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Paul Sud edited this page May 7, 2021 · 15 revisions

Environment Variables

Note: DCC refers to the ENCODE Data Coordination Center.

DCC API Keys

Only required if you need to interact with the ENCODE Portal in ways other than data retrieval or searching. You must have API keys as an ENCODE submitter; if you haven't any yet, please check with your DCC data wrangler.

This software needs your ENCODE DCC api key and secret key in order to POST and PATCH objects to the ENCODE Portal. They must be supplied via the environment variables DCC_API_KEY and DCC_SECRET_KEY. You can declare these in your startup file (i.e. .bashrc, .bash_profile), or whichever method that your prefer.

Other DCC related keys

DCC_MODE - The default value to pass to the connection.Connection class via the dcc_mode argument, which is used to indicate which instance of the Portal to connect to. This should be set to "prod" to use the production Portal, or "dev" to use the development Portal.

The following environment variables only matter when doing a POST operation (regarding encode_utils.connection.Connection.post):

  1. DCC_AWARD - The default value to use for the 'award' property in ENCODE profiles that include this. Only considered when not explicitly set in the payload.
  2. DCC_LAB - The default value to use for the 'lab' property in ENCODE profiles that include this. Only considered when not explicitly set in the payload.

AWS Keys

Only required if you are submitting data from AWS S3. You'll need to set

  1. AWS_ACCESS_KEY_ID
  2. AWS_SECRET_ACCESS_KEY These are needed so that encode-utils can calculate the md5sum and file size of S3 files you are submitting. Be sure to first register your S3 bucket with the DCC prior to submission, a process that is described here. When you upload a file to the DCC, you are using a temporary AWS user account, formally called a federated user, which is provided by the DCC and only works for uploading your file to a single, dedicated path in the DCC S3 bucket. Registering your bucket with the DCC is required so that the federated user can pull the specified file from your bucket at submission time.
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