A content-agnostic data exchange middle-ware for federated data warehouses.
This software is not designed for standalone usage. Rather it is to be used within federated data warehouse environments like e.g. research networks or multi-center clinical study registries in conjunction with local workflows and processing infrastructure.
The broker infrastructure contains two main components: The central component broker-server is used to publish information to be distributed. The local component broker-client is used by multiple parties to retrieve the published information and subsequently report status updates and response-data.
The middleware infrastructure is content-agnostic in the sense that it can be used with any format or kind of data. A typical scenario is submitting a query for data extraction (e.g. SQL) to the broker (server) to be received by multiple clients which in turn process the query and return status/progress information and resulting extracted data. Other use cases include distribution of metadata/terminology and processing of material transfer requests.
As all communication is based on RESTful HTTP endpoints, the broker-client is optional and can be replaced with simple HTTP calls.
Example for a typical scenario:
Analyst Broker-Server Broker-Client-1 Broker-Client-2 ....
submit query ---> publish query
|
| <----- ask for queries
| |
| -----> receive new query
| |
| <----- report status
| | (internal workflow
| | and query execution)
| <----- report results
|
(collect responses)
|
get status update <--- |
|
|
| <----------------------------- ask for queries
| |
| -----------------------------> receive new query
| |
| <----------------------------- report status
| | (internal workflow
| | and query execution)
| <----------------------------- report results
|
retrieve results <--- |
The easiest way to use the software is to download and run the pre-build binary distribution of broker-admin-dist.
To run the central broker component, first unpack the binary distribution broker-admin-dist-1.x.zip. For running the application, you need a Java 8 runtime environment or newer. We recommend to use the latest OpenJDK version (currently OpenJDK 15). Open a command shell in the extracted folder and run the script run_broker.sh for Linux/MingW/GitBash or run_broker.bat for Windows respectively. To change startup options (e.g port), edit the startup script.
To test the broker from an IDE, simply run the class broker-admin/src/test/java/org.aktin.broker.admin.standalone.TestServer. The port can be specified as command line argument and defaults to locahost:8080. Running the TestServer (instead of directly using the production src/main/java/org.aktin.broker.admin.standalone.HttpServer) will make sure that the system state and configuration files go to the target/ folder instead of cluttering the project directories as well as that example data is already available. In this test environment, the admin password is set to 'test'. Client API-Keys can be found under broker-admin/src/test/resources/api-keys.properties. For examples to use the broker, see below.
To build the project from its source code, you need a Java runtime environment (e.g. OpenJDK 15, minimum is Java 8) and the build-tool Apache Maven. To build the project, download/clone the repository source code and run mvn clean install via command shell in the main directory. After the build process is completed, you can find the broker binary distribution in the subfolder broker-admin-dist/target. To run the broker, see section Getting startet above.
Below, you will find examples for typical use cases. For accessing the broker from Java/JRE-Applications, you can use the broker-client dependency (https://mvnrepository.com/artifact/org.aktin/broker-client) which communicates with the broker via HTTP. To demonstrate the simplicity of the RESTful API, the command line tool curl is used in the following examples for direct HTTP communication.
This example performs authentication at the broker and creates a request containing query syntax which is to be distributed to all nodes.
# Admin authentication and store token in shell variable
TOKEN=`curl -s -H "Content-Type: application/xml" -X POST \
-d '<credentials><username>admin</username><password>CHANGEME</password></credentials>' \
http://localhost:8080/auth/login`
# Create a file containing the query syntax
echo "SELECT * FROM fhir_observation" > query1.sql
# submit the query
curl -i -H "Authorization: Bearer $TOKEN" -H "Content-Type: application/sql" -X POST \
-d @query1.sql http://localhost:8080/broker/request
# the response will contain a Location header for the newly created request.
# We will use this location below to publish the request
curl -si -H "Authorization: Bearer $TOKEN" -X POST http://localhost:8080/broker/request/1/publish
Documentation on the RESTful API of the request administration endpoint can be found in RequestAdminEndpoint.java
In this example, the client will authenticate via API-key and receives the published request.
