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cr-connect-workflow
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Merge pull request #129 from sartography/dev 

Dev --> Testing
This commit is contained in:
Aaron Louie 2020-06-29 08:34:29 -04:00 committed by GitHub
parent 1f41587e40 8f0115ac48
commit 464cd73376
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GPG Key ID: 4AEE18F83AFDEB23
53 changed files with 1637 additions and 549 deletions
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39
Pipfile
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@ -9,38 +9,41 @@ pbr = "*"
coverage = "*"
[packages]
alembic = "*"
connexion = {extras = ["swagger-ui"],version = "*"}
swagger-ui-bundle = "*"
coverage = "*"
docxtpl = "*"
flask = "*"
flask-admin = "*"
flask-bcrypt = "*"
flask-cors = "*"
flask-mail = "*"
flask-marshmallow = "*"
flask-migrate = "*"
flask-restful = "*"
gunicorn = "*"
httpretty = "*"
ldap3 = "*"
lxml = "*"
markdown = "*"
marshmallow = "*"
marshmallow-enum = "*"
marshmallow-sqlalchemy = "*"
openpyxl = "*"
pyjwt = "*"
requests = "*"
xlsxwriter = "*"
webtest = "*"
spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "deploy"}
alembic = "*"
coverage = "*"
sphinx = "*"
recommonmark = "*"
psycopg2-binary = "*"
docxtpl = "*"
python-dateutil = "*"
pandas = "*"
xlrd = "*"
ldap3 = "*"
gunicorn = "*"
werkzeug = "*"
psycopg2-binary = "*"
pyjwt = "*"
python-dateutil = "*"
recommonmark = "*"
requests = "*"
sentry-sdk = {extras = ["flask"],version = "==0.14.4"}
flask-mail = "*"
sphinx = "*"
spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "STG-26"}
swagger-ui-bundle = "*"
webtest = "*"
werkzeug = "*"
xlrd = "*"
xlsxwriter = "*"
[requires]
python_version = "3.7"

329
Pipfile.lock generated
View File

@ -1,7 +1,7 @@
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@ -161,6 +166,7 @@
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@ -182,6 +188,7 @@
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@ -237,6 +244,7 @@
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@ -261,6 +269,13 @@
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@ -369,6 +389,7 @@
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"sha256:427273b08efc16a85aa2b39892817e78e3ed074fcb89b2a51c4979bae7e7ba98",
"sha256:50c4ee32f0e1581828843267d8de35c3298e86ceecd5e9017dc45788be70a864",
"sha256:512a85c3c8c3995cc91af3e90f38f460da5d3cade8dc3a229c8e0879037547c9",
"sha256:57aa843b783179ab72e863512e14bdcba186641daf69e4e3a5761d705dcc35b1",
"sha256:621f58cd921cd71ba6215c42954ffaa8a918eecd8c535d97befa1a8acad986dd",
"sha256:6ac2558631a81b85e7fb7a44e5035347938b0a73f5fdc27a8566777d0792a6a4",
"sha256:716754d0b5490bdcf68e1e4925edc02ac07209883314ad01a137642ddb2056f1",
"sha256:736d41cfebedecc6f159fc4ac0769dc89528a989471dc1d378ba07d29a60ba1c",
"sha256:8619b86cb68b185a778635be5b3e6018623c0761dde4df2f112896424aa27bd8",
"sha256:87fad64529cde4f1914a5b9c383628e1a8f9e3930304c09cf22c2ae118a1280e",
"sha256:89494df7f93b1836cae210c42864b292f9b31eeabca4810193761990dc689cce",
"sha256:8cac7bb373a5f1423e28de3fd5fc8063b9c8ffe8957dc1b1a59cb90453db6da1",
"sha256:8fd452dc3d49b3cc54483e033de6c006c304432e6f84b74d7b2c68afa2569ae5",
"sha256:adad60eea2c4c2a1875eb6305a0b6e61a83163f8e233586a4d6a55221ef984fe",
"sha256:c26f95e7609b821b5f08a72dab929baa0d685406b953efd7c89423a511d5c413",
"sha256:cbe1324ef52ff26ccde2cb84b8593c8bf930069dfc06c1e616f1bfd4e47f48a3",
"sha256:d05c4adae06bd0c7f696ae3ec8d993ed8ffcc4e11a76b1b35a5af8a099bd2284",
"sha256:d98bc827a1293ae767c8f2f18be3bb5151fd37ddcd7da2a5f9581baeeb7a3fa1",
"sha256:da2fb75f64792c1fc64c82313a00c728a7c301efe6a60b7a9fe35b16b4368ce7",
"sha256:e4624d7edb2576cd72bb83636cd71c8ce544d8e272f308bd80885056972ca299",
"sha256:e89e0d9e106f8a9180a4ca92a6adde60c58b1b0299e1b43bd5e0312f535fbf33",
"sha256:f11c2437fb5f812d020932119ba02d9e2bc29a6eca01a055233a8b449e3e1e7d",
"sha256:f57be5673e12763dd400fea568608700a63ce1c6bd5bdbc3cc3a2c5fdb045274",
"sha256:fc728ece3d5c772c196fd338a99798e7efac7a04f9cb6416299a3638ee9a94cd"
],
"version": "==1.3.17"
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.3.18"
},
"swagger-ui-bundle": {
"hashes": [
@ -851,6 +976,7 @@
"sha256:3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527",
"sha256:88206b0eb87e6d677d424843ac5209e3fb9d0190d0ee169599165ec25e9d9115"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
"version": "==1.25.9"
},
"vine": {
@ -858,6 +984,7 @@
"sha256:133ee6d7a9016f177ddeaf191c1f58421a1dcc6ee9a42c58b34bed40e1d2cd87",
"sha256:ea4947cc56d1fd6f2095c8d543ee25dad966f78692528e68b4fada11ba3f98af"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.3.0"
},
"waitress": {
@ -865,6 +992,7 @@
"sha256:1bb436508a7487ac6cb097ae7a7fe5413aefca610550baf58f0940e51ecfb261",
"sha256:3d633e78149eb83b60a07dfabb35579c29aac2d24bb803c18b26fb2ab1a584db"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==1.4.4"
},
"webob": {
@ -872,6 +1000,7 @@
"sha256:a3c89a8e9ba0aeb17382836cdb73c516d0ecf6630ec40ec28288f3ed459ce87b",
"sha256:aa3a917ed752ba3e0b242234b2a373f9c4e2a75d35291dcbe977649bd21fd108"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.8.6"
},
"webtest": {
@ -890,6 +1019,13 @@
"index": "pypi",
"version": "==1.0.1"
},
"wtforms": {
"hashes": [
"sha256:6ff8635f4caeed9f38641d48cfe019d0d3896f41910ab04494143fc027866e1b",
"sha256:861a13b3ae521d6700dac3b2771970bd354a63ba7043ecc3a82b5288596a1972"
],
"version": "==2.3.1"
},
"xlrd": {
"hashes": [
"sha256:546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2",
@ -911,6 +1047,7 @@
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
],
"markers": "python_version >= '3.6'",
"version": "==3.1.0"
}
},
@ -920,6 +1057,7 @@
"sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c",
"sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==19.3.0"
},
"coverage": {
@ -972,6 +1110,7 @@
"sha256:68c70cc7167bdf5c7c9d8f6954a7837089c6a36bf565383919bb595efb8a17e5",
"sha256:b78134b2063dd214000685165d81c154522c3ee0a1c0d4d113c80361c234c5a2"
],
"markers": "python_version >= '3.5'",
"version": "==8.4.0"
},
"packaging": {
@ -979,6 +1118,7 @@
"sha256:4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8",
"sha256:998416ba6962ae7fbd6596850b80e17859a5753ba17c32284f67bfff33784181"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==20.4"
},
"pbr": {
@ -994,20 +1134,23 @@
"sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0",
"sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==0.13.1"
},
"py": {
"hashes": [
"sha256:a673fa23d7000440cc885c17dbd34fafcb7d7a6e230b29f6766400de36a33c44",
"sha256:f3b3a4c36512a4c4f024041ab51866f11761cc169670204b235f6b20523d4e6b"
"sha256:366389d1db726cd2fcfc79732e75410e5fe4d31db13692115529d34069a043c2",
"sha256:9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342"
],
"version": "==1.8.2"
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.9.0"
},
"pyparsing": {
"hashes": [
"sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1",
"sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
],
"markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.4.7"
},
"pytest": {
@ -1023,20 +1166,22 @@
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.15.0"
},
"wcwidth": {
"hashes": [
"sha256:79375666b9954d4a1a10739315816324c3e73110af9d0e102d906fdb0aec009f",
"sha256:8c6b5b6ee1360b842645f336d9e5d68c55817c26d3050f46b235ef2bc650e48f"
"sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784",
"sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"
],
"version": "==0.2.4"
"version": "==0.2.5"
},
"zipp": {
"hashes": [
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
],
"markers": "python_version >= '3.6'",
"version": "==3.1.0"
}
}

1
config/default.py
View File

@ -46,6 +46,7 @@ LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
# Email configuration
DEFAULT_SENDER = 'askresearch@virginia.edu'
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')

