redact" };
yield return new object[] { new Date("2000"), "1990", "Redact" };
yield return new object[] { new Date("2000-01-01"), null};
yield return new object[] { new Date("2010"), "2010-01-01"};
yield return new object[] { new Date("2010-01-01"), "2010-01-01" };
yield return new object[] { new Date("2010-01-02"), "2010-01-01" };
yield return new object[] { new Date("2020"), "2020-01-01" };
yield return new object[] { new Date("2020-05-20"), "2020-01-01" };
yield return new object[] { new Date("2020-01-01"), null, "Redact" };
yield return new object[] { new Date("2020-05-20"), null, "Redact" };
yield return new object[] { new Date("2021-05-20"), "2021-05-20", "Keep" };
}

Expand All @@ -88,10 +91,11 @@ public static IEnumerable<object[]> GetDateTimeNodesToGeneralizeWithRangeMapping
yield return new object[] { new FhirDateTime("2010-01-01"), null };
yield return new object[] { new FhirDateTime("2010-01-01T00:00:00Z"), null };
yield return new object[] { new FhirDateTime("2010-01-01T00:00:00+08:00"), "2010-01-01" };
yield return new object[] { new FhirDateTime("2010-01-01T00:00:00+08:00"), "2010-01-01" };
yield return new object[] { new FhirDateTime("2010-01-01T00:00:00+09:00"), null };
yield return new object[] { new FhirDateTime("2009-12-31T16:00:00Z"), "2010-01-01" };
yield return new object[] { new FhirDateTime("2020-01-01T00:00:00+08:00"), "2020-01-01" };
yield return new object[] { new FhirDateTime("2020-01-01"), "2020-01-01" };
yield return new object[] { new FhirDateTime("2020-01-01T00:00:00"), "2020-01-01" };
yield return new object[] { new FhirDateTime("2020-01-01T00:00:00+08:00"), null};
yield return new object[] { new FhirDateTime("2020-01-01"), null };
}

public static IEnumerable<object[]> GetTimeNodesToGeneralizeWithRangeMapping()
Expand Down Expand Up @@ -127,14 +131,18 @@ public static IEnumerable<object[]> GetDateTimeNodesToGeneralizeWithOmitDay()

public static IEnumerable<object[]> GetInvalidCasesExpressions()
{
yield return new object[] { new Integer(5), "{\"$this>='0' and $this<'20'\":\"20\"}" };
yield return new object[] { new Integer(5), "{\"$this>=0 and $this<20\":\"$this / 2\"}" };
yield return new object[] { new Integer(5), "{\"$this<5.5\":\"$this\"}" };
yield return new object[] { new Integer(5), "{\"$this>='0' and $this<'20'\":\"20\"}" };
yield return new object[] { new FhirDateTime("2015-01-01T00:00:00Z"), "{\"$this > @2015-1-1\":\"@2015-01-01\"}" };
yield return new object[] { new Date("2015-01-01"), "{\"$this > @2015-1-1\":\"@2015-01-01\"}" };
yield return new object[] { new FhirString("2015-01-01"), "{\"$this > @2015-01-01\":\"@2015-01-01\"}" };
}

public static IEnumerable<object[]> GetIntegerDecimalComparingCases()
{
yield return new object[] { new Integer(5), "{\"$this>=0 and $this<20\":\"$this / 2\"}", (decimal)2.5 };
yield return new object[] { new Integer(5), "{\"$this<5.5\":\"$this\"}", 5 };
}

public static IEnumerable<object[]> GetNodesToGeneralizeWithConflictSettings()
{
yield return new object[] { new Integer(18), 20 };
Expand Down Expand Up @@ -263,6 +271,25 @@ public void GivenAnIntegerNode_WhenGeneralizedWithApproximate_GeneralizedNodeSho
Assert.Equal(target, node.Value);
}


