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Merged
merged 2 commits into from
Sep 5, 2022
Merged

AC-506-export-task-does-not-support-folders-387 #394

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6514b81
Export task list files
lillie-dae Sep 2, 2022
590bf28
Merge branch 'develop' into AC-506-export-task-does-not-support-folde…
RemakingEden Sep 2, 2022
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6 changes: 3 additions & 3 deletions src/TaskManager/Plug-ins/Argo/packages.lock.json
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Expand Up @@ -28,9 +28,9 @@
},
"Microsoft.Extensions.ApiDescription.Client": {
"type": "Direct",
"requested": "[6.0.7, )",
"resolved": "6.0.7",
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"requested": "[6.0.8, )",
"resolved": "6.0.8",
"contentHash": "fN3zEuHjSql9w2Md29dYkmPbAijxr+LqxoOoJ9B8G2j+fHgAK/N0g89miIUwepwbk8izTi5m8cVyWTKQgkd+ww=="
},
"Monai.Deploy.Messaging": {
"type": "Direct",
Expand Down
12 changes: 6 additions & 6 deletions src/WorkflowManager/Database/packages.lock.json
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Expand Up @@ -49,15 +49,15 @@
},
"AWSSDK.Core": {
"type": "Transitive",
"resolved": "3.7.12.23",
"contentHash": "5n9mSVksj3vsv5hm7t/GUjv36iT0s0Wu9UCBn+onTKrnIpXZjVbsHBrxzEwA5Ru6Qg0j4Ah4R/+H6LcngTOVfg=="
"resolved": "3.7.12.27",
"contentHash": "pCX0yHPFuREXOqGaEQoCSlPZwsiijT1rBBiyk1pdD19Db8gVFglO7wMbxl37OhRNcLZprmtWJFvaDfuzeV10Wg=="
},
"AWSSDK.SecurityToken": {
"type": "Transitive",
"resolved": "3.7.1.187",
"contentHash": "Q8wBhVQJQsh7zeaO9KzYOFlWeSOEFRCuwtC//k6XP+8Lw3DIRqHG2HgiY5FyHUrsJrbbUM1uuLGNYG41r8pvDQ==",
"resolved": "3.7.1.191",
"contentHash": "tTIqJ/QKaPzTu5ZPdRFa2sW9p5F441RLV7nDdTAVVuu6oLyemna0bTtE+luGLaw17oE4GZHpa5n5p0oJmpzcxA==",
"dependencies": {
"AWSSDK.Core": "[3.7.12.23, 4.0.0)"
"AWSSDK.Core": "[3.7.12.27, 4.0.0)"
}
},
"DnsClient": {
Expand Down Expand Up @@ -807,7 +807,7 @@
"monai.deploy.workflowmanager.contracts": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Microsoft.Extensions.Configuration": "[6.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"MongoDB.Bson": "[2.17.1, )",
Expand Down
12 changes: 6 additions & 6 deletions src/WorkflowManager/Logging/packages.lock.json
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Expand Up @@ -41,15 +41,15 @@
},
"AWSSDK.Core": {
"type": "Transitive",
"resolved": "3.7.12.23",
"contentHash": "5n9mSVksj3vsv5hm7t/GUjv36iT0s0Wu9UCBn+onTKrnIpXZjVbsHBrxzEwA5Ru6Qg0j4Ah4R/+H6LcngTOVfg=="
"resolved": "3.7.12.27",
"contentHash": "pCX0yHPFuREXOqGaEQoCSlPZwsiijT1rBBiyk1pdD19Db8gVFglO7wMbxl37OhRNcLZprmtWJFvaDfuzeV10Wg=="
},
"AWSSDK.SecurityToken": {
"type": "Transitive",
"resolved": "3.7.1.187",
"contentHash": "Q8wBhVQJQsh7zeaO9KzYOFlWeSOEFRCuwtC//k6XP+8Lw3DIRqHG2HgiY5FyHUrsJrbbUM1uuLGNYG41r8pvDQ==",
"resolved": "3.7.1.191",
"contentHash": "tTIqJ/QKaPzTu5ZPdRFa2sW9p5F441RLV7nDdTAVVuu6oLyemna0bTtE+luGLaw17oE4GZHpa5n5p0oJmpzcxA==",
"dependencies": {
"AWSSDK.Core": "[3.7.12.23, 4.0.0)"
"AWSSDK.Core": "[3.7.12.27, 4.0.0)"
}
},
"JetBrains.Annotations": {
