OMERO Pixel Data Microservice

OMERO pixel data Vert.x asynchronous microservice server endpoint for OMERO.web.

Requirements

• OMERO 5.6.x+
• OMERO.web 5.6.x+
• Redis backed sessions
• Java 11+

Workflow

The microservice server endpoint for OMERO.web relies on the following workflow::

1. Setup of OMERO.web to use Redis backed sessions

2. Configuring the microservice endpoint

3. Ensure the microservice can communicate with your PostgreSQL instance

4. Ensure the microservice has read-write access to your OMERO server binary repository

5. Running the microservice endpoint for OMERO.web

6. Redirecting your OMERO.web installation to use the microservice endpoint

Build Artifacts

The latest artifacts, built by AppVeyor, can be found here::

• https://ci.appveyor.com/project/gs-jenkins/omero-ms-pixel-buffer/build/artifacts

Configuring and Running the Server

The pixel data microservice server endpoint piggybacks on the OMERO.web Django session and OMERO database. As such it is essential that as a prerequisite to running the server that your OMERO.web instance be configured to use Redis backed sessions and the microservice be able to communicate with your PostgreSQL instance. Filesystem backed sessions are not supported.

1. Configure the application by editing conf/config.yaml

2. Start the server::

    omero-ms-pixel-buffer
   

Configuring Logging

Logging is provided using the logback library. You can configure logging by copying the included logback.xml.example, editing as required, and then specifying the configuration when starting the microservice server::

cp logback.xml.example logback.xml
...
JAVA_OPTS="-Dlogback.configurationFile=/path/to/logback.xml" \
    omero-ms-pixel-buffer ...

Debugging the logback configuration can be done by providing the additional -Dlogback.debug=true property.

Using systemd

If you are using systemd you can place an appropriately modified version of the included omero-ms-pixel-buffer.service into your /etc/systemd/system directory and then execute::

systemctl daemon-reload
systemctl start omero-ms-pixel-buffer.service

Running systemctl status omero-ms-pixel-buffer.service will then produce output similar to the following::

# systemctl status omero-ms-pixel-buffer.service
● omero-ms-pixel-buffer.service - OMERO image region microservice server
   Loaded: loaded (/etc/systemd/system/omero-ms-pixel-buffer.service; disabled; vendor preset: disabled)
   Active: active (running) since Thu 2017-06-01 14:40:53 UTC; 8min ago
 Main PID: 9096 (java)
   CGroup: /system.slice/omero-ms-pixel-buffer.service
           └─9096 java -Dlogback.configurationFile=/opt/omero/omero-ms-pixel-buffer-0.2.0-SNAPSHOT/logback.xml -classpath /opt/omero/omero-ms-pixel-buffer-0.2.0-SNAPSHOT/lib/omero-ms-pixel-buffer-0.2.0-SNAPSHOT.jar:/opt/omero/omero-...

Jun 01 14:40:53 demo.glencoesoftware.com systemd[1]: Started OMERO image region microservice server.
Jun 01 14:40:53 demo.glencoesoftware.com systemd[1]: Starting OMERO image region microservice server...
Jun 01 14:40:54 demo.glencoesoftware.com omero-ms-pixel-buffer[9096]: Jun 01, 2017 2:40:54 PM io.vertx.core.spi.resolver.ResolverProvider
Jun 01 14:40:54 demo.glencoesoftware.com omero-ms-pixel-buffer[9096]: INFO: Using the default address resolver as the dns resolver could not be loaded
Jun 01 14:40:55 demo.glencoesoftware.com omero-ms-pixel-buffer[9096]: Jun 01, 2017 2:40:55 PM io.vertx.core.Launcher
Jun 01 14:40:55 demo.glencoesoftware.com omero-ms-pixel-buffer[9096]: INFO: Succeeded in deploying verticle

Redirecting OMERO.web to the Server

What follows is a snippet which can be placed in your nginx configuration, before your default OMERO.web location handler, to redirect both webgateway image region rendering currently used by OMERO.web to the image region microservice server endpoint::

upstream pixel_buffer_backend {
    server 127.0.0.1:8082 fail_timeout=0 max_fails=0;
}

...

location /tile/ {
    proxy_pass http://pixel_buffer_backend;
}

Development Installation

1. Clone the repository::

    git clone https://github.com/glencoesoftware/omero-ms-pixel-buffer.git
   

2. Run the Gradle build and utilize the artifacts as required::

    ./gradlew installDist
    cd build/install
    ...
   

3. Log in to the OMERO.web instance you would like to develop against with your web browser and with the developer tools find the sessionid cookie value. This is the OMERO.web session key.

4. Run single or multiple tile tests using curl::

    curl -H 'Cookie: sessionid=<omero_web_session_key>' \
        http://localhost:8082/tile/<image_id>/<z>/<c>/<t>?x=<x>&y=<y>&w=<w>&h=<h>&format=<format>&filename=<filename>
   

Valid formats, if missing the format will be raw pixels, include:

• png
• tif

If filename is missing, a suitable default based on the query string will be used.

Eclipse Configuration

1. Run the Gradle Eclipse task::

    ./gradlew eclipse
   

2. Configure your environment::

     mkdir conf
    cp src/dist/conf/config.yaml conf/
    # Edit as appropriate
   

3. Add a new Run Configuration with a main class of io.vertx.core.Launcher::

    run "com.glencoesoftware.omero.ms.pixelbuffer.PixelBufferMicroserviceVerticle"
   

Running Tests

Using Gradle run the unit tests:

./gradlew test

Reference

• https://github.com/glencoesoftware/omero-ms-core
• https://lettuce.io/
• http://vertx.io/