17
crc/__init__.py
View File

@ -4,6 +4,8 @@ import sentry_sdk
import connexion
from jinja2 import Environment, FileSystemLoader
from flask_admin import Admin
from flask_admin.contrib.sqla import ModelView
from flask_cors import CORS
from flask_marshmallow import Marshmallow
from flask_mail import Mail
@ -32,18 +34,24 @@ db = SQLAlchemy(app)
session = db.session
""":type: sqlalchemy.orm.Session"""
# Mail settings
mail = Mail(app)
migrate = Migrate(app, db)
ma = Marshmallow(app)
from crc import models
from crc import api
from crc.api import admin
connexion_app.add_api('api.yml', base_path='/v1.0')
# Convert list of allowed origins to list of regexes
origins_re = [r"^https?:\/\/%s(.*)" % o.replace('.', '\.') for o in app.config['CORS_ALLOW_ORIGINS']]
cors = CORS(connexion_app.app, origins=origins_re)
# Sentry error handling
if app.config['ENABLE_SENTRY']:
sentry_sdk.init(
dsn="https://25342ca4e2d443c6a5c49707d68e9f40@o401361.ingest.sentry.io/5260915",
@ -53,8 +61,6 @@ if app.config['ENABLE_SENTRY']:
# 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('APPLICATION_ROOT = ', app.config['APPLICATION_ROOT'])
@ -88,3 +94,10 @@ def clear_db():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
@app.cli.command()
def rrt_data_fix():
"""Finds all the empty task event logs, and populates
them with good wholesome data."""
from crc.services.workflow_service import WorkflowService
WorkflowService.fix_legacy_data_model_for_rrt()

21
crc/api.yml
View File

@ -626,6 +626,12 @@ paths:
schema:
type: string
format: uuid
- name: terminate_loop
in: query
required: false
description: Terminate the loop on a looping task
schema:
type: boolean
put:
operationId: crc.api.workflow.update_task
summary: Exclusively for User Tasks, submits form data as a flat set of key/values.
@ -917,6 +923,21 @@ paths:
application/json:
schema:
type: object
/health_attesting:
get:
operationId: crc.api.approval.get_health_attesting_csv
summary: Returns a CSV file with health attesting records
tags:
- Approvals
responses:
'200':
description: A CSV file
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
components:
securitySchemes:
jwt:

72
crc/api/admin.py Normal file
View File

@ -0,0 +1,72 @@
# Admin app
import json
from flask import url_for
from flask_admin import Admin
from flask_admin.contrib import sqla
from flask_admin.contrib.sqla import ModelView
from werkzeug.utils import redirect
from jinja2 import Markup
from crc import db, app
from crc.api.user import verify_token, verify_token_admin
from crc.models.approval import ApprovalModel
from crc.models.file import FileModel
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
from crc.models.workflow import WorkflowModel
class AdminModelView(sqla.ModelView):
can_create = False
can_edit = False
can_delete = False
page_size = 50 # the number of entries to display on the list view
column_exclude_list = ['bpmn_workflow_json', ]
column_display_pk = True
can_export = True
def is_accessible(self):
return verify_token_admin()
def inaccessible_callback(self, name, **kwargs):
# redirect to login page if user doesn't have access
return redirect(url_for('home'))
class UserView(AdminModelView):
column_filters = ['uid']
class StudyView(AdminModelView):
column_filters = ['id', 'primary_investigator_id']
column_searchable_list = ['title']
class ApprovalView(AdminModelView):
column_filters = ['study_id', 'approver_uid']
class WorkflowView(AdminModelView):
column_filters = ['study_id', 'id']
class FileView(AdminModelView):
column_filters = ['workflow_id']
def json_formatter(view, context, model, name):
value = getattr(model, name)
json_value = json.dumps(value, ensure_ascii=False, indent=2)
return Markup('<pre>{}</pre>'.format(json_value))
class TaskEventView(AdminModelView):
column_filters = ['workflow_id', 'action']
column_list = ['study_id', 'user_id', 'workflow_id', 'action', 'task_title', 'form_data', 'date']
column_formatters = {
'form_data': json_formatter,
}
admin = Admin(app)
admin.add_view(StudyView(StudyModel, db.session))
admin.add_view(ApprovalView(ApprovalModel, db.session))
admin.add_view(UserView(UserModel, db.session))
admin.add_view(WorkflowView(WorkflowModel, db.session))
admin.add_view(FileView(FileModel, db.session))
admin.add_view(TaskEventView(TaskEventModel, db.session))

76
crc/api/approval.py
View File

@ -1,9 +1,11 @@
import csv
import io
import json
import pickle
from base64 import b64decode
from datetime import datetime
from flask import g
from flask import g, make_response
from crc import db, session
from crc.api.common import ApiError
@ -88,71 +90,25 @@ def get_approvals_for_study(study_id=None):
return results
def get_health_attesting_csv():
records = ApprovalService.get_health_attesting_records()
si = io.StringIO()
cw = csv.writer(si)
cw.writerows(records)
output = make_response(si.getvalue())
output.headers["Content-Disposition"] = "attachment; filename=health_attesting.csv"
output.headers["Content-type"] = "text/csv"
return output
# ----- 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))
content = ApprovalService.get_not_really_csv_content()
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
return content
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 ---- #

86
crc/api/workflow.py
View File

@ -1,7 +1,7 @@
import uuid
from SpiffWorkflow.util.deep_merge import DeepMerge
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
@ -96,59 +96,10 @@ def delete_workflow_specification(spec_id):
session.commit()
def __get_workflow_api_model(processor: WorkflowProcessor, next_task = None):
"""Returns an API model representing the state of the current workflow, if requested, and
possible, next_task is set to the current_task."""
nav_dict = processor.bpmn_workflow.get_nav_list()
navigation = []
for nav_item in nav_dict:
spiff_task = processor.bpmn_workflow.get_task(nav_item['task_id'])
if 'description' in nav_item:
nav_item['title'] = nav_item.pop('description')
# fixme: duplicate code from the workflow_service. Should only do this in one place.
if ' ' in nav_item['title']:
nav_item['title'] = nav_item['title'].partition(' ')[2]
else:
nav_item['title'] = ""
if spiff_task:
nav_item['task'] = WorkflowService.spiff_task_to_api_task(spiff_task, add_docs_and_forms=False)
nav_item['title'] = nav_item['task'].title # Prefer the task title.
else:
nav_item['task'] = None
if not 'is_decision' in nav_item:
nav_item['is_decision'] = False
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(),
next_task=None,
navigation=navigation,
workflow_spec_id=processor.workflow_spec_id,
spec_version=processor.get_version_string(),
is_latest_spec=processor.is_latest_spec,
total_tasks=len(navigation),
completed_tasks=processor.workflow_model.completed_tasks,
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.
next_task = processor.next_task()
if next_task:
workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True)
return workflow_api
def get_workflow(workflow_id, soft_reset=False, hard_reset=False):
workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first()
processor = WorkflowProcessor(workflow_model, soft_reset=soft_reset, hard_reset=hard_reset)
workflow_api_model = __get_workflow_api_model(processor)
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
return WorkflowApiSchema().dump(workflow_api_model)
@ -161,21 +112,24 @@ def set_current_task(workflow_id, task_id):
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)
if task.state != task.COMPLETED and task.state != task.READY:
spiff_task = processor.bpmn_workflow.get_task(task_id)
if spiff_task.state != spiff_task.COMPLETED and spiff_task.state != spiff_task.READY:
raise ApiError("invalid_state", "You may not move the token to a task who's state is not "
"currently set to COMPLETE or READY.")
# Only reset the token if the task doesn't already have it.
if task.state == task.COMPLETED:
task.reset_token(reset_data=False) # we could optionally clear the previous data.
if spiff_task.state == spiff_task.COMPLETED:
spiff_task.reset_token(reset_data=True) # Don't try to copy the existing data back into this task.
processor.save()
WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_TOKEN_RESET)
workflow_api_model = __get_workflow_api_model(processor, task)
WorkflowService.log_task_action(user_uid, workflow_model, spiff_task,
WorkflowService.TASK_ACTION_TOKEN_RESET,
version=processor.get_version_string())
workflow_api_model = WorkflowService.processor_to_workflow_api(processor, spiff_task)
return WorkflowApiSchema().dump(workflow_api_model)
def update_task(workflow_id, task_id, body):
def update_task(workflow_id, task_id, body, terminate_loop=None):
workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
if workflow_model is None:
@ -187,17 +141,21 @@ def update_task(workflow_id, task_id, body):
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)
if task.state != task.READY:
spiff_task = processor.bpmn_workflow.get_task(task_id)
if spiff_task.state != spiff_task.READY:
raise ApiError("invalid_state", "You may not update a task unless it is in the READY state. "
"Consider calling a token reset to make this task Ready.")
task.update_data(body)
processor.complete_task(task)
if terminate_loop:
spiff_task.terminate_loop()
spiff_task.update_data(body)
processor.complete_task(spiff_task)
processor.do_engine_steps()
processor.save()
WorkflowService.log_task_action(user_uid, processor, task, WorkflowService.TASK_ACTION_COMPLETE)
workflow_api_model = __get_workflow_api_model(processor)
WorkflowService.log_task_action(user_uid, workflow_model, spiff_task, WorkflowService.TASK_ACTION_COMPLETE,
version=processor.get_version_string())
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
return WorkflowApiSchema().dump(workflow_api_model)

1
crc/models/api_models.py
View File

@ -36,6 +36,7 @@ class Task(object):
PROP_OPTIONS_FILE = "spreadsheet.name"
PROP_OPTIONS_VALUE_COLUMN = "spreadsheet.value.column"
PROP_OPTIONS_LABEL_COL = "spreadsheet.label.column"
PROP_OPTIONS_READ_ONLY = "read_only"
PROP_LDAP_LOOKUP = "ldap.lookup"
VALIDATION_REQUIRED = "required"
FIELD_TYPE_AUTO_COMPLETE = "autocomplete"

18
crc/models/email.py Normal file
View File

@ -0,0 +1,18 @@
from flask_marshmallow.sqla import SQLAlchemyAutoSchema
from marshmallow import EXCLUDE
from sqlalchemy import func
from crc import db
from crc.models.study import StudyModel
class EmailModel(db.Model):
__tablename__ = 'email'
id = db.Column(db.Integer, primary_key=True)
subject = db.Column(db.String)
sender = db.Column(db.String)
recipients = db.Column(db.String)
content = db.Column(db.String)
content_html = db.Column(db.String)
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=True)
study = db.relationship(StudyModel)

