Code Reference¶
studygovernor
Package¶
-
studygovernor.
create_app
(test_config=None, use_sentry=True)¶
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studygovernor.
load_app_config
(app, test_config)¶
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studygovernor.
set_config_defaults
(config)¶
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studygovernor.
set_default_config_value
(config, key, value, warning=None)¶
studygovernor.exceptions
Module¶
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exception
studygovernor.exceptions.
ConditionFunctionCallFailedError
(condition, function, args, kwargs, stacktrace)¶
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exception
studygovernor.exceptions.
ConditionFunctionReturnValueError
(condition, function, args, kwargs, return_value)¶ Bases:
studygovernor.exceptions.ConditionFunctionCallFailedError
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exception
studygovernor.exceptions.
ConditionNotMetError
(experiment, transition, condition)¶
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exception
studygovernor.exceptions.
CouldNotFindResourceError
(id_, type_, message=None)¶ Bases:
studygovernor.exceptions.StudyGovernorHTTPError
Could not find a resource
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code
= 404¶
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exception
studygovernor.exceptions.
NoValidTransitionError
(sourcestate, targetstate)¶
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exception
studygovernor.exceptions.
RESTResponseError
¶ Bases:
studygovernor.exceptions.StudyGovernorClientError
The REST response is not what was expected
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exception
studygovernor.exceptions.
StateChangeError
¶ Bases:
studygovernor.exceptions.StudyGovernorError
Exceptions encountered during a state change
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exception
studygovernor.exceptions.
StateNotFoundError
(requested_state)¶
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exception
studygovernor.exceptions.
StudyGovernorClientError
¶ Bases:
studygovernor.exceptions.StudyGovernorError
Error class for all client-side errors
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exception
studygovernor.exceptions.
StudyGovernorError
¶ Bases:
Exception
Base class for exceptions in the study governor codebase
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property
fields
¶
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marshal
(api_prefix)¶
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property
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exception
studygovernor.exceptions.
StudyGovernorHTTPError
(description, response=None)¶ Bases:
studygovernor.exceptions.StudyGovernorError
,werkzeug.exceptions.HTTPException
All exceptions that should lead to an HTTP error response
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code
= 500¶
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property
description
¶
-
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exception
studygovernor.exceptions.
StudyGovernorSSLError
¶ Bases:
studygovernor.exceptions.StudyGovernorClientError
There was a problem creating an SSL connection
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exception
studygovernor.exceptions.
UnknownConditionFunction
(condition, module, function)¶
studygovernor.fields
Module¶
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class
studygovernor.fields.
MappingField
(**kwargs)¶ Bases:
flask_restplus.fields.Raw
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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()
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-
class
studygovernor.fields.
ObjectUrl
(object_class, api_prefix=None, **kwargs)¶ Bases:
flask_restplus.fields.Raw
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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:
flask_restplus.fields.Raw
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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()
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studygovernor.util.filters
Module¶
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studygovernor.util.filters.
hyphenate_filter
(s)¶ Filter for lowercasing and hyphenating a string.
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studygovernor.util.filters.
json_format_filter
(s)¶ Filter for pretty formatting json’s.
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studygovernor.util.filters.
register_filters
(app)¶ Special function that registers all member of this module ending in “_filter”.
studygovernor.util.helpers
Module¶
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studygovernor.util.helpers.
get_object_from_arg
(id, model, model_name=None, skip_id=False, allow_none=False)¶
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studygovernor.util.helpers.
initialize_workflow
(workflow, app, verbose=False, force=True)¶
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studygovernor.util.helpers.
load_config_file
(app, file_path, silent=False)¶
studygovernor.models
Module¶
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class
studygovernor.models.
Action
(experiment=None, transition=None, freetext=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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end_time
¶
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experiment_id
¶
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freetext
¶
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id
¶
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return_value
¶
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start_time
¶
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success
¶
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transition_id
¶
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class
studygovernor.models.
Condition
(rule=None, freetext=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
-
check
(experiment)¶
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freetext
¶
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id
¶
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rule
¶
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transitions
¶
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class
studygovernor.models.
