From 85c20381eb5252b9475c4fe752786d23fb7205da Mon Sep 17 00:00:00 2001
From: Blair L Murri <BMurri@users.noreply.github.com>
Date: Mon, 10 Jul 2023 19:24:20 -0700
Subject: [PATCH 1/4] Publish node task runner Addresses #265

---
 Microsoft.GA4GH.TES.sln                       |   6 +
 .../PublishTesRunnerToTesApiArtifacts.csproj  | 135 ++++++++++++++++++
 2 files changed, 141 insertions(+)
 create mode 100644 src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj

diff --git a/Microsoft.GA4GH.TES.sln b/Microsoft.GA4GH.TES.sln
index c885de90e..c01a11c23 100644
--- a/Microsoft.GA4GH.TES.sln
+++ b/Microsoft.GA4GH.TES.sln
@@ -35,6 +35,8 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tes.Runner.Test", "src\Tes.
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tes.RunnerCLI", "src\Tes.RunnerCLI\Tes.RunnerCLI.csproj", "{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}"
 EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "PublishTesRunnerToTesApiArtifacts", "src\PublishTesRunnerToTesApiArtifacts\PublishTesRunnerToTesApiArtifacts.csproj", "{4A98F17B-0C4F-4412-8D48-54BA97601407}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -85,6 +87,10 @@ Global
 		{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}.Release|Any CPU.Build.0 = Release|Any CPU
+		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
diff --git a/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj b/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj
new file mode 100644
index 000000000..036d1600b
--- /dev/null
+++ b/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj
@@ -0,0 +1,135 @@
+<Project>
+  <Import Sdk="Microsoft.NET.Sdk" Project="Sdk.props"/>
+
+  <PropertyGroup>
+    <TargetFramework>net7.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+    <RuntimeIdentifiers>linux-x64</RuntimeIdentifiers>
+  </PropertyGroup>
+
+  <PropertyGroup Condition=" '$(ArtifactStagingDirectory)' != '' ">
+    <TesApiWebArchive>$(ArtifactStagingDirectory)\TesApi.Web</TesApiWebArchive>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Tes.RunnerCLI\Tes.RunnerCLI.csproj"
+          Targets="Publish;PublishItemsOutputGroup"
+          AdditionalProperties="PublishProfile=FolderProfile">
+        <ReferenceOutputAssembly>False</ReferenceOutputAssembly>
+        <OutputItemType>None</OutputItemType>
+        <CopyToOutputDirectory>Never</CopyToOutputDirectory>
+        <Private>False</Private>
+    </ProjectReference>
+    <ProjectReference Condition=" '$(TesApiWebArchive)' == '' "
+          Include="..\TesApi.Web\TesApi.Web.csproj"
+          Targets="Publish;PublishItemsOutputGroup"
+          AdditionalProperties="RuntimeIdentifiers=$(RuntimeIdentifiers)">
+        <ReferenceOutputAssembly>False</ReferenceOutputAssembly>
+        <OutputItemType>None</OutputItemType>
+        <CopyToOutputDirectory>Never</CopyToOutputDirectory>
+        <Private>False</Private>
+    </ProjectReference>
+    <None Condition=" '$(TesApiWebArchive)' != '' "
+          Include="$(TesApiWebArchive)\tesapi.dll"
+          MsBuildSourceProjectFile="$(TesApiWebArchive)\proj"
+          OutputPath="tesapi.dll"
+          TargetPath="tesapi.dll" />
+  </ItemGroup>
+
+  <!--<Target Name="__AssignPublishProperties" BeforeTargets="ResolveProjectReferences" AfterTargets="PrepareProjectReferences">
+    <ConvertToAbsolutePath Paths="$(OutputPath)scripts\">
+      <Output TaskParameter="AbsolutePaths" PropertyName="__TesRunnerPublishDir"/>
+    </ConvertToAbsolutePath>
+
+    <ItemGroup>
+      <__ProjectNotReferenced Include="@(_MSBuildProjectReferenceExistent)" />
+      <_MSBuildProjectReferenceExistent Remove="@(__ProjectNotReferenced)" />
+      <_MSBuildProjectReferenceExistent Include="@(__ProjectNotReferenced)">
+        <Properties>%(__ProjectNotReferenced.AdditionalProperties);PublishDir=$(__TesRunnerPublishDir);%(__ProjectNotReferenced.SetConfiguration);%(__ProjectNotReferenced.SetPlatform);%(__ProjectNotReferenced.SetTargetFramework)</Properties>
+        <AdditionalProperties></AdditionalProperties>
+        <GlobalPropertiesToRemove>%(__ProjectNotReferenced.GlobalPropertiesToRemove);PublishSingleFile;PublishTrimmed;SelfContained</GlobalPropertiesToRemove>
