sartography
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cr-connect-workflow
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Merge branch 'rrt/testing' into rrt/staging

This commit is contained in:
Aaron Louie 2020-06-02 08:50:27 -04:00
parent d661eca34f 211797b843
commit 761d70eaf3
13 changed files with 160 additions and 85 deletions
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1
Pipfile
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@ -38,6 +38,7 @@ xlrd = "*"
ldap3 = "*"
gunicorn = "*"
werkzeug = "*"
sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
[requires]
python_version = "3.7"

49
Pipfile.lock generated
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@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
"sha256": "979f996148ee181e3e0af2a3777aa1d00d0fd5d943d49df65963e694b8a88871"
"sha256": "54d9d51360f54762138a3acc7696badd1d711e7b1dde9e2d82aa706e40c17102"
},
"pipfile-spec": 6,
"requires": {
@ -32,10 +32,10 @@
},
"amqp": {
"hashes": [
"sha256:6e649ca13a7df3faacdc8bbb280aa9a6602d22fd9d545336077e573a1f4ff3b8",
"sha256:77f1aef9410698d20eaeac5b73a87817365f457a507d82edf292e12cbb83b08d"
"sha256:24dbaff8ce4f30566bb88976b398e8c4e77637171af3af6f1b9650f48890e60b",
"sha256:bb68f8d2bced8f93ccfd07d96c689b716b3227720add971be980accfc2952139"
],
"version": "==2.5.2"
"version": "==2.6.0"
},
"aniso8601": {
"hashes": [
@ -96,12 +96,18 @@
],
"version": "==3.6.3.0"
},
"blinker": {
"hashes": [
"sha256:471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6"
],
"version": "==1.4"
},
"celery": {
"hashes": [
"sha256:108a0bf9018a871620936c33a3ee9f6336a89f8ef0a0f567a9001f4aa361415f",
"sha256:5b4b37e276033fe47575107a2775469f0b721646a08c96ec2c61531e4fe45f2a"
"sha256:5147662e23dc6bc39c17a2cbc9a148debe08ecfb128b0eded14a0d9c81fc5742",
"sha256:df2937b7536a2a9b18024776a3a46fd281721813636c03a5177fa02fe66078f6"
],
"version": "==4.4.2"
"version": "==4.4.3"
},
"certifi": {
"hashes": [
@ -381,10 +387,10 @@
},
"kombu": {
"hashes": [
"sha256:2d1cda774126a044d91a7ff5fa6d09edf99f46924ab332a810760fe6740e9b76",
"sha256:598e7e749d6ab54f646b74b2d2df67755dee13894f73ab02a2a9feb8870c7cb2"
"sha256:ab0afaa5388dd2979cbc439d3623b86a4f7a58d41f621096bef7767c37bc2505",
"sha256:aece08f48706743aaa1b9d607fee300559481eafcc5ee56451aa0ef867a3be07"
],
"version": "==4.6.8"
"version": "==4.6.9"
},
"ldap3": {
"hashes": [
@ -704,6 +710,17 @@
"index": "pypi",
"version": "==2.23.0"
},
"sentry-sdk": {
"extras": [
"flask"
],
"hashes": [
"sha256:0e5e947d0f7a969314aa23669a94a9712be5a688ff069ff7b9fc36c66adc160c",
"sha256:799a8bf76b012e3030a881be00e97bc0b922ce35dde699c6537122b751d80e2c"
],
"index": "pypi",
"version": "==0.14.4"
},
"six": {
"hashes": [
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
@ -838,10 +855,10 @@
},
"waitress": {
"hashes": [
"sha256:045b3efc3d97c93362173ab1dfc159b52cfa22b46c3334ffc805dbdbf0e4309e",
"sha256:77ff3f3226931a1d7d8624c5371de07c8e90c7e5d80c5cc660d72659aaf23f38"
"sha256:1bb436508a7487ac6cb097ae7a7fe5413aefca610550baf58f0940e51ecfb261",
"sha256:3d633e78149eb83b60a07dfabb35579c29aac2d24bb803c18b26fb2ab1a584db"
],
"version": "==1.4.3"
"version": "==1.4.4"
},
"webob": {
"hashes": [
@ -966,10 +983,10 @@
},
"wcwidth": {
"hashes": [
"sha256:cafe2186b3c009a04067022ce1dcd79cb38d8d65ee4f4791b8888d6599d1bbe1",
"sha256:ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1"
"sha256:3de2e41158cb650b91f9654cbf9a3e053cee0719c9df4ddc11e4b568669e9829",
"sha256:b651b6b081476420e4e9ae61239ac4c1b49d0c5ace42b2e81dc2ff49ed50c566"
],
"version": "==0.1.9"
"version": "==0.2.2"
},
"zipp": {
"hashes": [

