Addi new docker containers (#589)

.github/workflows/tre-sql-pg-container.yaml

@@ -0,0 +1,39 @@
+name: TRE SQL PG Container
+
+on:
+  pull_request:
+    paths:
+      - 'src/Tre-SQL-PG/**'
+  push:
+    branches:
+      - main
+    paths:
+      - 'src/Tre-SQL-PG/**'
+
+permissions:
+  contents: write
+  pull-requests: read
+  actions: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  tre-hasura-container:
+    uses: SwanseaUniversityMedical/workflows/.github/workflows/pr-and-release-container.yaml@v1.4.2-containers
+    with:
+      job-name: tre-sqlpg-container
+      registry: ${{ vars.HARBOR_REGISTRY }}
+      registry-user: ${{ vars.HARBOR_USER }}
+      registry-repo: ${{ vars.HARBOR_PROJECT }}/${{ vars.HARBOR_REPO }}-tre-sqlpg
+      release-tag-format: 'DARE-TRE-SQLPG-Container-${version}'
+      cosign-public-key: ${{ vars.COSIGN_PUBLIC_KEY }}
+      slack-channel: ${{ vars.SLACK_CHANNEL }}
+      build-file: src/Tre-SQL-PG/Dockerfile
+      build-context: src
+    secrets:
+      cosign-private-key: ${{ secrets.COSIGN_PRIVATE_KEY }}
+      cosign-password: ${{ secrets.COSIGN_PASSWORD }}
+      registry-token: ${{ secrets.HARBOR_TOKEN }}
+      slack-token: ${{ secrets.SLACK_TOKEN }}

.github/workflows/tre-sql-trino-container.yaml

@@ -0,0 +1,39 @@
+name: TRE SQL Trino Container
+
+on:
+  pull_request:
+    paths:
+      - 'src/Tre-SQL-Trino/**'
+  push:
+    branches:
+      - main
+    paths:
+      - 'src/Tre-SQL-Trino/**'
+
+permissions:
+  contents: write
+  pull-requests: read
+  actions: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  tre-hasura-container:
+    uses: SwanseaUniversityMedical/workflows/.github/workflows/pr-and-release-container.yaml@v1.4.2-containers
+    with:
+      job-name: tre-sqltrino-container
+      registry: ${{ vars.HARBOR_REGISTRY }}
+      registry-user: ${{ vars.HARBOR_USER }}
+      registry-repo: ${{ vars.HARBOR_PROJECT }}/${{ vars.HARBOR_REPO }}-tre-sqltrino
+      release-tag-format: 'DARE-TRE-SQLTRINO-Container-${version}'
+      cosign-public-key: ${{ vars.COSIGN_PUBLIC_KEY }}
+      slack-channel: ${{ vars.SLACK_CHANNEL }}
+      build-file: src/Tre-SQL-Trino/Dockerfile
+      build-context: src
+    secrets:
+      cosign-private-key: ${{ secrets.COSIGN_PRIVATE_KEY }}
+      cosign-password: ${{ secrets.COSIGN_PASSWORD }}
+      registry-token: ${{ secrets.HARBOR_TOKEN }}
+      slack-token: ${{ secrets.SLACK_TOKEN }}

DARE-Control.sln

@@ -28,6 +28,10 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Data-Egress-UI", "src\Data-
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tre-Hasura", "src\Tre-Hasura\Tre-Hasura.csproj", "{3BAD3B69-2B08-4E09-BB8A-2611A0990062}"
 EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tre-SQL-PG", "src\Tre-SQL-PG\Tre-SQL-PG.csproj", "{C51CB601-57E5-445D-975E-62041FCF65A9}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Tre-SQL-Trino", "src\Tre-SQL-Trino\Tre-SQL-Trino.csproj", "{B47DC0A4-0691-456F-BBB2-7901E2398526}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -70,6 +74,14 @@ Global
 		{3BAD3B69-2B08-4E09-BB8A-2611A0990062}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{3BAD3B69-2B08-4E09-BB8A-2611A0990062}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{3BAD3B69-2B08-4E09-BB8A-2611A0990062}.Release|Any CPU.Build.0 = Release|Any CPU
+		{C51CB601-57E5-445D-975E-62041FCF65A9}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{C51CB601-57E5-445D-975E-62041FCF65A9}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{C51CB601-57E5-445D-975E-62041FCF65A9}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{C51CB601-57E5-445D-975E-62041FCF65A9}.Release|Any CPU.Build.0 = Release|Any CPU
+		{B47DC0A4-0691-456F-BBB2-7901E2398526}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{B47DC0A4-0691-456F-BBB2-7901E2398526}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{B47DC0A4-0691-456F-BBB2-7901E2398526}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{B47DC0A4-0691-456F-BBB2-7901E2398526}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -85,6 +97,8 @@ Global
 		{68369D1D-B5AE-4CED-944C-3FEF0EB23414} = {BCA7B4D1-726B-46EA-90D1-2BD3ACD5154A}
 		{80C9C407-D56A-4FD1-9FE3-58B046729ADC} = {ED66814A-91F3-4E06-AE48-B7A9F666659E}
 		{3BAD3B69-2B08-4E09-BB8A-2611A0990062} = {505AD4FB-0822-4989-9A01-1F56C3820D0D}
+		{C51CB601-57E5-445D-975E-62041FCF65A9} = {505AD4FB-0822-4989-9A01-1F56C3820D0D}
+		{B47DC0A4-0691-456F-BBB2-7901E2398526} = {505AD4FB-0822-4989-9A01-1F56C3820D0D}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {29E246A8-202C-4544-A30D-33E0AB416005}

src/Tre-Hasura/Program.cs

@@ -8,7 +8,7 @@
 using Tre_Hasura.Models;
 
