Merge pull request #780 from Project-MONAI/release/0.1.11

Release/0.1.11

Author: woodheadio

docs/api/rest/workflow-manager/payload.md

@@ -16,37 +16,197 @@
 
 # Workflow Manager - Payload APIs
 
-**TEMPLATE**
+## GET /payloads
 
-## GET/POST/PUT/DELETE /payloads/
+Returns a paginated list of Payloads with additional computed property of payloadStatus.
 
-*description*
+- If any of the workflow Instances status' attached to that payload are “Created” then the payloadStatus would be “In Progress”
+
+- If all workflow Instances status' attached to that payload are not “Created” then the payloadStatus would be “Complete”
+
+- If there are no workflow Instances attached to that payload then the payloadStatus would be “Complete”
 
 ### Parameters
 
-*parameters*
+(Query) pageNumber: int
+
+(Query) pageSize: int
+
+(Query) maxPageSize: int (default of 10)
+
+(Query) patientId: string
+
+(Query) patientName: string
 
 ### Responses
 
 Response Content Type: JSON
 
-*response type*
-
 | Code | Description                                                                                                                             |
 | ---- | --------------------------------------------------------------------------------------------------------------------------------------- |
-| 200  | Service is healthy.                                                                                                                     |
-| 503  | Service is unhealthy.                                                                                                                   |
+| 200  | List of payloads. | 
 | 500  | Server error. The response will be a [Problem details](https://datatracker.ietf.org/doc/html/rfc7807) object with server error details. |
 
 ### Example Request
 
 ```bash
-curl --location --request GET 'http://localhost:5000/workflows'
+curl --location --request GET 'http://localhost:5000/payloads'
 ```
 
 ### Example Response
 
 ```json
-*sample output*
+{
+  "PageNumber": 1,
+  "PageSize": 10,
+  "FirstPage": "/payload?pageNumber=1&pageSize=10",
+  "LastPage": "/payload?pageNumber=1&pageSize=10",
+  "TotalPages": 1,
+  "TotalRecords": 3,
+  "NextPage": null,
+  "PreviousPage": null,
+  "Data":
+    [
+      {
+        "Version": "1.0.0",
+        "id": "3042cac6-b8b8-4f65-a2b2-8ec340652c9b",
+        "payload_id": "c5c3636b-81dd-44a9-8c4b-71adec7d47b2",
+        "workflows": ["1e7b49f2-a3a2-4ded-b489-86ad9b2da9c8"],
+        "workflow_instance_ids": [],
+        "file_count": 50,
+        "correlation_id": "68ccea88-1f40-4eb3-ad23-7f444ac12910",
+        "bucket": "bucket_1",
+        "calling_aetitle": "Basic_AE",
+        "called_aetitle": "MIG",
+        "timestamp": "2023-05-03T12:47:59.046Z",
+        "files": [],
+        "patient_details":
+          {
+            "patient_id": "732ca351-6267-41e9-a6e8-21b3a74abe7c",
+            "patient_name": "Steve Jobs",
+            "patient_sex": "male",
+            "patient_dob": "1996-02-05T00:00:00Z",
+            "patient_age": null,
+            "patient_hospital_id": null
+          },
+        "payload_status": "Completed",
+        "payload_deleted": 1
+      },
+      {
+        "Version": "1.0.0",
+        "id": "2435a8d7-84f4-407d-9d0e-941bb87b0190",
+        "payload_id": "86c0f117-4021-412e-b163-0dc621df672a",
+        "workflows": ["3d517d26-118c-4241-beb8-6b51d462c746"],
+        "workflow_instance_ids": [],
+        "file_count": 3,
+        "correlation_id": "1ef12067-0fda-45c6-87b4-bcc4b245e8d9",
+        "bucket": "bucket_1",
+        "calling_aetitle": "Basic_AE",
+        "called_aetitle": "MIG",
+        "timestamp": "2023-05-03T12:47:59.046Z",
+        "files": [],
+        "patient_details":
+          {
+            "patient_id": "dae4a6d1-573d-4a3f-978f-ed056f628de6",
+            "patient_name": "Jane Doe",
+            "patient_sex": "female",
+            "patient_dob": null,
+            "patient_age": null,
+            "patient_hospital_id": null
+          },
+        "payload_status": "Completed",
+        "payload_deleted": 1
+      },
+      {
+        "Version": "1.0.0",
+        "id": "39d599bc-6635-4f94-9b55-b72a5b11c849",
+        "payload_id": "30a8e0c6-e6c4-458f-aa4d-b224b493d3c0",
+        "workflows": ["db52fafe-1035-436a-b4ff-50ab850f5f68"],
+        "workflow_instance_ids": [],
+        "file_count": 3,
+        "correlation_id": "40544d26-b4bb-4f67-b4ae-68ff3a237cf2",
+        "bucket": "bucket_2",
+        "calling_aetitle": "Basic_AE",
+        "called_aetitle": "MIG",
+        "timestamp": "2023-05-03T12:47:59.046Z",
+        "files": [],
+        "patient_details":
+          {
+            "patient_id": null,
+            "patient_name": null,
+            "patient_sex": null,
+            "patient_dob": null,
+            "patient_age": null,
+            "patient_hospital_id": null
+          },
+        "payload_status": "Completed",
+        "payload_deleted": 1
+      }
+    ],
+  "Succeeded": true,
+  "Errors": null,
+  "Message": null
+}
 ```
 
