Merge patch/0.1.0 into main (#55)

Fix #56, #68
* update changelog, setup doc, css style & oss licenses
* update docker image repo in appsettings.json
* include files in the export request message
* fix bug where workflow is empty in the workflow request message
* fix export pipeline stuck after Transform block

Signed-off-by: Victor Chang <[email protected]>

Author: mocsharp

docs/changelog.md

@@ -1,13 +1,20 @@
 # Changelog
 
-## 0.1.0 Initial Release
+## 0.1.1
 
-The MONAI Deploy Informatics Gateway upgrades the existing NVIDIA Clara Deploy DICOM Adapter to provide additional features and integrate with the MONAI Deploy platform. 
+[GitHub Milestone 0.1.1](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/6)
+
+- User guide updates & minor bug fixes.
+
+
+## 0.1.0
+
+The MONAI Deploy Informatics Gateway upgrades the existing NVIDIA Clara Deploy DICOM Adapter to provide additional features and integrate with the MONAI Deploy platform.
 
 - DICOM SCP (C-ECHO & C-STORE), SCU (C-STORE) support
 - ACR API with ability to retrieve data via DICOMweb & FHIR
 - Integrates with MinIO as the default storage service for storing received/retrieve data and for sharing among other subsystems in MONAI Deploy platform.
 - Integrates with RabbitMQ as the default messaging broker for exchanging requests among other subsystems.
 
 
-For a complete list of supported features, pleas refer to the [User Guide](./index.md).
+For a complete list of supported features, pleas refer to the [User Guide](./index.md).

docs/compliance/open-source-licenses.md

@@ -19,11 +19,11 @@ the repository and install it.
 
 ```bash
 # Download the CLI
-curl -LO https://url-to-cli
+curl -LO https://github.com/Project-MONAI/monai-deploy-informatics-gateway/releases/download/0.1.0/mig-cli-0.1.0-linux-x64.zip
+# Calculate the SHA256 checksum and verify the output with the checksum on the Releases page.
+sha256sum mig-cli-0.1.0-linux-x64.zip
 # Unzip the CLI
-unzip mig-cli-linux-0.1.0-x64.zip
-# Calculate the SHA256 checksum and compare with the one listed on the Releases page.
-sha256sum mig-cli
+unzip mig-cli-0.1.0-linux-x64.zip
 # Install it in bin
 sudo mv mig-cli /usr/local/bin
 ```
@@ -32,11 +32,11 @@ sudo mv mig-cli /usr/local/bin
 
 ```powershell
 # Download the CLI
-curl -LO https://url-to-cli
+curl -LO https://github.com/Project-MONAI/monai-deploy-informatics-gateway/releases/download/0.1.0/mig-cli-0.1.0-win-x64.zip
+# Calculate the SHA256 checksum and verify the output with the checksum on the Releases page.
+Get-FileHash mig-cli-0.1.0-win-x64.zip
 # Unzip the CLI
-Expand-Archive -Path mig-cli-win-0.1.0-x64.zip
-# Calculate the SHA256 checksum and compare with the one listed on the Releases page.
-Get-FileHash mig-cli.exe
+Expand-Archive -Path mig-cli-0.1.0-win-x64.zip
 ```
 
 ### Informatics Gateway Docker Image
@@ -56,8 +56,8 @@ docker pull ghcr.io/project-monai/monai-deploy-informatics-gateway:0.1.0
 Use the following command to initialize Informatics Gateway & default configuration:
 
 ```bash
-./mig-cli config init
-./mig-cli config endpoint http://localhost:5000
+mig-cli config init
+mig-cli config endpoint http://localhost:5000
 ```
 
 
@@ -77,61 +77,8 @@ For a complete reference of the `appsettings.jon`, please refer to [Configuratio
 
 The second command tells `mig-cli` where the endpoint is for the Informatics Gateway RESTful API.
 
