Adding dotnet format to repo

.github/workflows/dot_net_format.yml

@@ -0,0 +1,21 @@
+name: Format check on pull request
+on: pull_request
+jobs:
+  dotnet-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out code
+        uses: actions/[email protected]
+        with:
+          fetch-depth: 0
+
+      - name: Run dotnet format
+        shell: bash
+        run: |
+          allProjectFiles=$(find ./ -type f -name "*.csproj" | tr '\n' ' ');
+          if [ $? -ne 0 ]; then exit 1; fi
+          echo "$allProjectFiles"
+          for file in $allProjectFiles; do
+              dotnet format $file --verify-no-changes --verbosity detailed
+          done

README.md

@@ -1,23 +1,23 @@
-# Welcome to Cromwell on Azure
-![Logo](/docs/screenshots/logo.png)
-
-[Cromwell](https://cromwell.readthedocs.io/en/stable/) is a workflow management system for scientific workflows, orchestrating the computing tasks needed for genomics analysis. Originally developed by the [Broad Institute](https://github.com/broadinstitute/cromwell), Cromwell is also used in the GATK Best Practices genome analysis pipeline. Cromwell supports running scripts at various scales, including your local machine, a local computing cluster, and on the cloud. <br />
-
-Cromwell on Azure configures all Azure resources needed to run workflows through Cromwell on the Azure cloud, and uses the [GA4GH TES](https://cromwell.readthedocs.io/en/develop/backends/TES/) backend for orchestrating the tasks that create a workflow. The installation sets up a VM host to run the Cromwell server and uses Azure Batch to spin up virtual machines that run each task in a workflow. Cromwell workflows can be written using either the [WDL](https://github.com/openwdl/wdl) or the [CWL](https://www.commonwl.org/) scripting languages. To see examples of WDL scripts - see this ['Learn WDL'](https://github.com/openwdl/learn-wdl) repository on GitHub. To see examples of CWL scripts - see this ['CWL search result'](https://dockstore.org/search?descriptorType=CWL&searchMode=files) on Dockstore.<br />
-
-### Latest release
- * https://github.com/microsoft/CromwellOnAzure/releases
-
-### Documentation
-All documentation has been moved to our [wiki](https://github.com/microsoft/CromwellOnAzure/wiki)! 
-
-[Getting Started?](https://github.com/microsoft/CromwellOnAzure/wiki/Getting-Started)
-
-[Got Questions?](https://github.com/microsoft/CromwellOnAzure/wiki/FAQ-And-Troubleshooting)
-
-### Want to Contribute?
-Check out our [contributing guidelines](https://github.com/microsoft/CromwellOnAzure/blob/main/docs/contributing.md) and [Code of Conduct](https://github.com/microsoft/CromwellOnAzure/blob/main/CODE_OF_CONDUCT.md) and submit a PR! We'd love to have you.
-
-## Related Projects
-
-[Genomics Data Analysis with Jupyter Notebooks on Azure](https://github.com/microsoft/genomicsnotebook)<br/>
+# Welcome to Cromwell on Azure
+![Logo](/docs/screenshots/logo.png)
+
+[Cromwell](https://cromwell.readthedocs.io/en/stable/) is a workflow management system for scientific workflows, orchestrating the computing tasks needed for genomics analysis. Originally developed by the [Broad Institute](https://github.com/broadinstitute/cromwell), Cromwell is also used in the GATK Best Practices genome analysis pipeline. Cromwell supports running scripts at various scales, including your local machine, a local computing cluster, and on the cloud. <br />
+
+Cromwell on Azure configures all Azure resources needed to run workflows through Cromwell on the Azure cloud, and uses the [GA4GH TES](https://cromwell.readthedocs.io/en/develop/backends/TES/) backend for orchestrating the tasks that create a workflow. The installation sets up a VM host to run the Cromwell server and uses Azure Batch to spin up virtual machines that run each task in a workflow. Cromwell workflows can be written using either the [WDL](https://github.com/openwdl/wdl) or the [CWL](https://www.commonwl.org/) scripting languages. To see examples of WDL scripts - see this ['Learn WDL'](https://github.com/openwdl/learn-wdl) repository on GitHub. To see examples of CWL scripts - see this ['CWL search result'](https://dockstore.org/search?descriptorType=CWL&searchMode=files) on Dockstore.<br />
+
+### Latest release
+ * https://github.com/microsoft/CromwellOnAzure/releases
+
+### Documentation
+All documentation has been moved to our [wiki](https://github.com/microsoft/CromwellOnAzure/wiki)! 
+
+[Getting Started?](https://github.com/microsoft/CromwellOnAzure/wiki/Getting-Started)
+
+[Got Questions?](https://github.com/microsoft/CromwellOnAzure/wiki/FAQ-And-Troubleshooting)
+
+### Want to Contribute?
+Check out our [contributing guidelines](https://github.com/microsoft/CromwellOnAzure/blob/main/docs/contributing.md) and [Code of Conduct](https://github.com/microsoft/CromwellOnAzure/blob/main/CODE_OF_CONDUCT.md) and submit a PR! We'd love to have you.
+
+## Related Projects
+
+[Genomics Data Analysis with Jupyter Notebooks on Azure](https://github.com/microsoft/genomicsnotebook)<br/>