3
crc/models/ldap.py
View File

@ -29,6 +29,9 @@ class LdapModel(db.Model):
affiliation=", ".join(entry.uvaPersonIAMAffiliation),
sponsor_type=", ".join(entry.uvaPersonSponsoredType))
def proper_name(self):
return f'{self.display_name} - ({self.uid})'
class LdapSchema(SQLAlchemyAutoSchema):
class Meta:

1
crc/models/stats.py
View File

@ -17,6 +17,7 @@ class TaskEventModel(db.Model):
task_title = db.Column(db.String)
task_type = db.Column(db.String)
task_state = db.Column(db.String)
form_data = db.Column(db.JSON) # And form data submitted when the task was completed.
mi_type = db.Column(db.String)
mi_count = db.Column(db.Integer)
mi_index = db.Column(db.Integer)

91
crc/scripts/email.py Normal file
View File

@ -0,0 +1,91 @@
import markdown
from jinja2 import Template
from crc import app
from crc.api.common import ApiError
from crc.scripts.script import Script
from crc.services.ldap_service import LdapService
from crc.services.mails import send_mail
class Email(Script):
"""This Script allows to be introduced as part of a workflow and called from there, specifying
recipients and content """
def get_description(self):
return """
Creates an email, using the provided arguments (a list of UIDs)"
Each argument will be used to look up personal information needed for
the email creation.
Example:
Email Subject ApprvlApprvr1 PIComputingID
"""
def do_task_validate_only(self, task, *args, **kwargs):
self.get_subject(task, args)
self.get_users_info(task, args)
self.get_content(task)
def do_task(self, task, *args, **kwargs):
args = [arg for arg in args if type(arg) == str]
subject = self.get_subject(task, args)
recipients = self.get_users_info(task, args)
content, content_html = self.get_content(task)
if recipients:
send_mail(
subject=subject,
sender=app.config['DEFAULT_SENDER'],
recipients=recipients,
content=content,
content_html=content_html
)
def get_users_info(self, task, args):
if len(args) < 1:
raise ApiError(code="missing_argument",
message="Email script requires at least one argument. The "
"name of the variable in the task data that contains user"
"id to process. Multiple arguments are accepted.")
emails = []
for arg in args:
try:
uid = task.workflow.script_engine.evaluate_expression(task, arg)
except Exception as e:
app.logger.error(f'Workflow engines could not parse {arg}')
app.logger.error(str(e))
continue
user_info = LdapService.user_info(uid)
email = user_info.email_address
emails.append(user_info.email_address)
if not isinstance(email, str):
raise ApiError(code="invalid_argument",
message="The Email script requires at least 1 UID argument. The "
"name of the variable in the task data that contains subject and"
" user ids to process. This must point to an array or a string, but "
"it currently points to a %s " % emails.__class__.__name__)
return emails
def get_subject(self, task, args):
if len(args) < 1:
raise ApiError(code="missing_argument",
message="Email script requires at least one subject argument. The "
"name of the variable in the task data that contains subject"
" to process. Multiple arguments are accepted.")
subject = args[0]
if not isinstance(subject, str):
raise ApiError(code="invalid_argument",
message="The Email script requires 1 argument. The "
"the name of the variable in the task data that contains user"
"ids to process. This must point to an array or a string, but "
"it currently points to a %s " % subject.__class__.__name__)
return subject
def get_content(self, task):
content = task.task_spec.documentation
template = Template(content)
rendered = template.render(task.data)
rendered_markdown = markdown.markdown(rendered).replace('\n', '<br>')
return rendered, rendered_markdown

128
crc/services/approval_service.py
View File

@ -1,6 +1,9 @@
from datetime import datetime
import json
import pickle
from base64 import b64decode
from datetime import datetime, timedelta
from sqlalchemy import desc
from sqlalchemy import desc, func
from crc import app, db, session
from crc.api.common import ApiError
@ -109,16 +112,129 @@ class ApprovalService(object):
db_approvals = query.all()
return [Approval.from_model(approval_model) for approval_model in db_approvals]
@staticmethod
def get_approval_details(approval):
"""Returns a list of packed approval details, obtained from
the task data sent during the workflow """
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
if approval.status != ApprovalStatus.APPROVED.value:
return {}
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 = {
'Supervisor': pi_supervisor,
'PI_Details': pi_details,
'Review': review_complete
}
details['person_details'] = []
details['person_details'].append(pi_details)
for person in personnel:
uid = person['PersonnelComputingID']['value']
details['person_details'].append(LdapService.user_info(uid))
return details
@staticmethod
def get_health_attesting_records():
"""Return a list with prepared information related to all approvals """
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
health_attesting_rows = [
['university_computing_id',
'last_name',
'first_name',
'department',
'job_title',
'supervisor_university_computing_id']
]
for approval in approvals:
try:
details = ApprovalService.get_approval_details(approval)
if not details:
continue
for person in details['person_details']:
first_name = person.given_name
last_name = person.display_name.replace(first_name, '').strip()
record = [
person.uid,
last_name,
first_name,
'',
'Academic Researcher',
details['Supervisor'] if person.uid == details['person_details'][0].uid else 'askresearch'
]
if record not in health_attesting_rows:
health_attesting_rows.append(record)
except Exception as e:
app.logger.error("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
return health_attesting_rows
@staticmethod
def get_not_really_csv_content():
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
output = []
errors = []
for approval in approvals:
try:
details = ApprovalService.get_approval_details(approval)
for person in details['person_details']:
record = {
"study_id": approval.study_id,
"pi_uid": details['PI_Details'].uid,
"pi": details['PI_Details'].display_name,
"name": person.display_name,
"uid": person.uid,
"email": person.email_address,
"supervisor": details['Supervisor'] if person.uid == details['person_details'][0].uid else "",
"review_complete": details['Review'],
}
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 }
@staticmethod
def update_approval(approval_id, approver_uid):
"""Update a specific approval"""
"""Update a specific approval
NOTE: Actual update happens in the API layer, this
funtion is currently in charge of only sending
corresponding emails
"""
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()
if status == ApprovalStatus.APPROVED.value:
# second_approval = ApprovalModel().query.filter_by(
# study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,

42
crc/services/email_service.py Normal file
View File

@ -0,0 +1,42 @@
from datetime import datetime
from flask_mail import Message
from sqlalchemy import desc
from crc import app, db, mail, session
from crc.api.common import ApiError
from crc.models.study import StudyModel
from crc.models.email import EmailModel
class EmailService(object):
"""Provides common tools for working with an Email"""
@staticmethod
def add_email(subject, sender, recipients, content, content_html, study_id):
"""We will receive all data related to an email and store it"""
# Find corresponding study - if any
study = None
if type(study_id) == int:
study = db.session.query(StudyModel).get(study_id)
# Create EmailModel
email_model = EmailModel(subject=subject, sender=sender, recipients=str(recipients),
content=content, content_html=content_html, study=study)
# Send mail
try:
msg = Message(subject,
sender=sender,
recipients=recipients)
msg.body = content
msg.html = content_html
mail.send(msg)
except Exception as e:
app.logger.error(str(e))
db.session.add(email_model)
db.session.commit()

8
crc/services/file_service.py
View File

@ -3,7 +3,7 @@ import json
import os
from datetime import datetime
from uuid import UUID
from xml.etree import ElementTree
from lxml import etree
import flask
from SpiffWorkflow.bpmn.parser.ValidationException import ValidationException
@ -151,7 +151,7 @@ class FileService(object):
# If this is a BPMN, extract the process id.
if file_model.type == FileType.bpmn:
bpmn: ElementTree.Element = ElementTree.fromstring(binary_data)
bpmn: etree.Element = etree.fromstring(binary_data)
file_model.primary_process_id = FileService.get_process_id(bpmn)
new_file_data_model = FileDataModel(
@ -165,7 +165,7 @@ class FileService(object):
return file_model
@staticmethod
def get_process_id(et_root: ElementTree.Element):
def get_process_id(et_root: etree.Element):
process_elements = []
for child in et_root:
if child.tag.endswith('process') and child.attrib.get('isExecutable', False):
@ -179,7 +179,7 @@ class FileService(object):
# Look for the element that has the startEvent in it
for e in process_elements:
this_element: ElementTree.Element = e
this_element: etree.Element = e
for child_element in list(this_element):
if child_element.tag.endswith('startEvent'):
return this_element.attrib['id']

115
crc/services/mails.py
View File

@ -3,13 +3,15 @@ import os
from flask import render_template, render_template_string
from flask_mail import Message
from crc.services.email_service import EmailService
# 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)
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': "test"}
@ -20,109 +22,84 @@ def send_test_email(sender, recipients):
except Exception as e:
return str(e)
def send_mail(subject, sender, recipients, content, content_html, study_id=None):
EmailService.add_email(subject=subject, sender=sender, recipients=recipients,
content=content, content_html=content_html, study_id=study_id)
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
from crc import env
subject = 'Research Ramp-up Plan Submitted'
template = env.get_template('ramp_up_submission.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
msg.body = template.render(template_vars)
content = template.render(template_vars)
template = env.get_template('ramp_up_submission.html')
msg.html = template.render(template_vars)
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
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
from crc import env
subject = 'Research Ramp-up Plan Approval Request'
template = env.get_template('ramp_up_approval_request.txt')
template_vars = {'primary_investigator': primary_investigator}
msg.body = template.render(template_vars)
content = template.render(template_vars)
template = env.get_template('ramp_up_approval_request.html')
msg.html = template.render(template_vars)
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
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
from crc import env
subject = 'Research Ramp-up Plan Approval Request'
template = env.get_template('ramp_up_approval_request_first_review.txt')
template_vars = {'primary_investigator': primary_investigator}
msg.body = template.render(template_vars)
content = template.render(template_vars)
template = env.get_template('ramp_up_approval_request_first_review.html')
msg.html = template.render(template_vars)
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
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
subject = 'Research Ramp-up Plan Approved'
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)
content = template.render(template_vars)
template = env.get_template('ramp_up_approved.html')
msg.html = template.render(template_vars)
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
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
subject = 'Research Ramp-up Plan Denied'
from crc import env, mail
template = env.get_template('ramp_up_denied.txt')
template_vars = {'approver': approver}
msg.body = template.render(template_vars)
content = template.render(template_vars)
template = env.get_template('ramp_up_denied.html')
msg.html = template.render(template_vars)
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
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
subject = 'Research Ramp-up Plan Denied'
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)
content = template.render(template_vars)
template = env.get_template('ramp_up_denied_first_approver.html')
msg.html = template.render(template_vars)
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result

