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cr-connect-workflow
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Merge pull request #83 from sartography/dev 

Dev --> Staging
This commit is contained in:
Aaron Louie 2020-05-29 12:51:17 -04:00 committed by GitHub
parent 976285fa3b f88832da52
commit 1b77681af9
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88 changed files with 3923 additions and 1104 deletions
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43
Dockerfile
View File

@ -1,27 +1,22 @@
FROM python:3.7
FROM python:3.7-slim
ENV PATH=/root/.local/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
WORKDIR /app
COPY Pipfile Pipfile.lock /app/
# install node and yarn
RUN apt-get update
RUN apt-get -y install postgresql-client
RUN set -xe \
&& pip install pipenv \
&& apt-get update -q \
&& apt-get install -y -q \
gcc python3-dev libssl-dev \
curl postgresql-client git-core \
gunicorn3 postgresql-client \
&& pipenv install --dev \
&& apt-get remove -y gcc python3-dev libssl-dev \
&& apt-get autoremove -y \
&& apt-get clean -y \
&& rm -rf /var/lib/apt/lists/* \
&& mkdir -p /app \
&& useradd _gunicorn --no-create-home --user-group
# config project dir
RUN mkdir /crc-workflow
WORKDIR /crc-workflow
# install python requirements
RUN pip install pipenv
ADD Pipfile /crc-workflow/
ADD Pipfile.lock /crc-workflow/
RUN pipenv install --dev
# include rejoiner code (gets overriden by local changes)
COPY . /crc-workflow/
# run webserver by default
ENV FLASK_APP=./crc/__init__.py
CMD ["pipenv", "run", "python", "./run.py"]
# expose ports
EXPOSE 5000
COPY . /app/
WORKDIR /app

6
Pipfile
View File

@ -5,6 +5,7 @@ verify_ssl = true
[dev-packages]
pytest = "*"
pbr = "*"
[packages]
connexion = {extras = ["swagger-ui"],version = "*"}
@ -24,18 +25,19 @@ pyjwt = "*"
requests = "*"
xlsxwriter = "*"
webtest = "*"
spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "bug/the_horror"}
spiffworkflow = {editable = true,git = "https://github.com/sartography/SpiffWorkflow.git",ref = "deploy"}
alembic = "*"
coverage = "*"
sphinx = "*"
recommonmark = "*"
psycopg2-binary = "*"
docxtpl = "*"
flask-sso = "*"
python-dateutil = "*"
pandas = "*"
xlrd = "*"
ldap3 = "*"
gunicorn = "*"
werkzeug = "*"
[requires]
python_version = "3.7"

98
Pipfile.lock generated
View File

@ -1,7 +1,7 @@
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@ -96,12 +96,6 @@
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@ -241,11 +235,11 @@
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@ -302,17 +296,10 @@
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@ -320,6 +307,14 @@
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],
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"version": "==20.0.4"
},
"httpretty": {
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@ -550,25 +545,25 @@
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"version": "==1.0.3"
"version": "==1.0.4"
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"psycopg2-binary": {
"hashes": [
@ -711,10 +706,10 @@
},
"six": {
"hashes": [
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],
"version": "==1.14.0"
"version": "==1.15.0"
},
"snowballstemmer": {
"hashes": [
@ -732,11 +727,11 @@
},
"sphinx": {
"hashes": [
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"version": "==3.0.3"
"version": "==3.0.4"
},
"sphinxcontrib-applehelp": {
"hashes": [
@ -783,7 +778,7 @@
"spiffworkflow": {
"editable": true,
"git": "https://github.com/sartography/SpiffWorkflow.git",
"ref": "7dc54f1205de7006bdda6d966dc957e558f3c7f3"
"ref": "c8d87826d496af825a184bdc3f0a751e603cfe44"
},
"sqlalchemy": {
"hashes": [
@ -868,6 +863,7 @@
"sha256:2de2a5db0baeae7b2d2664949077c2ac63fbd16d98da0ff71837f7d1dea3fd43",
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],
"index": "pypi",
"version": "==1.0.1"
},
"xlrd": {
@ -924,6 +920,14 @@
],
"version": "==20.4"
},
"pbr": {
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],
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"version": "==5.4.5"
},
"pluggy": {
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@ -955,10 +959,10 @@
},
"six": {
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],
"version": "==1.14.0"
"version": "==1.15.0"
},
"wcwidth": {
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34
config/default.py
View File

@ -13,6 +13,9 @@ DEVELOPMENT = environ.get('DEVELOPMENT', default="true") == "true"
TESTING = environ.get('TESTING', default="false") == "true"
PRODUCTION = (environ.get('PRODUCTION', default="false") == "true") or (not DEVELOPMENT and not TESTING)
# Add trailing slash to base path
APPLICATION_ROOT = re.sub(r'//', '/', '/%s/' % environ.get('APPLICATION_ROOT', default="/").strip('/'))
DB_HOST = environ.get('DB_HOST', default="localhost")
DB_PORT = environ.get('DB_PORT', default="5432")
DB_NAME = environ.get('DB_NAME', default="crc_dev")
@ -22,39 +25,20 @@ SQLALCHEMY_DATABASE_URI = environ.get(
'SQLALCHEMY_DATABASE_URI',
default="postgresql://%s:%s@%s:%s/%s" % (DB_USER, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME)
)
TOKEN_AUTH_TTL_HOURS = environ.get('TOKEN_AUTH_TTL_HOURS', default=4)
TOKEN_AUTH_TTL_HOURS = int(environ.get('TOKEN_AUTH_TTL_HOURS', default=4))
TOKEN_AUTH_SECRET_KEY = environ.get('TOKEN_AUTH_SECRET_KEY', default="Shhhh!!! This is secret! And better darn well not show up in prod.")
FRONTEND_AUTH_CALLBACK = environ.get('FRONTEND_AUTH_CALLBACK', default="http://localhost:4200/session")
SWAGGER_AUTH_KEY = environ.get('SWAGGER_AUTH_KEY', default="SWAGGER")
#: Default attribute map for single signon.
SSO_LOGIN_URL = '/login'
SSO_ATTRIBUTE_MAP = {
'eppn': (False, 'eppn'), # dhf8r@virginia.edu
'uid': (True, 'uid'), # dhf8r
'givenName': (False, 'first_name'), # Daniel
'mail': (False, 'email_address'), # dhf8r@Virginia.EDU
'sn': (False, 'last_name'), # Funk
'affiliation': (False, 'affiliation'), # 'staff@virginia.edu;member@virginia.edu'
'displayName': (False, 'display_name'), # Daniel Harold Funk
'title': (False, 'title') # SOFTWARE ENGINEER V
}
# %s/%i placeholders expected for uva_id and study_id in various calls.
PB_BASE_URL = environ.get('PB_BASE_URL', default="http://localhost:5001/pb/")
PB_ENABLED = environ.get('PB_ENABLED', default="false") == "true"
PB_BASE_URL = environ.get('PB_BASE_URL', default="http://localhost:5001/pb/").strip('/') + '/' # Trailing slash required
PB_USER_STUDIES_URL = environ.get('PB_USER_STUDIES_URL', default=PB_BASE_URL + "user_studies?uva_id=%s")
PB_INVESTIGATORS_URL = environ.get('PB_INVESTIGATORS_URL', default=PB_BASE_URL + "investigators?studyid=%i")
PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL + "required_docs?studyid=%i")
PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu")
LDAP_TIMEOUT_SEC = environ.get('LDAP_TIMEOUT_SEC', default=3)
print('=== USING DEFAULT CONFIG: ===')
print('DB_HOST = ', DB_HOST)
print('CORS_ALLOW_ORIGINS = ', CORS_ALLOW_ORIGINS)
print('DEVELOPMENT = ', DEVELOPMENT)
print('TESTING = ', TESTING)
print('PRODUCTION = ', PRODUCTION)
print('PB_BASE_URL = ', PB_BASE_URL)
print('LDAP_URL = ', LDAP_URL)
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=3))

19
config/testing.py
View File

@ -1,11 +1,28 @@
import os
from os import environ
basedir = os.path.abspath(os.path.dirname(__file__))
NAME = "CR Connect Workflow"
DEVELOPMENT = True
TESTING = True
SQLALCHEMY_DATABASE_URI = "postgresql://crc_user:crc_pass@localhost:5432/crc_test"
TOKEN_AUTH_SECRET_KEY = "Shhhh!!! This is secret! And better darn well not show up in prod."
PB_ENABLED = False
# This is here, for when we are running the E2E Tests in the frontend code bases.
# which will set the TESTING envronment to true, causing this to execute, but we need
# to respect the environment variables in that case.
# when running locally the defaults apply, meaning we use crc_test for doing the tests
# locally, and we don't over-write the database. Did you read this far? Have a cookie!
DB_HOST = environ.get('DB_HOST', default="localhost")
DB_PORT = environ.get('DB_PORT', default="5432")
DB_NAME = environ.get('DB_NAME', default="crc_test")
DB_USER = environ.get('DB_USER', default="crc_user")
DB_PASSWORD = environ.get('DB_PASSWORD', default="crc_pass")
SQLALCHEMY_DATABASE_URI = environ.get(
'SQLALCHEMY_DATABASE_URI',
default="postgresql://%s:%s@%s:%s/%s" % (DB_USER, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME)
)
print('### USING TESTING CONFIG: ###')
print('SQLALCHEMY_DATABASE_URI = ', SQLALCHEMY_DATABASE_URI)

13
config/travis-testing.py
View File

@ -8,18 +8,7 @@ SQLALCHEMY_DATABASE_URI = "postgresql://postgres:@localhost:5432/crc_test"
TOKEN_AUTH_TTL_HOURS = 2
TOKEN_AUTH_SECRET_KEY = "Shhhh!!! This is secret! And better darn well not show up in prod."
FRONTEND_AUTH_CALLBACK = "http://localhost:4200/session" # Not Required
#: Default attribute map for single signon.
SSO_ATTRIBUTE_MAP = {
'eppn': (False, 'eppn'), # dhf8r@virginia.edu
'uid': (True, 'uid'), # dhf8r
'givenName': (False, 'first_name'), # Daniel
'mail': (False, 'email_address'), # dhf8r@Virginia.EDU
'sn': (False, 'last_name'), # Funk
'affiliation': (False, 'affiliation'), # 'staff@virginia.edu;member@virginia.edu'
'displayName': (False, 'display_name'), # Daniel Harold Funk
'title': (False, 'title') # SOFTWARE ENGINEER V
}
PB_ENABLED = False
print('+++ USING TRAVIS TESTING CONFIG: +++')
print('SQLALCHEMY_DATABASE_URI = ', SQLALCHEMY_DATABASE_URI)

22
crc/__init__.py
View File

@ -6,7 +6,6 @@ from flask_cors import CORS
from flask_marshmallow import Marshmallow
from flask_migrate import Migrate
from flask_sqlalchemy import SQLAlchemy
from flask_sso import SSO
logging.basicConfig(level=logging.INFO)
@ -31,17 +30,26 @@ session = db.session
migrate = Migrate(app, db)
ma = Marshmallow(app)
sso = SSO(app=app)
from crc import models
from crc import api
connexion_app.add_api('api.yml')
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)
print('=== USING THESE CONFIG SETTINGS: ===')
print('DB_HOST = ', )
print('CORS_ALLOW_ORIGINS = ', app.config['CORS_ALLOW_ORIGINS'])
print('DEVELOPMENT = ', app.config['DEVELOPMENT'])
print('TESTING = ', app.config['TESTING'])
print('PRODUCTION = ', app.config['PRODUCTION'])
print('PB_BASE_URL = ', app.config['PB_BASE_URL'])
print('LDAP_URL = ', app.config['LDAP_URL'])
print('APPLICATION_ROOT = ', app.config['APPLICATION_ROOT'])
print('PB_ENABLED = ', app.config['PB_ENABLED'])
@app.cli.command()
def load_example_data():
@ -49,3 +57,11 @@ def load_example_data():
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_all()
@app.cli.command()
def load_example_rrt_data():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_rrt()

137
crc/api.yml
View File

@ -56,7 +56,7 @@ paths:
required: false
schema:
type: string
- name: redirect_url
- name: redirect
in: query
required: false
schema:
@ -82,7 +82,7 @@ paths:
# /v1.0/study
/study:
get:
operationId: crc.api.study.all_studies
operationId: crc.api.study.user_studies
summary: Provides a list of studies related to the current user.
tags:
- Studies
@ -109,7 +109,24 @@ paths:
content:
application/json:
schema:
$ref: "#/components/schemas/Study"
type: array
items:
$ref: "#/components/schemas/Study"
/study/all:
get:
operationId: crc.api.study.all_studies
summary: Provides a list of studies
tags:
- Studies
responses:
'200':
description: An array of studies, with submitted files, ordered by the last modified date.
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Study"
/study/{study_id}:
parameters:
- name: study_id
@ -156,26 +173,6 @@ paths:
application/json:
schema:
$ref: "#/components/schemas/Study"
/study-update/{study_id}:
post:
operationId: crc.api.study.post_update_study_from_protocol_builder
summary: If the study is up-to-date with Protocol Builder, returns a 304 Not Modified. If out of date, return a 202 Accepted and study state changes to updating.
tags:
- Study Status
parameters:
- name: study_id
in: path
required: true
description: The id of the study that should be checked for updates.
schema:
type: integer
format: int32
responses:
'304':
description: Study is currently up to date and does not need to be reloaded from Protocol Builder
'202':
description: Request accepted, will preform an update. Study state set to "updating"
/workflow-specification:
get:
operationId: crc.api.workflow.all_specifications
@ -360,24 +357,12 @@ paths:
description: The unique id of a workflow specification
schema:
type: string
- name: study_id
in: query
required: false
description: The unique id of a study
schema:
type: integer
- name: workflow_id
in: query
required: false
description: The unique id of a workflow instance
schema:
type: integer
- name: task_id
in: query
required: false
description: The unique id of a workflow task
schema:
type: string
- name: form_field_key
in: query
required: false
@ -473,6 +458,12 @@ paths:
description: The id of the File requested
schema:
type: integer
- name: version
in: query
required: false
description: The version of the file, or none for latest version
schema:
type: integer
get:
operationId: crc.api.file.get_file_data
summary: Returns only the file contents
@ -681,7 +672,7 @@ paths:
application/json:
schema:
$ref: "#/components/schemas/Workflow"
/workflow/{workflow_id}/task/{task_id}/lookup/{field_id}:
/workflow/{workflow_id}/lookup/{field_id}:
parameters:
- name: workflow_id
in: path
@ -690,13 +681,6 @@ paths:
schema:
type: integer
format: int32
- name: task_id
in: path
required: true
description: The id of the task
schema:
type: string
format: uuid
- name: field_id
in: path
required: true
@ -755,13 +739,6 @@ paths:
schema:
type: string
/render_docx:
parameters:
- name: data
in: query
required: true
description: The json data to use in populating the template
schema:
type: string
put:
operationId: crc.api.tools.render_docx
security: [] # Disable security for this endpoint only.
@ -777,6 +754,9 @@ paths:
file:
type: string
format: binary
data:
type: string
format: json
responses:
'200':
description: Returns the generated document.
@ -802,6 +782,54 @@ paths:
type: array
items:
$ref: "#/components/schemas/Script"
/approval:
parameters:
- name: approver_uid
in: query
required: false
description: Restrict results to a given approver uid, maybe we restrict the use of this at somepoint.
schema:
type: string
get:
operationId: crc.api.approval.get_approvals
summary: Provides a list of workflows approvals
tags:
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
/approval/{approval_id}:
parameters:
- name: approval_id
in: path
required: true
description: The id of the approval in question.
schema:
type: integer
format: int32
put:
operationId: crc.api.approval.update_approval
summary: Updates an approval with the given parameters
tags:
- Approvals
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Approval'
responses:
'200':
description: Study updated successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/Approval"
components:
securitySchemes:
jwt:
@ -1209,7 +1237,10 @@ components:
readOnly: true
task:
$ref: "#/components/schemas/Task"
Approval:
properties:
id:
type: number
format: integer
example: 5

30
crc/api/approval.py Normal file
View File

@ -0,0 +1,30 @@
from crc import app, db, session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.approval import Approval, ApprovalModel, ApprovalSchema
from crc.services.approval_service import ApprovalService
def get_approvals(approver_uid = None):
if not approver_uid:
db_approvals = ApprovalService.get_all_approvals()
else:
db_approvals = ApprovalService.get_approvals_per_user(approver_uid)
approvals = [Approval.from_model(approval_model) for approval_model in db_approvals]
results = ApprovalSchema(many=True).dump(approvals)
return results
def update_approval(approval_id, body):
if approval_id is None:
raise ApiError('unknown_approval', 'Please provide a valid Approval ID.')
approval_model = session.query(ApprovalModel).get(approval_id)
if approval_model is None:
raise ApiError('unknown_approval', 'The approval "' + str(approval_id) + '" is not recognized.')
approval: Approval = ApprovalSchema().load(body)
approval.update_model(approval_model)
session.commit()
result = ApprovalSchema().dump(approval)
return result