Expand Down Expand Up @@ -741,7 +741,7 @@
"monai.deploy.workflowmanager.contracts": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Microsoft.Extensions.Configuration": "[6.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"MongoDB.Bson": "[2.17.1, )",
Expand Down
14 changes: 7 additions & 7 deletions src/WorkflowManager/PayloadListener/packages.lock.json
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Expand Up @@ -38,15 +38,15 @@
},
"AWSSDK.Core": {
"type": "Transitive",
"resolved": "3.7.12.23",
"contentHash": "5n9mSVksj3vsv5hm7t/GUjv36iT0s0Wu9UCBn+onTKrnIpXZjVbsHBrxzEwA5Ru6Qg0j4Ah4R/+H6LcngTOVfg=="
"resolved": "3.7.12.27",
"contentHash": "pCX0yHPFuREXOqGaEQoCSlPZwsiijT1rBBiyk1pdD19Db8gVFglO7wMbxl37OhRNcLZprmtWJFvaDfuzeV10Wg=="
},
"AWSSDK.SecurityToken": {
"type": "Transitive",
"resolved": "3.7.1.187",
"contentHash": "Q8wBhVQJQsh7zeaO9KzYOFlWeSOEFRCuwtC//k6XP+8Lw3DIRqHG2HgiY5FyHUrsJrbbUM1uuLGNYG41r8pvDQ==",
"resolved": "3.7.1.191",
"contentHash": "tTIqJ/QKaPzTu5ZPdRFa2sW9p5F441RLV7nDdTAVVuu6oLyemna0bTtE+luGLaw17oE4GZHpa5n5p0oJmpzcxA==",
"dependencies": {
"AWSSDK.Core": "[3.7.12.23, 4.0.0)"
"AWSSDK.Core": "[3.7.12.27, 4.0.0)"
}
},
"DnsClient": {
Expand Down Expand Up @@ -912,7 +912,7 @@
"monai.deploy.workflowmanager.contracts": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Microsoft.Extensions.Configuration": "[6.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"MongoDB.Bson": "[2.17.1, )",
Expand Down Expand Up @@ -951,7 +951,7 @@
"monai.deploy.workloadmanager.workfowexecuter": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Ardalis.GuardClauses": "[4.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"Monai.Deploy.Storage": "[0.2.1, )",
Expand Down
12 changes: 6 additions & 6 deletions src/WorkflowManager/Storage/packages.lock.json
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Expand Up @@ -27,15 +27,15 @@
},
"AWSSDK.Core": {
"type": "Transitive",
"resolved": "3.7.12.23",
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"resolved": "3.7.12.27",
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},
"AWSSDK.SecurityToken": {
"type": "Transitive",
"resolved": "3.7.1.187",
"contentHash": "Q8wBhVQJQsh7zeaO9KzYOFlWeSOEFRCuwtC//k6XP+8Lw3DIRqHG2HgiY5FyHUrsJrbbUM1uuLGNYG41r8pvDQ==",
"resolved": "3.7.1.191",
"contentHash": "tTIqJ/QKaPzTu5ZPdRFa2sW9p5F441RLV7nDdTAVVuu6oLyemna0bTtE+luGLaw17oE4GZHpa5n5p0oJmpzcxA==",
"dependencies": {
"AWSSDK.Core": "[3.7.12.23, 4.0.0)"
"AWSSDK.Core": "[3.7.12.27, 4.0.0)"
}
},
"JetBrains.Annotations": {
Expand Down Expand Up @@ -763,7 +763,7 @@
"monai.deploy.workflowmanager.contracts": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Microsoft.Extensions.Configuration": "[6.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"MongoDB.Bson": "[2.17.1, )",
Expand Down
24 changes: 21 additions & 3 deletions src/WorkflowManager/WorkflowExecuter/Services/WorkflowExecuterService.cs
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Expand Up @@ -339,20 +339,38 @@ private async Task HandleDicomExportAsync(WorkflowRevision workflow, WorkflowIns
return;
}

