Feature/net6.0 927 (#633)

* changing to net6.0 * circumventing the possible net6.0 bug * updated nuget, removed un-necessary stuff from proj files * using const to reduce string concatenation * removing None Remove section * updating some more interpreted strings to be net6.0 compatible
Illumina · Mar 22, 2022 · 68c7240 · 68c7240
1 parent 80f8c48
commit 68c7240
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Showing 38 changed files with 117 additions and 134 deletions.
diff --git a/AnnotationLambda/AnnotationLambda.csproj b/AnnotationLambda/AnnotationLambda.csproj
@@ -1,17 +1,17 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <GenerateRuntimeConfigurationFiles>true</GenerateRuntimeConfigurationFiles>
     <AWSProjectType>Lambda</AWSProjectType>
     <OutputPath>bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Amazon.Lambda.Core" Version="2.0.0" />
+    <PackageReference Include="Amazon.Lambda.Core" Version="2.1.0" />
     <PackageReference Include="Amazon.Lambda.Serialization.Json" Version="2.0.0" />
-    <PackageReference Include="AWSSDK.Lambda" Version="3.7.0.15" />
-    <PackageReference Include="AWSSDK.S3" Version="3.7.0.17" />
-    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.1.1" />
+    <PackageReference Include="AWSSDK.Lambda" Version="3.7.9.3" />
+    <PackageReference Include="AWSSDK.S3" Version="3.7.8.3" />
+    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.3.31" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Cloud\Cloud.csproj" />

diff --git a/CacheUtils/CacheUtils.csproj b/CacheUtils/CacheUtils.csproj
@@ -1,9 +1,9 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
   <ItemGroup>
@@ -12,9 +12,9 @@
     </Content>
   </ItemGroup>
   <ItemGroup>
-    <PackageReference Include="Microsoft.Extensions.Configuration" Version="5.0.0" />
-    <PackageReference Include="Microsoft.Extensions.Configuration.Binder" Version="5.0.0" />
-    <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="5.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration" Version="6.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration.Binder" Version="6.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="6.0.0" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\CommandLine\CommandLine.csproj" />

diff --git a/Cloud/Cloud.csproj b/Cloud/Cloud.csproj
@@ -1,14 +1,14 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Amazon.Lambda.Core" Version="2.0.0" />
+    <PackageReference Include="Amazon.Lambda.Core" Version="2.1.0" />
     <PackageReference Include="Amazon.Lambda.Serialization.Json" Version="2.0.0" />
-    <PackageReference Include="AWSSDK.S3" Version="3.7.0.17" />
-    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.1.1" />
+    <PackageReference Include="AWSSDK.S3" Version="3.7.8.3" />
+    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.3.31" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
   </ItemGroup>
   <ItemGroup>

diff --git a/CommandLine/CommandLine.csproj b/CommandLine/CommandLine.csproj
@@ -1,8 +1,8 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
   <ItemGroup>

diff --git a/Compression/Compression.csproj b/Compression/Compression.csproj
@@ -1,8 +1,8 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
     <ProjectReference Include="..\ErrorHandling\ErrorHandling.csproj" />

diff --git a/CustomAnnotationLambda/CustomAnnotationLambda.csproj b/CustomAnnotationLambda/CustomAnnotationLambda.csproj
@@ -1,15 +1,15 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <GenerateRuntimeConfigurationFiles>true</GenerateRuntimeConfigurationFiles>
     <AWSProjectType>Lambda</AWSProjectType>
     <OutputPath>bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Amazon.Lambda.Core" Version="2.0.0" />
+    <PackageReference Include="Amazon.Lambda.Core" Version="2.1.0" />
     <PackageReference Include="Amazon.Lambda.Serialization.Json" Version="2.0.0" />
-    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.1.1" />
+    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.3.31" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Cloud\Cloud.csproj" />

diff --git a/CustomStrValidationLambda/CustomStrValidationLambda.csproj b/CustomStrValidationLambda/CustomStrValidationLambda.csproj
@@ -1,11 +1,11 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <GenerateRuntimeConfigurationFiles>true</GenerateRuntimeConfigurationFiles>
     <AWSProjectType>Lambda</AWSProjectType>
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Amazon.Lambda.Core" Version="2.0.0" />
+    <PackageReference Include="Amazon.Lambda.Core" Version="2.1.0" />
     <PackageReference Include="Amazon.Lambda.Serialization.Json" Version="2.0.0" />
   </ItemGroup>
   <ItemGroup>

