Context

class pharmpy.workflows.Context(name, ref=None, common_options=None)

Bases: ABC

Context for runs

A database of results, metadata and run files for one tool run

Parameters:

• name (str) – Name of the context

• ref (str) – A reference (path) to the context

Attributes Summary

context_path
model_database	ModelDatabase to store results of models run in context

Methods Summary

abort_workflow(message)
call_workflow(workflow, unique_name)
create_subcontext(name)	Create a new subcontext of this context
exists(name[, ref])
get_model_context_path(model)
get_parent_context()	Get the parent context of this context
get_subcontext(name)	Get one of the subcontexts of this context
list_all_names()	Retrieve a list of all model names in the context
list_all_subcontexts()	Retrieve a list of the names of all subcontexts in the context
log_error(message[, model])	Add an error message to the log
log_info(message[, model])	Add an info message to the log
log_message(severity, message[, model])	Add a message to the log
log_warning(message[, model])	Add a warning message to the log
retrieve_annotation(name)	Retrieve an annotation for a model
retrieve_common_options()
retrieve_final_model_entry()
retrieve_input_model_entry()
retrieve_key(name)	Retrive the key corresponding to a model name
retrieve_log([level])	Retrieve the entire log all - the entire log current - only the current Context level lower - current and sub levels
retrieve_metadata()	Read tool metadata
retrieve_model_entry(name)
retrieve_results()	Retrieve tool results
store_annotation(name, annotation)	Store an annotation string (description) for a model
store_final_model_entry(me)
store_input_model_entry(me)
store_key(name, key)	Associate a key with a model name
store_message(severity, ctxpath, date, message)
store_metadata(metadata)	Store tool metadata
store_model_entry(me)
store_results(res)	Store tool results

Attributes Documentation

context_path

model_database

ModelDatabase to store results of models run in context

Methods Documentation

abort_workflow(message)

call_workflow(workflow, unique_name)

abstract create_subcontext(name)

Create a new subcontext of this context

abstract static exists(name, ref=None)

get_model_context_path(model)

abstract get_parent_context()

Get the parent context of this context

abstract get_subcontext(name)

Get one of the subcontexts of this context

abstract list_all_names()

Retrieve a list of all model names in the context

abstract list_all_subcontexts()

Retrieve a list of the names of all subcontexts in the context

log_error(message, model=None)

Add an error message to the log

log_info(message, model=None)

Add an info message to the log

Currently with echo to stdout. In the future this could be changed or be configurable.

log_message(severity, message, model=None)

Add a message to the log

log_warning(message, model=None)

Add a warning message to the log

abstract retrieve_annotation(name)

Retrieve an annotation for a model

abstract retrieve_common_options()

retrieve_final_model_entry()

retrieve_input_model_entry()

abstract retrieve_key(name)

Retrive the key corresponding to a model name

This key can be used to lookup the model in the model database

abstract retrieve_log(level='all')

Retrieve the entire log all - the entire log current - only the current Context level lower - current and sub levels

abstract retrieve_metadata()

Read tool metadata

retrieve_model_entry(name)

abstract retrieve_results()

Retrieve tool results

Returns:

Results – Tool results object

abstract store_annotation(name, annotation)

Store an annotation string (description) for a model

store_final_model_entry(me)

store_input_model_entry(me)

abstract store_key(name, key)

Associate a key with a model name

abstract store_message(severity, ctxpath, date, message)

abstract store_metadata(metadata)

Store tool metadata

Parameters:

metadata (dict) – Tool metadata dictionary

store_model_entry(me)

abstract store_results(res)

Store tool results

Parameters:

res (Results) – Tool results object