import datetime import glob import os import xml.etree.ElementTree as ElementTree from crc import app, db, session from crc.models.file import FileType, FileModel, FileDataModel, CONTENT_TYPES from crc.models.study import StudyModel from crc.models.user import UserModel from crc.models.workflow import WorkflowSpecModel from crc.services.file_service import FileService from crc.services.workflow_processor import WorkflowProcessor from crc.models.protocol_builder import ProtocolBuilderStatus class ExampleDataLoader: @staticmethod def clean_db(): session.flush() # Clear out any transactions before deleting it all to avoid spurious errors. for table in reversed(db.metadata.sorted_tables): session.execute(table.delete()) session.flush() def load_all(self): self.load_reference_documents() users = [ UserModel( uid='dhf8r', email_address='dhf8r@virginia.EDU', display_name='Daniel Harold Funk', affiliation='staff@virginia.edu;member@virginia.edu', eppn='dhf8r@virginia.edu', first_name='Daniel', last_name='Funk', title='SOFTWARE ENGINEER V' ) ] db.session.add_all(users) db.session.commit() studies = [ StudyModel( id=1, title='The impact of fried pickles on beer consumption in bipedal software developers.', last_updated=datetime.datetime.now(), protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS, primary_investigator_id='dhf8r', sponsor='Sartography Pharmaceuticals', ind_number='1234', user_uid='dhf8r' ), StudyModel( id=2, title='Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels', last_updated=datetime.datetime.now(), protocol_builder_status=ProtocolBuilderStatus.IN_PROCESS, primary_investigator_id='dhf8r', sponsor='Makerspace & Co.', ind_number='5678', user_uid='dhf8r' ), ] db.session.add_all(studies) db.session.commit() self.create_spec(id="crc2_training_session_enter_core_info", name="crc2_training_session_enter_core_info", display_name="CR Connect2 - Training Session - Core Info", description='Part of Milestone 3 Deliverable') self.create_spec(id="crc2_training_session_data_security_plan", name="crc2_training_session_data_security_plan", display_name="CR Connect2 - Training Session - Data Security Plan", description='Part of Milestone 3 Deliverable') self.create_spec(id="crc2_training_session_sponsor_funding_source", name="crc2_training_session_sponsor_funding_source", display_name="CR Connect2 - Training Session - Sponsor and/or Funding Source", description='Part of Milestone 3 Deliverable') def create_spec(self, id, name, display_name="", description="", filepath=None): """Assumes that a directory exists in static/bpmn with the same name as the given id. further assumes that the [id].bpmn is the primary file for the workflow. returns an array of data models to be added to the database.""" global file file_service = FileService() spec = WorkflowSpecModel(id=id, name=name, display_name=display_name, description=description, is_status=id == 'status') db.session.add(spec) db.session.commit() if not filepath: filepath = os.path.join(app.root_path, 'static', 'bpmn', id, "*") files = glob.glob(filepath) for file_path in files: noise, file_extension = os.path.splitext(file_path) filename = os.path.basename(file_path) is_status = filename.lower() == 'status.bpmn' is_primary = filename.lower() == id + '.bpmn' try: file = open(file_path, 'rb') data = file.read() content_type = CONTENT_TYPES[file_extension[1:]] file_service.add_workflow_spec_file(workflow_spec=spec, name=filename, content_type=content_type, binary_data=data, primary=is_primary, is_status=is_status) except IsADirectoryError as de: # Ignore sub directories pass finally: if file: file.close() return spec def load_reference_documents(self): file_path = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx') file = open(file_path, "rb") FileService.add_reference_file(FileService.IRB_PRO_CATEGORIES_FILE, binary_data=file.read(), content_type=CONTENT_TYPES['xls']) file.close()