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Merge branch 'dev' into feature/update_study_status_latest

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Carlos Lopez 2020-07-31 14:26:24 -06:00
commit 50b207307a
48 changed files with 1108 additions and 318 deletions
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5
Pipfile
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@ -38,13 +38,14 @@ recommonmark = "*"
requests = "*"
sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
sphinx = "*"
spiffworkflow = {git = "https://github.com/sartography/SpiffWorkflow.git",ref = "master"}
#spiffworkflow = {editable = true,path="/home/kelly/sartography/SpiffWorkflow/"}
swagger-ui-bundle = "*"
spiffworkflow = {editable = true, git = "https://github.com/sartography/SpiffWorkflow.git", ref = "master"}
webtest = "*"
werkzeug = "*"
xlrd = "*"
xlsxwriter = "*"
pygithub = "*"
python-box = "*"
[requires]
python_version = "3.7"

128
Pipfile.lock generated
View File

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@ -940,8 +948,9 @@
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@ -1114,13 +1121,12 @@
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3
README.md
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@ -18,6 +18,9 @@ Make sure all of the following are properly installed on your system:
- [Install pipenv](https://pipenv-es.readthedocs.io/es/stable/)
- [Add ${HOME}/.local/bin to your PATH](https://github.com/pypa/pipenv/issues/2122#issue-319600584)
### Running Postgres
### Project Initialization
1. Clone this repository.
2. In PyCharm:

3
config/default.py
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@ -46,6 +46,9 @@ PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL +
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
# Github token
GITHUB_TOKEN = environ.get('GITHUB_TOKEN', None)
# Email configuration
DEFAULT_SENDER = 'askresearch@virginia.edu'
FALLBACK_EMAILS = ['askresearch@virginia.edu', 'sartographysupport@googlegroups.com']

26
crc/api.yml
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@ -31,6 +31,13 @@ paths:
'304':
description: Redirection to the hosted frontend with an auth_token header.
/user:
parameters:
- name: admin_impersonate_uid
in: query
required: false
description: For admins, the unique uid of an existing user to impersonate.
schema:
type: string
get:
operationId: crc.api.user.get_current_user
summary: Returns the current user.
@ -38,11 +45,27 @@ paths:
- Users
responses:
'200':
description: The currently authenticated user.
description: The currently-authenticated user, or, if the current user is an admin and admin_impersonate_uid is provided, this will be the user with the given uid.
content:
application/json:
schema:
$ref: "#/components/schemas/User"
/list_users:
get:
operationId: crc.api.user.get_all_users
security:
- auth_admin: ['secret']
summary: Returns a list of all users in the database.
tags:
- Users
responses:
'200':
description: All users in the database.
content:
application/json:
schema:
type: array
$ref: "#/components/schemas/User"
# /v1.0/study
/study:
get:
@ -56,6 +79,7 @@ paths:
content:
application/json:
schema:
type: array
$ref: "#/components/schemas/Study"
post:
operationId: crc.api.study.add_study

24
crc/api/admin.py
View File

@ -3,19 +3,22 @@ import json
from flask import url_for
from flask_admin import Admin
from flask_admin.actions import action
from flask_admin.contrib import sqla
from flask_admin.contrib.sqla import ModelView
from sqlalchemy import desc
from werkzeug.utils import redirect
from jinja2 import Markup
from crc import db, app
from crc.api.user import verify_token, verify_token_admin
from crc.models.approval import ApprovalModel
from crc.models.file import FileModel
from crc.models.file import FileModel, FileDataModel
from crc.models.task_event import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
from crc.models.workflow import WorkflowModel
from crc.services.file_service import FileService
class AdminModelView(sqla.ModelView):
@ -34,26 +37,40 @@ class AdminModelView(sqla.ModelView):
# redirect to login page if user doesn't have access
return redirect(url_for('home'))
class UserView(AdminModelView):
column_filters = ['uid']
class StudyView(AdminModelView):
column_filters = ['id', 'primary_investigator_id']
column_searchable_list = ['title']
class ApprovalView(AdminModelView):
column_filters = ['study_id', 'approver_uid']
class WorkflowView(AdminModelView):
column_filters = ['study_id', 'id']
class FileView(AdminModelView):
column_filters = ['workflow_id']
column_filters = ['workflow_id', 'type']
@action('publish', 'Publish', 'Are you sure you want to publish this file(s)?')
def action_publish(self, ids):
FileService.publish_to_github(ids)
@action('update', 'Update', 'Are you sure you want to update this file(s)?')
def action_update(self, ids):
FileService.update_from_github(ids)
def json_formatter(view, context, model, name):
value = getattr(model, name)
json_value = json.dumps(value, ensure_ascii=False, indent=2)
return Markup('<pre>{}</pre>'.format(json_value))
return Markup(f'<pre>{json_value}</pre>')
class TaskEventView(AdminModelView):
column_filters = ['workflow_id', 'action']
@ -62,6 +79,7 @@ class TaskEventView(AdminModelView):
'form_data': json_formatter,
}
admin = Admin(app)
admin.add_view(StudyView(StudyModel, db.session))

3
crc/api/common.py
View File

@ -1,5 +1,6 @@
from SpiffWorkflow import WorkflowException
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from flask import g
from crc import ma, app
@ -65,3 +66,5 @@ class ApiErrorSchema(ma.Schema):
def handle_invalid_usage(error):
response = ApiErrorSchema().dump(error)
return response, error.status_code

8
crc/api/study.py
View File

@ -8,6 +8,7 @@ from crc.api.common import ApiError, ApiErrorSchema
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import Study, StudyModel, StudySchema, StudyStatus
from crc.services.study_service import StudyService
from crc.services.user_service import UserService
def add_study(body):
@ -17,7 +18,7 @@ def add_study(body):
if 'title' not in body:
raise ApiError("missing_title", "Can't create a new study without a title.")
study_model = StudyModel(user_uid=g.user.uid,
study_model = StudyModel(user_uid=UserService.current_user().uid,
title=body['title'],
primary_investigator_id=body['primary_investigator_id'],
last_updated=datetime.now(),
@ -65,8 +66,9 @@ def delete_study(study_id):
def user_studies():
"""Returns all the studies associated with the current user. """
StudyService.synch_with_protocol_builder_if_enabled(g.user)
studies = StudyService.get_studies_for_user(g.user)
user = UserService.current_user(allow_admin_impersonate=True)
StudyService.synch_with_protocol_builder_if_enabled(user)
studies = StudyService.get_studies_for_user(user)
results = StudySchema(many=True).dump(studies)
return results

81
crc/api/user.py
View File

@ -1,10 +1,11 @@
import flask
from flask import g, request
from crc import app, db
from crc import app, session
from crc.api.common import ApiError
from crc.models.user import UserModel, UserModelSchema
from crc.services.ldap_service import LdapService, LdapModel
from crc.services.user_service import UserService
"""
.. module:: crc.api.user
@ -35,6 +36,10 @@ def verify_token(token=None):
try:
token_info = UserModel.decode_auth_token(token)
g.user = UserModel.query.filter_by(uid=token_info['sub']).first()
# If the user is valid, store the token for this session
if g.user:
g.token = token
except:
raise failure_error
if g.user is not None:
@ -49,27 +54,31 @@ def verify_token(token=None):
if uid is not None:
db_user = UserModel.query.filter_by(uid=uid).first()
# If the user is valid, store the user and token for this session
if db_user is not None:
g.user = db_user
token = g.user.encode_auth_token().decode()
g.token = token
token_info = UserModel.decode_auth_token(token)
return token_info
else:
raise ApiError("no_user", "User not found. Please login via the frontend app before accessing this feature.",
status_code=403)
raise ApiError("no_user",
"User not found. Please login via the frontend app before accessing this feature.",
status_code=403)
else:
# Fall back to a default user if this is not production.
g.user = UserModel.query.first()
token = g.user.encode_auth_token()
token_info = UserModel.decode_auth_token(token)
return token_info
def verify_token_admin(token=None):
"""
Verifies the token for the user (if provided) in non-production environment. If in production environment,
checks that the user is in the list of authorized admins
Verifies the token for the user (if provided) in non-production environment.
If in production environment, checks that the user is in the list of authorized admins
Args:
token: Optional[str]
@ -77,21 +86,44 @@ def verify_token_admin(token=None):
Returns:
token: str
"""
# If this is production, check that the user is in the list of admins
if _is_production():
uid = _get_request_uid(request)
if uid is not None and uid in app.config['ADMIN_UIDS']:
return verify_token()
# If we're not in production, just use the normal verify_token method
else:
return verify_token(token)
verify_token(token)
if "user" in g and g.user.is_admin():
token = g.user.encode_auth_token()
token_info = UserModel.decode_auth_token(token)
return token_info
def get_current_user():
return UserModelSchema().dump(g.user)
def start_impersonating(uid):
if uid is not None and UserService.user_is_admin():
UserService.start_impersonating(uid)
user = UserService.current_user(allow_admin_impersonate=True)
return UserModelSchema().dump(user)
def stop_impersonating():
if UserService.user_is_admin():
UserService.stop_impersonating()
user = UserService.current_user(allow_admin_impersonate=False)
return UserModelSchema().dump(user)
def get_current_user(admin_impersonate_uid=None):
if UserService.user_is_admin():
if admin_impersonate_uid is not None:
UserService.start_impersonating(admin_impersonate_uid)
else:
UserService.stop_impersonating()
user = UserService.current_user(UserService.user_is_admin() and UserService.admin_is_impersonating())
return UserModelSchema().dump(user)
def get_all_users():
if "user" in g and g.user.is_admin():
all_users = session.query(UserModel).all()
return UserModelSchema(many=True).dump(all_users)
def login(
@ -134,7 +166,6 @@ def login(
# X-Forwarded-Server: dev.crconnect.uvadcos.io
# Connection: Keep-Alive
# If we're in production, override any uid with the uid from the SSO request headers
if _is_production():
uid = _get_request_uid(request)
@ -182,6 +213,8 @@ def _handle_login(user_info: LdapModel, redirect_url=None):
# Return the frontend auth callback URL, with auth token appended.
auth_token = user.encode_auth_token().decode()
g.token = auth_token
if redirect_url is not None:
if redirect_url.find("http://") != 0 and redirect_url.find("https://") != 0:
redirect_url = "http://" + redirect_url
@ -194,13 +227,13 @@ def _handle_login(user_info: LdapModel, redirect_url=None):
def _upsert_user(user_info):
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
user = session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
if user is None:
# Add new user
user = UserModel()
else:
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).with_for_update().first()
user = session.query(UserModel).filter(UserModel.uid == user_info.uid).with_for_update().first()
user.uid = user_info.uid
user.display_name = user_info.display_name
@ -208,8 +241,8 @@ def _upsert_user(user_info):
user.affiliation = user_info.affiliation
user.title = user_info.title
db.session.add(user)
db.session.commit()
session.add(user)
session.commit()
return user