-## Start/Stop Informatics Gateway
-
-To start or stop Informatics Gateway, use one of the following commands:
-
-```bash
-./mig-cli start
-./mig-cli stop
-```
-
-
 > [!Note]
-> To see available commands simply execute `./mig-cli` or `mig-cli.exe`.
-
-## Enable Incoming Associations
-
-The next step is to configure Informatics Gateway enable receiving of DICOM instances from external DICOM devices.
-
-1. Configure a listening AE Title to receive instances:
-
-```bash
-./mig-cli aet add -a BrainAET -grouping 0020,000E, -t 30
-```
-
-The command creates a new listening AE Title with AE Title `BrainAET`.  The listening AE Title
-will be grouping instances by the Series Instance UID (0020,000E) with a timeout value of 30 seconds.
-
-> [!Note]
-> `-grouping` is optional with default of 0020,000D.
-> `-t` is optional with default of 5 seconds.
-> For complete reference, please refer to the [Config API](../api/rest/config.md).
-
-2. Enable receiving DICOM instances from an external DICOM devices:
-
-```bash
-./mig-cli src add -n PACS-LA -a PACSLA001 --h 20.10.30.55 -p 104
-```
-
-This command above tells Informatics Gateway to accept instances from AE Title `PACSLA001` at IP `20.10.30.55` and port `104`.
-
-
-> [!Note]
-> By default, Informatics Gateway blocks all unknown sources.  
-> To allow all unknown sources, set `dicom>scp>rejectUnknownSources` to `false` in `appsettings.json`.
-
-## Export Processed Results
-
-If exporting via DIMSE is required, add a DICOM destination:
-
-```bash
-./mig-cli dst add -a WORKSTATION1 -h 100.200.10.20 -p 104
-```
-
-The command adds a DICOM export destination with AE Title `WORKSTATION1` at IP `100.200.10.20` and port `104`.
-
-
+> To see available commands simply execute `mig-cli` or `mig-cli.exe`.
 
 ## Storage Consideration & Configuration
 
@@ -144,8 +91,8 @@ The temporary storage location, by default, is set to `/payloads` in the `appset
 To change the temporary storage location, please locate `./InformaticsGateway/storage/temporary` property in the `appsettings.json` file.
 
 > [!Note]
-> Calculate the required temporary storage based on the number of studies and the size of each study. 
-> Please also consider the AE Title timeout if the AE Title needs to wait a long time before assembling & uploading 
+> Calculate the required temporary storage based on the number of studies and the size of each study.
+> Please also consider the AE Title timeout if the AE Title needs to wait a long time before assembling & uploading
 > the payload for final storage.
 
 
@@ -171,10 +118,10 @@ Locate the storage section of the configuration in `appsettings.json`:
     "storage": {
       "storageServiceCredentials": {
         "endpoint": "192.168.1.1:9000", # IP & port to MinIO instance
-        "accessKey": "admin", # Access key or username 
-        "accessToken": "password" # Access token or password 
+        "accessKey": "admin", # Access key or username
+        "accessToken": "password" # Access token or password
       },
-      "storageService": "Monai.Deploy.InformaticsGateway.Storage.MinIoStorageService, Monai.Deploy.InformaticsGateway.Storage.MinIo", # Fully qualified type name of the storage service 
+      "storageService": "Monai.Deploy.InformaticsGateway.Storage.MinIoStorageService, Monai.Deploy.InformaticsGateway.Storage.MinIo", # Fully qualified type name of the storage service
       "securedConnection": false, # Indicates if a secured connection is required to access MinIO
       "storageServiceBucketName": "igbucket" # The name of the bucket where data is uploaded to
     },
@@ -186,11 +133,11 @@ Locate the storage section of the configuration in `appsettings.json`:
 ### Message broker
 
 Informatics Gateway communicates with other MONAI Deploy components through a message broker.  The default messaging service
-included is provided by [RabbitMQ](https://www.rabbitmq.com/). To integrate with another storage service provider, please refer 
+included is provided by [RabbitMQ](https://www.rabbitmq.com/). To integrate with another storage service provider, please refer
 to the [Data Storage](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/blob/main/guidelines/srs.md#message-broker) section of the SRS.
 
 To use the default messaging service, please download and install RabbitMQ by following the
-[Get Started](https://www.rabbitmq.com/#getstarted) page. 
+[Get Started](https://www.rabbitmq.com/#getstarted) page.
 