+---
+
+## GET /payloads/{id}
+
+Returns specific payload for given id.
+
+### Parameters
+(Route) id: string - UUID
+
+### Responses
+
+Response Content Type: JSON
+
+| Code | Description                                                                                                                             |
+| ---- | --------------------------------------------------------------------------------------------------------------------------------------- |
+| 200  | List of payloads. | 
+| 400  | [Problem details](https://datatracker.ietf.org/doc/html/rfc7807) Failed to validate id. |
+| 404  | [Problem details](https://datatracker.ietf.org/doc/html/rfc7807) Failed to find payload with payload id. |
+| 500  | Server error. The response will be a [Problem details](https://datatracker.ietf.org/doc/html/rfc7807) object with server error details. |
+
+
+### Example Request
+
+```bash
+curl --location --request GET 'http://localhost:5000/payloads/3042cac6-b8b8-4f65-a2b2-8ec340652c9b'
+```
+
+### Example Response
+```json
+{
+  "Version": "1.0.0",
+  "id": "3042cac6-b8b8-4f65-a2b2-8ec340652c9b",
+  "payload_id": "c5c3636b-81dd-44a9-8c4b-71adec7d47b2",
+  "workflows": ["1e7b49f2-a3a2-4ded-b489-86ad9b2da9c8"],
+  "workflow_instance_ids": [],
+  "file_count": 50,
+  "correlation_id": "68ccea88-1f40-4eb3-ad23-7f444ac12910",
+  "bucket": "bucket_1",
+  "calling_aetitle": "Basic_AE",
+  "called_aetitle": "MIG",
+  "timestamp": "2023-05-03T12:47:59.046Z",
+  "files": [],
+  "patient_details":
+    {
+      "patient_id": "732ca351-6267-41e9-a6e8-21b3a74abe7c",
+      "patient_name": "Steve Jobs",
+      "patient_sex": "male",
+      "patient_dob": "1996-02-05T00:00:00Z",
+      "patient_age": null,
+      "patient_hospital_id": null
+    },
+}
+```
+
+---
+
+## DELETE /payloads/{id}
+
+TODO
+
+---

docs/setup/mwm-workflow-spec.md

@@ -48,7 +48,6 @@ Workflows can be created or updated via the [Workflow API](https://github.com/Pr
       - [Plugin](#plugin)
     - [Task Arguments](#task-arguments)
       - [Argo](#argo)
-        - [Resource Request Object](#resource-request-object)
     - [Clinical Review](#clinical-review)
     - [Router](#router-1)
     - [Export](#export-1)
@@ -69,6 +68,7 @@ Workflows can be created or updated via the [Workflow API](https://github.com/Pr
       - [Execution Context](#execution-context)
       - [Result Metadata \& Execution Stats - Using Dictionary Values](#result-metadata--execution-stats---using-dictionary-values)
       - [Argo Metadata](#argo-metadata)
+      - [Handled Exception Metadata](#handled-exception-metadata)
       - [DICOM Tags](#dicom-tags)
       - [Patient Details Context](#patient-details-context)
       - [Workflow Context](#workflow-context)
@@ -711,7 +711,7 @@ Conditional evaluators are logical statement strings that may be used to determi
 
