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cr-connect-workflow
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Merge pull request #86 from sartography/dev 

Dev --> Staging
This commit is contained in:
Aaron Louie 2020-06-12 17:07:18 -04:00 committed by GitHub
parent 1b77681af9 6ba5b8f272
commit 2c0cda1792
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GPG Key ID: 4AEE18F83AFDEB23
76 changed files with 3051 additions and 1201 deletions
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@ -38,6 +38,8 @@ xlrd = "*"
ldap3 = "*"
gunicorn = "*"
werkzeug = "*"
sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
flask-mail = "*"
[requires]
python_version = "3.7"

170
Pipfile.lock generated
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@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
"sha256": "979f996148ee181e3e0af2a3777aa1d00d0fd5d943d49df65963e694b8a88871"
"sha256": "6c89585086260ebcb41918b8ef3b1d9e189e1b492208d3ff000a138bc2f2fcee"
},
"pipfile-spec": 6,
"requires": {
@ -32,10 +32,10 @@
},
"amqp": {
"hashes": [
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"sha256:bb68f8d2bced8f93ccfd07d96c689b716b3227720add971be980accfc2952139"
],
"version": "==2.5.2"
"version": "==2.6.0"
},
"aniso8601": {
"hashes": [
@ -96,19 +96,25 @@
],
"version": "==3.6.3.0"
},
"blinker": {
"hashes": [
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],
"version": "==1.4"
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"celery": {
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"version": "==4.4.5"
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"certifi": {
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"version": "==2020.4.5.1"
"version": "==2020.4.5.2"
},
"cffi": {
"hashes": [
@ -270,13 +276,20 @@
"index": "pypi",
"version": "==3.0.8"
},
"flask-marshmallow": {
"flask-mail": {
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"index": "pypi",
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"version": "==0.9.1"
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"flask-marshmallow": {
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],
"index": "pypi",
"version": "==0.13.0"
},
"flask-migrate": {
"hashes": [
@ -338,18 +351,18 @@
},
"importlib-metadata": {
"hashes": [
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"markers": "python_version < '3.8'",
"version": "==1.6.0"
"version": "==1.6.1"
},
"inflection": {
"hashes": [
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],
"version": "==0.4.0"
"version": "==0.5.0"
},
"itsdangerous": {
"hashes": [
@ -381,10 +394,10 @@
},
"kombu": {
"hashes": [
"sha256:2d1cda774126a044d91a7ff5fa6d09edf99f46924ab332a810760fe6740e9b76",
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],
"version": "==4.6.8"
"version": "==4.6.10"
},
"ldap3": {
"hashes": [
@ -428,10 +441,10 @@
},
"mako": {
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"sha256:3139c5d64aa5d175dbafb95027057128b5fbd05a40c53999f3905ceb53366d9d",
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],
"version": "==1.1.2"
"version": "==1.1.3"
},
"markupsafe": {
"hashes": [
@ -473,11 +486,11 @@
},
"marshmallow": {
"hashes": [
"sha256:c2673233aa21dde264b84349dc2fd1dce5f30ed724a0a00e75426734de5b84ab",
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],
"index": "pypi",
"version": "==3.6.0"
"version": "==3.6.1"
},
"marshmallow-enum": {
"hashes": [
@ -489,37 +502,37 @@
},
"marshmallow-sqlalchemy": {
"hashes": [
"sha256:3247e41e424146340b03a369f2b7c6f0364477ccedc4e2481e84d5f3a8d3c67f",
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],
"index": "pypi",
"version": "==0.23.0"
"version": "==0.23.1"
},
"numpy": {
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],
"version": "==1.18.4"
"version": "==1.18.5"
},
"openapi-spec-validator": {
"hashes": [
@ -704,6 +717,17 @@
"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",
@ -727,11 +751,11 @@
},
"sphinx": {
"hashes": [
"sha256:779a519adbd3a70fc7c468af08c5e74829868b0a5b34587b33340e010291856c",
"sha256:ea64df287958ee5aac46be7ac2b7277305b0381d213728c3a49d8bb9b8415807"
"sha256:1c445320a3310baa5ccb8d957267ef4a0fc930dc1234db5098b3d7af14fbb242",
"sha256:7d3d5087e39ab5a031b75588e9859f011de70e213cd0080ccbc28079fb0786d1"
],
"index": "pypi",
"version": "==3.0.4"
"version": "==3.1.0"
},
"sphinxcontrib-applehelp": {
"hashes": [
@ -778,7 +802,7 @@
"spiffworkflow": {
"editable": true,
"git": "https://github.com/sartography/SpiffWorkflow.git",
"ref": "c8d87826d496af825a184bdc3f0a751e603cfe44"
"ref": "b8a064a0bb76c705a1be04ee9bb8ac7beee56eb0"
},
"sqlalchemy": {
"hashes": [
@ -838,10 +862,10 @@
},
"waitress": {
"hashes": [
"sha256:045b3efc3d97c93362173ab1dfc159b52cfa22b46c3334ffc805dbdbf0e4309e",
"sha256:77ff3f3226931a1d7d8624c5371de07c8e90c7e5d80c5cc660d72659aaf23f38"
"sha256:1bb436508a7487ac6cb097ae7a7fe5413aefca610550baf58f0940e51ecfb261",
"sha256:3d633e78149eb83b60a07dfabb35579c29aac2d24bb803c18b26fb2ab1a584db"
],
"version": "==1.4.3"
"version": "==1.4.4"
},
"webob": {
"hashes": [
@ -876,11 +900,11 @@
},
"xlsxwriter": {
"hashes": [
"sha256:488e1988ab16ff3a9cd58c7656d0a58f8abe46ee58b98eecea78c022db28656b",
"sha256:97ab487b81534415c5313154203f3e8a637d792b1e6a8201e8f7f71da0203c2a"
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],
"index": "pypi",
"version": "==1.2.8"
"version": "==1.2.9"
},
"zipp": {
"hashes": [
@ -900,11 +924,11 @@
},
"importlib-metadata": {
"hashes": [
"sha256:2a688cbaa90e0cc587f1df48bdc97a6eadccdcd9c35fb3f976a09e3b5016d90f",
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"sha256:15ec6c0fd909e893e3a08b3a7c76ecb149122fb14b7efe1199ddd4c7c57ea958"
],
"markers": "python_version < '3.8'",
"version": "==1.6.0"
"version": "==1.6.1"
},
"more-itertools": {
"hashes": [
@ -951,11 +975,11 @@
},
"pytest": {
"hashes": [
"sha256:95c710d0a72d91c13fae35dce195633c929c3792f54125919847fdcdf7caa0d3",
"sha256:eb2b5e935f6a019317e455b6da83dd8650ac9ffd2ee73a7b657a30873d67a698"
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],
"index": "pypi",
"version": "==5.4.2"
"version": "==5.4.3"
},
"six": {
"hashes": [
@ -966,10 +990,10 @@
},
"wcwidth": {
"hashes": [
"sha256:cafe2186b3c009a04067022ce1dcd79cb38d8d65ee4f4791b8888d6599d1bbe1",
"sha256:ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1"
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"sha256:8c6b5b6ee1360b842645f336d9e5d68c55817c26d3050f46b235ef2bc650e48f"
],
"version": "==0.1.9"
"version": "==0.2.4"
},
"zipp": {
"hashes": [

22
config/default.py
View File

@ -9,9 +9,13 @@ JSON_SORT_KEYS = False # CRITICAL. Do not sort the data when returning values
NAME = "CR Connect Workflow"
FLASK_PORT = environ.get('PORT0') or environ.get('FLASK_PORT', default="5000")
CORS_ALLOW_ORIGINS = re.split(r',\s*', environ.get('CORS_ALLOW_ORIGINS', default="localhost:4200, localhost:5002"))
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)
PRODUCTION = (environ.get('PRODUCTION', default="false") == "true")
TEST_UID = environ.get('TEST_UID', default="dhf8r")
ADMIN_UIDS = re.split(r',\s*', environ.get('ADMIN_UIDS', default="dhf8r,ajl2j,cah13us,cl3wf"))
# 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('/'))
@ -25,7 +29,7 @@ SQLALCHEMY_DATABASE_URI = environ.get(
'SQLALCHEMY_DATABASE_URI',
default="postgresql://%s:%s@%s:%s/%s" % (DB_USER, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME)
)
TOKEN_AUTH_TTL_HOURS = int(environ.get('TOKEN_AUTH_TTL_HOURS', default=4))
TOKEN_AUTH_TTL_HOURS = float(environ.get('TOKEN_AUTH_TTL_HOURS', default=24))
TOKEN_AUTH_SECRET_KEY = environ.get('TOKEN_AUTH_SECRET_KEY', default="Shhhh!!! This is secret! And better darn well not show up in prod.")
FRONTEND_AUTH_CALLBACK = environ.get('FRONTEND_AUTH_CALLBACK', default="http://localhost:4200/session")
SWAGGER_AUTH_KEY = environ.get('SWAGGER_AUTH_KEY', default="SWAGGER")
@ -39,6 +43,14 @@ PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL +
PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
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=3))
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
# Email configuration
FALLBACK_EMAILS = ['askresearch@virginia.edu', 'sartographysupport@googlegroups.com']
MAIL_DEBUG = environ.get('MAIL_DEBUG', default=True)
MAIL_SERVER = environ.get('MAIL_SERVER', default='smtp.mailtrap.io')
MAIL_PORT = environ.get('MAIL_PORT', default=2525)
MAIL_USE_SSL = environ.get('MAIL_USE_SSL', default=False)
MAIL_USE_TLS = environ.get('MAIL_USE_TLS', default=True)
MAIL_USERNAME = environ.get('MAIL_USERNAME', default='')
MAIL_PASSWORD = environ.get('MAIL_PASSWORD', default='')

3
config/testing.py
View File

@ -4,7 +4,6 @@ from os import environ
basedir = os.path.abspath(os.path.dirname(__file__))
NAME = "CR Connect Workflow"
DEVELOPMENT = True
TESTING = True
TOKEN_AUTH_SECRET_KEY = "Shhhh!!! This is secret! And better darn well not show up in prod."
PB_ENABLED = False
@ -23,8 +22,8 @@ SQLALCHEMY_DATABASE_URI = environ.get(
'SQLALCHEMY_DATABASE_URI',
default="postgresql://%s:%s@%s:%s/%s" % (DB_USER, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME)
)
ADMIN_UIDS = ['dhf8r']
print('### USING TESTING CONFIG: ###')
print('SQLALCHEMY_DATABASE_URI = ', SQLALCHEMY_DATABASE_URI)
print('DEVELOPMENT = ', DEVELOPMENT)
print('TESTING = ', TESTING)

2
config/travis-testing.py
View File

@ -2,7 +2,6 @@ import os
basedir = os.path.abspath(os.path.dirname(__file__))
NAME = "CR Connect Workflow"
DEVELOPMENT = True
TESTING = True
SQLALCHEMY_DATABASE_URI = "postgresql://postgres:@localhost:5432/crc_test"
TOKEN_AUTH_TTL_HOURS = 2
@ -12,6 +11,5 @@ PB_ENABLED = False
print('+++ USING TRAVIS TESTING CONFIG: +++')
print('SQLALCHEMY_DATABASE_URI = ', SQLALCHEMY_DATABASE_URI)
print('DEVELOPMENT = ', DEVELOPMENT)
print('TESTING = ', TESTING)
print('FRONTEND_AUTH_CALLBACK = ', FRONTEND_AUTH_CALLBACK)

37
crc/__init__.py
View File

@ -1,11 +1,15 @@
import logging
import os
import sentry_sdk
import connexion
from jinja2 import Environment, FileSystemLoader
from flask_cors import CORS
from flask_marshmallow import Marshmallow
from flask_mail import Mail
from flask_migrate import Migrate
from flask_sqlalchemy import SQLAlchemy
from sentry_sdk.integrations.flask import FlaskIntegration
logging.basicConfig(level=logging.INFO)
@ -40,16 +44,29 @@ 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()]
)
# Jinja environment definition, used to render mail templates
template_dir = os.getcwd() + '/crc/static/templates/mails'
env = Environment(loader=FileSystemLoader(template_dir))
# Mail settings
mail = Mail(app)
print('=== USING THESE CONFIG SETTINGS: ===')
print('DB_HOST = ', )
print('CORS_ALLOW_ORIGINS = ', app.config['CORS_ALLOW_ORIGINS'])
print('DEVELOPMENT = ', app.config['DEVELOPMENT'])
print('TESTING = ', app.config['TESTING'])
print('PRODUCTION = ', app.config['PRODUCTION'])
print('PB_BASE_URL = ', app.config['PB_BASE_URL'])
print('LDAP_URL = ', app.config['LDAP_URL'])
print('APPLICATION_ROOT = ', app.config['APPLICATION_ROOT'])
print('CORS_ALLOW_ORIGINS = ', app.config['CORS_ALLOW_ORIGINS'])
print('DB_HOST = ', app.config['DB_HOST'])
print('LDAP_URL = ', app.config['LDAP_URL'])
print('PB_BASE_URL = ', app.config['PB_BASE_URL'])
print('PB_ENABLED = ', app.config['PB_ENABLED'])
print('PRODUCTION = ', app.config['PRODUCTION'])
print('TESTING = ', app.config['TESTING'])
print('TEST_UID = ', app.config['TEST_UID'])
print('ADMIN_UIDS = ', app.config['ADMIN_UIDS'])
@app.cli.command()
def load_example_data():
@ -65,3 +82,9 @@ def load_example_rrt_data():
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_rrt()
@app.cli.command()
def clear_db():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()

202
crc/api.yml
View File

@ -9,54 +9,18 @@ servers:
security:
- jwt: ['secret']
paths:
/sso_backdoor:
/login:
get:
operationId: crc.api.user.backdoor
summary: A backdoor that allows someone to log in as a specific user, if they
are in a staging environment.
operationId: crc.api.user.login
summary: In production, logs the user in via SSO. If not in production, logs in as a specific user for testing.
security: [] # Disable security for this endpoint only.
parameters:
- name: uid
in: query
required: true
schema:
type: string
- name: email_address
in: query
required: false
schema:
type: string
- name: display_name
in: query
required: false
schema:
type: string
- name: affiliation
in: query
required: false
schema:
type: string
- name: eppn
in: query
required: false
schema:
type: string
- name: first_name
in: query
required: false
schema:
type: string
- name: last_name
in: query
required: false
schema:
type: string
- name: title
in: query
required: false
schema:
type: string
- name: redirect
- name: redirect_url
in: query
required: false
schema:
@ -150,6 +114,8 @@ paths:
$ref: "#/components/schemas/Study"
delete:
operationId: crc.api.study.delete_study
security:
- auth_admin: ['secret']
summary: Removes the given study completely.
tags:
- Studies
@ -173,6 +139,30 @@ paths:
application/json:
schema:
$ref: "#/components/schemas/Study"
/study/{study_id}/approvals:
parameters:
- name: study_id
in: path
required: true
description: The id of the study for which workflows should be returned.
schema:
type: integer
format: int32
get:
operationId: crc.api.approval.get_approvals_for_study
summary: Returns approvals for a single study
tags:
- Studies
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
/workflow-specification:
get:
operationId: crc.api.workflow.all_specifications
@ -227,6 +217,8 @@ paths:
$ref: "#/components/schemas/WorkflowSpec"
put:
operationId: crc.api.workflow.update_workflow_specification
security:
- auth_admin: ['secret']
summary: Modifies an existing workflow specification with the given parameters.
tags:
- Workflow Specifications
@ -244,6 +236,8 @@ paths:
$ref: "#/components/schemas/WorkflowSpec"
delete:
operationId: crc.api.workflow.delete_workflow_specification
security:
- auth_admin: ['secret']
summary: Removes an existing workflow specification
tags:
- Workflow Specifications
@ -289,6 +283,8 @@ paths:
$ref: "#/components/schemas/WorkflowSpecCategory"
post:
operationId: crc.api.workflow.add_workflow_spec_category
security:
- auth_admin: ['secret']
summary: Creates a new workflow spec category with the given parameters.
tags:
- Workflow Specification Category
@ -326,6 +322,8 @@ paths:
$ref: "#/components/schemas/WorkflowSpecCategory"
put:
operationId: crc.api.workflow.update_workflow_spec_category
security:
- auth_admin: ['secret']
summary: Modifies an existing workflow spec category with the given parameters.
tags:
- Workflow Specification Category
@ -343,6 +341,8 @@ paths:
$ref: "#/components/schemas/WorkflowSpecCategory"
delete:
operationId: crc.api.workflow.delete_workflow_spec_category
security:
- auth_admin: ['secret']
summary: Removes an existing workflow spec category
tags:
- Workflow Specification Category
@ -444,7 +444,7 @@ paths:
$ref: "#/components/schemas/File"
delete:
operationId: crc.api.file.delete_file
summary: Removes an existing file
summary: Removes an existing file. In the event the file can not be deleted, it is marked as "archived" in the database and is no longer returned unless specifically requested by id.
tags:
- Files
responses:
@ -542,6 +542,8 @@ paths:
example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
put:
operationId: crc.api.file.set_reference_file
security:
- auth_admin: ['secret']
summary: Update the contents of a named reference file.
tags:
- Files
@ -600,6 +602,8 @@ paths:
$ref: "#/components/schemas/Workflow"
delete:
operationId: crc.api.workflow.delete_workflow
security:
- auth_admin: ['secret']
summary: Removes an existing workflow
tags:
- Workflows and Tasks
@ -738,6 +742,26 @@ paths:
text/plain:
schema:
type: string
/send_email:
parameters:
- name: address
in: query
required: true
description: The address to send a test email to.
schema:
type: string
get:
operationId: crc.api.tools.send_email
summary: Sends an email so we can see if things work or not.
tags:
- Configurator Tools
responses:
'201':
description: Returns any error messages that might come back from sending the email.
content:
text/plain:
schema:
type: string
/render_docx:
put:
operationId: crc.api.tools.render_docx
@ -782,12 +806,62 @@ paths:
type: array
items:
$ref: "#/components/schemas/Script"
/approval:
/approval-counts:
parameters:
- name: approver_uid
- name: as_user
in: query
required: false
description: Restrict results to a given approver uid, maybe we restrict the use of this at somepoint.
description: If provided, returns the approval counts for that user.
schema:
type: string
get:
operationId: crc.api.approval.get_approval_counts
summary: Provides counts for approvals by status for the given user, or all users if no user is provided
tags:
- Approvals
responses:
'200':
description: An dictionary of Approval Statuses and the counts for each
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/ApprovalCounts"
/all_approvals:
parameters:
- name: status
in: query
required: false
description: If set to true, returns all the approvals with any status. Defaults to false, leaving out canceled approvals.
schema:
type: boolean
get:
operationId: crc.api.approval.get_all_approvals
summary: Provides a list of all workflows approvals
tags:
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
/approval:
parameters:
- name: status
in: query
required: false
description: If provided, returns just approvals for the given status.
schema:
type: string
- name: as_user
in: query
required: false
description: If provided, returns the approval results as they would appear for that user.
schema:
type: string
get:
@ -830,6 +904,19 @@ paths:
application/json:
schema:
$ref: "#/components/schemas/Approval"
/approval/csv:
get:
operationId: crc.api.approval.get_csv
summary: Provides a list of all users for all approved studies
tags:
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: object
components:
securitySchemes:
jwt:
@ -837,6 +924,11 @@ components:
scheme: bearer
bearerFormat: JWT
x-bearerInfoFunc: crc.api.user.verify_token
auth_admin:
type: http
scheme: bearer
bearerFormat: JWT
x-bearerInfoFunc: crc.api.user.verify_token_admin
schemas:
User:
properties:
@ -1243,4 +1335,26 @@ components:
type: number
format: integer
example: 5
ApprovalCounts:
properties:
PENDING:
type: number
format: integer
example: 5
APPROVED:
type: number
format: integer
example: 5
DECLINED:
type: number
format: integer
example: 5
CANCELED:
type: number
format: integer
example: 5
AWAITING:
type: number
format: integer
example: 5

