269 lines
10 KiB
Python
269 lines
10 KiB
Python
import datetime
|
|
import enum
|
|
import json
|
|
|
|
import marshmallow
|
|
from marshmallow import INCLUDE, fields
|
|
from marshmallow_enum import EnumField
|
|
from sqlalchemy import func
|
|
|
|
from crc import db, ma
|
|
from crc.api.common import ApiErrorSchema, ApiError
|
|
from crc.models.file import FileModel, SimpleFileSchema, FileSchema
|
|
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
|
|
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, WorkflowStatus, WorkflowSpecModel, \
|
|
WorkflowModel
|
|
from crc.services.file_service import FileService
|
|
from crc.services.user_service import UserService
|
|
|
|
|
|
class StudyStatus(enum.Enum):
|
|
in_progress = 'in_progress'
|
|
hold = 'hold'
|
|
open_for_enrollment = 'open_for_enrollment'
|
|
abandoned = 'abandoned'
|
|
|
|
|
|
class IrbStatus(enum.Enum):
|
|
incomplete_in_protocol_builder = 'incomplete in protocol builder'
|
|
completed_in_protocol_builder = 'completed in protocol builder'
|
|
hsr_assigned = 'hsr number assigned'
|
|
|
|
|
|
class StudyEventType(enum.Enum):
|
|
user = 'user'
|
|
automatic = 'automatic'
|
|
|
|
|
|
|
|
class StudyModel(db.Model):
|
|
__tablename__ = 'study'
|
|
id = db.Column(db.Integer, primary_key=True)
|
|
title = db.Column(db.String)
|
|
short_title = db.Column(db.String, nullable=True)
|
|
last_updated = db.Column(db.DateTime(timezone=True), server_default=func.now())
|
|
status = db.Column(db.Enum(StudyStatus))
|
|
irb_status = db.Column(db.Enum(IrbStatus))
|
|
primary_investigator_id = db.Column(db.String, nullable=True)
|
|
sponsor = db.Column(db.String, nullable=True)
|
|
hsr_number = db.Column(db.String, nullable=True)
|
|
ind_number = db.Column(db.String, nullable=True)
|
|
user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=False)
|
|
investigator_uids = db.Column(db.ARRAY(db.String), nullable=True)
|
|
requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
|
|
on_hold = db.Column(db.Boolean, default=False)
|
|
enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
|
|
#events = db.relationship("TaskEventModel")
|
|
events_history = db.relationship("StudyEvent", cascade="all, delete, delete-orphan")
|
|
|
|
def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
|
|
self.hsr_number = pbs.HSRNUMBER
|
|
self.title = pbs.TITLE
|
|
self.user_uid = pbs.NETBADGEID
|
|
self.last_updated = pbs.DATE_MODIFIED
|
|
|
|
self.irb_status = IrbStatus.incomplete_in_protocol_builder
|
|
|
|
|
|
class StudyAssociated(db.Model):
|
|
"""
|
|
This model allows us to associate people with a study, and optionally
|
|
give them edit access. This allows us to create a table with PI, D_CH, etc.
|
|
and give access to people other than the study owner.
