Adds user to example data. Requires login before adding/updating a study.
This commit is contained in:
Aaron Louie
parent
27d7afb656
commit
f3068e68db
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@ -12,6 +12,7 @@ from models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
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from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
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from crc.services import protocol_builder
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from crc.services.workflow_processor import WorkflowProcessor
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from services.protocol_builder import ProtocolBuilderService
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@auth.login_required
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@ -19,38 +20,24 @@ def all_studies():
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user = g.user
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""":type: crc.models.user.UserModel"""
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# Get studies matching this user from Protocol Builder
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pb_studies: List[ProtocolBuilderStudy] = protocol_builder.get_studies(user.uid)
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schema = StudyModelSchema(many=True)
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update_from_protocol_builder()
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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db_study_ids = list(map(lambda s: s.id, db_studies))
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for pb_study in pb_studies:
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if pb_study['HSRNUMBER'] not in db_study_ids:
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status = ProtocolBuilderStatus.complete._value_ if pb_study['Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
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add_study({
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'id': pb_study['HSRNUMBER'],
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'title': pb_study['TITLE'],
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'protocol_builder_status': status,
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'user_uid': pb_study['NETBADGEID'],
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'last_updated': pb_study['DATE_MODIFIED']
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})
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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return schema.dump(db_studies)
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return StudyModelSchema(many=True).dump(db_studies)
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@auth.login_required
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def add_study(body):
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study = StudyModelSchema().load(body, session=session)
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session.add(study)
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session.commit()
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# FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all.
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for spec in session.query(WorkflowSpecModel).all():
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WorkflowProcessor.create(study.id, spec.id)
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return StudyModelSchema().dump(study)
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@auth.login_required
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def update_study(study_id, body):
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if study_id is None:
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error = ApiError('unknown_study', 'Please provide a valid Study ID.')
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@ -68,6 +55,7 @@ def update_study(study_id, body):
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return StudyModelSchema().dump(study)
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@auth.login_required
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def get_study(study_id):
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study = session.query(StudyModel).filter_by(id=study_id).first()
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schema = StudyModelSchema()
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@ -76,12 +64,34 @@ def get_study(study_id):
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return schema.dump(study)
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@auth.login_required
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def update_from_protocol_builder():
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"""Call the """
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"""Updates the list of known studies for a given user based on data received from
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the protocol builder."""
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user = g.user
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""":type: crc.models.user.UserModel"""
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# Get studies matching this user from Protocol Builder
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pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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db_study_ids = list(map(lambda s: s.id, db_studies))
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for pb_study in pb_studies:
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if pb_study['HSRNUMBER'] not in db_study_ids:
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status = ProtocolBuilderStatus.complete._value_ if pb_study['Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
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add_study({
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'id': pb_study['HSRNUMBER'],
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'title': pb_study['TITLE'],
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'protocol_builder_status': status,
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'user_uid': pb_study['NETBADGEID'],
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'last_updated': pb_study['DATE_MODIFIED']
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})
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def post_update_study_from_protocol_builder(study_id):
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"""This will update the list of known studies based on data received from
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"""Update a single study based on data received from
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the protocol builder."""
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# todo: Actually get data from an external service here
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@ -1,16 +1,31 @@
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import datetime
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import glob
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import os
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import xml.etree.ElementTree as ElementTree
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from crc import app, db, session
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from crc.models.file import FileType, FileModel, FileDataModel
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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
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import xml.etree.ElementTree as ElementTree
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from crc.services.workflow_processor import WorkflowProcessor
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class ExampleDataLoader:
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def make_data(self):
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users = [
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UserModel(
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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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StudyModel(
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id=1,
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@ -19,7 +34,8 @@ class ExampleDataLoader:
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protocol_builder_status='in_process',
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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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ind_number='1234',
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user_uid='dhf8r'
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),
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StudyModel(
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id=2,
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@ -28,7 +44,8 @@ class ExampleDataLoader:
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protocol_builder_status='in_process',
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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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ind_number='5678',
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user_uid='dhf8r'
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),
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]
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@ -69,11 +86,11 @@ class ExampleDataLoader:
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description='How to take different paths based on input.')