173
crc/api/approval.py
View File

@ -1,19 +1,161 @@
from crc import app, db, session
import json
import pickle
from base64 import b64decode
from datetime import datetime
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.approval import Approval, ApprovalModel, ApprovalSchema
from flask import g
from crc import db, session
from crc.api.common import ApiError
from crc.models.approval import Approval, ApprovalModel, ApprovalSchema, ApprovalStatus
from crc.models.workflow import WorkflowModel
from crc.services.approval_service import ApprovalService
from crc.services.ldap_service import LdapService
def get_approvals(approver_uid = None):
if not approver_uid:
db_approvals = ApprovalService.get_all_approvals()
else:
db_approvals = ApprovalService.get_approvals_per_user(approver_uid)
# Returns counts of approvals in each status group assigned to the given user.
# The goal is to return results as quickly as possible.
def get_approval_counts(as_user=None):
uid = as_user or g.user.uid
db_user_approvals = db.session.query(ApprovalModel)\
.filter_by(approver_uid=uid)\
.filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
.all()
study_ids = [a.study_id for a in db_user_approvals]
db_other_approvals = db.session.query(ApprovalModel)\
.filter(ApprovalModel.study_id.in_(study_ids))\
.filter(ApprovalModel.approver_uid != uid)\
.filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
.all()
# Make a dict of the other approvals where the key is the study id and the value is the approval
# TODO: This won't work if there are more than 2 approvals with the same study_id
other_approvals = {}
for approval in db_other_approvals:
other_approvals[approval.study_id] = approval
counts = {}
for name, value in ApprovalStatus.__members__.items():
counts[name] = 0
for approval in db_user_approvals:
# Check if another approval has the same study id
if approval.study_id in other_approvals:
other_approval = other_approvals[approval.study_id]
# Other approval takes precedence over this one
if other_approval.id < approval.id:
if other_approval.status == ApprovalStatus.PENDING.name:
counts[ApprovalStatus.AWAITING.name] += 1
elif other_approval.status == ApprovalStatus.DECLINED.name:
counts[ApprovalStatus.DECLINED.name] += 1
elif other_approval.status == ApprovalStatus.CANCELED.name:
counts[ApprovalStatus.CANCELED.name] += 1
elif other_approval.status == ApprovalStatus.APPROVED.name:
counts[approval.status] += 1
else:
counts[approval.status] += 1
else:
counts[approval.status] += 1
return counts
def get_all_approvals(status=None):
approvals = ApprovalService.get_all_approvals(include_cancelled=status is True)
results = ApprovalSchema(many=True).dump(approvals)
return results
def get_approvals(status=None, as_user=None):
#status = ApprovalStatus.PENDING.value
user = g.user.uid
if as_user:
user = as_user
approvals = ApprovalService.get_approvals_per_user(user, status,
include_cancelled=False)
results = ApprovalSchema(many=True).dump(approvals)
return results
def get_approvals_for_study(study_id=None):
db_approvals = ApprovalService.get_approvals_for_study(study_id)
approvals = [Approval.from_model(approval_model) for approval_model in db_approvals]
results = ApprovalSchema(many=True).dump(approvals)
return results
# ----- Begin descent into madness ---- #
def get_csv():
"""A damn lie, it's a json file. A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
man to do just about anything"""
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
output = []
errors = []
for approval in approvals:
try:
if approval.status != ApprovalStatus.APPROVED.value:
continue
for related_approval in approval.related_approvals:
if related_approval.status != ApprovalStatus.APPROVED.value:
continue
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
data = json.loads(workflow.bpmn_workflow_json)
last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
personnel = extract_value(last_task, 'personnel')
training_val = extract_value(last_task, 'RequiredTraining')
pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
review_complete = 'AllRequiredTraining' in training_val
pi_uid = workflow.study.primary_investigator_id
pi_details = LdapService.user_info(pi_uid)
details = []
details.append(pi_details)
for person in personnel:
uid = person['PersonnelComputingID']['value']
details.append(LdapService.user_info(uid))
for person in details:
record = {
"study_id": approval.study_id,
"pi_uid": pi_details.uid,
"pi": pi_details.display_name,
"name": person.display_name,
"uid": person.uid,
"email": person.email_address,
"supervisor": "",
"review_complete": review_complete,
}
# We only know the PI's supervisor.
if person.uid == pi_details.uid:
record["supervisor"] = pi_supervisor
output.append(record)
except Exception as e:
errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
return {"results": output, "errors": errors }
def extract_value(task, key):
if key in task['data']:
return pickle.loads(b64decode(task['data'][key]['__bytes__']))
else:
return ""
def find_task(uuid, task):
if task['id']['__uuid__'] == uuid:
return task
for child in task['children']:
task = find_task(uuid, child)
if task:
return task
# ----- come back to the world of the living ---- #
def update_approval(approval_id, body):
if approval_id is None:
raise ApiError('unknown_approval', 'Please provide a valid Approval ID.')
@ -22,9 +164,18 @@ def update_approval(approval_id, body):
if approval_model is None:
raise ApiError('unknown_approval', 'The approval "' + str(approval_id) + '" is not recognized.')
approval: Approval = ApprovalSchema().load(body)
approval.update_model(approval_model)
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_model.status = body['status']
approval_model.message = body['message']
approval_model.date_approved = datetime.now()
session.add(approval_model)
session.commit()
result = ApprovalSchema().dump(approval)
# Called only to send emails
approver = body['approver']['uid']
ApprovalService.update_approval(approval_id, approver)
result = ApprovalSchema().dump(approval_model)
return result

20
crc/api/common.py
View File

@ -1,9 +1,12 @@
from SpiffWorkflow import WorkflowException
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from crc import ma, app
class ApiError(Exception):
def __init__(self, code, message, status_code=400,
file_name="", task_id="", task_name="", tag=""):
file_name="", task_id="", task_name="", tag="", task_data = {}):
self.status_code = status_code
self.code = code # a short consistent string describing the error.
self.message = message # A detailed message that provides more information.
@ -11,6 +14,7 @@ class ApiError(Exception):
self.task_name = task_name or "" # OPTIONAL: The name of the task in the BPMN Diagram.
self.file_name = file_name or "" # OPTIONAL: The file that caused the error.
self.tag = tag or "" # OPTIONAL: The XML Tag that caused the issue.
self.task_data = task_data or "" # OPTIONAL: A snapshot of data connected to the task when error ocurred.
Exception.__init__(self, self.message)
@classmethod
@ -20,6 +24,7 @@ class ApiError(Exception):
instance.task_id = task.task_spec.name or ""
instance.task_name = task.task_spec.description or ""
instance.file_name = task.workflow.spec.file or ""
instance.task_data = task.data
return instance
@classmethod
@ -32,10 +37,21 @@ class ApiError(Exception):
instance.file_name = task_spec._wf_spec.file
return instance
@classmethod
def from_workflow_exception(cls, code, message, exp: WorkflowException):
"""We catch a lot of workflow exception errors,
so consolidating the code, and doing the best things
we can with the data we have."""
if isinstance(exp, WorkflowTaskExecException):
return ApiError.from_task(code, message, exp.task)
else:
return ApiError.from_task_spec(code, message, exp.sender)
class ApiErrorSchema(ma.Schema):
class Meta:
fields = ("code", "message", "workflow_name", "file_name", "task_name", "task_id")
fields = ("code", "message", "workflow_name", "file_name", "task_name", "task_id",
"task_data")
@app.errorhandler(ApiError)

7
crc/api/file.py
View File

@ -12,8 +12,9 @@ from crc.services.file_service import FileService
def to_file_api(file_model):
"""Converts a FileModel object to something we can return via the aip"""
return File.from_models(file_model, FileService.get_file_data(file_model.id))
"""Converts a FileModel object to something we can return via the api"""
return File.from_models(file_model, FileService.get_file_data(file_model.id),
FileService.get_doc_dictionary())
def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None):
@ -121,7 +122,7 @@ def get_file_info(file_id):
def update_file_info(file_id, body):
if file_id is None:
raise ApiError('unknown_file', 'Please provide a valid File ID.')
raise ApiError('no_such_file', 'Please provide a valid File ID.')
file_model = session.query(FileModel).filter_by(id=file_id).first()

8
crc/api/study.py
View File

@ -48,12 +48,10 @@ def update_study(study_id, body):
def get_study(study_id):
study_service = StudyService()
study = study_service.get_study(study_id)
study = StudyService.get_study(study_id)
if (study is None):
raise ApiError("Study not found", status_code=404)
schema = StudySchema()
return schema.dump(study)
raise ApiError("unknown_study", 'The study "' + study_id + '" is not recognized.', status_code=404)
return StudySchema().dump(study)
def delete_study(study_id):

15
crc/api/tools.py
View File

@ -9,6 +9,8 @@ from crc.api.common import ApiError
from crc.scripts.complete_template import CompleteTemplate
from crc.scripts.script import Script
import crc.scripts
from crc.services.mails import send_test_email
def render_markdown(data, template):
"""
@ -20,9 +22,9 @@ def render_markdown(data, template):
data = json.loads(data)
return template.render(**data)
except UndefinedError as ue:
raise ApiError(code="undefined field", message=ue.message)
raise ApiError(code="undefined_field", message=ue.message)
except Exception as e:
raise ApiError(code="invalid", message=str(e))
raise ApiError(code="invalid_render", message=str(e))
def render_docx():
@ -42,9 +44,9 @@ def render_docx():
cache_timeout=-1 # Don't cache these files on the browser.
)
except ValueError as e:
raise ApiError(code="invalid", message=str(e))
raise ApiError(code="undefined_field", message=str(e))
except Exception as e:
raise ApiError(code="invalid", message=str(e))
raise ApiError(code="invalid_render", message=str(e))
def list_scripts():
@ -59,3 +61,8 @@ def list_scripts():
})
return script_meta
def send_email(address):
"""Just sends a quick test email to assure the system is working."""
if not address:
address = "dan@sartography.com"
return send_test_email(address, [address])

258
crc/api/user.py
View File

@ -1,41 +1,122 @@
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
from crc.models.user import UserModel, UserModelSchema
from crc.services.ldap_service import LdapService, LdapUserInfo
from crc.services.ldap_service import LdapService, LdapModel
"""
.. module:: crc.api.user
:synopsis: Single Sign On (SSO) user login and session handlers
"""
def verify_token(token):
failure_error = ApiError("invalid_token", "Unable to decode the token you provided. Please re-authenticate", status_code=403)
if (not 'PRODUCTION' in app.config or not app.config['PRODUCTION']) and token == app.config["SWAGGER_AUTH_KEY"]:
def verify_token(token=None):
"""
Verifies the token for the user (if provided). If in production environment and token is not provided,
gets user from the SSO headers and returns their token.
Args:
token: Optional[str]
Returns:
token: str
Raises:
ApiError. If not on production and token is not valid, returns an 'invalid_token' 403 error.
If on production and user is not authenticated, returns a 'no_user' 403 error.
"""
failure_error = ApiError("invalid_token", "Unable to decode the token you provided. Please re-authenticate",
status_code=403)
if not _is_production() and (token is None or 'user' not in g):
g.user = UserModel.query.first()
token = g.user.encode_auth_token()
try:
token_info = UserModel.decode_auth_token(token)
g.user = UserModel.query.filter_by(uid=token_info['sub']).first()
except:
raise failure_error
if g.user is not None:
return token_info
if token:
try:
token_info = UserModel.decode_auth_token(token)
g.user = UserModel.query.filter_by(uid=token_info['sub']).first()
except:
raise failure_error
if g.user is not None:
return token_info
else:
raise failure_error
# If there's no token and we're in production, get the user from the SSO headers and return their token
if not token and _is_production():
uid = _get_request_uid(request)
if uid is not None:
db_user = UserModel.query.filter_by(uid=uid).first()
if db_user is not None:
g.user = db_user
token = g.user.encode_auth_token().decode()
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)
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
Args:
token: Optional[str]
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:
raise failure_error
return verify_token(token)
def get_current_user():
return UserModelSchema().dump(g.user)
@app.route('/v1.0/login')
def sso_login():
# This what I see coming back:
def login(
uid=None,
redirect_url=None,
):
"""
In non-production environment, provides an endpoint for end-to-end system testing that allows the system
to simulate logging in as a specific user. In production environment, simply logs user in via single-sign-on
(SSO) Shibboleth authentication headers.
Args:
uid: Optional[str]
redirect_url: Optional[str]
Returns:
str. If not on production, returns the frontend auth callback URL, with auth token appended.
If on production and user is authenticated via SSO, returns the frontend auth callback URL,
with auth token appended.
Raises:
ApiError. If on production and user is not authenticated, returns a 404 error.
"""
# ----------------------------------------
# Shibboleth Authentication Headers
# ----------------------------------------
# X-Remote-Cn: Daniel Harold Funk (dhf8r)
# X-Remote-Sn: Funk
# X-Remote-Givenname: Daniel
@ -50,62 +131,52 @@ def sso_login():
# X-Forwarded-Host: dev.crconnect.uvadcos.io
# X-Forwarded-Server: dev.crconnect.uvadcos.io
# Connection: Keep-Alive
uid = request.headers.get("Uid")
if not uid:
uid = request.headers.get("X-Remote-Uid")
if not uid:
raise ApiError("invalid_sso_credentials", "'Uid' nor 'X-Remote-Uid' were present in the headers: %s"
% str(request.headers))
redirect = request.args.get('redirect')
app.logger.info("SSO_LOGIN: Full URL: " + request.url)
app.logger.info("SSO_LOGIN: User Id: " + uid)
app.logger.info("SSO_LOGIN: Will try to redirect to : " + str(redirect))
# If we're in production, override any uid with the uid from the SSO request headers
if _is_production():
uid = _get_request_uid(request)
ldap_service = LdapService()
info = ldap_service.user_info(uid)
if uid:
app.logger.info("SSO_LOGIN: Full URL: " + request.url)
app.logger.info("SSO_LOGIN: User Id: " + uid)
app.logger.info("SSO_LOGIN: Will try to redirect to : " + str(redirect_url))
ldap_info = LdapService().user_info(uid)
if ldap_info:
return _handle_login(ldap_info, redirect_url)
raise ApiError('404', 'unknown')
return _handle_login(info, redirect)
@app.route('/sso')
def sso():
response = ""
response += "<h1>Headers</h1>"
response += "<ul>"
for k,v in request.headers:
for k, v in request.headers:
response += "<li><b>%s</b> %s</li>\n" % (k, v)
response += "<h1>Environment</h1>"
for k,v in request.environ:
for k, v in request.environ:
response += "<li><b>%s</b> %s</li>\n" % (k, v)
return response
def _handle_login(user_info: LdapUserInfo, redirect_url=app.config['FRONTEND_AUTH_CALLBACK']):
"""On successful login, adds user to database if the user is not already in the system,
then returns the frontend auth callback URL, with auth token appended.
def _handle_login(user_info: LdapModel, redirect_url=None):
"""
On successful login, adds user to database if the user is not already in the system,
then returns the frontend auth callback URL, with auth token appended.
Args:
user_info - an ldap user_info object.
redirect_url: Optional[str]
Args:
user_info - an ldap user_info object.
redirect_url: Optional[str]
Returns:
Response. 302 - Redirects to the frontend auth callback URL, with auth token appended.
Returns:
Response. 302 - Redirects to the frontend auth callback URL, with auth token appended.
"""
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
if user is None:
# Add new user
user = UserModel()
user.uid = user_info.uid
user.display_name = user_info.display_name
user.email_address = user_info.email_address
user.affiliation = user_info.affiliation
user.title = user_info.title
db.session.add(user)
db.session.commit()
user = _upsert_user(user_info)
g.user = user
# Return the frontend auth callback URL, with auth token appended.
auth_token = user.encode_auth_token().decode()
@ -120,41 +191,44 @@ def _handle_login(user_info: LdapUserInfo, redirect_url=app.config['FRONTEND_AUT
return auth_token
def _upsert_user(user_info):
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
def backdoor(
uid=None,
affiliation=None,
display_name=None,
email_address=None,
eppn=None,
first_name=None,
last_name=None,
title=None,
redirect=None,
):
"""A backdoor for end-to-end system testing that allows the system to simulate logging in as a specific user.
Only works if the application is running in a non-production environment.
Args:
uid: str
affiliation: Optional[str]
display_name: Optional[str]
email_address: Optional[str]
eppn: Optional[str]
first_name: Optional[str]
last_name: Optional[str]
title: Optional[str]
redirect_url: Optional[str]
Returns:
str. If not on production, returns the frontend auth callback URL, with auth token appended.
Raises:
ApiError. If on production, returns a 404 error.
"""
if not 'PRODUCTION' in app.config or not app.config['PRODUCTION']:
ldap_info = LdapService().user_info(uid)
return _handle_login(ldap_info, redirect)
if user is None:
# Add new user
user = UserModel()
else:
raise ApiError('404', 'unknown')
user = db.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
user.email_address = user_info.email_address
user.affiliation = user_info.affiliation
user.title = user_info.title
db.session.add(user)
db.session.commit()
return user
def _get_request_uid(req):
uid = None
if _is_production():
if 'user' in g and g.user is not None:
return g.user.uid
uid = req.headers.get("Uid")
if not uid:
uid = req.headers.get("X-Remote-Uid")
if not uid:
raise ApiError("invalid_sso_credentials", "'Uid' nor 'X-Remote-Uid' were present in the headers: %s"
% str(req.headers))
return uid
def _is_production():
return 'PRODUCTION' in app.config and app.config['PRODUCTION']

44
crc/api/workflow.py
View File

@ -1,6 +1,8 @@
import uuid
from crc import session
from flask import g
from crc import session, app
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.api_models import WorkflowApi, WorkflowApiSchema, NavigationItem, NavigationItemSchema
from crc.models.file import FileModel, LookupDataSchema
@ -44,6 +46,13 @@ def validate_workflow_specification(spec_id):
try:
WorkflowService.test_spec(spec_id)
except ApiError as ae:
ae.message = "When populating all fields ... " + ae.message
errors.append(ae)
try:
# Run the validation twice, the second time, just populate the required fields.
WorkflowService.test_spec(spec_id, required_only=True)
except ApiError as ae:
ae.message = "When populating only required fields ... " + ae.message
errors.append(ae)
return ApiErrorSchema(many=True).dump(errors)
@ -112,6 +121,8 @@ def __get_workflow_api_model(processor: WorkflowProcessor, next_task = None):
navigation.append(NavigationItem(**nav_item))
NavigationItemSchema().dump(nav_item)
spec = session.query(WorkflowSpecModel).filter_by(id=processor.workflow_spec_id).first()
workflow_api = WorkflowApi(
id=processor.get_workflow_id(),
status=processor.get_status(),
@ -120,9 +131,10 @@ def __get_workflow_api_model(processor: WorkflowProcessor, next_task = None):
workflow_spec_id=processor.workflow_spec_id,
spec_version=processor.get_version_string(),
is_latest_spec=processor.is_latest_spec,
total_tasks=processor.workflow_model.total_tasks,
total_tasks=len(navigation),
completed_tasks=processor.workflow_model.completed_tasks,
last_updated=processor.workflow_model.last_updated
last_updated=processor.workflow_model.last_updated,
title=spec.display_name
)
if not next_task: # The Next Task can be requested to be a certain task, useful for parallel tasks.
# This may or may not work, sometimes there is no next task to complete.
@ -146,6 +158,7 @@ def delete_workflow(workflow_id):
def set_current_task(workflow_id, task_id):
workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
user_uid = __get_user_uid(workflow_model.study.user_uid)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
task = processor.bpmn_workflow.get_task(task_id)
@ -157,13 +170,21 @@ def set_current_task(workflow_id, task_id):
if task.state == task.COMPLETED:
task.reset_token(reset_data=False) # we could optionally clear the previous data.
processor.save()
WorkflowService.log_task_action(processor, task, WorkflowService.TASK_ACTION_TOKEN_RESET)
WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_TOKEN_RESET)
workflow_api_model = __get_workflow_api_model(processor, task)
return WorkflowApiSchema().dump(workflow_api_model)
def update_task(workflow_id, task_id, body):
workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
if workflow_model is None:
raise ApiError("invalid_workflow_id", "The given workflow id is not valid.", status_code=404)
elif workflow_model.study is None:
raise ApiError("invalid_study", "There is no study associated with the given workflow.", status_code=404)
user_uid = __get_user_uid(workflow_model.study.user_uid)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
task = processor.bpmn_workflow.get_task(task_id)
@ -174,7 +195,7 @@ def update_task(workflow_id, task_id, body):
processor.complete_task(task)
processor.do_engine_steps()
processor.save()
WorkflowService.log_task_action(processor, task, WorkflowService.TASK_ACTION_COMPLETE)
WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_COMPLETE)
workflow_api_model = __get_workflow_api_model(processor)
return WorkflowApiSchema().dump(workflow_api_model)
@ -228,4 +249,15 @@ def lookup(workflow_id, field_id, query, limit):
"""
workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
lookup_data = LookupService.lookup(workflow, field_id, query, limit)
return LookupDataSchema(many=True).dump(lookup_data)
return LookupDataSchema(many=True).dump(lookup_data)
def __get_user_uid(user_uid):
if 'user' in g:
if g.user.uid not in app.config['ADMIN_UIDS'] and user_uid != g.user.uid:
raise ApiError("permission_denied", "You are not authorized to edit the task data for this workflow.", status_code=403)
else:
return g.user.uid
else:
raise ApiError("logged_out", "You are no longer logged in.", status_code=401)

9
crc/models/api_models.py
View File

@ -31,10 +31,12 @@ class NavigationItem(object):
class Task(object):
PROP_OPTIONS_REPEAT = "repeat"
PROP_OPTIONS_FILE = "spreadsheet.name"
PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column"
PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column"
PROP_LDAP_LOOKUP = "ldap.lookup"
VALIDATION_REQUIRED = "required"
FIELD_TYPE_AUTO_COMPLETE = "autocomplete"
@ -117,7 +119,7 @@ class NavigationItemSchema(ma.Schema):
class WorkflowApi(object):
def __init__(self, id, status, next_task, navigation,
spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks, last_updated):
spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks, last_updated, title):
self.id = id
self.status = status
self.next_task = next_task # The next task that requires user input.
@ -128,13 +130,14 @@ class WorkflowApi(object):
self.total_tasks = total_tasks
self.completed_tasks = completed_tasks
self.last_updated = last_updated
self.title = title
class WorkflowApiSchema(ma.Schema):
class Meta:
model = WorkflowApi
fields = ["id", "status", "next_task", "navigation",
"workflow_spec_id", "spec_version", "is_latest_spec", "total_tasks", "completed_tasks",
"last_updated"]
"last_updated", "title"]
unknown = INCLUDE
status = EnumField(WorkflowStatus)
@ -145,7 +148,7 @@ class WorkflowApiSchema(ma.Schema):
def make_workflow(self, data, **kwargs):
keys = ['id', 'status', 'next_task', 'navigation',
'workflow_spec_id', 'spec_version', 'is_latest_spec', "total_tasks", "completed_tasks",
"last_updated"]
"last_updated", "title"]
filtered_fields = {key: data[key] for key in keys}
filtered_fields['next_task'] = TaskSchema().make_task(data['next_task'])
return WorkflowApi(**filtered_fields)