|
|
Task_Events will still work as they have previously
|
|
"""
|
|
__tablename__ = 'study_associated_user'
|
|
id = db.Column(db.Integer, primary_key=True)
|
|
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
|
|
uid = db.Column(db.String, db.ForeignKey('ldap_model.uid'), nullable=False)
|
|
role = db.Column(db.String, nullable=True)
|
|
send_email = db.Column(db.Boolean, nullable=True)
|
|
access = db.Column(db.Boolean, nullable=True)
|
|
|
|
class StudyEvent(db.Model):
|
|
__tablename__ = 'study_event'
|
|
id = db.Column(db.Integer, primary_key=True)
|
|
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
|
|
study = db.relationship(StudyModel, back_populates='events_history')
|
|
create_date = db.Column(db.DateTime(timezone=True), server_default=func.now())
|
|
status = db.Column(db.Enum(StudyStatus))
|
|
comment = db.Column(db.String, default='')
|
|
event_type = db.Column(db.Enum(StudyEventType))
|
|
user_uid = db.Column(db.String, db.ForeignKey('user.uid'), nullable=True)
|
|
|
|
|
|
class WorkflowMetadata(object):
|
|
def __init__(self, id, name = None, display_name = None, description = None, spec_version = None,
|
|
category_id = None, category_display_name = None, state: WorkflowState = None,
|
|
status: WorkflowStatus = None, total_tasks = None, completed_tasks = None,
|
|
is_review=None,display_order = None, state_message = None):
|
|
self.id = id
|
|
self.name = name
|
|
self.display_name = display_name
|
|
self.description = description
|
|
self.spec_version = spec_version
|
|
self.category_id = category_id
|
|
self.category_display_name = category_display_name
|
|
self.state = state
|
|
self.state_message = state_message
|
|
self.status = status
|
|
self.total_tasks = total_tasks
|
|
self.completed_tasks = completed_tasks
|
|
self.is_review = is_review
|
|
self.display_order = display_order
|
|
|
|
|
|
@classmethod
|
|
def from_workflow(cls, workflow: WorkflowModel):
|
|
is_review = FileService.is_workflow_review(workflow.workflow_spec_id)
|
|
instance = cls(
|
|
id=workflow.id,
|
|
name=workflow.workflow_spec.name,
|
|
display_name=workflow.workflow_spec.display_name,
|
|
description=workflow.workflow_spec.description,
|
|
spec_version=workflow.spec_version(),
|
|
category_id=workflow.workflow_spec.category_id,
|
|
category_display_name=workflow.workflow_spec.category.display_name,
|
|
state=WorkflowState.optional,
|
|
status=workflow.status,
|
|
total_tasks=workflow.total_tasks,
|
|
completed_tasks=workflow.completed_tasks,
|
|
is_review=is_review,
|
|
display_order=workflow.workflow_spec.display_order
|
|
)
|
|
return instance
|
|
|
|
|
|
class WorkflowMetadataSchema(ma.Schema):
|
|
state = EnumField(WorkflowState)
|
|
status = EnumField(WorkflowStatus)
|
|
class Meta:
|
|
model = WorkflowMetadata
|
|
additional = ["id", "name", "display_name", "description",
|
|
"total_tasks", "completed_tasks", "display_order",
|
|
"category_id", "is_review", "category_display_name", "state_message"]
|
|
unknown = INCLUDE
|
|
|
|
|
|
class Category(object):
|
|
def __init__(self, model: WorkflowSpecCategoryModel):
|
|
self.id = model.id
|
|
self.name = model.name
|
|
self.display_name = model.display_name
|
|
self.display_order = model.display_order
|
|
|
|
|
|
class CategorySchema(ma.Schema):
|
|
workflows = fields.List(fields.Nested(WorkflowMetadataSchema), dump_only=True)
|
|
class Meta:
|
|
model = Category
|
|
additional = ["id", "name", "display_name", "display_order"]
|
|
unknown = INCLUDE
|
|
|
|
|
|
class Study(object):
|
|
|
|
def __init__(self, title, short_title, last_updated, primary_investigator_id, user_uid,
|
|
id=None, status=None, irb_status=None, comment="",
|
|
sponsor="", hsr_number="", ind_number="", categories=[],
|
|
files=[], approvals=[], enrollment_date=None, events_history=[],
|
|
last_activity_user="",last_activity_date =None,create_user_display="", **argsv):
|
|
self.id = id
|
|
self.user_uid = user_uid
|
|
self.create_user_display = create_user_display
|
|
self.last_activity_date = last_activity_date
|
|
self.last_activity_user = last_activity_user
|
|
self.title = title
|
|
self.short_title = short_title
|
|
self.last_updated = last_updated
|
|
self.status = status
|
|
self.irb_status = irb_status
|
|
self.comment = comment
|
|
self.primary_investigator_id = primary_investigator_id
|
|
self.sponsor = sponsor
|
|
self.hsr_number = hsr_number
|
|
self.ind_number = ind_number
|
|
self.categories = categories
|
|
self.approvals = approvals
|
|
self.warnings = []
|
|
self.files = files
|
|
self.enrollment_date = enrollment_date
|
|
self.events_history = events_history
|
|
|
|
@classmethod
|
|
def from_model(cls, study_model: StudyModel):
|
|
if study_model is not None and len(study_model.__dict__.items()) > 0:
|
|
args = dict((k, v) for k, v in study_model.__dict__.items() if not k.startswith('_'))
|
|
args['events_history'] = study_model.events_history # For some reason this attribute is not picked up
|
|
instance = cls(**args)
|
|
return instance
|
|
else:
|
|
raise ApiError(code='empty_study_model',
|
|
message='There was a problem retrieving your study. StudyModel is empty.')
