aepsych.database

Submodules

aepsych.database.db module

class aepsych.database.db.Database(db_path=None)[source]

Bases: object

Initialize the database object.

Parameters:

db_path (str, optional) – The path to the database. Defaults to None.

get_engine()[source]

Get the engine for the database.

Returns:

The sessionmaker object for the database.

Return type:

sessionmaker

delete_db()[source]

Delete the database.

Return type:

None

is_update_required()[source]

Check if an update is required on the database.

Returns:

True if an update is required, False otherwise.

Return type:

bool

perform_updates()[source]

Perform updates on known tables. SQLAlchemy doesn’t do alters so they’re done the old fashioned way.

Return type:

None

session_scope()[source]

Provide a transactional scope around a series of operations.

execute_sql_query(query, vals)[source]

Execute an arbitrary query written in sql.

Parameters:

  • query (str) – The query to execute.

  • vals (Dict[str, str]) – The values to use in the query.

Returns:

The results of the query.

Return type:

List[Any]

get_master_records()[source]

Grab the list of master records.

Returns:

The list of master records.

Return type:

List[tables.DBMasterTable]

get_master_record(experiment_id)[source]

Grab the list of master record for a specific experiment (master) id.

Parameters:

experiment_id (int) – The experiment id.

Returns:

The master record or None if it doesn’t exist.

Return type:

tables.DBMasterTable or None

get_replay_for(master_id)[source]

Get the replay records for a specific master row.

Parameters:

master_id (int) – The master id.

Returns:

The replay records or None if they don’t exist.

Return type:

List[tables.DbReplayTable] or None

get_strats_for(master_id=0)[source]

Get the strat records for a specific master row.

Parameters:

master_id (int) – The master id. Defaults to 0.

Returns:

The strat records or None if they don’t exist.

Return type:

List[Any] or None

get_strat_for(master_id, strat_id=- 1)[source]

Get a specific strat record for a specific master row.

Parameters:

  • master_id (int) – The master id.

  • strat_id (int) – The strat id. Defaults to -1.

Returns:

The strat record.

Return type:

Any

get_config_for(master_id)[source]

Get the strat records for a specific master row.

Parameters:

master_id (int) – The master id.

Returns:

The config records.

Return type:

Any

get_raw_for(master_id)[source]

Get the raw data for a specific master row.

Parameters:

master_id (int) – The master id.

Returns:

The raw data or None if it doesn’t exist.

Return type:

List[tables.DbRawTable] or None

get_all_params_for(master_id)[source]

Get the parameters for all the iterations of a specific experiment.

Parameters:

master_id (int) – The master id.

Returns:

The parameters or None if they don’t exist.

Return type:

List[tables.DbRawTable] or None

get_param_for(master_id, iteration_id)[source]

Get the parameters for a specific iteration of a specific experiment.

Parameters:

  • master_id (int) – The master id.

  • iteration_id (int) – The iteration id.

Returns:

The parameters or None if they don’t exist.

Return type:

List[tables.DbRawTable] or None

get_all_outcomes_for(master_id)[source]

Get the outcomes for all the iterations of a specific experiment.

Parameters:

master_id (int) – The master id.

Returns:

The outcomes or None if they don’t exist.

Return type:

List[tables.DbRawTable] or None

get_outcome_for(master_id, iteration_id)[source]

Get the outcomes for a specific iteration of a specific experiment.

Parameters:

  • master_id (int) – The master id.

  • iteration_id (int) – The iteration id.

Returns:

The outcomes or None if they don’t exist.

Return type:

List[tables.DbRawTable] or None

record_setup(description, name, extra_metadata=None, id=None, request=None, participant_id=None)[source]

Record the setup of an experiment.

Parameters:

  • description (str) – The description of the experiment.

  • name (str) – The name of the experiment.

  • extra_metadata (str, optional) – Extra metadata. Defaults to None.

  • id (str, optional) – The id of the experiment. Defaults to None.

  • request (Dict[str, Any]) – The request. Defaults to None.

  • participant_id (int, optional) – The participant id. Defaults to None.

Returns:

The experiment id.

Return type:

str

record_message(master_table, type, request)[source]

Record a message in the database.

Parameters:

  • master_table (tables.DBMasterTable) – The master table.

  • type (str) – The type of the message.

  • request (Dict[str, Any]) – The request.

Return type:

None

record_raw(master_table, model_data, timestamp=None)[source]

Record raw data in the database.

Parameters:

  • master_table (tables.DBMasterTable) – The master table.

  • model_data (Any) – The model data.

  • timestamp (datetime.datetime, optional) – The timestamp. Defaults to None.

Returns:

The raw entry.

Return type:

tables.DbRawTable

record_param(raw_table, param_name, param_value)[source]

Record a parameter in the database.

Parameters:

  • raw_table (tables.DbRawTable) – The raw table.