 
-Console.WriteLine("Hello, World!");
+Console.WriteLine("TREFX Hashura Runner");
 var configuration = GetConfiguration();
 
 using IHost host = Host.CreateDefaultBuilder(args).ConfigureServices

src/Tre-SQL-PG/Dockerfile

@@ -0,0 +1,20 @@
+#See https://aka.ms/customizecontainer to learn how to customize your debug container and how Visual Studio uses this Dockerfile to build your images for faster debugging.
+
+FROM mcr.microsoft.com/dotnet/runtime:7.0 AS base
+WORKDIR /app
+
+FROM mcr.microsoft.com/dotnet/sdk:7.0 AS build
+WORKDIR /src
+COPY ["src/Tre-SQL-PG/Tre-SQL-PG.csproj", "src/Tre-SQL-PG/"]
+RUN dotnet restore "src/Tre-SQL-PG/Tre-SQL-PG.csproj"
+COPY . .
+WORKDIR "/src/src/Tre-SQL-PG"
+RUN dotnet build "Tre-SQL-PG.csproj" -c Release -o /app/build
+
+FROM build AS publish
+RUN dotnet publish "Tre-SQL-PG.csproj" -c Release -o /app/publish /p:UseAppHost=false
+
+FROM base AS final
+WORKDIR /app
+COPY --from=publish /app/publish .
+ENTRYPOINT ["dotnet", "Tre-SQL-PG.dll"]

src/Tre-SQL-PG/Program.cs

@@ -0,0 +1,89 @@
+using System;
+using System.Data;
+using System.IO;
+using Npgsql;
+
+Console.WriteLine("TREFX SQL Runner Module : Postgress");
+
+// Tre-SQL-PG.exe "--Query=select * from \"profileForm\"" --Output=data.csv
+
+var Token = "";
+var OutputFilename = "data.csv";
+var Query = "SELECT * FROM \"profileForm\"";
+string connectionString = "Host=localhost:5432;Username=admin;Password=admin;Database=assets3";
+
+foreach (var arg in args)
+{
+    Console.WriteLine("Arg = " + arg);
+
+    if (arg.StartsWith("--Output"))
+    {
+        OutputFilename = arg.Replace("--Output=", "");
+    }
+
+    if (arg.StartsWith("--Token_"))
+    {
+        Token = arg.Replace("--Token_", "");
+    }
+
+    if (arg.StartsWith("--Connection"))
+    {
+        connectionString = arg.Replace("--Connection=", "");
+    }
+
+    if (arg.StartsWith("--Query"))
+    {
+        Query = arg.Replace("--Query=", "");
+    }
+
+}
+
+Console.WriteLine("Query > " + Query);
+Console.WriteLine("Token > " + Token);
+Console.WriteLine("Output > " + OutputFilename);
+
+ExportToCsv(connectionString, Query, OutputFilename);
+
+Console.WriteLine("Completed");
+
+
+
+static void ExportToCsv(string connectionString, string sqlQuery, string csvFilePath)
+{
+    using (var connection = new NpgsqlConnection(connectionString))
+    {
+        connection.Open();
+        using (var command = new NpgsqlCommand(sqlQuery, connection))
+        {
+            using (var reader = command.ExecuteReader())
+            {
+                if (reader.HasRows)
+                {
+                    using (var streamWriter = new StreamWriter(csvFilePath))
+                    {
+                        // Write column headers
+                        for (int i = 0; i < reader.FieldCount; i++)
+                        {
+                            if (i > 0)
+                                streamWriter.Write(",");
+                            streamWriter.Write(reader.GetName(i));
+                        }
+                        streamWriter.WriteLine();
+
+                        // Write data rows
+                        while (reader.Read())
+                        {
+                            for (int i = 0; i < reader.FieldCount; i++)
+                            {
+                                if (i > 0)
+                                    streamWriter.Write(",");
+                                streamWriter.Write(reader[i].ToString());
+                            }
+                            streamWriter.WriteLine();
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

src/Tre-SQL-PG/Properties/launchSettings.json

@@ -0,0 +1,10 @@
+{
+  "profiles": {
+    "Tre-SQL-PG": {
+      "commandName": "Project"
+    },
+    "Docker": {
+      "commandName": "Docker"
+    }
+  }
+}