69
crc/api/file.py
View File

@ -1,51 +1,58 @@
import io
from typing import List
import connexion
from flask import send_file
from crc import session
from crc.api.common import ApiError
from crc.models.file import FileModelSchema, FileModel, FileDataModel
from crc.models.file import FileSchema, FileModel, File, FileModelSchema
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
def get_files(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):
if all(v is None for v in [workflow_spec_id, study_id, workflow_id, task_id, form_field_key]):
raise ApiError('missing_parameter',
'Please specify at least one of workflow_spec_id, study_id, '
'workflow_id, and task_id for this file in the HTTP parameters')
def to_file_api(file_model):
"""Converts a FileModel object to something we can return via the aip"""
return File.from_models(file_model, FileService.get_file_data(file_model.id))
results = FileService.get_files(workflow_spec_id, study_id, workflow_id, task_id, form_field_key)
return FileModelSchema(many=True).dump(results)
def get_files(workflow_spec_id=None, workflow_id=None, form_field_key=None):
if all(v is None for v in [workflow_spec_id, workflow_id, form_field_key]):
raise ApiError('missing_parameter',
'Please specify either a workflow_spec_id or a '
'workflow_id with an optional form_field_key')
file_models = FileService.get_files(workflow_spec_id=workflow_spec_id,
workflow_id=workflow_id,
irb_doc_code=form_field_key)
files = (to_file_api(model) for model in file_models)
return FileSchema(many=True).dump(files)
def get_reference_files():
results = FileService.get_files(is_reference=True)
return FileModelSchema(many=True).dump(results)
files = (to_file_api(model) for model in results)
return FileSchema(many=True).dump(files)
def add_file(workflow_spec_id=None, study_id=None, workflow_id=None, task_id=None, form_field_key=None):
all_none = all(v is None for v in [workflow_spec_id, study_id, workflow_id, task_id, form_field_key])
missing_some = (workflow_spec_id is None) and (None in [study_id, workflow_id, form_field_key])
if all_none or missing_some:
raise ApiError('missing_parameter',
'Please specify either a workflow_spec_id or all 3 of study_id, '
'workflow_id, and field_id for this file in the HTTP parameters')
if 'file' not in connexion.request.files:
raise ApiError('invalid_file',
'Expected a file named "file" in the multipart form request')
def add_file(workflow_spec_id=None, workflow_id=None, form_field_key=None):
file = connexion.request.files['file']
if workflow_spec_id:
if workflow_id:
if form_field_key is None:
raise ApiError('invalid_workflow_file',
'When adding a workflow related file, you must specify a form_field_key')
file_model = FileService.add_workflow_file(workflow_id=workflow_id, irb_doc_code=form_field_key,
name=file.filename, content_type=file.content_type,
binary_data=file.stream.read())
elif workflow_spec_id:
workflow_spec = session.query(WorkflowSpecModel).filter_by(id=workflow_spec_id).first()
file_model = FileService.add_workflow_spec_file(workflow_spec, file.filename, file.content_type,
file.stream.read())
else:
file_model = FileService.add_form_field_file(study_id, workflow_id, task_id, form_field_key, file.filename,
file.content_type, file.stream.read())
raise ApiError("invalid_file", "You must supply either a workflow spec id or a workflow_id and form_field_key.")
return FileModelSchema().dump(file_model)
return FileSchema().dump(to_file_api(file_model))
def get_reference_file(name):
@ -80,7 +87,7 @@ def set_reference_file(name):
file_model = file_models[0]
FileService.update_file(file_models[0], file.stream.read(), file.content_type)
return FileModelSchema().dump(file_model)
return FileSchema().dump(to_file_api(file_model))
def update_file_data(file_id):
@ -89,11 +96,11 @@ def update_file_data(file_id):
if file_model is None:
raise ApiError('no_such_file', 'The file id you provided does not exist')
file_model = FileService.update_file(file_model, file.stream.read(), file.content_type)
return FileModelSchema().dump(file_model)
return FileSchema().dump(to_file_api(file_model))
def get_file_data(file_id):
file_data = FileService.get_file_data(file_id)
def get_file_data(file_id, version=None):
file_data = FileService.get_file_data(file_id, version)
if file_data is None:
raise ApiError('no_such_file', 'The file id you provided does not exist')
return send_file(
@ -101,7 +108,7 @@ def get_file_data(file_id):
attachment_filename=file_data.file_model.name,
mimetype=file_data.file_model.content_type,
cache_timeout=-1, # Don't cache these files on the browser.
last_modified=file_data.last_updated
last_modified=file_data.date_created
)
@ -109,7 +116,7 @@ def get_file_info(file_id):
file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
if file_model is None:
raise ApiError('no_such_file', 'The file id you provided does not exist', status_code=404)
return FileModelSchema().dump(file_model)
return FileSchema().dump(to_file_api(file_model))
def update_file_info(file_id, body):
@ -124,7 +131,7 @@ def update_file_info(file_id, body):
file_model = FileModelSchema().load(body, session=session)
session.add(file_model)
session.commit()
return FileModelSchema().dump(file_model)
return FileSchema().dump(to_file_api(file_model))
def delete_file(file_id):

58
crc/api/study.py
View File

@ -1,25 +1,32 @@
from typing import List
from datetime import datetime
from connexion import NoContent
from flask import g
from sqlalchemy.exc import IntegrityError
from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudySchema, StudyModel, Study
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.study_service import StudyService
def add_study(body):
"""This should never get called, and is subject to deprication. Studies
should be added through the protocol builder only."""
study: Study = StudySchema().load(body)
study_model = StudyModel(**study.model_args())
"""Or any study like object. Body should include a title, and primary_investigator_id """
if 'primary_investigator_id' not in body:
raise ApiError("missing_pi", "Can't create a new study without a Primary Investigator.")
if 'title' not in body:
raise ApiError("missing_title", "Can't create a new study without a title.")
study_model = StudyModel(user_uid=g.user.uid,
title=body['title'],
primary_investigator_id=body['primary_investigator_id'],
last_updated=datetime.now(),
protocol_builder_status=ProtocolBuilderStatus.ACTIVE)
session.add(study_model)
errors = StudyService._add_all_workflow_specs_to_study(study)
errors = StudyService._add_all_workflow_specs_to_study(study_model)
session.commit()
study = StudyService().get_study(study_model.id)
study_data = StudySchema().dump(study)
study_data["errors"] = ApiErrorSchema(many=True).dump(errors)
return study_data
@ -43,7 +50,7 @@ def update_study(study_id, body):
def get_study(study_id):
study_service = StudyService()
study = study_service.get_study(study_id)
if(study is None):
if (study is None):
raise ApiError("Study not found", status_code=404)
schema = StudySchema()
return schema.dump(study)
@ -58,31 +65,16 @@ def delete_study(study_id):
raise ApiError(code="study_integrity_error", message=message)
def all_studies():
"""Returns all the studies associated with the current user. Assures we are
in sync with values read in from the protocol builder. """
StudyService.synch_all_studies_with_protocol_builder(g.user)
def user_studies():
"""Returns all the studies associated with the current user. """
StudyService.synch_with_protocol_builder_if_enabled(g.user)
studies = StudyService.get_studies_for_user(g.user)
results = StudySchema(many=True).dump(studies)
return results
def post_update_study_from_protocol_builder(study_id):
"""Update a single study based on data received from
the protocol builder."""
db_study = session.query(StudyModel).filter_by(study_id=study_id).all()
pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(g.user.uid)
pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study_id), None)
if pb_study:
db_study.update_from_protocol_builder(pb_study)
else:
db_study.inactive = True
db_study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
return NoContent, 304
def all_studies():
"""Returns all studies (regardless of user) with submitted files"""
studies = StudyService.get_all_studies_with_files()
results = StudySchema(many=True).dump(studies)
return results

3
crc/api/tools.py
View File

@ -25,13 +25,14 @@ def render_markdown(data, template):
raise ApiError(code="invalid", message=str(e))
def render_docx(data):
def render_docx():
"""
Provides a quick way to verify that a Jinja docx template will work properly on a given json
data structure. Useful for folks that are building these templates.
"""
try:
file = connexion.request.files['file']
data = connexion.request.form['data']
target_stream = CompleteTemplate().make_template(file, json.loads(data))
return send_file(
io.BytesIO(target_stream.read()),

112
crc/api/user.py
View File

@ -1,12 +1,13 @@
import json
import connexion
from flask import redirect, g
import flask
from flask import redirect, g, request
from crc import sso, app, db
from crc import app, db
from crc.api.common import ApiError
from crc.models.user import UserModel, UserModelSchema
from crc.services.ldap_service import LdapService, LdapUserInfo
"""
.. module:: crc.api.user
@ -32,53 +33,76 @@ def verify_token(token):
def get_current_user():
return UserModelSchema().dump(g.user)
@app.route('/v1.0/login')
def sso_login():
# This what I see coming back:
# X-Remote-Cn: Daniel Harold Funk (dhf8r)
# X-Remote-Sn: Funk
# X-Remote-Givenname: Daniel
# X-Remote-Uid: dhf8r
# Eppn: dhf8r@virginia.edu
# Cn: Daniel Harold Funk (dhf8r)
# Sn: Funk
# Givenname: Daniel
# Uid: dhf8r
# X-Remote-User: dhf8r@virginia.edu
# X-Forwarded-For: 128.143.0.10
# X-Forwarded-Host: dev.crconnect.uvadcos.io
# X-Forwarded-Server: dev.crconnect.uvadcos.io
# Connection: Keep-Alive
uid = request.headers.get("Uid")
if not uid:
uid = request.headers.get("X-Remote-Uid")
@sso.login_handler
def sso_login(user_info):
app.logger.info("Login from Shibboleth happening. " + json.dump(user_info))
# TODO: Get redirect URL from Shibboleth request header
_handle_login(user_info)
if not uid:
raise ApiError("invalid_sso_credentials", "'Uid' nor 'X-Remote-Uid' were present in the headers: %s"
% str(request.headers))
redirect = request.args.get('redirect')
app.logger.info("SSO_LOGIN: Full URL: " + request.url)
app.logger.info("SSO_LOGIN: User Id: " + uid)
app.logger.info("SSO_LOGIN: Will try to redirect to : " + str(redirect))
ldap_service = LdapService()
info = ldap_service.user_info(uid)
return _handle_login(info, redirect)
@app.route('/sso')
def sso():
response = ""
response += "<h1>Headers</h1>"
response += "<ul>"
for k,v in request.headers:
response += "<li><b>%s</b> %s</li>\n" % (k, v)
response += "<h1>Environment</h1>"
for k,v in request.environ:
response += "<li><b>%s</b> %s</li>\n" % (k, v)
return response
def _handle_login(user_info, redirect_url=app.config['FRONTEND_AUTH_CALLBACK']):
def _handle_login(user_info: LdapUserInfo, redirect_url=app.config['FRONTEND_AUTH_CALLBACK']):
"""On successful login, adds user to database if the user is not already in the system,
then returns the frontend auth callback URL, with auth token appended.
Args:
user_info (dict of {
uid: str,
affiliation: Optional[str],
display_name: Optional[str],
email_address: Optional[str],
eppn: Optional[str],
first_name: Optional[str],
last_name: Optional[str],
title: Optional[str],
}): Dictionary of user attributes
redirect_url: Optional[str]
user_info - an ldap user_info object.
redirect_url: Optional[str]
Returns:
Response. 302 - Redirects to the frontend auth callback URL, with auth token appended.
"""
uid = user_info['uid']
user = db.session.query(UserModel).filter(UserModel.uid == uid).first()
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
if user is None:
# Add new user
user = UserModelSchema().load(user_info, session=db.session)
else:
# Update existing user data
user = UserModelSchema().load(user_info, session=db.session, instance=user, partial=True)
user = UserModel()
# Build display_name if not set
if 'display_name' not in user_info or len(user_info['display_name']) == 0:
display_name_list = []
for prop in ['first_name', 'last_name']:
if prop in user_info and len(user_info[prop]) > 0:
display_name_list.append(user_info[prop])
user.display_name = ' '.join(display_name_list)
user.uid = user_info.uid
user.display_name = user_info.display_name
user.email_address = user_info.email_address
user.affiliation = user_info.affiliation
user.title = user_info.title
db.session.add(user)
db.session.commit()
@ -86,10 +110,17 @@ def _handle_login(user_info, redirect_url=app.config['FRONTEND_AUTH_CALLBACK']):
# Return the frontend auth callback URL, with auth token appended.
auth_token = user.encode_auth_token().decode()
if redirect_url is not None:
return redirect('%s/%s' % (redirect_url, auth_token))
if redirect_url.find("http://") != 0 and redirect_url.find("https://") != 0:
redirect_url = "http://" + redirect_url
url = '%s?token=%s' % (redirect_url, auth_token)
app.logger.info("SSO_LOGIN: REDIRECTING TO: " + url)
return flask.redirect(url, code=302)
else:
app.logger.info("SSO_LOGIN: NO REDIRECT, JUST RETURNING AUTH TOKEN.")
return auth_token
def backdoor(
uid=None,
affiliation=None,
@ -99,7 +130,7 @@ def backdoor(
first_name=None,
last_name=None,
title=None,
redirect_url=None,
redirect=None,
):
"""A backdoor for end-to-end system testing that allows the system to simulate logging in as a specific user.
Only works if the application is running in a non-production environment.
@ -122,11 +153,8 @@ def backdoor(
ApiError. If on production, returns a 404 error.
"""
if not 'PRODUCTION' in app.config or not app.config['PRODUCTION']:
user_info = {}
for key in UserModel.__dict__.keys():
if key in connexion.request.args:
user_info[key] = connexion.request.args[key]
return _handle_login(user_info, redirect_url)
ldap_info = LdapService().user_info(uid)
return _handle_login(ldap_info, redirect)
else:
raise ApiError('404', 'unknown')

28
crc/api/workflow.py
View File

@ -4,6 +4,7 @@ from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.api_models import WorkflowApi, WorkflowApiSchema, NavigationItem, NavigationItemSchema
from crc.models.file import FileModel, LookupDataSchema
from crc.models.stats import TaskEventModel
from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
WorkflowSpecCategoryModelSchema
from crc.services.file_service import FileService
@ -77,6 +78,8 @@ def delete_workflow_specification(spec_id):
for file in files:
FileService.delete_file(file.id)
session.query(TaskEventModel).filter(TaskEventModel.workflow_spec_id == spec_id).delete()
# Delete all stats and workflow models related to this specification
for workflow in session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id):
StudyService.delete_workflow(workflow)
@ -115,8 +118,8 @@ def __get_workflow_api_model(processor: WorkflowProcessor, next_task = None):
next_task=None,
navigation=navigation,
workflow_spec_id=processor.workflow_spec_id,
spec_version=processor.get_spec_version(),
is_latest_spec=processor.get_spec_version() == processor.get_latest_version_string(processor.workflow_spec_id),
spec_version=processor.get_version_string(),
is_latest_spec=processor.is_latest_spec,
total_tasks=processor.workflow_model.total_tasks,
completed_tasks=processor.workflow_model.completed_tasks,
last_updated=processor.workflow_model.last_updated
@ -216,26 +219,13 @@ def delete_workflow_spec_category(cat_id):
session.commit()
def lookup(workflow_id, task_id, field_id, query, limit):
def lookup(workflow_id, field_id, query, limit):
"""
given a field in a task, attempts to find the lookup table or function associated
with that field and runs a full-text query against it to locate the values and
labels that would be returned to a type-ahead box.
Tries to be fast, but first runs will be very slow.
"""
workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
if not workflow_model:
raise ApiError("unknown_workflow", "No workflow found with id: %i" % workflow_id)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
spiff_task = processor.bpmn_workflow.get_task(task_id)
if not spiff_task:
raise ApiError("unknown_task", "No task with %s found in workflow: %i" % (task_id, workflow_id))
field = None
for f in spiff_task.task_spec.form.fields:
if f.id == field_id:
field = f
if not field:
raise ApiError("unknown_field", "No field named %s in task %s" % (task_id, spiff_task.task_spec.name))
lookup_data = LookupService.lookup(spiff_task, field, query, limit)
workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
lookup_data = LookupService.lookup(workflow, field_id, query, limit)
return LookupDataSchema(many=True).dump(lookup_data)