var files = new List<VirtualFileInfo>();
foreach (var artifact in artifactValues)
{
if (artifact is not null)
{
var objects = await _storageService.ListObjectsAsync(
workflowInstance.BucketId,
artifact,
true);
if (objects.IsNullOrEmpty() is false)
{
files.AddRange(objects.ToList());
}
}
}

artifactValues = files.Select(f => f.FilePath).ToArray();

await DispatchDicomExport(workflowInstance, task, exportList, artifactValues, correlationId);
}

private string[] GetDicomExports(WorkflowRevision workflow, WorkflowInstance workflowInstance, TaskExecution task, string[]? exportDestinations)
{
var validExportDestinations = workflow.Workflow?.InformaticsGateway?.ExportDestinations;

#pragma warning disable CS8604 // Possible null reference argument.
if (exportDestinations.IsNullOrEmpty()
if (exportDestinations is null
|| exportDestinations.IsNullOrEmpty()
|| validExportDestinations is null
|| validExportDestinations.IsNullOrEmpty())
{
return Array.Empty<string>();
}
#pragma warning restore CS8604 // Possible null reference argument.

foreach (var exportDestination in exportDestinations)
{
Expand Down
14 changes: 7 additions & 7 deletions src/WorkflowManager/WorkflowExecuter/packages.lock.json
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Expand Up @@ -13,11 +13,11 @@
},
"AWSSDK.SecurityToken": {
"type": "Direct",
"requested": "[3.7.1.187, )",
"resolved": "3.7.1.187",
"contentHash": "Q8wBhVQJQsh7zeaO9KzYOFlWeSOEFRCuwtC//k6XP+8Lw3DIRqHG2HgiY5FyHUrsJrbbUM1uuLGNYG41r8pvDQ==",
"requested": "[3.7.1.191, )",
"resolved": "3.7.1.191",
"contentHash": "tTIqJ/QKaPzTu5ZPdRFa2sW9p5F441RLV7nDdTAVVuu6oLyemna0bTtE+luGLaw17oE4GZHpa5n5p0oJmpzcxA==",
"dependencies": {
"AWSSDK.Core": "[3.7.12.23, 4.0.0)"
"AWSSDK.Core": "[3.7.12.27, 4.0.0)"
}
},
"Monai.Deploy.Messaging": {
Expand Down Expand Up @@ -57,8 +57,8 @@
},
"AWSSDK.Core": {
"type": "Transitive",
"resolved": "3.7.12.23",
"contentHash": "5n9mSVksj3vsv5hm7t/GUjv36iT0s0Wu9UCBn+onTKrnIpXZjVbsHBrxzEwA5Ru6Qg0j4Ah4R/+H6LcngTOVfg=="
"resolved": "3.7.12.27",
"contentHash": "pCX0yHPFuREXOqGaEQoCSlPZwsiijT1rBBiyk1pdD19Db8gVFglO7wMbxl37OhRNcLZprmtWJFvaDfuzeV10Wg=="
},
"DnsClient": {
"type": "Transitive",
Expand Down Expand Up @@ -915,7 +915,7 @@
"monai.deploy.workflowmanager.contracts": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Microsoft.Extensions.Configuration": "[6.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"MongoDB.Bson": "[2.17.1, )",
Expand Down
26 changes: 13 additions & 13 deletions src/WorkflowManager/WorkflowManager/packages.lock.json
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Expand Up @@ -25,11 +25,11 @@
},
"Microsoft.AspNetCore.Mvc.NewtonsoftJson": {
"type": "Direct",
