Merge branch 'master' into release/2.2.1

SMI · Apr 7, 2020 · 7b28bbb · 7b28bbb
2 parents 855354a + a1945bd
commit 7b28bbb
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Showing 11 changed files with 68 additions and 52 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -1,20 +1,35 @@
-language: csharp
+language: generic
 mono: none
-dotnet: 2.2.100
+dist: bionic
+os: linux
 
 addons:
   postgresql: "10"
   apt:
     packages:
     - postgresql-10
     - postgresql-client-10
+    sources:
+    - sourceline: 'deb [arch=amd64] https://packages.microsoft.com/ubuntu/18.04/prod bionic main'
+      key_url: 'https://packages.microsoft.com/keys/microsoft.asc'
+    - sourceline: 'deb [arch=amd64,arm64,armhf] https://packages.microsoft.com/ubuntu/16.04/mssql-server-2017 xenial main'
 
 services:
-  - postgresql
-  - mysql
+- postgresql
+- mysql
+env:
+  global:
+  - MSSQL_SA_PASSWORD="YourStrong!Passw0rd"
+  - ACCEPT_EULA=Y
+  - MSSQL_PID='developer'
+cache:
+  directories:
+  - $HOME/.local/share/NuGet/
+  - $HOME/.nuget
 
 before_script:
-- sudo docker run --name=mssql-server-linux-latest -e 'ACCEPT_EULA=Y' -e 'MSSQL_SA_PASSWORD=YourStrong!Passw0rd' -p 1433:1433 -d microsoft/mssql-server-linux:2017-latest
+- sudo apt-get install -y --no-install-recommends mssql-tools mssql-server dotnet-runtime-2.2 dotnet-sdk-3.1
+- sudo /opt/mssql/bin/mssql-conf -n setup accept-eula
 
 script:
  - dotnet restore

diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -11,3 +11,4 @@
 
 - [Thomas Nind](https://github.com/tznind)
 - [Leandro Tramma](https://github.com/Tallmaris)
+- [James A Sutherland](https://github.com/jas88)
diff --git a/DicomTypeTranslation.Tests/DicomTypeTranslation.Tests.csproj b/DicomTypeTranslation.Tests/DicomTypeTranslation.Tests.csproj
@@ -1,7 +1,6 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <ProjectGuid>{877FAE0D-9EA7-4CA9-ADBB-B47913428ADE}</ProjectGuid>
-    <TargetFramework>netcoreapp2.2</TargetFramework>
+    <TargetFramework>netcoreapp3.1</TargetFramework>
     <AssemblyTitle>DicomTypeTranslation.Tests</AssemblyTitle>
     <Product>DicomTypeTranslation.Tests</Product>
     <Copyright>Copyright ©  2018</Copyright>
@@ -57,10 +56,12 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="fo-dicom.Json" Version="[4.0.4]" />
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.1.0" />
-    <PackageReference Include="NUnit" Version="3.11.0" />
-    <PackageReference Include="NUnit3TestAdapter" Version="3.13.0" />
-    <PackageReference Include="NunitXml.TestLogger" Version="2.1.36" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.5.0" />
+    <PackageReference Include="NUnit" Version="3.12.0" />
+    <PackageReference Include="NUnit3TestAdapter" Version="3.16.1"><IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
+<PrivateAssets>all</PrivateAssets>
+</PackageReference>
+    <PackageReference Include="NunitXml.TestLogger" Version="2.1.41" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\DicomTypeTranslation\DicomTypeTranslation.csproj" />

diff --git a/DicomTypeTranslation.Tests/JsonDicomConverterTests.cs b/DicomTypeTranslation.Tests/JsonDicomConverterTests.cs
@@ -7,7 +7,6 @@
 using Dicom.Serialization;
 using DicomTypeTranslation.Converters;
 using DicomTypeTranslation.Helpers;
-using DicomTypeTranslation.Tests.ElevationTests;
 using DicomTypeTranslation.Tests.Helpers;
 using Newtonsoft.Json;
 using Newtonsoft.Json.Linq;
@@ -24,7 +23,7 @@ public class JsonDicomConverterTests
 
         private readonly JsonConverter _jsonDicomConverter;
 