140
crc/models/approval.py Normal file
View File

@ -0,0 +1,140 @@
import enum
import marshmallow
from ldap3.core.exceptions import LDAPSocketOpenError
from marshmallow import INCLUDE
from sqlalchemy import func
from crc import db, ma
from crc.api.common import ApiError
from crc.models.file import FileDataModel
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowModel
from crc.services.ldap_service import LdapService
class ApprovalStatus(enum.Enum):
WAITING = "WAITING" # no one has done jack.
APPROVED = "APPROVED" # approved by the reviewer
DECLINED = "DECLINED" # rejected by the reviewer
CANCELED = "CANCELED" # The document was replaced with a new version and this review is no longer needed.
class ApprovalFile(db.Model):
file_data_id = db.Column(db.Integer, db.ForeignKey(FileDataModel.id), primary_key=True)
approval_id = db.Column(db.Integer, db.ForeignKey("approval.id"), primary_key=True)
approval = db.relationship("ApprovalModel")
file_data = db.relationship(FileDataModel)
class ApprovalModel(db.Model):
__tablename__ = 'approval'
id = db.Column(db.Integer, primary_key=True)
study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
study = db.relationship(StudyModel, backref='approval', cascade='all,delete')
workflow_id = db.Column(db.Integer, db.ForeignKey(WorkflowModel.id), nullable=False)
workflow = db.relationship(WorkflowModel)
approver_uid = db.Column(db.String) # Not linked to user model, as they may not have logged in yet.
status = db.Column(db.String)
message = db.Column(db.String, default='')
date_created = db.Column(db.DateTime(timezone=True), default=func.now())
version = db.Column(db.Integer) # Incremented integer, so 1,2,3 as requests are made.
approval_files = db.relationship(ApprovalFile, back_populates="approval",
cascade="all, delete, delete-orphan",
order_by=ApprovalFile.file_data_id)
class Approval(object):
def __init__(self, **kwargs):
self.__dict__.update(kwargs)
@classmethod
def from_model(cls, model: ApprovalModel):
# TODO: Reduce the code by iterating over model's dict keys
instance = cls()
instance.id = model.id
instance.study_id = model.study_id
instance.workflow_id = model.workflow_id
instance.version = model.version
instance.approver_uid = model.approver_uid
instance.status = model.status
instance.message = model.message
instance.date_created = model.date_created
instance.version = model.version
instance.title = ''
if model.study:
instance.title = model.study.title
instance.approver = {}
try:
ldap_service = LdapService()
principal_investigator_id = model.study.primary_investigator_id
user_info = ldap_service.user_info(principal_investigator_id)
except (ApiError, LDAPSocketOpenError) as exception:
user_info = None
instance.approver['display_name'] = 'Primary Investigator details'
instance.approver['department'] = 'currently not available'
if user_info:
# TODO: Rename approver to primary investigator
instance.approver['uid'] = model.approver_uid
instance.approver['display_name'] = user_info.display_name
instance.approver['title'] = user_info.title
instance.approver['department'] = user_info.department
instance.associated_files = []
for approval_file in model.approval_files:
associated_file = {}
associated_file['id'] = approval_file.file_data.file_model.id
associated_file['name'] = approval_file.file_data.file_model.name
associated_file['content_type'] = approval_file.file_data.file_model.content_type
instance.associated_files.append(associated_file)
return instance
def update_model(self, approval_model: ApprovalModel):
approval_model.status = self.status
approval_model.message = self.message
class ApprovalSchema(ma.Schema):
class Meta:
model = Approval
fields = ["id", "study_id", "workflow_id", "version", "title",
"version", "status", "message", "approver", "associated_files"]
unknown = INCLUDE
@marshmallow.post_load
def make_approval(self, data, **kwargs):
"""Loads the basic approval data for updates to the database"""
return Approval(**data)
# Carlos: Here is the data structure I was trying to imagine.
# If I were to continue down my current traing of thought, I'd create
# another class called just "Approval" that can take an ApprovalModel from the
# database and construct a data structure like this one, that can
# be provided to the API at an /approvals endpoint with GET and PUT
# dat = { "approvals": [
# {"id": 1,
# "study_id": 20,
# "workflow_id": 454,
# "study_title": "Dan Funk (dhf8r)", # Really it's just the name of the Principal Investigator
# "workflow_version": "21",
# "approver": { # Pulled from ldap
# "uid": "bgb22",
# "display_name": "Billy Bob (bgb22)",
# "title": "E42:He's a hoopy frood",
# "department": "E0:EN-Eng Study of Parallel Universes",
# },
# "files": [
# {
# "id": 124,
# "name": "ResearchRestart.docx",
# "content_type": "docx-something-whatever"
# }
# ]
# }
# ...
# ]

76
crc/models/file.py
View File

@ -1,16 +1,18 @@
import enum
from typing import cast
from marshmallow import INCLUDE, EXCLUDE
from marshmallow_enum import EnumField
from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from sqlalchemy import func, Index
from sqlalchemy.dialects.postgresql import UUID
from sqlalchemy.orm import deferred
from crc import db
from crc import db, ma
class FileType(enum.Enum):
bpmn = "bpmm"
bpmn = "bpmn"
csv = 'csv'
dmn = "dmn"
doc = "doc"
@ -55,15 +57,16 @@ CONTENT_TYPES = {
"zip": "application/zip"
}
class FileDataModel(db.Model):
__tablename__ = 'file_data'
id = db.Column(db.Integer, primary_key=True)
md5_hash = db.Column(UUID(as_uuid=True), unique=False, nullable=False)
data = db.Column(db.LargeBinary)
data = deferred(db.Column(db.LargeBinary)) # Don't load it unless you have to.
version = db.Column(db.Integer, default=0)
last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
date_created = db.Column(db.DateTime(timezone=True), default=func.now())
file_model_id = db.Column(db.Integer, db.ForeignKey('file.id'))
file_model = db.relationship("FileModel")
file_model = db.relationship("FileModel", foreign_keys=[file_model_id])
class FileModel(db.Model):
@ -78,42 +81,69 @@ class FileModel(db.Model):
primary_process_id = db.Column(db.String, nullable=True) # An id in the xml of BPMN documents, critical for primary BPMN.
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'), nullable=True)
workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=True)
study_id = db.Column(db.Integer, db.ForeignKey('study.id'), nullable=True)
task_id = db.Column(db.String, nullable=True)
irb_doc_code = db.Column(db.String, nullable=True) # Code reference to the irb_documents.xlsx reference file.
form_field_key = db.Column(db.String, nullable=True)
latest_version = db.Column(db.Integer, default=0)
class File(object):
@classmethod
def from_models(cls, model: FileModel, data_model: FileDataModel):
instance = cls()
instance.id = model.id
instance.name = model.name
instance.is_status = model.is_status
instance.is_reference = model.is_reference
instance.content_type = model.content_type
instance.primary = model.primary
instance.primary_process_id = model.primary_process_id
instance.workflow_spec_id = model.workflow_spec_id
instance.workflow_id = model.workflow_id
instance.irb_doc_code = model.irb_doc_code
instance.type = model.type
if data_model:
instance.last_modified = data_model.date_created
instance.latest_version = data_model.version
else:
instance.last_modified = None
instance.latest_version = None
return instance
class FileModelSchema(SQLAlchemyAutoSchema):
class Meta:
model = FileModel
load_instance = True
include_relationships = True
include_fk = True # Includes foreign keys
unknown = EXCLUDE
type = EnumField(FileType)
class FileSchema(ma.Schema):
class Meta:
model = File
fields = ["id", "name", "is_status", "is_reference", "content_type",
"primary", "primary_process_id", "workflow_spec_id", "workflow_id",
"irb_doc_code", "last_modified", "latest_version", "type"]
unknown = INCLUDE
type = EnumField(FileType)
class LookupFileModel(db.Model):
"""Takes the content of a file (like a xlsx, or csv file) and creates a key/value
store that can be used for lookups and searches. This table contains the metadata,
so we know the version of the file that was used, and what key column, and value column
were used to generate this lookup table. ie, the same xls file might have multiple
lookup file models, if different keys and labels are used - or someone decides to
make a change. We need to handle full text search over the label and value columns,
and not every column, because we don't know how much information will be in there. """
"""Gives us a quick way to tell what kind of lookup is set on a form field.
Connected to the file data model, so that if a new version of the same file is
created, we can update the listing."""
#fixme: What happens if they change the file associated with a lookup field?
__tablename__ = 'lookup_file'
id = db.Column(db.Integer, primary_key=True)
label_column = db.Column(db.String)
value_column = db.Column(db.String)
workflow_spec_id = db.Column(db.String)
field_id = db.Column(db.String)
is_ldap = db.Column(db.Boolean) # Allows us to run an ldap query instead of a db lookup.
file_data_model_id = db.Column(db.Integer, db.ForeignKey('file_data.id'))
dependencies = db.relationship("LookupDataModel", lazy="select", backref="lookup_file_model", cascade="all, delete, delete-orphan")
class LookupDataModel(db.Model):
__tablename__ = 'lookup_data'
id = db.Column(db.Integer, primary_key=True)
lookup_file_model_id = db.Column(db.Integer, db.ForeignKey('lookup_file.id'))
lookup_file_model = db.relationship(LookupFileModel)
value = db.Column(db.String)
label = db.Column(db.String)
# In the future, we might allow adding an additional "search" column if we want to search things not in label.
@ -139,3 +169,9 @@ class LookupDataSchema(SQLAlchemyAutoSchema):
include_relationships = False
include_fk = False # Includes foreign keys
class SimpleFileSchema(ma.Schema):
class Meta:
model = FileModel
fields = ["name"]

16
crc/models/study.py
View File

@ -5,6 +5,7 @@ from sqlalchemy import func
from crc import db, ma
from crc.api.common import ApiErrorSchema
from crc.models.file import FileModel, SimpleFileSchema
from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowState, WorkflowStatus, WorkflowSpecModel, \
WorkflowModel
@ -63,7 +64,7 @@ class WorkflowMetadata(object):
name=workflow.workflow_spec.name,
display_name=workflow.workflow_spec.display_name,
description=workflow.workflow_spec.description,
spec_version=workflow.spec_version,
spec_version=workflow.spec_version(),
category_id=workflow.workflow_spec.category_id,
state=WorkflowState.optional,
status=workflow.status,
@ -102,7 +103,8 @@ class CategorySchema(ma.Schema):
class Study(object):
def __init__(self, id, title, last_updated, primary_investigator_id, user_uid,
def __init__(self, title, last_updated, primary_investigator_id, user_uid,
id=None,
protocol_builder_status=None,
sponsor="", hsr_number="", ind_number="", categories=[], **argsv):
self.id = id
@ -116,11 +118,12 @@ class Study(object):
self.ind_number = ind_number
self.categories = categories
self.warnings = []
self.files = []
@classmethod
def from_model(cls, study_model: StudyModel):
args = {k: v for k, v in study_model.__dict__.items() if not k.startswith('_')}
id = study_model.id # Just read some value, in case the dict expired, otherwise dict may be empty.
args = dict((k, v) for k, v in study_model.__dict__.items() if not k.startswith('_'))
instance = cls(**args)
return instance
@ -139,10 +142,14 @@ class Study(object):
class StudySchema(ma.Schema):
id = fields.Integer(required=False, allow_none=True)
categories = fields.List(fields.Nested(CategorySchema), dump_only=True)
warnings = fields.List(fields.Nested(ApiErrorSchema), dump_only=True)
protocol_builder_status = EnumField(ProtocolBuilderStatus)
hsr_number = fields.String(allow_none=True)
sponsor = fields.String(allow_none=True)
ind_number = fields.String(allow_none=True)
files = fields.List(fields.Nested(SimpleFileSchema), dump_only=True)
class Meta:
model = Study
@ -154,3 +161,4 @@ class StudySchema(ma.Schema):
def make_study(self, data, **kwargs):
"""Can load the basic study data for updates to the database, but categories are write only"""
return Study(**data)

2
crc/models/user.py
View File

@ -19,6 +19,8 @@ class UserModel(db.Model):
last_name = db.Column(db.String, nullable=True)
title = db.Column(db.String, nullable=True)
# Add Department and School
def encode_auth_token(self):
"""

21
crc/models/workflow.py
View File

@ -5,6 +5,7 @@ from marshmallow import EXCLUDE
from marshmallow_sqlalchemy import SQLAlchemyAutoSchema
from crc import db
from crc.models.file import FileModel, FileDataModel
class WorkflowSpecCategoryModel(db.Model):
@ -67,16 +68,30 @@ class WorkflowStatus(enum.Enum):
complete = "complete"
class WorkflowSpecDependencyFile(db.Model):
"""Connects a workflow to the version of the specification files it depends on to execute"""
file_data_id = db.Column(db.Integer, db.ForeignKey(FileDataModel.id), primary_key=True)
workflow_id = db.Column(db.Integer, db.ForeignKey("workflow.id"), primary_key=True)
file_data = db.relationship(FileDataModel)
class WorkflowModel(db.Model):
__tablename__ = 'workflow'
id = db.Column(db.Integer, primary_key=True)
bpmn_workflow_json = db.Column(db.JSON)
status = db.Column(db.Enum(WorkflowStatus))
study_id = db.Column(db.Integer, db.ForeignKey('study.id'))
study = db.relationship("StudyModel", backref='workflow')
workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))
workflow_spec = db.relationship("WorkflowSpecModel")
spec_version = db.Column(db.String)
total_tasks = db.Column(db.Integer, default=0)
completed_tasks = db.Column(db.Integer, default=0)
# task_history = db.Column(db.ARRAY(db.String), default=[]) # The history stack of user completed tasks.
last_updated = db.Column(db.DateTime)
last_updated = db.Column(db.DateTime)
# Order By is important or generating hashes on reviews.
dependencies = db.relationship(WorkflowSpecDependencyFile, cascade="all, delete, delete-orphan",
order_by="WorkflowSpecDependencyFile.file_data_id")
def spec_version(self):
dep_ids = list(dep.file_data_id for dep in self.dependencies)
return "-".join(str(dep_ids))

32
crc/scripts/complete_template.py
View File

@ -27,24 +27,20 @@ Takes two arguments:
2. The 'code' of the IRB Document as set in the irb_documents.xlsx file."
"""
def do_task_validate_only(self, task, study_id, *args, **kwargs):
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, process the template, but do not store it in the database."""
self.process_template(task, study_id, None, *args, **kwargs)
def do_task(self, task, study_id, *args, **kwargs):
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
final_document_stream = self.process_template(task, study_id, workflow, *args, **kwargs)
file_name = args[0]
irb_doc_code = args[1]
FileService.add_task_file(study_id=study_id,
workflow_id=workflow_id,
workflow_spec_id=workflow.workflow_spec_id,
task_id=task.id,
name=file_name,
content_type=CONTENT_TYPES['docx'],
binary_data=final_document_stream.read(),
irb_doc_code=irb_doc_code)
FileService.add_workflow_file(workflow_id=workflow_id,
name=file_name,
content_type=CONTENT_TYPES['docx'],
binary_data=final_document_stream.read(),
irb_doc_code=irb_doc_code)
def process_template(self, task, study_id, workflow=None, *args, **kwargs):
"""Entry point, mostly worried about wiring it all up."""
@ -63,13 +59,13 @@ Takes two arguments:
file_data_model = None
if workflow is not None:
# Get the workflow's latest files
joined_file_data_models = WorkflowProcessor\
.get_file_models_for_version(workflow.workflow_spec_id, workflow.spec_version)
for joined_file_data in joined_file_data_models:
if joined_file_data.file_model.name == file_name:
file_data_model = session.query(FileDataModel).filter_by(id=joined_file_data.id).first()
# Get the workflow specification file with the given name.
file_data_models = FileService.get_spec_data_files(
workflow_spec_id=workflow.workflow_spec_id,
workflow_id=workflow.id)
for file_data in file_data_models:
if file_data.file_model.name == file_name:
file_data_model = file_data
if workflow is None or file_data_model is None:
file_data_model = FileService.get_workflow_file_data(task.workflow, file_name)

6
crc/scripts/fact_service.py
View File

@ -20,10 +20,10 @@ class FactService(Script):
response = requests.get('https://api.chucknorris.io/jokes/random')
return response.json()['value']
def do_task_validate_only(self, task, study_id, **kwargs):
self.do_task(task, study_id, **kwargs)
def do_task_validate_only(self, task, study_id, workflow_id, **kwargs):
self.do_task(task, study_id, workflow_id, **kwargs)
def do_task(self, task, study_id, **kwargs):
def do_task(self, task, study_id, workflow_id, **kwargs):
print(task.data)
if "type" not in task.data:

49
crc/scripts/request_approval.py Normal file
View File

@ -0,0 +1,49 @@
from crc.api.common import ApiError
from crc.scripts.script import Script
from crc.services.approval_service import ApprovalService
class RequestApproval(Script):
"""This still needs to be fully wired up as a Script task callable from the workflow
But the basic logic is here just to get the tests passing and logic sound. """
def get_description(self):
return """
Creates an approval request on this workflow, by the given approver_uid(s),"
Takes multiple arguments, which should point to data located in current task
or be quoted strings.
Example:
RequestApproval approver1 "dhf8r"
"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
self.get_uids(task, args)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
uids = self.get_uids(task, args)
if isinstance(uids, str):
ApprovalService.add_approval(study_id, workflow_id, args)
elif isinstance(uids, list):
for id in uids:
ApprovalService.add_approval(study_id, workflow_id, id)
def get_uids(self, task, args):
if len(args) < 1:
raise ApiError(code="missing_argument",
message="The RequestApproval script requires at least one argument. The "
"the name of the variable in the task data that contains user"
"id to process. Multiple arguments are accepted.")
uids = []
for arg in args:
id = task.workflow.script_engine.evaluate_expression(task, arg)
uids.append(id)
if not isinstance(id, str):
raise ApiError(code="invalid_argument",
message="The RequestApproval 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 " % uids.__class__.__name__)
return uids

4
crc/scripts/script.py
View File

@ -13,12 +13,12 @@ class Script(object):
raise ApiError("invalid_script",
"This script does not supply a description.")
def do_task(self, task, study_id, **kwargs):
def do_task(self, task, study_id, workflow_id, **kwargs):
raise ApiError("invalid_script",
"This is an internal error. The script you are trying to execute '%s' " % self.__class__.__name__ +
"does not properly implement the do_task function.")
def do_task_validate_only(self, task, study_id, **kwargs):
def do_task_validate_only(self, task, study_id, workflow_id, **kwargs):
raise ApiError("invalid_script",
"This is an internal error. The script you are trying to execute '%s' " % self.__class__.__name__ +
"does must provide a validate_only option that mimics the do_task, " +

4
crc/scripts/study_info.py
View File

@ -138,7 +138,7 @@ Returns information specific to the protocol.
documents_example=self.example_to_string("documents"),
)
def do_task_validate_only(self, task, study_id, *args, **kwargs):
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, pretend no results come back from pb"""
self.check_args(args)
# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
@ -184,7 +184,7 @@ Returns information specific to the protocol.
self.add_data_to_task(task=task, data=data["study"])
self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
def do_task(self, task, study_id, *args, **kwargs):
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
self.check_args(args)
cmd = args[0]

