# Set environment variable to testing before loading. # IMPORTANT - Environment must be loaded before app, models, etc.... import json import os import unittest import urllib.parse import datetime from crc.models.protocol_builder import ProtocolBuilderStatus from crc.models.study import StudyModel from crc.services.file_service import FileService from crc.services.study_service import StudyService from crc.services.workflow_processor import WorkflowProcessor os.environ["TESTING"] = "true" from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel from crc.models.user import UserModel from crc import app, db, session from example_data import ExampleDataLoader # UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES # import logging # logging.basicConfig() # logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO) class BaseTest(unittest.TestCase): """ Great class to inherit from, as it sets up and tears down classes efficiently when we have a database in place. """ auths = {} test_uid = "dhf8r" users = [ { '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' } ] studies = [ { 'id':0, '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' }, { 'id':1, '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' } ] @classmethod def setUpClass(cls): app.config.from_object('config.testing') cls.ctx = app.test_request_context() cls.app = app.test_client() db.create_all() @classmethod def tearDownClass(cls): db.drop_all() session.remove() pass def setUp(self): self.ctx.push() def tearDown(self): ExampleDataLoader.clean_db() # This does not seem to work, some colision of sessions. self.ctx.pop() self.auths = {} def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'): if user is None: uid = self.test_uid user_info = {'uid': self.test_uid, 'first_name': 'Daniel', 'last_name': 'Funk', 'email_address': 'dhf8r@virginia.edu'} else: uid = user.uid user_info = {'uid': user.uid, 'first_name': user.first_name, 'last_name': user.last_name, 'email_address': user.email_address} query_string = self.user_info_to_query_string(user_info, redirect_url) rv = self.app.get("/v1.0/sso_backdoor%s" % query_string, follow_redirects=False) self.assertTrue(rv.status_code == 302) self.assertTrue(str.startswith(rv.location, redirect_url)) user_model = session.query(UserModel).filter_by(uid=uid).first() self.assertIsNotNone(user_model.display_name) return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode()) def load_example_data(self): from example_data import ExampleDataLoader ExampleDataLoader.clean_db() ExampleDataLoader().load_all() for user_json in self.users: db.session.add(UserModel(**user_json)) db.session.commit() for study_json in self.studies: study_model = StudyModel(**study_json) db.session.add(study_model) StudyService._add_all_workflow_specs_to_study(study_model) db.session.commit() db.session.flush() specs = session.query(WorkflowSpecModel).all() self.assertIsNotNone(specs) for spec in specs: files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all() self.assertIsNotNone(files) self.assertGreater(len(files), 0) for spec in specs: files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all() self.assertIsNotNone(files) self.assertGreater(len(files), 0) for file in files: file_data = session.query(FileDataModel).filter_by(file_model_id=file.id).all() self.assertIsNotNone(file_data) self.assertGreater(len(file_data), 0) @staticmethod def load_test_spec(dir_name, master_spec=False, category_id=None): """Loads a spec into the database based on a directory in /tests/data""" if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0: return filepath = os.path.join(app.root_path, '..', 'tests', 'data', dir_name, "*") return ExampleDataLoader().create_spec(id=dir_name, name=dir_name, filepath=filepath, master_spec=master_spec, category_id=category_id) @staticmethod def protocol_builder_response(file_name): filepath = os.path.join(app.root_path, '..', 'tests', 'data', 'pb_responses', file_name) with open(filepath, 'r') as myfile: data = myfile.read() return data def assert_success(self, rv, msg=""): try: data = json.loads(rv.get_data(as_text=True)) self.assertTrue(200 <= rv.status_code < 300, "BAD Response: %i. \n %s" % (rv.status_code, json.dumps(data)) + ". " + msg) except: self.assertTrue(200 <= rv.status_code < 300, "BAD Response: %i." % rv.status_code + ". " + msg) def assert_failure(self, rv, status_code=0, error_code=""): self.assertFalse(200 <= rv.status_code < 300, "Incorrect Valid Response:" + rv.status + ".") if status_code != 0: self.assertEqual(status_code, rv.status_code) if error_code != "": data = json.loads(rv.get_data(as_text=True)) self.assertEqual(error_code, data["code"]) @staticmethod def user_info_to_query_string(user_info, redirect_url): query_string_list = [] items = user_info.items() for key, value in items: query_string_list.append('%s=%s' % (key, urllib.parse.quote(value))) query_string_list.append('redirect_url=%s' % redirect_url) return '?%s' % '&'.join(query_string_list) def replace_file(self, name, file_path): """Replaces a stored file with the given name with the contents of the file at the given path.""" file_service = FileService() file = open(file_path, "rb") data = file.read() file_model = db.session.query(FileModel).filter(FileModel.name == name).first() noise, file_extension = os.path.splitext(file_path) content_type = CONTENT_TYPES[file_extension[1:]] file_service.update_file(file_model, data, content_type) def create_workflow(self, workflow_name, study=None, category_id=None): if study == None: study = session.query(StudyModel).first() spec = self.load_test_spec(workflow_name, category_id=category_id) workflow_model = StudyService._create_workflow_model(study, spec) #processor = WorkflowProcessor(workflow_model) #workflow = session.query(WorkflowModel).filter_by(study_id=study.id, workflow_spec_id=workflow_name).first() return workflow_model def create_reference_document(self): file_path = os.path.join(app.root_path, '..', 'tests', 'data', '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()