3
config/default.py
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@ -13,6 +13,9 @@ DEVELOPMENT = environ.get('DEVELOPMENT', default="true") == "true"
TESTING = environ.get('TESTING', default="false") == "true"
PRODUCTION = (environ.get('PRODUCTION', default="false") == "true") or (not DEVELOPMENT and not TESTING)
# Sentry flag
ENABLE_SENTRY = environ.get('ENABLE_SENTRY', default="false") == "true"
# Add trailing slash to base path
APPLICATION_ROOT = re.sub(r'//', '/', '/%s/' % environ.get('APPLICATION_ROOT', default="/").strip('/'))

8
crc/__init__.py
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@ -1,11 +1,13 @@
import logging
import os
import sentry_sdk
import connexion
from flask_cors import CORS
from flask_marshmallow import Marshmallow
from flask_migrate import Migrate
from flask_sqlalchemy import SQLAlchemy
from sentry_sdk.integrations.flask import FlaskIntegration
logging.basicConfig(level=logging.INFO)
@ -40,6 +42,12 @@ connexion_app.add_api('api.yml', base_path='/v1.0')
origins_re = [r"^https?:\/\/%s(.*)" % o.replace('.', '\.') for o in app.config['CORS_ALLOW_ORIGINS']]
cors = CORS(connexion_app.app, origins=origins_re)
if app.config['ENABLE_SENTRY']:
sentry_sdk.init(
dsn="https://25342ca4e2d443c6a5c49707d68e9f40@o401361.ingest.sentry.io/5260915",
integrations=[FlaskIntegration()]
)
print('=== USING THESE CONFIG SETTINGS: ===')
print('DB_HOST = ', )
print('CORS_ALLOW_ORIGINS = ', app.config['CORS_ALLOW_ORIGINS'])

6
crc/api.yml
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@ -808,12 +808,12 @@ paths:
$ref: "#/components/schemas/Script"
/approval:
parameters:
- name: approver_uid
- name: everything
in: query
required: false
description: Restrict results to a given approver uid, maybe we restrict the use of this at somepoint.
description: If set to true, returns all the approvals known to the system.
schema:
type: string
type: boolean
get:
operationId: crc.api.approval.get_approvals
summary: Provides a list of workflows approvals

11
crc/api/approval.py
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@ -1,3 +1,5 @@
from flask import g
from crc import app, db, session
from crc.api.common import ApiError, ApiErrorSchema
@ -5,11 +7,11 @@ from crc.models.approval import Approval, ApprovalModel, ApprovalSchema
from crc.services.approval_service import ApprovalService
def get_approvals(approver_uid=None):
if not approver_uid:
def get_approvals(everything=False):
if everything:
db_approvals = ApprovalService.get_all_approvals()
else:
db_approvals = ApprovalService.get_approvals_per_user(approver_uid)
db_approvals = ApprovalService.get_approvals_per_user(g.user.uid)
approvals = [Approval.from_model(approval_model) for approval_model in db_approvals]
results = ApprovalSchema(many=True).dump(approvals)
@ -32,6 +34,9 @@ def update_approval(approval_id, body):
raise ApiError('unknown_approval', 'The approval "' + str(approval_id) + '" is not recognized.')
approval: Approval = ApprovalSchema().load(body)
if approval_model.approver_uid != g.user.uid:
raise ApiError("not_your_approval", "You may not modify this approval. It belongs to another user.")
approval.update_model(approval_model)
session.commit()

5
crc/api/user.py
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@ -1,8 +1,5 @@
import json
import connexion
import flask
from flask import redirect, g, request
from flask import g, request
from crc import app, db
from crc.api.common import ApiError