58
crc/scripts/update_study.py Normal file
View File

@ -0,0 +1,58 @@
import requests
from crc import db
from crc.api.common import ApiError
from crc.models.study import StudyModel
from crc.scripts.script import Script
class mock_study:
def __init__(self):
self.title = ""
self.principle_investigator_id = ""
class UpdateStudy(Script):
argument_error_message = "You must supply at least one argument to the " \
"update_study task, in the form [study_field]:[value]",
def get_description(self):
return """
Allows you to set specific attributes on the Study model by mapping them to
values in the task data. Should be called with the value to set (either title, or pi)
followed by a ":" and then the value to use in dot notation.
Example:
UpdateStudy title:PIComputingID.label pi:PIComputingID.value
"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
study = mock_study
self.__update_study(task, study, *args)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
self.__update_study(task, study, *args)
db.session.add(study)
def __update_study(self, task, study, *args):
if len(args) < 1:
raise ApiError.from_task("missing_argument", self.argument_error_message,
task=task)
for arg in args:
try:
field, value_lookup = arg.split(':')
except:
raise ApiError.from_task("invalid_argument", self.argument_error_message,
task=task)
value = task.workflow.script_engine.evaluate_expression(task, value_lookup)
if field.lower() == "title":
study.title = value
elif field.lower() == "pi":
study.primary_investigator_id = value
else:
raise ApiError.from_task("invalid_argument", self.argument_error_message,
task=task)

97
crc/services/approval_service.py Normal file
View File

@ -0,0 +1,97 @@
from datetime import datetime
from sqlalchemy import desc
from crc import db, session
from crc.api.common import ApiError
from crc.models.approval import ApprovalModel, ApprovalStatus, ApprovalFile
from crc.models.workflow import WorkflowModel
from crc.services.file_service import FileService
class ApprovalService(object):
"""Provides common tools for working with an Approval"""
@staticmethod
def get_approvals_per_user(approver_uid):
"""Returns a list of all approvals for the given user (approver)"""
db_approvals = session.query(ApprovalModel).filter_by(approver_uid=approver_uid).all()
return db_approvals
@staticmethod
def get_all_approvals():
"""Returns a list of all approvlas"""
db_approvals = session.query(ApprovalModel).all()
return db_approvals
@staticmethod
def update_approval(approval_id, approver_uid, status):
"""Update a specific approval"""
db_approval = session.query(ApprovalModel).get(approval_id)
if db_approval:
db_approval.status = status
session.add(db_approval)
session.commit()
# TODO: Log update action by approver_uid - maybe ?
return db_approval
@staticmethod
def add_approval(study_id, workflow_id, approver_uid):
"""we might have multiple approvals for a workflow, so I would expect this
method to get called multiple times for the same workflow. This will
only add a new approval if no approval already exists for the approver_uid,
unless the workflow has changed, at which point, it will CANCEL any
pending approvals and create a new approval for the latest version
of the workflow."""
# Find any existing approvals for this workflow and approver.
latest_approval_request = db.session.query(ApprovalModel). \
filter(ApprovalModel.workflow_id == workflow_id). \
filter(ApprovalModel.approver_uid == approver_uid). \
order_by(desc(ApprovalModel.version)).first()
# Construct as hash of the latest files to see if things have changed since
# the last approval.
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
workflow_data_files = FileService.get_workflow_data_files(workflow_id)
current_data_file_ids = list(data_file.id for data_file in workflow_data_files)
if len(current_data_file_ids) == 0:
raise ApiError("invalid_workflow_approval", "You can't create an approval for a workflow that has"
"no files to approve in it.")
# If an existing approval request exists and no changes were made, do nothing.
# If there is an existing approval request for a previous version of the workflow
# then add a new request, and cancel any waiting/pending requests.
if latest_approval_request:
request_file_ids = list(file.file_data_id for file in latest_approval_request.approval_files)
current_data_file_ids.sort()
request_file_ids.sort()
if current_data_file_ids == request_file_ids:
return # This approval already exists.
else:
latest_approval_request.status = ApprovalStatus.CANCELED.value
db.session.add(latest_approval_request)
version = latest_approval_request.version + 1
else:
version = 1
model = ApprovalModel(study_id=study_id, workflow_id=workflow_id,
approver_uid=approver_uid, status=ApprovalStatus.WAITING.value,
message="", date_created=datetime.now(),
version=version)
approval_files = ApprovalService._create_approval_files(workflow_data_files, model)
db.session.add(model)
db.session.add_all(approval_files)
db.session.commit()
@staticmethod
def _create_approval_files(workflow_data_files, approval):
"""Currently based exclusively on the status of files associated with a workflow."""
file_approval_models = []
for file_data in workflow_data_files:
file_approval_models.append(ApprovalFile(file_data_id=file_data.id,
approval=approval))
return file_approval_models

190
crc/services/file_service.py
View File

@ -5,13 +5,14 @@ from datetime import datetime
from uuid import UUID
from xml.etree import ElementTree
from SpiffWorkflow.bpmn.parser.ValidationException import ValidationException
from pandas import ExcelFile
from sqlalchemy import desc
from crc import session
from crc.api.common import ApiError
from crc.models.file import FileType, FileDataModel, FileModel, LookupFileModel, LookupDataModel
from crc.models.workflow import WorkflowSpecModel
from crc.services.workflow_processor import WorkflowProcessor
from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecDependencyFile
class FileService(object):
@ -40,22 +41,28 @@ class FileService(object):
return code in df['code'].values
@staticmethod
def add_form_field_file(study_id, workflow_id, task_id, form_field_key, name, content_type, binary_data):
"""Create a new file and associate it with a user task form field within a workflow.
Please note that the form_field_key MUST be a known file in the irb_documents.xslx reference document."""
if not FileService.is_allowed_document(form_field_key):
def add_workflow_file(workflow_id, irb_doc_code, name, content_type, binary_data):
"""Create a new file and associate it with the workflow
Please note that the irb_doc_code MUST be a known file in the irb_documents.xslx reference document."""
if not FileService.is_allowed_document(irb_doc_code):
raise ApiError("invalid_form_field_key",
"When uploading files, the form field id must match a known document in the "
"irb_docunents.xslx reference file. This code is not found in that file '%s'" % form_field_key)
"irb_docunents.xslx reference file. This code is not found in that file '%s'" % irb_doc_code)
file_model = FileModel(
study_id=study_id,
workflow_id=workflow_id,
task_id=task_id,
name=name,
form_field_key=form_field_key,
irb_doc_code=form_field_key
)
"""Assure this is unique to the workflow, task, and document code AND the Name
Because we will allow users to upload multiple files for the same form field
in some cases """
file_model = session.query(FileModel)\
.filter(FileModel.workflow_id == workflow_id)\
.filter(FileModel.name == name)\
.filter(FileModel.irb_doc_code == irb_doc_code).first()
if not file_model:
file_model = FileModel(
workflow_id=workflow_id,
name=name,
irb_doc_code=irb_doc_code
)
return FileService.update_file(file_model, binary_data, content_type)
@staticmethod
@ -76,18 +83,10 @@ class FileService(object):
return json.loads(df.to_json(orient='index'))
@staticmethod
def add_task_file(study_id, workflow_id, workflow_spec_id, task_id, name, content_type, binary_data,
irb_doc_code=None):
"""Create a new file and associate it with an executing task within a workflow."""
file_model = FileModel(
study_id=study_id,
workflow_id=workflow_id,
workflow_spec_id=workflow_spec_id,
task_id=task_id,
name=name,
irb_doc_code=irb_doc_code
)
return FileService.update_file(file_model, binary_data, content_type)
def get_workflow_files(workflow_id):
"""Returns all the file models associated with a running workflow."""
return session.query(FileModel).filter(FileModel.workflow_id == workflow_id).\
order_by(FileModel.id).all()
@staticmethod
def add_reference_file(name, content_type, binary_data):
@ -112,12 +111,12 @@ class FileService(object):
def update_file(file_model, binary_data, content_type):
session.flush() # Assure the database is up-to-date before running this.
file_data_model = session.query(FileDataModel). \
filter_by(file_model_id=file_model.id,
version=file_model.latest_version
).with_for_update().first()
latest_data_model = session.query(FileDataModel). \
filter(FileDataModel.file_model_id == file_model.id).\
order_by(desc(FileDataModel.date_created)).first()
md5_checksum = UUID(hashlib.md5(binary_data).hexdigest())
if (file_data_model is not None) and (md5_checksum == file_data_model.md5_hash):
if (latest_data_model is not None) and (md5_checksum == latest_data_model.md5_hash):
# This file does not need to be updated, it's the same file.
return file_model
@ -131,22 +130,20 @@ class FileService(object):
file_model.type = FileType[file_extension]
file_model.content_type = content_type
if file_data_model is None:
if latest_data_model is None:
version = 1
else:
version = file_data_model.version + 1
version = latest_data_model.version + 1
# If this is a BPMN, extract the process id.
if file_model.type == FileType.bpmn:
bpmn: ElementTree.Element = ElementTree.fromstring(binary_data)
file_model.primary_process_id = WorkflowProcessor.get_process_id(bpmn)
file_model.primary_process_id = FileService.get_process_id(bpmn)
file_model.latest_version = version
new_file_data_model = FileDataModel(
data=binary_data, file_model_id=file_model.id, file_model=file_model,
version=version, md5_hash=md5_checksum, last_updated=datetime.now()
version=version, md5_hash=md5_checksum, date_created=datetime.now()
)
session.add_all([file_model, new_file_data_model])
session.commit()
session.flush() # Assure the id is set on the model before returning it.
@ -154,46 +151,103 @@ class FileService(object):
return file_model
@staticmethod
def get_files(workflow_spec_id=None,
study_id=None, workflow_id=None, task_id=None, form_field_key=None,
def get_process_id(et_root: ElementTree.Element):
process_elements = []
for child in et_root:
if child.tag.endswith('process') and child.attrib.get('isExecutable', False):
process_elements.append(child)
if len(process_elements) == 0:
raise ValidationException('No executable process tag found')
# There are multiple root elements
if len(process_elements) > 1:
# Look for the element that has the startEvent in it
for e in process_elements:
this_element: ElementTree.Element = e
for child_element in list(this_element):
if child_element.tag.endswith('startEvent'):
return this_element.attrib['id']
raise ValidationException('No start event found in %s' % et_root.attrib['id'])
return process_elements[0].attrib['id']
@staticmethod
def get_files_for_study(study_id, irb_doc_code=None):
query = session.query(FileModel).\
join(WorkflowModel).\
filter(WorkflowModel.study_id == study_id)
if irb_doc_code:
query = query.filter(FileModel.irb_doc_code == irb_doc_code)
return query.all()
@staticmethod
def get_files(workflow_spec_id=None, workflow_id=None,
name=None, is_reference=False, irb_doc_code=None):
query = session.query(FileModel).filter_by(is_reference=is_reference)
if workflow_spec_id:
query = query.filter_by(workflow_spec_id=workflow_spec_id)
if all(v is None for v in [study_id, workflow_id, task_id, form_field_key]):
query = query.filter_by(
study_id=None,
workflow_id=None,
task_id=None,
form_field_key=None,
)
else:
if study_id:
query = query.filter_by(study_id=study_id)
if workflow_id:
query = query.filter_by(workflow_id=workflow_id)
if task_id:
query = query.filter_by(task_id=str(task_id))
if form_field_key:
query = query.filter_by(form_field_key=form_field_key)
if name:
query = query.filter_by(name=name)
elif workflow_id:
query = query.filter_by(workflow_id=workflow_id)
if irb_doc_code:
query = query.filter_by(irb_doc_code=irb_doc_code)
elif is_reference:
query = query.filter_by(is_reference=True)
if name:
query = query.filter_by(name=name)
query = query.order_by(FileModel.id)
results = query.all()
return results
@staticmethod
def get_file_data(file_id, file_model=None):
"""Returns the file_data that is associated with the file model id, if an actual file_model
is provided, uses that rather than looking it up again."""
if file_model is None:
file_model = session.query(FileModel).filter(FileModel.id == file_id).first()
return session.query(FileDataModel) \
.filter(FileDataModel.file_model_id == file_id) \
.filter(FileDataModel.version == file_model.latest_version) \
.first()
def get_spec_data_files(workflow_spec_id, workflow_id=None, name=None):
"""Returns all the FileDataModels related to a workflow specification.
If a workflow is specified, returns the version of the spec relatted
to that workflow, otherwise, returns the lastes files."""
if workflow_id:
query = session.query(FileDataModel) \
.join(WorkflowSpecDependencyFile) \
.filter(WorkflowSpecDependencyFile.workflow_id == workflow_id) \
.order_by(FileDataModel.id)
if name:
query = query.join(FileModel).filter(FileModel.name == name)
return query.all()
else:
"""Returns all the latest files related to a workflow specification"""
file_models = FileService.get_files(workflow_spec_id=workflow_spec_id)
latest_data_files = []
for file_model in file_models:
if name and file_model.name == name:
latest_data_files.append(FileService.get_file_data(file_model.id))
elif not name:
latest_data_files.append(FileService.get_file_data(file_model.id))
return latest_data_files
@staticmethod
def get_workflow_data_files(workflow_id=None):
"""Returns all the FileDataModels related to a running workflow -
So these are the latest data files that were uploaded or generated
that go along with this workflow. Not related to the spec in any way"""
file_models = FileService.get_files(workflow_id=workflow_id)
latest_data_files = []
for file_model in file_models:
latest_data_files.append(FileService.get_file_data(file_model.id))
return latest_data_files
@staticmethod
def get_file_data(file_id: int, version: int = None):
"""Returns the file data with the given version, or the lastest file, if version isn't provided."""
query = session.query(FileDataModel) \
.filter(FileDataModel.file_model_id == file_id)
if version:
query = query.filter(FileDataModel.version == version)
else:
query = query.order_by(desc(FileDataModel.date_created))
return query.first()
@staticmethod
def get_reference_file_data(file_name):
@ -202,7 +256,7 @@ class FileService(object):
filter(FileModel.name == file_name).first()
if not file_model:
raise ApiError("file_not_found", "There is no reference file with the name '%s'" % file_name)
return FileService.get_file_data(file_model.id, file_model)
return FileService.get_file_data(file_model.id)
@staticmethod
def get_workflow_file_data(workflow, file_name):

43
crc/services/ldap_service.py
View File

@ -8,23 +8,37 @@ from crc.api.common import ApiError
class LdapUserInfo(object):
def __init__(self, entry):
self.display_name = entry.displayName.value
self.given_name = ", ".join(entry.givenName)
self.email = entry.mail.value
self.telephone_number = ", ".join(entry.telephoneNumber)
self.title = ", ".join(entry.title)
self.department = ", ".join(entry.uvaDisplayDepartment)
self.affiliation = ", ".join(entry.uvaPersonIAMAffiliation)
self.sponsor_type = ", ".join(entry.uvaPersonSponsoredType)
self.uid = entry.uid.value
def __init__(self):
self.display_name = ''
self.given_name = ''
self.email_address = ''
self.telephone_number = ''
self.title = ''
self.department = ''
self.affiliation = ''
self.sponsor_type = ''
self.uid = ''
@classmethod
def from_entry(cls, entry):
instance = cls()
instance.display_name = entry.displayName.value
instance.given_name = ", ".join(entry.givenName)
instance.email_address = entry.mail.value
instance.telephone_number = ", ".join(entry.telephoneNumber)
instance.title = ", ".join(entry.title)
instance.department = ", ".join(entry.uvaDisplayDepartment)
instance.affiliation = ", ".join(entry.uvaPersonIAMAffiliation)
instance.sponsor_type = ", ".join(entry.uvaPersonSponsoredType)
instance.uid = entry.uid.value
return instance
class LdapService(object):
search_base = "ou=People,o=University of Virginia,c=US"
attributes = ['uid', 'cn', 'displayName', 'givenName', 'mail', 'objectClass', 'UvaDisplayDepartment',
attributes = ['uid', 'cn', 'sn', 'displayName', 'givenName', 'mail', 'objectClass', 'UvaDisplayDepartment',
'telephoneNumber', 'title', 'uvaPersonIAMAffiliation', 'uvaPersonSponsoredType']
uid_search_string = "(&(objectclass=person)(uid=%s))"
user_or_last_name_search_string = "(&(objectclass=person)(|(uid=%s*)(sn=%s*)))"
def __init__(self):
if app.config['TESTING']:
@ -50,10 +64,11 @@ class LdapService(object):
if len(self.conn.entries) < 1:
raise ApiError("missing_ldap_record", "Unable to locate a user with id %s in LDAP" % uva_uid)
entry = self.conn.entries[0]
return(LdapUserInfo(entry))
return LdapUserInfo.from_entry(entry)
def search_users(self, query, limit):
search_string = LdapService.uid_search_string % query
if len(query) < 3: return []
search_string = LdapService.user_or_last_name_search_string % (query, query)
self.conn.search(LdapService.search_base, search_string, attributes=LdapService.attributes)
# Entries are returned as a generator, accessing entries
@ -64,6 +79,6 @@ class LdapService(object):
for entry in self.conn.entries:
if count > limit:
break
results.append(LdapUserInfo(entry))
results.append(LdapUserInfo.from_entry(entry))
count += 1
return results