3
crc/services/study_service.py
View File

@ -181,8 +181,6 @@ class StudyService(object):
documents[code] = doc
return documents
@staticmethod
def get_investigators(study_id):
@ -224,7 +222,6 @@ class StudyService(object):
return FileModelSchema().dump(file)
@staticmethod
def synch_with_protocol_builder_if_enabled(user):
"""Assures that the studies we have locally for the given user are

38
crc/services/workflow_processor.py
View File

@ -1,5 +1,6 @@
import re
import xml.etree.ElementTree as ElementTree
from lxml import etree
import shlex
from datetime import datetime
from typing import List
@ -13,7 +14,6 @@ from SpiffWorkflow.camunda.parser.CamundaParser import CamundaParser
from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from SpiffWorkflow.specs import WorkflowSpec
from sqlalchemy import desc
from crc import session
from crc.api.common import ApiError
@ -36,7 +36,9 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
This allows us to reference custom code from the BPMN diagram.
"""
commands = script.split(" ")
# Shlex splits the whole string while respecting double quoted strings within
commands = shlex.split(script)
printable_comms = commands
path_and_command = commands[0].rsplit(".", 1)
if len(path_and_command) == 1:
module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
@ -102,14 +104,15 @@ class WorkflowProcessor(object):
def __init__(self, workflow_model: WorkflowModel, soft_reset=False, hard_reset=False, validate_only=False):
"""Create a Workflow Processor based on the serialized information available in the workflow model.
If soft_reset is set to true, it will try to use the latest version of the workflow specification.
If hard_reset is set to true, it will create a new Workflow, but embed the data from the last
completed task in the previous workflow.
If soft_reset is set to true, it will try to use the latest version of the workflow specification
without resetting to the beginning of the workflow. This will work for some minor changes to the spec.
If hard_reset is set to true, it will use the latest spec, and start the workflow over from the beginning.
which should work in casees where a soft reset fails.
If neither flag is set, it will use the same version of the specification that was used to originally
create the workflow model. """
self.workflow_model = workflow_model
if soft_reset or len(workflow_model.dependencies) == 0:
if soft_reset or len(workflow_model.dependencies) == 0: # Depenencies of 0 means the workflow was never started.
self.spec_data_files = FileService.get_spec_data_files(
workflow_spec_id=workflow_model.workflow_spec_id)
else:
@ -216,8 +219,6 @@ class WorkflowProcessor(object):
full_version = "v%s (%s)" % (version, files)
return full_version
def update_dependencies(self, spec_data_files):
existing_dependencies = FileService.get_spec_data_files(
workflow_spec_id=self.workflow_model.workflow_spec_id,
@ -267,12 +268,12 @@ class WorkflowProcessor(object):
for file_data in file_data_models:
if file_data.file_model.type == FileType.bpmn:
bpmn: ElementTree.Element = ElementTree.fromstring(file_data.data)
bpmn: etree.Element = etree.fromstring(file_data.data)
if file_data.file_model.primary:
process_id = FileService.get_process_id(bpmn)
parser.add_bpmn_xml(bpmn, filename=file_data.file_model.name)
elif file_data.file_model.type == FileType.dmn:
dmn: ElementTree.Element = ElementTree.fromstring(file_data.data)
dmn: etree.Element = etree.fromstring(file_data.data)
parser.add_dmn_xml(dmn, filename=file_data.file_model.name)
if process_id is None:
raise (ApiError(code="no_primary_bpmn_error",
@ -299,25 +300,12 @@ 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 they don't need to reenter all the previous data.
Returns the new version.
"""Recreate this workflow. This will be useful when a workflow specification changes.
"""
# 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)
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

158
crc/services/workflow_service.py
View File

@ -1,3 +1,4 @@
import copy
import string
from datetime import datetime
import random
@ -5,25 +6,26 @@ import random
import jinja2
from SpiffWorkflow import Task as SpiffTask, WorkflowException
from SpiffWorkflow.bpmn.specs.ManualTask import ManualTask
from SpiffWorkflow.bpmn.specs.MultiInstanceTask import MultiInstanceTask
from SpiffWorkflow.bpmn.specs.ScriptTask import ScriptTask
from SpiffWorkflow.bpmn.specs.UserTask import UserTask
from SpiffWorkflow.dmn.specs.BusinessRuleTask import BusinessRuleTask
from SpiffWorkflow.specs import CancelTask, StartTask
from flask import g
from SpiffWorkflow.util.deep_merge import DeepMerge
from jinja2 import Template
from crc import db, app
from crc.api.common import ApiError
from crc.models.api_models import Task, MultiInstanceType
from crc.models.api_models import Task, MultiInstanceType, NavigationItem, NavigationItemSchema, WorkflowApi
from crc.models.file import LookupDataModel
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
from crc.models.workflow import WorkflowModel, WorkflowStatus
from crc.models.workflow import WorkflowModel, WorkflowStatus, WorkflowSpecModel
from crc.services.file_service import FileService
from crc.services.lookup_service import LookupService
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor, CustomBpmnScriptEngine
from crc.services.workflow_processor import WorkflowProcessor
class WorkflowService(object):
@ -180,13 +182,87 @@ class WorkflowService(object):
def __get_options(self):
pass
@staticmethod
def _random_string(string_length=10):
"""Generate a random string of fixed length """
letters = string.ascii_lowercase
return ''.join(random.choice(letters) for i in range(string_length))
@staticmethod
def processor_to_workflow_api(processor: WorkflowProcessor, next_task=None):
"""Returns an API model representing the state of the current workflow, if requested, and
possible, next_task is set to the current_task."""
nav_dict = processor.bpmn_workflow.get_nav_list()
navigation = []
for nav_item in nav_dict:
spiff_task = processor.bpmn_workflow.get_task(nav_item['task_id'])
if 'description' in nav_item:
nav_item['title'] = nav_item.pop('description')
# fixme: duplicate code from the workflow_service. Should only do this in one place.
if ' ' in nav_item['title']:
nav_item['title'] = nav_item['title'].partition(' ')[2]
else:
nav_item['title'] = ""
if spiff_task:
nav_item['task'] = WorkflowService.spiff_task_to_api_task(spiff_task, add_docs_and_forms=False)
nav_item['title'] = nav_item['task'].title # Prefer the task title.
else:
nav_item['task'] = None
if not 'is_decision' in nav_item:
nav_item['is_decision'] = False
navigation.append(NavigationItem(**nav_item))
NavigationItemSchema().dump(nav_item)
spec = db.session.query(WorkflowSpecModel).filter_by(id=processor.workflow_spec_id).first()
workflow_api = WorkflowApi(
id=processor.get_workflow_id(),
status=processor.get_status(),
next_task=None,
navigation=navigation,
workflow_spec_id=processor.workflow_spec_id,
spec_version=processor.get_version_string(),
is_latest_spec=processor.is_latest_spec,
total_tasks=len(navigation),
completed_tasks=processor.workflow_model.completed_tasks,
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.
next_task = processor.next_task()
if next_task:
previous_form_data = WorkflowService.get_previously_submitted_data(processor.workflow_model.id, next_task)
DeepMerge.merge(next_task.data, previous_form_data)
workflow_api.next_task = WorkflowService.spiff_task_to_api_task(next_task, add_docs_and_forms=True)
return workflow_api
@staticmethod
def get_previously_submitted_data(workflow_id, spiff_task):
""" If the user has completed this task previously, find the form data for the last submission."""
query = db.session.query(TaskEventModel) \
.filter_by(workflow_id=workflow_id) \
.filter_by(task_name=spiff_task.task_spec.name) \
.filter_by(action=WorkflowService.TASK_ACTION_COMPLETE)
if hasattr(spiff_task, 'internal_data') and 'runtimes' in spiff_task.internal_data:
query = query.filter_by(mi_index=spiff_task.internal_data['runtimes'])
latest_event = query.order_by(TaskEventModel.date.desc()).first()
if latest_event:
if latest_event.form_data is not None:
return latest_event.form_data
else:
app.logger.error("missing_form_data", "We have lost data for workflow %i, "
"task %s, it is not in the task event model, "
"and it should be." % (workflow_id, spiff_task.task_spec.name))
return {}
else:
return {}
@staticmethod
def spiff_task_to_api_task(spiff_task, add_docs_and_forms=False):
task_type = spiff_task.task_spec.__class__.__name__
@ -218,8 +294,8 @@ class WorkflowService(object):
props = {}
if hasattr(spiff_task.task_spec, 'extensions'):
for id, val in spiff_task.task_spec.extensions.items():
props[id] = val
for key, val in spiff_task.task_spec.extensions.items():
props[key] = val
task = Task(spiff_task.id,
spiff_task.task_spec.name,
@ -318,21 +394,22 @@ class WorkflowService(object):
field.options.append({"id": d.value, "name": d.label})
@staticmethod
def log_task_action(user_uid, processor, spiff_task, action):
def log_task_action(user_uid, workflow_model, spiff_task, action, version):
task = WorkflowService.spiff_task_to_api_task(spiff_task)
workflow_model = processor.workflow_model
form_data = WorkflowService.extract_form_data(spiff_task.data, spiff_task)
task_event = TaskEventModel(
study_id=workflow_model.study_id,
user_uid=user_uid,
workflow_id=workflow_model.id,
workflow_spec_id=workflow_model.workflow_spec_id,
spec_version=processor.get_version_string(),
spec_version=version,
action=action,
task_id=task.id,
task_name=task.name,
task_title=task.title,
task_type=str(task.type),
task_state=task.state,
form_data=form_data,
mi_type=task.multi_instance_type.value, # Some tasks have a repeat behavior.
mi_count=task.multi_instance_count, # This is the number of times the task could repeat.
mi_index=task.multi_instance_index, # And the index of the currently repeating task.
@ -342,3 +419,64 @@ class WorkflowService(object):
db.session.add(task_event)
db.session.commit()
@staticmethod
def fix_legacy_data_model_for_rrt():
""" Remove this after use! This is just to fix RRT so the data is handled correctly.
Utility that is likely called via the flask command line, it will loop through all the
workflows in the system and attempt to add the right data into the task action log so that
users do not have to re fill out all of the forms if they start over or go back in the workflow.
Viciously inefficient, but should only have to run one time for RRT"""
workflows = db.session.query(WorkflowModel).all()
for workflow_model in workflows:
task_logs = db.session.query(TaskEventModel) \
.filter(TaskEventModel.workflow_id == workflow_model.id) \
.filter(TaskEventModel.action == WorkflowService.TASK_ACTION_COMPLETE) \
.order_by(TaskEventModel.date.desc()).all()
processor = WorkflowProcessor(workflow_model)
# Grab all the data from last task completed, which will be everything in this
# rrt situation because of how we were keeping all the data at the time.
latest_data = processor.next_task().data
# Move forward in the task spec tree, dropping any data that would have been
# added in subsequent tasks, just looking at form data, will not track the automated
# task data additions, hopefully this doesn't hang us.
for log in task_logs:
# if log.task_data is not None: # Only do this if the task event does not have data populated in it.
# continue
data = copy.deepcopy(latest_data) # Or you end up with insane crazy issues.
# In the simple case of RRT, there is exactly one task for the given task_spec
task = processor.bpmn_workflow.get_tasks_from_spec_name(log.task_name)[0]
data = WorkflowService.extract_form_data(data, task)
log.form_data = data
db.session.add(log)
db.session.commit()
@staticmethod
def extract_form_data(latest_data, task):
"""Removes data from latest_data that would be added by the child task or any of it's children."""
data = {}
if hasattr(task.task_spec, 'form'):
for field in task.task_spec.form.fields:
if field.has_property(Task.PROP_OPTIONS_READ_ONLY) and \
field.get_property(Task.PROP_OPTIONS_READ_ONLY).lower().strip() == "true":
continue # Don't add read-only data
elif field.has_property(Task.PROP_OPTIONS_REPEAT):
group = field.get_property(Task.PROP_OPTIONS_REPEAT)
if group in latest_data:
data[group] = latest_data[group]
elif isinstance(task.task_spec, MultiInstanceTask):
group = task.task_spec.elementVar
if group in latest_data:
data[group] = latest_data[group]
else:
if field.id in latest_data:
data[field.id] = latest_data[field.id]
return data