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workflow_specifications += \
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self.create_spec(id="docx",
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name="docx",
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display_name="Form with document generation",
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description='the name says it all')
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name="docx",
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display_name="Form with document generation",
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description='the name says it all')
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all_data = studies + workflow_specifications
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all_data = users + studies + workflow_specifications
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return all_data
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def create_spec(self, id, name, display_name="", description="", filepath=None):
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@ -112,7 +129,7 @@ class ExampleDataLoader:
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try:
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file = open(file_path, "rb")
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data = file.read()
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if(is_primary):
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if (is_primary):
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bpmn: ElementTree.Element = ElementTree.fromstring(data)
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spec.primary_process_id = WorkflowProcessor.get_process_id(bpmn)
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print("Locating Process Id for " + filename + " " + spec.primary_process_id)
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@ -121,7 +138,6 @@ class ExampleDataLoader:
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file.close()
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return models
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@staticmethod
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def clean_db():
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session.flush() # Clear out any transactions before deleting it all to avoid spurious errors.
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@ -3,11 +3,13 @@
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import json
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import os
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import unittest
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import urllib.parse
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os.environ["TESTING"] = "true"
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from crc.models.file import FileModel, FileDataModel
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from crc.models.workflow import WorkflowSpecModel
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os.environ["TESTING"] = "true"
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from crc.models.user import UserModel
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from crc import app, db, session
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from example_data import ExampleDataLoader
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@ -18,14 +20,13 @@ from example_data import ExampleDataLoader
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# logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
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# Great class to inherit from, as it sets up and tears down
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# classes efficiently when we have a database in place.
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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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auths = {}
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test_uid = "dhf8r"
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@classmethod
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def setUpClass(cls):
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@ -48,6 +49,25 @@ class BaseTest(unittest.TestCase):
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self.ctx.pop()
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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, 'first_name': 'Daniel', 'last_name': 'Funk',
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'email_address': 'dhf8r@virginia.edu'}
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else:
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uid = user.uid
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user_info = {'uid': user.uid, 'first_name': user.first_name, 'last_name': user.last_name,
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'email_address': user.email_address}
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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/sso_backdoor%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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return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
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def load_example_data(self):
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from example_data import ExampleDataLoader
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ExampleDataLoader.clean_db()
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@ -66,7 +86,8 @@ class BaseTest(unittest.TestCase):
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self.assertIsNotNone(file_data)
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self.assertGreater(len(file_data), 0)
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def load_test_spec(self, dir_name):
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@staticmethod
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def load_test_spec(dir_name):
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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
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@ -81,7 +102,8 @@ class BaseTest(unittest.TestCase):
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session.flush()
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return spec
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def protocol_builder_response(self, file_name):
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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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@ -102,3 +124,16 @@ class BaseTest(unittest.TestCase):
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"Incorrect Valid Response:" + rv.status + ".")
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if code != 0:
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self.assertEqual(code, rv.status_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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@ -1,31 +1,9 @@
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import urllib.parse
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from crc import db
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from crc.models.user import UserModel
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from tests.base_test import BaseTest
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class TestAuthentication(BaseTest):
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test_uid = "dhf8r"
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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, 'first_name': 'Daniel', 'last_name': 'Funk',
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'email_address': 'dhf8r@virginia.edu'}
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else:
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uid = user.uid
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user_info = {'uid': user.uid, 'first_name': user.first_name, 'last_name': user.last_name,
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'email_address': user.email_address}
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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/sso_backdoor%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 = UserModel.query.filter_by(uid=uid).first()
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self.assertIsNotNone(user_model.display_name)
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return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
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def test_auth_token(self):
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self.load_example_data()
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@ -35,12 +13,13 @@ class TestAuthentication(BaseTest):
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self.assertEqual("dhf8r", user.decode_auth_token(auth_token))