182
crc/services/lookup_service.py
View File

@ -1,13 +1,24 @@
import logging
import re
from pandas import ExcelFile
from sqlalchemy import func, desc
from sqlalchemy.sql.functions import GenericFunction
from crc import db
from crc.api.common import ApiError
from crc.models.api_models import Task
from crc.models.file import FileDataModel, LookupFileModel, LookupDataModel
from crc.models.workflow import WorkflowModel, WorkflowSpecDependencyFile
from crc.services.file_service import FileService
from crc.services.ldap_service import LdapService
from crc.services.workflow_processor import WorkflowProcessor
class TSRank(GenericFunction):
package = 'full_text'
name = 'ts_rank'
class LookupService(object):
"""Provides tools for doing lookups for auto-complete fields.
@ -24,33 +35,56 @@ class LookupService(object):
"""
@staticmethod
def lookup(spiff_task, field, query, limit):
"""Executes the lookup for the given field."""
if field.type != Task.FIELD_TYPE_AUTO_COMPLETE:
raise ApiError.from_task("invalid_field_type",
"Field '%s' must be an autocomplete field to use lookups." % field.label,
task=spiff_task)
# If this field has an associated options file, then do the lookup against that field.
if field.has_property(Task.PROP_OPTIONS_FILE):
lookup_table = LookupService.get_lookup_table(spiff_task, field)
return LookupService._run_lookup_query(lookup_table, query, limit)
# If this is a ldap lookup, use the ldap service to provide the fields to return.
elif field.has_property(Task.PROP_LDAP_LOOKUP):
return LookupService._run_ldap_query(query, limit)
else:
raise ApiError.from_task("unknown_lookup_option",
"Lookup supports using spreadsheet options or ldap options, and neither was"
"provided.")
def get_lookup_model(spiff_task, field):
workflow_id = spiff_task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
return LookupService.__get_lookup_model(workflow, field.id)
@staticmethod
def get_lookup_table(spiff_task, field):
""" Checks to see if the options are provided in a separate lookup table associated with the
def __get_lookup_model(workflow, field_id):
lookup_model = db.session.query(LookupFileModel) \
.filter(LookupFileModel.workflow_spec_id == workflow.workflow_spec_id) \
.filter(LookupFileModel.field_id == field_id).first()
# one more quick query, to see if the lookup file is still related to this workflow.
# if not, we need to rebuild the lookup table.
is_current = False
if lookup_model:
is_current = db.session.query(WorkflowSpecDependencyFile).\
filter(WorkflowSpecDependencyFile.file_data_id == lookup_model.file_data_model_id).count()
if not is_current:
if lookup_model:
db.session.delete(lookup_model)
# Very very very expensive, but we don't know need this till we do.
lookup_model = LookupService.create_lookup_model(workflow, field_id)
return lookup_model
@staticmethod
def lookup(workflow, field_id, query, limit):
lookup_model = LookupService.__get_lookup_model(workflow, field_id)
if lookup_model.is_ldap:
return LookupService._run_ldap_query(query, limit)
else:
return LookupService._run_lookup_query(lookup_model, query, limit)
@staticmethod
def create_lookup_model(workflow_model, field_id):
"""
This is all really expensive, but should happen just once (per file change).
Checks to see if the options are provided in a separate lookup table associated with the
workflow, and if so, assures that data exists in the database, and return a model than can be used
to locate that data.
Returns: an array of LookupData, suitable for returning to the api.
"""
processor = WorkflowProcessor(workflow_model) # VERY expensive, Ludicrous for lookup / type ahead
spiff_task, field = processor.find_task_and_field_by_field_id(field_id)
if field.has_property(Task.PROP_OPTIONS_FILE):
if not field.has_property(Task.PROP_OPTIONS_VALUE_COLUMN) or \
not field.has_property(Task.PROP_OPTIONS_LABEL_COL):
@ -65,67 +99,93 @@ class LookupService(object):
file_name = field.get_property(Task.PROP_OPTIONS_FILE)
value_column = field.get_property(Task.PROP_OPTIONS_VALUE_COLUMN)
label_column = field.get_property(Task.PROP_OPTIONS_LABEL_COL)
data_model = FileService.get_workflow_file_data(spiff_task.workflow, file_name)
lookup_model = LookupService.get_lookup_table_from_data_model(data_model, value_column, label_column)
return lookup_model
latest_files = FileService.get_spec_data_files(workflow_spec_id=workflow_model.workflow_spec_id,
workflow_id=workflow_model.id,
name=file_name)
if len(latest_files) < 1:
raise ApiError("missing_file", "Unable to locate the lookup data file '%s'" % file_name)
else:
data_model = latest_files[0]
lookup_model = LookupService.build_lookup_table(data_model, value_column, label_column,
workflow_model.workflow_spec_id, field_id)
elif field.has_property(Task.PROP_LDAP_LOOKUP):
lookup_model = LookupFileModel(workflow_spec_id=workflow_model.workflow_spec_id,
field_id=field_id,
is_ldap=True)
else:
raise ApiError("unknown_lookup_option",
"Lookup supports using spreadsheet options or ldap options, and neither "
"was provided.")
db.session.add(lookup_model)
db.session.commit()
return lookup_model
@staticmethod
def get_lookup_table_from_data_model(data_model: FileDataModel, value_column, label_column):
def build_lookup_table(data_model: FileDataModel, value_column, label_column, workflow_spec_id, field_id):
""" In some cases the lookup table can be very large. This method will add all values to the database
in a way that can be searched and returned via an api call - rather than sending the full set of
options along with the form. It will only open the file and process the options if something has
changed. """
xls = ExcelFile(data_model.data)
df = xls.parse(xls.sheet_names[0]) # Currently we only look at the fist sheet.
if value_column not in df:
raise ApiError("invalid_emum",
"The file %s does not contain a column named % s" % (data_model.file_model.name,
value_column))
if label_column not in df:
raise ApiError("invalid_emum",
"The file %s does not contain a column named % s" % (data_model.file_model.name,
label_column))
lookup_model = db.session.query(LookupFileModel) \
.filter(LookupFileModel.file_data_model_id == data_model.id) \
.filter(LookupFileModel.value_column == value_column) \
.filter(LookupFileModel.label_column == label_column).first()
if not lookup_model:
xls = ExcelFile(data_model.data)
df = xls.parse(xls.sheet_names[0]) # Currently we only look at the fist sheet.
if value_column not in df:
raise ApiError("invalid_emum",
"The file %s does not contain a column named % s" % (data_model.file_model.name,
value_column))
if label_column not in df:
raise ApiError("invalid_emum",
"The file %s does not contain a column named % s" % (data_model.file_model.name,
label_column))
lookup_model = LookupFileModel(label_column=label_column, value_column=value_column,
file_data_model_id=data_model.id)
db.session.add(lookup_model)
for index, row in df.iterrows():
lookup_data = LookupDataModel(lookup_file_model=lookup_model,
value=row[value_column],
label=row[label_column],
data=row.to_json())
db.session.add(lookup_data)
db.session.commit()
lookup_model = LookupFileModel(workflow_spec_id=workflow_spec_id,
field_id=field_id,
file_data_model_id=data_model.id,
is_ldap=False)
db.session.add(lookup_model)
for index, row in df.iterrows():
lookup_data = LookupDataModel(lookup_file_model=lookup_model,
value=row[value_column],
label=row[label_column],
data=row.to_json())
db.session.add(lookup_data)
db.session.commit()
return lookup_model
@staticmethod
def _run_lookup_query(lookup_file_model, query, limit):
db_query = LookupDataModel.query.filter(LookupDataModel.lookup_file_model == lookup_file_model)
query = re.sub('[^A-Za-z0-9 ]+', '', query)
print("Query: " + query)
query = query.strip()
if len(query) > 1:
if len(query) > 0:
if ' ' in query:
terms = query.split(' ')
new_terms = []
new_terms = ["'%s'" % query]
for t in terms:
new_terms.append(t + ":*")
query = '|'.join(new_terms)
new_terms.append("%s:*" % t)
new_query = ' | '.join(new_terms)
else:
query = "%s:*" % query
db_query = db_query.filter(LookupDataModel.label.match(query))
new_query = "%s:*" % query
# db_query = db_query.filter(text("lookup_data.label @@ to_tsquery('simple', '%s')" % query))
# Run the full text query
db_query = db_query.filter(LookupDataModel.label.match(new_query))
# But hackishly order by like, which does a good job of
# pulling more relevant matches to the top.
db_query = db_query.order_by(desc(LookupDataModel.label.like("%" + query + "%")))
#ORDER BY name LIKE concat('%', ticker, '%') desc, rank DESC
return db_query.limit(limit).all()
# db_query = db_query.order_by(desc(func.full_text.ts_rank(
# func.to_tsvector(LookupDataModel.label),
# func.to_tsquery(query))))
from sqlalchemy.dialects import postgresql
logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
result = db_query.limit(limit).all()
logging.getLogger('sqlalchemy.engine').setLevel(logging.ERROR)
return result
@staticmethod
def _run_ldap_query(query, limit):

62
crc/services/protocol_builder.py
View File

@ -5,8 +5,7 @@ import requests
from crc import app
from crc.api.common import ApiError
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStudySchema, ProtocolBuilderInvestigator, \
ProtocolBuilderRequiredDocument, ProtocolBuilderRequiredDocumentSchema
from crc.models.protocol_builder import ProtocolBuilderStudySchema, ProtocolBuilderRequiredDocument
class ProtocolBuilderService(object):
@ -15,8 +14,16 @@ class ProtocolBuilderService(object):
REQUIRED_DOCS_URL = app.config['PB_REQUIRED_DOCS_URL']
STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
@staticmethod
def is_enabled():
if isinstance(app.config['PB_ENABLED'], str):
return app.config['PB_ENABLED'].lower() == "true"
else:
return app.config['PB_ENABLED'] is True
@staticmethod
def get_studies(user_id) -> {}:
ProtocolBuilderService.__enabled_or_raise()
if not isinstance(user_id, str):
raise ApiError("invalid_user_id", "This user id is invalid: " + str(user_id))
response = requests.get(ProtocolBuilderService.STUDY_URL % user_id)
@ -30,40 +37,31 @@ class ProtocolBuilderService(object):
@staticmethod
def get_investigators(study_id) -> {}:
ProtocolBuilderService.check_args(study_id)
response = requests.get(ProtocolBuilderService.INVESTIGATOR_URL % study_id)
if response.ok and response.text:
pb_studies = json.loads(response.text)
return pb_studies
else:
raise ApiError("protocol_builder_error",
"Received an invalid response from the protocol builder (status %s): %s" %
(response.status_code, response.text))
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.INVESTIGATOR_URL)
@staticmethod
def get_required_docs(study_id) -> Optional[List[ProtocolBuilderRequiredDocument]]:
ProtocolBuilderService.check_args(study_id)
response = requests.get(ProtocolBuilderService.REQUIRED_DOCS_URL % study_id)
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.REQUIRED_DOCS_URL)
@staticmethod
def get_study_details(study_id) -> {}:
return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.STUDY_DETAILS_URL)
@staticmethod
def __enabled_or_raise():
if not ProtocolBuilderService.is_enabled():
raise ApiError("protocol_builder_disabled", "The Protocol Builder Service is currently disabled.")
@staticmethod
def __make_request(study_id, url):
ProtocolBuilderService.__enabled_or_raise()
if not isinstance(study_id, int):
raise ApiError("invalid_study_id", "This study id is invalid: " + str(study_id))
response = requests.get(url % study_id)
if response.ok and response.text:
return json.loads(response.text)
else:
raise ApiError("protocol_builder_error",
"Received an invalid response from the protocol builder (status %s): %s" %
(response.status_code, response.text))
@staticmethod
def get_study_details(study_id) -> {}:
ProtocolBuilderService.check_args(study_id)
response = requests.get(ProtocolBuilderService.STUDY_DETAILS_URL % study_id)
if response.ok and response.text:
pb_study_details = json.loads(response.text)
return pb_study_details
else:
raise ApiError("protocol_builder_error",
"Received an invalid response from the protocol builder (status %s): %s" %
(response.status_code, response.text))
@staticmethod
def check_args(study_id):
if not isinstance(study_id, int):
raise ApiError("invalid_study_id", "This study id is invalid: " + str(study_id))
"Received an invalid response from the protocol builder (status %s): %s when calling "
"url '%s'." %
(response.status_code, response.text, url))

119
crc/services/study_service.py
View File

@ -32,6 +32,17 @@ class StudyService(object):
studies.append(StudyService.get_study(study_model.id, study_model))
return studies
@staticmethod
def get_all_studies_with_files():
"""Returns a list of all studies"""
db_studies = session.query(StudyModel).all()
studies = []
for s in db_studies:
study = Study.from_model(s)
study.files = FileService.get_files_for_study(study.id)
studies.append(study)
return studies
@staticmethod
def get_study(study_id, study_model: StudyModel = None):
"""Returns a study model that contains all the workflows organized by category.
@ -42,6 +53,7 @@ class StudyService(object):
study = Study.from_model(study_model)
study.categories = StudyService.get_categories()
workflow_metas = StudyService.__get_workflow_metas(study_id)
study.files = FileService.get_files_for_study(study.id)
# Calling this line repeatedly is very very slow. It creates the
# master spec and runs it.
@ -58,16 +70,18 @@ class StudyService(object):
def delete_study(study_id):
session.query(TaskEventModel).filter_by(study_id=study_id).delete()
for workflow in session.query(WorkflowModel).filter_by(study_id=study_id):
StudyService.delete_workflow(workflow.id)
StudyService.delete_workflow(workflow)
session.query(StudyModel).filter_by(id=study_id).delete()
session.commit()
@staticmethod
def delete_workflow(workflow_id):
for file in session.query(FileModel).filter_by(workflow_id=workflow_id).all():
def delete_workflow(workflow):
for file in session.query(FileModel).filter_by(workflow_id=workflow.id).all():
FileService.delete_file(file.id)
session.query(TaskEventModel).filter_by(workflow_id=workflow_id).delete()
session.query(WorkflowModel).filter_by(id=workflow_id).delete()
for deb in workflow.dependencies:
session.delete(deb)
session.query(TaskEventModel).filter_by(workflow_id=workflow.id).delete()
session.query(WorkflowModel).filter_by(id=workflow.id).delete()
@staticmethod
def get_categories():
@ -110,23 +124,29 @@ class StudyService(object):
"""Returns a list of documents related to the study, and any file information
that is available.."""
# Get PB required docs
try:
pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id)
except requests.exceptions.ConnectionError as ce:
app.logger.error("Failed to connect to the Protocol Builder - %s" % str(ce))
# Get PB required docs, if Protocol Builder Service is enabled.
if ProtocolBuilderService.is_enabled():
try:
pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id)
except requests.exceptions.ConnectionError as ce:
app.logger.error("Failed to connect to the Protocol Builder - %s" % str(ce))
pb_docs = []
else:
pb_docs = []
# Loop through all known document types, get the counts for those files, and use pb_docs to mark those required.
# Loop through all known document types, get the counts for those files,
# and use pb_docs to mark those as required.
doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
documents = {}
for code, doc in doc_dictionary.items():
pb_data = next((item for item in pb_docs if int(item['AUXDOCID']) == int(doc['id'])), None)
doc['required'] = False
if pb_data:
doc['required'] = True
if ProtocolBuilderService.is_enabled():
pb_data = next((item for item in pb_docs if int(item['AUXDOCID']) == int(doc['id'])), None)
doc['required'] = False
if pb_data:
doc['required'] = True
doc['study_id'] = study_id
doc['code'] = code
@ -138,22 +158,19 @@ class StudyService(object):
doc['display_name'] = ' / '.join(name_list)
# For each file, get associated workflow status
doc_files = FileService.get_files(study_id=study_id, irb_doc_code=code)
doc_files = FileService.get_files_for_study(study_id=study_id, irb_doc_code=code)
doc['count'] = len(doc_files)
doc['files'] = []
for file in doc_files:
doc['files'].append({'file_id': file.id,
'task_id': file.task_id,
'workflow_id': file.workflow_id,
'workflow_spec_id': file.workflow_spec_id})
'workflow_id': file.workflow_id})
# update the document status to match the status of the workflow it is in.
if not 'status' in doc or doc['status'] is None:
if 'status' not in doc or doc['status'] is None:
workflow: WorkflowModel = session.query(WorkflowModel).filter_by(id=file.workflow_id).first()
doc['status'] = workflow.status.value
documents[code] = doc
return documents
@ -201,34 +218,40 @@ class StudyService(object):
@staticmethod
def synch_all_studies_with_protocol_builder(user):
def synch_with_protocol_builder_if_enabled(user):
"""Assures that the studies we have locally for the given user are
in sync with the studies available in protocol builder. """
# Get studies matching this user from Protocol Builder
pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
# Get studies from the database
db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
if ProtocolBuilderService.is_enabled():
# Update all studies from the protocol builder, create new studies as needed.
# Futher assures that every active study (that does exist in the protocol builder)
# has a reference to every available workflow (though some may not have started yet)
for pb_study in pb_studies:
db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None)
if not db_study:
db_study = StudyModel(id=pb_study.STUDYID)
session.add(db_study)
db_studies.append(db_study)
db_study.update_from_protocol_builder(pb_study)
StudyService._add_all_workflow_specs_to_study(db_study)
app.logger.info("The Protocol Builder is enabled. app.config['PB_ENABLED'] = " +
str(app.config['PB_ENABLED']))
# Mark studies as inactive that are no longer in Protocol Builder
for study in db_studies:
pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
if not pb_study:
study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
# Get studies matching this user from Protocol Builder
pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
db.session.commit()
# Get studies from the database
db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
# Update all studies from the protocol builder, create new studies as needed.
# Futher assures that every active study (that does exist in the protocol builder)
# has a reference to every available workflow (though some may not have started yet)
for pb_study in pb_studies:
db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None)
if not db_study:
db_study = StudyModel(id=pb_study.STUDYID)
session.add(db_study)
db_studies.append(db_study)
db_study.update_from_protocol_builder(pb_study)
StudyService._add_all_workflow_specs_to_study(db_study)
# Mark studies as inactive that are no longer in Protocol Builder
for study in db_studies:
pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
if not pb_study:
study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
db.session.commit()
@staticmethod
def __update_status_of_workflow_meta(workflow_metas, status):
@ -275,8 +298,8 @@ class StudyService(object):
return WorkflowProcessor.run_master_spec(master_specs[0], study_model)
@staticmethod
def _add_all_workflow_specs_to_study(study):
existing_models = session.query(WorkflowModel).filter(WorkflowModel.study_id == study.id).all()
def _add_all_workflow_specs_to_study(study_model:StudyModel):
existing_models = session.query(WorkflowModel).filter(WorkflowModel.study == study_model).all()
existing_specs = list(m.workflow_spec_id for m in existing_models)
new_specs = session.query(WorkflowSpecModel). \
filter(WorkflowSpecModel.is_master_spec == False). \
@ -285,15 +308,15 @@ class StudyService(object):
errors = []
for workflow_spec in new_specs:
try:
StudyService._create_workflow_model(study, workflow_spec)
StudyService._create_workflow_model(study_model, workflow_spec)
except WorkflowException as we:
errors.append(ApiError.from_task_spec("workflow_execution_exception", str(we), we.sender))
return errors
@staticmethod
def _create_workflow_model(study, spec):
def _create_workflow_model(study: StudyModel, spec):
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
study_id=study.id,
study=study,
workflow_spec_id=spec.id,
last_updated=datetime.now())
session.add(workflow_model)

