Update execution path #222
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BMurri
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May 11, 2023
BMurri
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May 11, 2023
ashanhol
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MattMcL4475
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May 15, 2023
| { | ||
| return $"{ExecutionsPathPrefix.TrimStart('/')}"; | ||
| } | ||
| return $"{storageAccountName}/{TesExecutionsPathPrefix.TrimStart('/')}/{task.Id}"; |
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instead of: /{TesExecutionsPathPrefix.TrimStart('/')}
more performant to do:
{TesExecutionsPathPrefix}
| var batchExecutionDirectoryPath = GetBatchExecutionDirectoryPath(task); | ||
| var metricsPath = $"/{batchExecutionDirectoryPath}/metrics.txt"; | ||
| var storageUploadPath = GetStorageUploadPath(task, defaultStorageAccountName); | ||
| var metricsPath = $"/{storageUploadPath}/metrics.txt"; |
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"metrics.txt" could be a constant, such as "const string metricFilename", because it's used a lot in the rest of this PR
| { | ||
| var blobsInExecutionDirectory = (await azureProxy.ListBlobsAsync(executionDirectoryUri)).Where(b => !b.EndsWith($"/{CromwellScriptFileName}")); | ||
| var cromwellExecutionDirectory = $"/{cromwellExecutionDirectoryPath.Split("/", StringSplitOptions.RemoveEmptyEntries)[0]}"; | ||
| additionalInputFiles = blobsInExecutionDirectory.Select(b => $"{cromwellExecutionDirectory}/{b}").Select(b => new TesInput { Content = null, Path = b, Url = b, Name = Path.GetFileName(b), Type = TesFileType.FILEEnum }).ToList(); |
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it's canonical in C# to use the full noun for the lambda parameter, instead of b it looks like it's a blobName , which would make those code more clear to read (it was probably me who originally did this :) )
| @@ -1013,18 +1009,24 @@ private async Task<CloudTask> ConvertTesTaskToBatchTaskAsync(string taskId, TesT | |||
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| return $" && echo $(date +%T) && {setVariables} && {downloadSingleFile} && {exitIfDownloadedFileIsNotFound} && {incrementTotalBytesTransferred}"; | |||
| })) | |||
| + $" && echo FileDownloadSizeInBytes=$total_bytes >> {metricsPath}"; | |||
| + $" && echo FileDownloadSizeInBytes=$total_bytes >> metrics.txt"; | |||
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metrics.txt could be a const
| @@ -1039,25 +1041,31 @@ private async Task<CloudTask> ConvertTesTaskToBatchTaskAsync(string taskId, TesT | |||
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| return $" && {{ {setVariables} && [ ! -e \"$path\" ] && : || {{ {blobxferCommand} && {incrementTotalBytesTransferred}; }} }}"; | |||
| })) | |||
| + $" && echo FileUploadSizeInBytes=$total_bytes >> {metricsPath}"; | |||
| + $" && echo FileUploadSizeInBytes=$total_bytes >> metrics.txt"; | |||
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metrics.txt could be a const
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| var executorImageIsPublic = containerRegistryProvider.IsImagePublic(executor.Image); | ||
| var dockerInDockerImageIsPublic = containerRegistryProvider.IsImagePublic(dockerInDockerImageName); | ||
| var blobXferImageIsPublic = containerRegistryProvider.IsImagePublic(blobxferImageName); | ||
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| var sb = new StringBuilder(); | ||
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| sb.AppendLinuxLine($"write_kv() {{ echo \"$1=$2\" >> $AZ_BATCH_TASK_WORKING_DIR{metricsPath}; }} && \\"); // Function that appends key=value pair to metrics.txt file | ||
| sb.AppendLinuxLine($"write_kv() {{ echo \"$1=$2\" >> $AZ_BATCH_TASK_WORKING_DIR/metrics.txt; }} && \\"); // Function that appends key=value pair to metrics.txt file |
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metrics.txt could be a const
| sb.AppendLinuxLine($"write_ts UploadEnd && \\"); | ||
| sb.AppendLinuxLine($"/bin/bash -c 'disk=( `df -k $AZ_BATCH_TASK_WORKING_DIR | tail -1` ) && echo DiskSizeInKiB=${{disk[1]}} >> $AZ_BATCH_TASK_WORKING_DIR{metricsPath} && echo DiskUsedInKiB=${{disk[2]}} >> $AZ_BATCH_TASK_WORKING_DIR{metricsPath}' && \\"); | ||
| sb.AppendLinuxLine($"/bin/bash -c 'disk=( `df -k $AZ_BATCH_TASK_WORKING_DIR | tail -1` ) && echo DiskSizeInKiB=${{disk[1]}} >> $AZ_BATCH_TASK_WORKING_DIR/metrics.txt && echo DiskUsedInKiB=${{disk[2]}} >> $AZ_BATCH_TASK_WORKING_DIR/metrics.txt' && \\"); |
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metrics.txt could be a const
| @@ -1156,6 +1164,9 @@ private async Task<CloudTask> ConvertTesTaskToBatchTaskAsync(string taskId, TesT | |||
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| return cloudTask; | |||
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| string MountBlobxferScriptAndMetrics(string scriptFileName) | |||
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metrics.txt could be a const
ashanhol
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May 15, 2023
Sister PR to microsoft/ga4gh-tes#222 Issue: microsoft/ga4gh-tes#112 Creates the tes-internal container for convenience to TES.
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Fixes #112
This PR further aims to untangle CoA from TES by separating cromwell's execution files from TES's batch files. The majority of this work is done in BatchScheduler.cs's
ConvertTesTaskToBatchTaskAsyncfunction.task.id/[file]cromwell-executions/assemble_refbased/0fb40b27-dffe-4d3f-b6da-02ea0b82aedd/call-align_to_ref/shard-0/execution/__batch/batch_scripttowd/batch_script.