-        private static readonly string _dcmDir = Path.Combine(TestContext.CurrentContext.TestDirectory , "TestDicomFiles");
+        private static readonly string _dcmDir = Path.Combine(TestContext.CurrentContext.TestDirectory, "TestDicomFiles");
 
         private readonly string _srDcmPath = Path.Combine(_dcmDir, "report01.dcm");
         private readonly string _imDcmPath = Path.Combine(_dcmDir, "image11.dcm");
@@ -91,14 +90,32 @@ private void VerifyJsonTripleTrip(DicomDataset originalDataset, bool expectFail
 
             // NOTE: Group length elements have been retired from the standard, and have never been included in any JSON conversion.
             // Remove them here to allow comparison between datasets.
-            originalDataset.RemoveGroupLengths();
+            RemoveGroupLengths(originalDataset);
 
             if (expectFail)
                 Assert.False(DicomDatasetHelpers.ValueEquals(originalDataset, recoDataset));
             else
                 Assert.True(DicomDatasetHelpers.ValueEquals(originalDataset, recoDataset));
         }
 
+        /// <summary>
+        /// Removes group length elements from the DICOM dataset. These have been retired in the DICOM standard.
+        /// </summary>
+        /// <remarks><see href="http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.2"/></remarks>
+        /// <param name="dataset">DICOM dataset</param>
+        private static void RemoveGroupLengths(DicomDataset dataset)
+        {
+            if (dataset == null)
+                return;
+
+            dataset.Remove(x => x.Tag.Element == 0x0000);
+
+            // Handle sequences
+            foreach (DicomSequence sq in dataset.Where(x => x.ValueRepresentation == DicomVR.SQ).Cast<DicomSequence>())
+                foreach (DicomDataset item in sq.Items)
+                    RemoveGroupLengths(item);
+        }
+
         private static void ValidatePrivateCreatorsExist(DicomDataset dataset)
         {
             foreach (DicomItem item in dataset)

diff --git a/DicomTypeTranslation.Tests/TestDatabases.xml b/DicomTypeTranslation.Tests/TestDatabases.xml
@@ -9,7 +9,7 @@
   </TestDatabase>
   <TestDatabase>
     <DatabaseType>MySql</DatabaseType>
-    <ConnectionString>server=127.0.0.1;Uid=root;Pwd=;Ssl-Mode=None</ConnectionString>
+    <ConnectionString>server=127.0.0.1;Uid=root;Pwd=;sslmode=None</ConnectionString>
   </TestDatabase>
   <!--         
   <TestDatabase>

diff --git a/DicomTypeTranslation/DicomTypeTranslation.csproj b/DicomTypeTranslation/DicomTypeTranslation.csproj
@@ -17,10 +17,10 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="fo-dicom.NetCore" Version="[4.0.4]" />
-    <PackageReference Include="HIC.FAnsiSql" Version="[0.10.12]" />
-    <PackageReference Include="MongoDB.Driver" Version="[2.8.1]" />
-    <PackageReference Include="Newtonsoft.Json" Version="[12.0.2]" />
-    <PackageReference Include="NLog" Version="[4.6.3]" />
-    <PackageReference Include="YamlDotNet" Version="[6.0.0]" />
+    <PackageReference Include="HIC.FAnsiSql" Version="0.11.1" />
+    <PackageReference Include="MongoDB.Driver" Version="2.10.2" />
+    <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
+    <PackageReference Include="NLog" Version="4.7.0" />
+    <PackageReference Include="YamlDotNet" Version="8.1.0" />
   </ItemGroup>
 </Project>
diff --git a/DicomTypeTranslation/HIC.DicomTypeTranslation.nuspec b/DicomTypeTranslation/HIC.DicomTypeTranslation.nuspec
@@ -14,11 +14,11 @@
     <tags>Dicom,ETL,SQL</tags>
     <dependencies>
       <dependency id="fo-dicom.NetCore" version="4.0.4" />
-      <dependency id="HIC.FAnsiSql" version="0.10.12" />
-      <dependency id="MongoDB.Driver" version="2.8.1" />
-      <dependency id="Newtonsoft.Json" version="12.0.2" />
-	  <dependency id="NLog" version="4.6.3" />
-	  <dependency id="YamlDotNet" version="6.0.0" />
+      <dependency id="HIC.FAnsiSql" version="0.11.1" />
+      <dependency id="MongoDB.Driver" version="2.10.2" />
+      <dependency id="Newtonsoft.Json" version="12.0.3" />
+	  <dependency id="NLog" version="4.7.0" />
+	  <dependency id="YamlDotNet" version="8.1.0" />
     </dependencies>
   </metadata>
   <files>