90
crc/models/approval.py
View File

@ -1,24 +1,28 @@
import enum
import marshmallow
from ldap3.core.exceptions import LDAPSocketOpenError
from marshmallow import INCLUDE
from marshmallow import INCLUDE, fields
from sqlalchemy import func
from crc import db, ma
from crc import db, ma, app
from crc.api.common import ApiError
from crc.models.file import FileDataModel
from crc.models.ldap import LdapSchema
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowModel
from crc.services.file_service import FileService
from crc.services.ldap_service import LdapService
class ApprovalStatus(enum.Enum):
WAITING = "WAITING" # no one has done jack.
PENDING = "PENDING" # no one has done jack.
APPROVED = "APPROVED" # approved by the reviewer
DECLINED = "DECLINED" # rejected by the reviewer
CANCELED = "CANCELED" # The document was replaced with a new version and this review is no longer needed.
# Used for overall status only, never set on a task.
AWAITING = "AWAITING" # awaiting another approval
class ApprovalFile(db.Model):
file_data_id = db.Column(db.Integer, db.ForeignKey(FileDataModel.id), primary_key=True)
@ -32,13 +36,14 @@ class ApprovalModel(db.Model):
__tablename__ = 'approval'
id = db.Column(db.Integer, primary_key=True)
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
study = db.relationship(StudyModel, backref='approval', cascade='all,delete')
study = db.relationship(StudyModel)
workflow_id = db.Column(db.Integer, db.ForeignKey(WorkflowModel.id), nullable=False)
workflow = db.relationship(WorkflowModel)
approver_uid = db.Column(db.String) # Not linked to user model, as they may not have logged in yet.
status = db.Column(db.String)
message = db.Column(db.String, default='')
date_created = db.Column(db.DateTime(timezone=True), default=func.now())
date_approved = db.Column(db.DateTime(timezone=True), default=None)
version = db.Column(db.Integer) # Incremented integer, so 1,2,3 as requests are made.
approval_files = db.relationship(ApprovalFile, back_populates="approval",
cascade="all, delete, delete-orphan",
@ -62,33 +67,37 @@ class Approval(object):
instance.status = model.status
instance.message = model.message
instance.date_created = model.date_created
instance.date_approved = model.date_approved
instance.version = model.version
instance.title = ''
instance.related_approvals = []
if model.study:
instance.title = model.study.title
instance.approver = {}
try:
ldap_service = LdapService()
principal_investigator_id = model.study.primary_investigator_id
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
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
instance.approver = LdapService.user_info(model.approver_uid)
instance.primary_investigator = LdapService.user_info(model.study.primary_investigator_id)
except ApiError as ae:
app.logger.error("Ldap lookup failed for approval record %i" % model.id)
doc_dictionary = FileService.get_doc_dictionary()
instance.associated_files = []
for approval_file in model.approval_files:
try:
# fixme: This is slow because we are doing a ton of queries to find the irb code.
extra_info = doc_dictionary[approval_file.file_data.file_model.irb_doc_code]
except:
extra_info = None
associated_file = {}
associated_file['id'] = approval_file.file_data.file_model.id
associated_file['name'] = approval_file.file_data.file_model.name
if extra_info:
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'] = '(' + 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)
@ -100,10 +109,17 @@ class Approval(object):
class ApprovalSchema(ma.Schema):
approver = fields.Nested(LdapSchema, dump_only=True)
primary_investigator = fields.Nested(LdapSchema, dump_only=True)
related_approvals = fields.List(fields.Nested('ApprovalSchema', allow_none=True, dump_only=True))
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", "date_approved",
"related_approvals"]
unknown = INCLUDE
@marshmallow.post_load
@ -111,30 +127,4 @@ class ApprovalSchema(ma.Schema):
"""Loads the basic approval data for updates to the database"""
return Approval(**data)
# Carlos: Here is the data structure I was trying to imagine.
# If I were to continue down my current traing of thought, I'd create
# another class called just "Approval" that can take an ApprovalModel from the
# database and construct a data structure like this one, that can
# be provided to the API at an /approvals endpoint with GET and PUT
# dat = { "approvals": [
# {"id": 1,
# "study_id": 20,
# "workflow_id": 454,
# "study_title": "Dan Funk (dhf8r)", # Really it's just the name of the Principal Investigator
# "workflow_version": "21",
# "approver": { # Pulled from ldap
# "uid": "bgb22",
# "display_name": "Billy Bob (bgb22)",
# "title": "E42:He's a hoopy frood",
# "department": "E0:EN-Eng Study of Parallel Universes",
# },
# "files": [
# {
# "id": 124,
# "name": "ResearchRestart.docx",
# "content_type": "docx-something-whatever"
# }
# ]
# }
# ...
# ]

19
crc/models/file.py
View File

@ -82,11 +82,14 @@ class FileModel(db.Model):
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=True)
irb_doc_code = db.Column(db.String, nullable=True) # Code reference to the irb_documents.xlsx reference file.
# A request was made to delete the file, but we can't because there are
# active approvals or running workflows that depend on it. So we archive
# it instead, hide it in the interface.
archived = db.Column(db.Boolean, default=False, nullable=False)
class File(object):
@classmethod
def from_models(cls, model: FileModel, data_model: FileDataModel):
def from_models(cls, model: FileModel, data_model: FileDataModel, doc_dictionary):
instance = cls()
instance.id = model.id
instance.name = model.name
@ -99,6 +102,15 @@ class File(object):
instance.workflow_id = model.workflow_id
instance.irb_doc_code = model.irb_doc_code
instance.type = model.type
if model.irb_doc_code and model.irb_doc_code in doc_dictionary:
instance.category = "/".join(filter(None, [doc_dictionary[model.irb_doc_code]['category1'],
doc_dictionary[model.irb_doc_code]['category2'],
doc_dictionary[model.irb_doc_code]['category3']]))
instance.description = doc_dictionary[model.irb_doc_code]['description']
instance.download_name = ".".join([instance.category, model.type.value])
else:
instance.category = ""
instance.description = ""
if data_model:
instance.last_modified = data_model.date_created
instance.latest_version = data_model.version
@ -122,7 +134,8 @@ class FileSchema(ma.Schema):
model = File
fields = ["id", "name", "is_status", "is_reference", "content_type",
"primary", "primary_process_id", "workflow_spec_id", "workflow_id",
"irb_doc_code", "last_modified", "latest_version", "type"]
"irb_doc_code", "last_modified", "latest_version", "type", "categories",
"description", "category", "description", "download_name"]
unknown = INCLUDE
type = EnumField(FileType)

39
crc/models/ldap.py Normal file
View File

@ -0,0 +1,39 @@
from flask_marshmallow.sqla import SQLAlchemyAutoSchema
from marshmallow import EXCLUDE
from sqlalchemy import func
from crc import db
class LdapModel(db.Model):
uid = db.Column(db.String, primary_key=True)
display_name = db.Column(db.String)
given_name = db.Column(db.String)
email_address = db.Column(db.String)
telephone_number = db.Column(db.String)
title = db.Column(db.String)
department = db.Column(db.String)
affiliation = db.Column(db.String)
sponsor_type = db.Column(db.String)
date_cached = db.Column(db.DateTime(timezone=True), default=func.now())
@classmethod
def from_entry(cls, entry):
return LdapModel(uid=entry.uid.value,
display_name=entry.displayName.value,
given_name=", ".join(entry.givenName),
email_address=entry.mail.value,
telephone_number=entry.telephoneNumber.value,
title=", ".join(entry.title),
department=", ".join(entry.uvaDisplayDepartment),
affiliation=", ".join(entry.uvaPersonIAMAffiliation),
sponsor_type=", ".join(entry.uvaPersonSponsoredType))
class LdapSchema(SQLAlchemyAutoSchema):
class Meta:
model = LdapModel
load_instance = True
include_relationships = True
include_fk = True # Includes foreign keys
unknown = EXCLUDE

13
crc/models/study.py
View File

@ -5,7 +5,7 @@ from sqlalchemy import func
from crc import db, ma
from crc.api.common import ApiErrorSchema
from crc.models.file import FileModel, SimpleFileSchema
from crc.models.file import FileModel, SimpleFileSchema, FileSchema
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, WorkflowStatus, WorkflowSpecModel, \
WorkflowModel
@ -106,7 +106,8 @@ class Study(object):
def __init__(self, title, last_updated, primary_investigator_id, user_uid,
id=None,
protocol_builder_status=None,
sponsor="", hsr_number="", ind_number="", categories=[], **argsv):
sponsor="", hsr_number="", ind_number="", categories=[],
files=[], approvals=[], **argsv):
self.id = id
self.user_uid = user_uid
self.title = title
@ -117,8 +118,9 @@ class Study(object):
self.hsr_number = hsr_number
self.ind_number = ind_number
self.categories = categories
self.approvals = approvals
self.warnings = []
self.files = []
self.files = files
@classmethod
def from_model(cls, study_model: StudyModel):
@ -149,12 +151,13 @@ class StudySchema(ma.Schema):
hsr_number = fields.String(allow_none=True)
sponsor = fields.String(allow_none=True)
ind_number = fields.String(allow_none=True)
files = fields.List(fields.Nested(SimpleFileSchema), dump_only=True)
files = fields.List(fields.Nested(FileSchema), dump_only=True)
approvals = fields.List(fields.Nested('ApprovalSchema'), dump_only=True)
class Meta:
model = Study
additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
"sponsor", "ind_number"]
"sponsor", "ind_number", "approvals", "files"]
unknown = INCLUDE
@marshmallow.post_load

10
crc/models/user.py
View File

@ -19,7 +19,7 @@ class UserModel(db.Model):
last_name = db.Column(db.String, nullable=True)
title = db.Column(db.String, nullable=True)
# Add Department and School
# TODO: Add Department and School
def encode_auth_token(self):
@ -27,7 +27,7 @@ class UserModel(db.Model):
Generates the Auth Token
:return: string
"""
hours = int(app.config['TOKEN_AUTH_TTL_HOURS'])
hours = float(app.config['TOKEN_AUTH_TTL_HOURS'])
payload = {
'exp': datetime.datetime.utcnow() + datetime.timedelta(hours=hours, minutes=0, seconds=0),
'iat': datetime.datetime.utcnow(),
@ -36,7 +36,7 @@ class UserModel(db.Model):
return jwt.encode(
payload,
app.config.get('TOKEN_AUTH_SECRET_KEY'),
algorithm='HS256'
algorithm='HS256',
)
@staticmethod
@ -50,9 +50,9 @@ class UserModel(db.Model):
payload = jwt.decode(auth_token, app.config.get('TOKEN_AUTH_SECRET_KEY'), algorithms='HS256')
return payload
except jwt.ExpiredSignatureError:
raise ApiError('token_expired', 'The Authentication token you provided expired, and must be renewed.')
raise ApiError('token_expired', 'The Authentication token you provided expired and must be renewed.')
except jwt.InvalidTokenError:
raise ApiError('token_invalid', 'The Authentication token you provided. You need a new token. ')
raise ApiError('token_invalid', 'The Authentication token you provided is invalid. You need a new token. ')
class UserModelSchema(SQLAlchemyAutoSchema):

17
crc/scripts/complete_template.py
View File

@ -29,7 +29,8 @@ Takes two arguments:
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, process the template, but do not store it in the database."""
self.process_template(task, study_id, None, *args, **kwargs)
workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
self.process_template(task, study_id, workflow, *args, **kwargs)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
@ -62,13 +63,13 @@ Takes two arguments:
# Get the workflow specification file with the given name.
file_data_models = FileService.get_spec_data_files(
workflow_spec_id=workflow.workflow_spec_id,
workflow_id=workflow.id)
for file_data in file_data_models:
if file_data.file_model.name == file_name:
file_data_model = file_data
if workflow is None or file_data_model is None:
file_data_model = FileService.get_workflow_file_data(task.workflow, file_name)
workflow_id=workflow.id,
name=file_name)
if len(file_data_models) > 0:
file_data_model = file_data_models[0]
else:
raise ApiError(code="invalid_argument",
message="Uable to locate a file with the given name.")
# Get images from file/files fields
if len(args) == 3:

6
crc/scripts/request_approval.py
View File

@ -11,7 +11,8 @@ 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.
or be quoted strings. The order is important. Approvals will be processed
in this order.
Example:
RequestApproval approver1 "dhf8r"
@ -26,7 +27,8 @@ RequestApproval approver1 "dhf8r"
ApprovalService.add_approval(study_id, workflow_id, args)
elif isinstance(uids, list):
for id in uids:
ApprovalService.add_approval(study_id, workflow_id, id)
if id: ## Assure it's not empty or null
ApprovalService.add_approval(study_id, workflow_id, id)
def get_uids(self, task, args):
if len(args) < 1:

192
crc/services/approval_service.py
View File

@ -2,37 +2,168 @@ from datetime import datetime
from sqlalchemy import desc
from crc import db, session
from crc import app, db, session
from crc.api.common import ApiError
from crc.models.approval import ApprovalModel, ApprovalStatus, ApprovalFile
from crc.models.approval import ApprovalModel, ApprovalStatus, ApprovalFile, Approval
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowModel
from crc.services.file_service import FileService
from crc.services.ldap_service import LdapService
from crc.services.mails import (
send_ramp_up_submission_email,
send_ramp_up_approval_request_email,
send_ramp_up_approval_request_first_review_email,
send_ramp_up_approved_email,
send_ramp_up_denied_email,
send_ramp_up_denied_email_to_approver
)
class ApprovalService(object):
"""Provides common tools for working with an Approval"""
@staticmethod
def get_approvals_per_user(approver_uid):
"""Returns a list of all approvals for the given user (approver)"""
db_approvals = session.query(ApprovalModel).filter_by(approver_uid=approver_uid).all()
return db_approvals
def __one_approval_from_study(study, approver_uid = None, status=None,
include_cancelled=True):
"""Returns one approval, with all additional approvals as 'related_approvals',
the main approval can be pinned to an approver with an optional argument.
Will return null if no approvals exist on the study."""
main_approval = None
related_approvals = []
query = db.session.query(ApprovalModel).filter(ApprovalModel.study_id == study.id)
if not include_cancelled:
query=query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
approvals = query.all() # All non-cancelled approvals.
for approval_model in approvals:
if approval_model.approver_uid == approver_uid:
main_approval = approval_model
else:
related_approvals.append(approval_model)
# IF WE ARE JUST RETURNING ALL OF THE APPROVALS PER STUDY
if not main_approval and len(related_approvals) > 0:
main_approval = related_approvals[0]
related_approvals = related_approvals[1:]
if main_approval is not None: # May be null if the study has no approvals.
final_status = ApprovalService.__calculate_overall_approval_status(main_approval, related_approvals)
if status and final_status != status: return # Now that we are certain of the status, filter on it.
main_approval = Approval.from_model(main_approval)
main_approval.status = final_status
for ra in related_approvals:
main_approval.related_approvals.append(Approval.from_model(ra))
return main_approval
@staticmethod
def get_all_approvals():
"""Returns a list of all approvlas"""
db_approvals = session.query(ApprovalModel).all()
return db_approvals
def __calculate_overall_approval_status(approval, related):
# In the case of pending approvals, check to see if there is a related approval
# that proceeds this approval - and if it is declined, or still pending, then change
# the state of the approval to be Declined, or Waiting respectively.
if approval.status == ApprovalStatus.PENDING.value:
for ra in related:
if ra.id < approval.id:
if ra.status == ApprovalStatus.DECLINED.value or ra.status == ApprovalStatus.CANCELED.value:
return ra.status # If any prior approval id declined or cancelled so is this approval.
elif ra.status == ApprovalStatus.PENDING.value:
return ApprovalStatus.AWAITING.value # if any prior approval is pending, then this is waiting.
return approval.status
else:
return approval.status
@staticmethod
def update_approval(approval_id, approver_uid, status):
def get_approvals_per_user(approver_uid, status=None, include_cancelled=False):
"""Returns a list of approval objects (not db models) for the given
approver. """
studies = db.session.query(StudyModel).join(ApprovalModel).\
filter(ApprovalModel.approver_uid == approver_uid).all()
approvals = []
for study in studies:
approval = ApprovalService.__one_approval_from_study(study, approver_uid,
status, include_cancelled)
if approval:
approvals.append(approval)
return approvals
@staticmethod
def get_all_approvals(include_cancelled=True):
"""Returns a list of all approval objects (not db models), one record
per study, with any associated approvals grouped under the first approval."""
studies = db.session.query(StudyModel).all()
approvals = []
for study in studies:
approval = ApprovalService.__one_approval_from_study(study, include_cancelled=include_cancelled)
if approval:
approvals.append(approval)
return approvals
@staticmethod
def get_approvals_for_study(study_id, include_cancelled=True):
"""Returns an array of Approval objects for the study, it does not
compute the related approvals."""
query = session.query(ApprovalModel).filter_by(study_id=study_id)
if not include_cancelled:
query = query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
db_approvals = query.all()
return [Approval.from_model(approval_model) for approval_model in db_approvals]
@staticmethod
def update_approval(approval_id, approver_uid):
"""Update a specific approval"""
db_approval = session.query(ApprovalModel).get(approval_id)
status = db_approval.status
if db_approval:
db_approval.status = status
session.add(db_approval)
session.commit()
# db_approval.status = status
# session.add(db_approval)
# session.commit()
if status == ApprovalStatus.APPROVED.value:
# second_approval = ApprovalModel().query.filter_by(
# study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,
# status=ApprovalStatus.PENDING.value, version=db_approval.version).first()
# if second_approval:
# send rrp approval request for second approver
ldap_service = LdapService()
pi_user_info = ldap_service.user_info(db_approval.study.primary_investigator_id)
approver_info = ldap_service.user_info(approver_uid)
# send rrp submission
mail_result = send_ramp_up_approved_email(
'askresearch@virginia.edu',
[pi_user_info.email_address],
f'{approver_info.display_name} - ({approver_info.uid})'
)
if mail_result:
app.logger.error(mail_result)
elif status == ApprovalStatus.DECLINED.value:
ldap_service = LdapService()
pi_user_info = ldap_service.user_info(db_approval.study.primary_investigator_id)
approver_info = ldap_service.user_info(approver_uid)
# send rrp submission
mail_result = send_ramp_up_denied_email(
'askresearch@virginia.edu',
[pi_user_info.email_address],
f'{approver_info.display_name} - ({approver_info.uid})'
)
if mail_result:
app.logger.error(mail_result)
first_approval = ApprovalModel().query.filter_by(
study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,
status=ApprovalStatus.APPROVED.value, version=db_approval.version).first()
if first_approval:
# Second approver denies
first_approver_info = ldap_service.user_info(first_approval.approver_uid)
approver_email = [first_approver_info.email_address] if first_approver_info.email_address else app.config['FALLBACK_EMAILS']
# send rrp denied by second approver email to first approver
mail_result = send_ramp_up_denied_email_to_approver(
'askresearch@virginia.edu',
approver_email,
f'{pi_user_info.display_name} - ({pi_user_info.uid})',
f'{approver_info.display_name} - ({approver_info.uid})'
)
if mail_result:
app.logger.error(mail_result)
# TODO: Log update action by approver_uid - maybe ?
return db_approval
@ -78,14 +209,43 @@ class ApprovalService(object):
version = 1
model = ApprovalModel(study_id=study_id, workflow_id=workflow_id,
approver_uid=approver_uid, status=ApprovalStatus.WAITING.value,
approver_uid=approver_uid, status=ApprovalStatus.PENDING.value,
message="", date_created=datetime.now(),
version=version)
approval_files = ApprovalService._create_approval_files(workflow_data_files, model)
# Check approvals count
approvals_count = ApprovalModel().query.filter_by(study_id=study_id, workflow_id=workflow_id,
version=version).count()
db.session.add(model)
db.session.add_all(approval_files)
db.session.commit()
# Send first email
if approvals_count == 0:
ldap_service = LdapService()
pi_user_info = ldap_service.user_info(model.study.primary_investigator_id)
approver_info = ldap_service.user_info(approver_uid)
# send rrp submission
mail_result = send_ramp_up_submission_email(
'askresearch@virginia.edu',
[pi_user_info.email_address],
f'{approver_info.display_name} - ({approver_info.uid})'
)
if mail_result:
app.logger.error(mail_result)
# send rrp approval request for first approver
# enhance the second part in case it bombs
approver_email = [approver_info.email_address] if approver_info.email_address else app.config['FALLBACK_EMAILS']
mail_result = send_ramp_up_approval_request_first_review_email(
'askresearch@virginia.edu',
approver_email,
f'{pi_user_info.display_name} - ({pi_user_info.uid})'
)
if mail_result:
app.logger.error(mail_result)
@staticmethod
def _create_approval_files(workflow_data_files, approval):
"""Currently based exclusively on the status of files associated with a workflow."""