276
crc/services/workflow_processor.py
View File

@ -1,8 +1,7 @@
import random
import re
import string
import xml.etree.ElementTree as ElementTree
from datetime import datetime
from typing import List
from SpiffWorkflow import Task as SpiffTask, WorkflowException
from SpiffWorkflow.bpmn.BpmnScriptEngine import BpmnScriptEngine
@ -13,14 +12,15 @@ from SpiffWorkflow.bpmn.workflow import BpmnWorkflow
from SpiffWorkflow.camunda.parser.CamundaParser import CamundaParser
from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from SpiffWorkflow.operators import Operator
from SpiffWorkflow.specs import WorkflowSpec
from sqlalchemy import desc
from crc import session
from crc.api.common import ApiError
from crc.models.file import FileDataModel, FileModel, FileType
from crc.models.workflow import WorkflowStatus, WorkflowModel
from crc.models.workflow import WorkflowStatus, WorkflowModel, WorkflowSpecDependencyFile
from crc.scripts.script import Script
from crc.services.file_service import FileService
class CustomBpmnScriptEngine(BpmnScriptEngine):
@ -48,6 +48,11 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
mod = __import__(module_name, fromlist=[class_name])
klass = getattr(mod, class_name)
study_id = task.workflow.data[WorkflowProcessor.STUDY_ID_KEY]
if WorkflowProcessor.WORKFLOW_ID_KEY in task.workflow.data:
workflow_id = task.workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY]
else:
workflow_id = None
if not isinstance(klass(), Script):
raise ApiError.from_task("invalid_script",
"This is an internal error. The script '%s:%s' you called " %
@ -57,14 +62,22 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
if task.workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY]:
"""If this is running a validation, and not a normal process, then we want to
mimic running the script, but not make any external calls or database changes."""
klass().do_task_validate_only(task, study_id, *commands[1:])
klass().do_task_validate_only(task, study_id, workflow_id, *commands[1:])
else:
klass().do_task(task, study_id, *commands[1:])
klass().do_task(task, study_id, workflow_id, *commands[1:])
except ModuleNotFoundError:
raise ApiError.from_task("invalid_script",
"Unable to locate Script: '%s:%s'" % (module_name, class_name),
task=task)
def evaluate_expression(self, task, expression):
"""
Evaluate the given expression, within the context of the given task and
return the result.
"""
exp, valid = self.validateExpression(expression)
return self._eval(exp, **task.data)
@staticmethod
def camel_to_snake(camel):
camel = camel.strip()
@ -87,7 +100,7 @@ class WorkflowProcessor(object):
STUDY_ID_KEY = "study_id"
VALIDATION_PROCESS_KEY = "validate_only"
def __init__(self, workflow_model: WorkflowModel, soft_reset=False, hard_reset=False):
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
@ -95,18 +108,22 @@ class WorkflowProcessor(object):
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
orig_version = workflow_model.spec_version
if soft_reset or workflow_model.spec_version is None:
self.workflow_model.spec_version = WorkflowProcessor.get_latest_version_string(
workflow_model.workflow_spec_id)
spec = self.get_spec(workflow_model.workflow_spec_id, workflow_model.spec_version)
if soft_reset or len(workflow_model.dependencies) == 0:
self.spec_data_files = FileService.get_spec_data_files(
workflow_spec_id=workflow_model.workflow_spec_id)
else:
self.spec_data_files = FileService.get_spec_data_files(
workflow_spec_id=workflow_model.workflow_spec_id,
workflow_id=workflow_model.id)
spec = self.get_spec(self.spec_data_files, workflow_model.workflow_spec_id)
self.workflow_spec_id = workflow_model.workflow_spec_id
try:
self.bpmn_workflow = self.__get_bpmn_workflow(workflow_model, spec)
self.bpmn_workflow = self.__get_bpmn_workflow(workflow_model, spec, validate_only)
self.bpmn_workflow.script_engine = self._script_engine
if not self.WORKFLOW_ID_KEY in self.bpmn_workflow.data:
if self.WORKFLOW_ID_KEY not in self.bpmn_workflow.data:
if not workflow_model.id:
session.add(workflow_model)
session.commit()
@ -119,71 +136,63 @@ class WorkflowProcessor(object):
self.save()
except KeyError as ke:
if soft_reset:
# Undo the soft-reset.
workflow_model.spec_version = orig_version
raise ApiError(code="unexpected_workflow_structure",
message="Failed to deserialize workflow"
" '%s' version %s, due to a mis-placed or missing task '%s'" %
(self.workflow_spec_id, workflow_model.spec_version, str(ke)) +
" This is very likely due to a soft reset where there was a structural change.")
(self.workflow_spec_id, self.get_version_string(), str(ke)) +
" This is very likely due to a soft reset where there was a structural change.")
if hard_reset:
# Now that the spec is loaded, get the data and rebuild the bpmn with the new details
workflow_model.spec_version = self.hard_reset()
self.hard_reset()
workflow_model.bpmn_workflow_json = WorkflowProcessor._serializer.serialize_workflow(self.bpmn_workflow)
self.save()
if soft_reset:
self.save()
def __get_bpmn_workflow(self, workflow_model: WorkflowModel, spec: WorkflowSpec):
# set whether this is the latest spec file.
if self.spec_data_files == FileService.get_spec_data_files(workflow_spec_id=workflow_model.workflow_spec_id):
self.is_latest_spec = True
else:
self.is_latest_spec = False
def __get_bpmn_workflow(self, workflow_model: WorkflowModel, spec: WorkflowSpec, validate_only=False):
if workflow_model.bpmn_workflow_json:
bpmn_workflow = self._serializer.deserialize_workflow(workflow_model.bpmn_workflow_json, workflow_spec=spec)
else:
bpmn_workflow = BpmnWorkflow(spec, script_engine=self._script_engine)
bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = workflow_model.study_id
bpmn_workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY] = False
bpmn_workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY] = validate_only
bpmn_workflow.do_engine_steps()
return bpmn_workflow
def save(self):
"""Saves the current state of this processor to the database """
workflow_model = self.workflow_model
workflow_model.bpmn_workflow_json = self.serialize()
self.workflow_model.bpmn_workflow_json = self.serialize()
complete_states = [SpiffTask.CANCELLED, SpiffTask.COMPLETED]
tasks = list(self.get_all_user_tasks())
workflow_model.status = self.get_status()
workflow_model.total_tasks = len(tasks)
workflow_model.completed_tasks = sum(1 for t in tasks if t.state in complete_states)
workflow_model.last_updated = datetime.now()
session.add(workflow_model)
self.workflow_model.status = self.get_status()
self.workflow_model.total_tasks = len(tasks)
self.workflow_model.completed_tasks = sum(1 for t in tasks if t.state in complete_states)
self.workflow_model.last_updated = datetime.now()
self.update_dependencies(self.spec_data_files)
session.add(self.workflow_model)
session.commit()
@staticmethod
def run_master_spec(spec_model, study):
"""Executes a BPMN specification for the given study, without recording any information to the database
Useful for running the master specification, which should not persist. """
version = WorkflowProcessor.get_latest_version_string(spec_model.id)
spec = WorkflowProcessor.get_spec(spec_model.id, version)
try:
bpmn_workflow = BpmnWorkflow(spec, script_engine=WorkflowProcessor._script_engine)
bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = study.id
bpmn_workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY] = False
bpmn_workflow.do_engine_steps()
except WorkflowException as we:
raise ApiError.from_task_spec("error_running_master_spec", str(we), we.sender)
if not bpmn_workflow.is_completed():
raise ApiError("master_spec_not_automatic",
"The master spec should only contain fully automated tasks, it failed to complete.")
return bpmn_workflow.last_task.data
def get_version_string(self):
# this could potentially become expensive to load all the data in the data models.
# in which case we might consider using a deferred loader for the actual data, but
# trying not to pre-optimize.
file_data_models = FileService.get_spec_data_files(self.workflow_model.workflow_spec_id,
self.workflow_model.id)
return WorkflowProcessor.__get_version_string_for_data_models(file_data_models)
@staticmethod
def get_parser():
parser = MyCustomParser()
return parser
def get_latest_version_string_for_spec(spec_id):
file_data_models = FileService.get_spec_data_files(spec_id)
return WorkflowProcessor.__get_version_string_for_data_models(file_data_models)
@staticmethod
def get_latest_version_string(workflow_spec_id):
def __get_version_string_for_data_models(file_data_models):
"""Version is in the format v[VERSION] (FILE_ID_LIST)
For example, a single bpmn file with only one version would be
v1 (12) Where 12 is the id of the file data model that is used to create the
@ -192,10 +201,6 @@ class WorkflowProcessor(object):
a Spec that includes a BPMN, DMN, an a Word file all on the first
version would be v1.1.1 (12.45.21)"""
# this could potentially become expensive to load all the data in the data models.
# in which case we might consider using a deferred loader for the actual data, but
# trying not to pre-optimize.
file_data_models = WorkflowProcessor.__get_latest_file_models(workflow_spec_id)
major_version = 0 # The version of the primary file.
minor_version = [] # The versions of the minor files if any.
file_ids = []
@ -211,103 +216,78 @@ class WorkflowProcessor(object):
full_version = "v%s (%s)" % (version, files)
return full_version
@staticmethod
def get_file_models_for_version(workflow_spec_id, version):
file_id_strings = re.findall('\((.*)\)', version)[0].split(".")
file_ids = [int(i) for i in file_id_strings]
files = session.query(FileDataModel)\
.join(FileModel) \
.filter(FileModel.workflow_spec_id == workflow_spec_id)\
.filter(FileDataModel.id.in_(file_ids)).all()
if len(files) != len(file_ids):
raise ApiError("invalid_version",
"The version '%s' of workflow specification '%s' is invalid. " %
(version, workflow_spec_id) +
" Unable to locate the correct files to recreate it.")
return files
def update_dependencies(self, spec_data_files):
existing_dependencies = FileService.get_spec_data_files(
workflow_spec_id=self.workflow_model.workflow_spec_id,
workflow_id=self.workflow_model.id)
# Don't save the dependencies if they haven't changed.
if existing_dependencies == spec_data_files:
return
# Remove all existing dependencies, and replace them.
self.workflow_model.dependencies = []
for file_data in spec_data_files:
self.workflow_model.dependencies.append(WorkflowSpecDependencyFile(file_data_id=file_data.id))
@staticmethod
def __get_latest_file_models(workflow_spec_id):
"""Returns all the latest files related to a workflow specification"""
return session.query(FileDataModel) \
.join(FileModel) \
.filter(FileModel.workflow_spec_id == workflow_spec_id)\
.filter(FileDataModel.version == FileModel.latest_version)\
.order_by(FileModel.id)\
.all()
def run_master_spec(spec_model, study):
"""Executes a BPMN specification for the given study, without recording any information to the database
Useful for running the master specification, which should not persist. """
spec_data_files = FileService.get_spec_data_files(spec_model.id)
spec = WorkflowProcessor.get_spec(spec_data_files, spec_model.id)
try:
bpmn_workflow = BpmnWorkflow(spec, script_engine=WorkflowProcessor._script_engine)
bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = study.id
bpmn_workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY] = False
bpmn_workflow.do_engine_steps()
except WorkflowException as we:
raise ApiError.from_task_spec("error_running_master_spec", str(we), we.sender)
if not bpmn_workflow.is_completed():
raise ApiError("master_spec_not_automatic",
"The master spec should only contain fully automated tasks, it failed to complete.")
return bpmn_workflow.last_task.data
@staticmethod
def get_spec(workflow_spec_id, version=None):
"""Returns the requested version of the specification,
or the latest version if none is specified."""
def get_parser():
parser = MyCustomParser()
return parser
@staticmethod
def get_spec(file_data_models: List[FileDataModel], workflow_spec_id):
"""Returns a SpiffWorkflow specification for the given workflow spec,
using the files provided. The Workflow_spec_id is only used to generate
better error messages."""
parser = WorkflowProcessor.get_parser()
process_id = None
if version is None:
file_data_models = WorkflowProcessor.__get_latest_file_models(workflow_spec_id)
else:
file_data_models = WorkflowProcessor.get_file_models_for_version(workflow_spec_id, version)
for file_data in file_data_models:
if file_data.file_model.type == FileType.bpmn:
bpmn: ElementTree.Element = ElementTree.fromstring(file_data.data)
if file_data.file_model.primary:
process_id = WorkflowProcessor.get_process_id(bpmn)
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)
parser.add_dmn_xml(dmn, filename=file_data.file_model.name)
if process_id is None:
raise(ApiError(code="no_primary_bpmn_error",
message="There is no primary BPMN model defined for workflow %s" % workflow_spec_id))
raise (ApiError(code="no_primary_bpmn_error",
message="There is no primary BPMN model defined for workflow %s" % workflow_spec_id))
try:
spec = parser.get_spec(process_id)
except ValidationException as ve:
raise ApiError(code="workflow_validation_error",
message="Failed to parse Workflow Specification '%s' %s." % (workflow_spec_id, version) +
message="Failed to parse Workflow Specification '%s'" % workflow_spec_id +
"Error is %s" % str(ve),
file_name=ve.filename,
task_id=ve.id,
tag=ve.tag)
return spec
@staticmethod
def populate_form_with_random_data(task, task_api):
"""populates a task with random data - useful for testing a spec."""
if not hasattr(task.task_spec, 'form'): return
form_data = {}
for field in task_api.form.fields:
if field.type == "enum":
if len(field.options) > 0:
form_data[field.id] = random.choice(field.options)
else:
raise ApiError.from_task("invalid_enum", "You specified an enumeration field (%s),"
" with no options" % field.id,
task)
elif field.type == "long":
form_data[field.id] = random.randint(1, 1000)
elif field.type == 'boolean':
form_data[field.id] = random.choice([True, False])
elif field.type == 'file':
form_data[field.id] = random.randint(1, 100)
elif field.type == 'files':
form_data[field.id] = random.randrange(1, 100)
else:
form_data[field.id] = WorkflowProcessor._random_string()
if task.data is None:
task.data = {}
task.data.update(form_data)
@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 status_of(bpmn_workflow):
if bpmn_workflow.is_completed():
@ -325,8 +305,8 @@ class WorkflowProcessor(object):
Returns the new version.
"""
version = WorkflowProcessor.get_latest_version_string(self.workflow_spec_id)
spec = WorkflowProcessor.get_spec(self.workflow_spec_id) # Force latest version by NOT specifying version
self.spec_data_files = FileService.get_spec_data_files(workflow_spec_id=self.workflow_spec_id)
spec = WorkflowProcessor.get_spec(self.spec_data_files, self.workflow_spec_id)
# spec = WorkflowProcessor.get_spec(self.workflow_spec_id, version)
bpmn_workflow = BpmnWorkflow(spec, script_engine=self._script_engine)
bpmn_workflow.data = self.bpmn_workflow.data
@ -334,14 +314,10 @@ class WorkflowProcessor(object):
task.data = self.bpmn_workflow.last_task.data
bpmn_workflow.do_engine_steps()
self.bpmn_workflow = bpmn_workflow
return version
def get_status(self):
return self.status_of(self.bpmn_workflow)
def get_spec_version(self):
return self.workflow_model.spec_version
def do_engine_steps(self):
try:
self.bpmn_workflow.do_engine_steps()
@ -422,32 +398,18 @@ class WorkflowProcessor(object):
return [t for t in all_tasks
if not self.bpmn_workflow._is_engine_task(t.task_spec) and t.state in [t.COMPLETED, t.CANCELLED]]
@staticmethod
def get_process_id(et_root: ElementTree.Element):
process_elements = []
for child in et_root:
if child.tag.endswith('process') and child.attrib.get('isExecutable', False):
process_elements.append(child)
if len(process_elements) == 0:
raise ValidationException('No executable process tag found')
# There are multiple root elements
if len(process_elements) > 1:
# Look for the element that has the startEvent in it
for e in process_elements:
this_element: ElementTree.Element = e
for child_element in list(this_element):
if child_element.tag.endswith('startEvent'):
return this_element.attrib['id']
raise ValidationException('No start event found in %s' % et_root.attrib['id'])
return process_elements[0].attrib['id']
def get_nav_item(self, task):
for nav_item in self.bpmn_workflow.get_nav_list():
if nav_item['task_id'] == task.id:
return nav_item
def find_task_and_field_by_field_id(self, field_id):
"""Tracks down a form field by name in the workflow spec,
only looks at ready tasks. Returns a tuple of the task, and form"""
for spiff_task in self.bpmn_workflow.get_tasks():
if hasattr(spiff_task.task_spec, "form"):
for field in spiff_task.task_spec.form.fields:
if field.id == field_id:
return spiff_task, field
raise ApiError("invalid_field",
"Unable to find a task in the workflow with a lookup field called: %s" % field_id)