2
crc/static/templates/mails/ramp_up_denied.txt
View File

@ -1 +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.
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.

8
docker_run.sh
View File

@ -23,8 +23,16 @@ if [ "$RESET_DB_RRT" = "true" ]; then
pipenv run flask load-example-rrt-data
fi
if [ "$FIX_RRT_DATA" = "true" ]; then
echo 'Fixing RRT data...'
pipenv run flask rrt-data-fix
fi
# THIS MUST BE THE LAST COMMAND!
if [ "$APPLICATION_ROOT" = "/" ]; then
pipenv run gunicorn --bind 0.0.0.0:$PORT0 wsgi:app
else
pipenv run gunicorn -e SCRIPT_NAME="$APPLICATION_ROOT" --bind 0.0.0.0:$PORT0 wsgi:app
fi

28
migrations/versions/1fdd1bdb600e_.py Normal file
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@ -0,0 +1,28 @@
"""empty message
Revision ID: 1fdd1bdb600e
Revises: 17597692d0b0
Create Date: 2020-06-17 16:44:16.427988
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '1fdd1bdb600e'
down_revision = '17597692d0b0'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('task_event', sa.Column('task_data', sa.JSON(), nullable=True))
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_column('task_event', 'task_data')
# ### end Alembic commands ###

38
migrations/versions/5acd138e969c_.py Normal file
View File

@ -0,0 +1,38 @@
"""empty message
Revision ID: 5acd138e969c
Revises: de30304ff5e6
Create Date: 2020-06-24 21:36:15.128632
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '5acd138e969c'
down_revision = 'de30304ff5e6'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('email',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('subject', sa.String(), nullable=True),
sa.Column('sender', sa.String(), nullable=True),
sa.Column('recipients', sa.String(), nullable=True),
sa.Column('content', sa.String(), nullable=True),
sa.Column('content_html', sa.String(), nullable=True),
sa.Column('study_id', sa.Integer(), nullable=True),
sa.ForeignKeyConstraint(['study_id'], ['study.id'], ),
sa.PrimaryKeyConstraint('id')
)
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('email')
# ### end Alembic commands ###

30
migrations/versions/de30304ff5e6_.py Normal file
View File

@ -0,0 +1,30 @@
"""empty message
Revision ID: de30304ff5e6
Revises: 1fdd1bdb600e
Create Date: 2020-06-18 16:19:11.133665
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision = 'de30304ff5e6'
down_revision = '1fdd1bdb600e'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('task_event', sa.Column('form_data', sa.JSON(), nullable=True))
op.drop_column('task_event', 'task_data')
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('task_event', sa.Column('task_data', postgresql.JSON(astext_type=sa.Text()), autoincrement=False, nullable=True))
op.drop_column('task_event', 'form_data')
# ### end Alembic commands ###

0
tests/test_approvals_api.py → tests/approval/test_approvals_api.py
View File

26
tests/test_approvals_service.py → tests/approval/test_approvals_service.py
View File

@ -57,6 +57,32 @@ class TestApprovalsService(BaseTest):
self.assertEqual(1, models[0].version)
self.assertEqual(2, models[1].version)
def test_get_health_attesting_records(self):
self.load_example_data()
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="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
records = ApprovalService.get_health_attesting_records()
self.assertEqual(len(records), 1)
def test_get_not_really_csv_content(self):
self.load_example_data()
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="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
records = ApprovalService.get_not_really_csv_content()
self.assertEqual(len(records), 2)
def test_new_approval_sends_proper_emails(self):
self.assertEqual(1, 1)

0
tests/test_request_approval_script.py → tests/approval/test_request_approval_script.py
View File

15
tests/base_test.py
View File

@ -290,7 +290,7 @@ class BaseTest(unittest.TestCase):
self.assertEqual(workflow.workflow_spec_id, workflow_api.workflow_spec_id)
return workflow_api
def complete_form(self, workflow_in, task_in, dict_data, error_code=None, user_uid="dhf8r"):
def complete_form(self, workflow_in, task_in, dict_data, error_code=None, terminate_loop=None, user_uid="dhf8r"):
prev_completed_task_count = workflow_in.completed_tasks
if isinstance(task_in, dict):
task_id = task_in["id"]
@ -299,7 +299,12 @@ class BaseTest(unittest.TestCase):
user = session.query(UserModel).filter_by(uid=user_uid).first()
self.assertIsNotNone(user)
if terminate_loop:
rv = self.app.put('/v1.0/workflow/%i/task/%s/data?terminate_loop=true' % (workflow_in.id, task_id),
headers=self.logged_in_headers(user=user),
content_type="application/json",
data=json.dumps(dict_data))
else:
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",
@ -316,6 +321,8 @@ class BaseTest(unittest.TestCase):
# 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)
# presumably, we also need to deal with sequential items here too . .
if not task_in.multi_instance_type == 'looping':
self.assertEqual(prev_completed_task_count + 1, workflow.completed_tasks)
# Assure a record exists in the Task Events
@ -335,6 +342,7 @@ class BaseTest(unittest.TestCase):
self.assertEqual(task_in.name, event.task_name)
self.assertEqual(task_in.title, event.task_title)
self.assertEqual(task_in.type, event.task_type)
if not task_in.multi_instance_type == 'looping':
self.assertEqual("COMPLETED", event.task_state)
# Not sure what voodoo is happening inside of marshmallow to get me in this state.
@ -344,6 +352,9 @@ class BaseTest(unittest.TestCase):
self.assertEqual(task_in.multi_instance_type, event.mi_type)
self.assertEqual(task_in.multi_instance_count, event.mi_count)
if task_in.multi_instance_type == 'looping' and not terminate_loop:
self.assertEqual(task_in.multi_instance_index+1, event.mi_index)
else:
self.assertEqual(task_in.multi_instance_index, event.mi_index)
self.assertEqual(task_in.process_name, event.process_name)
self.assertIsNotNone(event.date)

