Code Reference#

`studygovernor` Package#

studygovernor.convert_to_bool(value)#

Return type:: Union[str, bool]

studygovernor.create_app(test_config=None, use_sentry=True)#

studygovernor.load_app_config(app, test_config)#

studygovernor.load_config_from_env()#

studygovernor.set_config_defaults(config)#

studygovernor.set_default_config_value(config, key, value, warning=None)#

studygovernor.uia_username_mapper(identity)#

Return type:: str

`studygovernor.callbacks` Module#

studygovernor.callbacks.check_json_serializable(data)#

Check if given data is JSON serializable

Parameters:: data (Any) – Data to check
Return type:: bool
Returns:: Bool indicating the data is serializable

studygovernor.callbacks.clean_config(config)#

Clean a config so that it is guaranteed to be serializable

Return type:: Dict[str, Union[bool, float, int, str, None, List[Union[bool, float, int, str, None]], Dict[str, Union[bool, float, int, str, None]]]]

studygovernor.callbacks.clean_value(value)#

Return type:: Union[bool, float, int, str, None]

studygovernor.callbacks.dispatch_callback(callback_execution, config)#: Dispatch the callback to the appropriate backend.

studygovernor.callbacks.master_callback(*, callback_function, callback_arguments, callback_execution_url, callback_execution_secret, config)#

studygovernor.callbacks.replace_mapping(string, mapping)#

Performs multiple substitutions in a string, will use each key-value pair a replacements.

Parameters:

string (str) – String to perform substitutions on
mapping (Mapping[str, str]) – The mapping containing all replacements pairs

Returns:

Updated string after replacements

studygovernor.callbacks.update_callback_execution(url, secret, data)#

`studygovernor.exceptions` Module#

exception studygovernor.exceptions.ConditionFunctionCallFailedError(condition, stacktrace)#: Bases: StateChangeError

exception studygovernor.exceptions.ConditionFunctionReturnValueError(condition, function, args, kwargs, return_value)#: Bases: ConditionFunctionCallFailedError

exception studygovernor.exceptions.ConditionNotMetError(experiment, transition, condition)#: Bases: StateChangeError

exception studygovernor.exceptions.CouldNotFindResourceError(id_, type_, message=None)#

Bases: StudyGovernorHTTPError

Could not find a resource

code: int | None = 404#

exception studygovernor.exceptions.NoValidTransitionError(sourcestate, targetstate)#: Bases: StateChangeError

exception studygovernor.exceptions.RESTResponseError#

Bases: StudyGovernorClientError

The REST response is not what was expected

exception studygovernor.exceptions.StateChangeError#

Bases: StudyGovernorError

Exceptions encountered during a state change

exception studygovernor.exceptions.StateNotFoundError(requested_state)#: Bases: StateChangeError

exception studygovernor.exceptions.StudyGovernorClientError#

Bases: StudyGovernorError

Error class for all client-side errors

exception studygovernor.exceptions.StudyGovernorError#

Bases: Exception

Base class for exceptions in the study governor codebase

property fields#

marshal(api_prefix)#

exception studygovernor.exceptions.StudyGovernorHTTPError(description, response=None)#

Bases: StudyGovernorError, HTTPException

All exceptions that should lead to an HTTP error response

code: int | None = 500#

property description#

exception studygovernor.exceptions.StudyGovernorSSLError#

Bases: StudyGovernorClientError

There was a problem creating an SSL connection

exception studygovernor.exceptions.UnknownConditionFunction(condition, module, function)#: Bases: StateChangeError

`studygovernor.fields` Module#

class studygovernor.fields.MappingField(**kwargs)#

Bases: Raw

format(value)#

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters:: value – The value to format
Raises:: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

class studygovernor.fields.ObjectUrl(object_class, api_prefix=None, **kwargs)#

Bases: Raw

format(value)#

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters:: value – The value to format
Raises:: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

class studygovernor.fields.OptionalDatetime(dt_format='iso8601', **kwargs)#

Bases: DateTime

format(value)#

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters:: value – The value to format
Raises:: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

class studygovernor.fields.SubUrl(object_class, subfield, **kwargs)#

Bases: Raw

format(value)#

Formats a field’s value. No-op by default - field classes that modify how the value of existing object keys should be presented should override this and apply the appropriate formatting.