22
crc/api/workflow.py
View File

@ -13,6 +13,7 @@ from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, Workflow
from crc.services.file_service import FileService
from crc.services.lookup_service import LookupService
from crc.services.study_service import StudyService
from crc.services.user_service import UserService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
@ -141,7 +142,7 @@ def set_current_task(workflow_id, task_id):
task_id = uuid.UUID(task_id)
spiff_task = processor.bpmn_workflow.get_task(task_id)
_verify_user_and_role(processor, spiff_task)
user_uid = g.user.uid
user_uid = UserService.current_user(allow_admin_impersonate=True).uid
if spiff_task.state != spiff_task.COMPLETED and spiff_task.state != spiff_task.READY:
raise ApiError("invalid_state", "You may not move the token to a task who's state is not "
"currently set to COMPLETE or READY.")
@ -184,7 +185,8 @@ def update_task(workflow_id, task_id, body, terminate_loop=None):
processor.save()
# Log the action, and any pending task assignments in the event of lanes in the workflow.
WorkflowService.log_task_action(g.user.uid, processor, spiff_task, WorkflowService.TASK_ACTION_COMPLETE)
user = UserService.current_user(allow_admin_impersonate=False) # Always log as the real user.
WorkflowService.log_task_action(user.uid, processor, spiff_task, WorkflowService.TASK_ACTION_COMPLETE)
WorkflowService.update_task_assignments(processor)
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
@ -244,19 +246,11 @@ def lookup(workflow_id, field_id, query=None, value=None, limit=10):
def _verify_user_and_role(processor, spiff_task):
"""Assures the currently logged in user can access the given workflow and task, or
raises an error.
Allow administrators to modify tasks, otherwise assure that the current user
is allowed to edit or update the task. Will raise the appropriate error if user
is not authorized. """
if 'user' not in g:
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
if g.user.uid in app.config['ADMIN_UIDS']:
return g.user.uid
raises an error. """
user = UserService.current_user(allow_admin_impersonate=True)
allowed_users = WorkflowService.get_users_assigned_to_task(processor, spiff_task)
if g.user.uid not in allowed_users:
if user.uid not in allowed_users:
raise ApiError.from_task("permission_denied",
f"This task must be completed by '{allowed_users}', "
f"but you are {g.user.uid}", spiff_task)
f"but you are {user.uid}", spiff_task)

15
crc/models/user.py
View File

@ -1,6 +1,7 @@
import datetime
import jwt
from marshmallow import fields
from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from crc import db, app
@ -21,6 +22,10 @@ class UserModel(db.Model):
# TODO: Add Department and School
def is_admin(self):
# Currently admin abilities are set in the configuration, but this
# may change in the future.
return self.uid in app.config['ADMIN_UIDS']
def encode_auth_token(self):
"""
@ -60,4 +65,14 @@ class UserModelSchema(SQLAlchemyAutoSchema):
model = UserModel
load_instance = True
include_relationships = True
is_admin = fields.Method('get_is_admin', dump_only=True)
def get_is_admin(self, obj):
return obj.is_admin()
class AdminSessionModel(db.Model):
__tablename__ = 'admin_session'
id = db.Column(db.Integer, primary_key=True)
token = db.Column(db.String, unique=True)
admin_impersonate_uid = db.Column(db.String)

2
crc/scripts/fact_service.py
View File

@ -40,7 +40,7 @@ class FactService(Script):
else:
details = "unknown fact type."
self.add_data_to_task(task, details)
#self.add_data_to_task(task, details)
print(details)
return details

50
crc/scripts/ldap.py Normal file
View File

@ -0,0 +1,50 @@
import copy
from crc import app
from crc.api.common import ApiError
from crc.scripts.script import Script
from crc.services.ldap_service import LdapService
class Ldap(Script):
"""This Script allows to be introduced as part of a workflow and called from there, taking
a UID (or several) as input and looking it up through LDAP to return the person's details """
def get_description(self):
return """
Attempts to create a dictionary with person details, using the
provided argument (a UID) and look it up through LDAP.
Examples:
supervisor_info = ldap(supervisor_uid) // Sets the supervisor information to ldap details for the given uid.
"""
def do_task_validate_only(self, task, *args, **kwargs):
return self.set_users_info_in_task(task, args)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
return self.set_users_info_in_task(task, args)
def set_users_info_in_task(self, task, args):
if len(args) != 1:
raise ApiError(code="missing_argument",
message="Ldap takes a single argument, the "
"UID for the person we want to look up")
uid = args[0]
user_info_dict = {}
user_info = LdapService.user_info(uid)
user_info_dict = {
"display_name": user_info.display_name,
"given_name": user_info.given_name,
"email_address": user_info.email_address,
"telephone_number": user_info.telephone_number,
"title": user_info.title,
"department": user_info.department,
"affiliation": user_info.affiliation,
"sponsor_type": user_info.sponsor_type,
"uid": user_info.uid,
"proper_name": user_info.proper_name()
}
return user_info_dict

2
crc/scripts/request_approval.py
View File

@ -11,7 +11,7 @@ class RequestApproval(Script):
return """
Creates an approval request on this workflow, by the given approver_uid(s),"
Takes multiple arguments, which should point to data located in current task
or be quoted strings. The order is important. Approvals will be processed
or be quoted strings. The order is important. Approvals will be processed
in this order.
Example:

47
crc/scripts/script.py
View File

@ -23,6 +23,53 @@ class Script(object):
"This is an internal error. The script you are trying to execute '%s' " % self.__class__.__name__ +
"does must provide a validate_only option that mimics the do_task, " +
"but does not make external calls or database updates." )
@staticmethod
def generate_augmented_list(task, study_id,workflow_id):
"""
this makes a dictionary of lambda functions that are closed over the class instance that
They represent. This is passed into PythonScriptParser as a list of helper functions that are
available for running. In general, they maintain the do_task call structure that they had, but
they always return a value rather than updating the task data.
We may be able to remove the task for each of these calls if we are not using it other than potentially
updating the task data.
"""
def make_closure(subclass,task,study_id,workflow_id):
instance = subclass()
return lambda *a : subclass.do_task(instance,task,study_id,workflow_id,*a)
execlist = {}
subclasses = Script.get_all_subclasses()
for x in range(len(subclasses)):
subclass = subclasses[x]
execlist[subclass.__module__.split('.')[-1]] = make_closure(subclass,task,study_id,
workflow_id)
return execlist
@staticmethod
def generate_augmented_validate_list(task, study_id, workflow_id):
"""
this makes a dictionary of lambda functions that are closed over the class instance that
They represent. This is passed into PythonScriptParser as a list of helper functions that are
available for running. In general, they maintain the do_task call structure that they had, but
they always return a value rather than updating the task data.
We may be able to remove the task for each of these calls if we are not using it other than potentially
updating the task data.
"""
def make_closure_validate(subclass,task,study_id,workflow_id):
instance = subclass()
return lambda *a : subclass.do_task_validate_only(instance,task,study_id,workflow_id,*a)
execlist = {}
subclasses = Script.get_all_subclasses()
for x in range(len(subclasses)):
subclass = subclasses[x]
execlist[subclass.__module__.split('.')[-1]] = make_closure_validate(subclass,task,study_id,
workflow_id)
return execlist
@staticmethod
def get_all_subclasses():