Experiment
(subject=None, label=None, scandate=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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actions
¶
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external_experiment_links
¶
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property
external_ids
¶
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find_external_id
(external_system_name)¶
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id
¶
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init_state
()¶
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label
¶
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scandate
¶
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scans
¶
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set_state
(target_state, api_prefix='api_v1', freetext=None)¶
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property
state
¶
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subject
¶
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subject_id
¶
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class
studygovernor.models.
ExternalExperimentLinks
(external_id=None, experiment=None, external_system=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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experiment
¶
-
experiment_id
¶
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external_id
¶
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external_system
¶
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external_system_id
¶
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id
¶
-
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class
studygovernor.models.
ExternalSubjectLinks
(external_id=None, subject=None, external_system=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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external_id
¶
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external_system
¶
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external_system_id
¶
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id
¶
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subject
¶
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subject_id
¶
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class
studygovernor.models.
ExternalSystem
(id=None, system_name=None, url=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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external_experiment_links
¶
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external_subject_links
¶
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id
¶
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system_name
¶
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url
¶
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class
studygovernor.models.
Role
(**kwargs)¶ Bases:
sqlalchemy.ext.declarative.api.Model
,studygovernor.auth.models.BaseRole
This implements the BaseRole from the .auth.models module. In this specific case, the BaseRole is sufficient.
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description
¶
-
id
¶
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name
¶
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permissions
¶
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update_datetime
¶
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users
¶
-
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class
studygovernor.models.
Scan
(experiment=None, scantype=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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experiment
¶
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experiment_id
¶
-
id
¶
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scantype
¶
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scantype_id
¶
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class
studygovernor.models.
Scantype
(id=None, modality=None, protocol=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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id
¶
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modality
¶
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protocol
¶
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scans
¶
-
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class
studygovernor.models.
State
(id=None, label=None, callback=None, lifespan=None, freetext=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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callback
¶
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property
experiments
¶
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freetext
¶
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get_transition_to
(target_state)¶
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id
¶
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label
¶
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lifespan
¶
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property
lifespan_timedelta
¶
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transition_destinations
¶
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transition_sources
¶
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class
studygovernor.models.
Subject
(label=None, date_of_birth=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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date_of_birth
¶
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experiments
¶
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property
external_ids
¶
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external_subject_links
¶
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id
¶
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label
¶
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class
studygovernor.models.
Transition
(id=None, source_state=None, destination_state=None, conditions=None)¶ Bases:
sqlalchemy.ext.declarative.api.Model
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actions
¶
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conditions
¶
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destination_state
¶
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destination_state_id
¶
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id
¶
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source_state
¶
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source_state_id
¶
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class
studygovernor.models.
User
(**kwargs)¶ Bases:
sqlalchemy.ext.declarative.api.Model
,studygovernor.auth.models.BaseUser
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active
¶
-
confirmed_at
¶
-
create_datetime
¶
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create_time
¶
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current_login_at
¶
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current_login_ip
¶
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email
¶
-
fs_uniquifier
¶
-
id
¶
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last_login_at
¶
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last_login_ip
¶
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login_count
¶
-
name
¶
-
password
¶
-
roles
¶
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tf_phone_number
¶
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tf_primary_method
¶
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tf_totp_secret
¶
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update_datetime
¶
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username
¶
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studygovernor.views
Module¶
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studygovernor.views.
forbidden_error
(error)¶
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studygovernor.views.
index
()¶
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studygovernor.views.
page_not_found_error
(error)¶
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studygovernor.views.
user
(id)¶
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studygovernor.views.
users
()¶
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studygovernor.views.
web_action
(id)¶
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studygovernor.views.
web_experiment
(id)¶
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studygovernor.views.
web_experiments
()¶
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studygovernor.views.
web_state
(id)¶
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studygovernor.views.
web_states
()¶
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studygovernor.views.
web_subject
(id)¶
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studygovernor.views.
web_subjects
()¶
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studygovernor.views.
web_transition
(id)¶
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studygovernor.views.
web_transitions
()¶