[Theory]
[MemberData(nameof(GetIntegerDecimalComparingCases))]
public void GivenIntegerDecimalComparingCases_WhenGeneralized_GeneralizedNodeShouldBeReturned(Base data, string cases, object target)
{
var node = ElementNode.FromElement(data.ToTypedElement());

GeneralizeProcessor processor = new GeneralizeProcessor();
var context = new ProcessContext
{
VisitedNodes = new HashSet<ElementNode>()
};
var settings = new Dictionary<string, object> { { "cases", cases } };

var processResult = processor.Process(node, context, settings);
Assert.True(processResult.IsGeneralized);
Assert.Equal(target, node.Value);
}

[Theory]
[MemberData(nameof(GetStringNodesToGeneralizeWithValueSet))]
public void GivenAStringNode_WhenGeneralizedWithValueSet_GeneralizedNodeShouldBeReturned(Base data, object target, string otherValues = "redact")
Expand Down
4 changes: 2 additions & 2 deletions ...icrosoft.Health.Fhir.Anonymizer.Shared.Core.UnitTests/Processors/PerturbProcessorTests.cs
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Expand Up @@ -90,7 +90,7 @@ public static IEnumerable<object[]> GetQuantityNodesToPerturbFixedSpan()
};
yield return new object[]
{
new SimpleQuantity { Value = decimal.Parse("25,162.1378") },
new Quantity { Value = decimal.Parse("25,162.1378") },
2.26,
2,
25161.01,
Expand Down Expand Up @@ -134,7 +134,7 @@ public static IEnumerable<object[]> GetQuantityNodesToPerturbProportionalSpan()
};
yield return new object[]
{
new SimpleQuantity { Value = decimal.Parse("25,162.1378") },
new Quantity { Value = decimal.Parse("25,162.1378") },
1,
2,
12581.07,
Expand Down
2 changes: 1 addition & 1 deletion ...ealth.Fhir.Anonymizer.Shared.Core.UnitTests/Processors/Settings/GeneralizeSettingTests.cs
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Expand Up @@ -14,6 +14,7 @@ public static IEnumerable<object[]> GetGeneralizeFhirRuleConfigs()
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this<=10 and $this>=0\": \"10\"}" }, { "otherValues", "Keep" } }, "{\r\n \"$this<=10 and $this>=0\": \"10\"\r\n}", "Keep" };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this<=10 and $this>=0\": \"10\"}" }, { "otherValues", "Redact" } }, "{\r\n \"$this<=10 and $this>=0\": \"10\"\r\n}", "Redact" };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"\": \"\"}" }, { "otherValues", "Redact" } }, "{\r\n \"\": \"\"\r\n}", "Redact" };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this = @2015-01-01T00:00\": \"@2015-01-01T00:00:00Z\"}" } }, "{\r\n \"$this = @2015-01-01T00:00\": \"@2015-01-01T00:00:00Z\"\r\n}", "Redact" };
}