src/Tre-SQL-PG/Tre-SQL-PG.csproj

@@ -0,0 +1,18 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>net7.0</TargetFramework>
+    <RootNamespace>Tre_SQL_PG</RootNamespace>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+    <DockerDefaultTargetOS>Linux</DockerDefaultTargetOS>
+    <DockerfileContext>..\..</DockerfileContext>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Microsoft.VisualStudio.Azure.Containers.Tools.Targets" Version="1.18.1" />
+    <PackageReference Include="Npgsql" Version="8.0.2" />
+  </ItemGroup>
+
+</Project>

src/Tre-SQL-Trino/Dockerfile

@@ -0,0 +1,20 @@
+#See https://aka.ms/customizecontainer to learn how to customize your debug container and how Visual Studio uses this Dockerfile to build your images for faster debugging.
+
+FROM mcr.microsoft.com/dotnet/runtime:7.0 AS base
+WORKDIR /app
+
+FROM mcr.microsoft.com/dotnet/sdk:7.0 AS build
+WORKDIR /src
+COPY ["src/Tre-SQL-Trino/Tre-SQL-Trino.csproj", "src/Tre-SQL-Trino/"]
+RUN dotnet restore "src/Tre-SQL-Trino/Tre-SQL-Trino.csproj"
+COPY . .
+WORKDIR "/src/src/Tre-SQL-Trino"
+RUN dotnet build "Tre-SQL-Trino.csproj" -c Release -o /app/build
+
+FROM build AS publish
+RUN dotnet publish "Tre-SQL-Trino.csproj" -c Release -o /app/publish /p:UseAppHost=false
+
+FROM base AS final
+WORKDIR /app
+COPY --from=publish /app/publish .
+ENTRYPOINT ["dotnet", "Tre-SQL-Trino.dll"]

src/Tre-SQL-Trino/Program.cs

@@ -0,0 +1,110 @@
+using System;
+using System.Data;
+using System.IO;
+using System.Net.Http;
+using Newtonsoft.Json;
+using Newtonsoft.Json.Linq;
+using System.Threading.Tasks;
+
+Console.WriteLine("TREFX SQL Runner Module : Trino");
+
+// Tre-SQL-Trino.exe "--Query=select * from \"profileForm\"" --Output=data.csv
+
+string trinoUrl = "http://trino-server:8080/v1/statement";
+var Token = "";
+var OutputFilename = "data.csv";
+var Query = "SELECT * FROM \"profileForm\"";
+
+foreach (var arg in args)
+{
+    Console.WriteLine("Arg = " + arg);
+
+    if (arg.StartsWith("--Output"))
+    {
+        OutputFilename = arg.Replace("--Output=", "");
+    }
+
+    if (arg.StartsWith("--Token_"))
+    {
+        Token = arg.Replace("--Token_", "");
+    }
+
+    if (arg.StartsWith("--Connection"))
+    {
+        trinoUrl = arg.Replace("--Connection=", "");
+    }
+
+    if (arg.StartsWith("--Query"))
+    {
+        Query = arg.Replace("--Query=", "");
+    }
+
+}
+
+Console.WriteLine("Query > " + Query);
+Console.WriteLine("Token > " + Token);
+Console.WriteLine("Output > " + OutputFilename);
+
+await ExportToCsv(trinoUrl, Query, OutputFilename);
+
+Console.WriteLine("Completed");
+
+
+static async Task ExportToCsv(string trinoUrl, string sqlQuery, string csvFilePath)
+{
+    using (var httpClient = new HttpClient())
+    {
+        var requestBody = new
+        {
+            query = sqlQuery
+        };
+
+        var requestContent = new StringContent(JsonConvert.SerializeObject(requestBody));
+        requestContent.Headers.ContentType = new System.Net.Http.Headers.MediaTypeHeaderValue("application/json");
+
+        using (var response = await httpClient.PostAsync(trinoUrl, requestContent))
+        {
+            response.EnsureSuccessStatusCode();
+
+            using (var responseStream = await response.Content.ReadAsStreamAsync())
+            using (var streamReader = new StreamReader(responseStream))
+            using (var jsonReader = new JsonTextReader(streamReader))
+            {
+                var jsonSerializer = new JsonSerializer();
+
+                using (var streamWriter = new StreamWriter(csvFilePath))
+                using (var csvWriter = new CsvHelper.CsvWriter(streamWriter, System.Globalization.CultureInfo.InvariantCulture))
+                {
+                    while (jsonReader.Read())
+                    {
+                        if (jsonReader.TokenType == JsonToken.StartObject)
+                        {
+                            // Deserialize JSON response into a dynamic object
+                            var jsonObject = jsonSerializer.Deserialize<JObject>(jsonReader);
+
+                            // Write column headers
+                            var columns = jsonObject["columns"];
+                            foreach (var column in columns)
+                            {
+                                csvWriter.WriteField(column["name"].ToString());
+                            }
+                            csvWriter.NextRecord();
+
+                            // Write data rows
+                            var data = jsonObject["data"];
+                            foreach (var rowData in data)
+                            {
+                                foreach (var value in rowData)
+                                {
+                                    csvWriter.WriteField(value.ToString());
+                                }
+                                csvWriter.NextRecord();
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+