pydetecdiv.persistence.repository

Definition of the Repository interface accessible from the Business-logic layer and that must be implemented by concrete repositories.

class pydetecdiv.persistence.repository.ShallowDb

Bases: ABC

Abstract class used as an interface to encapsulate project persistence access

abstractmethod create() → None

Abstract method enforcing the implementation in all shallow persistence connectors of a create() method for creating the database if it does not exist

abstractmethod commit() → None

Abstract method enforcing the implementation of a method to save creations and updates of objects in repository on disk

abstractmethod rollback() → None

Abstract method enforcing the implementation of a method cancelling operations that have not been committed

abstractmethod close() → None

Abstract method enforcing the implementation of a close() method in all shallow persistence connectors

abstractmethod import_images(image_files: list[str], data_dir_path: str, destination: str, author: str = '', date: datetime = 'now', in_place: bool = False, img_format: str = 'imagetiff') → Popen

Import images specified in a list of files into a destination

Parameters:

• image_files – list of image files to import

• data_dir_path – path for the current project raw data directory

• destination – destination directory to import files into

• author – the user importing the data

• date – the date of import

• in_place – boolean indicating whether image files should be copied (False) or kept in place (True)

• img_format – the file format

Returns:

the list of imported files. This list can be used to roll the copy back if needed

abstractmethod save_object(class_name: str, record: dict[str, Any]) → int

Abstract method enforcing the implementation of a save_object() method in all shallow persistence connectors

Parameters:

• class_name – the class name of the object to save

• record – the record representing the object

abstractmethod delete_object(class_name: str, id_: int) → None

Abstract method enforcing the implementation of a delete_object() method in all shallow persistence connectors

Parameters:

• class_name – the class name of the object to delete

• id_ – the id of the object to delete

abstractmethod count_records(class_name: str) → int

Get the number of objects of a given class in the current project

Parameters:

class_name – the class name of the objects whose count will be returned

Returns:

the number of objects

abstractmethod get_dataframe(class_name: str, id_list: list[int] = None) → DataFrame

Abstract method enforcing the implementation of a method returning a pandas DataFrame containing the list of objects of a given class in the current project whose id is in id_list

Parameters:

• class_name – the class name of the objects whose list will be returned

• id_list – the list of ids of objects to retrieve

Returns:

a DataFrame containing the list of objects

abstractmethod get_record(class_name: str, id_: int = None, uuid: str = None) → dict[str, Any] | None

Abstract method enforcing the implementation of a method returning an object record of a given class whose id is id_

Parameters:

• class_name – the class of the requested object

• id_ – the id of the requested object

Returns:

a record (i.e. dictionary) containing the data for the requested object

abstractmethod get_records(class_name: str, id_list: list[int] = None) → list[dict[str, Any]]

Abstract method enforcing the implementation of a method returning the list of all object records of a given class specified by its name or a list of objects whose id is in id_list

Parameters:

• class_name – the class name of the requested objects

• id_list – the list of ids for objects

Returns:

a list of records (i.e. dictionaries) containing the data for the requested objects

abstractmethod get_linked_records(cls_name: str, parent_cls_name: str, parent_id: int) → list[dict[str, Any]]

Abstract method enforcing the implementation of a method returning the list of records for all objects of class

defined by class_name that are linked to object of class parent_class_name with id_ = parent_id

Parameters:

• cls_name – the class name of the objects to retrieve records for

• parent_cls_name – the class nae of the parent object

• parent_id – the id of the parent object

Returns:

a list of records

abstractmethod link(class1_name: str, id_1: int, class2_name: str, id_2: int) → None

Create a link between two domain-specific objects. There must be a direct link defined in Linker class, otherwise, the link cannot be created.

Parameters:

• class1_name – the class name of the first object to link

• id_1 – the id of the first object to link

• class2_name – the class name of the second object to link

• id_2 – the id of the second object to link

abstractmethod unlink(class1_name: str, id_1: int, class2_name: str, id_2: int) → None

Remove the link between two domain-specific objects. There must be a direct link defined in Linker class, otherwise, the link cannot be removed.

