private void VerifyPostFiles(ProcessedTriggerInfo processedTriggerInfo, CromwellOnAzureEnvironment environment)
{
var files = RetrievePostFiles(processedTriggerInfo, environment);
Assert.AreEqual(processedTriggerInfo.WorkflowInputs.Count + 1, files.Count, "unexpected number of files");
Assert.AreEqual("workflowSource", files[0].ParameterName, $"unexpected ParameterName for the 0th file");
Assert.AreEqual(processedTriggerInfo.WorkflowSource.Filename, files[0].Filename, $"unexpected Filename for the 0th file");
AssertBytesEqual(processedTriggerInfo.WorkflowSource.Data, files[0].Data, "files[0].Data");
for (var i = 0; i < processedTriggerInfo.WorkflowInputs.Count; i++)
{
var ip1 = i + 1;
if (i == 0)
{
Assert.AreEqual("workflowInputs", files[ip1].ParameterName, $"unexpected ParameterName for file #{ip1}");
}
else
{
Assert.AreEqual("workflowInputs_" + ip1, files[ip1].ParameterName, $"unexpected ParameterName for file #{ip1}");
}
Assert.AreEqual(processedTriggerInfo.WorkflowInputs[i].Filename, files[ip1].Filename, $"unexpected Filename for file #{ip1}");
AssertBytesEqual(processedTriggerInfo.WorkflowInputs[i].Data, files[ip1].Data, $"files[{ip1}].Data");
}
}
private async Task <(string, byte[])> GetBlobFileNameAndDataUsingMocksAsync(string url, string accountAuthority)
{
var serviceCollection = new ServiceCollection()
.AddLogging(loggingBuilder => loggingBuilder.AddConsole());
var serviceProvider = serviceCollection.BuildServiceProvider();
var azStorageMock = new Mock <IAzureStorage>();
azStorageMock.Setup(az => az
.DownloadBlockBlobAsync(It.IsAny <string>()))
.Returns(Task.FromResult(blobData));
azStorageMock.Setup(az => az
.DownloadFileUsingHttpClientAsync(It.IsAny <string>()))
.Returns(Task.FromResult(httpClientData));
azStorageMock.SetupGet(az => az.AccountAuthority).Returns(accountAuthority);
var environment = new CromwellOnAzureEnvironment(
serviceProvider.GetRequiredService <ILoggerFactory>(),
azStorageMock.Object,
new CromwellApiClient.CromwellApiClient("http://cromwell:8000"));
return(await environment.GetBlobFileNameAndData(url));
}
private static async Task <(string newTriggerName, Workflow newTriggerContent)> ProcessAbortRequestAsync(Guid workflowId, ICromwellApiClient cromwellApiClient)
{
string newTriggerName = null;
Workflow newTriggerContent = null;
var loggerFactory = new Mock <ILoggerFactory>();
var azureStorage = new Mock <IAzureStorage>();
var repository = new Mock <IRepository <TesTask> >();
loggerFactory
.Setup(f => f.CreateLogger(It.IsAny <string>()))
.Returns(new Mock <ILogger>().Object);
azureStorage
.Setup(az => az.GetWorkflowsByStateAsync(WorkflowState.Abort))
.Returns(Task.FromResult(new[] {
new TriggerFile {
Uri = $"http://tempuri.org/workflows/abort/{workflowId}.json",
ContainerName = "workflows",
Name = $"abort/{workflowId}.json",
LastModified = DateTimeOffset.UtcNow
}
}.AsEnumerable()));
azureStorage
.Setup(az => az.DownloadBlobTextAsync(It.IsAny <string>(), $"abort/{workflowId}.json"))
.Returns(Task.FromResult(string.Empty));
azureStorage
.Setup(az => az.UploadFileTextAsync(It.IsAny <string>(), "workflows", It.IsAny <string>()))
.Callback((string content, string container, string blobName) => {
newTriggerName = blobName;
newTriggerContent = content is not null ? JsonConvert.DeserializeObject <Workflow>(content) : null;
});
var cromwellOnAzureEnvironment = new CromwellOnAzureEnvironment(loggerFactory.Object, azureStorage.Object, cromwellApiClient, repository.Object, Enumerable.Repeat(azureStorage.Object, 1));
await cromwellOnAzureEnvironment.ProcessAndAbortWorkflowsAsync();
return(newTriggerName, newTriggerContent);
}
private CromwellOnAzureEnvironment SetCromwellOnAzureEnvironment(string accountAuthority)
{
var serviceCollection = new ServiceCollection()
.AddLogging(loggingBuilder => loggingBuilder.AddConsole());
var serviceProvider = serviceCollection.BuildServiceProvider();