"requested": "[6.0.7, )",
"resolved": "6.0.7",
"contentHash": "zkt7EFRR5fZQUc6taa8sO8aG+EF7XQ6Z7+fPW3gXCh6l7+vyDpZ9PbTODYMsXaS1tOjP1b+jJgf7hY/kaciO4Q==",
"requested": "[6.0.8, )",
"resolved": "6.0.8",
"contentHash": "2imWU1FEnirRogFvtu+wV11xJuC0u7aNprpNQygQLTZvnSlaLPTJhUUrqskFVn6PRDv3kCE4peaBJKwseNv71w==",
"dependencies": {
"Microsoft.AspNetCore.JsonPatch": "6.0.7",
"Microsoft.AspNetCore.JsonPatch": "6.0.8",
"Newtonsoft.Json": "13.0.1",
"Newtonsoft.Json.Bson": "1.0.2"
}
Expand Down Expand Up @@ -186,15 +186,15 @@
},
"AWSSDK.Core": {
"type": "Transitive",
"resolved": "3.7.12.23",
"contentHash": "5n9mSVksj3vsv5hm7t/GUjv36iT0s0Wu9UCBn+onTKrnIpXZjVbsHBrxzEwA5Ru6Qg0j4Ah4R/+H6LcngTOVfg=="
"resolved": "3.7.12.27",
"contentHash": "pCX0yHPFuREXOqGaEQoCSlPZwsiijT1rBBiyk1pdD19Db8gVFglO7wMbxl37OhRNcLZprmtWJFvaDfuzeV10Wg=="
},
"AWSSDK.SecurityToken": {
"type": "Transitive",
"resolved": "3.7.1.187",
"contentHash": "Q8wBhVQJQsh7zeaO9KzYOFlWeSOEFRCuwtC//k6XP+8Lw3DIRqHG2HgiY5FyHUrsJrbbUM1uuLGNYG41r8pvDQ==",
"resolved": "3.7.1.191",
"contentHash": "tTIqJ/QKaPzTu5ZPdRFa2sW9p5F441RLV7nDdTAVVuu6oLyemna0bTtE+luGLaw17oE4GZHpa5n5p0oJmpzcxA==",
"dependencies": {
"AWSSDK.Core": "[3.7.12.23, 4.0.0)"
"AWSSDK.Core": "[3.7.12.27, 4.0.0)"
}
},
"Crc32.NET": {
Expand Down Expand Up @@ -325,8 +325,8 @@
},
"Microsoft.AspNetCore.JsonPatch": {
"type": "Transitive",
"resolved": "6.0.7",
"contentHash": "ybv3udO2SaGW74NKIxj06ozTtcEJf2yOCNj4OGY/ZvB+LG/mZGBVKrwZYaZBXaWR9dakrf4+M3LiMAhasTEamg==",
"resolved": "6.0.8",
"contentHash": "OihHbIG+WAxk0U3jwPxCgh2tQqpeODYis3D0SnwIshpkKoZFhifCwfDNcsTBoppx4Y6ic0dcxkGiHO5NZWtXiw==",
"dependencies": {
"Microsoft.CSharp": "4.7.0",
"Newtonsoft.Json": "13.0.1"
Expand Down Expand Up @@ -1687,7 +1687,7 @@
"monai.deploy.workflowmanager.contracts": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Microsoft.Extensions.Configuration": "[6.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"MongoDB.Bson": "[2.17.1, )",
Expand Down Expand Up @@ -1747,7 +1747,7 @@
"monai.deploy.workloadmanager.workfowexecuter": {
"type": "Project",
"dependencies": {
"AWSSDK.SecurityToken": "[3.7.1.187, )",
"AWSSDK.SecurityToken": "[3.7.1.191, )",
"Ardalis.GuardClauses": "[4.0.1, )",
"Monai.Deploy.Messaging": "[0.1.3-rc0012, )",
"Monai.Deploy.Storage": "[0.2.1, )",
Expand Down
14 changes: 13 additions & 1 deletion tests/UnitTests/WorkflowExecuter.Tests/Services/WorkflowExecuterServiceTests.cs
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Expand Up @@ -37,6 +37,7 @@
using Monai.Deploy.WorkflowManager.Storage.Services;
using Monai.Deploy.WorkflowManager.ConditionsResolver.Parser;
using Monai.Deploy.WorkflowManager.Common.Interfaces;
using System.Threading;