|
|
|
|
def model_args(self):
|
|
"""Arguments that can be passed into the Study Model to update it."""
|
|
self_dict = self.__dict__.copy()
|
|
del self_dict["categories"]
|
|
del self_dict["warnings"]
|
|
return self_dict
|
|
|
|
|
|
class StudyForUpdateSchema(ma.Schema):
|
|
|
|
id = fields.Integer(required=False, allow_none=True)
|
|
status = EnumField(StudyStatus, by_value=True)
|
|
hsr_number = fields.String(allow_none=True)
|
|
sponsor = fields.String(allow_none=True)
|
|
ind_number = fields.String(allow_none=True)
|
|
enrollment_date = fields.DateTime(allow_none=True)
|
|
comment = fields.String(allow_none=True)
|
|
|
|
class Meta:
|
|
model = Study
|
|
unknown = INCLUDE
|
|
|
|
@marshmallow.post_load
|
|
def make_study(self, data, **kwargs):
|
|
"""Can load the basic study data for updates to the database, but categories are write only"""
|
|
return Study(**data)
|
|
|
|
|
|
class StudyEventSchema(ma.Schema):
|
|
|
|
id = fields.Integer(required=False)
|
|
create_date = fields.DateTime()
|
|
status = EnumField(StudyStatus, by_value=True)
|
|
comment = fields.String(allow_none=True)
|
|
event_type = EnumField(StudyEvent, by_value=True)
|
|
|
|
|
|
class StudySchema(ma.Schema):
|
|
|
|
id = fields.Integer(required=False, allow_none=True)
|
|
categories = fields.List(fields.Nested(CategorySchema), dump_only=True)
|
|
warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
|
|
protocol_builder_status = EnumField(StudyStatus, by_value=True)
|
|
status = EnumField(StudyStatus, by_value=True)
|
|
hsr_number = fields.String(allow_none=True)
|
|
short_title = fields.String(allow_none=True)
|
|
sponsor = fields.String(allow_none=True)
|
|
ind_number = fields.String(allow_none=True)
|
|
files = fields.List(fields.Nested(FileSchema), dump_only=True)
|
|
enrollment_date = fields.Date(allow_none=True)
|
|
events_history = fields.List(fields.Nested('StudyEventSchema'), dump_only=True)
|
|
|
|
class Meta:
|
|
model = Study
|
|
additional = ["id", "title", "short_title", "last_updated", "primary_investigator_id", "user_uid",
|
|
"sponsor", "ind_number", "files", "enrollment_date",
|
|
"create_user_display", "last_activity_date","last_activity_user",
|
|
"events_history"]
|
|
unknown = INCLUDE
|
|
|
|
@marshmallow.post_load
|
|
def make_study(self, data, **kwargs):
|
|
"""Can load the basic study data for updates to the database, but categories are write only"""
|
|
return Study(**data)
|
|
|