135
crc/services/workflow_service.py
View File

@ -1,4 +1,6 @@
import string
from datetime import datetime
import random
import jinja2
from SpiffWorkflow import Task as SpiffTask, WorkflowException
@ -15,9 +17,14 @@ from crc import db, app
from crc.api.common import ApiError
from crc.models.api_models import Task, MultiInstanceType
from crc.models.file import LookupDataModel
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel
from crc.models.user import UserModel
from crc.models.workflow import WorkflowModel, WorkflowStatus
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
@ -34,30 +41,127 @@ class WorkflowService(object):
But for now, this contains tools for converting spiff-workflow models into our
own API models with additional information and capabilities."""
@classmethod
def test_spec(cls, spec_id):
@staticmethod
def make_test_workflow(spec_id):
user = db.session.query(UserModel).filter_by(uid="test").first()
if not user:
db.session.add(UserModel(uid="test"))
study = db.session.query(StudyModel).filter_by(user_uid="test").first()
if not study:
db.session.add(StudyModel(user_uid="test", title="test"))
db.session.commit()
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
workflow_spec_id=spec_id,
last_updated=datetime.now(),
study=study)
return workflow_model
@staticmethod
def delete_test_data():
for study in db.session.query(StudyModel).filter(StudyModel.user_uid=="test"):
StudyService.delete_study(study.id)
db.session.commit()
db.session.query(UserModel).filter_by(uid="test").delete()
@staticmethod
def test_spec(spec_id):
"""Runs a spec through it's paces to see if it results in any errors. Not fool-proof, but a good
sanity check."""
version = WorkflowProcessor.get_latest_version_string(spec_id)
spec = WorkflowProcessor.get_spec(spec_id, version)
bpmn_workflow = BpmnWorkflow(spec, script_engine=CustomBpmnScriptEngine())
bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY] = 1
bpmn_workflow.data[WorkflowProcessor.WORKFLOW_ID_KEY] = spec_id
bpmn_workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY] = True
while not bpmn_workflow.is_completed():
workflow_model = WorkflowService.make_test_workflow(spec_id)
try:
processor = WorkflowProcessor(workflow_model, validate_only=True)
except WorkflowException as we:
WorkflowService.delete_test_data()
raise ApiError.from_task_spec("workflow_execution_exception", str(we),
we.sender)
while not processor.bpmn_workflow.is_completed():
try:
bpmn_workflow.do_engine_steps()
tasks = bpmn_workflow.get_tasks(SpiffTask.READY)
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) # Assure we try to process the documenation, and raise those errors.
WorkflowProcessor.populate_form_with_random_data(task, task_api)
WorkflowService.populate_form_with_random_data(task, task_api)
task.complete()
except WorkflowException as we:
WorkflowService.delete_test_data()
raise ApiError.from_task_spec("workflow_execution_exception", str(we),
we.sender)
WorkflowService.delete_test_data()
@staticmethod
def populate_form_with_random_data(task, task_api):
"""populates a task with random data - useful for testing a spec."""
if not hasattr(task.task_spec, 'form'): return
form_data = {}
for field in task_api.form.fields:
if field.type == "enum":
if len(field.options) > 0:
random_choice = random.choice(field.options)
if isinstance(random_choice, dict):
form_data[field.id] = random.choice(field.options)['id']
else:
# fixme: why it is sometimes an EnumFormFieldOption, and other times not?
form_data[field.id] = random_choice.id ## Assume it is an EnumFormFieldOption
else:
raise ApiError.from_task("invalid_enum", "You specified an enumeration field (%s),"
" with no options" % field.id,
task)
elif field.type == "autocomplete":
lookup_model = LookupService.get_lookup_model(task, field)
if field.has_property(Task.PROP_LDAP_LOOKUP):
form_data[field.id] = {
"label": "dhf8r",
"value": "Dan Funk",
"data": {
"uid": "dhf8r",
"display_name": "Dan Funk",
"given_name": "Dan",
"email_address": "dhf8r@virginia.edu",
"department": "Depertment of Psychocosmographictology",
"affiliation": "Rousabout",
"sponsor_type": "Staff"
}
}
elif lookup_model:
data = db.session.query(LookupDataModel).filter(
LookupDataModel.lookup_file_model == lookup_model).limit(10).all()
options = []
for d in data:
options.append({"id": d.value, "name": d.label})
form_data[field.id] = random.choice(options)
else:
raise ApiError.from_task("invalid_autocomplete", "The settings for this auto complete field "
"are incorrect: %s " % field.id, task)
elif field.type == "long":
form_data[field.id] = random.randint(1, 1000)
elif field.type == 'boolean':
form_data[field.id] = random.choice([True, False])
elif field.type == 'file':
form_data[field.id] = random.randint(1, 100)
elif field.type == 'files':
form_data[field.id] = random.randrange(1, 100)
else:
form_data[field.id] = WorkflowService._random_string()
if task.data is None:
task.data = {}
task.data.update(form_data)
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 spiff_task_to_api_task(spiff_task, add_docs_and_forms=False):
@ -176,12 +280,12 @@ class WorkflowService(object):
@staticmethod
def process_options(spiff_task, field):
lookup_model = LookupService.get_lookup_table(spiff_task, field)
# If this is an auto-complete field, do not populate options, a lookup will happen later.
if field.type == Task.FIELD_TYPE_AUTO_COMPLETE:
pass
else:
elif field.has_property(Task.PROP_OPTIONS_FILE):
lookup_model = LookupService.get_lookup_model(spiff_task, field)
data = db.session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_model).all()
if not hasattr(field, 'options'):
field.options = []
@ -197,7 +301,7 @@ class WorkflowService(object):
user_uid=g.user.uid,
workflow_id=workflow_model.id,
workflow_spec_id=workflow_model.workflow_spec_id,
spec_version=workflow_model.spec_version,
spec_version=processor.get_version_string(),
action=action,
task_id=task.id,
task_name=task.name,
@ -212,3 +316,4 @@ class WorkflowService(object):
)
db.session.add(task_event)
db.session.commit()

105
crc/static/bpmn/core_info/core_info.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_0be39yr" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<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:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_0be39yr" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_1cme33c" isExecutable="false">
<bpmn:parallelGateway id="ParallelGateway_0ecwf3g">
<bpmn:incoming>Flow_1wqp7vf</bpmn:incoming>
@ -36,10 +36,9 @@
</camunda:formField>
<camunda:formField id="ProtocolOwnerName" label="Protocol Owner Name" type="autocomplete">
<camunda:properties>
<camunda:property id="enum.options.file" value="SponsorList.xls" />
<camunda:property id="enum.options.value.column" value="CUSTOMER_NUMBER" />
<camunda:property id="enum.options.label.column" value="CUSTOMER_NAME" />
<camunda:property id="enum.options.lookup" value="True" />
<camunda:property id="spreadsheet.name" value="SponsorList.xls" />
<camunda:property id="spreadsheet.value.column" value="CUSTOMER_NUMBER" />
<camunda:property id="spreadsheet.label.column" value="CUSTOMER_NAME" />
<camunda:property id="help" value="#### How To:\nYou can find the name by typing any part (at least 3 characters) of the name.\n\nNote: This source of this list is in the Integration System (Oracle) and the information is owned by and managed by the OSP team.\n\nIf you are not finding the name or need to make any changes.\n1. Email &#39;Information Team listserve&#39; osp-infoteam@virginia.edu with the Subject Line &#34;Requesting New Sponsor Setup&#34; and provide the following information:\n - Sponsor Legal Name, Address, Sponsor Classification (Federal Government, Foreign Entity, Foundation, Industry, Local Government, Other Colleges &#38; Universities or State Government) as stated in the agreement/notification.\n - Copies of the agreement from the sponsor (contract, award letter, email, etc.).\n2. Once all the required information is received, OSP will add the name to the list.\n3. The updated list should be available for your selection in the workflow within 2 business days." />
<camunda:property id="description" value="The protocol owner name is always an entity. For example, if this is a UVA Primary Investigator - Investigator initiated study, the Protocol Owner Name will be &#34;University of Virginia&#34;" />
</camunda:properties>
@ -235,104 +234,104 @@
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1cme33c">
<bpmndi:BPMNEdge id="Flow_1wqp7vf_di" bpmnElement="Flow_1wqp7vf">
<di:waypoint x="450" y="325" />
<di:waypoint x="495" y="325" />
<di:waypoint x="820" y="325" />
<di:waypoint x="865" y="325" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1tfyk5m_di" bpmnElement="Flow_1tfyk5m">
<di:waypoint x="300" y="325" />
<di:waypoint x="350" y="325" />
<di:waypoint x="670" y="325" />
<di:waypoint x="720" y="325" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1d4dncx_di" bpmnElement="Flow_1d4dncx">
<di:waypoint x="520" y="300" />
<di:waypoint x="520" y="250" />
<di:waypoint x="620" y="250" />
<di:waypoint x="890" y="300" />
<di:waypoint x="890" y="250" />
<di:waypoint x="990" y="250" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_16v64sg_di" bpmnElement="Flow_16v64sg">
<di:waypoint x="140" y="325" />
<di:waypoint x="200" y="325" />
<di:waypoint x="510" y="325" />
<di:waypoint x="570" y="325" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_09h1imz_di" bpmnElement="Flow_09h1imz">
<di:waypoint x="-20" y="325" />
<di:waypoint x="40" y="325" />
<di:waypoint x="350" y="325" />
<di:waypoint x="410" y="325" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1v7oplk_di" bpmnElement="SequenceFlow_1v7oplk">
<di:waypoint x="845" y="325" />
<di:waypoint x="898" y="325" />
<di:waypoint x="1215" y="325" />
<di:waypoint x="1268" y="325" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0rw17h2_di" bpmnElement="SequenceFlow_0rw17h2">
<di:waypoint x="720" y="500" />
<di:waypoint x="820" y="500" />
<di:waypoint x="820" y="350" />
<di:waypoint x="1090" y="500" />
<di:waypoint x="1190" y="500" />
<di:waypoint x="1190" y="350" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0gsy7mo_di" bpmnElement="SequenceFlow_0gsy7mo">
<di:waypoint x="720" y="380" />
<di:waypoint x="820" y="380" />
<di:waypoint x="820" y="350" />
<di:waypoint x="1090" y="380" />
<di:waypoint x="1190" y="380" />
<di:waypoint x="1190" y="350" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1o39rt4_di" bpmnElement="SequenceFlow_1o39rt4">
<di:waypoint x="720" y="250" />
<di:waypoint x="820" y="250" />
<di:waypoint x="820" y="300" />
<di:waypoint x="1090" y="250" />
<di:waypoint x="1190" y="250" />
<di:waypoint x="1190" y="300" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_02nbqkn_di" bpmnElement="SequenceFlow_02nbqkn">
<di:waypoint x="720" y="130" />
<di:waypoint x="820" y="130" />
<di:waypoint x="820" y="300" />
<di:waypoint x="1090" y="130" />
<di:waypoint x="1190" y="130" />
<di:waypoint x="1190" y="300" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0xj8i4c_di" bpmnElement="SequenceFlow_0xj8i4c">
<di:waypoint x="520" y="350" />
<di:waypoint x="520" y="500" />
<di:waypoint x="620" y="500" />
<di:waypoint x="890" y="350" />
<di:waypoint x="890" y="500" />
<di:waypoint x="990" y="500" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1idbomg_di" bpmnElement="SequenceFlow_1idbomg">
<di:waypoint x="520" y="350" />
<di:waypoint x="520" y="380" />
<di:waypoint x="620" y="380" />
<di:waypoint x="890" y="350" />
<di:waypoint x="890" y="380" />
<di:waypoint x="990" y="380" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0f61fxp_di" bpmnElement="SequenceFlow_0f61fxp">
<di:waypoint x="520" y="300" />
<di:waypoint x="520" y="130" />
<di:waypoint x="620" y="130" />
<di:waypoint x="890" y="300" />
<di:waypoint x="890" y="130" />
<di:waypoint x="990" y="130" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1r3yrhy_di" bpmnElement="SequenceFlow_1r3yrhy">
<di:waypoint x="-182" y="325" />
<di:waypoint x="-120" y="325" />
<di:waypoint x="188" y="325" />
<di:waypoint x="250" y="325" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="ParallelGateway_0ecwf3g_di" bpmnElement="ParallelGateway_0ecwf3g">
<dc:Bounds x="495" y="300" width="50" height="50" />
<dc:Bounds x="865" y="300" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ParallelGateway_01234ff_di" bpmnElement="ParallelGateway_01234ff">
<dc:Bounds x="795" y="300" width="50" height="50" />
<dc:Bounds x="1165" y="300" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_16uwhzg_di" bpmnElement="EndEvent_16uwhzg">
<dc:Bounds x="898" y="307" width="36" height="36" />
<dc:Bounds x="1268" y="307" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="StartEvent_1mhzkcr_di" bpmnElement="StartEvent_1mhzkcr">
<dc:Bounds x="-218" y="307" width="36" height="36" />
<dc:Bounds x="152" y="307" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_1y1qon7_di" bpmnElement="UserTask_1y1qon7">
<dc:Bounds x="620" y="340" width="100" height="80" />
<dc:Bounds x="990" y="340" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_01zzzg9_di" bpmnElement="UserTask_01zzzg9">
<dc:Bounds x="620" y="460" width="100" height="80" />
<dc:Bounds x="990" y="460" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_0gtuk1e_di" bpmnElement="UserTask_EnterMultiSiteInfo">
<dc:Bounds x="620" y="210" width="100" height="80" />
<dc:Bounds x="990" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_0ebxkp7_di" bpmnElement="UserTask_0ebxkp7">
<dc:Bounds x="620" y="90" width="100" height="80" />
<dc:Bounds x="990" y="90" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0vthni9_di" bpmnElement="Activity_10nxpt2">
<dc:Bounds x="-120" y="285" width="100" height="80" />
<dc:Bounds x="250" y="285" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0spxv8q_di" bpmnElement="Activity_PBMultiSiteCheckQ12">
<dc:Bounds x="40" y="285" width="100" height="80" />
<dc:Bounds x="410" y="285" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0ah6heg_di" bpmnElement="Activity_PBMultiSiteCheckQ14">
<dc:Bounds x="200" y="285" width="100" height="80" />
<dc:Bounds x="570" y="285" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0x7b58m_di" bpmnElement="Activity_PBMultiSiteCheckQ28">
<dc:Bounds x="350" y="285" width="100" height="80" />
<dc:Bounds x="720" y="285" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
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<?xml version="1.0" encoding="UTF-8"?>
<definitions xmlns="http://www.omg.org/spec/DMN/20151101/dmn.xsd" id="Definitions_0crc2o7" name="DRD" namespace="http://camunda.org/schema/1.0/dmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<decision id="Decision_ApprovalInfo" name="Approval Info">
<decisionTable id="decisionTable_1">
<input id="input_1" label="School">
<inputExpression id="inputExpression_1" typeRef="string">
<text>PISchool</text>
</inputExpression>
</input>
<output id="OutputClause_1138fqx" label="School" name="ApprvlSchool" typeRef="string" />
<output id="output_1" label="Approver 1" name="ApprvlApprvr1" typeRef="string" />
<output id="OutputClause_0d10p7n" label="Approver 1 Name" name="ApprvlApprvrName1" typeRef="string" />
<output id="OutputClause_0dcb1cr" label="Approver 1 Role" name="ApprvlApprovrRole1" typeRef="string" />
<output id="OutputClause_0mftsw9" label="Approver 2" name="ApprvlApprvr2" typeRef="string" />
<output id="OutputClause_0orlpz9" label="Approver 2 Name" name="ApprvlApprvrName2" typeRef="string" />
<output id="OutputClause_0iuw224" label="Approver 2 Role" name="ApprvlApprvrRole2" typeRef="string" />
<rule id="DecisionRule_1wge2nn">
<inputEntry id="UnaryTests_0mfg1fu">
<text>"Architecture"</text>
</inputEntry>
<outputEntry id="LiteralExpression_074qb28">
<text>"Architecture"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0vb9mia">
<text>PISupervisor.data.uid</text>
</outputEntry>
<outputEntry id="LiteralExpression_00k4by2">
<text>PISupervisor.data.display_name</text>
</outputEntry>
<outputEntry id="LiteralExpression_1pqm0u2">
<text>"Supervisor"</text>
</outputEntry>
<outputEntry id="LiteralExpression_17oc2op">
<text>"agc9a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1b0mjy0">
<text>"Anselmo Canfora"</text>
</outputEntry>
<outputEntry id="LiteralExpression_08dc6cz">
<text>"Associate Research Dean"</text>
</outputEntry>
</rule>
<rule id="DecisionRule_1u9orsf">
<inputEntry id="UnaryTests_08ormp3">
<text>"Arts &amp; Sciences"</text>
</inputEntry>
<outputEntry id="LiteralExpression_0ua8d03">
<text>"Arts &amp; Sciences"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1ejs3h2">
<text>PISupervisor.data.uid</text>
</outputEntry>
<outputEntry id="LiteralExpression_1v7dfzn">
<text>PISupervisor.data.display_name</text>
</outputEntry>
<outputEntry id="LiteralExpression_0h7eq4l">
<text>"Supervisor"</text>
</outputEntry>
<outputEntry id="LiteralExpression_06pynb2">
<text>"dh2t"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1b047rf">
<text>"David Hill"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0x965p2">
<text>"Associate Research Dean"</text>
</outputEntry>
</rule>
<rule id="DecisionRule_0k7lbs6">
<inputEntry id="UnaryTests_1tws5wb">
<text>"Commerce"</text>
</inputEntry>
<outputEntry id="LiteralExpression_0y7bv69">
<text>"Commerce"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0sz476a">
<text>"dcs8f"</text>
</outputEntry>
<outputEntry id="LiteralExpression_11bvybc">
<text>"David Smith"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0wbcswk">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0htwmws">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_0do7f3z">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0ntf026">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_0pcsd6s">
<inputEntry id="UnaryTests_07uijrb">
<text>"Darden"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1he7hp6">
<text>"Darden"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0hdskgi">
<text>"mw4m"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1urv25e">
<text>"Maureen Wellen"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1uxxdv0">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0q81xjf">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_0qypltu">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1rp7s1w">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_0qlavkb">
<inputEntry id="UnaryTests_1775ht5">
<text>"Data Science"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1fxauop">
<text>"Data Science"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0w0ksry">
<text>"cws3v"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1mnndve">
<text>"Claudia Scholz"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0847zci">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1xjonk2">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_0g81mjb">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1rb6200">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_0vw6027">
<inputEntry id="UnaryTests_1hsal1b">
<text>"Education"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1uwd4hj">
<text>"Education"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1t3c4oj">
<text>PISupervisor.data.uid</text>
</outputEntry>
<outputEntry id="LiteralExpression_045f3hz">
<text>PISupervisor.data.display_name</text>
</outputEntry>
<outputEntry id="LiteralExpression_0vkosy7">
<text>"Supervisor"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1sj3i3e">
<text>"cpb8g"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1f1zg5p">
<text>"Catherine Bradshaw"</text>
</outputEntry>
<outputEntry id="LiteralExpression_11ml53c">
<text>"Associate Research Dean"</text>
</outputEntry>
</rule>
<rule id="DecisionRule_1rgdbw3">
<inputEntry id="UnaryTests_022jcbh">
<text>"Engineering"</text>
</inputEntry>
<outputEntry id="LiteralExpression_0lzmt29">
<text>"Engineering"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0v4df1x">
<text>"sb5mc"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1biq8m6">
<text>"Susan Barker"</text>
</outputEntry>
<outputEntry id="LiteralExpression_16kmec1">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1bjsn8g">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_1ycmwd4">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1rm1jw7">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_1hy1sby">
<inputEntry id="UnaryTests_1u52cey">
<text>"Law"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1w3vu2k">
<text>"Law"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1nrqe2j">
<text>"kendrick"</text>
</outputEntry>
<outputEntry id="LiteralExpression_02ckxvj">
<text>"Leslie Kendrick"</text>
</outputEntry>
<outputEntry id="LiteralExpression_19n45lv">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0nppbew">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_08qy2v8">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0n1f5l1">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_1nmyhfi">
<inputEntry id="UnaryTests_0uqd08s">
<text>"Leadership &amp; Public Policy"</text>
</inputEntry>
<outputEntry id="LiteralExpression_0dy02ei">
<text>"Leadership &amp; Public Policy"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0rxrqkb">
<text>"jps3va"</text>
</outputEntry>
<outputEntry id="LiteralExpression_05wkbco">
<text>"Jay Shimshack"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0ejmi7q">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1ph2wlx">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_1q9esl3">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0i6fih4">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_17uxicj">
<inputEntry id="UnaryTests_0kttpy1">
<text>"Medicine"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1ops4nm">
<text>"Medicine"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1cwa3r0">
<text>PISupervisor.data.uid</text>
</outputEntry>
<outputEntry id="LiteralExpression_1y0r1vs">
<text>PISupervisor.data.display_name</text>
</outputEntry>
<outputEntry id="LiteralExpression_0ouvo17">
<text>"Supervisor"</text>
</outputEntry>
<outputEntry id="LiteralExpression_18rte97">
<text>"mas3x"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0j7fp1z">
<text>"Margaret Shupnik"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1rxh2p0">
<text>"Associate Research Dean"</text>
</outputEntry>
</rule>
<rule id="DecisionRule_1t4241f">
<inputEntry id="UnaryTests_0xwnrta">
<text>"Nursing"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1va63rh">
<text>"Nursing"</text>
</outputEntry>
<outputEntry id="LiteralExpression_125fuie">
<text>"jla7e"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1p94oot">
<text>"Jeanne Alhusen"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0h1e3bv">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0e8b9ui">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_0xky8fm">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1mq49yg">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_0jnp1wp">
<inputEntry id="UnaryTests_164zt99">
<text>"Continuing Education"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1h81xwr">
<text>"Continuing Education"</text>
</outputEntry>
<outputEntry id="LiteralExpression_12sudp0">
<text>"ado4v"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0j7x2td">
<text>"Angela  Orebaugh"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1jkrv7z">
<text>"Associate Research Dean"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0qelytu">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_1tffqsf">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_19tc8kf">
<text></text>
</outputEntry>
</rule>
<rule id="DecisionRule_1ynkili">
<inputEntry id="UnaryTests_1dupb6e">
<text>"Provost Office"</text>
</inputEntry>
<outputEntry id="LiteralExpression_1w13wuw">
<text>"Provost Office"</text>
</outputEntry>
<outputEntry id="LiteralExpression_13xizrn">
<text>"rammk"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0ixvqzn">
<text>"Melur Ramasubramanian"</text>
</outputEntry>
<outputEntry id="LiteralExpression_166hajt">
<text>"VP of Research"</text>
</outputEntry>
<outputEntry id="LiteralExpression_1xazzzn">
<text></text>
</outputEntry>
<outputEntry id="LiteralExpression_14uq3iz">
<text>"n/a"</text>
</outputEntry>
<outputEntry id="LiteralExpression_0zr3ar6">
<text></text>
</outputEntry>
</rule>
</decisionTable>
</decision>
</definitions>

