sartography
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cr-connect-workflow
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cr-connect-workflow/tests/base_test.py

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# Set environment variable to testing before loading.
# IMPORTANT - Environment must be loaded before app, models, etc....
import os
from sqlalchemy import Sequence
os.environ["TESTING"] = "true"
import json
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.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()
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.
"""
if not app.config['TESTING']:
raise (Exception("INVALID TEST CONFIGURATION. This is almost always in import order issue."
"The first class to import in each test should be the base_test.py file."))
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.ACTIVE,
'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.ACTIVE,
'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()
cls.ctx.push()
db.create_all()
@classmethod
def tearDownClass(cls):
cls.ctx.pop()
db.drop_all()
pass
def setUp(self):
pass
def tearDown(self):
ExampleDataLoader.clean_db()
session.flush()
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}
else:
uid = user.uid
user_info = {'uid': user.uid}
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, use_crc_data=False, use_rrt_data=False):
"""use_crc_data will cause this to load the mammoth collection of documents
we built up developing crc, use_rrt_data will do the same for hte rrt project,
otherwise it depends on a small setup for running tests."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
if use_crc_data:
ExampleDataLoader().load_all()
elif use_rrt_data:
ExampleDataLoader().load_rrt()
else:
ExampleDataLoader().load_test_data()
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.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
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 session.query(WorkflowSpecModel).filter_by(id=dir_name).first()
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=%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_user(self, uid="dhf8r", email="daniel.h.funk@gmail.com", display_name="Hoopy Frood"):
user = session.query(UserModel).filter(UserModel.uid == uid).first()
if user is None:
user = UserModel(uid=uid, email_address=email, display_name=display_name)
db.session.add(user)
db.session.commit()
return user
def create_study(self, uid="dhf8r", title="Beer conception in the bipedal software engineer"):
study = session.query(StudyModel).first()
if study is None:
user = self.create_user(uid=uid)
study = StudyModel(title=title, protocol_builder_status=ProtocolBuilderStatus.ACTIVE,
user_uid=user.uid)
db.session.add(study)
db.session.commit()
return study
def create_workflow(self, workflow_name, study=None, category_id=None):
db.session.flush()
spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
if spec is None:
spec = self.load_test_spec(workflow_name, category_id=category_id)
if study is None:
study = self.create_study()
workflow_model = StudyService._create_workflow_model(study, spec)
return workflow_model
def create_reference_document(self):
file_path = os.path.join(app.root_path, 'static', 'reference', 'irb_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()
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