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Setup

This section outlines the steps to download and install the Informatics Gateway using the CLI and Docker image.

Runtime Requirements

  • Docker 20.10.12 or higher

For development requirements, refer to the Informatics Gateway README.md.

Installation

Informatics Gateway CLI

Download and install the Informatics Gateway CLI from the Releases section of the repository and install it.

On Linux

# Download the 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-0.1.0-linux-x64.zip
# Install it in bin
sudo mv mig-cli /usr/local/bin

On Windows

# Download the 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-0.1.0-win-x64.zip

Informatics Gateway Docker Image

Navigate to the monai-deploy-informatics-gateway package page and locate the version to download.

# for the latest build
docker pull ghcr.io/project-monai/monai-deploy-informatics-gateway:latest
# or for a versioned build
docker pull ghcr.io/project-monai/monai-deploy-informatics-gateway:0.1.0

Configure Informatics Gateway

Use the following commands to initialize the Informatics Gateway and default configuration:

mig-cli config init
mig-cli config endpoint http://localhost:5000
mig-cli.exe config init
mig-cli.exe config endpoint http://localhost:5000

The first command extracts the default appsettings.json file into the home directory:

  • Linux: ~/.mig/appsettings.json
  • Windows: C:\Users\[username]\.mig\appsettings.json

This file is mapped into the Docker container and used by the Informatics Gateway when mig-cli is used to launch the application.

For a complete reference of the appsettings.json file, refer to the Configuration Schema.

The second command passes the endpoint for the Informatics Gateway RESTful API to mig-cli.

Note

To see available commands, simply execute mig-cli or mig-cli.exe.

Storage Consideration & Configuration

The Informatics Gateway operates on two storage locations. In the first location, the incoming data for data grouping is temporarily stored. In the second location, the Informatics Gateway uploads grouped datasets to final storage shared by other MONAI Deploy sub-systems.

Temporary Storage of Incoming Dataset

By default, the temporary storage location is set to /payloads in the appsettings.json file.

To change the temporary storage location, locate the ./InformaticsGateway/storage/temporary property in the appsettings.json file and modify it.

Note

You will need to calculate the required temporary storage based on the number of studies and the size of each study. Also, consider changing the AE Title timeout if the AE Title needs to wait a long time before assembling and uploading the payload for final storage.

Note

Before running the Informatics Gateway, adjust the values of watermarkPercent and reserveSpaceGB based on the expected number of studies and size of each study. The suggested value for reserveSpaceGB is 2x to 3x the size of a single study multiplied by the number of configured AE Titles.

Shared Storage

Informatics Gateway includes MinIO as the default storage service provider. To integrate with another storage service provider, please refer to the Data Storage section of the SRS.

Download and install MinIO by following the quickstart guide. Once MinIO is installed and configured, modify the storage configuration to enable communication between the Informatics Gateway and MinIO.

Locate the storage section of the configuration in appsettings.json:

{
  "ConnectionStrings": {
    "InformaticsGatewayDatabase": "Data Source=migdev.db"
  },
  "InformaticsGateway": {
    "dicom": { ... },
    "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
      },
      "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
    },
    ...
  }
}

Message broker

The nformatics Gateway communicates with other MONAI Deploy components through a message broker. The default messaging service included is provided by RabbitMQ. To integrate with another storage service provider, refer to the Data Storage section of the SRS.

To use the default messaging service, download and install RabbitMQ by following the Get Started page.

Before launching Informatics Gateway, update appsettings.json to configure the publisher and subscriber settings. The Informatics Gateway publishes all messages to an exchange under the specified virtual host. Therefore, please confirm the values before starting Informatics Gateway.

{
  "InformaticsGateway": {
    "messaging": {
      "publisherSettings": {
        "endpoint": "localhost",
        "username": "username",
        "password": "password",
        "virtualHost": "monaideploy",
        "exchange": "monaideploy"
      },
      "subscriberSettings": {
        "endpoint": "localhost",
        "username": "username",
        "password": "password",
        "virtualHost": "monaideploy",
        "exchange": "monaideploy",
        "exportRequestQueue": "export_tasks"
      }
    },
  }
}

Start/Stop Informatics Gateway

To start or stop the Informatics Gateway, update the value of DockerImagePrefix in appsettings.json with the repository name of the Docker image:

{
    ...,
    "Cli": {
        "DockerImagePrefix": "ghcr.io/project-monai/monai-deploy-informatics-gateway"
    }
}

Lastly, use one of the following commands to start or stop the Informatics Gateway:

mig-cli start
mig-cli stop

Enable Incoming Associations

The next step is to configure the Informatics Gateway to enable receiving of DICOM instances from external DICOM devices.

  1. Configure a listening AE Title to receive instances:
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 group instances by the Series Instance UID (0020,000E) with a timeout value of 30 seconds.

Note

-grouping is optional, with a default value of 0020,000D. -t is optional, with a default value of 5 seconds. For complete reference, refer to the Config API.

  1. Enable the receiving of DICOM instances from external DICOM devices:
mig-cli src add -n PACS-LA -a PACSLA001 --h 20.10.30.55

The above command tells the 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

The 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 same as the host IP address. In this 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:

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.