+      </_MSBuildProjectReferenceExistent>
+    </ItemGroup>
+  </Target>-->
+
+  <Import Sdk="Microsoft.NET.Sdk" Project="Sdk.targets"/>
+
+  <UsingTask TaskName="ConvertNoneToPublishDir" TaskFactory="RoslynCodeTaskFactory" AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.Core.dll">
+    <ParameterGroup>
+      <PublishedFiles ParameterType="Microsoft.Build.Framework.ITaskItem[]" Required="true" />
+      <PublishedDirectories ParameterType="Microsoft.Build.Framework.ITaskItem[]" Output="true" />
+    </ParameterGroup>
+    <Task>
+      <!--<Reference Include="System.Linq"/>-->
+      <Using Namespace="System.Linq" />
+      <Using Namespace="System.IO" />
+      <Using Namespace="Microsoft.Build.Framework" />
+      <Using Namespace="Microsoft.Build.Utilities" />
+      <Code Type="Fragment" Language="cs">
+        <![CDATA[
+            var dirs = new List<ITaskItem>();
+            foreach (var file in PublishedFiles)
+            {
+                Log.LogMessage(MessageImportance.Normal, "Parsing {0}", file.ItemSpec);
+                var dirInfo = Directory.GetParent(Path.Combine(Directory.GetParent(file.GetMetadata("MsBuildSourceProjectFile")).FullName, file.GetMetadata("OutputPath")));
+                var dir = new TaskItem(dirInfo.FullName);
+                file.CopyMetadataTo(dir);
+                dirs.Add(dir);
+            }
+            //PublishedDirectories = Enumerable.DistinctBy(dirs, item => item.ItemSpec).ToArray();
+            PublishedDirectories = dirs.ToArray();
+        ]]>
+      </Code>
+    </Task>
+  </UsingTask>
+
+  <UsingTask TaskName="GenerateMD5" TaskFactory="RoslynCodeTaskFactory" AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.Core.dll">
+    <ParameterGroup>
+      <InputFile ParameterType="Microsoft.Build.Framework.ITaskItem" Required="true" />
+      <MD5Hash Output="true" />
+    </ParameterGroup>
+    <Task>
+      <Using Namespace="System" />
+      <Using Namespace="System.IO" />
+      <Using Namespace="System.Security.Cryptography" />
+      <Using Namespace="Microsoft.Build.Framework" />
+      <Code Type="Fragment" Language="cs">
+        <![CDATA[
+            Log.LogMessage(MessageImportance.Normal, "Computing MD5 hash for {0}", InputFile.ItemSpec);
+            var md5spc = MD5.Create();
+            MD5Hash = Convert.ToBase64String(md5spc.ComputeHash(File.ReadAllBytes(InputFile.ItemSpec)));
+            Log.LogMessage(MessageImportance.Normal, "Computed MD5 hash is {0}", MD5Hash);
+        ]]>
+      </Code>
+  </Task>
+
+  </UsingTask>
+
+  <Target Name="Compile">
+    <ConvertNoneToPublishDir PublishedFiles="@(None)">
+      <Output ItemName="__PublishDirs" TaskParameter="PublishedDirectories"/>
+    </ConvertNoneToPublishDir>
+    <ItemGroup>
+      <IntermediateAssembly Remove="@(IntermediateAssembly)" />
+        <__tRunnerPath Include="@(__PublishDirs)" Condition="Exists('%(__PublishDirs.Identity)/tRunner') and '%(__PublishDirs.TargetPath)' == 'tRunner'" />
+        <__tRunnerFiles Include="%(__tRunnerPath.FullPath)\**\*" />
+        <__tesapiScriptsPath Include="@(__PublishDirs->'%(FullPath)\scripts')"  Condition="Exists('%(__PublishDirs.Identity)/tesapi.dll') and '%(__PublishDirs.TargetPath)' == 'tesapi.dll'" />
+    </ItemGroup>
+    <Copy SourceFiles="@(__tRunnerFiles)"
+          DestinationFolder="@(__tesapiScriptsPath)"
+          SkipUnchangedFiles="false"
+          Condition=" '%(__tRunnerFiles.Filename)%(__tRunnerFiles.Extension)' == 'tRunner' "/>
+    <GenerateMD5 InputFile="@(__tesapiScriptsPath->'%(FullPath)\tRunner')">
+      <Output TaskParameter="MD5Hash" PropertyName="__TRunnerMD5Hash" />
+    </GenerateMD5>
+    <WriteLinesToFile Lines="$(__TRunnerMD5Hash)" File="@(__tesapiScriptsPath->'%(FullPath)\TRunnerMD5Hash.txt')" WriteOnlyWhenDifferent="true" Overwrite="true" />
+    <ItemGroup>
+      <FileWrites Include="@(__tesapiScriptsPath->'%(FullPath)\TRunnerMD5Hash.txt')" />
+      <FileWrites Include="@(__tesapiScriptsPath->'%(FullPath)\tRunner')" />
+    </ItemGroup>
+  </Target>
+
+  <Target Name="CopyFilesToOutputDirectory" />
+    
+</Project>