64
crc/services/file_service.py
View File

@ -5,11 +5,13 @@ from datetime import datetime
from uuid import UUID
from xml.etree import ElementTree
import flask
from SpiffWorkflow.bpmn.parser.ValidationException import ValidationException
from pandas import ExcelFile
from sqlalchemy import desc
from sqlalchemy.exc import IntegrityError
from crc import session
from crc import session, app
from crc.api.common import ApiError
from crc.models.file import FileType, FileDataModel, FileModel, LookupFileModel, LookupDataModel
from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecDependencyFile
@ -20,6 +22,14 @@ class FileService(object):
DOCUMENT_LIST = "irb_documents.xlsx"
INVESTIGATOR_LIST = "investigators.xlsx"
__doc_dictionary = None
@staticmethod
def get_doc_dictionary():
if not FileService.__doc_dictionary:
FileService.__doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
return FileService.__doc_dictionary
@staticmethod
def add_workflow_spec_file(workflow_spec: WorkflowSpecModel,
name, content_type, binary_data, primary=False, is_status=False):
@ -35,10 +45,8 @@ class FileService(object):
@staticmethod
def is_allowed_document(code):
data_model = FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
xls = ExcelFile(data_model.data)
df = xls.parse(xls.sheet_names[0])
return code in df['code'].values
doc_dict = FileService.get_doc_dictionary()
return code in doc_dict
@staticmethod
def add_workflow_file(workflow_id, irb_doc_code, name, content_type, binary_data):
@ -86,6 +94,7 @@ class FileService(object):
def get_workflow_files(workflow_id):
"""Returns all the file models associated with a running workflow."""
return session.query(FileModel).filter(FileModel.workflow_id == workflow_id).\
filter(FileModel.archived == False).\
order_by(FileModel.id).all()
@staticmethod
@ -117,7 +126,11 @@ class FileService(object):
md5_checksum = UUID(hashlib.md5(binary_data).hexdigest())
if (latest_data_model is not None) and (md5_checksum == latest_data_model.md5_hash):
# This file does not need to be updated, it's the same file.
# This file does not need to be updated, it's the same file. If it is arhived,
# then de-arvhive it.
file_model.archived = False
session.add(file_model)
session.commit()
return file_model
# Verify the extension
@ -129,6 +142,7 @@ class FileService(object):
else:
file_model.type = FileType[file_extension]
file_model.content_type = content_type
file_model.archived = False # Unarchive the file if it is archived.
if latest_data_model is None:
version = 1
@ -178,7 +192,8 @@ class FileService(object):
def get_files_for_study(study_id, irb_doc_code=None):
query = session.query(FileModel).\
join(WorkflowModel).\
filter(WorkflowModel.study_id == study_id)
filter(WorkflowModel.study_id == study_id).\
filter(FileModel.archived == False)
if irb_doc_code:
query = query.filter(FileModel.irb_doc_code == irb_doc_code)
return query.all()
@ -198,6 +213,9 @@ class FileService(object):
if name:
query = query.filter_by(name=name)
query = query.filter(FileModel.archived == False)
query = query.order_by(FileModel.id)
results = query.all()
@ -260,11 +278,12 @@ class FileService(object):
@staticmethod
def get_workflow_file_data(workflow, file_name):
"""Given a SPIFF Workflow Model, tracks down a file with the given name in the database and returns its data"""
"""This method should be deleted, find where it is used, and remove this method.
Given a SPIFF Workflow Model, tracks down a file with the given name in the database and returns its data"""
workflow_spec_model = FileService.find_spec_model_in_db(workflow)
if workflow_spec_model is None:
raise ApiError(code="workflow_model_error",
raise ApiError(code="unknown_workflow",
message="Something is wrong. I can't find the workflow you are using.")
file_data_model = session.query(FileDataModel) \
@ -295,12 +314,21 @@ class FileService(object):
@staticmethod
def delete_file(file_id):
data_models = session.query(FileDataModel).filter_by(file_model_id=file_id).all()
for dm in data_models:
lookup_files = session.query(LookupFileModel).filter_by(file_data_model_id=dm.id).all()
for lf in lookup_files:
session.query(LookupDataModel).filter_by(lookup_file_model_id=lf.id).delete()
session.query(LookupFileModel).filter_by(id=lf.id).delete()
session.query(FileDataModel).filter_by(file_model_id=file_id).delete()
session.query(FileModel).filter_by(id=file_id).delete()
session.commit()
try:
data_models = session.query(FileDataModel).filter_by(file_model_id=file_id).all()
for dm in data_models:
lookup_files = session.query(LookupFileModel).filter_by(file_data_model_id=dm.id).all()
for lf in lookup_files:
session.query(LookupDataModel).filter_by(lookup_file_model_id=lf.id).delete()
session.query(LookupFileModel).filter_by(id=lf.id).delete()
session.query(FileDataModel).filter_by(file_model_id=file_id).delete()
session.query(FileModel).filter_by(id=file_id).delete()
session.commit()
except IntegrityError as ie:
# We can't delete the file or file data, because it is referenced elsewhere,
# but we can at least mark it as deleted on the table.
session.rollback()
file_model = session.query(FileModel).filter_by(id=file_id).first()
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)))

144
crc/services/ldap_service.py
View File

@ -1,84 +1,90 @@
import os
from crc import app
from ldap3 import Connection, Server, MOCK_SYNC
from attr import asdict
from ldap3.core.exceptions import LDAPExceptionError
from crc import app, db
from ldap3 import Connection, Server, MOCK_SYNC, RESTARTABLE
from crc.api.common import ApiError
from crc.models.ldap import LdapModel, LdapSchema
class LdapUserInfo(object):
def __init__(self):
self.display_name = ''
self.given_name = ''
self.email_address = ''
self.telephone_number = ''
self.title = ''
self.department = ''
self.affiliation = ''
self.sponsor_type = ''
self.uid = ''
@classmethod
def from_entry(cls, entry):
instance = cls()
instance.display_name = entry.displayName.value
instance.given_name = ", ".join(entry.givenName)
instance.email_address = entry.mail.value
instance.telephone_number = ", ".join(entry.telephoneNumber)
instance.title = ", ".join(entry.title)
instance.department = ", ".join(entry.uvaDisplayDepartment)
instance.affiliation = ", ".join(entry.uvaPersonIAMAffiliation)
instance.sponsor_type = ", ".join(entry.uvaPersonSponsoredType)
instance.uid = entry.uid.value
return instance
class LdapService(object):
search_base = "ou=People,o=University of Virginia,c=US"
attributes = ['uid', 'cn', 'sn', 'displayName', 'givenName', 'mail', 'objectClass', 'UvaDisplayDepartment',
'telephoneNumber', 'title', 'uvaPersonIAMAffiliation', 'uvaPersonSponsoredType']
uid_search_string = "(&(objectclass=person)(uid=%s))"
user_or_last_name_search_string = "(&(objectclass=person)(|(uid=%s*)(sn=%s*)))"
user_or_last_name_search = "(&(objectclass=person)(|(uid=%s*)(sn=%s*)))"
cn_single_search = '(&(objectclass=person)(cn=%s*))'
cn_double_search = '(&(objectclass=person)(&(cn=%s*)(cn=*%s*)))'
temp_cache = {}
conn = None
def __init__(self):
if app.config['TESTING']:
server = Server('my_fake_server')
self.conn = Connection(server, client_strategy=MOCK_SYNC)
file_path = os.path.abspath(os.path.join(app.root_path, '..', 'tests', 'data', 'ldap_response.json'))
self.conn.strategy.entries_from_json(file_path)
self.conn.bind()
@staticmethod
def __get_conn():
if not LdapService.conn:
if app.config['TESTING']:
server = Server('my_fake_server')
conn = Connection(server, client_strategy=MOCK_SYNC)
file_path = os.path.abspath(os.path.join(app.root_path, '..', 'tests', 'data', 'ldap_response.json'))
conn.strategy.entries_from_json(file_path)
conn.bind()
else:
server = Server(app.config['LDAP_URL'], connect_timeout=app.config['LDAP_TIMEOUT_SEC'])
conn = Connection(server, auto_bind=True,
receive_timeout=app.config['LDAP_TIMEOUT_SEC'],
client_strategy=RESTARTABLE)
LdapService.conn = conn
return LdapService.conn
@staticmethod
def user_info(uva_uid):
user_info = db.session.query(LdapModel).filter(LdapModel.uid == uva_uid).first()
if not user_info:
app.logger.info("No cache for " + uva_uid)
search_string = LdapService.uid_search_string % uva_uid
conn = LdapService.__get_conn()
conn.search(LdapService.search_base, search_string, attributes=LdapService.attributes)
if len(conn.entries) < 1:
raise ApiError("missing_ldap_record", "Unable to locate a user with id %s in LDAP" % uva_uid)
entry = conn.entries[0]
user_info = LdapModel.from_entry(entry)
db.session.add(user_info)
db.session.commit()
return user_info
@staticmethod
def search_users(query, limit):
if len(query.strip()) < 3:
return []
elif query.endswith(' '):
search_string = LdapService.cn_single_search % (query.strip())
elif query.strip().count(',') == 1:
f, l = query.split(",")
search_string = LdapService.cn_double_search % (l.strip(), f.strip())
elif query.strip().count(' ') == 1:
f,l = query.split(" ")
search_string = LdapService.cn_double_search % (f, l)
else:
server = Server(app.config['LDAP_URL'], connect_timeout=app.config['LDAP_TIMEOUT_SEC'])
self.conn = Connection(server,
auto_bind=True,
receive_timeout=app.config['LDAP_TIMEOUT_SEC'],
)
def __del__(self):
if self.conn:
self.conn.unbind()
def user_info(self, uva_uid):
search_string = LdapService.uid_search_string % uva_uid
self.conn.search(LdapService.search_base, search_string, attributes=LdapService.attributes)
if len(self.conn.entries) < 1:
raise ApiError("missing_ldap_record", "Unable to locate a user with id %s in LDAP" % uva_uid)
entry = self.conn.entries[0]
return LdapUserInfo.from_entry(entry)
def search_users(self, query, limit):
if len(query) < 3: return []
search_string = LdapService.user_or_last_name_search_string % (query, query)
self.conn.search(LdapService.search_base, search_string, attributes=LdapService.attributes)
# Entries are returned as a generator, accessing entries
# can make subsequent calls to the ldap service, so limit
# those here.
count = 0
# Search by user_id or last name
search_string = LdapService.user_or_last_name_search % (query, query)
results = []
for entry in self.conn.entries:
if count > limit:
break
results.append(LdapUserInfo.from_entry(entry))
count += 1
app.logger.info(search_string)
try:
conn = LdapService.__get_conn()
conn.search(LdapService.search_base, search_string, attributes=LdapService.attributes)
# Entries are returned as a generator, accessing entries
# can make subsequent calls to the ldap service, so limit
# those here.
count = 0
for entry in conn.entries:
if count > limit:
break
results.append(LdapSchema().dump(LdapModel.from_entry(entry)))
count += 1
except LDAPExceptionError as le:
app.logger.info("Failed to execute ldap search. %s", str(le))
return results

10
crc/services/lookup_service.py
View File

@ -103,7 +103,7 @@ class LookupService(object):
workflow_id=workflow_model.id,
name=file_name)
if len(latest_files) < 1:
raise ApiError("missing_file", "Unable to locate the lookup data file '%s'" % file_name)
raise ApiError("invalid_enum", "Unable to locate the lookup data file '%s'" % file_name)
else:
data_model = latest_files[0]
@ -189,15 +189,15 @@ class LookupService(object):
@staticmethod
def _run_ldap_query(query, limit):
users = LdapService().search_users(query, limit)
users = LdapService.search_users(query, limit)
"""Converts the user models into something akin to the
LookupModel in models/file.py, so this can be returned in the same way
we return a lookup data model."""
user_list = []
for user in users:
user_list.append( {"value": user.uid,
"label": user.display_name + " (" + user.uid + ")",
"data": user.__dict__
user_list.append( {"value": user['uid'],
"label": user['display_name'] + " (" + user['uid'] + ")",
"data": user
})
return user_list

128
crc/services/mails.py Normal file
View File

@ -0,0 +1,128 @@
import os
from flask import render_template, render_template_string
from flask_mail import Message
# TODO: Extract common mailing code into its own function
def send_test_email(sender, recipients):
try:
msg = Message('Research Ramp-up Plan test',
sender=sender,
recipients=recipients)
from crc import env, mail
template = env.get_template('ramp_up_approval_request_first_review.txt')
template_vars = {'primary_investigator': "test"}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approval_request_first_review.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
def send_ramp_up_submission_email(sender, recipients, approver_1, approver_2=None):
try:
msg = Message('Research Ramp-up Plan Submitted',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_submission.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_submission.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
def send_ramp_up_approval_request_email(sender, recipients, primary_investigator):
try:
msg = Message('Research Ramp-up Plan Approval Request',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_approval_request.txt')
template_vars = {'primary_investigator': primary_investigator}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approval_request.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
def send_ramp_up_approval_request_first_review_email(sender, recipients, primary_investigator):
try:
msg = Message('Research Ramp-up Plan Approval Request',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_approval_request_first_review.txt')
template_vars = {'primary_investigator': primary_investigator}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approval_request_first_review.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
def send_ramp_up_approved_email(sender, recipients, approver_1, approver_2=None):
try:
msg = Message('Research Ramp-up Plan Approved',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_approved.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approved.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
def send_ramp_up_denied_email(sender, recipients, approver):
try:
msg = Message('Research Ramp-up Plan Denied',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_denied.txt')
template_vars = {'approver': approver}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_denied.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
def send_ramp_up_denied_email_to_approver(sender, recipients, primary_investigator, approver_2):
try:
msg = Message('Research Ramp-up Plan Denied',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_denied_first_approver.txt')
template_vars = {'primary_investigator': primary_investigator, 'approver_2': approver_2}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_denied_first_approver.html')
msg.html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)

2
crc/services/protocol_builder.py
View File

@ -25,7 +25,7 @@ class ProtocolBuilderService(object):
def get_studies(user_id) -> {}:
ProtocolBuilderService.__enabled_or_raise()
if not isinstance(user_id, str):
raise ApiError("invalid_user_id", "This user id is invalid: " + str(user_id))
raise ApiError("protocol_builder_error", "This user id is invalid: " + str(user_id))
response = requests.get(ProtocolBuilderService.STUDY_URL % user_id)
if response.ok and response.text:
pb_studies = ProtocolBuilderStudySchema(many=True).loads(response.text)

24
crc/services/study_service.py
View File

@ -4,11 +4,13 @@ from typing import List
import requests
from SpiffWorkflow import WorkflowException
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from ldap3.core.exceptions import LDAPSocketOpenError
from crc import db, session, app
from crc.api.common import ApiError
from crc.models.file import FileModel, FileModelSchema
from crc.models.file import FileModel, FileModelSchema, File
from crc.models.ldap import LdapSchema
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
@ -18,6 +20,8 @@ from crc.services.file_service import FileService
from crc.services.ldap_service import LdapService
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.approval_service import ApprovalService
from crc.models.approval import Approval
class StudyService(object):
@ -53,7 +57,11 @@ class StudyService(object):
study = Study.from_model(study_model)
study.categories = StudyService.get_categories()
workflow_metas = StudyService.__get_workflow_metas(study_id)
study.files = FileService.get_files_for_study(study.id)
study.approvals = ApprovalService.get_approvals_for_study(study.id)
files = FileService.get_files_for_study(study.id)
files = (File.from_models(model, FileService.get_file_data(model.id),
FileService.get_doc_dictionary()) for model in files)
study.files = list(files)
# Calling this line repeatedly is very very slow. It creates the
# master spec and runs it.
@ -78,8 +86,8 @@ class StudyService(object):
def delete_workflow(workflow):
for file in session.query(FileModel).filter_by(workflow_id=workflow.id).all():
FileService.delete_file(file.id)
for deb in workflow.dependencies:
session.delete(deb)
for dep in workflow.dependencies:
session.delete(dep)
session.query(TaskEventModel).filter_by(workflow_id=workflow.id).delete()
session.query(WorkflowModel).filter_by(id=workflow.id).delete()
@ -174,6 +182,7 @@ class StudyService(object):
return documents
@staticmethod
def get_investigators(study_id):
@ -197,8 +206,7 @@ class StudyService(object):
@staticmethod
def get_ldap_dict_if_available(user_id):
try:
ldap_service = LdapService()
return ldap_service.user_info(user_id).__dict__
return LdapSchema().dump(LdapService().user_info(user_id))
except ApiError as ae:
app.logger.info(str(ae))
return {"error": str(ae)}
@ -309,8 +317,10 @@ class StudyService(object):
for workflow_spec in new_specs:
try:
StudyService._create_workflow_model(study_model, workflow_spec)
except WorkflowTaskExecException as wtee:
errors.append(ApiError.from_task("workflow_startup_exception", str(wtee), wtee.task))
except WorkflowException as we:
errors.append(ApiError.from_task_spec("workflow_execution_exception", str(we), we.sender))
errors.append(ApiError.from_task_spec("workflow_startup_exception", str(we), we.sender))
return errors
@staticmethod

28
crc/services/workflow_processor.py
View File

@ -299,21 +299,27 @@ class WorkflowProcessor(object):
return WorkflowStatus.waiting
def hard_reset(self):
"""Recreate this workflow, but keep the data from the last completed task and add it back into the first task.
This may be useful when a workflow specification changes, and users need to review all the
prior steps, but don't need to reenter all the previous data.
"""Recreate this workflow, but keep the data from the last completed task and add
it back into the first task. This may be useful when a workflow specification changes,
and users need to review all the prior steps, but they don't need to reenter all the previous data.
Returns the new version.
"""
# Create a new workflow based on the latest specs.
self.spec_data_files = FileService.get_spec_data_files(workflow_spec_id=self.workflow_spec_id)
spec = WorkflowProcessor.get_spec(self.spec_data_files, self.workflow_spec_id)
# spec = WorkflowProcessor.get_spec(self.workflow_spec_id, version)
bpmn_workflow = BpmnWorkflow(spec, script_engine=self._script_engine)
bpmn_workflow.data = self.bpmn_workflow.data
for task in bpmn_workflow.get_tasks(SpiffTask.READY):
task.data = self.bpmn_workflow.last_task.data
bpmn_workflow.do_engine_steps()
self.bpmn_workflow = bpmn_workflow
new_spec = WorkflowProcessor.get_spec(self.spec_data_files, self.workflow_spec_id)
new_bpmn_workflow = BpmnWorkflow(new_spec, script_engine=self._script_engine)
new_bpmn_workflow.data = self.bpmn_workflow.data
# Reset the current workflow to the beginning - which we will consider to be the first task after the root
# element. This feels a little sketchy, but I think it is safe to assume root will have one child.
first_task = self.bpmn_workflow.task_tree.children[0]
first_task.reset_token(reset_data=False)
for task in new_bpmn_workflow.get_tasks(SpiffTask.READY):
task.data = first_task.data
new_bpmn_workflow.do_engine_steps()
self.bpmn_workflow = new_bpmn_workflow
def get_status(self):
return self.status_of(self.bpmn_workflow)