     NOT_CONTAINS (Valid for integers and strings compared to lists)
 
-more information on conditionals can be found  [Conditionals Docs](guidelines\mwm-conditionals.md)
+more information on conditionals can be found  [Conditionals Docs](..\..\guidelines\mwm-conditionals.md)
 
 ### Context
 The workflow metadata is any data that can be used by Evaluators. This includes metadata added by previous tasks, but can also include metadata about the input files (most notably DICOM tags).
@@ -799,6 +799,33 @@ An example format of the metadata.json can be found below:
 
 execution stats are populated from the argo execution values returned automatically.
 
+#### Handled Exception Metadata
+Application models can throw handled exceptions, to do this your application model should output the properties "exception" and "exception_message" to the `metadata.json`
+
+Example...
+```json
+{
+  "exception": "NoDicomFilesException",
+  "exception_message": "No dicom files found."
+}
+```
+
+We recommend your application exits execution once the metadata.json has been written.
+
+This exception can be used in the workflow task destinations queries for example like the following examples...
+
+```python
+{{ context.executions.task_id.result.exception }} == 'NoDicomFilesException' && {{ context.executions.task_id.result.exception_message }} == 'No dicom files found.'
+```
+
+```python
+{{ context.executions.task_id.result.exception_message }} CONTAINS 'No dicom files'
+```
+
+```python
+{{ context.executions.task_id.result.exception }} == NULL
+```
+
 
 #### DICOM Tags
 When the input data is DICOM, Evaluators can use DICOM tag values in conditional statements.

src/AssemblyInfo.cs

@@ -18,4 +18,4 @@
 
 [assembly: AssemblyFileVersion("0.0.0.0")]
 [assembly: AssemblyVersion("0.0.0.0")]
-[assembly: AssemblyInformationalVersion("0.0.0-development")]
+[assembly: AssemblyInformationalVersion("0.0.0-development")]

src/Monai.Deploy.WorkflowManager.sln

@@ -82,6 +82,10 @@ Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Monai.Deploy.WorkflowManage
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Monai.Deploy.WorkflowManager.Common.Tests", "..\tests\UnitTests\Common.Tests\Monai.Deploy.WorkflowManager.Common.Tests.csproj", "{75A4AEDA-0386-4B2D-9DBA-BC9AE733660E}"
 EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Monai.Deploy.WorkflowManager.Services", "WorkflowManager\Monai.Deploy.WorkflowManager.Services\Monai.Deploy.WorkflowManager.Services.csproj", "{526FF10C-1C7F-4C26-8E8A-D7ACD65F5467}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Monai.Deploy.WorkflowManager.Services.Tests", "..\tests\UnitTests\WorkflowManager.Services.Tests\Monai.Deploy.WorkflowManager.Services.Tests.csproj", "{0D40F7D6-3747-4280-8EB3-9F3A18AC1125}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU
@@ -228,6 +232,14 @@ Global
 		{75A4AEDA-0386-4B2D-9DBA-BC9AE733660E}.Debug|Any CPU.Build.0 = Debug|Any CPU
 		{75A4AEDA-0386-4B2D-9DBA-BC9AE733660E}.Release|Any CPU.ActiveCfg = Release|Any CPU
 		{75A4AEDA-0386-4B2D-9DBA-BC9AE733660E}.Release|Any CPU.Build.0 = Release|Any CPU
+		{526FF10C-1C7F-4C26-8E8A-D7ACD65F5467}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{526FF10C-1C7F-4C26-8E8A-D7ACD65F5467}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{526FF10C-1C7F-4C26-8E8A-D7ACD65F5467}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{526FF10C-1C7F-4C26-8E8A-D7ACD65F5467}.Release|Any CPU.Build.0 = Release|Any CPU
+		{0D40F7D6-3747-4280-8EB3-9F3A18AC1125}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{0D40F7D6-3747-4280-8EB3-9F3A18AC1125}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{0D40F7D6-3747-4280-8EB3-9F3A18AC1125}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{0D40F7D6-3747-4280-8EB3-9F3A18AC1125}.Release|Any CPU.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -269,6 +281,8 @@ Global
 		{81E3F943-B992-4C81-AA09-A17C05081236} = {37A19144-CEA5-47A2-9FFD-22C522E8B895}
 		{C853A9E3-C53D-4B1A-BFDA-228689A8C94C} = {71DDEE7B-E213-4E39-A7F4-4646783A27F7}
 		{75A4AEDA-0386-4B2D-9DBA-BC9AE733660E} = {71DDEE7B-E213-4E39-A7F4-4646783A27F7}
+		{526FF10C-1C7F-4C26-8E8A-D7ACD65F5467} = {AC5B198A-C3F2-4AD2-B532-E71B4630BDD5}
+		{0D40F7D6-3747-4280-8EB3-9F3A18AC1125} = {71DDEE7B-E213-4E39-A7F4-4646783A27F7}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {DC0D56C8-D8CB-45CE-B528-F3DCF86D63ED}