var azStorageMock = new Mock <IAzureStorage>();
azStorageMock.Setup(az => az
.DownloadBlockBlobAsync(It.IsAny <string>()))
.Returns(Task.FromResult(blobData));
azStorageMock.Setup(az => az
.DownloadFileUsingHttpClientAsync(It.IsAny <string>()))
.Returns(Task.FromResult(httpClientData));
azStorageMock.SetupGet(az => az.AccountAuthority).Returns(accountAuthority);
var accountName = accountAuthority;
var subdomainEndIndex = accountAuthority.IndexOf(".");
if (subdomainEndIndex > 0)
{
accountName = accountAuthority.Substring(0, subdomainEndIndex);
}
azStorageMock.SetupGet(az => az.AccountName).Returns(accountName);
var environment = new CromwellOnAzureEnvironment(
serviceProvider.GetRequiredService <ILoggerFactory>(),
azStorageMock.Object,
new CromwellApiClient.CromwellApiClient("http://cromwell:8000"));
return(environment);
}
private static List <CromwellApiClient.CromwellApiClient.FileToPost> RetrievePostFiles(ProcessedTriggerInfo processedTriggerInfo, CromwellOnAzureEnvironment environment)
{
var cromwellApiClient = (CromwellApiClient.CromwellApiClient)environment.cromwellApiClient;
return(cromwellApiClient.AccumulatePostFiles(
processedTriggerInfo.WorkflowSource.Filename,
processedTriggerInfo.WorkflowSource.Data,
processedTriggerInfo.WorkflowInputs.Select(a => a.Filename).ToList(),
processedTriggerInfo.WorkflowInputs.Select(a => a.Data).ToList(),
processedTriggerInfo.WorkflowOptions.Filename,
processedTriggerInfo.WorkflowOptions.Data,
processedTriggerInfo.WorkflowDependencies.Filename,
processedTriggerInfo.WorkflowDependencies.Data));
}
public async Task NewWorkflowsThatFailToParseAsJsonAreAnotatedAndMovedToFailedSubdirectory()
{
const string badJason = @"{'WorkflowUrl': 'https://tempuri.org/inputs/bam-to-unmapped-bams.wdl' 'WorkflowInputsUrl': 'https://tempuri.org/inputs/bam-to-unmapped-bams.inputs.json'}";
const string errPrefix = "\nError(s): ";
var cromwellApiClient = new Mock <ICromwellApiClient>();
var triesToPost = false;
cromwellApiClient
.Setup(ac => ac.PostWorkflowAsync(It.IsAny <string>(), It.IsAny <byte[]>(), It.IsAny <List <string> >(), It.IsAny <List <byte[]> >(), It.IsAny <string>(), It.IsAny <byte[]>(), It.IsAny <string>(), It.IsAny <byte[]>()))
.Callback(() => triesToPost = true)
.Throws(new Exception("Should never get here."));
string newTriggerName = null;
string newTriggerContent = null;
var loggerFactory = new Mock <ILoggerFactory>();
var azureStorage = new Mock <IAzureStorage>();
var repository = new Mock <IRepository <TesTask> >();
loggerFactory
.Setup(f => f.CreateLogger(It.IsAny <string>()))
.Returns(new Mock <ILogger>().Object);
azureStorage
.Setup(az => az.GetWorkflowsByStateAsync(WorkflowState.New))
.Returns(Task.FromResult(new[] {
new TriggerFile {
Uri = $"http://tempuri.org/workflows/new/Sample.json",
ContainerName = "workflows",
Name = $"new/Sample.json",
LastModified = DateTimeOffset.UtcNow
}
}.AsEnumerable()));
azureStorage
.Setup(az => az.DownloadBlobTextAsync(It.IsAny <string>(), $"new/Sample.json"))
.Returns(Task.FromResult(badJason));
azureStorage
.Setup(az => az.UploadFileTextAsync(It.IsAny <string>(), "workflows", It.IsAny <string>()))
.Callback((string content, string container, string blobName) => {
newTriggerName = blobName;
newTriggerContent = content;
});
var deleted = false;
azureStorage
.Setup(az => az.DeleteBlobIfExistsAsync(It.IsAny <string>(), $"new/Sample.json"))
.Callback(() => deleted = true);
var cromwellOnAzureEnvironment = new CromwellOnAzureEnvironment(loggerFactory.Object, azureStorage.Object, cromwellApiClient.Object, repository.Object, Enumerable.Repeat(azureStorage.Object, 1));
await cromwellOnAzureEnvironment.ProcessAndAbortWorkflowsAsync();
Assert.IsTrue(newTriggerName.StartsWith("failed/"));
Assert.IsTrue(deleted);
Assert.IsFalse(triesToPost);
Assert.IsTrue((badJason + errPrefix).Length < newTriggerContent.Length);
Assert.IsTrue(newTriggerContent.StartsWith(badJason + errPrefix));
}