54
crc/scripts/study_info.py
View File

@ -8,7 +8,7 @@ from crc.scripts.script import Script
from crc.services.file_service import FileService
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.study_service import StudyService
from box import Box
class StudyInfo(Script):
"""Please see the detailed description that is provided below. """
@ -149,11 +149,11 @@ Returns information specific to the protocol.
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, pretend no results come back from pb"""
self.check_args(args)
self.check_args(args,2)
# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
FileService.get_reference_file_data(FileService.INVESTIGATOR_LIST)
data = {
data = Box({
"study":{
"info": {
"id": 12,
@ -195,38 +195,50 @@ Returns information specific to the protocol.
'id': 0,
}
}
}
self.add_data_to_task(task=task, data=data["study"])
self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
})
if args[0]=='documents':
return StudyService().get_documents_status(study_id)
return data['study'][args[0]]
#self.add_data_to_task(task=task, data=data["study"])
#self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
self.check_args(args)
self.check_args(args,2)
prefix = None
if len(args) > 1:
prefix = args[1]
cmd = args[0]
study_info = {}
if self.__class__.__name__ in task.data:
study_info = task.data[self.__class__.__name__]
# study_info = {}
# if self.__class__.__name__ in task.data:
# study_info = task.data[self.__class__.__name__]
retval = None
if cmd == 'info':
study = session.query(StudyModel).filter_by(id=study_id).first()
schema = StudySchema()
self.add_data_to_task(task, {cmd: schema.dump(study)})
retval = schema.dump(study)
if cmd == 'investigators':
self.add_data_to_task(task, {cmd: StudyService().get_investigators(study_id)})
retval = StudyService().get_investigators(study_id)
if cmd == 'roles':
self.add_data_to_task(task, {cmd: StudyService().get_investigators(study_id, all=True)})
retval = StudyService().get_investigators(study_id, all=True)
if cmd == 'details':
self.add_data_to_task(task, {cmd: self.pb.get_study_details(study_id)})
retval = self.pb.get_study_details(study_id)
if cmd == 'approvals':
self.add_data_to_task(task, {cmd: StudyService().get_approvals(study_id)})
retval = StudyService().get_approvals(study_id)
if cmd == 'documents':
self.add_data_to_task(task, {cmd: StudyService().get_documents_status(study_id)})
retval = StudyService().get_documents_status(study_id)
if cmd == 'protocol':
self.add_data_to_task(task, {cmd: StudyService().get_protocol(study_id)})
retval = StudyService().get_protocol(study_id)
if isinstance(retval,dict) and prefix is not None:
return Box({x:retval[x] for x in retval.keys() if x[:len(prefix)] == prefix})
elif isinstance(retval,dict):
return Box(retval)
else:
return retval
def check_args(self, args):
if len(args) != 1 or (args[0] not in StudyInfo.type_options):
def check_args(self, args, maxlen=1):
if len(args) < 1 or len(args) > maxlen or (args[0] not in StudyInfo.type_options):
raise ApiError(code="missing_argument",
message="The StudyInfo script requires a single argument which must be "
"one of %s" % ",".join(StudyInfo.type_options))

49
crc/services/file_service.py
View File

@ -2,6 +2,7 @@ import hashlib
import json
import os
from datetime import datetime
from github import Github, UnknownObjectException
from uuid import UUID
from lxml import etree
@ -333,3 +334,51 @@ class FileService(object):
file_model.archived = True
session.commit()
app.logger.info("Failed to delete file, so archiving it instead. %i, due to %s" % (file_id, str(ie)))
@staticmethod
def update_from_github(file_ids):
gh_token = app.config['GITHUB_TOKEN']
_github = Github(gh_token)
repo = _github.get_user().get_repo('crispy-fiesta')
for file_id in file_ids:
file_data_model = FileDataModel.query.filter_by(
file_model_id=file_id
).order_by(
desc(FileDataModel.version)
).first()
try:
repo_file = repo.get_contents(file_data_model.file_model.name)
except UnknownObjectException:
# TODO: Add message indicating file is not in the repo
pass
else:
file_data_model.data = repo_file.decoded_content
session.add(file_data_model)
session.commit()
@staticmethod
def publish_to_github(file_ids):
gh_token = app.config['GITHUB_TOKEN']
_github = Github(gh_token)
repo = _github.get_user().get_repo('crispy-fiesta')
for file_id in file_ids:
file_data_model = FileDataModel.query.filter_by(file_model_id=file_id).first()
try:
repo_file = repo.get_contents(file_data_model.file_model.name)
except UnknownObjectException:
repo.create_file(
path=file_data_model.file_model.name,
message=f'Creating {file_data_model.file_model.name}',
content=file_data_model.data
)
return {'created': True}
else:
updated = repo.update_file(
path=repo_file.path,
message=f'Updating {file_data_model.file_model.name}',
content=file_data_model.data,
sha=repo_file.sha
)
return {'updated': True}

117
crc/services/user_service.py Normal file
View File

@ -0,0 +1,117 @@
from flask import g
from crc import session
from crc.api.common import ApiError
from crc.models.user import UserModel, AdminSessionModel
class UserService(object):
"""Provides common tools for working with users"""
# Returns true if the current user is logged in.
@staticmethod
def has_user():
return 'token' in g and \
bool(g.token) and \
'user' in g and \
bool(g.user)
# Returns true if the current user is an admin.
@staticmethod
def user_is_admin():
return UserService.has_user() and g.user.is_admin()
# Returns true if the current admin user is impersonating another user.
@staticmethod
def admin_is_impersonating():
if UserService.user_is_admin():
adminSession: AdminSessionModel = UserService.get_admin_session()
return adminSession is not None
else:
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
# Returns true if the given user uid is different from the current user's uid.
@staticmethod
def is_different_user(uid):
return UserService.has_user() and uid is not None and uid is not g.user.uid
@staticmethod
def current_user(allow_admin_impersonate=False) -> UserModel:
if not UserService.has_user():
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
# Admins can pretend to be different users and act on a user's behalf in
# some circumstances.
if UserService.user_is_admin() and allow_admin_impersonate and UserService.admin_is_impersonating():
return UserService.get_admin_session_user()
else:
return g.user
# Admins can pretend to be different users and act on a user's behalf in some circumstances.
# This method allows an admin user to start impersonating another user with the given uid.
# Stops impersonating if the uid is None or invalid.
@staticmethod
def start_impersonating(uid=None):
if not UserService.has_user():
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
if not UserService.user_is_admin():
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
if uid is None:
raise ApiError("invalid_uid", "Please provide a valid user uid.")
if not UserService.admin_is_impersonating() and UserService.is_different_user(uid):
# Impersonate the user if the given uid is valid.
impersonate_user = session.query(UserModel).filter(UserModel.uid == uid).first()
if impersonate_user is not None:
g.impersonate_user = impersonate_user
# Store the uid and user session token.
session.add(AdminSessionModel(token=g.token, admin_impersonate_uid=uid))
session.commit()
else:
raise ApiError("invalid_uid", "The uid provided is not valid.")
@staticmethod
def stop_impersonating():
if not UserService.has_user():
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)
# Clear out the current impersonating user.
if 'impersonate_user' in g:
del g.impersonate_user
admin_session: AdminSessionModel = UserService.get_admin_session()
if admin_session:
session.delete(admin_session)
session.commit()
@staticmethod
def in_list(uids, allow_admin_impersonate=False):
"""Returns true if the current user's id is in the given list of ids. False if there
is no user, or the user is not in the list."""
if UserService.has_user(): # If someone is logged in, lock tasks that don't belong to them.
user = UserService.current_user(allow_admin_impersonate)
if user.uid in uids:
return True
return False
@staticmethod
def get_admin_session() -> AdminSessionModel:
if UserService.user_is_admin():
return session.query(AdminSessionModel).filter(AdminSessionModel.token == g.token).first()
else:
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)
@staticmethod
def get_admin_session_user() -> UserModel:
if UserService.user_is_admin():
admin_session = UserService.get_admin_session()
if admin_session is not None:
return session.query(UserModel).filter(UserModel.uid == admin_session.admin_impersonate_uid).first()
else:
raise ApiError("unauthorized", "You do not have permissions to do this.", status_code=403)

