transmart-packer

Run data transformation jobs for TranSMART.

Install

First make virtual environment to install dependencies using Python3.6+

pip install transmart-packer

Or from source:

git clone https://github.com/thehyve/transmart-packer.git
cd transmart-packer
pip install .

Dependencies

a Redis server running on localhost (or update packer/config.py)

Running

From root dir run:

redis-server

celery -A packer.tasks worker --loglevel=info

transmart-packer

Environment variables:

Variable	Description
`TRANSMART_URL`	The URL of the TranSMART API server
`KEYCLOAK_SERVER_URL`	Keycloak server URL, e.g., `https://keycloak-dwh-test.thehyve.net`
`KEYCLOAK_REALM`	The Keycloak realm, e.g., `transmart-dev`
`KEYCLOAK_CLIENT_ID`	The Keycloak client ID (default: `transmart-client`)
`REDIS_URL`	Redis server URL (default: `redis://localhost:6379`)
`DATA_DIR`	Directory to write export data (default: `/tmp/packer/`)
`LOG_CFG`	Logging configuration (default: `packer/logging.yaml`)
`CLIENT_ORIGIN_URL`	URLs to restrict cross-origin requests to (CORS) (default: `*`)

An optional variable VERIFY_CERT can be used to specify the path of a certificate collection file (.pem) used to verify HTTP requests.

Alternatively, you could build and run the stack from code using docker-compose.

# Downloads redis image and creates image with project dependencies.
docker-compose build

# After build is complete, start via:
docker-compose up

On code change the webserver will automatically restart, but the Celery workers will not. After updating the Celery task logic, you will need to restart the Docker container.

Usage

Available handlers:

Path	Description
`GET /jobs`	List all known jobs for this user.
`POST /jobs/create`	Create a new job by providing job_type and job_parameters, creates the job and returns a task_id.
`GET /jobs/status/<task_id>`	Get status details for a specific task.
`GET /jobs/cancel/<task_id>`	Cancel scheduled or abort a running task.
`GET /jobs/data/<task_id>`	Download the data that this task produced.
`WS /jobs/subscribe`	Open websocket connection to get live updates on job progress.

To start the toy job "add" on the localhost machine make call to http://localhost:8999/jobs/create?job_type=add&job_parameters={%22x%22:500,%22y%22:1501}.

Development

Components

Overview of the components of transmart-packer and the interaction with external components.

Testing

To run the test suite, we have to start redis-server and celery workers with the commands above. Then you can run:

python setup.py test

Extending

New jobs can be added by adding a new Celery function to the jobs folder and adding the function to the jobs registry. See the packer/jobs/example.py to learn how.

Existing jobs

Basic export job

Export transmart api client observation dataframe to tsv file

{
    "job_type":"basic_export",
    "job_parameters": {
        "constraint": {
            "type":"study_name",
            "studyId":"CSR"

        },
        "custom_name":"name of the export"
    }
}

CSR export

The Central Subject Registry (CSR) data model specific export. The model contains individual, diagnosis, biosource and biomaterial entities, following the hierarchy: patient > diagnosis > biosource > biomaterial. The entities IDs are first 4 columns of the export file. The rest of the columns are concepts. Higher level concepts (e.g Age that is specific to Patient level) get distributed to all rows specific to lower levels (e.g. Diagnosis)

See the CSR test study as an example.

{
    "job_type":"csr_export",
    "job_parameters": {
        "constraint": {
            "type":"study_name",
            "studyId":"CSR"

        },
        "custom_name":"name of the export",
        "row_filter": {
            "type":"patient_set",
            "subjectIds": ["P2", "P6"]
        }
    }
}

where:

job_parameters.constraint - any transmart v2 api constraint or composition of them that used to get data from transmart.
job_parameters.custom_name (optional) - name of the export job and the output tsv file.
job_parameters.row_filter (optional) - any transmart v2 api constraint or composition of them to fetch keys ([[[[patient], diagnosis], biosource], biomaterial]) that will make it to the end result. e.g. Given the CSR study and query above only rows specific to P2 and P6 patients will end up to the result table such as P2, D2, BS2, BM2, ... row. Please note that keys do not have to be equals in length. A row gets selected if only part of keys matches. e.g. P1 vs P1, D1

Adding new entity to CSR data model:

When the CSR data model is extended with new entities, the export transformation code has to be changed as well in order to include a column with the ID of the new entity as one of the identifying columns.

In order to do this, table_transformations/csr_transformations.py file has to be modified. Required changes:

extend the ID_COLUMNS list,
modify from_obs_df_to_csr_df(obs: DataFrame) function in order to properly rename columns.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.

cpavanrun/transmart-packer