LocalDirectoryDatabase#

class pharmpy.workflows.LocalDirectoryDatabase(path='.', file_extension='.mod')[source]#

Bases: NonTransactionalModelDatabase

ModelDatabase implementation for single local directory

All files will be stored in the same directory. It is assumed that all files connected to a model are named modelname + extension. This means that care must be taken to keep filenames unique. Clashing filenames will be overwritten. It is recommended to use the LocalModelDirectoryDatabase instead.

Parameters:

  • path (str or Path) – Path to the database directory. Will be created if it does not exist.

  • file_extension (str) – File extension to use for model files.

Methods Summary

list_all_files(name)

Lists all file names related to a model run

retrieve_all_files(name, destination_path[, ...])

Retrieve all files related to a model run

retrieve_file(name, filename, destination_path)

Retrieve one file related to a model run

retrieve_model(name)

Read a model from the database

retrieve_model_entry(name)

Read model entry from the database

retrieve_modelfit_results(name)

Read modelfit results from the database

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

Methods Documentation

list_all_files(name)[source]#

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

retrieve_all_files(name, destination_path, force=False)[source]#

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)

retrieve_file(name, filename, destination_path, force=False)[source]#

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)

retrieve_model(name)[source]#

Read a model from the database

Parameters:

model_name (str) – Name of the model

Returns:

Model – Retrieved model object

retrieve_model_entry(name)[source]#

Read model entry from the database

Parameters:

model_name (str) – Name of the model

Returns:

ModelEntry – Retrieved model entry object

retrieve_modelfit_results(name)[source]#

Read modelfit results from the database

Parameters:

model_name (str) – Name of the model

Returns:

Results – Retrieved model results object

store_local_file(model, path, new_filename=None)[source]#

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.

store_metadata(model, metadata)[source]#

Store metadata

Parameters:

  • model (Model) – Pharmpy model object

  • metadata (Dict) – A dictionary with metadata

store_model(model)[source]#

Store a model object

Parameters:

model (Model) – Pharmpy model object

store_model_entry(model_entry)[source]#

Store model entry of the model entry bound to this transaction

Parameters:

model_entry (ModelEntry) – Pharmpy ModelEntry object

store_modelfit_results(model)[source]#

Store modelfit results

Parameters:

model (Model) – Pharmpy model object