Cosmos Indexing Integration

Microsoft.Health.Dicom.sln

@@ -28,9 +28,13 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Dicom.Core
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Dicom.Api", "src\Microsoft.Health.Dicom.Api\Microsoft.Health.Dicom.Api.csproj", "{B0570D75-E376-44AC-870B-87ECB54F0AE3}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Microsoft.Health.Dicom.Api.UnitTests", "src\Microsoft.Health.Dicom.Api.UnitTests\Microsoft.Health.Dicom.Api.UnitTests.csproj", "{D7B538E5-8B3B-487C-8F6A-475F80C50DFE}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Dicom.Api.UnitTests", "src\Microsoft.Health.Dicom.Api.UnitTests\Microsoft.Health.Dicom.Api.UnitTests.csproj", "{D7B538E5-8B3B-487C-8F6A-475F80C50DFE}"
 EndProject
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Microsoft.Health.Dicom.Core.UnitTests", "src\Microsoft.Health.Dicom.Core.UnitTests\Microsoft.Health.Dicom.Core.UnitTests.csproj", "{FA0484A7-AA0C-4CC6-A75F-1D6B23DD847D}"
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Dicom.Core.UnitTests", "src\Microsoft.Health.Dicom.Core.UnitTests\Microsoft.Health.Dicom.Core.UnitTests.csproj", "{FA0484A7-AA0C-4CC6-A75F-1D6B23DD847D}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Dicom.CosmosDb", "src\Microsoft.Health.Dicom.CosmosDb\Microsoft.Health.Dicom.CosmosDb.csproj", "{E78AB378-6CF4-442A-BC34-81A1B7431ECD}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Microsoft.Health.Dicom.CosmosDb.UnitTests", "src\Microsoft.Health.Dicom.CosmosDb.UnitTests\Microsoft.Health.Dicom.CosmosDb.UnitTests.csproj", "{FA0B32A4-E623-4B24-902D-BFDC6E42E612}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
@@ -78,6 +82,14 @@ Global
 		{FA0484A7-AA0C-4CC6-A75F-1D6B23DD847D}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{FA0484A7-AA0C-4CC6-A75F-1D6B23DD847D}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{FA0484A7-AA0C-4CC6-A75F-1D6B23DD847D}.Release|Any CPU.Build.0 = Release|Any CPU
+		{E78AB378-6CF4-442A-BC34-81A1B7431ECD}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{E78AB378-6CF4-442A-BC34-81A1B7431ECD}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{E78AB378-6CF4-442A-BC34-81A1B7431ECD}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{E78AB378-6CF4-442A-BC34-81A1B7431ECD}.Release|Any CPU.Build.0 = Release|Any CPU
+		{FA0B32A4-E623-4B24-902D-BFDC6E42E612}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{FA0B32A4-E623-4B24-902D-BFDC6E42E612}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{FA0B32A4-E623-4B24-902D-BFDC6E42E612}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{FA0B32A4-E623-4B24-902D-BFDC6E42E612}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -93,6 +105,8 @@ Global
 		{B0570D75-E376-44AC-870B-87ECB54F0AE3} = {176641B3-297C-4E04-A83D-8F80F80485E8}
 		{D7B538E5-8B3B-487C-8F6A-475F80C50DFE} = {176641B3-297C-4E04-A83D-8F80F80485E8}
 		{FA0484A7-AA0C-4CC6-A75F-1D6B23DD847D} = {176641B3-297C-4E04-A83D-8F80F80485E8}
+		{E78AB378-6CF4-442A-BC34-81A1B7431ECD} = {176641B3-297C-4E04-A83D-8F80F80485E8}
+		{FA0B32A4-E623-4B24-902D-BFDC6E42E612} = {176641B3-297C-4E04-A83D-8F80F80485E8}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		RESX_SortFileContentOnSave = True