src/Shared/Configuration/InformaticsGatewayConfiguration.cs

@@ -0,0 +1,26 @@
+/*
+ * Copyright 2022 MONAI Consortium
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+using Microsoft.Extensions.Configuration;
+
+namespace Monai.Deploy.WorkflowManager.Configuration
+{
+    public class InformaticsGatewayConfiguration
+    {
+        [ConfigurationKeyName("apiHost")]
+        public string ApiHost { get; set; }
+    }
+}

src/Shared/Shared/ApiControllerBase.cs

@@ -22,7 +22,6 @@
 using Monai.Deploy.WorkflowManager.Shared.Filter;
 using Monai.Deploy.WorkflowManager.Shared.Wrappers;
 using Monai.Deploy.WorkflowManager.Shared.Services;
-using Microsoft.AspNetCore.Routing;
 
 namespace Monai.Deploy.WorkflowManager.ControllersShared
 {
@@ -85,7 +84,7 @@ public PagedResponse<IEnumerable<T>> CreatePagedReponse<T>(IEnumerable<T> pagedD
 
         public StatsPagedResponse<IEnumerable<T>> CreateStatsPagedReponse<T>(IEnumerable<T> pagedData, PaginationFilter validFilter, long totalRecords, IUriService uriService, string route)
         {
-            var response = new StatsPagedResponse<IEnumerable<T>>(pagedData, validFilter.PageNumber, validFilter.PageSize.Value);
+            var response = new StatsPagedResponse<IEnumerable<T>>(pagedData, validFilter.PageNumber, validFilter.PageSize ?? 10);
             response.SetUp(validFilter, totalRecords, uriService, route);
             return response;
         }

src/Shared/Shared/Filter/TimeFilter.cs

@@ -0,0 +1,25 @@
+/*
+ * Copyright 2023 MONAI Consortium
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+namespace Monai.Deploy.WorkflowManager.Shared.Filter
+{
+    public class TimeFilter : PaginationFilter
+    {
+        public DateTime StartTime { get; set; }
+
+        public DateTime EndTime { get; set; }
+    }
+}

src/Shared/Shared/MonaiServiceLocator.cs

@@ -41,7 +41,7 @@ public Dictionary<string, ServiceStatus> GetServiceStatus()
             return _runningServices.ToDictionary(k => k.ServiceName, v => v.Status);
         }
 
-        private IMonaiService GetService(Type type)
+        private IMonaiService? GetService(Type type)
         {
             Guard.Against.Null(type, nameof(type));
 
@@ -58,7 +58,7 @@ private static List<Type> LocateTypes()
                                             serviceType.IsAssignableFrom(p) &&
                                             p != serviceType &&
                                             !p.IsAbstract &&
-                                            p.FullName.StartsWith("Monai", StringComparison.InvariantCulture));
+                                            p.FullName is not null && p.FullName.StartsWith("Monai", StringComparison.InvariantCulture));
             return services.Distinct().ToList();
         }