Parameters:: value – The value to format
Raises:: MarshallingError – In case of formatting problem

Ex:

class TitleCase(Raw):
    def format(self, value):
        return unicode(value).title()

`studygovernor.util.filters` Module#

studygovernor.util.filters.hyphenate_filter(s)#: Filter for lowercasing and hyphenating a string.

studygovernor.util.filters.json_format_filter(s)#: Filter for pretty formatting json’s.

studygovernor.util.filters.python_code_filter(s)#

studygovernor.util.filters.register_filters(app)#: Special function that registers all member of this module ending in “_filter”.

studygovernor.util.filters.yaml_dump_filter(s)#: Filter for pretty formatting json’s.

`studygovernor.util.helpers` Module#

studygovernor.util.helpers.create_workflow(workflow_definition, verbose=False)#

studygovernor.util.helpers.get_object_from_arg(id, model, model_name=None, skip_id=False, allow_none=False, filters=None)#

Return type:: TypeVar(T)

studygovernor.util.helpers.get_uri(route, id, blueprint=None)#

studygovernor.util.helpers.has_permission_all(*args)#

studygovernor.util.helpers.has_permission_any(*args)#

studygovernor.util.helpers.http_auth_optional(realm)#

Decorator that protects endpoints using Basic HTTP authentication.

Parameters:: realm – optional realm name

If authentication fails, this version will continue normally! This is to enable secondary fall-back with tokens.

Once authenticated, if so configured, CSRF protection will be tested.

… warning::: Auth is optional, so this will not prohibit access to the route without further logic!

studygovernor.util.helpers.initialize_workflow(workflow, app, verbose=False, force=True, upgrade=False)#

studygovernor.util.helpers.upgrade_workflow(workflow, workflow_definition, db, verbose=False)#

`studygovernor.models` Module#

class studygovernor.models.Action(**kwargs)#

Bases: Model

property api_uri: str#

Return type:: str

end_time#

executions#

experiment#

experiment_id#

freetext#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

return_value#

start_time#

success#

transition#

transition_id#

property web_uri: str#

Return type:: str

class studygovernor.models.Callback(**kwargs)#

Bases: Model

” Data model representing the definition of a callback. This defines how a callback should be executed, but is not linked to a specific execution.

callback_arguments#

condition#

description#

executions#

function#

id#

initial_delay#

label#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

run_timeout#

state#

state_id#

variable_map#

wait_timeout#

class studygovernor.models.CallbackExecution(**kwargs)#

Bases: Model

Data model representing one execution of a callback. Links back to the callback definition and the source action.

action: Mapped[Action]#

action_id#

property api_uri: str#

Return type:: str

callback: Mapped[Callback]#

callback_id#

property cohort#

created#

property experiment#

property external_systems#

finished#

id#

result#

result_log#

result_values#

run_log#

run_start#

secret_key#

status#

property subject#

uri(blueprint=None)#

Return type:: str

wait_start#

property web_uri: str#

Return type:: str

class studygovernor.models.CallbackExecutionResult(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)#

Bases: str, Enum

” Defined the valid result categories for a callback execution

property badge_class#

failed = 'failed'#

none = 'none'#

success = 'success'#

timeout = 'timeout'#

class studygovernor.models.CallbackExecutionStatus(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)#

Bases: str, Enum

” Defined the valid states for callback execution

property badge_class#

created = 'created'#

finished = 'finished'#

queued = 'queued'#

property resolved#

running = 'running'#

skipped = 'skipped'#

waiting = 'waiting'#

class studygovernor.models.Cohort(**kwargs)#

Bases: Model

description#

external_system_urls#

property external_urls#

id#

label#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

subjects#

class studygovernor.models.Experiment(**kwargs)#

Bases: Model

actions#

property api_uri: str#

Return type:: str

external_experiment_links#

property external_ids#

find_external_id(external_system_name)#

id#

label#

property last_action: Action#

Return type:: Action

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

scandate#

scans#

property state: State#

Return type:: State

subject#

subject_id#

property variable_map#

variables#

property web_uri: str#

Return type:: str

class studygovernor.models.ExternalCohortUrls(**kwargs)#

Bases: Model

cohort#

cohort_id#

external_system#

external_system_id#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

url#

class studygovernor.models.ExternalExperimentLinks(external_id=None, experiment=None, external_system=None)#