format/Setup Pre-commit.md

@@ -0,0 +1,12 @@
+# Set up Pre-commit
+To set up dotnet format to run locally on 'git commit', you need to perform the following actions. You should only need to do this once unless you remove and clone the repo again. 
+
+## Git pre-commit hook to reformat
+Navigate to GIT-REPO-LOCATION/format. Run the "dotnet-format-pre-commit.cmd" to copy the pre-commit file into the GIT-REPO-LOCATION/.git/hooks directory. Verify that the file has been copied as expeted into GIT-REPO-LOCATION/.git/hooks. The cmd script assumes it is being run from the **GIT-REPO-LOCATION/format** directory
+
+```
+cd GIT-REPO-LOCATION/format
+.\dotnet-format-pre-commit.cmd
+```
+
+After running this, when you go to commit, dotnet format should run automatically and correct any formatting that needs attention. 

format/dotnet-format-pre-commit.cmd

@@ -0,0 +1,2 @@
+:: copy pre-commit dotnet format command into local hooks
+echo F | xcopy "pre-commit" "..\.git\hooks\pre-commit"

format/pre-commit

@@ -0,0 +1,26 @@
+#!/bin/sh
+
+LC_ALL=C
+# Select files to format
+NATIVE_FILES=$(git diff --cached --name-only --diff-filter=ACM "*.h" "*.hpp" "*.c" "*.cpp" "*.inl" | sed 's| |\\ |g')
+MANAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM "*.cs" "*.vb" | sed 's| |\\ |g')
+
+exec 1>&2
+
+if [[ -n "$NATIVE_FILES" ]]; then
+    # Format all selected files
+    echo "$NATIVE_FILES" | cat | xargs | sed -e 's/ /,/g' | xargs "./artifacts/tools/clang-format" -style=file -i
+
+    # Add back the modified files to staging
+    echo "$NATIVE_FILES" | xargs git add
+fi
+if [[ -n "$MANAGED_FILES" ]]; then
+    # Format all selected files
+    echo "$MANAGED_FILES" | cat | xargs | sed -e 's/ /,/g' | dotnet format -v m
+
+    # Add back the modified files to staging
+    echo "$MANAGED_FILES" | xargs git add
+fi
+
+
+exit 0

src/TriggerService.Tests/ProcessNewWorkflowTests.cs

@@ -196,9 +196,9 @@ public async Task NewWorkflowsThatFailToParseAsJsonAreAnotatedAndMovedToFailedSu
 