diff --git a/DicomTypeTranslation/Helpers/DicomDatasetHelpers.cs b/DicomTypeTranslation/Helpers/DicomDatasetHelpers.cs
@@ -1,4 +1,4 @@
-
+
 using Dicom;
 using Dicom.IO.Buffer;
 using JetBrains.Annotations;
@@ -18,6 +18,7 @@ public static class DicomDatasetHelpers
         /// Checks  the correct fo-dicom library is present for the platform at runtime
         /// </summary>
         /// <returns></returns>
+        [Obsolete("This is likely no longer needed since we explicitly build (and fo-dicom provides) packages for both Windows & Linux")]
         [UsedImplicitly]
         public static bool CorrectFoDicomVersion()
         {
@@ -32,25 +33,6 @@ public static bool CorrectFoDicomVersion()
             }
         }
 
-        /// <summary>
-        /// Removes group length elements from the DICOM dataset. These have been retired in the DICOM standard.
-        /// </summary>
-        /// <remarks><see href="http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.2"/></remarks>
-        /// <param name="dataset">DICOM dataset</param>
-        public static void RemoveGroupLengths(this DicomDataset dataset)
-        {
-            if (dataset == null)
-                return;
-
-            dataset.Remove(x => x.Tag.Element == 0x0000);
-
-            // Handle sequences
-            foreach (DicomSequence sq in dataset.Where(x => x.ValueRepresentation == DicomVR.SQ).Cast<DicomSequence>())
-                foreach (DicomDataset item in sq.Items)
-                    item.RemoveGroupLengths();
-        }
-
-
         /// <summary>
         /// Returns true if the elements in <paramref name="a"/> are the same set of tags and values as <paramref name="b"/>
         /// </summary>

diff --git a/DicomTypeTranslation/TableCreation/SystemTypeTypeConverter.cs b/DicomTypeTranslation/TableCreation/SystemTypeTypeConverter.cs
@@ -14,7 +14,7 @@ public bool Accepts(Type type)
 
         public object ReadYaml(IParser parser, Type type)
         {
-            var scalar = parser.Expect<Scalar>();
+            var scalar = parser.Consume<Scalar>();
             return Type.GetType(scalar.Value);
         }
 

