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 from crc.models.file import FileModel, SimpleFileSchema from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, WorkflowStatus, WorkflowSpecModel, \ WorkflowModel class StudyModel(db.Model): __tablename__ = 'study' id = db.Column(db.Integer, primary_key=True) title = db.Column(db.String) last_updated = db.Column(db.DateTime(timezone=True), default=func.now()) protocol_builder_status = db.Column(db.Enum(ProtocolBuilderStatus)) 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) 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.protocol_builder_status = ProtocolBuilderStatus.INCOMPLETE if pbs.Q_COMPLETE: self.protocol_builder_status = ProtocolBuilderStatus.ACTIVE if pbs.HSRNUMBER: self.protocol_builder_status = ProtocolBuilderStatus.OPEN if self.on_hold: self.protocol_builder_status = ProtocolBuilderStatus.HOLD class WorkflowMetadata(object): def __init__(self, id, name, display_name, description, spec_version, category_id, state: WorkflowState, status: WorkflowStatus, total_tasks, completed_tasks, display_order): 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.state = state self.status = status self.total_tasks = total_tasks self.completed_tasks = completed_tasks self.display_order = display_order @classmethod def from_workflow(cls, workflow: WorkflowModel): 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, state=WorkflowState.optional, status=workflow.status, total_tasks=workflow.total_tasks, completed_tasks=workflow.completed_tasks, 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"] 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, last_updated, primary_investigator_id, user_uid, id=None, protocol_builder_status=None, sponsor="", hsr_number="", ind_number="", categories=[], **argsv): self.id = id self.user_uid = user_uid self.title = title self.last_updated = last_updated self.protocol_builder_status = protocol_builder_status self.primary_investigator_id = primary_investigator_id self.sponsor = sponsor self.hsr_number = hsr_number self.ind_number = ind_number self.categories = categories self.warnings = [] self.files = [] @classmethod def from_model(cls, study_model: StudyModel): id = study_model.id # Just read some value, in case the dict expired, otherwise dict may be empty. args = dict((k, v) for k, v in study_model.__dict__.items() if not k.startswith('_')) instance = cls(**args) return instance def update_model(self, study_model: StudyModel): for k,v in self.__dict__.items(): if not k.startswith('_'): study_model.__dict__[k] = v 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 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(ProtocolBuilderStatus) hsr_number = fields.String(allow_none=True) sponsor = fields.String(allow_none=True) ind_number = fields.String(allow_none=True) files = fields.List(fields.Nested(SimpleFileSchema), dump_only=True) class Meta: model = Study additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid", "sponsor", "ind_number"] 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)