67
tests/data/email/email.bpmn Normal file
View File

@ -0,0 +1,67 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_0y2dq4f" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_0tad5ma" name="Set Recipients" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_1synsig</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:endEvent id="Event_0izrcj4">
<bpmn:incoming>Flow_1xlrgne</bpmn:incoming>
</bpmn:endEvent>
<bpmn:scriptTask id="Activity_0s5v97n" name="Email Recipients">
<bpmn:documentation># Dear Approver
## you have been requested for approval
---
New request submitted by {{ PIComputingID }}
Email content to be delivered to {{ ApprvlApprvr1 }}
---</bpmn:documentation>
<bpmn:incoming>Flow_08n2npe</bpmn:incoming>
<bpmn:outgoing>Flow_1xlrgne</bpmn:outgoing>
<bpmn:script>Email "Camunda Email Subject" ApprvlApprvr1 PIComputingID</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1synsig" sourceRef="StartEvent_1" targetRef="Activity_1l9vih3" />
<bpmn:sequenceFlow id="Flow_1xlrgne" sourceRef="Activity_0s5v97n" targetRef="Event_0izrcj4" />
<bpmn:sequenceFlow id="Flow_08n2npe" sourceRef="Activity_1l9vih3" targetRef="Activity_0s5v97n" />
<bpmn:userTask id="Activity_1l9vih3" name="Set Recipients">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="ApprvlApprvr1" label="Approver" type="string" />
<camunda:formField id="PIComputingID" label="Primary Investigator" type="string" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_1synsig</bpmn:incoming>
<bpmn:outgoing>Flow_08n2npe</bpmn:outgoing>
</bpmn:userTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0tad5ma">
<bpmndi:BPMNEdge id="Flow_08n2npe_di" bpmnElement="Flow_08n2npe">
<di:waypoint x="370" y="117" />
<di:waypoint x="450" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1xlrgne_di" bpmnElement="Flow_1xlrgne">
<di:waypoint x="550" y="117" />
<di:waypoint x="662" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1synsig_di" bpmnElement="Flow_1synsig">
<di:waypoint x="215" y="117" />
<di:waypoint x="270" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_0izrcj4_di" bpmnElement="Event_0izrcj4">
<dc:Bounds x="662" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_04imfm6_di" bpmnElement="Activity_0s5v97n">
<dc:Bounds x="450" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0xugr62_di" bpmnElement="Activity_1l9vih3">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

45
tests/data/looping_task/looping_task.bpmn Normal file
View File

@ -0,0 +1,45 @@
<?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_1v9xfjq" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
<bpmn:process id="looping_task" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_0vlor2k</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:userTask id="GetNames" name="Get Names" camunda:formKey="GetNamesForm">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="GetNames_CurrentVar.Name" type="string" />
<camunda:formField id="GetNames_CurrentVar.Nickname" type="string" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0vlor2k</bpmn:incoming>
<bpmn:outgoing>Flow_1tvod7v</bpmn:outgoing>
<bpmn:standardLoopCharacteristics />
</bpmn:userTask>
<bpmn:endEvent id="Event_End">
<bpmn:incoming>Flow_1tvod7v</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_1tvod7v" sourceRef="GetNames" targetRef="Event_End" />
<bpmn:sequenceFlow id="Flow_0vlor2k" sourceRef="StartEvent_1" targetRef="GetNames" />
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="looping_task">
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1mpvzb7_di" bpmnElement="GetNames">
<dc:Bounds x="250" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_0dhdik5_di" bpmnElement="Event_End">
<dc:Bounds x="402" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_1tvod7v_di" bpmnElement="Flow_1tvod7v">
<di:waypoint x="350" y="117" />
<di:waypoint x="402" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0vlor2k_di" bpmnElement="Flow_0vlor2k">
<di:waypoint x="215" y="117" />
<di:waypoint x="250" y="117" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

8
tests/data/multi_instance/multi_instance.bpmn
View File

@ -8,8 +8,8 @@
<bpmn:endEvent id="Event_End" name="Event_End">
<bpmn:incoming>Flow_0ugjw69</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MutiInstanceTask" targetRef="Event_End" />
<bpmn:userTask id="MutiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
<bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MultiInstanceTask" targetRef="Event_End" />
<bpmn:userTask id="MultiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
<bpmn:documentation># Please provide addtional information about:
## Investigator ID: {{investigator.NETBADGEID}}
## Role: {{investigator.INVESTIGATORTYPEFULL}}</bpmn:documentation>
@ -25,7 +25,7 @@
<bpmn:outgoing>Flow_0ugjw69</bpmn:outgoing>
<bpmn:multiInstanceLoopCharacteristics isSequential="true" camunda:collection="StudyInfo.investigators" camunda:elementVariable="investigator" />
</bpmn:userTask>
<bpmn:sequenceFlow id="SequenceFlow_1p568pp" sourceRef="Task_1v0e2zu" targetRef="MutiInstanceTask" />
<bpmn:sequenceFlow id="SequenceFlow_1p568pp" sourceRef="Task_1v0e2zu" targetRef="MultiInstanceTask" />
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
@ -58,7 +58,7 @@
<dc:Bounds x="585" y="142" width="54" height="14" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1iyilui_di" bpmnElement="MutiInstanceTask">
<bpmndi:BPMNShape id="Activity_1iyilui_di" bpmnElement="MultiInstanceTask">
<dc:Bounds x="430" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_0cbbirp_di" bpmnElement="Task_1v0e2zu">

8
tests/data/multi_instance_parallel/multi_instance_parallel.bpmn
View File

@ -8,8 +8,8 @@
<bpmn:endEvent id="Event_End" name="Event_End">
<bpmn:incoming>Flow_0ugjw69</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MutiInstanceTask" targetRef="Event_End" />
<bpmn:userTask id="MutiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
<bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MultiInstanceTask" targetRef="Event_End" />
<bpmn:userTask id="MultiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
<bpmn:documentation># Please provide addtional information about:
## Investigator ID: {{investigator.user_id}}
## Role: {{investigator.type_full}}</bpmn:documentation>
@ -22,7 +22,7 @@
<bpmn:outgoing>Flow_0ugjw69</bpmn:outgoing>
<bpmn:multiInstanceLoopCharacteristics camunda:collection="StudyInfo.investigators" camunda:elementVariable="investigator" />
</bpmn:userTask>
<bpmn:sequenceFlow id="SequenceFlow_1p568pp" sourceRef="Task_1v0e2zu" targetRef="MutiInstanceTask" />
<bpmn:sequenceFlow id="SequenceFlow_1p568pp" sourceRef="Task_1v0e2zu" targetRef="MultiInstanceTask" />
<bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
<bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
@ -55,7 +55,7 @@
<dc:Bounds x="575" y="142" width="54" height="14" />
</bpmndi:BPMNLabel>
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1iyilui_di" bpmnElement="MutiInstanceTask">
<bpmndi:BPMNShape id="Activity_1iyilui_di" bpmnElement="MultiInstanceTask">
<dc:Bounds x="410" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_0cbbirp_di" bpmnElement="Task_1v0e2zu">

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

@ -175,9 +175,6 @@ Your random fact is:
<bpmndi:BPMNShape id="UserTask_186s7tw_di" bpmnElement="Task_User_Select_Type">
<dc:Bounds x="270" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<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>
@ -187,6 +184,9 @@ Your random fact is:
<bpmndi:BPMNShape id="TextAnnotation_1234e5n_di" bpmnElement="TextAnnotation_1234e5n">
<dc:Bounds x="570" y="120" width="100" height="68" />
</bpmndi:BPMNShape>
<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:BPMNEdge id="Association_1cfasjp_di" bpmnElement="Association_1cfasjp">
<di:waypoint x="344" y="210" />
<di:waypoint x="359" y="184" />

39
tests/emails/test_email_script.py Normal file
View File

@ -0,0 +1,39 @@
from tests.base_test import BaseTest
from crc.models.email import EmailModel
from crc.services.file_service import FileService
from crc.scripts.email import Email
from crc.services.workflow_processor import WorkflowProcessor
from crc.api.common import ApiError
from crc import db, mail
class TestEmailScript(BaseTest):
def test_do_task(self):
workflow = self.create_workflow('email')
task_data = {
'PIComputingID': 'dhf8r',
'ApprvlApprvr1': 'lb3dp'
}
task = self.get_workflow_api(workflow).next_task
with mail.record_messages() as outbox:
self.complete_form(workflow, task, task_data)
self.assertEqual(len(outbox), 1)
self.assertEqual(outbox[0].subject, 'Camunda Email Subject')
# PI is present
self.assertIn(task_data['PIComputingID'], outbox[0].body)
self.assertIn(task_data['PIComputingID'], outbox[0].html)
# Approver is present
self.assertIn(task_data['ApprvlApprvr1'], outbox[0].body)
self.assertIn(task_data['ApprvlApprvr1'], outbox[0].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 1)

34
tests/emails/test_email_service.py Normal file
View File

@ -0,0 +1,34 @@
from tests.base_test import BaseTest
from crc import session
from crc.models.approval import ApprovalModel, ApprovalStatus
from crc.models.email import EmailModel
from crc.services.email_service import EmailService
class TestEmailService(BaseTest):
def test_add_email(self):
self.load_example_data()
study = self.create_study()
workflow = self.create_workflow('random_fact')
subject = 'Email Subject'
sender = 'sender@sartography.com'
recipients = ['recipient@sartography.com', 'back@sartography.com']
content = 'Content for this email'
content_html = '<p>Hypertext Markup Language content for this email</p>'
EmailService.add_email(subject=subject, sender=sender, recipients=recipients,
content=content, content_html=content_html, study_id=study.id)
email_model = EmailModel.query.first()
self.assertEqual(email_model.subject, subject)
self.assertEqual(email_model.sender, sender)
self.assertEqual(email_model.recipients, str(recipients))
self.assertEqual(email_model.content, content)
self.assertEqual(email_model.content_html, content_html)
self.assertEqual(email_model.study, study)
# TODO: Create email model without study

