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Add germline integration test #632

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merged 3 commits into from
Apr 7, 2023
Merged

Add germline integration test #632

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ff71913
add germline
MattMcL4475 Apr 7, 2023
2940c7e
update workflow name
MattMcL4475 Apr 7, 2023
a351d4c
Merge branch 'main' into task/AddGermlineToIntegrationTest
MattMcL4475 Apr 7, 2023
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52 changes: 38 additions & 14 deletions src/TriggerService.Tests/IntegrationTests.cs
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
using System;
// Copyright (c) Microsoft Corporation.
// Licensed under the MIT License.

using System;
using System.Net.Http;
using System.Threading.Tasks;
using Azure.Storage.Blobs;
Expand Down Expand Up @@ -26,21 +29,24 @@ public async Task RunScaleTestWithMutect2Async()
const int countOfWorkflowsToRun = 100;
const string triggerFile = "https://raw.githubusercontent.com/microsoft/gatk4-somatic-snvs-indels-azure/main-azure/mutect2.trigger.json";
const string workflowFriendlyName = $"mutect2";
const string containerName = "workflows";

var n = DateTime.UtcNow;
var date = $"{n.Year}-{n.Month}-{n.Day}-{n.Hour}-{n.Minute}";
using var httpClient = new HttpClient();
var triggerFileJson = await (await httpClient.GetAsync(triggerFile)).Content.ReadAsStringAsync();
await StartWorkflowsAsync(countOfWorkflowsToRun, triggerFile, workflowFriendlyName);
}

for (var i = 1; i <= countOfWorkflowsToRun; i++)
{
// example: new/mutect2-001-of-100-2023-4-7-3-9.0fb0858a-3166-4a22-85b6-4337df2f53c5.json
var blobName = $"new/{workflowFriendlyName}-{i:D3}-of-{countOfWorkflowsToRun:D3}-{date}.json";
var blobClient = new BlobServiceClient(new Uri($"https://{testStorageAccountName}.blob.core.windows.net/{containerName}/{blobName}?{workflowsContainerSasToken.TrimStart('?')}"));
var container = blobClient.GetBlobContainerClient(containerName);
await container.GetBlobClient(blobName).UploadAsync(BinaryData.FromString(triggerFileJson), true);
}
/// <summary>
/// To run this test, specify a testStorageAccountName, a workflowsContainerSasToken, and remove the [Ignore] attribute
/// </summary>
/// <returns></returns>
[Ignore]
[TestCategory("Integration")]
[TestMethod]
public async Task RunScaleTestWithWholeGenomeGermlineSingleSampleAsync()
{
const int countOfWorkflowsToRun = 1500;
const string triggerFile = "https://raw.githubusercontent.com/microsoft/gatk4-genome-processing-pipeline-azure/main-azure/WholeGenomeGermlineSingleSample.trigger.json";
const string workflowFriendlyName = $"wgs-germline";

await StartWorkflowsAsync(countOfWorkflowsToRun, triggerFile, workflowFriendlyName);
}

[Ignore]
Expand Down Expand Up @@ -76,5 +82,23 @@ public async Task DeleteOldBatchPoolsAsync()

Console.WriteLine($"Deleted {count} pools.");
}

private static async Task StartWorkflowsAsync(int countOfWorkflowsToRun, string triggerFile, string workflowFriendlyName)
{
const string containerName = "workflows";
var n = DateTime.UtcNow;
var date = $"{n.Year}-{n.Month}-{n.Day}-{n.Hour}-{n.Minute}";
using var httpClient = new HttpClient();
var triggerFileJson = await (await httpClient.GetAsync(triggerFile)).Content.ReadAsStringAsync();

for (var i = 1; i <= countOfWorkflowsToRun; i++)
{
// example: new/mutect2-001-of-100-2023-4-7-3-9.0fb0858a-3166-4a22-85b6-4337df2f53c5.json
var blobName = $"new/{workflowFriendlyName}-{i:D4}-of-{countOfWorkflowsToRun:D4}-{date}.json";
var blobClient = new BlobServiceClient(new Uri($"https://{testStorageAccountName}.blob.core.windows.net/{containerName}/{blobName}?{workflowsContainerSasToken.TrimStart('?')}"));
var container = blobClient.GetBlobContainerClient(containerName);
await container.GetBlobClient(blobName).UploadAsync(BinaryData.FromString(triggerFileJson), true);
}
}
}
}