build/build.yml

@@ -2,39 +2,36 @@ parameters:
   packageArtifacts: true
 
 steps:
-- task: DotNetCoreInstaller@0
-  inputs:
-    version: '2.2.103' 
-
-- script: dotnet build --configuration $(buildConfiguration) --version-suffix $(build.buildNumber) /warnaserror
-  displayName: 'dotnet build $(buildConfiguration)'
-
-# To run the tests we install NPM to run the 'azurite' emulator (https://github.com/Azure/Azurite).
-# This allows us to test the blob storage providers without an Azure instance.
-- task: NodeTool@0
-  displayName: 'Use Node 8.x'
-  inputs:
-    versionSpec: 8.x
-    checkLatest: true
-
-- script: npm install -g azurite@2.7.0
-  displayName: 'Install Azurite v2.7.0'
-
-# We start the Azurite as a separate process as the start call is blocking.
-- script: azurite -s &
-  condition: and(succeeded(), eq( variables['Agent.OS'], 'Linux' ))
-  displayName: 'Start Azurite Storage Emulator (Linux)'
-
-- script: start azurite -s
-  condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
-  displayName: 'Start Azurite Storage Emulator (Windows)'
-
-- task: DotNetCoreCLI@2
-  displayName: 'dotnet test UnitTests'
-  inputs:
-    command: test
-    projects: '**\*Tests*.csproj'
-    arguments: '--configuration $(buildConfiguration)'
-
-- ${{ if eq(parameters.packageArtifacts, 'true') }}:
-  - template: package.yml
+
+  - task: NuGetToolInstaller@0
+    displayName: 'Use NuGet 4.7.1'
+    inputs:
+      versionSpec: 4.7.1
+      checkLatest: true
+
+  - task: DotNetCoreInstaller@0
+    inputs:
+      version: '2.2.103' 
+
+  - task:  DotNetCoreCLI@2
+    displayName: 'donet restore'
+    inputs:
+      command: restore
+      restoreSolution: '**\*.sln'
+      feedsToUse: config
+      nugetConfigPath: nuget.config
+
+  - script: dotnet build --configuration $(buildConfiguration) --version-suffix $(build.buildNumber) /warnaserror
+    displayName: 'dotnet build $(buildConfiguration)'
+
+  - task: DotNetCoreCLI@2
+    displayName: 'dotnet test UnitTests'
+    inputs:
+      command: test
+      projects: '**/*UnitTests/*.csproj'
+      arguments: '--configuration $(buildConfiguration)'
+
+  - template: test.yml
+
+  - ${{ if eq(parameters.packageArtifacts, 'true') }}:
+    - template: package.yml

build/test.yml

@@ -0,0 +1,53 @@
+
+steps:
+
+  # To run the tests we install NPM to run the 'azurite' emulator (https://github.com/Azure/Azurite).
+  # This allows us to test the blob storage providers without an Azure instance.
+  - task: NodeTool@0
+    displayName: 'Use Node 8.x'
+    inputs:
+      versionSpec: 8.x
+      checkLatest: true
+
+  - script: npm install -g azurite@2.7.0
+    displayName: 'Install Azurite v2.7.0'
+
+  # We start the Azurite as a separate process as the start call is blocking.
+  - script: azurite -s &
+    condition: and(succeeded(), eq( variables['Agent.OS'], 'Linux' ))
+    displayName: 'Start Azurite Storage Emulator (Linux)'
+
+  - script: start azurite -s
+    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
+    displayName: 'Start Azurite Storage Emulator (Windows)'
+
+  # Currently the Cosmos DB Emulator only runs on Windows. Therefore all end to end testing
+  # is performed on windows.
+  - powershell: |
+      $cosmosemulator=[Environment]::GetEnvironmentVariable("ProgramFiles") + "\Azure Cosmos DB Emulator\CosmosDB.Emulator.exe"
+      & $cosmosemulator /noui
+      $location = 'https://localhost:8081/_explorer/index.html'
+      $statusCode = [int]0
+      while ($statusCode -ne 200)
+      {
+        Try
+        {
+          $req = [system.Net.WebRequest]::Create($location)
+          $response = $req.GetResponse()
+          $statusCode = [int]$response.StatusCode
+          $location + " status code: " + $statusCode
+          $response.Close()
+        } Catch {
+          $PSItem.ToString()
+        }
+      }    
+    displayName: 'Start Installed Cosmos Emulator'
+    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
+
+  - task: DotNetCoreCLI@2
+    displayName: 'Run all tests (Windows)'
+    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
+    inputs:
+      command: test
+      projects: '**\*Tests*.csproj'
+      arguments: '--configuration $(buildConfiguration)'

src/Microsoft.Health.Dicom.Blob/Features/Storage/DicomBlobDataStore.cs

@@ -13,6 +13,7 @@
 using Microsoft.Extensions.Logging;
 using Microsoft.Extensions.Options;
 using Microsoft.Health.Blob.Configs;
+using Microsoft.Health.Dicom.Core.Features.Persistence;
 
 namespace Microsoft.Health.Dicom.Blob.Features.Storage
 {

src/Microsoft.Health.Dicom.Core.UnitTests/Features/Persistence/DicomAttributeIdExtensionsTests.cs

