wtsi-hgi / asclepius Goto Github PK

iRODS is a dependency which both the planner and executor initialise in the same way:

• asclepius/planner/planner.py

  Lines 22 to 30 in 815d467

  	ssl_settings = {'ssl_context':
  	ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH)}
  	coll_buffer = []
  	objects = []
  	collections = []
  	with iRODSSession(irods_env_file=ENV_FILE, **ssl_settings) as session:

• asclepius/executor/executor.py

  Lines 25 to 29 in 815d467

  	from irods.session import iRODSSession
  	env_file = os.path.expanduser('/nfs/users/nfs_m/mercury/.irods/irods_environment.json')
  	ssl_context = ssl.create_default_context(purpose=ssl.Purpose.SERVER_AUTH, cafile=None, capath=None, cadata=None)
  	ssl_settings = {'ssl_context': ssl_context}
  	with iRODSSession(irods_env_file=env_file, **ssl_settings) as session:

Consider making a suite of common classes, one of which would be an iRODS wrapper -- others include things like time handing, logging and the AVU model, etc. -- that can be injected into the planner and executor classes, respectively. Then, if the implementation of the iRODS wrapper needs to change (for whatever reason), its interface can remain and no downstream changes will need to be made to its dependants.

For example, in the above examples, the way each module is defining the iRODS environment configuration path is different: one loads from a central configuration and another has it hard-coded. A unified interface would resolve this bifurcation in a single place without having to change code everywhere. This unified interface could then, say, be extended to source the iRODS environment configuration following the following precedence (highest priority first):

1. From the IRODS_ENVIRONMENT_FILE environment variable;
2. From a specified file, say in some configuration file;
3. Finally falling back to the default of ~/.irods/irods_environment.json (or failing, if this doesn't exist).