From 70f46d98c0834bdcdb61e86a8e1d9756597cfa52 Mon Sep 17 00:00:00 2001
From: Blair L Murri <BMurri@users.noreply.github.com>
Date: Mon, 10 Jul 2023 19:47:08 -0700
Subject: [PATCH 2/4] remove changes to solution file

---
 Microsoft.GA4GH.TES.sln | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/Microsoft.GA4GH.TES.sln b/Microsoft.GA4GH.TES.sln
index c01a11c23..c885de90e 100644
--- a/Microsoft.GA4GH.TES.sln
+++ b/Microsoft.GA4GH.TES.sln
@@ -35,8 +35,6 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tes.Runner.Test", "src\Tes.
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tes.RunnerCLI", "src\Tes.RunnerCLI\Tes.RunnerCLI.csproj", "{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}"
 EndProject
-Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "PublishTesRunnerToTesApiArtifacts", "src\PublishTesRunnerToTesApiArtifacts\PublishTesRunnerToTesApiArtifacts.csproj", "{4A98F17B-0C4F-4412-8D48-54BA97601407}"
-EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -87,10 +85,6 @@ Global
 		{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{D5DFB5A4-2E18-456A-9A29-5BD8C82DF250}.Release|Any CPU.Build.0 = Release|Any CPU
-		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{4A98F17B-0C4F-4412-8D48-54BA97601407}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

From 3b7f7f0ca1a2af27633e0c5a3b9ea5d83c85c9df Mon Sep 17 00:00:00 2001
From: Blair L Murri <BMurri@users.noreply.github.com>
Date: Mon, 10 Jul 2023 21:03:49 -0700
Subject: [PATCH 3/4] Remove fragile publishing from tesapi.web project

---
 src/TesApi.Web/TesApi.Web.csproj | 80 +-------------------------------
 1 file changed, 1 insertion(+), 79 deletions(-)

diff --git a/src/TesApi.Web/TesApi.Web.csproj b/src/TesApi.Web/TesApi.Web.csproj
index 305af8fbf..8167d1e4e 100644
--- a/src/TesApi.Web/TesApi.Web.csproj
+++ b/src/TesApi.Web/TesApi.Web.csproj
@@ -62,16 +62,6 @@
 