@@ -0,0 +1,72 @@
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+
+using System;
+using Dicom;
+using Microsoft.Health.Dicom.Core.Features.Persistence;
+using Xunit;
+
+namespace Microsoft.Health.Dicom.Core.UnitTests.Features.Persistence
+{
+    public class DicomAttributeIdExtensionsTests
+    {
+        [Fact]
+        public void GivenDatasetAndInvalidParameters_WhenFetchedAttributeValues_ArgumentExceptionIsThrown()
+        {
+            var dicomDataset = new DicomDataset();
+            Assert.Throws<ArgumentNullException>(() => dicomDataset.TryGetValues((DicomAttributeId)null, out object[] values));
+        }
+
+        [Fact]
+        public void GivenDataset_WhenFetchingMissingAttribute_FalseIsReturned()
+        {
+            var dicomDataset = new DicomDataset();
+            var result = dicomDataset.TryGetValues(new DicomAttributeId(DicomTag.PatientName), out object[] values);
+
+            Assert.False(result);
+            Assert.Null(values);
+        }
+
+        [Fact]
+        public void GivenDatasetWithSequence_WhenFetchingAttributeValues_IsReturnedCorrectly()
+        {
+            var sequence1 = new DicomSequence(
+                DicomTag.ReferencedPatientSequence,
+                new DicomDataset() { { DicomTag.PatientName, "Patient1" } },
+                new DicomDataset() { { DicomTag.PatientName, "Patient2" } },
+                new DicomDataset() { { DicomTag.PatientName, "Patient3" } });
+
+            var fetchedValues1 = new DicomDataset() { sequence1 }.TryGetValues(
+                                        new DicomAttributeId(DicomTag.ReferencedPatientSequence, DicomTag.PatientName),
+                                        out object[] values1);
+            Assert.True(fetchedValues1);
+            Assert.Equal(3, values1.Length);
+            Assert.Contains("Patient1", values1);
+            Assert.Contains("Patient2", values1);
+            Assert.Contains("Patient3", values1);
+
+            var sequence2 = new DicomSequence(
+                DicomTag.ReferencedStudySequence,
+                new DicomDataset() { { DicomTag.StudyDate, new DateTime(2019, 6, 25) } },
+                new DicomDataset() { { new DicomSequence(DicomTag.ReferencedStudySequence, new DicomDataset() { { DicomTag.StudyDate, new DateTime(2019, 6, 24) } }) } },
+                new DicomDataset() { { DicomTag.StudyDate, new DateTime(2019, 6, 23) } });
+
+            var fetchedValues2 = new DicomDataset() { sequence2 }.TryGetValues(
+                                        new DicomAttributeId(DicomTag.ReferencedStudySequence, DicomTag.StudyDate),
+                                        out object[] values2);
+            Assert.True(fetchedValues2);
+            Assert.Equal(2, values2.Length);
+            Assert.Contains(new DateTime(2019, 6, 25), values2);
+            Assert.Contains(new DateTime(2019, 6, 23), values2);
+
+            var fetchedValues3 = new DicomDataset() { sequence2 }.TryGetValues(
+                                        new DicomAttributeId(DicomTag.ReferencedStudySequence, DicomTag.ReferencedStudySequence, DicomTag.StudyDate),
+                                        out object[] values3);
+            Assert.True(fetchedValues3);
+            Assert.Single(values3);
+            Assert.Contains(new DateTime(2019, 6, 24), values3);
+        }
+    }
+}

src/Microsoft.Health.Dicom.Core.UnitTests/Features/Persistence/DicomAttributeIdTests.cs

