import glob import glob import os from crc import app, db, session from crc.models.file import CONTENT_TYPES from crc.models.ldap import LdapModel from crc.models.user import UserModel from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel from crc.services.document_service import DocumentService from crc.services.file_service import FileService from crc.services.study_service import StudyService class ExampleDataLoader: @staticmethod def clean_db(): session.flush() # Clear out any transactions before deleting it all to avoid spurious errors. engine = session.bind.engine connection = engine.connect() for table in reversed(db.metadata.sorted_tables): if engine.dialect.has_table(connection, table): session.execute(table.delete()) session.commit() session.flush() def load_all(self): self.load_reference_documents() categories = [ WorkflowSpecCategoryModel( id=0, display_name='From PB', display_order=0 ), WorkflowSpecCategoryModel( id=1, display_name='Core Info', display_order=1 ), WorkflowSpecCategoryModel( id=2, display_name='Approvals', display_order=2 ), WorkflowSpecCategoryModel( id=3, display_name='Data Security Plan', display_order=3 ), WorkflowSpecCategoryModel( id=4, display_name='Finance', display_order=4 ), WorkflowSpecCategoryModel( id=5, display_name='Notifications', display_order=5 ), WorkflowSpecCategoryModel( id=6, display_name='Status', display_order=6 ), ] db.session.execute("select setval('workflow_spec_category_id_seq',7);") db.session.add_all(categories) db.session.commit() # Pass IRB Review self.create_spec(id="irb_api_personnel", display_name="Personnel", description="TBD", category_id=0, display_order=0) self.create_spec(id="irb_api_details", display_name="Protocol Builder Data", description="TBD", category_id=0, display_order=1) self.create_spec(id="documents_approvals", display_name="Documents & Approvals", description="Status of all approvals and documents required from Protocol Builder", category_id=0, display_order=2) self.create_spec(id="ide_supplement", display_name="IDE Supplement Info", description="Supplemental information for the IDE number entered in Protocol Builder", category_id=0, display_order=3) self.create_spec(id="ind_update", display_name="IND Supplement Info", description="Supplement information for the Investigational New Drug(s) specified in Protocol Builder", category_id=0, display_order=4) # Core Info self.create_spec(id="protocol", display_name="Protocol", description="Upload the Study Protocol here.", category_id=1, display_order=0) self.create_spec(id="non_uva_approval", display_name="Non-UVA Institutional Approval", description="TBD", category_id=1, display_order=1) self.create_spec(id="core_info", display_name="Core Info", description="TBD", category_id=1, display_order=2) # Approvals self.create_spec(id="ids_full_submission", display_name="Investigational Drug Service (IDS) Full Submission", description="TBD", category_id=2, display_order=0) self.create_spec(id="ids_waiver", display_name="Investigational Drug Service (IDS) Waiver", description="TBD", category_id=2, display_order=1) self.create_spec(id="rsc_hire_submission", display_name="RSC/HIRE Submission", description="TBD", category_id=2, display_order=2) self.create_spec(id="rsc_hire_committee", display_name="RSC/HIRE Committee", description="TBD", category_id=2, display_order=3) self.create_spec(id="department_chair_approval", display_name="Department Chair Approval", description="TBD", category_id=2, display_order=4) # Data Security Plan self.create_spec(id="data_security_plan", display_name="Data Security Plan", description="Create and generate Data Security Plan", category_id=3, display_order=0) # Finance self.create_spec(id="sponsor_funding_source", display_name="Sponsor Funding Source", description="TBD", category_id=4, display_order=0) self.create_spec(id="finance", display_name="Finance Data", description="TBD", category_id=4, display_order=1) # Notifications self.create_spec(id="notifications", display_name="Notifications", description="TBD", category_id=5, display_order=0) # Status self.create_spec(id="enrollment_date", display_name="Enrollment Date", description="Study enrollment date", category_id=6, display_order=0) self.create_spec(id="abandoned", display_name="Abandoned", description="Place