117
tests/emails/test_mails.py Normal file
View File

@ -0,0 +1,117 @@
from tests.base_test import BaseTest
from crc import mail, session
from crc.models.approval import ApprovalModel, ApprovalStatus
from crc.models.email import EmailModel
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):
"""Initial setup shared by all TestApprovals tests"""
self.load_example_data()
self.study = self.create_study()
self.workflow = self.create_workflow('random_fact')
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):
with mail.record_messages() as outbox:
send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1)
self.assertEqual(len(outbox), 1)
self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Submitted')
self.assertIn(self.approver_1, outbox[0].body)
self.assertIn(self.approver_1, outbox[0].html)
send_ramp_up_submission_email(self.sender, self.recipients, self.approver_1, self.approver_2)
self.assertEqual(len(outbox), 2)
self.assertIn(self.approver_1, outbox[1].body)
self.assertIn(self.approver_1, outbox[1].html)
self.assertIn(self.approver_2, outbox[1].body)
self.assertIn(self.approver_2, outbox[1].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 2)
def test_send_ramp_up_approval_request_email(self):
with mail.record_messages() as outbox:
send_ramp_up_approval_request_email(self.sender, self.recipients, self.primary_investigator)
self.assertEqual(len(outbox), 1)
self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Approval Request')
self.assertIn(self.primary_investigator, outbox[0].body)
self.assertIn(self.primary_investigator, outbox[0].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 1)
def test_send_ramp_up_approval_request_first_review_email(self):
with mail.record_messages() as outbox:
send_ramp_up_approval_request_first_review_email(
self.sender, self.recipients, self.primary_investigator
)
self.assertEqual(len(outbox), 1)
self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Approval Request')
self.assertIn(self.primary_investigator, outbox[0].body)
self.assertIn(self.primary_investigator, outbox[0].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 1)
def test_send_ramp_up_approved_email(self):
with mail.record_messages() as outbox:
send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1)
self.assertEqual(len(outbox), 1)
self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Approved')
self.assertIn(self.approver_1, outbox[0].body)
self.assertIn(self.approver_1, outbox[0].html)
send_ramp_up_approved_email(self.sender, self.recipients, self.approver_1, self.approver_2)
self.assertEqual(len(outbox), 2)
self.assertIn(self.approver_1, outbox[1].body)
self.assertIn(self.approver_1, outbox[1].html)
self.assertIn(self.approver_2, outbox[1].body)
self.assertIn(self.approver_2, outbox[1].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 2)
def test_send_ramp_up_denied_email(self):
with mail.record_messages() as outbox:
send_ramp_up_denied_email(self.sender, self.recipients, self.approver_1)
self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Denied')
self.assertIn(self.approver_1, outbox[0].body)
self.assertIn(self.approver_1, outbox[0].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 1)
def test_send_send_ramp_up_denied_email_to_approver(self):
with mail.record_messages() as outbox:
send_ramp_up_denied_email_to_approver(
self.sender, self.recipients, self.primary_investigator, self.approver_2
)
self.assertEqual(outbox[0].subject, 'Research Ramp-up Plan Denied')
self.assertIn(self.primary_investigator, outbox[0].body)
self.assertIn(self.primary_investigator, outbox[0].html)
self.assertIn(self.approver_2, outbox[0].body)
self.assertIn(self.approver_2, outbox[0].html)
db_emails = EmailModel.query.count()
self.assertEqual(db_emails, 1)

4
tests/test_file_service.py → tests/files/test_file_service.py
View File

@ -61,14 +61,14 @@ class TestFileService(BaseTest):
# Archive the file
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
self.assertEqual(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))
self.assertEqual(0, len(file_models))
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,

16
tests/test_files_api.py → tests/files/test_files_api.py
View File

@ -91,7 +91,6 @@ class TestFilesApi(BaseTest):
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
def test_archive_file_no_longer_shows_up(self):
self.load_example_data()
self.create_reference_document()
@ -109,21 +108,16 @@ class TestFilesApi(BaseTest):
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))))
self.assertEqual(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))
self.assertEqual(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))))
self.assertEqual(0, len(json.loads(rv.get_data(as_text=True))))
def test_set_reference_file(self):
file_name = "irb_document_types.xls"
@ -285,8 +279,8 @@ class TestFilesApi(BaseTest):
.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))
self.assertEqual(1, len(approvals))
self.assertEqual(1, len(approvals[0].approval_files))
def test_change_primary_bpmn(self):

0
tests/test_study_api.py → tests/study/test_study_api.py
View File

0
tests/test_study_details_documents.py → tests/study/test_study_details_documents.py
View File

0
tests/test_study_service.py → tests/study/test_study_service.py
View File

0
tests/test_update_study_script.py → tests/study/test_update_study_script.py
View File

54
tests/test_looping_task.py Normal file
View File

@ -0,0 +1,54 @@
from unittest.mock import patch
from crc import session
from crc.models.api_models import MultiInstanceType
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowStatus
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
class TestWorkflowProcessorLoopingTask(BaseTest):
"""Tests the Workflow Processor as it deals with a Looping task"""
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, required_only=False)
def get_processor(self, study_model, spec_model):
workflow_model = StudyService._create_workflow_model(study_model, spec_model)
return WorkflowProcessor(workflow_model)
def test_create_and_complete_workflow(self):
# This depends on getting a list of investigators back from the protocol builder.
workflow = self.create_workflow('looping_task')
task = self.get_workflow_api(workflow).next_task
self.assertEqual("GetNames", task.name)
self.assertEqual(task.multi_instance_type, 'looping')
self.assertEqual(1, task.multi_instance_index)
self.complete_form(workflow,task,{'GetNames_CurrentVar':{'Name': 'Peter Norvig', 'Nickname': 'Pete'}})
task = self.get_workflow_api(workflow).next_task
self.assertEqual(task.multi_instance_type,'looping')
self.assertEqual(2, task.multi_instance_index)
self.complete_form(workflow,
task,
{'GetNames_CurrentVar':{'Name': 'Stuart Russell', 'Nickname': 'Stu'}},
terminate_loop=True)
task = self.get_workflow_api(workflow).next_task
self.assertEqual(task.name,'Event_End')
self.assertEqual(workflow.completed_tasks,workflow.total_tasks)
self.assertEqual(task.data, {'GetNames_CurrentVar': 2,
'GetNames': {'1': {'Name': 'Peter Norvig',
'Nickname': 'Pete'},
'2': {'Name': 'Stuart Russell',
'Nickname': 'Stu'}}})

55
tests/test_mails.py
View File

@ -1,55 +0,0 @@
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)

84
tests/test_tasks_api.py
View File

@ -4,14 +4,86 @@ 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.workflow import WorkflowStatus
from crc.services.workflow_service import WorkflowService
from crc.models.stats import TaskEventModel
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.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("dhf8r", 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 vodoo 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)
# Assure that there is data in the form_data
self.assertIsNotNone(event.form_data)
workflow = WorkflowApiSchema().load(json_data)
return workflow
def test_get_current_user_tasks(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
@ -299,13 +371,13 @@ class TestTasksApi(BaseTest):
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"})
workflow_api = self.complete_form(workflow, task, {"FieldA": "Dan"})
task = workflow_api.next_task
self.assertIsNotNone(task)
self.assertEqual("Activity_B", task.name)
self.assertEqual("Sub Workflow Example", task.process_name)
workflow_api = self.complete_form(workflow, task, {"name": "Dan"})
workflow_api = self.complete_form(workflow, task, {"FieldB": "Dan"})
self.assertEqual(WorkflowStatus.complete, workflow_api.status)
def test_update_task_resets_token(self):
@ -368,12 +440,14 @@ class TestTasksApi(BaseTest):
self.assertEqual(9, len(ready_items))
self.assertEqual("UserTask", workflow_api.next_task.type)
self.assertEqual("MutiInstanceTask",workflow_api.next_task.name)
self.assertEqual("MultiInstanceTask",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'])
self.complete_form(workflow, task, {"investigator":{"email": "dhf8r@virginia.edu"}})
data = workflow_api.next_task.data
data['investigator']['email'] = "dhf8r@virginia.edu"
self.complete_form(workflow, task, data)
#tasks = self.get_workflow_api(workflow).user_tasks
workflow = self.get_workflow_api(workflow)

53
tests/test_workflow_processor.py → tests/workflow/test_workflow_processor.py
View File

@ -270,53 +270,6 @@ class TestWorkflowProcessor(BaseTest):
processor = self.get_processor(study, workflow_spec_model)
self.assertTrue(processor.get_version_string().startswith('v2.1.1'))
def test_restart_workflow(self):
self.load_example_data()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
processor = self.get_processor(study, workflow_spec_model)
self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id)
task = processor.next_task()
task.data = {"key": "Value"}
processor.complete_task(task)
task_before_restart = processor.next_task()
processor.hard_reset()
task_after_restart = processor.next_task()
self.assertNotEqual(task.get_name(), task_before_restart.get_name())
self.assertEqual(task.get_name(), task_after_restart.get_name())
self.assertEqual(task.data, task_after_restart.data)
def test_soft_reset(self):
self.load_example_data()
# Start the two_forms workflow, and enter some data in the first form.
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
processor = self.get_processor(study, workflow_spec_model)
self.assertEqual(processor.workflow_model.workflow_spec_id, workflow_spec_model.id)
task = processor.next_task()
task.data = {"color": "blue"}
processor.complete_task(task)
# Modify the specification, with a minor text change.
file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'two_forms', 'mods', 'two_forms_text_mod.bpmn')
self.replace_file("two_forms.bpmn", file_path)
# Setting up another processor should not error out, but doesn't pick up the update.
processor.workflow_model.bpmn_workflow_json = processor.serialize()
processor2 = WorkflowProcessor(processor.workflow_model)
self.assertEqual("Step 1", processor2.bpmn_workflow.last_task.task_spec.description)
self.assertNotEqual("# This is some documentation I wanted to add.",
processor2.bpmn_workflow.last_task.task_spec.documentation)
# You can do a soft update and get the right response.
processor3 = WorkflowProcessor(processor.workflow_model, soft_reset=True)
self.assertEqual("Step 1", processor3.bpmn_workflow.last_task.task_spec.description)
self.assertEqual("# This is some documentation I wanted to add.",
processor3.bpmn_workflow.last_task.task_spec.documentation)
def test_hard_reset(self):
self.load_example_data()
@ -344,8 +297,10 @@ class TestWorkflowProcessor(BaseTest):
# Do a hard reset, which should bring us back to the beginning, but retain the data.
processor3 = WorkflowProcessor(processor.workflow_model, hard_reset=True)
self.assertEqual("Step 1", processor3.next_task().task_spec.description)
self.assertEqual({"color": "blue"}, processor3.next_task().data)
processor3.complete_task(processor3.next_task())
self.assertTrue(processor3.is_latest_spec) # Now at version 2.
task = processor3.next_task()
task.data = {"color": "blue"}
processor3.complete_task(task)
self.assertEqual("New Step", processor3.next_task().task_spec.description)
self.assertEqual("blue", processor3.next_task().data["color"])