@@ -0,0 +1,67 @@
+// -------------------------------------------------------------------------------------------------
+// Copyright (c) Microsoft Corporation. All rights reserved.
+// Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+// -------------------------------------------------------------------------------------------------
+using System;
+using Dicom;
+using Microsoft.Health.Dicom.Core.Features.Persistence;
+using Newtonsoft.Json;
+using Xunit;
+
+namespace Microsoft.Health.Dicom.Core.UnitTests.Features.Persistence
+{
+    public class DicomAttributeIdTests
+    {
+        [Fact]
+        public void GivenDicomAttributeId_WhenConstructingWithInvalidParameters_ArgumentExceptionThrown()
+        {
+            Assert.Throws<ArgumentNullException>(() => new DicomAttributeId((DicomTag[])null));
+            Assert.Throws<ArgumentException>(() => new DicomAttributeId(Array.Empty<DicomTag>()));
+            Assert.Throws<FormatException>(() => new DicomAttributeId(DicomTag.RightImageSequence));
+            Assert.Throws<FormatException>(() => new DicomAttributeId(DicomTag.RightImageSequence, DicomTag.ROIContourSequence));
+            Assert.Throws<FormatException>(() => new DicomAttributeId(DicomTag.StudyDate, DicomTag.RightLensSequence));
+
+            Assert.Throws<ArgumentNullException>(() => new DicomAttributeId((string)null));
+            Assert.Throws<ArgumentException>(() => new DicomAttributeId(string.Empty));
+            Assert.Throws<FormatException>(() => new DicomAttributeId("0020000D.0020000D"));
+            Assert.Throws<FormatException>(() => new DicomAttributeId("INVALID"));
+            Assert.Throws<FormatException>(() => new DicomAttributeId("INVALID.INVALID"));
+
+            Assert.Throws<ArgumentOutOfRangeException>(() => new DicomAttributeId(DicomTag.StudyDate).GetDicomTag(-1));
+            Assert.Throws<ArgumentOutOfRangeException>(() => new DicomAttributeId(DicomTag.StudyDate).GetDicomTag(1));
+        }
+
+        [Fact]
+        public void GivenValidDicomAttributeId_WhenSerialized_IsDeserializedCorrectly()
+        {
+            SerializeAndDeserialize(new DicomAttributeId(DicomTag.StudyDate));
+            SerializeAndDeserialize(new DicomAttributeId(DicomTag.RelatedSeriesSequence, DicomTag.RegistrationSequence, DicomTag.RegisteredLocalizerUnits));
+            SerializeAndDeserialize(new DicomAttributeId(DicomTag.RegionPixelShiftSequence, DicomTag.NumberOfVerticalPixels));
+            SerializeAndDeserialize(new DicomAttributeId("0020000D"));
+            SerializeAndDeserialize(new DicomAttributeId("00101002.00100020"));
+            SerializeAndDeserialize(new DicomAttributeId("00101002.00100024.00400032"));
+            SerializeAndDeserialize(new DicomAttributeId("StudyInstanceUID"));
+            SerializeAndDeserialize(new DicomAttributeId("OtherPatientIDsSequence.PatientID"));
+            SerializeAndDeserialize(new DicomAttributeId("OtherPatientIDsSequence.IssuerOfPatientIDQualifiersSequence.UniversalEntityID"));
+        }
+
+        [Fact]
+        public void GivenValidDicomAttributeId_WhenCompared_IsComparedCorrectly()
+        {
+            Assert.Equal(new DicomAttributeId(DicomTag.StudyInstanceUID), new DicomAttributeId("StudyInstanceUID"));
+            Assert.Equal(new DicomAttributeId(DicomTag.OtherPatientIDsSequence, DicomTag.PatientID), new DicomAttributeId("OtherPatientIDsSequence.PatientID"));
+
+            Assert.Equal(
+                new DicomAttributeId(DicomTag.OtherPatientIDsSequence, DicomTag.IssuerOfPatientIDQualifiersSequence, DicomTag.UniversalEntityID),
+                new DicomAttributeId("OtherPatientIDsSequence.IssuerOfPatientIDQualifiersSequence.UniversalEntityID"));
+        }
+
+        private void SerializeAndDeserialize(DicomAttributeId dicomAttributeId)
+        {
+            var json = JsonConvert.SerializeObject(dicomAttributeId);
+            var deserialized = JsonConvert.DeserializeObject<DicomAttributeId>(json);
+
+            Assert.Equal(dicomAttributeId, deserialized);
+        }
+    }
+}