 Before launching Informatics Gateway, update `appsettings.json` to configure the publisher and subscriber settings.
 IG publishes all messages to an *exchange* under the specified *virtual host*. Therefore, please confirm the values before starting
@@ -219,3 +166,69 @@ Informatics Gateway.
   }
 }
 ```
+
+## Start/Stop Informatics Gateway
+
+To start or stop Informatics Gateway, update the value of `DockerImagePrefix` in `appsettings.json` with the repository name of the Docker image:
+
+```json
+{
+    ...,
+    "Cli": {
+        "DockerImagePrefix": "ghcr.io/project-monai/monai-deploy-informatics-gateway"
+    }
+}
+```
+
+
+Lastly, use one of the following commands start or stop Informatics Gateway:
+
+```bash
+mig-cli start
+mig-cli stop
+```
+
+
+## Enable Incoming Associations
+
+The next step is to configure Informatics Gateway enable receiving of DICOM instances from external DICOM devices.
+
+1. Configure a listening AE Title to receive instances:
+
+```bash
+mig-cli aet add -a BrainAET -grouping 0020,000E, -t 30
+```
+
+The command creates a new listening AE Title with AE Title `BrainAET`.  The listening AE Title
+will be grouping instances by the Series Instance UID (0020,000E) with a timeout value of 30 seconds.
+
+> [!Note]
+> `-grouping` is optional with default of 0020,000D.
+> `-t` is optional with default of 5 seconds.
+> For complete reference, please refer to the [Config API](../api/rest/config.md).
+
+2. Enable receiving DICOM instances from an external DICOM devices:
+
+```bash
+mig-cli src add -n PACS-LA -a PACSLA001 --h 20.10.30.55
+```
+
+This command above tells Informatics Gateway to accept instances from AE Title `PACSLA001` at IP `20.10.30.55` and port `104`.
+
+> [!Note]
+> By default, Informatics Gateway blocks all unknown sources.
+> To allow all unknown sources, set `dicom>scp>rejectUnknownSources` to `false` in `appsettings.json`.
+
+> [!WARNING]
+> Informatics Gateway validates both the source IP address and AE Title when `rejectUnknownSources` is set to `true`.
+> When running Informatics Gateway in a container and data is coming from the localhost, the IP address may not be the host's IP address. In such a case, open the log file and locate the association that failed; the log should indicate the correct IP address under `Remote host`.
+
+## Export Processed Results
+
+If exporting via DIMSE is required, add a DICOM destination:
+
+```bash
+mig-cli dst add -a WORKSTATION1 -h 100.200.10.20 -p 104
+```
+
+The command adds a DICOM export destination with AE Title `WORKSTATION1` at IP `100.200.10.20` and port `104`.

docs/setup/setup.md

@@ -1,10 +1,10 @@
 /* COLOR VARIABLES*/
 
 :root {
-    --header-bg-color: #76b900;
+    --header-bg-color: #03a3a3;
     --header-ft-color: #fff;
-    --highlight-light: #76b900;
-    --highlight-dark: #76b900;
+    --highlight-light: #03a3a3;
+    --highlight-dark: #03a3a3;
     --accent-dim: #e0e0e0;
     --accent-super-dim: #f3f3f3;
     --font-color: #34393e;
@@ -39,7 +39,7 @@ a:hover,
 a:focus {
     color: var(--highlight-light);
     text-decoration: none;
-    color: #569700;
+    color: #03a3a3;
     background-color: #eff7e0;
 }
 
@@ -298,7 +298,7 @@ pre {
     font-size: 13px;
     word-break: break-all;
     word-wrap: break-word;
-    background-color: #fffaef;
+    background-color: #eef9f9;
     border-radius: 4px;
     border: none;
     box-shadow: var(--card-box-shadow);
@@ -333,4 +333,4 @@ pre {
     margin-top: 2em;
     border-bottom: 8px solid var(--highlight-dark);
     padding: 0 10px;
-}
+}

docs/templates/material/styles/main.css

@@ -10,6 +10,7 @@
 // limitations under the License.
 
 using Ardalis.GuardClauses;
+using Monai.Deploy.InformaticsGateway.Common;
 using System;
 using System.Collections.Generic;
 using System.Diagnostics;
@@ -61,13 +62,7 @@ public enum PayloadState
 
         public int Count { get => _fileCount; }
 
-        public IEnumerable<string> Workflows
-        {
-            get
-            {
-                return Files.SelectMany(x => x.Workflows).Distinct();
-            }
-        }
+        public ISet<string> Workflows { get; private set; }
 
         public string CorrelationId { get; init; }
 
@@ -87,6 +82,7 @@ public Payload(string key, string correlationId, uint timeout)
             State = PayloadState.Created;
             Files = new List<FileStorageInfo>();
             UploadedFiles = new List<BlockStorageInfo>();
+            Workflows = new HashSet<string>();
         }
 
         public void Add(FileStorageInfo value)
@@ -98,6 +94,15 @@ public void Add(FileStorageInfo value)
             _lastReceived.Start();
             _fileCount = Files.Count;
 
+            if (!value.Workflows.IsNullOrEmpty())
+            {
+                foreach (var workflow in value.Workflows)
+                {
+
+                    Workflows.Add(workflow);
+                }
+            }
+
             if (Files.Count == 1)
             {
                 DateTimeCreated = value.Received;

src/Api/Storage/Payload.cs

@@ -35,12 +35,5 @@ public class MessageBrokerConfigurationKeys
         /// </summary>
         [JsonProperty(PropertyName = "exportRequestPrefix")]
         public string ExportRequestPrefix { get; set; } = "md.export.request";
-
-        /// <summary>
-        /// Gets or sets the name of the request queue.
-        /// Defaults to `export_tasks`
-        /// </summary>
-        [JsonProperty(PropertyName = "exportRequestQueue")]
-        public string ExportRequestQueue { get; set; } = "export_tasks";
     }
 }