namespace Monai.Deploy.WorkflowManager.WorkflowExecuter.Tests.Services
{
Expand Down Expand Up @@ -378,7 +379,13 @@ public async Task ProcessPayload_WithExportTask_DispatchesExport()
_workflowInstanceRepository.Setup(w => w.UpdateTasksAsync(It.IsAny<string>(), It.IsAny<List<TaskExecution>>())).ReturnsAsync(true);
_workflowInstanceRepository.Setup(w => w.GetByWorkflowsIdsAsync(It.IsAny<List<string>>())).ReturnsAsync(new List<WorkflowInstance>());
_workflowInstanceRepository.Setup(w => w.UpdateTaskStatusAsync(It.IsAny<string>(), It.IsAny<string>(), It.IsAny<TaskExecutionStatus>())).ReturnsAsync(true);
_artifactMapper.Setup(a => a.ConvertArtifactVariablesToPath(It.IsAny<Artifact[]>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<bool>())).ReturnsAsync(new Dictionary<string, string>() { { "dicomexport", "/dcm" } });
var dcmInfo = new Dictionary<string, string>() { { "dicomexport", "/dcm" } };
_artifactMapper.Setup(a => a.ConvertArtifactVariablesToPath(It.IsAny<Artifact[]>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<bool>())).ReturnsAsync(dcmInfo);
_storageService.Setup(w => w.ListObjectsAsync(workflowRequest.Bucket, "/dcm", true, It.IsAny<CancellationToken>()))
.ReturnsAsync(new List<VirtualFileInfo>()
{
new VirtualFileInfo("testfile.dcm", "/dcm/testfile.dcm", "test", ulong.MaxValue)
});

var result = await WorkflowExecuterService.ProcessPayload(workflowRequest, new Payload() { Id = Guid.NewGuid().ToString() });

Expand Down Expand Up @@ -1038,6 +1045,11 @@ public async Task ProcessTaskUpdate_ValidTaskUpdateEventWithExportTaskDestinatio
_workflowRepository.Setup(w => w.GetByWorkflowIdAsync(workflowInstance.WorkflowId)).ReturnsAsync(workflow);
_payloadService.Setup(p => p.GetByIdAsync(It.IsAny<string>())).ReturnsAsync(new Payload { PatientDetails = new PatientDetails { } });
_artifactMapper.Setup(a => a.ConvertArtifactVariablesToPath(It.IsAny<Artifact[]>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<bool>())).ReturnsAsync(new Dictionary<string, string> { { "dicomexport", "/dcm" } });
_storageService.Setup(w => w.ListObjectsAsync(It.IsAny<string>(), "/dcm", true, It.IsAny<CancellationToken>()))
.ReturnsAsync(new List<VirtualFileInfo>()
{
new VirtualFileInfo("testfile.dcm", "/dcm/testfile.dcm", "test", ulong.MaxValue)
});

var response = await WorkflowExecuterService.ProcessTaskUpdate(updateEvent);

Expand Down
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