37
crc/models/approval.py
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@ -68,24 +68,33 @@ class Approval(object):
if model.study:
instance.title = model.study.title
principal_investigator_id = model.study.primary_investigator_id
instance.approver = {}
try:
ldap_service = LdapService()
user_info = ldap_service.user_info(principal_investigator_id)
except (ApiError, LDAPSocketOpenError) as exception:
user_info = None
instance.approver['display_name'] = 'Primary Investigator details'
instance.approver['department'] = 'currently not available'
if user_info:
# TODO: Rename approver to primary investigator
user_info = ldap_service.user_info(model.approver_uid)
instance.approver['uid'] = model.approver_uid
instance.approver['display_name'] = user_info.display_name
instance.approver['title'] = user_info.title
instance.approver['department'] = user_info.department
except (ApiError, LDAPSocketOpenError) as exception:
user_info = None
instance.approver['display_name'] = 'Unknown'
instance.approver['department'] = 'currently not available'
instance.primary_investigator = {}
try:
ldap_service = LdapService()
user_info = ldap_service.user_info(model.study.primary_investigator_id)
instance.primary_investigator['uid'] = model.approver_uid
instance.primary_investigator['display_name'] = user_info.display_name
instance.primary_investigator['title'] = user_info.title
instance.primary_investigator['department'] = user_info.department
except (ApiError, LDAPSocketOpenError) as exception:
user_info = None
instance.primary_investigator['display_name'] = 'Primary Investigator details'
instance.primary_investigator['department'] = 'currently not available'
# TODO: Organize it properly, move it to services
doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
instance.associated_files = []
@ -98,12 +107,13 @@ class Approval(object):
associated_file['id'] = approval_file.file_data.file_model.id
if extra_info:
irb_doc_code = approval_file.file_data.file_model.irb_doc_code
associated_file['name'] = '_'.join((irb_doc_code, approval_file.file_data.file_model.name))
associated_file['name'] = '_'.join((extra_info['category1'],
approval_file.file_data.file_model.name))
associated_file['description'] = extra_info['description']
else:
associated_file['name'] = approval_file.file_data.file_model.name
associated_file['description'] = 'No description available'
associated_file['name'] = '(' + principal_investigator_id + ')' + associated_file['name']
associated_file['name'] = '(' + model.study.primary_investigator_id + ')' + associated_file['name']
associated_file['content_type'] = approval_file.file_data.file_model.content_type
instance.associated_files.append(associated_file)
@ -118,7 +128,8 @@ class ApprovalSchema(ma.Schema):
class Meta:
model = Approval
fields = ["id", "study_id", "workflow_id", "version", "title",
"version", "status", "message", "approver", "associated_files"]
"status", "message", "approver", "primary_investigator",
"associated_files", "date_created"]
unknown = INCLUDE
@marshmallow.post_load

1
crc/scripts/request_approval.py
View File

@ -26,6 +26,7 @@ RequestApproval approver1 "dhf8r"
ApprovalService.add_approval(study_id, workflow_id, args)
elif isinstance(uids, list):
for id in uids:
if id: ## Assure it's not empty or null
ApprovalService.add_approval(study_id, workflow_id, id)
def get_uids(self, task, args):

3
package-lock.json generated Normal file
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@ -0,0 +1,3 @@
{
"lockfileVersion": 1
}