             var cromwellOnAzureEnvironment = new TriggerHostedService(
                 logger,
-                triggerServiceOptions.Object, 
-                cromwellApiClient2, 
-                tesTaskRepository, 
+                triggerServiceOptions.Object,
+                cromwellApiClient2,
+                tesTaskRepository,
                 storageUtility.Object);
 
             await cromwellOnAzureEnvironment.ProcessAndAbortWorkflowsAsync();

src/TriggerService.Tests/TriggerEngineTests.cs

@@ -98,7 +98,7 @@ public async Task TriggerEngineRunsAndOnlyLogsAvailabilityOncePerSystemUponAvail
                 .Setup(x => x.GetStorageAccountsUsingMsiAsync(It.IsAny<string>()))
                 .Returns(Task.FromResult((new List<IAzureStorage>(), azureStorage.Object)));
 
-            var triggerHostedService = new TriggerHostedService(logger, triggerServiceOptions.Object, cromwellApiClient, tesTaskRepository, storageUtility.Object); 
+            var triggerHostedService = new TriggerHostedService(logger, triggerServiceOptions.Object, cromwellApiClient, tesTaskRepository, storageUtility.Object);
 
             //var engine = new TriggerHostedService(loggerFactory, environment.Object, TimeSpan.FromMilliseconds(25), TimeSpan.FromMilliseconds(25));
             _ = Task.Run(() => triggerHostedService.StartAsync(new System.Threading.CancellationToken()));

src/TriggerService/WorkflowState.cs

@@ -1,4 +1,4 @@
-// Copyright (c) Microsoft Corporation.
+// Copyright (c) Microsoft Corporation.
 // Licensed under the MIT License.
 
 namespace TriggerService

src/deploy-cromwell-on-azure/Deployer.cs

@@ -1310,7 +1310,7 @@ private Task<IPrivateDnsZone> CreatePrivateDnsZoneAsync(INetwork virtualNetwork,
         private Task ExecuteQueriesOnAzurePostgreSQLDbFromK8(IKubernetes kubernetesClient, string podName, string aksNamespace)
             => Execute(
                 $"Executing script to create users in tes_db and cromwell_db...",
-                async () => 
+                async () =>
                 {
                     var cromwellScript = GetCreateCromwellUserString();
                     var tesScript = GetCreateTesUserString();
@@ -1844,7 +1844,7 @@ void ValidateHelmInstall(string helmPath, string featureName)
             if (!configuration.ManualHelmDeployment)
             {
                 ValidateHelmInstall(configuration.HelmBinaryPath, nameof(configuration.HelmBinaryPath));
-            }      
+            }
 
             if (!configuration.Update)
             {

src/deploy-cromwell-on-azure/MountableContainer.cs

@@ -6,86 +6,86 @@
 
 namespace CromwellOnAzureDeployer
 {
-        /// <summary>
-        /// Represents a container to mount with blob-csi-driver. 
-        /// </summary>
-        public class MountableContainer
-        {
-            public string StorageAccount { get; set; }
-            public string ContainerName { get; set; }
-            public string SasToken { get; set; }
-            public string ResourceGroupName { get; set; }
+    /// <summary>
+    /// Represents a container to mount with blob-csi-driver. 
+    /// </summary>
+    public class MountableContainer
+    {
+        public string StorageAccount { get; set; }
+        public string ContainerName { get; set; }
+        public string SasToken { get; set; }
+        public string ResourceGroupName { get; set; }
 
-            public MountableContainer() { }
+        public MountableContainer() { }
 
-            public MountableContainer(Dictionary<string, string> dictionary)
+        public MountableContainer(Dictionary<string, string> dictionary)
+        {
+            if (dictionary.ContainsKey("accountName"))
             {
-                if (dictionary.ContainsKey("accountName"))
-                {
-                    StorageAccount = dictionary["accountName"];
-                }
-
-                if (dictionary.ContainsKey("containerName"))
-                {
-                    ContainerName = dictionary["containerName"];
-                }
-
-                if (dictionary.ContainsKey("resourceGroup"))
-                {
-                    ResourceGroupName = dictionary["resourceGroup"];
-                }
+                StorageAccount = dictionary["accountName"];
+            }
 