110
crc/services/workflow_processor.py
View File

@ -17,6 +17,7 @@ from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from SpiffWorkflow.specs import WorkflowSpec
import crc
from crc import session, app
from crc.api.common import ApiError
from crc.models.file import FileDataModel, FileModel, FileType
@ -28,64 +29,71 @@ from crc import app
class CustomBpmnScriptEngine(BpmnScriptEngine):
"""This is a custom script processor that can be easily injected into Spiff Workflow.
Rather than execute arbitrary code, this assumes the script references a fully qualified python class
such as myapp.RandomFact. """
It will execute python code read in from the bpmn. It will also make any scripts in the
scripts directory available for execution. """
def execute(self, task: SpiffTask, script, data):
"""
Functions in two modes.
1. If the command is proceeded by #! then this is assumed to be a python script, and will
attempt to load that python module and execute the do_task method on that script. Scripts
must be located in the scripts package and they must extend the script.py class.
2. If not proceeded by the #! this will attempt to execute the script directly and assumes it is
valid Python.
"""
# Shlex splits the whole string while respecting double quoted strings within
if not script.startswith('#!'):
try:
super().execute(task, script, data)
except SyntaxError as e:
raise ApiError.from_task('syntax_error',
f'If you are running a pre-defined script, please'
f' proceed the script with "#!", otherwise this is assumed to be'
f' pure python: {script}, {e.msg}', task=task)
else:
self.run_predefined_script(task, script[2:], data) # strip off the first two characters.
def run_predefined_script(self, task: SpiffTask, script, data):
commands = shlex.split(script)
path_and_command = commands[0].rsplit(".", 1)
if len(path_and_command) == 1:
module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
class_name = path_and_command[0]
study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
else:
module_name = "crc.scripts." + path_and_command[0] + "." + self.camel_to_snake(path_and_command[1])
class_name = path_and_command[1]
workflow_id = None
try:
mod = __import__(module_name, fromlist=[class_name])
klass = getattr(mod, class_name)
study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
else:
workflow_id = None
if not isinstance(klass(), Script):
raise ApiError.from_task("invalid_script",
"This is an internal error. The script '%s:%s' you called " %
(module_name, class_name) +
"does not properly implement the CRC Script class.",
task=task)
if task.workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY]:
"""If this is running a validation, and not a normal process, then we want to
mimic running the script, but not make any external calls or database changes."""
klass().do_task_validate_only(task, study_id, workflow_id, *commands[1:])
augmentMethods = Script.generate_augmented_validate_list(task, study_id, workflow_id)
else:
klass().do_task(task, study_id, workflow_id, *commands[1:])
except ModuleNotFoundError:
raise ApiError.from_task("invalid_script",
"Unable to locate Script: '%s:%s'" % (module_name, class_name),
task=task)
augmentMethods = Script.generate_augmented_list(task, study_id, workflow_id)
super().execute(task, script, data, externalMethods=augmentMethods)
except SyntaxError as e:
raise ApiError('syntax_error',
f'Something is wrong with your python script '
f'please correct the following:'
f' {script}, {e.msg}')
except NameError as e:
raise ApiError('name_error',
f'something you are referencing does not exist:'
f' {script}, {e.name}')
# else:
# self.run_predefined_script(task, script[2:], data) # strip off the first two characters.
# def run_predefined_script(self, task: SpiffTask, script, data):
# commands = shlex.split(script)
# path_and_command = commands[0].rsplit(".", 1)
# if len(path_and_command) == 1:
# module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
# class_name = path_and_command[0]
# else:
# module_name = "crc.scripts." + path_and_command[0] + "." + self.camel_to_snake(path_and_command[1])
# class_name = path_and_command[1]
# try:
# mod = __import__(module_name, fromlist=[class_name])
# klass = getattr(mod, class_name)
# study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
# if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
# workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
# else:
# workflow_id = None
#
# if not isinstance(klass(), Script):
# raise ApiError.from_task("invalid_script",
# "This is an internal error. The script '%s:%s' you called " %
# (module_name, class_name) +
# "does not properly implement the CRC Script class.",
# task=task)
# if task.workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY]:
# """If this is running a validation, and not a normal process, then we want to
# mimic running the script, but not make any external calls or database changes."""
# klass().do_task_validate_only(task, study_id, workflow_id, *commands[1:])
# else:
# klass().do_task(task, study_id, workflow_id, *commands[1:])
# except ModuleNotFoundError:
# raise ApiError.from_task("invalid_script",
# "Unable to locate Script: '%s:%s'" % (module_name, class_name),
# task=task)
def evaluate_expression(self, task, expression):
"""

5
crc/services/workflow_service.py
View File

@ -30,6 +30,7 @@ from crc.models.workflow import WorkflowModel, WorkflowStatus, WorkflowSpecModel
from crc.services.file_service import FileService
from crc.services.lookup_service import LookupService
from crc.services.study_service import StudyService
from crc.services.user_service import UserService
from crc.services.workflow_processor import WorkflowProcessor
@ -238,7 +239,7 @@ class WorkflowService(object):
nav_item['title'] = nav_item['task'].title # Prefer the task title.
user_uids = WorkflowService.get_users_assigned_to_task(processor, spiff_task)
if 'user' not in g or not g.user or g.user.uid not in user_uids:
if not UserService.in_list(user_uids, allow_admin_impersonate=True):
nav_item['state'] = WorkflowService.TASK_STATE_LOCKED
else:
@ -271,7 +272,7 @@ class WorkflowService(object):
workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True)
# Update the state of the task to locked if the current user does not own the task.
user_uids = WorkflowService.get_users_assigned_to_task(processor, next_task)
if 'user' not in g or not g.user or g.user.uid not in user_uids:
if not UserService.in_list(user_uids, allow_admin_impersonate=True):
workflow_api.next_task.state = WorkflowService.TASK_STATE_LOCKED
return workflow_api

3
crc/static/bpmn/core_info/core_info.bpmn
View File

@ -212,7 +212,8 @@
<bpmn:scriptTask id="Activity_10nxpt2" name="Load Study Details">
<bpmn:incoming>SequenceFlow_1r3yrhy</bpmn:incoming>
<bpmn:outgoing>Flow_09h1imz</bpmn:outgoing>
<bpmn:script>#! StudyInfo details</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['details'] = study_info('details')</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_PBMultiSiteCheckQ12" name="PB Multi-Site Check Q12" camunda:decisionRef="Decision_core_info_multi_site_q12">
<bpmn:incoming>Flow_09h1imz</bpmn:incoming>

2
crc/static/bpmn/data_security_plan/data_security_plan.bpmn
View File

@ -453,7 +453,7 @@ Indicate all the possible formats in which you will transmit your data outside o
<bpmn:incoming>SequenceFlow_0k2r83n</bpmn:incoming>
<bpmn:incoming>SequenceFlow_0t6xl9i</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_16kyite</bpmn:outgoing>
<bpmn:script>#! CompleteTemplate NEW_DSP_template.docx Study_DataSecurityPlan</bpmn:script>
<bpmn:script>complete_template('NEW_DSP_template.docx','Study_DataSecurityPlan')</bpmn:script>
</bpmn:scriptTask>
<bpmn:manualTask id="Task_0q6ir2l" name="View Instructions">
<bpmn:documentation>##### Instructions

5
crc/static/bpmn/documents_approvals/documents_approvals.bpmn
View File

@ -53,12 +53,13 @@
<bpmn:scriptTask id="Activity_0a14x7j" name="Load Approvals">
<bpmn:incoming>Flow_0c7ryff</bpmn:incoming>
<bpmn:outgoing>Flow_142jtxs</bpmn:outgoing>
<bpmn:script>#! StudyInfo approvals</bpmn:script>
<bpmn:script>StudyInfo['approvals'] = study_info('approvals')</bpmn:script>
</bpmn:scriptTask>
<bpmn:scriptTask id="Activity_1aju60t" name="Load Documents">
<bpmn:incoming>Flow_1k3su2q</bpmn:incoming>
<bpmn:outgoing>Flow_0c7ryff</bpmn:outgoing>
<bpmn:script>#! StudyInfo documents</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['documents'] = study_info('documents')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_142jtxs" sourceRef="Activity_0a14x7j" targetRef="Activity_DisplayDocsAndApprovals" />
<bpmn:sequenceFlow id="Flow_0c7ryff" sourceRef="Activity_1aju60t" targetRef="Activity_0a14x7j" />

3
crc/static/bpmn/ide_supplement/ide_supplement.bpmn
View File

@ -36,7 +36,8 @@
<bpmn:scriptTask id="ScriptTask_1fn00ox" name="Load IRB Details">
<bpmn:incoming>SequenceFlow_1dhb8f4</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1uzcl1f</bpmn:outgoing>
<bpmn:script>#! StudyInfo details</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['details'] = study_info('details')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1uzcl1f" sourceRef="ScriptTask_1fn00ox" targetRef="Task_SupplementIDE" />
<bpmn:exclusiveGateway id="ExclusiveGateway_1fib89p" name="IS_IDE = True and Number Provided?&#10;&#10;">

3
crc/static/bpmn/ids_full_submission/ids_full_submission.bpmn
View File

@ -217,7 +217,8 @@ Protocol Owner: **(need to insert value here)**</bpmn:documentation>
<bpmn:scriptTask id="Activity_LoadDocuments" name="Load Documents">
<bpmn:incoming>SequenceFlow_1dexemq</bpmn:incoming>
<bpmn:outgoing>Flow_1x9d2mo</bpmn:outgoing>
<bpmn:script>#! StudyInfo documents</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['documents'] = study_info('documents')</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">

3
crc/static/bpmn/ind_update/ind_update.bpmn
View File

@ -12,7 +12,8 @@
<bpmn:scriptTask id="ScriptTask_LoadIRBDetails" name="Load IRB Details">
<bpmn:incoming>SequenceFlow_1dhb8f4</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1uzcl1f</bpmn:outgoing>
<bpmn:script>#! StudyInfo details</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['details'] = study_info('details')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1uzcl1f" sourceRef="ScriptTask_LoadIRBDetails" targetRef="Task_SupplementIDE" />
<bpmn:businessRuleTask id="Task_SupplementIDE" name="Current IND Status" camunda:decisionRef="decision_ind_check">