145
crc/services/workflow_service.py
View File

@ -7,7 +7,6 @@ from SpiffWorkflow import Task as SpiffTask, WorkflowException
from SpiffWorkflow.bpmn.specs.ManualTask import ManualTask
from SpiffWorkflow.bpmn.specs.ScriptTask import ScriptTask
from SpiffWorkflow.bpmn.specs.UserTask import UserTask
from SpiffWorkflow.bpmn.workflow import BpmnWorkflow
from SpiffWorkflow.dmn.specs.BusinessRuleTask import BusinessRuleTask
from SpiffWorkflow.specs import CancelTask, StartTask
from flask import g
@ -17,7 +16,6 @@ from crc import db, app
from crc.api.common import ApiError
from crc.models.api_models import Task, MultiInstanceType
from crc.models.file import LookupDataModel
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
@ -39,7 +37,9 @@ class WorkflowService(object):
the workflow Processor should be hidden behind this service.
This will help maintain a structure that avoids circular dependencies.
But for now, this contains tools for converting spiff-workflow models into our
own API models with additional information and capabilities."""
own API models with additional information and capabilities and
handles the testing of a workflow specification by completing it with
random selections, attempting to mimic a front end as much as possible. """
@staticmethod
def make_test_workflow(spec_id):
@ -58,15 +58,23 @@ class WorkflowService(object):
@staticmethod
def delete_test_data():
for study in db.session.query(StudyModel).filter(StudyModel.user_uid=="test"):
for study in db.session.query(StudyModel).filter(StudyModel.user_uid == "test"):
StudyService.delete_study(study.id)
db.session.commit()
db.session.query(UserModel).filter_by(uid="test").delete()
user = db.session.query(UserModel).filter_by(uid="test").first()
if user:
db.session.delete(user)
@staticmethod
def test_spec(spec_id):
"""Runs a spec through it's paces to see if it results in any errors. Not fool-proof, but a good
sanity check."""
def test_spec(spec_id, required_only=False):
"""Runs a spec through it's paces to see if it results in any errors.
Not fool-proof, but a good sanity check. Returns the final data
output form the last task if successful.
required_only can be set to true, in which case this will run the
spec, only completing the required fields, rather than everything.
"""
workflow_model = WorkflowService.make_test_workflow(spec_id)
@ -74,8 +82,7 @@ class WorkflowService(object):
processor = WorkflowProcessor(workflow_model, validate_only=True)
except WorkflowException as we:
WorkflowService.delete_test_data()
raise ApiError.from_task_spec("workflow_execution_exception", str(we),
we.sender)
raise ApiError.from_workflow_exception("workflow_validation_exception", str(we), we)
while not processor.bpmn_workflow.is_completed():
try:
@ -85,38 +92,57 @@ class WorkflowService(object):
task_api = WorkflowService.spiff_task_to_api_task(
task,
add_docs_and_forms=True) # Assure we try to process the documenation, and raise those errors.
WorkflowService.populate_form_with_random_data(task, task_api)
WorkflowService.populate_form_with_random_data(task, task_api, required_only)
task.complete()
except WorkflowException as we:
WorkflowService.delete_test_data()
raise ApiError.from_task_spec("workflow_execution_exception", str(we),
we.sender)
raise ApiError.from_workflow_exception("workflow_validation_exception", str(we), we)
WorkflowService.delete_test_data()
return processor.bpmn_workflow.last_task.data
@staticmethod
def populate_form_with_random_data(task, task_api):
def populate_form_with_random_data(task, task_api, required_only):
"""populates a task with random data - useful for testing a spec."""
if not hasattr(task.task_spec, 'form'): return
form_data = {}
form_data = task.data # Just like with the front end, we start with what was already there, and modify it.
for field in task_api.form.fields:
if field.type == "enum":
if len(field.options) > 0:
random_choice = random.choice(field.options)
if isinstance(random_choice, dict):
form_data[field.id] = random.choice(field.options)['id']
else:
# fixme: why it is sometimes an EnumFormFieldOption, and other times not?
form_data[field.id] = random_choice.id ## Assume it is an EnumFormFieldOption
if required_only and (not field.has_validation(Task.VALIDATION_REQUIRED) or
field.get_validation(Task.VALIDATION_REQUIRED).lower().strip() != "true"):
continue # Don't include any fields that aren't specifically marked as required.
if field.has_property("read_only") and field.get_property("read_only").lower().strip() == "true":
continue # Don't mess about with read only fields.
if field.has_property(Task.PROP_OPTIONS_REPEAT):
group = field.get_property(Task.PROP_OPTIONS_REPEAT)
if group not in form_data:
form_data[group] = [{},{},{}]
for i in range(3):
form_data[group][i][field.id] = WorkflowService.get_random_data_for_field(field, task)
else:
form_data[field.id] = WorkflowService.get_random_data_for_field(field, task)
if task.data is None:
task.data = {}
task.data.update(form_data)
@staticmethod
def get_random_data_for_field(field, task):
if field.type == "enum":
if len(field.options) > 0:
random_choice = random.choice(field.options)
if isinstance(random_choice, dict):
return random.choice(field.options)['id']
else:
raise ApiError.from_task("invalid_enum", "You specified an enumeration field (%s),"
" with no options" % field.id,
task)
elif field.type == "autocomplete":
lookup_model = LookupService.get_lookup_model(task, field)
if field.has_property(Task.PROP_LDAP_LOOKUP):
form_data[field.id] = {
# fixme: why it is sometimes an EnumFormFieldOption, and other times not?
return random_choice.id ## Assume it is an EnumFormFieldOption
else:
raise ApiError.from_task("invalid_enum", "You specified an enumeration field (%s),"
" with no options" % field.id, task)
elif field.type == "autocomplete":
lookup_model = LookupService.get_lookup_model(task, field)
if field.has_property(Task.PROP_LDAP_LOOKUP): # All ldap records get the same person.
return {
"label": "dhf8r",
"value": "Dan Funk",
"data": {
@ -126,32 +152,30 @@ class WorkflowService(object):
"email_address": "dhf8r@virginia.edu",
"department": "Depertment of Psychocosmographictology",
"affiliation": "Rousabout",
"sponsor_type": "Staff"
"sponsor_type": "Staff"}
}
}
elif lookup_model:
data = db.session.query(LookupDataModel).filter(
LookupDataModel.lookup_file_model == lookup_model).limit(10).all()
options = []
for d in data:
options.append({"id": d.value, "name": d.label})
form_data[field.id] = random.choice(options)
else:
raise ApiError.from_task("invalid_autocomplete", "The settings for this auto complete field "
"are incorrect: %s " % field.id, task)
elif field.type == "long":
form_data[field.id] = random.randint(1, 1000)
elif field.type == 'boolean':
form_data[field.id] = random.choice([True, False])
elif field.type == 'file':
form_data[field.id] = random.randint(1, 100)
elif field.type == 'files':
form_data[field.id] = random.randrange(1, 100)
elif lookup_model:
data = db.session.query(LookupDataModel).filter(
LookupDataModel.lookup_file_model == lookup_model).limit(10).all()
options = []
for d in data:
options.append({"id": d.value, "label": d.label})
return random.choice(options)
else:
form_data[field.id] = WorkflowService._random_string()
if task.data is None:
task.data = {}
task.data.update(form_data)
raise ApiError.from_task("unknown_lookup_option", "The settings for this auto complete field "
"are incorrect: %s " % field.id, task)
elif field.type == "long":
return random.randint(1, 1000)
elif field.type == 'boolean':
return random.choice([True, False])
elif field.type == 'file':
# fixme: produce some something sensible for files.
return random.randint(1, 100)
# fixme: produce some something sensible for files.
elif field.type == 'files':
return random.randrange(1, 100)
else:
return WorkflowService._random_string()
def __get_options(self):
pass
@ -272,10 +296,11 @@ class WorkflowService(object):
template = Template(raw_doc)
return template.render(**spiff_task.data)
except jinja2.exceptions.TemplateError as ue:
# return "Error processing template. %s" % ue.message
raise ApiError(code="template_error", message="Error processing template for task %s: %s" %
(spiff_task.task_spec.name, str(ue)), status_code=500)
raise ApiError.from_task(code="template_error", message="Error processing template for task %s: %s" %
(spiff_task.task_spec.name, str(ue)), task=spiff_task)
except TypeError as te:
raise ApiError.from_task(code="template_error", message="Error processing template for task %s: %s" %
(spiff_task.task_spec.name, str(te)), task=spiff_task)
# TODO: Catch additional errors and report back.
@staticmethod
@ -293,12 +318,12 @@ class WorkflowService(object):
field.options.append({"id": d.value, "name": d.label})
@staticmethod
def log_task_action(processor, spiff_task, action):
def log_task_action(user_uid, processor, spiff_task, action):
task = WorkflowService.spiff_task_to_api_task(spiff_task)
workflow_model = processor.workflow_model
task_event = TaskEventModel(
study_id=workflow_model.study_id,
user_uid=g.user.uid,
user_uid=user_uid,
workflow_id=workflow_model.id,
workflow_spec_id=workflow_model.workflow_spec_id,
spec_version=processor.get_version_string(),

BIN
crc/static/bpmn/research_rampup/ResearchRampUpPlan.docx
View File

Binary file not shown.

54
crc/static/bpmn/research_rampup/exclusive_area_monitors.dmn Normal file
View File

@ -0,0 +1,54 @@
<?xml version="1.0" encoding="UTF-8"?>
<definitions xmlns="http://www.omg.org/spec/DMN/20151101/dmn.xsd" id="Definitions_06veek1" name="DRD" namespace="http://camunda.org/schema/1.0/dmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<decision id="Decision_ExclusiveAMCheck" name="Exclusive AM Check">
<decisionTable id="decisionTable_1">
<input id="InputClause_1z0jy2o" label="How Many Exclusive Spaces?">
<inputExpression id="LiteralExpression_0tvij2j" typeRef="integer" expressionLanguage="python">
<text>len(exclusive)</text>
</inputExpression>
</input>
<input id="input_1" label="Number Without Area Monitor">
<inputExpression id="inputExpression_1" typeRef="integer" expressionLanguage="python">
<text>sum([1 for x in exclusive if x.get('ExclusiveSpaceAMComputingID',None) == None])</text>
</inputExpression>
</input>
<output id="output_1" label="All Possible Area Monitors Entered" name="isAllExclusiveAreaMonitors" typeRef="boolean" />
<rule id="DecisionRule_07162mr">
<description>No exclusvie spaces without Area Monitor</description>
<inputEntry id="UnaryTests_1892rx8">
<text>&gt;0</text>
</inputEntry>
<inputEntry id="UnaryTests_1jqxc3u">
<text>0</text>
</inputEntry>
<outputEntry id="LiteralExpression_16l50ps">
<text>true</text>
</outputEntry>
</rule>
<rule id="DecisionRule_0ifa4wu">
<description>One or more exclusive space without an Area Monitor</description>
<inputEntry id="UnaryTests_1jakyab">
<text>&gt;0</text>
</inputEntry>
<inputEntry id="UnaryTests_0szbwxc">
<text>&gt; 0</text>
</inputEntry>
<outputEntry id="LiteralExpression_0td8sa6">
<text>false</text>
</outputEntry>
</rule>
<rule id="DecisionRule_026r0im">
<description>No exclusive spaces entered</description>
<inputEntry id="UnaryTests_0c670b6">
<text>0</text>
</inputEntry>
<inputEntry id="UnaryTests_0j06ysc">
<text></text>
</inputEntry>
<outputEntry id="LiteralExpression_1apwzvv">
<text>true</text>
</outputEntry>
</rule>
</decisionTable>
</decision>
</definitions>

713
crc/static/bpmn/research_rampup/research_rampup.bpmn
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54
crc/static/bpmn/research_rampup/shared_area_monitors.dmn Normal file
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@ -0,0 +1,54 @@
<?xml version="1.0" encoding="UTF-8"?>
<definitions xmlns="http://www.omg.org/spec/DMN/20151101/dmn.xsd" id="Definitions_06veek1" name="DRD" namespace="http://camunda.org/schema/1.0/dmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<decision id="Decision_SharedAMCheck" name="Shared AM Check">
<decisionTable id="decisionTable_1">
<input id="InputClause_1koybx6" label="How Many Shared Spaces">
<inputExpression id="LiteralExpression_1mjo0y4" typeRef="integer" expressionLanguage="python">
<text>len(shared)</text>
</inputExpression>
</input>
<input id="input_1" label="Number Without Area Monitor">
<inputExpression id="inputExpression_1" typeRef="integer" expressionLanguage="python">
<text>sum([1 for x in shared if x.get('SharedSpaceAMComputingID',None) == None])</text>
</inputExpression>
</input>
<output id="output_1" label="All Possible Shared Area Monitors Entered" name="isAllSharedAreaMonitors" typeRef="boolean" />
<rule id="DecisionRule_07162mr">
<description>No shared spaces without Area Monitor</description>
<inputEntry id="UnaryTests_1p4ab2l">
<text>&gt;0</text>
</inputEntry>
<inputEntry id="UnaryTests_1jqxc3u">
<text>0</text>
</inputEntry>
<outputEntry id="LiteralExpression_16l50ps">
<text>true</text>
</outputEntry>
</rule>
<rule id="DecisionRule_0ifa4wu">
<description>One or more shared space without an Area Monitor</description>
<inputEntry id="UnaryTests_06bujee">
<text>&gt;0</text>
</inputEntry>
<inputEntry id="UnaryTests_0szbwxc">
<text>&gt; 0</text>
</inputEntry>
<outputEntry id="LiteralExpression_0td8sa6">
<text>false</text>
</outputEntry>
</rule>
<rule id="DecisionRule_1uh85sk">
<description>No shared spaces entered</description>
<inputEntry id="UnaryTests_15grk62">
<text>0</text>
</inputEntry>
<inputEntry id="UnaryTests_1gaiomm">
<text></text>
</inputEntry>
<outputEntry id="LiteralExpression_1iep8ai">
<text>true</text>
</outputEntry>
</rule>
</decisionTable>
</decision>
</definitions>

BIN
crc/static/reference/rrt_documents.xlsx
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2
crc/static/templates/mails/ramp_up_approval_request.html Normal file
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@ -0,0 +1,2 @@
<p>A Research Ramp-up approval request from {{ primary_investigator }} is now available for your review in your
<a href="https://rrt.uvadcos.io/app/approvals">Research Ramp-up Toolkit]</a></p>

2
crc/static/templates/mails/ramp_up_approval_request.txt Normal file
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@ -0,0 +1,2 @@
A Research Ramp-up approval request from {{ primary_investigator }} is now available for your review in your
Research Ramp-up Toolkit: https://rrt.uvadcos.io/app/approvals.

2
crc/static/templates/mails/ramp_up_approval_request_first_review.html Normal file
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@ -0,0 +1,2 @@
<p>A Research Ramp-up approval request from {{ primary_investigator }} and is now available for your review in your
<a href="https://rrt.uvadcos.io/app/approvals">Research Ramp-up Toolkit</a>.</p>

2
crc/static/templates/mails/ramp_up_approval_request_first_review.txt Normal file
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@ -0,0 +1,2 @@
A Research Ramp-up approval request from {{ primary_investigator }} is now available for your review in your
Research Ramp-up Toolkit at https://rrt.uvadcos.io/app/approvals.

1
crc/static/templates/mails/ramp_up_approved.html Normal file
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@ -0,0 +1 @@
<p>Your Research Ramp-up Plan has been approved by {{ approver_1 }} {% if approver_2 %}and {{ approver_2 }} {% endif %}</p>

1
crc/static/templates/mails/ramp_up_approved.txt Normal file
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@ -0,0 +1 @@
Your Research Ramp-up Plan has been approved by {{ approver_1 }} {% if approver_2 %}and {{ approver_2 }} {% endif %}

1
crc/static/templates/mails/ramp_up_denied.html Normal file
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@ -0,0 +1 @@
<p>Your Research Ramp-up Plan has been denied by {{ approver }}. Please return to the Research Ramp-up Plan application and review the comments from {{ approver }} on the home page. Next, open the application and locate the first step where changes are needed. Continue to complete additional steps saving your work along the way. Review your revised Research Ramp-up Plan and res-submit for approval.</p>

1
crc/static/templates/mails/ramp_up_denied.txt Normal file
View File

@ -0,0 +1 @@
Your Research Ramp-up Plan has been denied by {{ approver_1 }}. Please return to the Research Ramp-up Plan application and review the comments from {{ approver_1 }} on the home page. Next, open the application and locate the first step where changes are needed. Continue to complete additional steps saving your work along the way. Review your revised Research Ramp-up Plan and res-submit for approval.

1
crc/static/templates/mails/ramp_up_denied_first_approver.html Normal file
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@ -0,0 +1 @@
<p>The Research Ramp-up Plan submitted by {{ primary_investigator }} was denied by {{ approver_2 }} and returned for requested updates. You may see comments related to this denial in on your Research Ramp-up Toolkit Approval dashboard.</p>

1
crc/static/templates/mails/ramp_up_denied_first_approver.txt Normal file
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@ -0,0 +1 @@
The Research Ramp-up Plan submitted by {{ primary_investigator }} was denied by {{ approver_2 }} and returned for requested updates. You may see comments related to this denial in on your Research Ramp-up Toolkit Approval dashboard.

5
crc/static/templates/mails/ramp_up_submission.html Normal file
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@ -0,0 +1,5 @@
<p>Your Research Ramp-up Plan (RRP) has been submitted for review by {{ approver_1 }} {% if approver_2 %}and {{ approver_2 }} {% endif %}. After completion of the review step you will receive email notification of its approval or if additional information and/or modifications are required, along with instructions on how to proceed. Return to the Research Ramp-up Plan application to proceed as instructed.</p>
<p>In the meantime, please make sure all required training has been completed and needed supplies secured. You will be asked to confirm that both of these requirements have been met before reopening the research space approved in your RRP.</p>
<p>Additionally, if there are any unknown Area Monitors for the spaces listed in your RRP, please contact your approvers to determine either who they are or how you can find out. Missing Area Monitors will need to be entered before proceeding as well.</p>

5
crc/static/templates/mails/ramp_up_submission.txt Normal file
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@ -0,0 +1,5 @@
Your Research Ramp-up Plan (RRP) has been submitted for review by {{ approver_1 }} {% if approver_2 %}and {{ approver_2 }} {% endif %}. After completion of the review step you will receive email notification of its approval or if additional information and/or modifications are required, along with instructions on how to proceed. Return to the Research Ramp-up Plan application to proceed as instructed.
In the meantime, please make sure all required training has been completed and needed supplies secured. You will be asked to confirm that both of these requirements have been met before reopening the research space approved in your RRP.
Additionally, if there are any unknown Area Monitors for the spaces listed in your RRP, please contact your approvers to determine either who they are or how you can find out. Missing Area Monitors will need to be entered before proceeding as well.

42
migrations/versions/13424d5a6de8_.py Normal file
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@ -0,0 +1,42 @@
"""empty message
Revision ID: 13424d5a6de8
Revises: 5064b72284b7
Create Date: 2020-06-02 18:17:29.990159
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '13424d5a6de8'
down_revision = '5064b72284b7'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('ldap_model',
sa.Column('uid', sa.String(), nullable=False),
sa.Column('display_name', sa.String(), nullable=True),
sa.Column('given_name', sa.String(), nullable=True),
sa.Column('email_address', sa.String(), nullable=True),
sa.Column('telephone_number', sa.String(), nullable=True),
sa.Column('title', sa.String(), nullable=True),
sa.Column('department', sa.String(), nullable=True),
sa.Column('affiliation', sa.String(), nullable=True),
sa.Column('sponsor_type', sa.String(), nullable=True),
sa.Column('date_cached', sa.DateTime(timezone=True), nullable=True),
sa.PrimaryKeyConstraint('uid')
)
op.add_column('approval', sa.Column('date_approved', sa.DateTime(timezone=True), nullable=True))
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_column('approval', 'date_approved')
op.drop_table('ldap_model')
# ### end Alembic commands ###

28
migrations/versions/17597692d0b0_.py Normal file
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@ -0,0 +1,28 @@
"""empty message
Revision ID: 17597692d0b0
Revises: 13424d5a6de8
Create Date: 2020-06-03 17:33:56.454339
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '17597692d0b0'
down_revision = '13424d5a6de8'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('file', sa.Column('archived', sa.Boolean(), nullable=True, default=False))
op.execute("UPDATE file SET archived = false")
op.alter_column('file', 'archived', nullable=False)
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_column('file', 'archived')
# ### end Alembic commands ###

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

145
tests/base_test.py
View File

@ -2,24 +2,27 @@
# IMPORTANT - Environment must be loaded before app, models, etc....
import os
from sqlalchemy import Sequence
os.environ["TESTING"] = "true"
import json
import unittest
import urllib.parse
import datetime
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudyModel
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
from crc.models.user import UserModel
from flask import g
from sqlalchemy import Sequence
from crc import app, db, session
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType
from crc.models.approval import ApprovalModel, ApprovalStatus
from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.workflow_service import WorkflowService
from example_data import ExampleDataLoader
#UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
@ -95,7 +98,7 @@ class BaseTest(unittest.TestCase):
def tearDown(self):
ExampleDataLoader.clean_db()
session.flush()
g.user = None
self.auths = {}
def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
@ -107,23 +110,28 @@ class BaseTest(unittest.TestCase):
user_info = {'uid': user.uid}
query_string = self.user_info_to_query_string(user_info, redirect_url)
rv = self.app.get("/v1.0/sso_backdoor%s" % query_string, follow_redirects=False)
rv = self.app.get("/v1.0/login%s" % query_string, follow_redirects=False)
self.assertTrue(rv.status_code == 302)
self.assertTrue(str.startswith(rv.location, redirect_url))
user_model = session.query(UserModel).filter_by(uid=uid).first()
self.assertIsNotNone(user_model.display_name)
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')
return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
def load_example_data(self, use_crc_data=False):
def load_example_data(self, use_crc_data=False, use_rrt_data=False):
"""use_crc_data will cause this to load the mammoth collection of documents
we built up developing crc, otherwise it depends on a small setup for
running tests."""
we built up developing crc, use_rrt_data will do the same for hte rrt project,
otherwise it depends on a small setup for running tests."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
if(use_crc_data):
if use_crc_data:
ExampleDataLoader().load_all()
elif use_rrt_data:
ExampleDataLoader().load_rrt()
else:
ExampleDataLoader().load_test_data()
@ -158,6 +166,7 @@ class BaseTest(unittest.TestCase):
@staticmethod
def load_test_spec(dir_name, master_spec=False, category_id=None):
"""Loads a spec into the database based on a directory in /tests/data"""
if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
return session.query(WorkflowSpecModel).filter_by(id=dir_name).first()
filepath = os.path.join(app.root_path, '..', 'tests', 'data', dir_name, "*")
@ -197,7 +206,7 @@ class BaseTest(unittest.TestCase):
for key, value in items:
query_string_list.append('%s=%s' % (key, urllib.parse.quote(value)))
query_string_list.append('redirect=%s' % redirect_url)
query_string_list.append('redirect_url=%s' % redirect_url)
return '?%s' % '&'.join(query_string_list)
@ -221,12 +230,12 @@ class BaseTest(unittest.TestCase):
db.session.commit()
return user
def create_study(self, uid="dhf8r", title="Beer conception in the bipedal software engineer"):
study = session.query(StudyModel).first()
def create_study(self, uid="dhf8r", title="Beer conception 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, protocol_builder_status=ProtocolBuilderStatus.ACTIVE,
user_uid=user.uid)
user_uid=user.uid, primary_investigator_id=primary_investigator_id)
db.session.add(study)
db.session.commit()
return study
@ -248,3 +257,97 @@ class BaseTest(unittest.TestCase):
binary_data=file.read(),
content_type=CONTENT_TYPES['xls'])
file.close()
def create_approval(
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()
return approval
def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False, user_uid="dhf8r"):
user = session.query(UserModel).filter_by(uid=user_uid).first()
self.assertIsNotNone(user)
rv = self.app.get('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' %
(workflow.id, str(soft_reset), str(hard_reset)),
headers=self.logged_in_headers(user),
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
workflow_api = WorkflowApiSchema().load(json_data)
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, user_uid="dhf8r"):
prev_completed_task_count = workflow_in.completed_tasks
if isinstance(task_in, dict):
task_id = task_in["id"]
else:
task_id = task_in.id
user = session.query(UserModel).filter_by(uid=user_uid).first()
self.assertIsNotNone(user)
rv = self.app.put('/v1.0/workflow/%i/task/%s/data' % (workflow_in.id, task_id),
headers=self.logged_in_headers(user=user),
content_type="application/json",
data=json.dumps(dict_data))
if error_code:
self.assert_failure(rv, error_code=error_code)
return
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
# Assure stats are updated on the model
workflow = WorkflowApiSchema().load(json_data)
# The total number of tasks may change over time, as users move through gateways
# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
self.assertIsNotNone(workflow.total_tasks)
self.assertEqual(prev_completed_task_count + 1, workflow.completed_tasks)
# Assure a record exists in the Task Events
task_events = session.query(TaskEventModel) \
.filter_by(workflow_id=workflow.id) \
.filter_by(task_id=task_id) \
.order_by(TaskEventModel.date.desc()).all()
self.assertGreater(len(task_events), 0)
event = task_events[0]
self.assertIsNotNone(event.study_id)
self.assertEqual(user_uid, event.user_uid)
self.assertEqual(workflow.id, event.workflow_id)
self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEqual(workflow.spec_version, event.spec_version)
self.assertEqual(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEqual(task_in.id, task_id)
self.assertEqual(task_in.name, event.task_name)
self.assertEqual(task_in.title, event.task_title)
self.assertEqual(task_in.type, event.task_type)
self.assertEqual("COMPLETED", event.task_state)
# Not sure what voodoo is happening inside of marshmallow to get me in this state.
if isinstance(task_in.multi_instance_type, MultiInstanceType):
self.assertEqual(task_in.multi_instance_type.value, event.mi_type)
else:
self.assertEqual(task_in.multi_instance_type, event.mi_type)
self.assertEqual(task_in.multi_instance_count, event.mi_count)
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