-                if (dictionary.ContainsKey("sasToken"))
-                {
-                    SasToken = dictionary["sasToken"];
-                }
+            if (dictionary.ContainsKey("containerName"))
+            {
+                ContainerName = dictionary["containerName"];
             }
 
-            public Dictionary<string, string> ToDictionary()
+            if (dictionary.ContainsKey("resourceGroup"))
             {
-                var dictionary = new Dictionary<string, string>();
+                ResourceGroupName = dictionary["resourceGroup"];
+            }
 
-                if (StorageAccount is not null)
-                {
-                    dictionary["accountName"] = StorageAccount;
-                }
+            if (dictionary.ContainsKey("sasToken"))
+            {
+                SasToken = dictionary["sasToken"];
+            }
+        }
 
-                if (ContainerName is not null)
-                {
-                    dictionary["containerName"] = ContainerName;
-                }
+        public Dictionary<string, string> ToDictionary()
+        {
+            var dictionary = new Dictionary<string, string>();
 
-                if (ResourceGroupName is not null)
-                {
-                    dictionary["resourceGroup"] = ResourceGroupName;
-                }
+            if (StorageAccount is not null)
+            {
+                dictionary["accountName"] = StorageAccount;
+            }
 
-                if (SasToken is not null)
-                {
-                    dictionary["sasToken"] = SasToken;
-                }
+            if (ContainerName is not null)
+            {
+                dictionary["containerName"] = ContainerName;
+            }
 
-                return dictionary;
+            if (ResourceGroupName is not null)
+            {
+                dictionary["resourceGroup"] = ResourceGroupName;
             }
 
-            public override bool Equals(object other)
+            if (SasToken is not null)
             {
-                return string.Equals(StorageAccount, ((MountableContainer)other).StorageAccount, StringComparison.OrdinalIgnoreCase) &&
-                    string.Equals(ContainerName, ((MountableContainer)other).ContainerName, StringComparison.OrdinalIgnoreCase) &&
-                    string.Equals(SasToken, ((MountableContainer)other).SasToken, StringComparison.OrdinalIgnoreCase) &&
-                    string.Equals(ResourceGroupName, ((MountableContainer)other).ResourceGroupName, StringComparison.OrdinalIgnoreCase);
+                dictionary["sasToken"] = SasToken;
             }
 
-            public override int GetHashCode()
+            return dictionary;
+        }
+
+        public override bool Equals(object other)
+        {
+            return string.Equals(StorageAccount, ((MountableContainer)other).StorageAccount, StringComparison.OrdinalIgnoreCase) &&
+                string.Equals(ContainerName, ((MountableContainer)other).ContainerName, StringComparison.OrdinalIgnoreCase) &&
+                string.Equals(SasToken, ((MountableContainer)other).SasToken, StringComparison.OrdinalIgnoreCase) &&
+                string.Equals(ResourceGroupName, ((MountableContainer)other).ResourceGroupName, StringComparison.OrdinalIgnoreCase);
+        }
+
+        public override int GetHashCode()
+        {
+            if (SasToken is null)
+            {
+                return HashCode.Combine(StorageAccount.GetHashCode(), ContainerName.GetHashCode(), ResourceGroupName.GetHashCode());
+            }
+            else
             {
-                if (SasToken is null)
-                {
-                    return HashCode.Combine(StorageAccount.GetHashCode(), ContainerName.GetHashCode(), ResourceGroupName.GetHashCode());
-                }
-                else
-                {
-                    return HashCode.Combine(StorageAccount.GetHashCode(), ContainerName.GetHashCode(), SasToken.GetHashCode());
-                }
+                return HashCode.Combine(StorageAccount.GetHashCode(), ContainerName.GetHashCode(), SasToken.GetHashCode());
             }
         }
+    }
 }