Environment Variables

The command-line client and the client bindings use a set of environment variables in order to communicate with the API server and to store state on the current default project and directory. These settings are usually set when you run dx login and can be later changed through other dx commands. To display the currently used settings in human-readable format, you can use the dx env command:

$ dx env
Auth token used         adLTkSNkjxoAerREqbB1dVkspQzCOuug
API server protocol     https
API server host         api.dnanexus.com
API server port         443
Current workspace       project-9zVpbQf4Zg2641v5BGY00001
Current workspace name  "Scratch Project"
Current folder          /
Current user            alice

To print the bash commands for setting the environment variables to match what dx is using, you can run the same command with the --bash flag.

$ dx env --bash
export DX_SECURITY_CONTEXT='{"auth_token_type": "bearer", "auth_token": "adLTkSNkjxoAerREqbB1dVkspQzCOuug"}'
export DX_APISERVER_PROTOCOL=https
export DX_APISERVER_HOST=api.dnanexus.com
export DX_APISERVER_PORT=443
export DX_PROJECT_CONTEXT_ID=project-9zVpbQf4Zg2641v5BGY00001

Running a dx command from the command-line will not (and cannot) overwrite your shell's environment variables, so it stores them in a file at ~/.dnanexus_config/environment.

Prioritization of configuration files

The following is a list in order of which DNAnexus utilities load values from configuration sources:

  1. Command line options (if available)
  2. Environment variables already set in the shell
  3. ~/.dnanexus_config/environment.json (dx configuration file)
  4. Hardcoded defaults

Overriding the dx Configuration File

Note that the dx command will always prioritize the environment variables that are currently set in the shell. This means that if you have set your environment variable for DX_SECURITY_CONTEXT and subsequently use dx login to log in as a different user, it will still use the original environment variable. If not run in a script, it will print a warning to stderr whenever the environment variables and its stored state have a mismatch. To get out of this situation, the best approach is often to run source ~/.dnanexus_config/unsetenv. Setting environment variables is generally an approach within a shell script or part of a job environment in the cloud.

In the interaction below, environment variables have already been set, but the user then uses dx to log in which is still overridden by the shell's environment variables.

$ dx ls -l Project: Sample Project (project-9zVpbQf4Zg2641v5BGY00001) Folder : / <Contents of Sample Project> $ dx login Acquiring credentials from https://auth.dnanexus.com Username: alice Password: Note: Use "dx select --level VIEW" or "dx select --public" to select from projects for which you only have VIEW permissions. Available projects: 0) SAM importer test (CONTRIBUTE) 1) Scratch Project (ADMINISTER) 2) Mouse (ADMINISTER) Pick a numbered choice [1]: 2 Setting current project to: Mouse $ dx ls WARNING: The following environment variables were found to be different than the values last stored by dx: DX_SECURITY_CONTEXT, DX_PROJECT_CONTEXT_ID To use the values stored by dx, unset the environment variables in your shell by running "source ~/.dnanexus_config/unsetenv". To clear the dx-stored values, run "dx clearenv". Project: Sample Project (project-9zVpbQf4Zg2641v5BGY00001) Folder : / <Contents of Sample Project> $ source ~/.dnanexus_config/unsetenv $ dx ls -l Project: Mouse (project-9zVpbQf4Zg2641v5BGY00001) Folder : / <Contents of Mouse>

Clearing dx-set variables

If you instead want to discard the values which dx has stored, the command dx clearenv removes the dx-generated configuration file ~/.dnanexus_config/environment.json for you.

Command line options

Most dx commands have the following additional flags to temporarily override the values of the respective variables.

$ dx --env-help
usage: dx command ... [--apiserver-host APISERVER_HOST]
                      [--apiserver-port APISERVER_PORT]
                      [--apiserver-protocol APISERVER_PROTOCOL]
                      [--project-context-id PROJECT_CONTEXT_ID]
                      [--workspace-id WORKSPACE_ID]
                      [--security-context SECURITY_CONTEXT]
                      [--auth-token AUTH_TOKEN]

optional arguments:
  --apiserver-host APISERVER_HOST
                        API server host
  --apiserver-port APISERVER_PORT
                        API server port
  --apiserver-protocol APISERVER_PROTOCOL
                        API server protocol (http or https)
  --project-context-id PROJECT_CONTEXT_ID
                        Default project or project context ID
  --workspace-id WORKSPACE_ID
                        Workspace ID (for jobs only)
  --security-context SECURITY_CONTEXT
                        JSON string of security context
  --auth-token AUTH_TOKEN
                        Authentication token

For example, you can temporarily override the current default project used:

$ dx env --project-context-id project-B0VK6F6gpqG6z7JGkbqQ000Q
Auth token used         R54BN6Ws6Zl3Y0VqBA9o1qweUswYW5o4
API server protocol     https
API server host         api.dnanexus.com
API server port         443
Current workspace       project-B0VK6F6gpqG6z7JGkbqQ000Q
Current folder          /

Last edited by Katherine Lai (klai), 2013-02-27 02:24:23

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