ModelDatabase

class pharmpy.workflows.ModelDatabase

Bases: ABC

Baseclass for databases for models and results of model runs

Primary key is the model name, which means that models with the same name will be counted as the same model.

Currently the model database is centered around storing and retrieving files belonging to the model or results from fitting the model. This doesn’t mean that implementations have to use a file system to store the files.

Methods Summary

list_all_files(model)	Lists all file names related to a model run
retrieve_all_files(model, destination_path)	Retrieve all files related to a model run
retrieve_file(model, filename, destination_path)	Retrieve one file related to a model run
retrieve_model(model)	Read a model from the database
retrieve_model_entry(model)	Read model entry from the database
retrieve_modelfit_results(model)	Read modelfit results from the database
snapshot(model)	Creates a readable snapshot context for a given model.
store_local_file(model, path[, new_filename])	Store a file from the local machine
store_metadata(model, metadata)	Store metadata
store_model(model)	Store a model object
store_model_entry(model_entry)	Store model entry of the model entry bound to this transaction
store_modelfit_results(model)	Store modelfit results
transaction(obj)	Creates a writable transaction context for a given model.

Methods Documentation

abstractmethod list_all_files(model)

Lists all file names related to a model run

Note that this will not return a list of full paths, only the name of the files

Parameters:

model (Model, ModelHash) – Model object or ModelHash

Returns:

list[str] – List of file names

abstractmethod retrieve_all_files(model, destination_path, force=False)

Retrieve all files related to a model run

Parameters:

• model (Model, ModelHash) – Model object or ModelHash

• destination_path (Path) – Destination path

• force (bool) – Force overwrite of files (default False)

abstractmethod retrieve_file(model, filename, destination_path, force=False)

Retrieve one file related to a model run

Parameters:

• model (Model, ModelHash) – Model object or ModelHash

• filename (str) – Name of file

• destination_path (Path) – Destination path

• force (bool) – Force overwrite of file (default False)

abstractmethod retrieve_model(model)

Read a model from the database

Parameters:

model_name (str) – Name of the model

Returns:

Model – Retrieved model object

abstractmethod retrieve_model_entry(model)

Read model entry from the database

Parameters:

model_name (str) – Name of the model

Returns:

ModelEntry – Retrieved model entry object

abstractmethod retrieve_modelfit_results(model)

Read modelfit results from the database

Parameters:

model_name (str) – Name of the model

Returns:

Results – Retrieved model results object

abstractmethod snapshot(model)

Creates a readable snapshot context for a given model.

Parameters:

model_name (str) – Name of the Pharmpy model object

abstractmethod store_local_file(model, path, new_filename=None)

Store a file from the local machine

Parameters:

• model (Model) – Pharmpy model object

• path (Path) – Path to file

• new_filename (str|None) – Filename to give to the file. Optional, defaults to original filename given by path.

abstractmethod store_metadata(model, metadata)

Store metadata

Parameters:

• model (Model) – Pharmpy model object

• metadata (Dict) – A dictionary with metadata

abstractmethod store_model(model)

Store a model object

Parameters:

model (Model) – Pharmpy model object

abstractmethod store_model_entry(model_entry)

Store model entry of the model entry bound to this transaction

Parameters:

model_entry (ModelEntry) – Pharmpy ModelEntry object

abstractmethod store_modelfit_results(model)

Store modelfit results

Parameters:

model (Model) – Pharmpy model object

abstractmethod transaction(obj)

Creates a writable transaction context for a given model.

Parameters:

obj (Model | ModelEntry | ModelHash) – Pharmpy model, ModelEntry or ModelHash object