3
crc/static/bpmn/irb_api_details/irb_api_details.bpmn
View File

@ -8,7 +8,8 @@
<bpmn:scriptTask id="ScriptTask_02924vs" name="Load IRB Details">
<bpmn:incoming>SequenceFlow_1fmyo77</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_18nr0gf</bpmn:outgoing>
<bpmn:script>#! StudyInfo details</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['details'] = study_info('details')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1fmyo77" sourceRef="StartEvent_1" targetRef="ScriptTask_02924vs" />
<bpmn:sequenceFlow id="SequenceFlow_18nr0gf" sourceRef="ScriptTask_02924vs" targetRef="Activity_FromIRB-API" />

3
crc/static/bpmn/irb_api_personnel/irb_api_personnel.bpmn
View File

@ -7,7 +7,8 @@
<bpmn:scriptTask id="ScriptTask_LoadPersonnel" name="Load IRB Personnel">
<bpmn:incoming>Flow_0kcrx5l</bpmn:incoming>
<bpmn:outgoing>Flow_1dcsioh</bpmn:outgoing>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_1qor16n">
<bpmn:documentation>## The following information was gathered:

6
crc/static/bpmn/research_rampup/research_rampup.bpmn
View File

@ -598,7 +598,7 @@ Use the EHS [Lab Safety Plan During COVID 19 template](https://www.google.com/ur
This step is internal to the system and do not require and user interaction</bpmn:documentation>
<bpmn:incoming>Flow_11uqavk</bpmn:incoming>
<bpmn:outgoing>Flow_0aqgwvu</bpmn:outgoing>
<bpmn:script>#! CompleteTemplate ResearchRampUpPlan.docx RESEARCH_RAMPUP</bpmn:script>
<bpmn:script>complete_template('ResearchRampUpPlan.docx','RESEARCH_RAMPUP')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_0aqgwvu" sourceRef="Activity_GenerateRRP" targetRef="Activity_AcknowledgePlanReview" />
<bpmn:sequenceFlow id="Flow_0j4rs82" sourceRef="Activity_SubmitPlan" targetRef="Activity_0absozl" />
@ -755,7 +755,7 @@ Notify the Area Monitor for
This step is internal to the system and do not require and user interaction</bpmn:documentation>
<bpmn:incoming>Flow_0j4rs82</bpmn:incoming>
<bpmn:outgoing>Flow_07ge8uf</bpmn:outgoing>
<bpmn:script>#!RequestApproval ApprvlApprvr1 ApprvlApprvr2</bpmn:script>
<bpmn:script>request_approval('ApprvlApprvr1','ApprvlApprvr2')</bpmn:script>
</bpmn:scriptTask>
<bpmn:scriptTask id="Activity_1u58hox" name="Update Request">
<bpmn:documentation>#### Script Task
@ -764,7 +764,7 @@ This step is internal to the system and do not require and user interaction</bpm
This step is internal to the system and do not require and user interaction</bpmn:documentation>
<bpmn:incoming>Flow_16y8glw</bpmn:incoming>
<bpmn:outgoing>Flow_0uc4o6c</bpmn:outgoing>
<bpmn:script>#! UpdateStudy title:PIComputingID.label pi:PIComputingID.value</bpmn:script>
<bpmn:script>update_study('title:PIComputingID.label','pi:PIComputingID.value')</bpmn:script>
</bpmn:scriptTask>
<bpmn:userTask id="PersonnelSchedule" name="Upload Weekly Personnel Schedule(s)" camunda:formKey="Personnel Weekly Schedule">
<bpmn:documentation>#### Weekly Personnel Schedule(s)

9
crc/static/bpmn/top_level_workflow/top_level_workflow.bpmn
View File

@ -11,7 +11,8 @@
<bpmn:scriptTask id="Task_Load_Requirements" name="Load Documents From PB">
<bpmn:incoming>SequenceFlow_1ees8ka</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_17ct47v</bpmn:outgoing>
<bpmn:script>#! StudyInfo documents</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['documents'] = study_info('documents')</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_1yqy50i" name="Enter Core Info&#10;" camunda:decisionRef="enter_core_info">
<bpmn:incoming>Flow_1m8285h</bpmn:incoming>
@ -62,7 +63,8 @@
<bpmn:scriptTask id="Activity_0f295la" name="Load Details from PB">
<bpmn:incoming>Flow_0pwtiqm</bpmn:incoming>
<bpmn:outgoing>Flow_0eq6px2</bpmn:outgoing>
<bpmn:script>#! StudyInfo details</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['details'] = study_info('details')</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_0ahlc3u" name="IDE Supplement" camunda:decisionRef="decision_ide_menu_check">
<bpmn:incoming>Flow_14ce1d7</bpmn:incoming>
@ -91,7 +93,8 @@
<bpmn:scriptTask id="Activity_0g3qa1c" name="Load Personnel from PB">
<bpmn:incoming>Flow_1qyrmzn</bpmn:incoming>
<bpmn:outgoing>Flow_0vo6ul1</bpmn:outgoing>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1ybicki" sourceRef="Activity_13ep6ar" targetRef="Event_135x8jg" />
<bpmn:businessRuleTask id="Activity_13ep6ar" name="Personnel" camunda:decisionRef="personnel">

2
migrations/versions/1c3f88dbccc3_.py
View File

@ -11,7 +11,7 @@ from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision = '1c3f88dbccc3'
down_revision = '2e7b377cbc7b'
down_revision = 'ab06a94e5d4c'
branch_labels = None
depends_on = None

34
migrations/versions/ab06a94e5d4c_.py Normal file
View File

@ -0,0 +1,34 @@
"""empty message
Revision ID: ab06a94e5d4c
Revises: 2e7b377cbc7b
Create Date: 2020-07-30 11:23:46.601338
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'ab06a94e5d4c'
down_revision = '2e7b377cbc7b'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('admin_session',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('token', sa.String(), nullable=True),
sa.Column('admin_impersonate_uid', sa.String(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('token')
)
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('admin_session')
# ### end Alembic commands ###

2
setup.py
View File

@ -1,3 +1,3 @@
from setuptools import setup
setup(setup_requires=["pbr"], pbr=True)
setup(setup_requires=["pbr"], pbr=True, install_requires=['box'])