Bases: Model

experiment#

experiment_id#

external_id#

external_system#

external_system_id#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

class studygovernor.models.ExternalSubjectLinks(external_id=None, subject=None, external_system=None)#

Bases: Model

external_id#

external_system#

external_system_id#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

subject#

subject_id#

class studygovernor.models.ExternalSystem(id=None, system_name=None, url=None)#

Bases: Model

external_cohort_urls#

external_experiment_links#

external_subject_links#

history#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

system_name#

url#

class studygovernor.models.ExternalSystemHistory(**kwargs)#

Bases: Model

external_system#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

system_id#

timestamp#

url#

class studygovernor.models.Role(**kwargs)#

Bases: Model, BaseRole

This implements the BaseRole from the .auth.models module. In this specific case, the BaseRole is sufficient.

description: str | None#

id: int#

name: str#

permissions: list[str] | None#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

update_datetime: datetime#

class studygovernor.models.Scan(experiment=None, scantype=None)#

Bases: Model

experiment#

experiment_id#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

scantype#

scantype_id#

class studygovernor.models.Scantype(id=None, modality=None, protocol=None)#

Bases: Model

id#

modality#

protocol#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

scans#

class studygovernor.models.State(**kwargs)#

Bases: Model

callbacks#

property experiments#

freetext#

get_transition_to(target_state)#

id#

label#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

transition_destinations#

transition_sources#

workflow#

workflow_id#

class studygovernor.models.Subject(**kwargs)#

Bases: Model

property api_uri: str#

Return type:: str

cohort#

cohort_id#

date_of_birth#

experiments#

property external_ids#

external_subject_links#

id#

label#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

property web_uri: str#

Return type:: str

class studygovernor.models.Transition(id=None, source_state=None, destination_state=None, condition=None)#

Bases: Model

actions#

condition#

destination_state#

destination_state_id#

id#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

source_state#

source_state_id#

class studygovernor.models.User(**kwargs)#

Bases: Model, BaseUser

active: bool#

confirmed_at: datetime | None#

create_datetime: datetime#

create_time#

current_login_at: datetime#

current_login_ip: str | None#

email: str#

fs_uniquifier: str#

id: int#

last_login_at: datetime#

last_login_ip: str | None#

login_count: int#

name#

password: str | None#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

roles: list[RoleMixin]#

tf_phone_number: str | None#

tf_primary_method: str | None#

tf_totp_secret: str | None#

update_datetime: datetime#

username: str | None#

class studygovernor.models.Variable(**kwargs)#

Bases: Model

experiment#

experiment_id#

id#

label#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

type#

value#

class studygovernor.models.VariableType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)#

Bases: Enum

bool = 'bool'#

date = 'date'#

datetime = 'datetime'#

float = 'float'#

int = 'int'#

json = 'json'#

none = 'none'#

classmethod pack(value)#

Return type:: Tuple[VariableType, str]

str = 'str'#

time = 'time'#

classmethod unpack(value, var_type)#

Return type:: Any

class studygovernor.models.Workflow(**kwargs)#

Bases: Model

id#

label#

query: t.ClassVar[Query]#: A SQLAlchemy query for a model. Equivalent to db.session.query(Model). Can be customized per-model by overriding query_class.

Warning

The query interface is considered legacy in SQLAlchemy. Prefer using session.execute(select()) instead.

states#

studygovernor.models.log_history(mapper, connection, target)#

Code Reference#

studygovernor Package#

studygovernor.callbacks Module#

studygovernor.exceptions Module#

studygovernor.fields Module#

studygovernor.util.filters Module#

studygovernor.util.helpers Module#

studygovernor.models Module#

`studygovernor` Package#

`studygovernor.callbacks` Module#

`studygovernor.exceptions` Module#

`studygovernor.fields` Module#

`studygovernor.util.filters` Module#

`studygovernor.util.helpers` Module#

`studygovernor.models` Module#