diff --git a/Packages.md b/Packages.md
@@ -9,12 +9,12 @@
 
 | Package | Source Code | Version | License | Purpose | Additional Risk Assessment |
 | ------- | ------------| --------| ------- | ------- | -------------------------- |
-| HIC.FAnsiSql |[GitHub](https://github.com/HicServices/FAnsiSql) | [0.10.12](https://www.nuget.org/packages/HIC.FansiSql/0.10.12) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Handles assigning translating database types and DBMS interactions|
-|[MongoDB.Driver](https://docs.mongodb.com/ecosystem/drivers/csharp/)| [GitHub](https://github.com/mongodb/mongo-csharp-driver) |[2.8.1](https://www.nuget.org/packages/MongoDB.Driver/2.8.1)| [Apache 2.0](http://www.apache.org/licenses/LICENSE-2.0) | Types for writting dicom tags into MongoDb databases|
+| HIC.FAnsiSql |[GitHub](https://github.com/HicServices/FAnsiSql) | [0.11.1](https://www.nuget.org/packages/HIC.FansiSql/0.11.1) | [GPL 3.0](https://www.gnu.org/licenses/gpl-3.0.html) | Handles assigning translating database types and DBMS interactions|
+|[MongoDB.Driver](https://docs.mongodb.com/ecosystem/drivers/csharp/)| [GitHub](https://github.com/mongodb/mongo-csharp-driver) |[2.10.2](https://www.nuget.org/packages/MongoDB.Driver/2.10.2)| [Apache 2.0](http://www.apache.org/licenses/LICENSE-2.0) | Types for writting dicom tags into MongoDb databases|
 | fo-dicom.NetCore | [GitHub](https://github.com/fo-dicom/fo-dicom) |[4.0.4](https://www.nuget.org/packages/fo-dicom.NetCore/4.0.4)|[MS-PL](https://opensource.org/licenses/MS-PL) | Handles reading/writing dicom tags from dicom datasets | |
 | fo-dicom.Json | [GitHub](https://github.com/fo-dicom/fo-dicom) |[4.0.4](https://www.nuget.org/packages/fo-dicom.Json/4.0.4)|[MS-PL](https://opensource.org/licenses/MS-PL) | Handles serializing dicom datasets | |
-| YamlDotNet | [GitHub](https://github.com/aaubry/YamlDotNet)  | [6.0.0](https://www.nuget.org/packages/YamlDotNet/6.0.0) | [MIT](https://opensource.org/licenses/MIT) |Loading configuration files|
-| [NLog](https://nlog-project.org/) | [GitHub](https://github.com/NLog/NLog) | [4.6.3](https://www.nuget.org/packages/NLog/4.6.3) | [BSD 3-Clause](https://github.com/NLog/NLog/blob/dev/LICENSE.txt) | Flexible user configurable logging | |
-| [Newtonsoft.Json](https://www.newtonsoft.com/json) | [GitHub](https://github.com/JamesNK/Newtonsoft.Json) | [12.0.2](https://www.nuget.org/packages/Newtonsoft.Json/12.0.2) | [MIT](https://opensource.org/licenses/MIT) | Serialization of objects for sharing/transmission |
+| YamlDotNet | [GitHub](https://github.com/aaubry/YamlDotNet)  | [8.1.0](https://www.nuget.org/packages/YamlDotNet/8.1.0) | [MIT](https://opensource.org/licenses/MIT) |Loading configuration files|
+| [NLog](https://nlog-project.org/) | [GitHub](https://github.com/NLog/NLog) | [4.7.0](https://www.nuget.org/packages/NLog/4.7.0) | [BSD 3-Clause](https://github.com/NLog/NLog/blob/dev/LICENSE.txt) | Flexible user configurable logging | |
+| [Newtonsoft.Json](https://www.newtonsoft.com/json) | [GitHub](https://github.com/JamesNK/Newtonsoft.Json) | [12.0.3](https://www.nuget.org/packages/Newtonsoft.Json/12.0.3) | [MIT](https://opensource.org/licenses/MIT) | Serialization of objects for sharing/transmission |
 | [Nunit](https://nunit.org/) |[GitHub](https://github.com/nunit/nunit) | [3.11.0](https://www.nuget.org/packages/NUnit/3.11.0) | [MIT](https://opensource.org/licenses/MIT) | Unit testing |
 | NUnit3TestAdapter | [GitHub](https://github.com/nunit/nunit3-vs-adapter)| [3.13.0](https://www.nuget.org/packages/NUnit3TestAdapter/3.13.0) | [MIT](https://opensource.org/licenses/MIT) | Run unit tests from within Visual Studio |
diff --git a/rakefile.rb b/rakefile.rb
@@ -22,7 +22,7 @@
           </TestDatabase>
           <TestDatabase>
             <DatabaseType>MySql</DatabaseType>
-            <ConnectionString>Server=#{MYSQLDB};Uid=#{MYSQLUSR};Pwd=#{MYSQLPASS};Ssl-Mode=Required</ConnectionString>
+            <ConnectionString>Server=#{MYSQLDB};Uid=#{MYSQLUSR};Pwd=#{MYSQLPASS};sslmode=Required</ConnectionString>
           </TestDatabase>
           <!--<TestDatabase>
             <DatabaseType>Oracle</DatabaseType>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,3 +11,4 @@

		- [Thomas Nind](https://github.com/tznind)
		- [Leandro Tramma](https://github.com/Tallmaris)
		- [James A Sutherland](https://github.com/jas88)