113
tests/base_test.py
View File

@ -18,14 +18,16 @@ from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
from crc.models.task_event import TaskEventModel
from crc.models.study import StudyModel, StudyStatus
from crc.models.user import UserModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecCategoryModel
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.user_service import UserService
from crc.services.workflow_service import WorkflowService
from example_data import ExampleDataLoader
#UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
# UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
import logging
logging.basicConfig()
@ -36,22 +38,32 @@ class BaseTest(unittest.TestCase):
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."))
"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'
}
'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'
},
{
'uid': 'lbd3p',
'email_address': 'lbd3p@virginia.EDU',
'display_name': 'Laura Barnes',
'affiliation': 'staff@virginia.edu;member@virginia.edu',
'eppn': 'lbd3p@virginia.edu',
'first_name': 'Laura',
'last_name': 'Barnes',
'title': 'Associate Professor of Systems and Information Engineering'
},
]
studies = [
@ -77,7 +89,6 @@ class BaseTest(unittest.TestCase):
}
]
@classmethod
def setUpClass(cls):
app.config.from_object('config.testing')
@ -97,7 +108,7 @@ class BaseTest(unittest.TestCase):
def tearDown(self):
ExampleDataLoader.clean_db()
g.user = None
self.logout()
self.auths = {}
def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
@ -117,7 +128,8 @@ class BaseTest(unittest.TestCase):
self.assertIsNotNone(user_model.display_name)
self.assertEqual(user_model.uid, uid)
self.assertTrue('user' in g, 'User should be in Flask globals')
self.assertEqual(uid, g.user.uid, 'Logged in user should match given user uid')
user = UserService.current_user(allow_admin_impersonate=True)
self.assertEqual(uid, user.uid, 'Logged in user should match given user uid')
return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
@ -134,16 +146,21 @@ class BaseTest(unittest.TestCase):
else:
ExampleDataLoader().load_test_data()
for user_json in self.users:
db.session.add(UserModel(**user_json))
db.session.commit()
# If in production mode, only add the first user.
if app.config['PRODUCTION']:
session.add(UserModel(**self.users[0]))
else:
for user_json in self.users:
session.add(UserModel(**user_json))
session.commit()
for study_json in self.studies:
study_model = StudyModel(**study_json)
db.session.add(study_model)
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()
session.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
session.commit()
session.flush()
specs = session.query(WorkflowSpecModel).all()
self.assertIsNotNone(specs)
@ -167,8 +184,8 @@ class BaseTest(unittest.TestCase):
"""Loads a spec into the database based on a directory in /tests/data"""
if category_id is None:
category = WorkflowSpecCategoryModel(name="test", display_name="Test Workflows", display_order=0)
db.session.add(category)
db.session.commit()
session.add(category)
session.commit()
category_id = category.id
if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
@ -216,14 +233,13 @@ class BaseTest(unittest.TestCase):
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()
file_model = 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)
@ -232,18 +248,19 @@ class BaseTest(unittest.TestCase):
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()
session.add(user)
session.commit()
return user
def create_study(self, uid="dhf8r", title="Beer consumption in the bipedal software engineer", primary_investigator_id="lb3dp"):
def create_study(self, uid="dhf8r", title="Beer consumption in the bipedal software engineer",
primary_investigator_id="lb3dp"):
study = session.query(StudyModel).filter_by(user_uid=uid).filter_by(title=title).first()
if study is None:
user = self.create_user(uid=uid)
study = StudyModel(title=title, status=StudyStatus.in_progress,
user_uid=user.uid, primary_investigator_id=primary_investigator_id)
db.session.add(study)
db.session.commit()
session.add(study)
session.commit()
return study
def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
@ -270,8 +287,8 @@ class BaseTest(unittest.TestCase):
return full_study
def create_workflow(self, workflow_name, display_name=None, study=None, category_id=None, as_user="dhf8r"):
db.session.flush()
spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
session.flush()
spec = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
if spec is None:
if display_name is None:
display_name = workflow_name
@ -290,21 +307,22 @@ class BaseTest(unittest.TestCase):
file.close()
def create_approval(
self,
study=None,
workflow=None,
approver_uid=None,
status=None,
version=None,
self,
study=None,
workflow=None,
approver_uid=None,
status=None,
version=None,
):
study = study or self.create_study()
workflow = workflow or self.create_workflow()
approver_uid = approver_uid or self.test_uid
status = status or ApprovalStatus.PENDING.value
version = version or 1
approval = ApprovalModel(study=study, workflow=workflow, approver_uid=approver_uid, status=status, version=version)
db.session.add(approval)
db.session.commit()
approval = ApprovalModel(study=study, workflow=workflow, approver_uid=approver_uid, status=status,
version=version)
session.add(approval)
session.commit()
return approval
def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False, do_engine_steps=True, user_uid="dhf8r"):
@ -322,7 +340,6 @@ class BaseTest(unittest.TestCase):
self.assertEqual(workflow.workflow_spec_id, workflow_api.workflow_spec_id)
return workflow_api
def complete_form(self, workflow_in, task_in, dict_data, error_code=None, terminate_loop=None, user_uid="dhf8r"):
prev_completed_task_count = workflow_in.completed_tasks
if isinstance(task_in, dict):
@ -387,12 +404,18 @@ class BaseTest(unittest.TestCase):
self.assertEqual(task_in.multi_instance_count, event.mi_count)
if task_in.multi_instance_type == 'looping' and not terminate_loop:
self.assertEqual(task_in.multi_instance_index+1, event.mi_index)
self.assertEqual(task_in.multi_instance_index + 1, event.mi_index)
else:
self.assertEqual(task_in.multi_instance_index, event.mi_index)
self.assertEqual(task_in.process_name, event.process_name)
self.assertIsNotNone(event.date)
workflow = WorkflowApiSchema().load(json_data)
return workflow
def logout(self):
if 'user' in g:
del g.user
if 'impersonate_user' in g:
del g.impersonate_user

2
tests/data/docx/docx.bpmn
View File

@ -27,7 +27,7 @@
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_1i7hk1a</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_11c35oq</bpmn:outgoing>
<bpmn:script>#! CompleteTemplate Letter.docx AD_CoCApp</bpmn:script>
<bpmn:script>complete_template('Letter.docx','AD_CoCApp')</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0evb22x">
<bpmn:incoming>SequenceFlow_11c35oq</bpmn:incoming>

2
tests/data/email/email.bpmn
View File

@ -20,7 +20,7 @@ Email content to be delivered to {{ ApprvlApprvr1 }}
---</bpmn:documentation>
<bpmn:incoming>Flow_08n2npe</bpmn:incoming>
<bpmn:outgoing>Flow_1xlrgne</bpmn:outgoing>
<bpmn:script>#! Email "Camunda Email Subject" ApprvlApprvr1 PIComputingID</bpmn:script>
<bpmn:script>email("Camunda Email Subject",'ApprvlApprvr1','PIComputingID')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1synsig" sourceRef="StartEvent_1" targetRef="Activity_1l9vih3" />
<bpmn:sequenceFlow id="Flow_1xlrgne" sourceRef="Activity_0s5v97n" targetRef="Event_0izrcj4" />

2
tests/data/invalid_script/invalid_script.bpmn
View File

@ -11,7 +11,7 @@
<bpmn:scriptTask id="Invalid_Script_Task" name="An Invalid Script Reference">
<bpmn:incoming>SequenceFlow_1pnq3kg</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_12pf6um</bpmn:outgoing>
<bpmn:script>#! NoSuchScript withArg1</bpmn:script>
<bpmn:script>no_such_script('withArg1')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_12pf6um" sourceRef="Invalid_Script_Task" targetRef="EndEvent_063bpg6" />
</bpmn:process>

70
tests/data/ldap_replace/ldap_replace.bpmn Normal file
View File

@ -0,0 +1,70 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0y2dq4f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_0tad5ma" name="Set Recipients" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_1synsig</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:endEvent id="Event_0izrcj4">
<bpmn:incoming>Flow_11e7jgz</bpmn:incoming>
</bpmn:endEvent>
<bpmn:scriptTask id="Activity_0s5v97n" name="Ldap Replace">
<bpmn:incoming>Flow_08n2npe</bpmn:incoming>
<bpmn:outgoing>Flow_1xlrgne</bpmn:outgoing>
<bpmn:script>Supervisor = ldap(Supervisor)
Investigator = ldap(Investigator)</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1synsig" sourceRef="StartEvent_1" targetRef="Activity_1l9vih3" />
<bpmn:sequenceFlow id="Flow_1xlrgne" sourceRef="Activity_0s5v97n" targetRef="Activity_0f78ek5" />
<bpmn:sequenceFlow id="Flow_08n2npe" sourceRef="Activity_1l9vih3" targetRef="Activity_0s5v97n" />
<bpmn:userTask id="Activity_1l9vih3" name="Set UIDs">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="Supervisor" label="Approver" type="string" />
<camunda:formField id="Investigator" label="Primary Investigator" type="string" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_1synsig</bpmn:incoming>
<bpmn:outgoing>Flow_08n2npe</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_11e7jgz" sourceRef="Activity_0f78ek5" targetRef="Event_0izrcj4" />
<bpmn:userTask id="Activity_0f78ek5" name="Read UIDs">
<bpmn:incoming>Flow_1xlrgne</bpmn:incoming>
<bpmn:outgoing>Flow_11e7jgz</bpmn:outgoing>
</bpmn:userTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0tad5ma">
<bpmndi:BPMNEdge id="Flow_11e7jgz_di" bpmnElement="Flow_11e7jgz">
<di:waypoint x="720" y="117" />
<di:waypoint x="802" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_08n2npe_di" bpmnElement="Flow_08n2npe">
<di:waypoint x="370" y="117" />
<di:waypoint x="450" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1xlrgne_di" bpmnElement="Flow_1xlrgne">
<di:waypoint x="550" y="117" />
<di:waypoint x="620" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1synsig_di" bpmnElement="Flow_1synsig">
<di:waypoint x="215" y="117" />
<di:waypoint x="270" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_0izrcj4_di" bpmnElement="Event_0izrcj4">
<dc:Bounds x="802" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_04imfm6_di" bpmnElement="Activity_0s5v97n">
<dc:Bounds x="450" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0xugr62_di" bpmnElement="Activity_1l9vih3">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_17h05g6_di" bpmnElement="Activity_0f78ek5">
<dc:Bounds x="620" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

3
tests/data/multi_instance/multi_instance.bpmn
View File

@ -29,7 +29,8 @@
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">

5
tests/data/multi_instance_parallel/multi_instance_parallel.bpmn
View File

@ -11,7 +11,7 @@
<bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MultiInstanceTask" targetRef="Event_End" />
<bpmn:userTask id="MultiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
<bpmn:documentation># Please provide addtional information about:
## Investigator ID: {{investigator.user_id}}
## Investigator ID: {{investigator.user_id}}
## Role: {{investigator.type_full}}</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
@ -29,7 +29,8 @@
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
<bpmn:script>#! StudyInfo investigators</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['investigators'] = study_info('investigators')</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">

2
tests/data/random_fact/random_fact.bpmn
View File

@ -132,7 +132,7 @@ Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0641sh6</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0t29gjo</bpmn:outgoing>
<bpmn:script>#! FactService</bpmn:script>
<bpmn:script>FactService = fact_service()</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0u1cgrf">
<bpmn:documentation># Great Job!