37
tests/data/decision_table/decision_table.bpmn
View File

@ -1,5 +1,5 @@
<?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_1elv5t1" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
<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_1elv5t1" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_15vbyda" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1ma1wxb</bpmn:outgoing>
@ -8,7 +8,11 @@
<bpmn:userTask id="get_num_presents" name="Get number of presents" camunda:formKey="present_question">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="num_presents" label="How many presents will my dog Ginger leave for me today?" type="long" defaultValue="0" />
<camunda:formField id="num_presents" label="How many presents will my dog Ginger leave for me today?" type="long" defaultValue="0">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_1ma1wxb</bpmn:incoming>
@ -26,38 +30,37 @@ Based on the information you provided (Ginger left {{num_presents}}, we recommen
## {{message}}
We hope you both have an excellent day!
</bpmn:documentation>
We hope you both have an excellent day!</bpmn:documentation>
<bpmn:incoming>SequenceFlow_0grui6f</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_0grui6f" sourceRef="Task_0sgafty" targetRef="EndEvent_0tsqkyu" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_15vbyda">
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1ma1wxb_di" bpmnElement="SequenceFlow_1ma1wxb">
<di:waypoint x="215" y="117" />
<di:waypoint x="270" y="117" />
<bpmndi:BPMNEdge id="SequenceFlow_0grui6f_di" bpmnElement="SequenceFlow_0grui6f">
<di:waypoint x="530" y="117" />
<di:waypoint x="592" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="UserTask_15w5gb3_di" bpmnElement="get_num_presents">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1uxaqwp_di" bpmnElement="SequenceFlow_1uxaqwp">
<di:waypoint x="370" y="117" />
<di:waypoint x="430" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1ma1wxb_di" bpmnElement="SequenceFlow_1ma1wxb">
<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="UserTask_15w5gb3_di" bpmnElement="get_num_presents">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="BusinessRuleTask_10c5wgr_di" bpmnElement="Task_0sgafty">
<dc:Bounds x="430" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0tsqkyu_di" bpmnElement="EndEvent_0tsqkyu">
<dc:Bounds x="592" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_0grui6f_di" bpmnElement="SequenceFlow_0grui6f">
<di:waypoint x="530" y="117" />
<di:waypoint x="592" y="117" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

6
tests/data/exclusive_gateway/exclusive_gateway.bpmn
View File

@ -8,7 +8,11 @@
<bpmn:userTask id="Task_Has_Bananas" name="Enter Do You Have Bananas" camunda:formKey="bananas_form">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="has_bananas" label="Do you have bananas?" type="boolean" />
<camunda:formField id="has_bananas" label="Do you have bananas?" type="boolean">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_1pnq3kg</bpmn:incoming>

44
tests/data/random_fact/random_fact.bpmn
View File

@ -1,5 +1,5 @@
<?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_1gjhqt9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
<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_1gjhqt9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_1ds61df" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0c7wlth</bpmn:outgoing>
@ -108,6 +108,9 @@ Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="type" label="Type" type="enum" defaultValue="cat">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
<camunda:value id="norris" name="Chuck Norris" />
<camunda:value id="cat" name="Cat Fact" />
<camunda:value id="buzzword" name="Business Buzzword" />
@ -121,8 +124,7 @@ Autoconverted link https://github.com/nodeca/pica (enable linkify to see)
<bpmn:outgoing>SequenceFlow_0641sh6</bpmn:outgoing>
</bpmn:userTask>
<bpmn:scriptTask id="Task_Get_Fact_From_API" name="Display Fact">
<bpmn:documentation>
</bpmn:documentation>
<bpmn:documentation />
<bpmn:extensionElements>
<camunda:inputOutput>
<camunda:inputParameter name="Fact.type" />
@ -155,6 +157,18 @@ Your random fact is:
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1ds61df">
<bpmndi:BPMNEdge id="SequenceFlow_0t29gjo_di" bpmnElement="SequenceFlow_0t29gjo">
<di:waypoint x="570" y="250" />
<di:waypoint x="692" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0641sh6_di" bpmnElement="SequenceFlow_0641sh6">
<di:waypoint x="370" y="250" />
<di:waypoint x="470" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0c7wlth_di" bpmnElement="SequenceFlow_0c7wlth">
<di:waypoint x="188" y="250" />
<di:waypoint x="270" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="152" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
@ -164,35 +178,23 @@ Your random fact is:
<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
<dc:Bounds x="470" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0u1cgrf_di" bpmnElement="EndEvent_0u1cgrf">
<dc:Bounds x="692" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="TextAnnotation_09fq7kh_di" bpmnElement="TextAnnotation_09fq7kh">
<dc:Bounds x="330" y="116" width="99.99202297383536" height="68.28334396936822" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="TextAnnotation_1234e5n_di" bpmnElement="TextAnnotation_1234e5n">
<dc:Bounds x="570" y="120" width="100" height="68" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Association_1cfasjp_di" bpmnElement="Association_1cfasjp">
<di:waypoint x="344" y="210" />
<di:waypoint x="359" y="184" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="TextAnnotation_1234e5n_di" bpmnElement="TextAnnotation_1234e5n">
<dc:Bounds x="570" y="120" width="100" height="68" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Association_1qirnyy_di" bpmnElement="Association_1qirnyy">
<di:waypoint x="561" y="210" />
<di:waypoint x="584" y="188" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="EndEvent_0u1cgrf_di" bpmnElement="EndEvent_0u1cgrf">
<dc:Bounds x="692" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_0c7wlth_di" bpmnElement="SequenceFlow_0c7wlth">
<di:waypoint x="188" y="250" />
<di:waypoint x="270" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0641sh6_di" bpmnElement="SequenceFlow_0641sh6">
<di:waypoint x="370" y="250" />
<di:waypoint x="470" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0t29gjo_di" bpmnElement="SequenceFlow_0t29gjo">
<di:waypoint x="570" y="250" />
<di:waypoint x="692" y="250" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

47
tests/data/repeat_form/repeat_form.bpmn Normal file
View File

@ -0,0 +1,47 @@
<?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_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Repeat" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="Task_14svgcu" />
<bpmn:endEvent id="EndEvent_0q4qzl9">
<bpmn:incoming>SequenceFlow_02vev7n</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_02vev7n" sourceRef="Task_14svgcu" targetRef="EndEvent_0q4qzl9" />
<bpmn:userTask id="Task_14svgcu" name="Repeating Form" camunda:formKey="RepeatForm">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="name" label="Add a cat name" type="string" defaultValue="couger buttons">
<camunda:properties>
<camunda:property id="repeat" value="cats" />
</camunda:properties>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_02vev7n</bpmn:outgoing>
</bpmn:userTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Repeat">
<bpmndi:BPMNEdge id="SequenceFlow_02vev7n_di" bpmnElement="SequenceFlow_02vev7n">
<di:waypoint x="370" y="117" />
<di:waypoint x="432" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
<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="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
<dc:Bounds x="432" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_18ly1yq_di" bpmnElement="Task_14svgcu">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

48
tests/data/required_fields/required_fields.bpmn Normal file
View File

@ -0,0 +1,48 @@
<?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_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Required" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="Task_Required_Fields" />
<bpmn:endEvent id="EndEvent_0q4qzl9">
<bpmn:incoming>SequenceFlow_02vev7n</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="SequenceFlow_02vev7n" sourceRef="Task_Required_Fields" targetRef="EndEvent_0q4qzl9" />
<bpmn:userTask id="Task_Required_Fields" name="Required fields" camunda:formKey="RequiredForm">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="string_required" label="String" type="string" defaultValue="some string">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="string_not_required" type="string" defaultValue="If ya like, I don&#39;t care." />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_02vev7n</bpmn:outgoing>
</bpmn:userTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Required">
<bpmndi:BPMNEdge id="SequenceFlow_02vev7n_di" bpmnElement="SequenceFlow_02vev7n">
<di:waypoint x="370" y="117" />
<di:waypoint x="432" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
<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="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
<dc:Bounds x="432" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_18ly1yq_di" bpmnElement="Task_Required_Fields">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

293
tests/test_approvals_api.py
View File

@ -1,113 +1,260 @@
import json
import random
import string
from flask import g
from tests.base_test import BaseTest
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
}
from crc import session, db
from crc.models.approval import ApprovalModel, ApprovalStatus
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowModel
class TestApprovals(BaseTest):
def setUp(self):
"""Initial setup shared by all TestApprovals tests"""
self.load_example_data()
self.study = self.create_study()
self.workflow = self.create_workflow('random_fact')
# TODO: Move to base_test as a helper
self.approval = ApprovalModel(
study=self.study,
workflow=self.workflow,
approver_uid='arc93',
status=ApprovalStatus.WAITING.value,
version=1
)
session.add(self.approval)
self.approval_2 = ApprovalModel(
study=self.study,
workflow=self.workflow,
approver_uid='dhf8r',
status=ApprovalStatus.WAITING.value,
version=1
# Add a study with 2 approvers
study_workflow_approvals_1 = self._create_study_workflow_approvals(
user_uid="dhf8r", title="first study", primary_investigator_id="lb3dp",
approver_uids=["lb3dp", "dhf8r"], statuses=[ApprovalStatus.PENDING.value, ApprovalStatus.PENDING.value]
)
session.add(self.approval_2)
self.study = study_workflow_approvals_1['study']
self.workflow = study_workflow_approvals_1['workflow']
self.approval = study_workflow_approvals_1['approvals'][0]
self.approval_2 = study_workflow_approvals_1['approvals'][1]
session.commit()
# Add a study with 1 approver
study_workflow_approvals_2 = self._create_study_workflow_approvals(
user_uid="dhf8r", title="second study", primary_investigator_id="dhf8r",
approver_uids=["lb3dp"], statuses=[ApprovalStatus.PENDING.value]
)
self.unrelated_study = study_workflow_approvals_2['study']
self.unrelated_workflow = study_workflow_approvals_2['workflow']
self.approval_3 = study_workflow_approvals_2['approvals'][0]
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))
# Stored approvals are 2
# Stored approvals are 3
approvals_count = ApprovalModel.query.count()
self.assertEqual(approvals_count, 2)
self.assertEqual(approvals_count, 3)
# but Dan's approvals should be only 1
self.assertEqual(len(response), 1)
# Confirm approver UID matches returned payload
approval = ApprovalSchema().load(response[0])
self.assertEqual(approval.approver['uid'], approver_uid)
approval = response[0]
self.assertEqual(approval['approver']['uid'], approver_uid)
def test_list_approvals_per_admin(self):
"""All approvals will be returned"""
rv = self.app.get('/v1.0/approval', headers=self.logged_in_headers())
def test_list_approvals_as_user(self):
"""All approvals as different user"""
rv = self.app.get('/v1.0/approval?as_user=lb3dp', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
# Returned approvals should match what's in the db
approvals_count = ApprovalModel.query.count()
# Returned approvals should match what's in the db for user ld3dp, we should get one
# approval back per study (2 studies), and that approval should have one related approval.
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(1, len(response[0]['related_approvals'])) # this approval has a related approval.
self.assertEqual(self.approval.status, ApprovalStatus.WAITING.value)
def test_update_approval_fails_if_not_the_approver(self):
approval = session.query(ApprovalModel).filter_by(approver_uid='lb3dp').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)
def test_csv_export(self):
self.load_test_spec('two_forms')
self._add_lots_of_random_approvals(n=50, workflow_spec_name='two_forms')
# Get all workflows
workflows = db.session.query(WorkflowModel).filter_by(workflow_spec_id='two_forms').all()
# For each workflow, complete all tasks
for workflow in workflows:
workflow_api = self.get_workflow_api(workflow, user_uid=workflow.study.user_uid)
self.assertEqual('two_forms', workflow_api.workflow_spec_id)
# Log current user out.
g.user = None
self.assertIsNone(g.user)
# Complete the form for Step one and post it.
self.complete_form(workflow, workflow_api.next_task, {"color": "blue"}, error_code=None, user_uid=workflow.study.user_uid)
# Get the next Task
workflow_api = self.get_workflow_api(workflow, user_uid=workflow.study.user_uid)
self.assertEqual("StepTwo", workflow_api.next_task.name)
# Get all user Tasks and check that the data have been saved
task = workflow_api.next_task
self.assertIsNotNone(task.data)
for val in task.data.values():
self.assertIsNotNone(val)
rv = self.app.get(f'/v1.0/approval/csv', headers=self.logged_in_headers())
self.assert_success(rv)
def test_all_approvals(self):
self._add_lots_of_random_approvals()
not_canceled = session.query(ApprovalModel).filter(ApprovalModel.status != 'CANCELED').all()
not_canceled_study_ids = []
for a in not_canceled:
if a.study_id not in not_canceled_study_ids:
not_canceled_study_ids.append(a.study_id)
rv_all = self.app.get(f'/v1.0/all_approvals?status=false', headers=self.logged_in_headers())
self.assert_success(rv_all)
all_data = json.loads(rv_all.get_data(as_text=True))
self.assertEqual(len(all_data), len(not_canceled_study_ids), 'Should return all non-canceled approvals, grouped by study')
all_approvals = session.query(ApprovalModel).all()
all_approvals_study_ids = []
for a in all_approvals:
if a.study_id not in all_approvals_study_ids:
all_approvals_study_ids.append(a.study_id)
rv_all = self.app.get(f'/v1.0/all_approvals?status=true', headers=self.logged_in_headers())
self.assert_success(rv_all)
all_data = json.loads(rv_all.get_data(as_text=True))
self.assertEqual(len(all_data), len(all_approvals_study_ids), 'Should return all approvals, grouped by study')
def test_approvals_counts(self):
statuses = [name for name, value in ApprovalStatus.__members__.items()]
self._add_lots_of_random_approvals()
# Get the counts
rv_counts = self.app.get(f'/v1.0/approval-counts', headers=self.logged_in_headers())
self.assert_success(rv_counts)
counts = json.loads(rv_counts.get_data(as_text=True))
# Get the actual approvals
rv_approvals = self.app.get(f'/v1.0/approval', headers=self.logged_in_headers())
self.assert_success(rv_approvals)
approvals = json.loads(rv_approvals.get_data(as_text=True))
# Tally up the number of approvals in each status category
manual_counts = {}
for status in statuses:
manual_counts[status] = 0
for approval in approvals:
manual_counts[approval['status']] += 1
# Numbers in each category should match
for status in statuses:
self.assertEqual(counts[status], manual_counts[status], 'Approval counts for status %s should match' % status)
# Total number of approvals should match
total_counts = sum(counts[status] for status in statuses)
self.assertEqual(total_counts, len(approvals), 'Total approval counts for user should match number of approvals for user')
def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
workflow_spec_name="random_fact"):
study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
approvals = []
for i in range(len(approver_uids)):
approvals.append(self.create_approval(
study=study,
workflow=workflow,
approver_uid=approver_uids[i],
status=statuses[i],
version=1
))
return {
'study': study,
'workflow': workflow,
'approvals': approvals,
}
def _add_lots_of_random_approvals(self, n=100, workflow_spec_name="random_fact"):
num_studies_before = db.session.query(StudyModel).count()
statuses = [name for name, value in ApprovalStatus.__members__.items()]
# Add a whole bunch of approvals with random statuses
for i in range(n):
approver_uids = random.choices(["lb3dp", "dhf8r"])
self._create_study_workflow_approvals(
user_uid=random.choice(["lb3dp", "dhf8r"]),
title="".join(random.choices(string.ascii_lowercase, k=64)),
primary_investigator_id=random.choice(["lb3dp", "dhf8r"]),
approver_uids=approver_uids,
statuses=random.choices(statuses, k=len(approver_uids)),
workflow_spec_name=workflow_spec_name
)
session.flush()
num_studies_after = db.session.query(StudyModel).count()
self.assertEqual(num_studies_after, num_studies_before + n)

32
tests/test_approvals_service.py
View File

@ -15,13 +15,14 @@ class TestApprovalsService(BaseTest):
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
self.assertEquals(1, db.session.query(ApprovalModel).count())
self.assertEqual(1, db.session.query(ApprovalModel).count())
model = db.session.query(ApprovalModel).first()
self.assertEquals(workflow.study_id, model.study_id)
self.assertEquals(workflow.id, model.workflow_id)
self.assertEquals("dhf8r", model.approver_uid)
self.assertEquals(1, model.version)
self.assertEqual(workflow.study_id, model.study_id)
self.assertEqual(workflow.id, model.workflow_id)
self.assertEqual("dhf8r", model.approver_uid)
self.assertEqual(1, model.version)
def test_new_requests_dont_add_if_approval_exists_for_current_workflow(self):
self.create_reference_document()
@ -32,9 +33,9 @@ class TestApprovalsService(BaseTest):
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
self.assertEquals(1, db.session.query(ApprovalModel).count())
self.assertEqual(1, db.session.query(ApprovalModel).count())
model = db.session.query(ApprovalModel).first()
self.assertEquals(1, model.version)
self.assertEqual(1, model.version)
def test_new_approval_requests_after_file_modification_create_new_requests(self):
self.load_example_data()
@ -51,9 +52,20 @@ class TestApprovalsService(BaseTest):
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
self.assertEquals(2, db.session.query(ApprovalModel).count())
self.assertEqual(2, db.session.query(ApprovalModel).count())
models = db.session.query(ApprovalModel).order_by(ApprovalModel.version).all()
self.assertEquals(1, models[0].version)
self.assertEquals(2, models[1].version)
self.assertEqual(1, models[0].version)
self.assertEqual(2, models[1].version)
def test_new_approval_sends_proper_emails(self):
self.assertEqual(1, 1)
def test_new_approval_failed_ldap_lookup(self):
# failed lookup should send email to sartographysupport@googlegroups.com + Cheryl
self.assertEqual(1, 1)
def test_approve_approval_sends_proper_emails(self):
self.assertEqual(1, 1)
def test_deny_approval_sends_proper_emails(self):
self.assertEqual(1, 1)

