icgc-argo / Daco2Ego

Utility and service to load DACO list into Ego.

Daco2Ego

Utility and service to load DACO list into Ego.

Installation instructions:

1. Go to the machine you want to run Daco2Ego on, create a daco2ego user, grant it permissions to read it's input files from the directory where they're stored, (eg. from /nfs/icgc-dcc), and copy over a configuration file with the right values set. (See the example file for the fields to fill in.)

2. scp over the crontab file, and add it to the daco2ego user's crontab.

scp crontab daco2ego@<host>:crontab
ssh daco2ego@<host>
crontab crontab 

That's it!

Development

Requires Python 3.6 due to the use of format strings.

To test with a local ego and dac-api (http), enable insecure transport. In daco2ego.py, below the other imports, add:

import os
os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = '1'

Make sure to remove in production!

Tests

Test ego client

File: test_ego_client.py

Can be run against a local ego instance, if OAUTHLIB_INSECURE_TRANSPORT is enabled (see Development note). Requires a test config file, to be created in /python/tests/test_ego.conf. Add in the applicable values:

{
  "client": {
    "base_url": "<your_local_ego>",
    "client_id": "<daco2ego_client_id>",
    "client_secret": "<daco2ego_client_secret>",
    "daco_group": "<daco_group_name>",
    "cloud_group":"<daco_cloud_group_name>"
  }
}

Test daco client

File: test_daco_client.py

No test config required

Test daco2ego

File: test_daco2ego.py

Requires a test config file, to be created in /python/tests/test.conf, required:

  {
    "client":
      {
        "base_url": "https://ego/v1/",
        "dac_api_url": "https://dac-api/v1"
      }
  }