public static IEnumerable<object[]> GetInvalidGeneralizeFhirRuleConfigs()
Expand All @@ -23,7 +24,6 @@ public static IEnumerable<object[]> GetInvalidGeneralizeFhirRuleConfigs()
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this sub 1\": \"10\"}" } } };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this<10\"+ \"10++\"}" } } };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this<10\": \"10\"}" }, { "otherValues", "unknown" } } };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"$this = @2015-01-01T00:00\": \"@2015-01-01T00:00:00Z\"}" }} };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "cases", "{\"\": \"\"}" }, { "otherValues", "Redact" } } };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "method", "generalize" }, { "otherValues", "Keep" } } };
yield return new object[] { new Dictionary<string, object>() { { "path", "Patient.birthDate" }, { "cases", "{\"$this<10\": \"10\"}" }, { "otherValues", "Keep" } } };
Expand Down
4 changes: 2 additions & 2 deletions ...rosoft.Health.Fhir.Anonymizer.Shared.Core.UnitTests/Visitors/AnonymizationVisitorTests.cs
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Expand Up @@ -563,8 +563,8 @@ private Observation CreateTestObservation()
observation.ReferenceRange.Add(
new Observation.ReferenceRangeComponent
{
Low = new SimpleQuantity { Value = 10, Unit = "TestUnit" },
High = new SimpleQuantity { Value = 100},
Low = new Quantity { Value = 10, Unit = "TestUnit" },
High = new Quantity { Value = 100},
});
return observation;
}
Expand Down
3 changes: 0 additions & 3 deletions src/Microsoft.Health.Fhir.Anonymizer.Shared.Core/Processors/GeneralizeProcessor.cs
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Expand Up @@ -4,8 +4,6 @@
using Hl7.Fhir.ElementModel;
using Hl7.Fhir.Model;
using Hl7.FhirPath;
using Hl7.Fhir.Serialization;
using Hl7.Fhir.Support.Model;
using Microsoft.Health.Fhir.Anonymizer.Core.Models;
using Microsoft.Health.Fhir.Anonymizer.Core.Processors.Settings;
using Microsoft.Health.Fhir.Anonymizer.Core.AnonymizerConfigurations;
Expand All @@ -27,7 +25,6 @@ public ProcessResult Process(ElementNode node, ProcessContext context = null, Di
}

var generalizeSetting = GeneralizeSetting.CreateFromRuleSettings(settings);
node.Value = PrimitiveTypeConverter.ConvertTo(node.Value, Primitives.GetNativeRepresentation(node.InstanceType));
foreach (var eachCase in generalizeSetting.Cases)
{
try
Expand Down
4 changes: 2 additions & 2 deletions ...nonymizer.Stu3.Core.UnitTests/Microsoft.Health.Fhir.Anonymizer.Stu3.Core.UnitTests.csproj
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Expand Up @@ -11,8 +11,8 @@
<PrivateAssets>all</PrivateAssets>
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
</PackageReference>
<PackageReference Include="Hl7.Fhir.STU3" Version="1.7.0" />
<PackageReference Include="Hl7.FhirPath" Version="1.7.0" />
<PackageReference Include="Hl7.Fhir.STU3" Version="2.0.3" />
<PackageReference Include="Hl7.FhirPath" Version="2.0.3" />
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.2.0" />
<PackageReference Include="NUnit3TestAdapter" Version="3.15.1" />
<PackageReference Include="xunit" Version="2.4.0" />
Expand Down
4 changes: 2 additions & 2 deletions ...rosoft.Health.Fhir.Anonymizer.Stu3.Core/Microsoft.Health.Fhir.Anonymizer.Stu3.Core.csproj
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Expand Up @@ -8,8 +8,8 @@

<ItemGroup>
<PackageReference Include="Ensure.That" Version="9.2.0" />
<PackageReference Include="Hl7.Fhir.STU3" Version="1.7.0" />
<PackageReference Include="Hl7.FhirPath" Version="1.7.0" />
<PackageReference Include="Hl7.Fhir.STU3" Version="2.0.3" />
<PackageReference Include="Hl7.FhirPath" Version="2.0.3" />
<PackageReference Include="MathNet.Numerics" Version="4.11.0" />
<PackageReference Include="Microsoft.Extensions.Logging" Version="3.1.2" />
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
Expand Down
4 changes: 2 additions & 2 deletions ...nymizer.Stu3.FunctionalTests/Microsoft.Health.Fhir.Anonymizer.Stu3.FunctionalTests.csproj
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Expand Up @@ -11,8 +11,8 @@
<PrivateAssets>all</PrivateAssets>
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
</PackageReference>
<PackageReference Include="Hl7.Fhir.STU3" Version="1.7.0" />
<PackageReference Include="Hl7.FhirPath" Version="1.7.0" />
<PackageReference Include="Hl7.Fhir.STU3" Version="2.0.3" />
<PackageReference Include="Hl7.FhirPath" Version="2.0.3" />
<PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.4.0" />
<PackageReference Include="xunit" Version="2.4.0" />
Expand Down
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