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def test_auth_creates_user(self):
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new_uid = 'czn1z';
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self.load_example_data()
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user = db.session.query(UserModel).filter(UserModel.uid == self.test_uid).first()
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user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
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self.assertIsNone(user)
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user_info = {'uid': self.test_uid, 'first_name': 'Daniel', 'last_name': 'Funk',
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'email_address': 'dhf8r@virginia.edu'}
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user_info = {'uid': new_uid, 'first_name': 'Cordi', 'last_name': 'Nator',
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'email_address': 'czn1z@virginia.edu'}
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redirect_url = 'http://worlds.best.website/admin'
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query_string = self.user_info_to_query_string(user_info, redirect_url)
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url = '/v1.0/sso_backdoor%s' % query_string
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@ -48,7 +27,7 @@ class TestAuthentication(BaseTest):
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self.assertTrue(rv_1.status_code == 302)
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self.assertTrue(str.startswith(rv_1.location, redirect_url))
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user = db.session.query(UserModel).filter(UserModel.uid == self.test_uid).first()
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user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
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self.assertIsNotNone(user)
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self.assertIsNotNone(user.display_name)
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self.assertIsNotNone(user.email_address)
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@ -69,15 +48,3 @@ class TestAuthentication(BaseTest):
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user = UserModel(uid="ajl2j", first_name='Aaron', last_name='Louie', email_address='ajl2j@virginia.edu')
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rv = self.app.get('/v1.0/user', headers=self.logged_in_headers(user, redirect_url='http://omg.edu/lolwut'))
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self.assert_success(rv)
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def user_info_to_query_string(self, 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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@ -1,8 +1,7 @@
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import json
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from datetime import datetime, tzinfo, timezone
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from datetime import datetime, timezone
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from crc import session
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from crc.models.file import FileModel
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from crc.models.study import StudyModel, StudyModelSchema
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from models.protocol_builder import ProtocolBuilderStatus
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from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowStatus, \
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@ -21,7 +20,8 @@ class TestStudyApi(BaseTest):
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self.load_example_data()
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study = {
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"id": 12345,
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"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents for Interstellar Spacecraft",
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"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
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"for Interstellar Spacecraft",
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"last_updated": datetime.now(tz=timezone.utc),
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"protocol_builder_status": ProtocolBuilderStatus.in_process,
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"primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
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@ -30,6 +30,7 @@ class TestStudyApi(BaseTest):
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}
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rv = self.app.post('/v1.0/study',
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content_type="application/json",
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headers=self.logged_in_headers(),
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data=json.dumps(StudyModelSchema().dump(study)))
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self.assert_success(rv)
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db_study = session.query(StudyModel).filter_by(id=12345).first()
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@ -41,16 +42,15 @@ class TestStudyApi(BaseTest):
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self.assertEqual(study["sponsor"], db_study.sponsor)
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self.assertEqual(study["ind_number"], db_study.ind_number)
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def test_update_study(self):
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self.load_example_data()
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study: StudyModel = session.query(StudyModel).first()
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study.title = "Pilot Study of Fjord Placement for Single Fraction Outcomes to Cortisol Susceptibility"
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study.protocol_builder_status = ProtocolBuilderStatus.complete
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rv = self.app.put('/v1.0/study/%i' % study.id,
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content_type="application/json",
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data=json.dumps(StudyModelSchema().dump(study)))
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content_type="application/json",
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headers=self.logged_in_headers(),
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data=json.dumps(StudyModelSchema().dump(study)))
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self.assert_success(rv)
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db_study = session.query(StudyModel).filter_by(id=study.id).first()
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self.assertIsNotNone(db_study)
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@ -62,6 +62,7 @@ class TestStudyApi(BaseTest):
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study = session.query(StudyModel).first()
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rv = self.app.get('/v1.0/study/%i' % study.id,
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follow_redirects=True,
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headers=self.logged_in_headers(),
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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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@ -80,7 +81,9 @@ class TestStudyApi(BaseTest):
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study = session.query(StudyModel).first()
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self.assertEqual(0, session.query(WorkflowModel).count())
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spec = session.query(WorkflowSpecModel).first()
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rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
|
||||
rv = self.app.post('/v1.0/study/%i/workflows' % study.id,
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(),
|
||||
data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
|
||||
self.assert_success(rv)
|
||||
self.assertEqual(1, session.query(WorkflowModel).count())
|
||||
|
|
@ -98,7 +101,9 @@ class TestStudyApi(BaseTest):
|
|||
self.load_example_data()
|
||||
study = session.query(StudyModel).first()
|
||||
spec = session.query(WorkflowSpecModel).first()
|
||||
rv = self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
|
||||
rv = self.app.post('/v1.0/study/%i/workflows' % study.id,
|
||||
content_type="application/json",
|
||||
headers=self.logged_in_headers(),
|
||||
data=json.dumps(WorkflowSpecModelSchema().dump(spec)))
|
||||
self.assertEqual(1, session.query(WorkflowModel).count())
|
||||
json_data = json.loads(rv.get_data(as_text=True))
|
||||
|
|
|
|||
Loading…
Reference in New Issue