mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-22 20:58:28 +00:00
d85ca1ce51
Add the lane information to the Task model. Drop the foreign key constraint on the user_uid in the task log, as we might create tasks for users before they ever log into the system. Add a new endpoint to the API called task events. It should be possible to query this and get a list of all tasks that need a users attention. The task events returned include detailed information about the workflow and study as sub-models Rename all the actions in event log to things that are easier to pass over the api as arguments, make this backwards compatible, updating existing names in the database via the migration. Throughly test the navigation and task details as control of the workflow is passed between two lanes.
390 lines
16 KiB
Python
390 lines
16 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
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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, 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 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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return ExampleDataLoader().create_spec(id=dir_name, name=dir_name, filepath=filepath, master_spec=master_spec,
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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, 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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spec = self.load_test_spec(workflow_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, 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('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' %
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(workflow.id, str(soft_reset), str(hard_reset)),
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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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