Environment Interface Proposal

Environment Interface Proposal

Concept

Each logged in user of the Model SEED has a persistent environment that includes the following settings:

1. A workspace directory
2. A default biochemistry
3. A default model
4. A default mapping
5. A default SEED
6. A default ModelSEED
7. A default FBA

Command summary

1. mseed login: logs into the environment with a specified username and password (e.g. mseed login chenry mypassword)
2. mseed logout: logs out of the environment
3. mseed env: prints current environment settings
4. mseed setenv: sets environment parameter (e.g. mseed setenv models/chenry/Seed83333.1)
5. mseed saveenv: saves the environment settings to a specified name (e.g. mseed printenv MySettings)
6. mseed loadenv: loads environment settings from a specified name (e.g. mseed loadevn MySettings)

Environment related global options

1. A saved environment may be bootstrapped onto any Model SEED command using the -env option followed by the name of the environment (e.g. mseed bio list media -env environments/chenry/Default).
2. An environment may also be specified entirely in the command line (e.g. mseed bio list media -env "models/chenry/Seed83333.1;bio/chenry/main;mapping/chenry/main;seed/pubseed;mseed/local").