   <ItemGroup>
     <ProjectReference Include="..\CommonUtilities\CommonUtilities.csproj" />
-
-    <ProjectReference Include="..\Tes.RunnerCLI\Tes.RunnerCLI.csproj"
-		      Targets="Publish"
-		      AdditionalProperties="PublishProfile=FolderProfile">
-      <ReferenceOutputAssembly>False</ReferenceOutputAssembly>
-      <OutputItemType>None</OutputItemType>
-      <CopyToOutputDirectory>Never</CopyToOutputDirectory>
-      <Private>False</Private>
-    </ProjectReference>
-
     <ProjectReference Include="..\Tes\Tes.csproj" />
   </ItemGroup>
 
@@ -80,72 +70,4 @@
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
   </ItemGroup>
-
-  <UsingTask TaskName="GenerateMD5" TaskFactory="RoslynCodeTaskFactory" AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.Core.dll">
-    <ParameterGroup>
-      <InputFile ParameterType="Microsoft.Build.Framework.ITaskItem" Required="true" />
-      <MD5Hash Output="true" />
-    </ParameterGroup>
-    <Task>
-      <!--<Reference Include="" />-->
-      <Using Namespace="System" />
-      <Using Namespace="System.IO" />
-      <Using Namespace="System.Security.Cryptography" />
-      <Using Namespace="Microsoft.Build.Framework" />
-      <Code Type="Fragment" Language="cs">
-        <![CDATA[
-            Log.LogMessage(MessageImportance.Normal, "Computing MD5 hash for {0}", InputFile.ItemSpec);
-            var md5spc = MD5.Create();
-            MD5Hash = Convert.ToBase64String(md5spc.ComputeHash(File.ReadAllBytes(InputFile.ItemSpec)));
-            Log.LogMessage(MessageImportance.Normal, "Computed MD5 hash is {0}", MD5Hash);
-        ]]>
-      </Code>
-    </Task>
-  </UsingTask>
-
-  <Target Name="__AssignPublishProperties" BeforeTargets="ResolveProjectReferences" AfterTargets="PrepareProjectReferences">
-    <ConvertToAbsolutePath Paths="$(OutputPath)scripts\">
-      <Output TaskParameter="AbsolutePaths" PropertyName="__TesRunnerPublishDir"/>
-    </ConvertToAbsolutePath>
-
-    <ItemGroup>
-      <__ProjectNotReferenced Include="@(_MSBuildProjectReferenceExistent)" Condition=" '%(Filename)' == 'Tes.RunnerCLI' "/>
-      <_MSBuildProjectReferenceExistent Remove="@(__ProjectNotReferenced)"/>
-      <_MSBuildProjectReferenceExistent Include="@(__ProjectNotReferenced)">
-        <Properties>%(__ProjectNotReferenced.AdditionalProperties);PublishDir=$(__TesRunnerPublishDir);%(__ProjectNotReferenced.SetConfiguration);%(__ProjectNotReferenced.SetPlatform);%(__ProjectNotReferenced.SetTargetFramework)</Properties>
-        <AdditionalProperties></AdditionalProperties>
-        <GlobalPropertiesToRemove>%(__ProjectNotReferenced.GlobalPropertiesToRemove);PublishSingleFile;PublishTrimmed;SelfContained</GlobalPropertiesToRemove>
-      </_MSBuildProjectReferenceExistent>
-    </ItemGroup>
-  </Target>
-
-  <Target Name="__GetPublishedProjectMD5Hash" AfterTargets="ResolveProjectReferences;AssignTargetPaths;__AdjustCopyToOutputDirectoryItemsOptimization">
-    <ItemGroup>
-      <__TRunnerMD5Hash Include="$(IntermediateOutputPath)TRunnerMD5Hash.txt" />
-    </ItemGroup>
-
-    <GenerateMD5 InputFile="$(__TesRunnerPublishDir)tRunner">
-      <Output TaskParameter="MD5Hash" PropertyName="__TRunnerMD5Hash" />
-    </GenerateMD5>
-
-    <WriteLinesToFile Lines="$(__TRunnerMD5Hash)" File="@(__TRunnerMD5Hash)" WriteOnlyWhenDifferent="true" Overwrite="true" />
-
-    <ItemGroup>
-      <FileWrites Include="@(__TRunnerMD5Hash)" />
-      <ContentWithTargetPath Include="@(__TRunnerMD5Hash->'%(FullPath)')">
-        <TargetPath>scripts\TRunnerMD5Hash.txt</TargetPath>
-        <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
-      </ContentWithTargetPath>
-    </ItemGroup>
-  </Target>
-
-  <Target Name="CopyNodeRunnerToPublishDir" BeforeTargets="ComputeResolvedFilesToPublishList">
-    <ItemGroup>
-      <ResolvedFileToPublish Include="$(__TesRunnerPublishDir)tRunner">
-        <RelativePath>scripts\tRunner</RelativePath>
-        <CopyToPublishDirectory>PreserveNewest</CopyToPublishDirectory>
-      </ResolvedFileToPublish>
-    </ItemGroup>
-  </Target>
-
-</Project>
\ No newline at end of file
+</Project>