24
tests/data/study_details/study_details.bpmn
View File

@ -8,12 +8,19 @@
<bpmn:scriptTask id="Task_Script_Load_Study_Details" name="Load Study Info">
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
<bpmn:script>#! StudyInfo info</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['info'] = study_info('info')</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Details" targetRef="EndEvent_171dj09" />
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Details" targetRef="Activity_0w91u9s" />
<bpmn:endEvent id="EndEvent_171dj09">
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
<bpmn:incoming>Flow_0ochvmi</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_0ochvmi" sourceRef="Activity_0w91u9s" targetRef="EndEvent_171dj09" />
<bpmn:scriptTask id="Activity_0w91u9s" name="StudyInfo as Script">
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
<bpmn:outgoing>Flow_0ochvmi</bpmn:outgoing>
<bpmn:script>study = study_info('info','p')</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
@ -29,10 +36,17 @@
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
<di:waypoint x="370" y="117" />
<di:waypoint x="402" y="117" />
<di:waypoint x="430" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="EndEvent_171dj09_di" bpmnElement="EndEvent_171dj09">
<dc:Bounds x="402" y="99" width="36" height="36" />
<dc:Bounds x="622" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_0ochvmi_di" bpmnElement="Flow_0ochvmi">
<di:waypoint x="530" y="117" />
<di:waypoint x="622" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="Activity_1wtk4bb_di" bpmnElement="Activity_0w91u9s">
<dc:Bounds x="430" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>

3
tests/data/top_level_workflow/top_level_workflow.bpmn
View File

@ -11,7 +11,8 @@
<bpmn:scriptTask id="Task_Load_Requirements" name="Load Required Documents From PM">
<bpmn:incoming>SequenceFlow_1ees8ka</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_17ct47v</bpmn:outgoing>
<bpmn:script>#! StudyInfo documents</bpmn:script>
<bpmn:script>StudyInfo = {}
StudyInfo['documents'] = study_info('documents')</bpmn:script>
</bpmn:scriptTask>
<bpmn:businessRuleTask id="Activity_1yqy50i" name="Enter Core Info&#10;" camunda:decisionRef="enter_core_info">
<bpmn:incoming>Flow_1m8285h</bpmn:incoming>

95
tests/files/test_file_service.py
View File

@ -1,9 +1,45 @@
from github import UnknownObjectException
from sqlalchemy import desc
from tests.base_test import BaseTest
from unittest.mock import patch, Mock
from crc import db
from crc.models.file import FileDataModel
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
class FakeGithubCreates(Mock):
def get_user(var):
class FakeUser(Mock):
def get_repo(var, name):
class FakeRepo(Mock):
def get_contents(var, filename):
raise UnknownObjectException(status='Failure', data='Failed data')
def update_file(var, path, message, content, sha):
pass
return FakeRepo()
return FakeUser()
class FakeGithub(Mock):
def get_user(var):
class FakeUser(Mock):
def get_repo(var, name):
class FakeRepo(Mock):
def get_contents(var, filename):
fake_file = Mock()
fake_file.decoded_content = b'Some bytes'
fake_file.path = '/el/path/'
fake_file.data = 'Serious data'
fake_file.sha = 'Sha'
return fake_file
def update_file(var, path, message, content, sha):
pass
return FakeRepo()
return FakeUser()
class TestFileService(BaseTest):
"""Largely tested via the test_file_api, and time is tight, but adding new tests here."""
@ -103,3 +139,62 @@ class TestFileService(BaseTest):
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEqual(2, len(file_models))
@patch('crc.services.file_service.Github')
def test_update_from_github(self, mock_github):
mock_github.return_value = FakeGithub()
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file_model = FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
FileService.update_from_github([file_model.id])
file_model_data = FileDataModel.query.filter_by(
file_model_id=file_model.id
).order_by(
desc(FileDataModel.version)
).first()
self.assertEqual(file_model_data.data, b'Some bytes')
@patch('crc.services.file_service.Github')
def test_publish_to_github_creates(self, mock_github):
mock_github.return_value = FakeGithubCreates()
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file_model = FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
result = FileService.publish_to_github([file_model.id])
self.assertEqual(result['created'], True)
@patch('crc.services.file_service.Github')
def test_publish_to_github_updates(self, mock_github):
mock_github.return_value = FakeGithub()
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file_model = FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
result = FileService.publish_to_github([file_model.id])
self.assertEqual(result['updated'], True)

70
tests/ldap/test_ldap_lookup_script.py Normal file
View File

@ -0,0 +1,70 @@
from tests.base_test import BaseTest
from crc.services.workflow_processor import WorkflowProcessor
from crc.scripts.ldap import Ldap
from crc.api.common import ApiError
from crc import db, mail
class TestLdapLookupScript(BaseTest):
def test_get_existing_user_details(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
script = Ldap()
user_details = script.do_task(task, workflow.study_id, workflow.id, "dhf8r")
self.assertEqual(user_details['display_name'], 'Dan Funk')
self.assertEqual(user_details['given_name'], 'Dan')
self.assertEqual(user_details['email_address'], 'dhf8r@virginia.edu')
self.assertEqual(user_details['telephone_number'], '+1 (434) 924-1723')
self.assertEqual(user_details['title'], 'E42:He\'s a hoopy frood')
self.assertEqual(user_details['department'], 'E0:EN-Eng Study of Parallel Universes')
self.assertEqual(user_details['affiliation'], 'faculty')
self.assertEqual(user_details['sponsor_type'], 'Staff')
self.assertEqual(user_details['uid'], 'dhf8r')
self.assertEqual(user_details['proper_name'], 'Dan Funk - (dhf8r)')
def test_get_invalid_user_details(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {
'PIComputingID': 'rec3z'
}
script = Ldap()
with(self.assertRaises(ApiError)):
user_details = script.do_task(task, workflow.study_id, workflow.id, "PIComputingID")
def test_bpmn_task_receives_user_details(self):
workflow = self.create_workflow('ldap_replace')
task_data = {
'Supervisor': 'dhf8r',
'Investigator': 'lb3dp'
}
task = self.get_workflow_api(workflow).next_task
self.complete_form(workflow, task, task_data)
task = self.get_workflow_api(workflow).next_task
self.assertEqual(task.data['Supervisor']['display_name'], 'Dan Funk')
self.assertEqual(task.data['Supervisor']['given_name'], 'Dan')
self.assertEqual(task.data['Supervisor']['email_address'], 'dhf8r@virginia.edu')
self.assertEqual(task.data['Supervisor']['telephone_number'], '+1 (434) 924-1723')
self.assertEqual(task.data['Supervisor']['title'], 'E42:He\'s a hoopy frood')
self.assertEqual(task.data['Supervisor']['department'], 'E0:EN-Eng Study of Parallel Universes')
self.assertEqual(task.data['Supervisor']['affiliation'], 'faculty')
self.assertEqual(task.data['Supervisor']['sponsor_type'], 'Staff')
self.assertEqual(task.data['Supervisor']['uid'], 'dhf8r')
self.assertEqual(task.data['Supervisor']['proper_name'], 'Dan Funk - (dhf8r)')