# list available requests
curl -is -H "Authorization: Bearer xxxApiKey123" http://localhost:8080/broker/my/request
# retrieve first request
curl -is -H "Authorization: Bearer xxxApiKey123" http://localhost:8080/broker/my/request/1
# update status to retrieved
curl -is -H "Authorization: Bearer xxxApiKey123" -X POST \
http://localhost:8080/broker/my/request/1/status/retrievedThis example demonstrates, how the client can supply arbitrary data as a result to a request.
# Create a file containing the query results
echo -e "a;b\n1;2\n3;4\n" > result1.csv
# submit the file contents
curl -i -H "Authorization: Bearer xxxApiKey123" -H "Content-Type: text/csv" -X PUT \
-d @result1.csv http://localhost:8080/aggregator/my/request/1/result
# update status to completed
curl -is -H "Authorization: Bearer xxxApiKey123" -X POST \
http://localhost:8080/broker/my/request/1/status/completed
A different client may also reject a query. (Note the different API-key to indicate a different client)
curl -is -H "Authorization: Bearer xxxApiKey567" -X POST \
http://localhost:8080/broker/my/request/1/status/rejected
Possible request states are documented in broker-api/RequestStatus
Once one or more clients have responded to a request e.g. by supplying result data, the submitter can retrieve the results either via individual REST calls or more conveniently via ZIP bundle:
# assuming authentication was already done (see first example)
# retrieve a download ID for the bundle containing all results and status updates
BUNDLE_ID=`curl -s -H "Authorization: Bearer $TOKEN" http://localhost:8080/broker/export/request-bundle/1`
# download the results bundle
curl -s -H "Authorization: Bearer $TOKEN" --output results.zip \
http://localhost:8080/broker/download/$BUNDLE_ID
The broker includes a minimal web frontent, which can be used to view the status of connected nodes, manage requests and responses and download results. This frontent serves only as a built-in minimal user interface - for a better user experience, external customized frontents should be used.
To access the frontend, go to http://localhost:8080/admin/html/index.html once the broker is running. For login, use the username admin. The admin password is specified in the startup script and defaults to CHANGEME.
The minimal web frontend currently only supports the org.aktin.broker.auth.cred.CredentialTokenAuthProvider.
Without this auth provider, the frontend will not function. Nevertheless, the broker will be fully function
To use broker functionality in java client applications, you can use the broker-client dependency (https://mvnrepository.com/artifact/org.aktin/broker-client).
The client library comes with two runnable implementations:
org.aktin.broker.client.live.sysproc.CLIfor a command line implementation with executes custom OS processes to automatically handle requests.org.aktin.broker.client.live.util.AdminListenerwhich connects to the server and listens/prints any changes and updates. For more information, see broker-client/README.md
For a code example of other clients, see the following implementations:
- https://github.com/li2b2/li2b2-shrine/tree/master/node/i2b2/i2b2-node
- https://github.com/li2b2/li2b2-shrine/tree/master/node/dktk/dktk-node
Multiple authentication/authorization providers are supported. Default method is API key authentication.
Client now retrieves keycloak token. Broker does no longer use the introspection endpoint but checks the token itself.
To get it running, the following is needed:
keycloak.json: get it from keycloak. Go to your client there, and click on the "installation" tab and select "keycloak oidc json" format. Copy the file to the target folder (where sysproc.properties is copied to as well) add the OpenIdAuthProvider to the list of providers.
In run_broker.sh, add -Dbroker.auth.provider=org.aktin.broker.auth.apikey.ApiKeyPropertiesAuthProvider,org.aktin.broker.auth.cred.CredentialTokenAuthProvider,org.aktin.broker.auth.openid.OpenIdAuthProvider or if wanted, add it to the defaultconfig
adapt openid-config.properties (broker-admin) to contain the correct urls to your keycloak and copy
it to the place where you extracted the broker admin dist zip to (place it where api-keys.properties is)