81
tests/test_workflow_processor_multi_instance.py → tests/workflow/test_workflow_processor_multi_instance.py
View File

@ -1,13 +1,13 @@
from unittest.mock import patch
from tests.base_test import BaseTest
from crc import session
from crc import session, db
from crc.models.api_models import MultiInstanceType
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowStatus
from crc.models.workflow import WorkflowStatus, WorkflowModel
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
class TestWorkflowProcessorMultiInstance(BaseTest):
@ -32,7 +32,7 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
'error': 'Unable to locate a user with id asd3v in LDAP'}}
def _populate_form_with_random_data(self, task):
WorkflowProcessor.populate_form_with_random_data(task)
WorkflowService.populate_form_with_random_data(task)
def get_processor(self, study_model, spec_model):
workflow_model = StudyService._create_workflow_model(study_model, spec_model)
@ -51,51 +51,72 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
self.assertIsNotNone(processor)
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
processor.bpmn_workflow.do_engine_steps()
next_user_tasks = processor.next_user_tasks()
self.assertEqual(1, len(next_user_tasks))
task = next_user_tasks[0]
workflow_api = WorkflowService.processor_to_workflow_api(processor)
self.assertIsNotNone(workflow_api)
self.assertIsNotNone(workflow_api.next_task)
# 1st investigator
api_task = workflow_api.next_task
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
self.assertEqual("dhf8r", task.data["investigator"]["user_id"])
self.assertEqual("MutiInstanceTask", task.get_name())
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual(MultiInstanceType.sequential, api_task.multi_instance_type)
self.assertEqual("dhf8r", api_task.data["investigator"]["user_id"])
self.assertEqual("MultiInstanceTask", api_task.name)
self.assertEqual(3, api_task.multi_instance_count)
self.assertEqual(1, api_task.multi_instance_index)
task = processor.get_current_user_tasks()[0]
self.assertEqual(task.id, api_task.id)
task.update_data({"investigator": {"email": "asd3v@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
workflow_api = WorkflowService.processor_to_workflow_api(processor)
task = next_user_tasks[0]
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MutiInstanceTask", api_task.name)
task.update_data({"investigator":{"email":"asdf32@virginia.edu"}})
# 2nd investigator
api_task = workflow_api.next_task
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
self.assertEqual(None, api_task.data["investigator"]["user_id"])
self.assertEqual("MultiInstanceTask", api_task.name)
self.assertEqual(3, api_task.multi_instance_count)
self.assertEqual(2, api_task.multi_instance_index)
task = processor.get_current_user_tasks()[0]
self.assertEqual(task.id, api_task.id)
task.update_data({"investigator": {"email": "asdf32@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
workflow_api = WorkflowService.processor_to_workflow_api(processor)
task = next_user_tasks[0]
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MutiInstanceTask", task.get_name())
task.update_data({"investigator":{"email":"dhf8r@virginia.edu"}})
# 3rd investigator
api_task = workflow_api.next_task
self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
self.assertEqual("asd3v", api_task.data["investigator"]["user_id"])
self.assertEqual("MultiInstanceTask", api_task.name)
self.assertEqual(3, api_task.multi_instance_count)
self.assertEqual(3, api_task.multi_instance_index)
task = processor.get_current_user_tasks()[0]
self.assertEqual(task.id, api_task.id)
task.update_data({"investigator": {"email": "dhf8r@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
task = processor.bpmn_workflow.last_task
workflow_api = WorkflowService.processor_to_workflow_api(processor)
# Last task
api_task = workflow_api.next_task
expected = self.mock_investigator_response
expected['PI']['email'] = "asd3v@virginia.edu"
expected['SC_I']['email'] = "asdf32@virginia.edu"
expected['DC']['email'] = "dhf8r@virginia.edu"
self.assertEqual(expected,
task.data['StudyInfo']['investigators'])
self.assertEqual(expected, api_task.data['StudyInfo']['investigators'])
self.assertEqual(WorkflowStatus.complete, processor.get_status())
def refresh_processor(self, processor):
"""Saves the processor, and returns a new one read in from the database"""
processor.save()
processor = WorkflowProcessor(processor.workflow_model)
return processor
@patch('crc.services.study_service.StudyService.get_investigators')
def test_create_and_complete_workflow_parallel(self, mock_study_service):
"""Unlike the test above, the parallel task allows us to complete the items in any order."""
@ -107,11 +128,15 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
workflow_spec_model = self.load_test_spec("multi_instance_parallel")
study = session.query(StudyModel).first()
processor = self.get_processor(study, workflow_spec_model)
processor = self.refresh_processor(processor)
processor.bpmn_workflow.do_engine_steps()
# In the Parallel instance, there should be three tasks, all of them in the ready state.
next_user_tasks = processor.next_user_tasks()
self.assertEqual(3, len(next_user_tasks))
# There should be six tasks in the navigation: start event, the script task, end event, and three tasks
# for the three executions of hte multi-instance.
self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list()))
# We can complete the tasks out of order.
task = next_user_tasks[2]
@ -124,20 +149,23 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
task.update_data({"investigator": {"email": "dhf8r@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list()))
task = next_user_tasks[0]
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MutiInstanceTask", api_task.name)
self.assertEqual("MultiInstanceTask", api_task.name)
task.update_data({"investigator":{"email":"asd3v@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list()))
task = next_user_tasks[1]
api_task = WorkflowService.spiff_task_to_api_task(task)
self.assertEqual("MutiInstanceTask", task.get_name())
self.assertEqual("MultiInstanceTask", task.get_name())
task.update_data({"investigator":{"email":"asdf32@virginia.edu"}})
processor.complete_task(task)
processor.do_engine_steps()
self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list()))
# Completing the tasks out of order, still provides the correct information.
expected = self.mock_investigator_response
@ -148,3 +176,4 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
task.data['StudyInfo']['investigators'])
self.assertEqual(WorkflowStatus.complete, processor.get_status())
self.assertEquals(6, len(processor.bpmn_workflow.get_nav_list()))

53
tests/test_workflow_service.py → tests/workflow/test_workflow_service.py
View File

@ -1,7 +1,14 @@
import json
from tests.base_test import BaseTest
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from SpiffWorkflow import Task as SpiffTask, WorkflowException
from example_data import ExampleDataLoader
from crc import db
from crc.models.stats import TaskEventModel
from crc.models.api_models import Task
class TestWorkflowService(BaseTest):
@ -79,3 +86,49 @@ class TestWorkflowService(BaseTest):
task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, task_api, required_only=False)
self.assertTrue(isinstance(task.data["sponsor"], dict))
def test_fix_legacy_data_model_for_rrt(self):
ExampleDataLoader().load_rrt() # Make sure the research_rampup is loaded, as it's not a test spec.
workflow = self.create_workflow('research_rampup')
processor = WorkflowProcessor(workflow, validate_only=True)
# Use the test spec code to complete the workflow of research rampup.
while not processor.bpmn_workflow.is_completed():
processor.bpmn_workflow.do_engine_steps()
tasks = processor.bpmn_workflow.get_tasks(SpiffTask.READY)
for task in tasks:
task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, task_api, False)
task.complete()
# create the task events
WorkflowService.log_task_action('dhf8r', workflow, task,
WorkflowService.TASK_ACTION_COMPLETE,
version=processor.get_version_string())
processor.save()
db.session.commit()
WorkflowService.fix_legacy_data_model_for_rrt()
# All tasks should now have data associated with them.
task_logs = db.session.query(TaskEventModel) \
.filter(TaskEventModel.workflow_id == workflow.id) \
.filter(TaskEventModel.action == WorkflowService.TASK_ACTION_COMPLETE) \
.order_by(TaskEventModel.date).all() # Get them back in order.
self.assertEqual(17, len(task_logs))
for log in task_logs:
task = processor.bpmn_workflow.get_tasks_from_spec_name(log.task_name)[0]
self.assertIsNotNone(log.form_data)
# Each task should have the data in the form for that task in the task event.
if hasattr(task.task_spec, 'form'):
for field in task.task_spec.form.fields:
if field.has_property(Task.PROP_OPTIONS_REPEAT):
self.assertIn(field.get_property(Task.PROP_OPTIONS_REPEAT), log.form_data)
else:
self.assertIn(field.id, log.form_data)
# Some spot checks:
# The first task should be empty, with all the data removed.
self.assertEqual({}, task_logs[0].form_data)

0
tests/test_workflow_spec_api.py → tests/workflow/test_workflow_spec_api.py
View File

0
tests/test_workflow_spec_validation_api.py → tests/workflow/test_workflow_spec_validation_api.py
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