201
tests/test_authentication.py
View File

@ -1,29 +1,73 @@
from tests.base_test import BaseTest
import json
from calendar import timegm
from datetime import timezone, datetime, timedelta
from crc import db
import jwt
from tests.base_test import BaseTest
from crc import db, app
from crc.api.common import ApiError
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudySchema, StudyModel
from crc.models.user import UserModel
class TestAuthentication(BaseTest):
def test_auth_token(self):
self.load_example_data()
user = UserModel(uid="dhf8r")
auth_token = user.encode_auth_token()
self.assertTrue(isinstance(auth_token, bytes))
self.assertEqual("dhf8r", user.decode_auth_token(auth_token).get("sub"))
def tearDown(self):
# Assure we set the production flag back to false.
app.config['PRODUCTION'] = False
super().tearDown()
def test_backdoor_auth_creates_user(self):
new_uid = 'lb3dp' ## Assure this user id is in the fake responses from ldap.
def test_auth_token(self):
# Save the orginal timeout setting
orig_ttl = float(app.config['TOKEN_AUTH_TTL_HOURS'])
self.load_example_data()
# Set the timeout to something else
new_ttl = 4.0
app.config['TOKEN_AUTH_TTL_HOURS'] = new_ttl
user_1 = UserModel(uid="dhf8r")
expected_exp_1 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple())
auth_token_1 = user_1.encode_auth_token()
self.assertTrue(isinstance(auth_token_1, bytes))
self.assertEqual("dhf8r", user_1.decode_auth_token(auth_token_1).get("sub"))
actual_exp_1 = user_1.decode_auth_token(auth_token_1).get("exp")
self.assertTrue(expected_exp_1 - 1000 <= actual_exp_1 <= expected_exp_1 + 1000)
# Set the timeout to something else
neg_ttl = -0.01
app.config['TOKEN_AUTH_TTL_HOURS'] = neg_ttl
user_2 = UserModel(uid="dhf8r")
expected_exp_2 = timegm((datetime.utcnow() + timedelta(hours=neg_ttl)).utctimetuple())
auth_token_2 = user_2.encode_auth_token()
self.assertTrue(isinstance(auth_token_2, bytes))
with self.assertRaises(ApiError) as api_error:
with self.assertRaises(jwt.exceptions.ExpiredSignatureError):
user_2.decode_auth_token(auth_token_2)
self.assertEqual(api_error.exception.status_code, 400, 'Should raise an API Error if token is expired')
# Set the timeout back to where it was
app.config['TOKEN_AUTH_TTL_HOURS'] = orig_ttl
user_3 = UserModel(uid="dhf8r")
expected_exp_3 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple())
auth_token_3 = user_3.encode_auth_token()
self.assertTrue(isinstance(auth_token_3, bytes))
actual_exp_3 = user_3.decode_auth_token(auth_token_1).get("exp")
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.
self.load_example_data()
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
self.assertIsNone(user)
user_info = {'uid': new_uid, 'first_name': 'Cordi', 'last_name': 'Nator',
'email_address': 'czn1z@virginia.edu'}
'email_address': 'czn1z@virginia.edu'}
redirect_url = 'http://worlds.best.website/admin'
query_string = self.user_info_to_query_string(user_info, redirect_url)
url = '/v1.0/sso_backdoor%s' % query_string
url = '/v1.0/login%s' % query_string
rv_1 = self.app.get(url, follow_redirects=False)
self.assertTrue(rv_1.status_code == 302)
self.assertTrue(str.startswith(rv_1.location, redirect_url))
@ -38,22 +82,30 @@ class TestAuthentication(BaseTest):
self.assertTrue(rv_2.status_code == 302)
self.assertTrue(str.startswith(rv_2.location, redirect_url))
def test_normal_auth_creates_user(self):
new_uid = 'lb3dp' # This user is in the test ldap system.
def test_production_auth_creates_user(self):
# Switch production mode on
app.config['PRODUCTION'] = True
self.load_example_data()
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
new_uid = 'lb3dp' # This user is in the test ldap system.
user = db.session.query(UserModel).filter_by(uid=new_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(UserModel.uid == new_uid).first()
self.assertIsNotNone(user)
self.assertEquals(new_uid, user.uid)
self.assertEquals("Laura Barnes", user.display_name)
self.assertEquals("lb3dp@virginia.edu", user.email_address)
self.assertEquals("E0:Associate Professor of Systems and Information Engineering", user.title)
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)
# Switch production mode back off
app.config['PRODUCTION'] = False
def test_current_user_status(self):
self.load_example_data()
@ -67,3 +119,108 @@ 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)
def test_admin_can_access_admin_only_endpoints(self):
# Switch production mode on
app.config['PRODUCTION'] = True
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_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
rv_add_study = self.app.post(
'/v1.0/study',
content_type="application/json",
headers=admin_token_headers,
data=json.dumps(StudySchema().dump(admin_study)),
follow_redirects=False
)
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()
self.assertIsNotNone(db_admin_study)
rv_del_study = self.app.delete(
'/v1.0/study/%i' % db_admin_study.id,
follow_redirects=False,
headers=admin_token_headers
)
self.assert_success(rv_del_study, 'Admin user should be able to delete a study')
# Switch production mode back off
app.config['PRODUCTION'] = False
def test_nonadmin_cannot_access_admin_only_endpoints(self):
# Switch production mode on
app.config['PRODUCTION'] = True
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_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
non_admin_study = self._make_fake_study(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')
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()
self.assertIsNotNone(db_non_admin_study)
rv_non_admin_del_study = self.app.delete(
'/v1.0/study/%i' % db_non_admin_study.id,
follow_redirects=False,
headers=non_admin_token_headers
)
self.assert_failure(rv_non_admin_del_study, 401)
# Switch production mode back off
app.config['PRODUCTION'] = False
def _make_fake_study(self, uid):
return {
"title": "blah",
"last_updated": datetime.now(tz=timezone.utc),
"protocol_builder_status": ProtocolBuilderStatus.ACTIVE,
"primary_investigator_id": uid,
"user_uid": uid,
}

2
tests/test_complete_template_script.py
View File

@ -17,7 +17,7 @@ class TestCompleteTemplate(unittest.TestCase):
data = {"name": "Dan"}
data_copy = copy.deepcopy(data)
script.rich_text_update(data_copy)
self.assertEquals(data, data_copy)
self.assertEqual(data, data_copy)
def test_rich_text_update_new_line(self):
script = CompleteTemplate()

46
tests/test_file_service.py
View File

@ -1,8 +1,9 @@
from tests.base_test import BaseTest
from crc import db
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
class TestFileService(BaseTest):
"""Largely tested via the test_file_api, and time is tight, but adding new tests here."""
@ -22,11 +23,11 @@ class TestFileService(BaseTest):
binary_data=b'5678', irb_doc_code=irb_code)
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
self.assertEqual(1, len(file_models))
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_data))
self.assertEquals(2, file_data[0].version)
self.assertEqual(1, len(file_data))
self.assertEqual(2, file_data[0].version)
def test_add_file_from_form_increments_version_and_replaces_on_subsequent_add_with_same_name(self):
@ -46,12 +47,43 @@ class TestFileService(BaseTest):
name="anything.png", content_type="text",
binary_data=b'5678')
def test_replace_archive_file_unarchives_the_file_and_updates(self):
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.
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
# Archive the file
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
file_model = file_models[0]
file_model.archived = True
db.session.add(file_model)
# Assure that the file no longer comes back.
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(0, len(file_models))
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEqual(1, len(file_models))
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_data))
self.assertEquals(2, file_data[0].version)
self.assertEqual(1, len(file_data))
self.assertEqual(2, file_data[0].version)
self.assertEqual(b'5678', file_data[0].data)
def test_add_file_from_form_allows_multiple_files_with_different_names(self):
self.load_example_data()
@ -70,4 +102,4 @@ class TestFileService(BaseTest):
name="a_different_thing.png", content_type="text",
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(2, len(file_models))
self.assertEqual(2, len(file_models))

73
tests/test_files_api.py
View File

@ -3,12 +3,14 @@ import json
from tests.base_test import BaseTest
from crc import session
from crc import session, db
from crc.models.file import FileModel, FileType, FileSchema, FileModelSchema
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
from example_data import ExampleDataLoader
from crc.services.approval_service import ApprovalService
from crc.models.approval import ApprovalModel, ApprovalStatus
class TestFilesApi(BaseTest):
@ -46,6 +48,7 @@ class TestFilesApi(BaseTest):
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(2, len(json_data))
def test_create_file(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()
@ -89,6 +92,39 @@ class TestFilesApi(BaseTest):
self.assert_success(rv)
def test_archive_file_no_longer_shows_up(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
correct_name = task.task_spec.form.fields[0].id
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
rv = self.app.post('/v1.0/file?study_id=%i&workflow_id=%s&task_id=%i&form_field_key=%s' %
(workflow.study_id, workflow.id, task.id, correct_name), data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEquals(1, len(json.loads(rv.get_data(as_text=True))))
file_model = db.session.query(FileModel).filter(FileModel.workflow_id == workflow.id).all()
self.assertEquals(1, len(file_model))
file_model[0].archived = True
db.session.commit()
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEquals(0, len(json.loads(rv.get_data(as_text=True))))
def test_set_reference_file(self):
file_name = "irb_document_types.xls"
data = {'file': (io.BytesIO(b"abcdef"), "does_not_matter.xls")}
@ -218,6 +254,41 @@ class TestFilesApi(BaseTest):
rv = self.app.get('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
self.assertEqual(404, rv.status_code)
def test_delete_file_after_approval(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anotother_anything.png", content_type="text",
binary_data=b'1234', irb_doc_code="Study_App_Doc")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
file = session.query(FileModel).\
filter(FileModel.workflow_id == workflow.id).\
filter(FileModel.name == "anything.png").first()
self.assertFalse(file.archived)
rv = self.app.get('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.delete('/v1.0/file/%i' % file.id, headers=self.logged_in_headers())
self.assert_success(rv)
session.refresh(file)
self.assertTrue(file.archived)
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
approvals = session.query(ApprovalModel)\
.filter(ApprovalModel.status == ApprovalStatus.PENDING.value)\
.filter(ApprovalModel.study_id == workflow.study_id).all()
self.assertEquals(1, len(approvals))
self.assertEquals(1, len(approvals[0].approval_files))
def test_change_primary_bpmn(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()

13
tests/test_ldap_service.py
View File

@ -1,22 +1,19 @@
import os
from tests.base_test import BaseTest
from crc import app
from crc.api.common import ApiError
from crc.services.ldap_service import LdapService
from tests.base_test import BaseTest
from ldap3 import Server, Connection, ALL, MOCK_SYNC
class TestLdapService(BaseTest):
def setUp(self):
self.ldap_service = LdapService()
pass
def tearDown(self):
pass
def test_get_single_user(self):
user_info = self.ldap_service.user_info("lb3dp")
user_info = LdapService.user_info("lb3dp")
self.assertIsNotNone(user_info)
self.assertEqual("lb3dp", user_info.uid)
self.assertEqual("Laura Barnes", user_info.display_name)
@ -30,7 +27,7 @@ class TestLdapService(BaseTest):
def test_find_missing_user(self):
try:
user_info = self.ldap_service.user_info("nosuch")
user_info = LdapService.user_info("nosuch")
self.assertFalse(True, "An API error should be raised.")
except ApiError as ae:
self.assertEquals("missing_ldap_record", ae.code)
self.assertEqual("missing_ldap_record", ae.code)

53
tests/test_lookup_service.py
View File

@ -31,7 +31,7 @@ class TestLookupService(BaseTest):
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(28, len(lookup_data))
self.assertEqual(28, len(lookup_data))
def test_updates_to_file_cause_lookup_rebuild(self):
spec = BaseTest.load_test_spec('enum_options_with_search')
@ -43,7 +43,7 @@ class TestLookupService(BaseTest):
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(28, len(lookup_data))
self.assertEqual(28, len(lookup_data))
# Update the workflow specification file.
file_path = os.path.join(app.root_path, '..', 'tests', 'data',
@ -59,7 +59,7 @@ class TestLookupService(BaseTest):
lookup_records = session.query(LookupFileModel).all()
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(4, len(lookup_data))
self.assertEqual(4, len(lookup_data))
@ -70,49 +70,50 @@ class TestLookupService(BaseTest):
processor.do_engine_steps()
results = LookupService.lookup(workflow, "AllTheNames", "", limit=10)
self.assertEquals(10, len(results), "Blank queries return everything, to the limit")
self.assertEqual(10, len(results), "Blank queries return everything, to the limit")
results = LookupService.lookup(workflow, "AllTheNames", "medicines", limit=10)
self.assertEquals(1, len(results), "words in the middle of label are detected.")
self.assertEquals("The Medicines Company", results[0].label)
self.assertEqual(1, len(results), "words in the middle of label are detected.")
self.assertEqual("The Medicines Company", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "UVA", limit=10)
self.assertEquals(1, len(results), "Beginning of label is found.")
self.assertEquals("UVA - INTERNAL - GM USE ONLY", results[0].label)
self.assertEqual(1, len(results), "Beginning of label is found.")
self.assertEqual("UVA - INTERNAL - GM USE ONLY", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "uva", limit=10)
self.assertEquals(1, len(results), "case does not matter.")
self.assertEquals("UVA - INTERNAL - GM USE ONLY", results[0].label)
self.assertEqual(1, len(results), "case does not matter.")
self.assertEqual("UVA - INTERNAL - GM USE ONLY", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "medici", limit=10)
self.assertEquals(1, len(results), "partial words are picked up.")
self.assertEquals("The Medicines Company", results[0].label)
self.assertEqual(1, len(results), "partial words are picked up.")
self.assertEqual("The Medicines Company", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "Genetics Savings", limit=10)
self.assertEquals(1, len(results), "multiple terms are picked up..")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
self.assertEqual(1, len(results), "multiple terms are picked up..")
self.assertEqual("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "Genetics Sav", limit=10)
self.assertEquals(1, len(results), "prefix queries still work with partial terms")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
self.assertEqual(1, len(results), "prefix queries still work with partial terms")
self.assertEqual("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "Gen Sav", limit=10)
self.assertEquals(1, len(results), "prefix queries still work with ALL the partial terms")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
self.assertEqual(1, len(results), "prefix queries still work with ALL the partial terms")
self.assertEqual("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "Inc", limit=10)
self.assertEquals(7, len(results), "short terms get multiple correct results.")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
self.assertEqual(7, len(results), "short terms get multiple correct results.")
self.assertEqual("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "reaction design", limit=10)
self.assertEquals(5, len(results), "all results come back for two terms.")
self.assertEquals("Reaction Design", results[0].label, "Exact matches come first.")
self.assertEqual(5, len(results), "all results come back for two terms.")
self.assertEqual("Reaction Design", results[0].label, "Exact matches come first.")
results = LookupService.lookup(workflow, "AllTheNames", "1 Something", limit=10)
self.assertEquals("1 Something", results[0].label, "Exact matches are prefered")
self.assertEqual("1 Something", results[0].label, "Exact matches are prefered")
results = LookupService.lookup(workflow, "AllTheNames", "1 (!-Something", limit=10)
self.assertEquals("1 Something", results[0].label, "special characters don't flake out")
self.assertEqual("1 Something", results[0].label, "special characters don't flake out")
# 1018 10000 Something Industry
@ -123,6 +124,6 @@ class TestLookupService(BaseTest):
# Fixme: Stop words are taken into account on the query side, and haven't found a fix yet.
#results = WorkflowService.run_lookup_query(lookup_table.id, "in", limit=10)
#self.assertEquals(7, len(results), "stop words are not removed.")
#self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
#self.assertEqual(7, len(results), "stop words are not removed.")
#self.assertEqual("Genetics Savings & Clone, Inc.", results[0].label)

55
tests/test_mails.py Normal file
View File

@ -0,0 +1,55 @@
from tests.base_test import BaseTest
from crc.services.mails import (
send_ramp_up_submission_email,
send_ramp_up_approval_request_email,
send_ramp_up_approval_request_first_review_email,
send_ramp_up_approved_email,
send_ramp_up_denied_email,
send_ramp_up_denied_email_to_approver
)
class TestMails(BaseTest):
def setUp(self):
self.sender = 'sender@sartography.com'
self.recipients = ['recipient@sartography.com']
self.primary_investigator = 'Dr. Bartlett'
self.approver_1 = 'Max Approver'
self.approver_2 = 'Close Reviewer'
def test_send_ramp_up_submission_email(self):
send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1)
self.assertTrue(True)
send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1, self.approver_2)
self.assertTrue(True)
def test_send_ramp_up_approval_request_email(self):
send_ramp_up_approval_request_email(self.sender, self.recipients, self.primary_investigator)
self.assertTrue(True)
def test_send_ramp_up_approval_request_first_review_email(self):
send_ramp_up_approval_request_first_review_email(
self.sender, self.recipients, self.primary_investigator
)
self.assertTrue(True)
def test_send_ramp_up_approved_email(self):
send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1)
self.assertTrue(True)
send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1, self.approver_2)
self.assertTrue(True)
def test_send_ramp_up_denied_email(self):
send_ramp_up_denied_email(self.sender, self.recipients, self.approver_1)
self.assertTrue(True)
def test_send_send_ramp_up_denied_email_to_approver(self):
send_ramp_up_denied_email_to_approver(
self.sender, self.recipients, self.primary_investigator, self.approver_2
)
self.assertTrue(True)

22
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
@ -24,7 +24,23 @@ class TestRequestApprovalScript(BaseTest):
binary_data=b'1234')
script = RequestApproval()
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
self.assertEquals(2, db.session.query(ApprovalModel).count())
self.assertEqual(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.assertEqual(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."""
@ -48,5 +64,5 @@ class TestRequestApprovalScript(BaseTest):
script = RequestApproval()
script.do_task_validate_only(task, workflow.study_id, workflow.id, "study.approval1")
self.assertEquals(0, db.session.query(ApprovalModel).count())
self.assertEqual(0, db.session.query(ApprovalModel).count())

42
tests/test_study_api.py
View File

@ -1,5 +1,6 @@
import json
from tests.base_test import BaseTest
from datetime import datetime, timezone
from unittest.mock import patch
@ -8,8 +9,9 @@ from crc.models.protocol_builder import ProtocolBuilderStatus, \
ProtocolBuilderStudySchema
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel, StudySchema
from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecCategoryModel
from crc.services.protocol_builder import ProtocolBuilderService
from crc.models.workflow import WorkflowSpecModel, WorkflowModel
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
class TestStudyApi(BaseTest):
@ -68,6 +70,34 @@ class TestStudyApi(BaseTest):
self.assertEqual(0, workflow["total_tasks"])
self.assertEqual(0, workflow["completed_tasks"])
def test_get_study_has_details_about_files(self):
# Set up the study and attach a file to it.
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.
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="png",
binary_data=b'1234', irb_doc_code=irb_code)
api_response = self.app.get('/v1.0/study/%i' % workflow.study_id,
headers=self.logged_in_headers(), content_type="application/json")
self.assert_success(api_response)
study = StudySchema().loads(api_response.get_data(as_text=True))
self.assertEqual(1, len(study.files))
self.assertEqual("UVA Compliance/PRC Approval", study.files[0]["category"])
self.assertEqual("Cancer Center's PRC Approval Form", study.files[0]["description"])
self.assertEqual("UVA Compliance/PRC Approval.png", study.files[0]["download_name"])
# TODO: WRITE A TEST FOR STUDY FILES
def test_get_study_has_details_about_approvals(self):
# TODO: WRITE A TEST FOR STUDY APPROVALS
pass
def test_add_study(self):
self.load_example_data()
study = self.add_test_study()
@ -150,10 +180,10 @@ class TestStudyApi(BaseTest):
db_studies_after = session.query(StudyModel).all()
num_db_studies_after = len(db_studies_after)
self.assertGreater(num_db_studies_after, num_db_studies_before)
self.assertEquals(num_abandoned, 1)
self.assertEquals(num_open, 1)
self.assertEquals(num_active, 1)
self.assertEquals(num_incomplete, 1)
self.assertEqual(num_abandoned, 1)
self.assertEqual(num_open, 1)
self.assertEqual(num_active, 1)
self.assertEqual(num_incomplete, 1)
self.assertEqual(len(json_data), num_db_studies_after)
self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)

26
tests/test_study_service.py
View File

@ -153,14 +153,16 @@ class TestStudyService(BaseTest):
self.assertEqual(1, docs["UVACompl_PRCAppr"]['count'])
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0])
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0]['file_id'])
self.assertEquals(workflow.id, docs["UVACompl_PRCAppr"]['files'][0]['workflow_id'])
self.assertEqual(workflow.id, docs["UVACompl_PRCAppr"]['files'][0]['workflow_id'])
def test_get_all_studies(self):
user = self.create_user_with_study_and_workflow()
study = db.session.query(StudyModel).filter_by(user_uid=user.uid).first()
self.assertIsNotNone(study)
# Add a document to the study with the correct code.
workflow1 = self.create_workflow('docx')
workflow2 = self.create_workflow('empty_workflow')
workflow1 = self.create_workflow('docx', study=study)
workflow2 = self.create_workflow('empty_workflow', study=study)
# Add files to both workflows.
FileService.add_workflow_file(workflow_id=workflow1.id,
@ -174,8 +176,8 @@ class TestStudyService(BaseTest):
binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
studies = StudyService().get_all_studies_with_files()
self.assertEquals(1, len(studies))
self.assertEquals(3, len(studies[0].files))
self.assertEqual(1, len(studies))
self.assertEqual(3, len(studies[0].files))
@ -191,17 +193,17 @@ class TestStudyService(BaseTest):
workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
investigators = StudyService().get_investigators(workflow.study_id)
self.assertEquals(9, len(investigators))
self.assertEqual(9, len(investigators))
# dhf8r is in the ldap mock data.
self.assertEquals("dhf8r", investigators['PI']['user_id'])
self.assertEquals("Dan Funk", investigators['PI']['display_name']) # Data from ldap
self.assertEquals("Primary Investigator", investigators['PI']['label']) # Data from xls file.
self.assertEquals("Always", investigators['PI']['display']) # Data from xls file.
self.assertEqual("dhf8r", investigators['PI']['user_id'])
self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.
# asd3v is not in ldap, so an error should be returned.
self.assertEquals("asd3v", investigators['DC']['user_id'])
self.assertEquals("Unable to locate a user with id asd3v in LDAP", investigators['DC']['error']) # Data from ldap
self.assertEqual("asd3v", investigators['DC']['user_id'])
self.assertEqual("Unable to locate a user with id asd3v in LDAP", investigators['DC']['error']) # Data from ldap
# No value is provided for Department Chair
self.assertIsNone(investigators['DEPT_CH']['user_id'])