Parameters:

• class1_name – the class name of the first object to unlink

• id_1 – the id of the first object to unlink

• class2_name – the class name of the second object to unlink

• id_2 – the id of the second object to unlink

pydetecdiv.persistence.sqlalchemy

Concrete Repositories using a SQL database with the sqlalchemy toolkit

class pydetecdiv.persistence.sqlalchemy.repositories.ShallowSQLite3(dbname: str = None)

Bases: ShallowDb

A concrete shallow SQLite3 persistence inheriting ShallowDb and implementing SQLite3-specific engine

property session: Session

Property returning the sqlalchemy Session object attached to the repository

Returns:

commit() → None

Commit the current transaction

rollback() → None

Rollback the current transaction

executescript(script)

Reads a string containing several SQL statements in a free format

Parameters:

script (str) – the string representing the SQL script to be executed

create() → None

Gets SqlAlchemy classes defining the project database schema and creates the database if it does not exist.

close() → None

Close the current connexion

import_images(image_files: list[str], data_dir_path: str, destination: str, author: str = '', date: datetime = 'now', in_place: bool = False, img_format: str = 'imagetiff') → Popen

Import images specified in a list of files into a destination

Parameters:

• image_files (list of str) – list of image files to import

• data_dir_path (path or str) – path for the current project raw data directory

• destination (str) – destination directory to import files into

• author (str) – the user importing the data

• date (str) – the date of import

• in_place (bool) – boolean indicating whether image files should be copied (False) or kept in place (True)

• img_format (str) – the file format

Returns:

the list of imported files. This list can be used to roll the copy back if needed

Return type:

list of str

annotate_data(dataset: <module 'pydetecdiv.domain.Dataset' from '/home/fred/PycharmProjects/pyDetecDiv/src/pydetecdiv/domain/Dataset.py'>, source: str, keys_: tuple[str, ...], regex: str) → DataFrame

Method to annotate data files in a dataset according to a regular expression applied to a source. The resulting key-value pairs are placed in a key_val column.

Parameters:

• dataset (Dataset object) – the dataset whose data should be annotated

• source (str or callable returning a str) – the database field or combination of fields to apply the regular expression to

• keys (tuple of str) – the list of classes created objects belong to

• regex (regular expression str) – regular expression defining the annotations

Returns:

list of annotated Data records in a dataframe

Return type:

pandas.DataFrame

save_object(class_name: str, record: dict[str, object]) → int

Save the object represented by the record

Parameters:

• class_name (str) – the class name of the object to save into SQL database

• record (dict) – the record representing the object

Returns:

the id of the created or updated object

Return type:

int

delete_object(class_name: str, id_: int) → None

Delete an object of class name = class_name with id = id_

Parameters:

• class_name – the class name of the object to delete

• id_ – the id of the object to delete

count_records(class_name: str) → int

Get the number of objects of a given class in the current project

Parameters:

class_name (str) – the class name of the objects whose count will be returned

Returns:

the number of objects

Return type:

int

get_dataframe(class_name: str, id_list: list[int] = None) → DataFrame

Get a DataFrame containing the list of all domain objects of a given class in the current project

Parameters:

• class_name (str) – the class name of the objects whose list will be returned

• id_list (a list of int) – the list of ids of objects to retrieve

Returns:

a DataFrame containing the list of objects

Return type:

DataFrame containing the records representing the requested domain-specific objects

get_record(class_name: str, id_: int = None, uuid: str = None) → dict[str, Any] | None

A method returning an object record of a given class from its id

Parameters:

• class_name (str) – the class name of object to get the record of

• id (int) – the id of the requested object

Returns:

the object record

Return type:

dict (record)

get_record_by_name(class_name: str, name: str = None) → dict[str, Any] | None

Return a record from its name

Parameters:

• class_name (str) – class name of the corresponding DSO object

• name (str) – the name of the requested record

Returns:

the record

Return type:

dict

get_records(class_name: str, id_list: list[int] = None) → list[dict[str, Any]]

A method returning the list of all object records of a given class or select those whose id is in id_list

Parameters:

• class_name (str) – the class name of objects to get records of

• id_list (a list of int) – the list of ids of objects to retrieve

Returns:

a list of records

Return type:

list of dictionaries (records)

get_linked_records(cls_name: str, parent_cls_name: str, parent_id: int) → list[dict[str, Any]]

A method returning the list of records for all objects of class defined by cls_name that are linked to object of class parent_cls_name with id_ = parent_id

Parameters:

• cls_name – the class name of the objects to retrieve records for

• parent_cls_name – the class nae of the parent object

• parent_id – the id of the parent object

Returns:

a list of records

link(class1_name: str, id_1: int, class2_name: str, id_2: int) → None

Create a link between two domain-specific objects. There must be a direct link defined in Linker class, otherwise, the link cannot be created.

Parameters:

• class1_name (str) – the class name of the first object to link

• id_1 (int) – the id of the first object to link

• class2_name (str) – the class name of the second object to link

• id_2 (int) – the id of the second object to link

unlink(class1_name: str, id_1: int, class2_name: str, id_2: int) → None

Remove the link between two domain-specific objects. There must be a direct link defined in Linker class, otherwise, the link cannot be removed.

Parameters:

• class1_name (str) – the class name of the first object to unlink

• id_1 (int) – the id of the first object to unlink

• class2_name (str) – the class name of the second object to unlink

• id_2 (int) – the id of the second object to unlink