diff --git a/Downloader/Downloader.csproj b/Downloader/Downloader.csproj
@@ -1,15 +1,15 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
   <ItemGroup>
-    <PackageReference Include="Microsoft.Extensions.Configuration" Version="5.0.0" />
-    <PackageReference Include="Microsoft.Extensions.Configuration.FileExtensions" Version="5.0.0" />
-    <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="5.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration" Version="6.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration.FileExtensions" Version="6.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="6.0.0" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\CommandLine\CommandLine.csproj" />

diff --git a/ErrorHandling/ErrorHandling.csproj b/ErrorHandling/ErrorHandling.csproj
@@ -1,11 +1,11 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
-    <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+    <TargetFramework>net6.0</TargetFramework>
+    <OutputPath>..\bin\$(Configuration)</OutputPath>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
   <ItemGroup>
-    <PackageReference Include="AWSSDK.S3" Version="3.7.0.17" />
+    <PackageReference Include="AWSSDK.S3" Version="3.7.8.3" />
   </ItemGroup>
 </Project>
diff --git a/GeneAnnotationLambda/GeneAnnotationLambda.csproj b/GeneAnnotationLambda/GeneAnnotationLambda.csproj
@@ -1,15 +1,15 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <GenerateRuntimeConfigurationFiles>true</GenerateRuntimeConfigurationFiles>
     <AWSProjectType>Lambda</AWSProjectType>
     <OutputPath>bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="Amazon.Lambda.Serialization.Json" Version="2.0.0" />
-    <PackageReference Include="AWSSDK.Core" Version="3.7.0.16" />
-    <PackageReference Include="AWSSDK.Lambda" Version="3.7.0.15" />
+    <PackageReference Include="AWSSDK.Core" Version="3.7.8.5" />
+    <PackageReference Include="AWSSDK.Lambda" Version="3.7.9.3" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Cloud\Cloud.csproj" />

diff --git a/Genome/Genome.csproj b/Genome/Genome.csproj
@@ -1,8 +1,8 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
   <ItemGroup>

diff --git a/IO/IO.csproj b/IO/IO.csproj
@@ -1,18 +1,14 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
     <AllowUnsafeBlocks>true</AllowUnsafeBlocks>
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
   <ItemGroup>
-    <PackageReference Include="AWSSDK.Core" Version="3.7.0.16" />
-    <PackageReference Include="AWSSDK.S3" Version="3.7.0.17" />
-    <PackageReference Include="IsExternalInit" Version="1.0.0">
-      <PrivateAssets>all</PrivateAssets>
-      <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
-    </PackageReference>
+    <PackageReference Include="AWSSDK.Core" Version="3.7.8.5" />
+    <PackageReference Include="AWSSDK.S3" Version="3.7.8.3" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\ErrorHandling\ErrorHandling.csproj" />

diff --git a/Intervals/Intervals.csproj b/Intervals/Intervals.csproj
@@ -1,8 +1,8 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
 </Project>
diff --git a/Jasix/Jasix.csproj b/Jasix/Jasix.csproj
@@ -1,9 +1,9 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />

diff --git a/Jist/Jist.csproj b/Jist/Jist.csproj
@@ -2,7 +2,7 @@
 
     <PropertyGroup>
         <OutputType>Exe</OutputType>
-        <TargetFramework>netcoreapp3.1</TargetFramework>
+        <TargetFramework>net6.0</TargetFramework>
         <OutputPath>..\bin\$(Configuration)</OutputPath>
     </PropertyGroup>
 

diff --git a/MitoHeteroplasmy/MitoHeteroplasmy.csproj b/MitoHeteroplasmy/MitoHeteroplasmy.csproj
@@ -1,8 +1,8 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
-    <LangVersion>latest</LangVersion>
+    <TargetFramework>net6.0</TargetFramework>
+
   </PropertyGroup>
   <ItemGroup>
     <EmbeddedResource Include="Resources\MitoHeteroplasmy.tsv.gz" />

diff --git a/Nirvana/Nirvana.csproj b/Nirvana/Nirvana.csproj
@@ -1,14 +1,14 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Microsoft.Extensions.Configuration" Version="5.0.0" />
-    <PackageReference Include="Microsoft.Extensions.Configuration.Binder" Version="5.0.0" />
-    <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="5.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration" Version="6.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration.Binder" Version="6.0.0" />
+    <PackageReference Include="Microsoft.Extensions.Configuration.Json" Version="6.0.0" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Cloud\Cloud.csproj" />