study into Abandoned status", category_id=6, display_order=1) # Top Level (Master Status) Workflow self.create_spec(id="top_level_workflow", display_name="Top Level Workflow", description="Determines the status of other workflows in a study", category_id=None, master_spec=True) def load_rrt(self): file_path = os.path.join(app.root_path, 'static', 'reference', 'rrt_documents.xlsx') file = open(file_path, "rb") FileService.add_reference_file(FileService.DOCUMENT_LIST, binary_data=file.read(), content_type=CONTENT_TYPES['xls']) file.close() category = WorkflowSpecCategoryModel( id=0, display_name='Research Ramp-up Category', display_order=0 ) db.session.add(category) db.session.commit() self.create_spec(id="rrt_top_level_workflow", display_name="Top Level Workflow", description="Does nothing, we don't use the master workflow here.", category_id=None, master_spec=True) self.create_spec(id="research_rampup", display_name="Research Ramp-up Toolkit", description="Process for creating a new research ramp-up request.", category_id=0, master_spec=False) def load_test_data(self): self.load_reference_documents() category = WorkflowSpecCategoryModel( id=0, display_name='Test Category', display_order=0, admin=False ) db.session.add(category) db.session.commit() self.create_spec(id="empty_workflow", display_name="Top Level Workflow", description="Does nothing, we don't use the master workflow here.", category_id=None, master_spec=True, from_tests = True) self.create_spec(id="random_fact", display_name="Random Fact", description="The workflow for a Random Fact.", category_id=0, display_order=0, master_spec=False, from_tests=True) def create_spec(self, id, display_name="", description="", filepath=None, master_spec=False, category_id=None, display_order=None, from_tests=False, standalone=False, library=False): """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, display_name=display_name, description=description, is_master_spec=master_spec, category_id=category_id, display_order=display_order, standalone=standalone, library=library) db.session.add(spec) db.session.commit() if not filepath and not from_tests: filepath = os.path.join(app.root_path, 'static', 'bpmn', id, "*.*") if not filepath and from_tests: filepath = os.path.join(app.root_path, '..', 'tests', 'data', id, "*.*") files = glob.glob(filepath) for file_path in files: if os.path.isdir(file_path): continue # Don't try to process sub directories 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' file = None 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(DocumentService.DOCUMENT_LIST, binary_data=file.read(), content_type=CONTENT_TYPES['xls']) file.close() file_path = os.path.join(app.root_path, 'static', 'reference', 'investigators.xlsx') file = open(file_path, "rb") FileService.add_reference_file(StudyService.INVESTIGATOR_LIST, binary_data=file.read(), content_type=CONTENT_TYPES['xls']) file.close() def load_default_user(self): ldap_info = LdapModel(uid="dhf8r", email_address="dhf8r@virginia.edu", display_name="Development User") user = UserModel(uid="dhf8r", ldap_info=ldap_info) db.session.add(ldap_info) db.session.add(user) db.session.commit() def ldap(): return "x"; def study_info(i): return {"x":"Y"}; me = ldap() investigators = study_info('investigators') pi = investigators.get('PI', None) is_me_pi = False if pi is not None: hasPI = True if pi['uid'] == me['uid']: is_me_pi = True else: hasPI = False dc = investigators.get('DEPT_CH', None) pcs = {} is_me_pc = False for k in investigators.keys(): if k in ['SC_I','SC_II','IRBC']: investigator = investigators.get(k) if investigator['uid'] != me['uid']: pcs[k] = investigator else: is_me_pc = True is_me_pc_role = investigator['label'] del(investigator) cnt_pcs = len(pcs.keys()) acs = {} is_me_ac = False for k in investigators.keys(): if k == 'AS_C': investigator = investigators.get(k) if investigator['uid'] != me['uid']: acs[k] = investigator else: is_me_ac = True is_me_ac_role = investigator['label'] del investigator cnt_acs = len(acs.keys()) subs = {} is_me_subs = False for k in investigators.keys(): if k[:2] == 'SI': investigator = investigators.get(k) if investigator['uid'] != me['uid']: subs[k] = investigator else: is_me_subs = True del investigator cnt_subs = len(subs.keys()) del investigators