Use the TES Wizard to submit an analysis

Simple SQL Query

The Simple SQL Query TES Wizard mode creates a TES task that executes a Postgres SQL Runner  container image. To submit a SQL query TES Task you need to set:

• Name

• Description (optional)

• TREs to submit to

• A SQL Query

  An example for a SQL query to get the number of records and the total value of the measurement values for the concept “Airway resistance —during inspiration” in the TRE OMOP CDM DB is:

  WITH user_query AS (
  SELECT value_as_number FROM public.measurement WHERE
    measurement_concept_id = 21490742
    AND value_as_number IS NOT NULL
    )
  SELECT COUNT(*) AS n, SUM(value_as_number) AS total FROM user_query;

Example of the Simple SQL Query TES Wizard mode:

Custom Image

Apart from the mandatory inputs for TES Name and TREs selection, the custom image wizard provides several more options for running tasks.

1. Data input (optional)

If the TREs support it, you can provide a path to download extra data for input.

• Path: a textbox to provide the path from which to collect data
• Type: a selection box where you can choose whether your input is a FILE or DIRECTORY.

2. Data output

You can specify where your output is stored. The TRE agent will amend this to comply with egress policy.

• Path: a textbox to provide the path to which output data should be sent
• Type: a selection box where you can choose whether your output is a FILE or DIRECTORY.
• URL: A text box to specify a URL for storing your data.

3. Executors

This section contains details of your executor(s).

• Docker image: Executors are containers. This textbox allows you to specify which.
• Workdir: The working directory used by this container.
• Commands: A textbox for the commands to pass to the container

4. Environment variables

Some containers will need some environment variables to be passed to them to work. You do not need to specify all of these; for example for many TREs, you will not have database credentials and these will be populated for you.

--body-json {"code":"GENERIC","analysis":"DISTRIBUTION","uuid":"123","collection":"test","owner":"me"} --no-encode

--body-json
{"code":"GENERIC","analysis":"DISTRIBUTION","uuid":"123","collection":"test","owner":"me"}
--no-encode

Raw JSON

The Raw JSON wizard has the simplest interface: a single text box for writing a TES message as a JSON object. This also includes JSON syntax highlighting and formatting.

"tags": {
    "project": "Testing",
    "tres": "DEMO 01" // or "DEMO TRE 01|DEMO TRE 02"
}

Example of the Raw JSON TES Wizard mode: