400 lines
17 KiB
Python
400 lines
17 KiB
Python
# Set environment variable to testing before loading.
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# IMPORTANT - Environment must be loaded before app, models, etc....
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import os
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os.environ["TESTING"] = "true"
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import json
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import unittest
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import urllib.parse
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import datetime
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from flask import g
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from sqlalchemy import Sequence
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from crc import app, db, session
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from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
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from crc.models.approval import ApprovalModel, ApprovalStatus
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from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
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from crc.models.protocol_builder import ProtocolBuilderStatus
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from crc.models.task_event import TaskEventModel
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from crc.models.study import StudyModel
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from crc.models.user import UserModel
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from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
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from crc.services.file_service import FileService
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from crc.services.study_service import StudyService
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from crc.services.workflow_service import WorkflowService
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from example_data import ExampleDataLoader
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#UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
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import logging
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logging.basicConfig()
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class BaseTest(unittest.TestCase):
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""" Great class to inherit from, as it sets up and tears down classes
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efficiently when we have a database in place.
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"""
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if not app.config['TESTING']:
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raise (Exception("INVALID TEST CONFIGURATION. This is almost always in import order issue."
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"The first class to import in each test should be the base_test.py file."))
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auths = {}
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test_uid = "dhf8r"
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users = [
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{
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'uid':'dhf8r',
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'email_address':'dhf8r@virginia.EDU',
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'display_name':'Daniel Harold Funk',
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'affiliation':'staff@virginia.edu;member@virginia.edu',
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'eppn':'dhf8r@virginia.edu',
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'first_name':'Daniel',
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'last_name':'Funk',
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'title':'SOFTWARE ENGINEER V'
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}
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]
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studies = [
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{
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'id':0,
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'title':'The impact of fried pickles on beer consumption in bipedal software developers.',
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'last_updated':datetime.datetime.now(),
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'protocol_builder_status':ProtocolBuilderStatus.active,
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'primary_investigator_id':'dhf8r',
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'sponsor':'Sartography Pharmaceuticals',
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'ind_number':'1234',
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'user_uid':'dhf8r'
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},
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{
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'id':1,
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'title':'Requirement of hippocampal neurogenesis for the behavioral effects of soft pretzels',
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'last_updated':datetime.datetime.now(),
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'protocol_builder_status':ProtocolBuilderStatus.active,
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'primary_investigator_id':'dhf8r',
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'sponsor':'Makerspace & Co.',
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'ind_number':'5678',
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'user_uid':'dhf8r'
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}
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]
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@classmethod
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def setUpClass(cls):
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app.config.from_object('config.testing')
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cls.ctx = app.test_request_context()
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cls.app = app.test_client()
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cls.ctx.push()
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db.create_all()
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@classmethod
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def tearDownClass(cls):
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cls.ctx.pop()
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db.drop_all()
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pass
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def setUp(self):
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pass
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def tearDown(self):
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ExampleDataLoader.clean_db()
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g.user = None
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self.auths = {}
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def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
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if user is None:
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uid = self.test_uid
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user_info = {'uid': self.test_uid}
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else:
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uid = user.uid
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user_info = {'uid': user.uid}
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query_string = self.user_info_to_query_string(user_info, redirect_url)
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rv = self.app.get("/v1.0/login%s" % query_string, follow_redirects=False)
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self.assertTrue(rv.status_code == 302)
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self.assertTrue(str.startswith(rv.location, redirect_url))
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user_model = session.query(UserModel).filter_by(uid=uid).first()
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self.assertIsNotNone(user_model.display_name)
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self.assertEqual(user_model.uid, uid)
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self.assertTrue('user' in g, 'User should be in Flask globals')
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self.assertEqual(uid, g.user.uid, 'Logged in user should match given user uid')
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return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
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def load_example_data(self, use_crc_data=False, use_rrt_data=False):
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"""use_crc_data will cause this to load the mammoth collection of documents
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we built up developing crc, use_rrt_data will do the same for hte rrt project,
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otherwise it depends on a small setup for running tests."""
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from example_data import ExampleDataLoader
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ExampleDataLoader.clean_db()
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if use_crc_data:
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ExampleDataLoader().load_all()
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elif use_rrt_data:
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ExampleDataLoader().load_rrt()
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else:
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ExampleDataLoader().load_test_data()
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for user_json in self.users:
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db.session.add(UserModel(**user_json))
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db.session.commit()
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for study_json in self.studies:
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study_model = StudyModel(**study_json)
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db.session.add(study_model)
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StudyService._add_all_workflow_specs_to_study(study_model)
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db.session.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
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db.session.commit()
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db.session.flush()
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specs = session.query(WorkflowSpecModel).all()
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self.assertIsNotNone(specs)
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for spec in specs:
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files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all()
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self.assertIsNotNone(files)
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self.assertGreater(len(files), 0)
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for spec in specs:
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files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all()
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self.assertIsNotNone(files)
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self.assertGreater(len(files), 0)
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for file in files:
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file_data = session.query(FileDataModel).filter_by(file_model_id=file.id).all()
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self.assertIsNotNone(file_data)
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self.assertGreater(len(file_data), 0)
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@staticmethod
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def load_test_spec(dir_name, display_name=None, master_spec=False, category_id=None):
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"""Loads a spec into the database based on a directory in /tests/data"""
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if category_id is None:
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category = WorkflowSpecCategoryModel(name="test", display_name="Test Workflows", display_order=0)
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db.session.add(category)
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db.session.commit()
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category_id = category.id
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if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
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return session.query(WorkflowSpecModel).filter_by(id=dir_name).first()
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filepath = os.path.join(app.root_path, '..', 'tests', 'data', dir_name, "*")
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if display_name is None:
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display_name = dir_name
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return ExampleDataLoader().create_spec(id=dir_name, name=dir_name, filepath=filepath, master_spec=master_spec,
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display_name=display_name, category_id=category_id)
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@staticmethod
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def protocol_builder_response(file_name):
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filepath = os.path.join(app.root_path, '..', 'tests', 'data', 'pb_responses', file_name)
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with open(filepath, 'r') as myfile:
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data = myfile.read()
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return data
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def assert_success(self, rv, msg=""):
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try:
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data = json.loads(rv.get_data(as_text=True))
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self.assertTrue(200 <= rv.status_code < 300,
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"BAD Response: %i. \n %s" %
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(rv.status_code, json.dumps(data)) + ". " + msg)
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except:
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self.assertTrue(200 <= rv.status_code < 300,
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"BAD Response: %i." % rv.status_code + ". " + msg)
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def assert_failure(self, rv, status_code=0, error_code=""):
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self.assertFalse(200 <= rv.status_code < 300,
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"Incorrect Valid Response:" + rv.status + ".")
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if status_code != 0:
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self.assertEqual(status_code, rv.status_code)
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if error_code != "":
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data = json.loads(rv.get_data(as_text=True))
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self.assertEqual(error_code, data["code"])
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@staticmethod
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def user_info_to_query_string(user_info, redirect_url):
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query_string_list = []
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items = user_info.items()
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for key, value in items:
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query_string_list.append('%s=%s' % (key, urllib.parse.quote(value)))
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query_string_list.append('redirect_url=%s' % redirect_url)
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return '?%s' % '&'.join(query_string_list)
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def replace_file(self, name, file_path):
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"""Replaces a stored file with the given name with the contents of the file at the given path."""
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file_service = FileService()
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file = open(file_path, "rb")
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data = file.read()
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file_model = db.session.query(FileModel).filter(FileModel.name == name).first()
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noise, file_extension = os.path.splitext(file_path)
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content_type = CONTENT_TYPES[file_extension[1:]]
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file_service.update_file(file_model, data, content_type)
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def create_user(self, uid="dhf8r", email="daniel.h.funk@gmail.com", display_name="Hoopy Frood"):
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user = session.query(UserModel).filter(UserModel.uid == uid).first()
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if user is None:
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user = UserModel(uid=uid, email_address=email, display_name=display_name)
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db.session.add(user)
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db.session.commit()
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return user
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def create_study(self, uid="dhf8r", title="Beer consumption in the bipedal software engineer", primary_investigator_id="lb3dp"):
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study = session.query(StudyModel).filter_by(user_uid=uid).filter_by(title=title).first()
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if study is None:
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user = self.create_user(uid=uid)
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study = StudyModel(title=title, protocol_builder_status=ProtocolBuilderStatus.active,
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user_uid=user.uid, primary_investigator_id=primary_investigator_id)
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db.session.add(study)
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db.session.commit()
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return study
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def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
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workflow_spec_name="random_fact"):
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study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
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workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
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approvals = []
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for i in range(len(approver_uids)):
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approvals.append(self.create_approval(
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study=study,
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workflow=workflow,
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approver_uid=approver_uids[i],
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status=statuses[i],
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version=1
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))
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full_study = {
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'study': study,
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'workflow': workflow,
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'approvals': approvals,
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}
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return full_study
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def create_workflow(self, workflow_name, display_name=None, study=None, category_id=None, as_user="dhf8r"):
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db.session.flush()
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spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
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if spec is None:
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if display_name is None:
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display_name = workflow_name
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spec = self.load_test_spec(workflow_name, display_name, category_id=category_id)
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if study is None:
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study = self.create_study(uid=as_user)
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workflow_model = StudyService._create_workflow_model(study, spec)
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return workflow_model
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def create_reference_document(self):
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file_path = os.path.join(app.root_path, 'static', 'reference', 'irb_documents.xlsx')
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file = open(file_path, "rb")
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FileService.add_reference_file(FileService.DOCUMENT_LIST,
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binary_data=file.read(),
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content_type=CONTENT_TYPES['xls'])
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file.close()
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def create_approval(
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self,
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study=None,
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workflow=None,
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approver_uid=None,
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status=None,
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version=None,
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):
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study = study or self.create_study()
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workflow = workflow or self.create_workflow()
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approver_uid = approver_uid or self.test_uid
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status = status or ApprovalStatus.PENDING.value
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version = version or 1
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approval = ApprovalModel(study=study, workflow=workflow, approver_uid=approver_uid, status=status, version=version)
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db.session.add(approval)
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db.session.commit()
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return approval
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def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False, do_engine_steps=True, user_uid="dhf8r"):
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user = session.query(UserModel).filter_by(uid=user_uid).first()
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self.assertIsNotNone(user)
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rv = self.app.get(f'/v1.0/workflow/{workflow.id}'
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f'?soft_reset={str(soft_reset)}'
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f'&hard_reset={str(hard_reset)}'
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f'&do_engine_steps={str(do_engine_steps)}',
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headers=self.logged_in_headers(user),
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content_type="application/json")
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self.assert_success(rv)
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json_data = json.loads(rv.get_data(as_text=True))
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workflow_api = WorkflowApiSchema().load(json_data)
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self.assertEqual(workflow.workflow_spec_id, workflow_api.workflow_spec_id)
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return workflow_api
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def complete_form(self, workflow_in, task_in, dict_data, error_code=None, terminate_loop=None, user_uid="dhf8r"):
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prev_completed_task_count = workflow_in.completed_tasks
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if isinstance(task_in, dict):
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task_id = task_in["id"]
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else:
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task_id = task_in.id
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user = session.query(UserModel).filter_by(uid=user_uid).first()
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self.assertIsNotNone(user)
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if terminate_loop:
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rv = self.app.put('/v1.0/workflow/%i/task/%s/data?terminate_loop=true' % (workflow_in.id, task_id),
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headers=self.logged_in_headers(user=user),
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content_type="application/json",
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data=json.dumps(dict_data))
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else:
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rv = self.app.put('/v1.0/workflow/%i/task/%s/data' % (workflow_in.id, task_id),
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headers=self.logged_in_headers(user=user),
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content_type="application/json",
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data=json.dumps(dict_data))
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if error_code:
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self.assert_failure(rv, error_code=error_code)
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return
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self.assert_success(rv)
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json_data = json.loads(rv.get_data(as_text=True))
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# Assure task events are updated on the model
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workflow = WorkflowApiSchema().load(json_data)
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# The total number of tasks may change over time, as users move through gateways
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# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
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self.assertIsNotNone(workflow.total_tasks)
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# presumably, we also need to deal with sequential items here too . .
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if not task_in.multi_instance_type == 'looping':
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self.assertEqual(prev_completed_task_count + 1, workflow.completed_tasks)
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# Assure a record exists in the Task Events
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task_events = session.query(TaskEventModel) \
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.filter_by(workflow_id=workflow.id) \
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.filter_by(task_id=task_id) \
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.filter_by(action=WorkflowService.TASK_ACTION_COMPLETE) \
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.order_by(TaskEventModel.date.desc()).all()
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self.assertGreater(len(task_events), 0)
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event = task_events[0]
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self.assertIsNotNone(event.study_id)
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self.assertEqual(user_uid, event.user_uid)
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self.assertEqual(workflow.id, event.workflow_id)
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self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)
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self.assertEqual(workflow.spec_version, event.spec_version)
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self.assertEqual(WorkflowService.TASK_ACTION_COMPLETE, event.action)
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self.assertEqual(task_in.id, task_id)
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self.assertEqual(task_in.name, event.task_name)
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self.assertEqual(task_in.title, event.task_title)
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self.assertEqual(task_in.type, event.task_type)
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if not task_in.multi_instance_type == 'looping':
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self.assertEqual("COMPLETED", event.task_state)
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# Not sure what voodoo is happening inside of marshmallow to get me in this state.
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if isinstance(task_in.multi_instance_type, MultiInstanceType):
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self.assertEqual(task_in.multi_instance_type.value, event.mi_type)
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else:
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self.assertEqual(task_in.multi_instance_type, event.mi_type)
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self.assertEqual(task_in.multi_instance_count, event.mi_count)
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if task_in.multi_instance_type == 'looping' and not terminate_loop:
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self.assertEqual(task_in.multi_instance_index+1, event.mi_index)
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else:
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self.assertEqual(task_in.multi_instance_index, event.mi_index)
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self.assertEqual(task_in.process_name, event.process_name)
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self.assertIsNotNone(event.date)
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workflow = WorkflowApiSchema().load(json_data)
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return workflow
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