  • param_name (str) – The parameter name.

  • param_value (str) – The parameter value.

Return type:

None

record_outcome(raw_table, outcome_name, outcome_value)[source]

Record an outcome in the database.

Parameters:

  • raw_table (tables.DbRawTable) – The raw table.

  • outcome_name (str) – The outcome name.

  • outcome_value (float) – The outcome value.

Return type:

None

record_strat(master_table, strat)[source]

Record a strategy in the database.

Parameters:
Return type:

None

record_config(master_table, config)[source]

Record a config in the database.

Parameters:
Return type:

None

list_master_records()[source]

List the master records.

Return type:

None

aepsych.database.tables module

class aepsych.database.tables.Base(**kwargs)

Bases: object

The base class of the class hierarchy.

When called, it accepts no arguments and returns a new featureless instance that has no instance attributes and cannot be given any.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

metadata = MetaData()
registry = <sqlalchemy.orm.decl_api.registry object>
class aepsych.database.tables.DBMasterTable(**kwargs)[source]

Bases: Base

Master table to keep track of all experiments and unique keys associated with the experiment

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

unique_id
experiment_name
experiment_description
experiment_id
participant_id
extra_metadata
children_replay
children_strat
children_config
children_raw
classmethod from_sqlite(row)[source]

Create a DBMasterTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DBMasterTable object.

Return type:

DBMasterTable

static update(engine)[source]

Update the master table schema to include extra_metadata and participant_id columns.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]

Check if the master table schema requires an update.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

bool

class aepsych.database.tables.DbReplayTable(**kwargs)[source]

Bases: Base

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

use_extra_info = False
unique_id
timestamp
message_type
message_contents
extra_info
master_table_id
parent
classmethod from_sqlite(row)[source]

Create a DbReplayTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DbReplayTable object.

Return type:

DbReplayTable

static update(engine)[source]

Update the replay_data table schema to include an extra_info column and convert old configs.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]

Check if the replay_data table schema requires an update.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

bool

class aepsych.database.tables.DbStratTable(**kwargs)[source]

Bases: Base

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

unique_id
timestamp
strat
master_table_id
parent
classmethod from_sqlite(row)[source]

Create a DbStratTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DbStratTable object.

Return type:

DbStratTable

static update(engine)[source]

Update the strat_data table schema.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]

Check if the strat_data table schema requires an update.(always False)

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

bool

class aepsych.database.tables.DbConfigTable(**kwargs)[source]

Bases: Base

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

unique_id
timestamp
config
master_table_id
parent
classmethod from_sqlite(row)[source]

Create a DbConfigTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DbConfigTable object.

Return type:

DbConfigTable

static update(engine)[source]

Update the config_data table schema.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]

Check if the config_data table schema requires an update.(always False)

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

bool

class aepsych.database.tables.DbRawTable(**kwargs)[source]

Bases: Base

Fact table to store the raw data of each iteration of an experiment.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

unique_id
timestamp
model_data
master_table_id
parent
children_param
children_outcome
classmethod from_sqlite(row)[source]

Create a DbRawTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DbRawTable object.

Return type:

DbRawTable

static update(db, engine)[source]

Update the raw table with data from the replay table.

Parameters:

  • db (Any) – The database object.

  • engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]

Check if the raw table is empty, and data already exists.

Parameters:

engine (Engine) – The sqlalchemy engine.

Returns:

True if the raw table is empty and data already exists, False otherwise.

Return type:

bool

class aepsych.database.tables.DbParamTable(**kwargs)[source]

Bases: Base

Dimension table to store the parameters of each iteration of an experiment. Supports multiple parameters per iteration, and multiple stimuli per parameter.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

unique_id
param_name
param_value
iteration_id
parent
classmethod from_sqlite(row)[source]

Create a DbParamTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DbParamTable object.

Return type:

DbParamTable

static update(engine)[source]

Update the param_data table schema.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]

Check if the param_data table schema requires an update.(always False)

Parameters:

engine (Engine) – The sqlalchemy engine.

Returns:

True if the param_data table schema requires an update, False otherwise.

Return type:

bool

class aepsych.database.tables.DbOutcomeTable(**kwargs)[source]

Bases: Base

Dimension table to store the outcomes of each iteration of an experiment. Supports multiple outcomes per iteration.

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

unique_id
outcome_name
outcome_value
iteration_id
parent
classmethod from_sqlite(row)[source]

Create a DbOutcomeTable object from a row in the sqlite database.

Parameters:

row (Dict[str, Any]) – A row from the sqlite database.

Returns:

A DbOutcomeTable object.

Return type:

DbOutcomeTable

static update(engine)[source]

Update the outcome_data table schema.

Parameters:

engine (Engine) – The sqlalchemy engine.

Return type:

None

static requires_update(engine)[source]
Parameters:

engine (Engine) –

Return type:

bool

Module contents