100
tests/test_approvals_api.py
View File

@ -5,35 +5,6 @@ from crc import app, db, session
from crc.models.approval import ApprovalModel, ApprovalSchema, ApprovalStatus
APPROVAL_PAYLOAD = {
'id': None,
'approver': {
'uid': 'bgb22',
'display_name': 'Billy Bob (bgb22)',
'title': 'E42:He\'s a hoopy frood',
'department': 'E0:EN-Eng Study of Parallel Universes'
},
'title': 'El Study',
'status': 'DECLINED',
'version': 1,
'message': 'Incorrect documents',
'associated_files': [
{
'id': 42,
'name': 'File 1',
'content_type': 'document'
},
{
'id': 43,
'name': 'File 2',
'content_type': 'document'
}
],
'workflow_id': 1,
'study_id': 1
}
class TestApprovals(BaseTest):
def setUp(self):
"""Initial setup shared by all TestApprovals tests"""
@ -64,7 +35,7 @@ class TestApprovals(BaseTest):
def test_list_approvals_per_approver(self):
"""Only approvals associated with approver should be returned"""
approver_uid = self.approval_2.approver_uid
rv = self.app.get(f'/v1.0/approval?approver_uid={approver_uid}', headers=self.logged_in_headers())
rv = self.app.get(f'/v1.0/approval', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
@ -82,7 +53,7 @@ class TestApprovals(BaseTest):
def test_list_approvals_per_admin(self):
"""All approvals will be returned"""
rv = self.app.get('/v1.0/approval', headers=self.logged_in_headers())
rv = self.app.get('/v1.0/approval?everything=true', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
@ -90,24 +61,67 @@ class TestApprovals(BaseTest):
# Returned approvals should match what's in the db
approvals_count = ApprovalModel.query.count()
response_count = len(response)
self.assertEqual(approvals_count, response_count)
self.assertEqual(2, response_count)
def test_update_approval(self):
"""Approval status will be updated"""
approval_id = self.approval.id
data = dict(APPROVAL_PAYLOAD)
data['id'] = approval_id
rv = self.app.get('/v1.0/approval', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
response_count = len(response)
self.assertEqual(1, response_count)
self.assertEqual(self.approval.status, ApprovalStatus.PENDING.value)
def test_update_approval_fails_if_not_the_approver(self):
approval = session.query(ApprovalModel).filter_by(approver_uid='arc93').first()
data = {'id': approval.id,
"approver_uid": "dhf8r",
'message': "Approved. I like the cut of your jib.",
'status': ApprovalStatus.APPROVED.value}
rv = self.app.put(f'/v1.0/approval/{approval_id}',
self.assertEqual(approval.status, ApprovalStatus.PENDING.value)
rv = self.app.put(f'/v1.0/approval/{approval.id}',
content_type="application/json",
headers=self.logged_in_headers(),
headers=self.logged_in_headers(), # As dhf8r
data=json.dumps(data))
self.assert_failure(rv)
def test_accept_approval(self):
approval = session.query(ApprovalModel).filter_by(approver_uid='dhf8r').first()
data = {'id': approval.id,
"approver_uid": "dhf8r",
'message': "Approved. I like the cut of your jib.",
'status': ApprovalStatus.APPROVED.value}
self.assertEqual(approval.status, ApprovalStatus.PENDING.value)
rv = self.app.put(f'/v1.0/approval/{approval.id}',
content_type="application/json",
headers=self.logged_in_headers(), # As dhf8r
data=json.dumps(data))
self.assert_success(rv)
session.refresh(self.approval)
session.refresh(approval)
# Updated record should now have the data sent to the endpoint
self.assertEqual(self.approval.message, data['message'])
self.assertEqual(self.approval.status, ApprovalStatus.DECLINED.value)
self.assertEqual(approval.message, data['message'])
self.assertEqual(approval.status, ApprovalStatus.APPROVED.value)
def test_decline_approval(self):
approval = session.query(ApprovalModel).filter_by(approver_uid='dhf8r').first()
data = {'id': approval.id,
"approver_uid": "dhf8r",
'message': "Approved. I find the cut of your jib lacking.",
'status': ApprovalStatus.DECLINED.value}
self.assertEqual(approval.status, ApprovalStatus.PENDING.value)
rv = self.app.put(f'/v1.0/approval/{approval.id}',
content_type="application/json",
headers=self.logged_in_headers(), # As dhf8r
data=json.dumps(data))
self.assert_success(rv)
session.refresh(approval)
# Updated record should now have the data sent to the endpoint
self.assertEqual(approval.message, data['message'])
self.assertEqual(approval.status, ApprovalStatus.DECLINED.value)

18
tests/test_request_approval_script.py
View File

@ -1,6 +1,6 @@
from crc.services.file_service import FileService
from tests.base_test import BaseTest
from crc.services.file_service import FileService
from crc.scripts.request_approval import RequestApproval
from crc.services.workflow_processor import WorkflowProcessor
from crc.api.common import ApiError
@ -26,6 +26,22 @@ class TestRequestApprovalScript(BaseTest):
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
self.assertEquals(2, db.session.query(ApprovalModel).count())
def test_do_task_with_blank_second_approver(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"study": {"approval1": "dhf8r", 'approval2':''}}
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code="UVACompl_PRCAppr",
name="anything.png", content_type="text",
binary_data=b'1234')
script = RequestApproval()
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
self.assertEquals(1, db.session.query(ApprovalModel).count())
def test_do_task_with_incorrect_argument(self):
"""This script should raise an error if it can't figure out the approvers."""
self.load_example_data()

1
tests/test_tasks_api.py
View File

@ -10,7 +10,6 @@ from crc.models.api_models import WorkflowApiSchema, MultiInstanceType, TaskSche
from crc.models.file import FileModelSchema
from crc.models.stats import TaskEventModel
from crc.models.workflow import WorkflowStatus
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.workflow_service import WorkflowService