157
tests/test_tasks_api.py
View File

@ -4,86 +4,14 @@ import random
from unittest.mock import patch
from tests.base_test import BaseTest
from crc import session, app
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType, TaskSchema
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
class TestTasksApi(BaseTest):
def get_workflow_api(self, workflow, soft_reset=False, hard_reset=False):
rv = self.app.get('/v1.0/workflow/%i?soft_reset=%s&hard_reset=%s' %
(workflow.id, str(soft_reset), str(hard_reset)),
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
workflow_api = WorkflowApiSchema().load(json_data)
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):
prev_completed_task_count = workflow_in.completed_tasks
if isinstance(task_in, dict):
task_id = task_in["id"]
else:
task_id = task_in.id
rv = self.app.put('/v1.0/workflow/%i/task/%s/data' % (workflow_in.id, task_id),
headers=self.logged_in_headers(),
content_type="application/json",
data=json.dumps(dict_data))
if error_code:
self.assert_failure(rv, error_code=error_code)
return
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
# Assure stats are updated on the model
workflow = WorkflowApiSchema().load(json_data)
# The total number of tasks may change over time, as users move through gateways
# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
self.assertIsNotNone(workflow.total_tasks)
self.assertEquals(prev_completed_task_count + 1, workflow.completed_tasks)
# Assure a record exists in the Task Events
task_events = session.query(TaskEventModel) \
.filter_by(workflow_id=workflow.id) \
.filter_by(task_id=task_id) \
.order_by(TaskEventModel.date.desc()).all()
self.assertGreater(len(task_events), 0)
event = task_events[0]
self.assertIsNotNone(event.study_id)
self.assertEquals("dhf8r", event.user_uid)
self.assertEquals(workflow.id, event.workflow_id)
self.assertEquals(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEquals(workflow.spec_version, event.spec_version)
self.assertEquals(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEquals(task_in.id, task_id)
self.assertEquals(task_in.name, event.task_name)
self.assertEquals(task_in.title, event.task_title)
self.assertEquals(task_in.type, event.task_type)
self.assertEquals("COMPLETED", event.task_state)
# Not sure what vodoo is happening inside of marshmallow to get me in this state.
if isinstance(task_in.multi_instance_type, MultiInstanceType):
self.assertEquals(task_in.multi_instance_type.value, event.mi_type)
else:
self.assertEquals(task_in.multi_instance_type, event.mi_type)
self.assertEquals(task_in.multi_instance_count, event.mi_count)
self.assertEquals(task_in.multi_instance_index, event.mi_index)
self.assertEquals(task_in.process_name, event.process_name)
self.assertIsNotNone(event.date)
workflow = WorkflowApiSchema().load(json_data)
return workflow
def test_get_current_user_tasks(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
@ -156,14 +84,14 @@ class TestTasksApi(BaseTest):
self.assertIsNotNone(workflow_api.navigation)
nav = workflow_api.navigation
self.assertEquals(5, len(nav))
self.assertEquals("Do You Have Bananas", nav[0]['title'])
self.assertEquals("Bananas?", nav[1]['title'])
self.assertEquals("FUTURE", nav[1]['state'])
self.assertEquals("yes", nav[2]['title'])
self.assertEquals("NOOP", nav[2]['state'])
self.assertEquals("no", nav[3]['title'])
self.assertEquals("NOOP", nav[3]['state'])
self.assertEqual(5, len(nav))
self.assertEqual("Do You Have Bananas", nav[0]['title'])
self.assertEqual("Bananas?", nav[1]['title'])
self.assertEqual("FUTURE", nav[1]['state'])
self.assertEqual("yes", nav[2]['title'])
self.assertEqual("NOOP", nav[2]['state'])
self.assertEqual("no", nav[3]['title'])
self.assertEqual("NOOP", nav[3]['state'])
def test_navigation_with_exclusive_gateway(self):
self.load_example_data()
@ -173,19 +101,20 @@ class TestTasksApi(BaseTest):
workflow_api = self.get_workflow_api(workflow)
self.assertIsNotNone(workflow_api.navigation)
nav = workflow_api.navigation
self.assertEquals(7, len(nav))
self.assertEquals("Task 1", nav[0]['title'])
self.assertEquals("Which Branch?", nav[1]['title'])
self.assertEquals("a", nav[2]['title'])
self.assertEquals("Task 2a", nav[3]['title'])
self.assertEquals("b", nav[4]['title'])
self.assertEquals("Task 2b", nav[5]['title'])
self.assertEquals("Task 3", nav[6]['title'])
self.assertEqual(7, len(nav))
self.assertEqual("Task 1", nav[0]['title'])
self.assertEqual("Which Branch?", nav[1]['title'])
self.assertEqual("a", nav[2]['title'])
self.assertEqual("Task 2a", nav[3]['title'])
self.assertEqual("b", nav[4]['title'])
self.assertEqual("Task 2b", nav[5]['title'])
self.assertEqual("Task 3", nav[6]['title'])
def test_document_added_to_workflow_shows_up_in_file_list(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('docx')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
data = {
@ -204,12 +133,12 @@ class TestTasksApi(BaseTest):
json_data = json.loads(rv.get_data(as_text=True))
files = FileModelSchema(many=True).load(json_data, session=session)
self.assertTrue(len(files) == 1)
# Assure we can still delete the study even when there is a file attached to a workflow.
rv = self.app.delete('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers())
self.assert_success(rv)
def test_get_documentation_populated_in_end(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
@ -287,8 +216,8 @@ class TestTasksApi(BaseTest):
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
workflow = self.get_workflow_api(workflow)
self.assertEquals('Task_Manual_One', workflow.next_task.name)
self.assertEquals('ManualTask', workflow_api.next_task.type)
self.assertEqual('Task_Manual_One', workflow.next_task.name)
self.assertEqual('ManualTask', workflow_api.next_task.type)
self.assertTrue('Markdown' in workflow_api.next_task.documentation)
self.assertTrue('Dan' in workflow_api.next_task.documentation)
@ -298,7 +227,7 @@ class TestTasksApi(BaseTest):
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
self.assertEquals("JustAValue", task.properties['JustAKey'])
self.assertEqual("JustAValue", task.properties['JustAKey'])
@patch('crc.services.protocol_builder.requests.get')
@ -318,13 +247,13 @@ class TestTasksApi(BaseTest):
# get the first form in the two form workflow.
workflow = self.get_workflow_api(workflow)
navigation = self.get_workflow_api(workflow).navigation
self.assertEquals(4, len(navigation)) # Start task, form_task, multi_task, end task
self.assertEquals("UserTask", workflow.next_task.type)
self.assertEquals(MultiInstanceType.sequential.value, workflow.next_task.multi_instance_type)
self.assertEquals(9, workflow.next_task.multi_instance_count)
self.assertEqual(4, len(navigation)) # Start task, form_task, multi_task, end task
self.assertEqual("UserTask", workflow.next_task.type)
self.assertEqual(MultiInstanceType.sequential.value, workflow.next_task.multi_instance_type)
self.assertEqual(9, workflow.next_task.multi_instance_count)
# Assure that the names for each task are properly updated, so they aren't all the same.
self.assertEquals("Primary Investigator", workflow.next_task.properties['display_name'])
self.assertEqual("Primary Investigator", workflow.next_task.properties['display_name'])
def test_lookup_endpoint_for_task_field_enumerations(self):
@ -366,18 +295,18 @@ class TestTasksApi(BaseTest):
navigation = workflow_api.navigation
task = workflow_api.next_task
self.assertEquals(2, len(navigation))
self.assertEquals("UserTask", task.type)
self.assertEquals("Activity_A", task.name)
self.assertEquals("My Sub Process", task.process_name)
self.assertEqual(2, len(navigation))
self.assertEqual("UserTask", task.type)
self.assertEqual("Activity_A", task.name)
self.assertEqual("My Sub Process", task.process_name)
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
task = workflow_api.next_task
self.assertIsNotNone(task)
self.assertEquals("Activity_B", task.name)
self.assertEquals("Sub Workflow Example", task.process_name)
self.assertEqual("Activity_B", task.name)
self.assertEqual("Sub Workflow Example", task.process_name)
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
self.assertEquals(WorkflowStatus.complete, workflow_api.status)
self.assertEqual(WorkflowStatus.complete, workflow_api.status)
def test_update_task_resets_token(self):
self.load_example_data()
@ -387,7 +316,7 @@ class TestTasksApi(BaseTest):
first_task = self.get_workflow_api(workflow).next_task
self.complete_form(workflow, first_task, {"has_bananas": True})
workflow = self.get_workflow_api(workflow)
self.assertEquals('Task_Num_Bananas', workflow.next_task.name)
self.assertEqual('Task_Num_Bananas', workflow.next_task.name)
# Trying to re-submit the initial task, and answer differently, should result in an error.
self.complete_form(workflow, first_task, {"has_bananas": False}, error_code="invalid_state")
@ -408,18 +337,18 @@ class TestTasksApi(BaseTest):
workflow = WorkflowApiSchema().load(json_data)
# Assure the Next Task is the one we just reset the token to be on.
self.assertEquals("Task_Has_Bananas", workflow.next_task.name)
self.assertEqual("Task_Has_Bananas", workflow.next_task.name)
# Go ahead and get that workflow one more time, it should still be right.
workflow = self.get_workflow_api(workflow)
# Assure the Next Task is the one we just reset the token to be on.
self.assertEquals("Task_Has_Bananas", workflow.next_task.name)
self.assertEqual("Task_Has_Bananas", workflow.next_task.name)
# The next task should be a different value.
self.complete_form(workflow, workflow.next_task, {"has_bananas": False})
workflow = self.get_workflow_api(workflow)
self.assertEquals('Task_Why_No_Bananas', workflow.next_task.name)
self.assertEqual('Task_Why_No_Bananas', workflow.next_task.name)
@patch('crc.services.protocol_builder.requests.get')
def test_parallel_multi_instance(self, mock_get):
@ -434,13 +363,13 @@ class TestTasksApi(BaseTest):
workflow = self.create_workflow('multi_instance_parallel')
workflow_api = self.get_workflow_api(workflow)
self.assertEquals(12, len(workflow_api.navigation))
self.assertEqual(12, len(workflow_api.navigation))
ready_items = [nav for nav in workflow_api.navigation if nav['state'] == "READY"]
self.assertEquals(9, len(ready_items))
self.assertEqual(9, len(ready_items))
self.assertEquals("UserTask", workflow_api.next_task.type)
self.assertEquals("MutiInstanceTask",workflow_api.next_task.name)
self.assertEquals("more information", workflow_api.next_task.title)
self.assertEqual("UserTask", workflow_api.next_task.type)
self.assertEqual("MutiInstanceTask",workflow_api.next_task.name)
self.assertEqual("more information", workflow_api.next_task.title)
for i in random.sample(range(9), 9):
task = TaskSchema().load(ready_items[i]['task'])
@ -448,5 +377,5 @@ class TestTasksApi(BaseTest):
#tasks = self.get_workflow_api(workflow).user_tasks
workflow = self.get_workflow_api(workflow)
self.assertEquals(WorkflowStatus.complete, workflow.status)
self.assertEqual(WorkflowStatus.complete, workflow.status)

2
tests/test_tools_api.py
View File

@ -28,7 +28,7 @@ class TestStudyApi(BaseTest):
content_type='multipart/form-data')
self.assert_success(rv)
self.assertIsNotNone(rv.data)
self.assertEquals('application/octet-stream', rv.content_type)
self.assertEqual('application/octet-stream', rv.content_type)
def test_list_scripts(self):
rv = self.app.get('/v1.0/list_scripts')

4
tests/test_update_study_script.py
View File

@ -19,5 +19,5 @@ class TestUpdateStudyScript(BaseTest):
script = UpdateStudy()
script.do_task(task, workflow.study_id, workflow.id, "title:details.label", "pi:details.value")
self.assertEquals("My New Title", workflow.study.title)
self.assertEquals("dhf8r", workflow.study.primary_investigator_id)
self.assertEqual("My New Title", workflow.study.title)
self.assertEqual("dhf8r", workflow.study.primary_investigator_id)

2
tests/test_workflow_processor.py
View File

@ -25,7 +25,7 @@ class TestWorkflowProcessor(BaseTest):
def _populate_form_with_random_data(self, task):
api_task = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, api_task)
WorkflowService.populate_form_with_random_data(task, api_task, required_only=False)
def get_processor(self, study_model, spec_model):
workflow_model = StudyService._create_workflow_model(study_model, spec_model)

24
tests/test_workflow_processor_multi_instance.py
View File

@ -57,13 +57,13 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
task = next_user_tasks[0]
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
self.assertEquals("dhf8r", task.data["investigator"]["user_id"])
self.assertEqual("dhf8r", task.data["investigator"]["user_id"])
self.assertEqual("MutiInstanceTask", task.get_name())
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEquals(MultiInstanceType.sequential, api_task.multi_instance_type)
self.assertEquals(3, api_task.multi_instance_count)
self.assertEquals(1, api_task.multi_instance_index)
self.assertEqual(MultiInstanceType.sequential, api_task.multi_instance_type)
self.assertEqual(3, api_task.multi_instance_count)
self.assertEqual(1, api_task.multi_instance_index)
task.update_data({"investigator":{"email":"asd3v@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
@ -72,8 +72,8 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MutiInstanceTask", api_task.name)
task.update_data({"investigator":{"email":"asdf32@virginia.edu"}})
self.assertEquals(3, api_task.multi_instance_count)
self.assertEquals(2, api_task.multi_instance_index)
self.assertEqual(3, api_task.multi_instance_count)
self.assertEqual(2, api_task.multi_instance_index)
processor.complete_task(task)
processor.do_engine_steps()
@ -81,8 +81,8 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MutiInstanceTask", task.get_name())
task.update_data({"investigator":{"email":"dhf8r@virginia.edu"}})
self.assertEquals(3, api_task.multi_instance_count)
self.assertEquals(3, api_task.multi_instance_index)
self.assertEqual(3, api_task.multi_instance_count)
self.assertEqual(3, api_task.multi_instance_index)
processor.complete_task(task)
processor.do_engine_steps()
task = processor.bpmn_workflow.last_task
@ -91,7 +91,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
expected['PI']['email'] = "asd3v@virginia.edu"
expected['SC_I']['email'] = "asdf32@virginia.edu"
expected['DC']['email'] = "dhf8r@virginia.edu"
self.assertEquals(expected,
self.assertEqual(expected,
task.data['StudyInfo']['investigators'])
self.assertEqual(WorkflowStatus.complete, processor.get_status())
@ -117,10 +117,10 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
task = next_user_tasks[2]
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
self.assertEquals("asd3v", task.data["investigator"]["user_id"]) # The last of the tasks
self.assertEqual("asd3v", task.data["investigator"]["user_id"]) # The last of the tasks
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEquals(MultiInstanceType.parallel, api_task.multi_instance_type)
self.assertEqual(MultiInstanceType.parallel, api_task.multi_instance_type)
task.update_data({"investigator":{"email":"dhf8r@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
@ -144,7 +144,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
expected['PI']['email'] = "asd3v@virginia.edu"
expected['SC_I']['email'] = "asdf32@virginia.edu"
expected['DC']['email'] = "dhf8r@virginia.edu"
self.assertEquals(expected,
self.assertEqual(expected,
task.data['StudyInfo']['investigators'])
self.assertEqual(WorkflowStatus.complete, processor.get_status())

8
tests/test_workflow_service.py
View File

@ -66,9 +66,9 @@ class TestWorkflowService(BaseTest):
task = processor.next_task()
WorkflowService.process_options(task, task.task_spec.form.fields[0])
options = task.task_spec.form.fields[0].options
self.assertEquals(28, len(options))
self.assertEquals('1000', options[0]['id'])
self.assertEquals("UVA - INTERNAL - GM USE ONLY", options[0]['name'])
self.assertEqual(28, len(options))
self.assertEqual('1000', options[0]['id'])
self.assertEqual("UVA - INTERNAL - GM USE ONLY", options[0]['name'])
def test_random_data_populate_form_on_auto_complete(self):
self.load_example_data()
@ -77,5 +77,5 @@ class TestWorkflowService(BaseTest):
processor.do_engine_steps()
task = processor.next_task()
task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, task_api)
WorkflowService.populate_form_with_random_data(task, task_api, required_only=False)
self.assertTrue(isinstance(task.data["sponsor"], dict))

49
tests/test_workflow_spec_validation_api.py
View File

@ -3,17 +3,16 @@ from unittest.mock import patch
from tests.base_test import BaseTest
from crc.services.protocol_builder import ProtocolBuilderService
from crc import session, app
from crc.api.common import ApiErrorSchema
from crc.models.protocol_builder import ProtocolBuilderStudySchema
from crc.models.workflow import WorkflowSpecModel
from crc.services.workflow_service import WorkflowService
class TestWorkflowSpecValidation(BaseTest):
def validate_workflow(self, workflow_name):
self.load_example_data()
spec_model = self.load_test_spec(workflow_name)
rv = self.app.get('/v1.0/workflow-specification/%s/validate' % spec_model.id, headers=self.logged_in_headers())
self.assert_success(rv)
@ -22,6 +21,7 @@ class TestWorkflowSpecValidation(BaseTest):
def test_successful_validation_of_test_workflows(self):
app.config['PB_ENABLED'] = False # Assure this is disabled.
self.load_example_data()
self.assertEqual(0, len(self.validate_workflow("parallel_tasks")))
self.assertEqual(0, len(self.validate_workflow("decision_table")))
self.assertEqual(0, len(self.validate_workflow("docx")))
@ -49,6 +49,13 @@ class TestWorkflowSpecValidation(BaseTest):
self.load_example_data(use_crc_data=True)
app.config['PB_ENABLED'] = True
self.validate_all_loaded_workflows()
def test_successful_validation_of_rrt_workflows(self):
self.load_example_data(use_rrt_data=True)
self.validate_all_loaded_workflows()
def validate_all_loaded_workflows(self):
workflows = session.query(WorkflowSpecModel).all()
errors = []
for w in workflows:
@ -59,28 +66,54 @@ class TestWorkflowSpecValidation(BaseTest):
errors.extend(ApiErrorSchema(many=True).load(json_data))
self.assertEqual(0, len(errors), json.dumps(errors))
def test_invalid_expression(self):
self.load_example_data()
errors = self.validate_workflow("invalid_expression")
self.assertEqual(1, len(errors))
self.assertEqual("workflow_execution_exception", errors[0]['code'])
self.assertEqual(2, len(errors))
self.assertEqual("workflow_validation_exception", errors[0]['code'])
self.assertEqual("ExclusiveGateway_003amsm", errors[0]['task_id'])
self.assertEqual("Has Bananas Gateway", errors[0]['task_name'])
self.assertEqual("invalid_expression.bpmn", errors[0]['file_name'])
self.assertEqual('ExclusiveGateway_003amsm: Error evaluating expression \'this_value_does_not_exist==true\', '
self.assertEqual('When populating all fields ... ExclusiveGateway_003amsm: Error evaluating expression \'this_value_does_not_exist==true\', '
'name \'this_value_does_not_exist\' is not defined', errors[0]["message"])
self.assertIsNotNone(errors[0]['task_data'])
self.assertIn("has_bananas", errors[0]['task_data'])
def test_validation_error(self):
self.load_example_data()
errors = self.validate_workflow("invalid_spec")
self.assertEqual(1, len(errors))
self.assertEqual(2, len(errors))
self.assertEqual("workflow_validation_error", errors[0]['code'])
self.assertEqual("StartEvent_1", errors[0]['task_id'])
self.assertEqual("invalid_spec.bpmn", errors[0]['file_name'])
def test_invalid_script(self):
self.load_example_data()
errors = self.validate_workflow("invalid_script")
self.assertEqual(1, len(errors))
self.assertEqual("workflow_execution_exception", errors[0]['code'])
self.assertEqual(2, len(errors))
self.assertEqual("workflow_validation_exception", errors[0]['code'])
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'])
def test_repeating_sections_correctly_populated(self):
self.load_example_data()
spec_model = self.load_test_spec('repeat_form')
final_data = WorkflowService.test_spec(spec_model.id)
self.assertIsNotNone(final_data)
self.assertIn('cats', final_data)
def test_required_fields(self):
self.load_example_data()
spec_model = self.load_test_spec('required_fields')
final_data = WorkflowService.test_spec(spec_model.id)
self.assertIsNotNone(final_data)
self.assertIn('string_required', final_data)
self.assertIn('string_not_required', final_data)
final_data = WorkflowService.test_spec(spec_model.id, required_only=True)
self.assertIsNotNone(final_data)
self.assertIn('string_required', final_data)
self.assertNotIn('string_not_required', final_data)