From 3bc84e9206fc3bdb3052ad705596826a6657304a Mon Sep 17 00:00:00 2001
From: Blair L Murri <BMurri@users.noreply.github.com>
Date: Wed, 12 Jul 2023 11:37:57 -0700
Subject: [PATCH 4/4] Remove commented out code

---
 .../PublishTesRunnerToTesApiArtifacts.csproj    | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj b/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj
index 036d1600b..99a7011d2 100644
--- a/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj
+++ b/src/PublishTesRunnerToTesApiArtifacts/PublishTesRunnerToTesApiArtifacts.csproj
@@ -37,22 +37,6 @@
           TargetPath="tesapi.dll" />
   </ItemGroup>
 
-  <!--<Target Name="__AssignPublishProperties" BeforeTargets="ResolveProjectReferences" AfterTargets="PrepareProjectReferences">
-    <ConvertToAbsolutePath Paths="$(OutputPath)scripts\">
-      <Output TaskParameter="AbsolutePaths" PropertyName="__TesRunnerPublishDir"/>
-    </ConvertToAbsolutePath>
-
-    <ItemGroup>
-      <__ProjectNotReferenced Include="@(_MSBuildProjectReferenceExistent)" />
-      <_MSBuildProjectReferenceExistent Remove="@(__ProjectNotReferenced)" />
-      <_MSBuildProjectReferenceExistent Include="@(__ProjectNotReferenced)">
-        <Properties>%(__ProjectNotReferenced.AdditionalProperties);PublishDir=$(__TesRunnerPublishDir);%(__ProjectNotReferenced.SetConfiguration);%(__ProjectNotReferenced.SetPlatform);%(__ProjectNotReferenced.SetTargetFramework)</Properties>
-        <AdditionalProperties></AdditionalProperties>
-        <GlobalPropertiesToRemove>%(__ProjectNotReferenced.GlobalPropertiesToRemove);PublishSingleFile;PublishTrimmed;SelfContained</GlobalPropertiesToRemove>
-      </_MSBuildProjectReferenceExistent>
-    </ItemGroup>
-  </Target>-->
-
   <Import Sdk="Microsoft.NET.Sdk" Project="Sdk.targets"/>
 
   <UsingTask TaskName="ConvertNoneToPublishDir" TaskFactory="RoslynCodeTaskFactory" AssemblyFile="$(MSBuildToolsPath)\Microsoft.Build.Tasks.Core.dll">
@@ -77,7 +61,6 @@
                 file.CopyMetadataTo(dir);
                 dirs.Add(dir);
             }
-            //PublishedDirectories = Enumerable.DistinctBy(dirs, item => item.ItemSpec).ToArray();
             PublishedDirectories = dirs.ToArray();
         ]]>
       </Code>