199
tests/test_authentication.py
View File

@ -5,7 +5,7 @@ from datetime import timezone, datetime, timedelta
import jwt
from tests.base_test import BaseTest
from crc import db, app
from crc import app, session
from crc.api.common import ApiError
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudySchema, StudyModel, StudyStatus
@ -13,6 +13,8 @@ from crc.models.user import UserModel
class TestAuthentication(BaseTest):
admin_uid = 'dhf8r'
non_admin_uid = 'lb3dp'
def tearDown(self):
# Assure we set the production flag back to false.
@ -58,9 +60,9 @@ class TestAuthentication(BaseTest):
self.assertTrue(expected_exp_3 - 1000 <= actual_exp_3 <= expected_exp_3 + 1000)
def test_non_production_auth_creates_user(self):
new_uid = 'lb3dp' ## Assure this user id is in the fake responses from ldap.
new_uid = self.non_admin_uid ## Assure this user id is in the fake responses from ldap.
self.load_example_data()
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
user = session.query(UserModel).filter(UserModel.uid == new_uid).first()
self.assertIsNone(user)
user_info = {'uid': new_uid, 'first_name': 'Cordi', 'last_name': 'Nator',
@ -72,7 +74,7 @@ class TestAuthentication(BaseTest):
self.assertTrue(rv_1.status_code == 302)
self.assertTrue(str.startswith(rv_1.location, redirect_url))
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
user = session.query(UserModel).filter(UserModel.uid == new_uid).first()
self.assertIsNotNone(user)
self.assertIsNotNone(user.display_name)
self.assertIsNotNone(user.email_address)
@ -88,21 +90,20 @@ class TestAuthentication(BaseTest):
self.load_example_data()
new_uid = 'lb3dp' # This user is in the test ldap system.
user = db.session.query(UserModel).filter_by(uid=new_uid).first()
# User should not be in the system yet.
user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
self.assertIsNone(user)
redirect_url = 'http://worlds.best.website/admin'
headers = dict(Uid=new_uid)
db.session.flush()
rv = self.app.get('v1.0/login', follow_redirects=False, headers=headers)
self.assert_success(rv)
user = db.session.query(UserModel).filter_by(uid=new_uid).first()
self.assertIsNotNone(user)
self.assertEqual(new_uid, user.uid)
self.assertEqual("Laura Barnes", user.display_name)
self.assertEqual("lb3dp@virginia.edu", user.email_address)
self.assertEqual("E0:Associate Professor of Systems and Information Engineering", user.title)
# Log in
non_admin_user = self._login_as_non_admin()
# User should be in the system now.
redirect_url = 'http://worlds.best.website/admin'
rv_user = self.app.get('/v1.0/user', headers=self.logged_in_headers(non_admin_user, redirect_url=redirect_url))
self.assert_success(rv_user)
user_data = json.loads(rv_user.get_data(as_text=True))
self.assertEqual(self.non_admin_uid, user_data['uid'])
self.assertFalse(user_data['is_admin'])
# Switch production mode back off
app.config['PRODUCTION'] = False
@ -119,6 +120,8 @@ class TestAuthentication(BaseTest):
user = UserModel(uid="dhf8r", first_name='Dan', last_name='Funk', email_address='dhf8r@virginia.edu')
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers(user, redirect_url='http://omg.edu/lolwut'))
self.assert_success(rv)
user_data = json.loads(rv.get_data(as_text=True))
self.assertTrue(user_data['is_admin'])
def test_admin_can_access_admin_only_endpoints(self):
# Switch production mode on
@ -126,21 +129,8 @@ class TestAuthentication(BaseTest):
self.load_example_data()
admin_uids = app.config['ADMIN_UIDS']
self.assertGreater(len(admin_uids), 0)
admin_uid = admin_uids[0]
self.assertEqual(admin_uid, 'dhf8r') # This user is in the test ldap system.
admin_headers = dict(Uid=admin_uid)
rv = self.app.get('v1.0/login', follow_redirects=False, headers=admin_headers)
self.assert_success(rv)
admin_user = db.session.query(UserModel).filter(UserModel.uid == admin_uid).first()
self.assertIsNotNone(admin_user)
self.assertEqual(admin_uid, admin_user.uid)
admin_study = self._make_fake_study(admin_uid)
admin_user = self._login_as_admin()
admin_study = self._make_fake_study(admin_user.uid)
admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
rv_add_study = self.app.post(
@ -153,7 +143,7 @@ class TestAuthentication(BaseTest):
self.assert_success(rv_add_study, 'Admin user should be able to add a study')
new_admin_study = json.loads(rv_add_study.get_data(as_text=True))
db_admin_study = db.session.query(StudyModel).filter_by(id=new_admin_study['id']).first()
db_admin_study = session.query(StudyModel).filter_by(id=new_admin_study['id']).first()
self.assertIsNotNone(db_admin_study)
rv_del_study = self.app.delete(
@ -173,26 +163,9 @@ class TestAuthentication(BaseTest):
self.load_example_data()
# Non-admin user should not be able to delete a study
non_admin_uid = 'lb3dp'
admin_uids = app.config['ADMIN_UIDS']
self.assertGreater(len(admin_uids), 0)
self.assertNotIn(non_admin_uid, admin_uids)
non_admin_headers = dict(Uid=non_admin_uid)
rv = self.app.get(
'v1.0/login',
follow_redirects=False,
headers=non_admin_headers
)
self.assert_success(rv)
non_admin_user = db.session.query(UserModel).filter_by(uid=non_admin_uid).first()
self.assertIsNotNone(non_admin_user)
non_admin_user = self._login_as_non_admin()
non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
non_admin_study = self._make_fake_study(non_admin_uid)
non_admin_study = self._make_fake_study(non_admin_user.uid)
rv_add_study = self.app.post(
'/v1.0/study',
@ -203,7 +176,7 @@ class TestAuthentication(BaseTest):
self.assert_success(rv_add_study, 'Non-admin user should be able to add a study')
new_non_admin_study = json.loads(rv_add_study.get_data(as_text=True))
db_non_admin_study = db.session.query(StudyModel).filter_by(id=new_non_admin_study['id']).first()
db_non_admin_study = session.query(StudyModel).filter_by(id=new_non_admin_study['id']).first()
self.assertIsNotNone(db_non_admin_study)
rv_non_admin_del_study = self.app.delete(
@ -216,6 +189,87 @@ class TestAuthentication(BaseTest):
# Switch production mode back off
app.config['PRODUCTION'] = False
def test_list_all_users(self):
self.load_example_data()
rv = self.app.get('/v1.0/user')
self.assert_failure(rv, 401)
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers())
self.assert_success(rv)
all_users = session.query(UserModel).all()
rv = self.app.get('/v1.0/list_users', headers=self.logged_in_headers())
self.assert_success(rv)
user_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(len(user_data), len(all_users))
def test_admin_can_impersonate_another_user(self):
# Switch production mode on
app.config['PRODUCTION'] = True
self.load_example_data()
admin_user = self._login_as_admin()
admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
# User should not be in the system yet.
non_admin_user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
self.assertIsNone(non_admin_user)
# Admin should not be able to impersonate non-existent user
rv_1 = self.app.get(
'/v1.0/user?admin_impersonate_uid=' + self.non_admin_uid,
content_type="application/json",
headers=admin_token_headers,
follow_redirects=False
)
self.assert_failure(rv_1, 400)
# Add the non-admin user now
self.logout()
non_admin_user = self._login_as_non_admin()
self.assertEqual(non_admin_user.uid, self.non_admin_uid)
non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
# Add a study for the non-admin user
non_admin_study = self._make_fake_study(self.non_admin_uid)
rv_add_study = self.app.post(
'/v1.0/study',
content_type="application/json",
headers=non_admin_token_headers,
data=json.dumps(StudySchema().dump(non_admin_study))
)
self.assert_success(rv_add_study, 'Non-admin user should be able to add a study')
self.logout()
# Admin should be able to impersonate user now
admin_user = self._login_as_admin()
rv_2 = self.app.get(
'/v1.0/user?admin_impersonate_uid=' + self.non_admin_uid,
content_type="application/json",
headers=admin_token_headers,
follow_redirects=False
)
self.assert_success(rv_2)
user_data_2 = json.loads(rv_2.get_data(as_text=True))
self.assertEqual(user_data_2['uid'], self.non_admin_uid, 'Admin user should impersonate non-admin user')
# Study endpoint should return non-admin user's studies
rv_study = self.app.get(
'/v1.0/study',
content_type="application/json",
headers=admin_token_headers,
follow_redirects=False
)
self.assert_success(rv_study, 'Admin user should be able to get impersonated user studies')
study_data = json.loads(rv_study.get_data(as_text=True))
self.assertGreaterEqual(len(study_data), 1)
self.assertEqual(study_data[0]['user_uid'], self.non_admin_uid)
# Switch production mode back off
app.config['PRODUCTION'] = False
def _make_fake_study(self, uid):
return {
"title": "blah",
@ -224,3 +278,42 @@ class TestAuthentication(BaseTest):
"primary_investigator_id": uid,
"user_uid": uid,
}
def _login_as_admin(self):
admin_uids = app.config['ADMIN_UIDS']
self.assertGreater(len(admin_uids), 0)
self.assertIn(self.admin_uid, admin_uids)
admin_headers = dict(Uid=self.admin_uid)
rv = self.app.get('v1.0/login', follow_redirects=False, headers=admin_headers)
self.assert_success(rv)
admin_user = session.query(UserModel).filter(UserModel.uid == self.admin_uid).first()
self.assertIsNotNone(admin_user)
self.assertEqual(self.admin_uid, admin_user.uid)
self.assertTrue(admin_user.is_admin())
return admin_user
def _login_as_non_admin(self):
admin_uids = app.config['ADMIN_UIDS']
self.assertGreater(len(admin_uids), 0)
self.assertNotIn(self.non_admin_uid, admin_uids)
non_admin_headers = dict(Uid=self.non_admin_uid)
rv = self.app.get(
'v1.0/login?uid=' + self.non_admin_uid,
follow_redirects=False,
headers=non_admin_headers
)
self.assert_success(rv)
user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first()
self.assertIsNotNone(user)
self.assertFalse(user.is_admin())
self.assertIsNotNone(user)
self.assertEqual(self.non_admin_uid, user.uid)
self.assertEqual("Laura Barnes", user.display_name)
self.assertEqual("lb3dp@virginia.edu", user.email_address)
self.assertEqual("E0:Associate Professor of Systems and Information Engineering", user.title)
return user

2
tests/test_ldap_service.py
View File

@ -30,4 +30,4 @@ class TestLdapService(BaseTest):
user_info = LdapService.user_info("nosuch")
self.assertFalse(True, "An API error should be raised.")
except ApiError as ae:
self.assertEqual("missing_ldap_record", ae.code)
self.assertEqual("missing_ldap_record", ae.code)

2
tests/workflow/test_workflow_spec_validation_api.py
View File

@ -90,7 +90,7 @@ class TestWorkflowSpecValidation(BaseTest):
errors = self.validate_workflow("invalid_script")
self.assertEqual(2, len(errors))
self.assertEqual("workflow_validation_exception", errors[0]['code'])
self.assertTrue("NoSuchScript" in errors[0]['message'])
#self.assertTrue("NoSuchScript" in errors[0]['message'])
self.assertEqual("Invalid_Script_Task", errors[0]['task_id'])
self.assertEqual("An Invalid Script Reference", errors[0]['task_name'])
self.assertEqual("invalid_script.bpmn", errors[0]['file_name'])