diff --git a/NirvanaLambda/NirvanaLambda.csproj b/NirvanaLambda/NirvanaLambda.csproj
@@ -1,16 +1,16 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <GenerateRuntimeConfigurationFiles>true</GenerateRuntimeConfigurationFiles>
     <AWSProjectType>Lambda</AWSProjectType>
     <OutputPath>bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Amazon.Lambda.Core" Version="2.0.0" />
+    <PackageReference Include="Amazon.Lambda.Core" Version="2.1.0" />
     <PackageReference Include="Amazon.Lambda.Serialization.Json" Version="2.0.0" />
-    <PackageReference Include="AWSSDK.Lambda" Version="3.7.0.15" />
-    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.1.1" />
+    <PackageReference Include="AWSSDK.Lambda" Version="3.7.9.3" />
+    <PackageReference Include="AWSSDK.SimpleNotificationService" Version="3.7.3.31" />
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\Genome\Genome.csproj" />

diff --git a/OptimizedCore/OptimizedCore.csproj b/OptimizedCore/OptimizedCore.csproj
@@ -1,12 +1,12 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
     <AllowUnsafeBlocks>true</AllowUnsafeBlocks>
   </PropertyGroup>
   <ItemGroup>
-    <PackageReference Include="Microsoft.Extensions.ObjectPool" Version="6.0.0-preview.6.21355.2" />
+    <PackageReference Include="Microsoft.Extensions.ObjectPool" Version="6.0.2" />
   </ItemGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
 </Project>
diff --git a/Phantom/Phantom.csproj b/Phantom/Phantom.csproj
@@ -1,8 +1,8 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />

diff --git a/ReferenceSequence/ReferenceSequence.csproj b/ReferenceSequence/ReferenceSequence.csproj
@@ -1,9 +1,9 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <ItemGroup>
     <ProjectReference Include="..\CommandLine\CommandLine.csproj" />

diff --git a/RepeatExpansions/RepeatExpansionPhenotype.cs b/RepeatExpansions/RepeatExpansionPhenotype.cs
@@ -41,8 +41,13 @@ public string GetAnnotation(int repeatNumber)
 
         private string GetJson(double percentile, IEnumerable<string> classifications)
         {
-            string joined = string.Join(",", classifications.Select(classification => "\"" + classification + "\""));
-            return $"{{\"phenotype\":\"{_phenotype}\",\"omimId\":{_omimId},\"classifications\":[{joined}],\"percentile\":{percentile:0.00}}}";
+            // in net6.0, the compiler gets confused if you have }}}. Should the first two }s be a closing brace or the second? This results in a bug.
+            // we can circumvent it by taking the leading and trailing parenthesis out of the main expression and adding them separately
+            const char openCurly  = '{';
+            const char closeCurly = '}';
+            string     joined     = string.Join(",", classifications.Select(classification => "\"" + classification + "\""));
+            return $"{openCurly}\"phenotype\":\"{_phenotype}\",\"omimId\":{_omimId},\"classifications\":[{joined}],\"percentile\":{percentile:0.00}{closeCurly}";
+
         }
 
         private IEnumerable<string> GetClassifications(int repeatNumber)

diff --git a/RepeatExpansions/RepeatExpansions.csproj b/RepeatExpansions/RepeatExpansions.csproj
@@ -1,14 +1,10 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>netcoreapp3.1</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <OutputPath>..\bin\$(Configuration)</OutputPath>
-    <LangVersion>latest</LangVersion>
+
   </PropertyGroup>
   <Import Project="..\CommonAssemblyInfo.props" />
-  <ItemGroup>
-    <None Remove="RepeatExpansions.GRCh37.tsv" />
-    <None Remove="RepeatExpansions.GRCh38.tsv" />
-  </ItemGroup>
   <ItemGroup>
     <EmbeddedResource Include="Resources\RepeatExpansions.GRCh37.tsv" />
     <EmbeddedResource Include="Resources\RepeatExpansions.GRCh38.tsv" />

diff --git a/SAUtils/ExtractCosmicSvs/CosmicCnvItem.cs b/SAUtils/ExtractCosmicSvs/CosmicCnvItem.cs
@@ -57,7 +57,7 @@ private static IEnumerable<string> GetJsonStrings(IDictionary<string, int> dicti
         {
             foreach (var kvp in dictionary)
             {
-                yield return $"{{\"{kvp.Key.Replace('_', ' ')}\":{kvp.Value}}}";
+                yield return $"{JsonObject.OpenBrace}\"{kvp.Key.Replace('_', ' ')}\":{kvp.Value}{JsonObject.CloseBrace}";
             }
         }
-Original file line number
+Diff line change
@@ Expand Up @@
             {
                 foreach (var kvp in dictionary)
                 {
-                    yield return $"{{\"{kvp.Key.Replace('_', ' ')}\":{kvp.Value}}}";
+                    yield return $"{JsonObject.OpenBrace}\"{kvp.Key.Replace('_', ' ')}\":{kvp.Value}{JsonObject.CloseBrace}";
                 }
             }
@@ Expand Down @@