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<?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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_1oogn9j" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:process id="Process_0ssahs9" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_05ja25w</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:manualTask id="ManualTask_Instructions" name="Read RRP Instructions">
<bpmn:documentation>## **Beta Stage: All data entered will be destroyed before public launch**
### UNIVERSITY OF VIRGINIA RESEARCH
[From Research Ramp-up Guidance](https://research.virginia.edu/research-ramp-guidance)
#### Support
Report problems and/or submit questions to: askresearch@virginia.edu
#### Research Guidance
Our general principle is that only research activities requiring on-Grounds presence would be conducted on-Grounds. All other research-related work would continue to be performed by telework until restrictions are lifted. Separate school, department and building specific plans should supplement these guidelines.
For research that needs to be on Grounds, the plan is to ramp up in phases with emphasis on safety. The goal of this document is to provide a central framework for resuming activities while allowing for coordinated school specific implementation strategies.
The success of the ramp up depends on each researcher placing the safety of themselves and the people around them first, while conducting their research. In order to reduce our risks as much as possible, this must be a partnership between the researchers and the administration.
Schools are developing a process for the approval of ramp up requests and enforcement of safety guidelines described in this document. The VPR office is working with the schools to provide the necessary support for business process infrastructure, and working with the COO’s office to coordinate the acquisition of supplies necessary including face coverings and sanitizing supplies.
**Instructions for Submitting:**
1. The Research Ramp-up Plan allows for one request to be entered for a single Principle Investigator. In the form that follows enter the Primary Investigator this request is for and other identifying information. The PI's School and Supervisor will be used as needed for approval routing.
2. Provide all available information in the forms that follow to provide an overview of where the research will resume, who will be involved, what supporting resources will be needed and what steps have been taken to assure compliance with [Research Ramp-up Guidance](https://research.virginia.edu/research-ramp-guidance).
3. After all forms have been completed, you will be presented with the option to create your Research Recovery Plan in Word format. Download the document and review it. If you see any corrections that need to be made, return to the corresponding form and make the correction.
4. Once the generated Research Recovery Plan is finalize, proceed to the Plan Submission step to submit your plan for approval.</bpmn:documentation>
<bpmn:incoming>SequenceFlow_05ja25w</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_0h50bp3</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:userTask id="Activity-PI_Info" name="Enter PI Info" camunda:formKey="PI Information">
<bpmn:documentation>#### Primary Investigator Information
Enter the following information for the PI submitting this request</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="PIComputingID" label="Primary Investigator" type="autocomplete">
<camunda:properties>
<camunda:property id="placeholder" value="wxy0z or Smith" />
<camunda:property id="ldap.lookup" value="true" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
<camunda:constraint name="description" config="Find the PI by entering Computing ID or Last Name." />
<camunda:constraint name="ldap.lookup" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="PISchool" label="PI&#39;s School" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="SchoolList.xls" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="School Name" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptArchitecture" label="PI&#39;s Primary Architecture Department" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="DepartmentList-Architecture.xlsx" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Label" />
<camunda:property id="hide_expression" value="(model.PISchool &#38;&#38; model.PISchool !== &#34;Architecture&#34;) || model.PISchool === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptArtsSciences" label="PI&#39;s Primary Arts &#38; Sciences Department" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="DepartmentList-ArtsSciences.xlsx" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Label" />
<camunda:property id="hide_expression" value="(model.PISchool &#38;&#38; model.PISchool !== &#34;Arts &#38; Sciences&#34;) || model.PISchool === null" />
<camunda:property id="description" value="Type key words to find department" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptEducation" label="PI&#39;s Primary Education Department" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="DepartmentList-Education.xlsx" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Label" />
<camunda:property id="hide_expression" value="(model.PISchool &#38;&#38; model.PISchool !== &#34;Education&#34;) || model.PISchool === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptEngineering" label="PI&#39;s Primary Engineering Department" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="DepartmentList-Engineering.xlsx" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Label" />
<camunda:property id="hide_expression" value="(model.PISchool &#38;&#38; model.PISchool !== &#34;Engineering&#34;) || model.PISchool === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptMedicine" label="PI&#39;s Primary Medicine Department/Center" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="DepartmentList-Medicine.xlsx" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Label" />
<camunda:property id="hide_expression" value="(model.PISchool &#38;&#38; model.PISchool !== &#34;Medicine&#34;) || model.PISchool === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptProvostOffice" label="PI&#39;s Primary Provost Office Department/Center" type="enum">
<camunda:properties>
<camunda:property id="spreadsheet.name" value="DepartmentList-ProvostOffice.xlsx" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Label" />
<camunda:property id="hide_expression" value="(model.PISchool &#38;&#38; model.PISchool !== &#34;Provost Office&#34;) || model.PISchool === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PIPrimaryDeptOther" label="Primary Department " type="string">
<camunda:properties>
<camunda:property id="hide_expression" value="(model.PIPrimaryDeptArchitecture === null &#38;&#38; model.PIPrimaryDeptArtsSciences === null &#38;&#38; model.PIPrimaryDeptEducation === null &#38;&#38; model.PIPrimaryDeptEngineering === null &#38;&#38; model.PIPrimaryDeptMedicine === null &#38;&#38; model.PIPrimaryDeptProvostOffice === null) || (model.PIPrimaryDeptArchitecture !== &#34;Other&#34; &#38;&#38; model.PIPrimaryDeptArtsSciences !== &#34;Other&#34; &#38;&#38; model.PIPrimaryDeptEducation !== &#34;Other&#34; &#38;&#38; model.PIPrimaryDeptEngineering !== &#34;Other&#34; &#38;&#38; model.PIPrimaryDeptMedicine !== &#34;Other&#34; &#38;&#38; model.PIPrimaryDeptProvostOffice !== &#34;Other&#34;)" />
<camunda:property id="description" value="Enter the PI&#39;s Primary Department " />
</camunda:properties>
</camunda:formField>
<camunda:formField id="PISupervisor" label="Pi&#39;s Supervisor" type="autocomplete">
<camunda:properties>
<camunda:property id="description" value="Find the PI&#39;s Supervisor by entering Computing I D or Last Name." />
<camunda:property id="ldap.lookup" value="true" />
<camunda:property id="placeholder" value="wxy0z or Smith" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="Required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_0h50bp3</bpmn:incoming>
<bpmn:outgoing>Flow_16y8glw</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="SequenceFlow_0h50bp3" sourceRef="ManualTask_Instructions" targetRef="Activity-PI_Info" />
<bpmn:sequenceFlow id="SequenceFlow_05ja25w" sourceRef="StartEvent_1" targetRef="ManualTask_Instructions" />
<bpmn:userTask id="Personnel" name="Enter Personnel" camunda:formKey="Personnel">
<bpmn:documentation>#### People for whom you are requesting access
Provide information on all researchers you are requesting approval for reentry into the previously entered lab/research and/or office space(s) for conducting research on-Grounds. (If there are personnel already working in the space, include them).
**Note: no undergraduates will be allowed to work on-Grounds during Phase I.**
#### Exclusive Space previously entered
{% for es in exclusive %}
{{ es.ExclusiveSpaceRoomID + " " + es.ExclusiveSpaceBuilding.label }}
{% else %}
No exclusive space entered
{% endfor %}
#### Shared Space previously entered
{% for ss in shared %}
{{ ss.SharedSpaceRoomID + " " + ss.SharedSpaceBuilding.label }}
{% else %}
No shared space entered
{% endfor %}</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="PersonnelComputingID" label="Computer ID" type="autocomplete">
<camunda:properties>
<camunda:property id="repeat" value="Personnel" />
<camunda:property id="ldap.lookup" value="true" />
<camunda:property id="description" value="Find by entering Computing ID or Last Name." />
<camunda:property id="placeholder" value="wxy0z or Smith" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="PersonnelType" label="Personnel Type" type="enum">
<camunda:properties>
<camunda:property id="repeat" value="Personnel" />
</camunda:properties>
<camunda:value id="Faculty" name="Faculty" />
<camunda:value id="AcademicResearcher" name="Academic Researcher" />
<camunda:value id="Staff" name="Staff" />
<camunda:value id="Postdoc" name="Postdoc" />
<camunda:value id="DoctoralStudent" name="Doctoral Student" />
<camunda:value id="UndeGraduate" name="Undergraduate" />
</camunda:formField>
<camunda:formField id="PersonnelSpace" label="Space they will work in" type="textarea">
<camunda:properties>
<camunda:property id="rows" value="2" />
<camunda:property id="autosize" value="true" />
<camunda:property id="description" value="Provide building and room number for each lab space this person will work in" />
<camunda:property id="repeat" value="Personnel" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="PersonnelJustification" label="Research Justification" type="textarea">
<camunda:properties>
<camunda:property id="description" value="Provide a brief description of this person’s research and justification why this is critical research." />
<camunda:property id="rows" value="3" />
<camunda:property id="autosize" value="true" />
<camunda:property id="repeat" value="Personnel" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="PersonnelWeeklySchedule" label="Personnel Weekly Schedule" type="files">
<camunda:properties>
<camunda:property id="description" value="Upload a file or files of proposed weekly schedules for all personnel which are representative of compliance with ramp-up guidance." />
</camunda:properties>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_1eiud85</bpmn:incoming>
<bpmn:outgoing>Flow_1nbjr72</bpmn:outgoing>
</bpmn:userTask>
<bpmn:userTask id="UserTask_CoreResource" name="Enter Core Resources" camunda:formKey="Core Resources">
<bpmn:documentation>#### If applicable, provide a list of any [Core Resources](https://research.virginia.edu/research-core-resources) you will utilize space or instruments in and name/email of contact person in the core you have coordinated your plan with. (Core facility managers are responsible for developing a plan for their space)</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="isCoreResourcesUse" label="Core Resources Use" type="boolean">
<camunda:properties>
<camunda:property id="description" value="Will you need access to core resources to resume research?" />
<camunda:property id="help" value="[From Research Ramp-up Guidance](https://research.virginia.edu/research-ramp-guidance)\n#### ADDITIONAL CONSIDERATIONS FOR A SUCCESSFUL RAMP-UP:\n##### Lab-based Research\n- (1) Core facilities operational\n\n[EHS Lab Ramp up Checklist for Laboratories](https://research.virginia.edu/sites/vpr/files/2020-05/EHS.LabRampUpChecklistForLaboratories_0_0.pdf)\n##### General\n- Note that shared facilities, such as stockrooms or core labs, may be on different ramp up schedules or in more demand than during normal operation." />
</camunda:properties>
</camunda:formField>
<camunda:formField id="CoreResources" label="Core Resources" type="textarea">
<camunda:properties>
<camunda:property id="rows" value="10" />
<camunda:property id="autosize" value="true" />
<camunda:property id="hide_expression" value="!model.isCoreResourcesUse | model.isCoreResourcesUse == null" />
</camunda:properties>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_15zy1q7</bpmn:incoming>
<bpmn:outgoing>Flow_12ie6w0</bpmn:outgoing>
</bpmn:userTask>
<bpmn:endEvent id="EndEvent_09wp7av">
<bpmn:documentation>#### End of Workflow
Place instruction here,</bpmn:documentation>
<bpmn:incoming>Flow_05w8yd6</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_1e2qi9s" sourceRef="Activity_AcknowledgePlanReview" targetRef="Activity_ApprovalInfo" />
<bpmn:manualTask id="Activity_AcknowledgePlanReview" name="Acknowledge Plan Review">
<bpmn:documentation>Your Research Ramp-up Plan has been generated and is available in the Files pop-out found in the upper right hand corner of this application Click on the file name link to download the MS Word file, open and review. If changes are needed, choose the appropriate menu choice to make your edits, clicking Save when done. Note that you will need to revisit subsequent steps so the application can check to see if your edits impacted future workflow decisions. All your data will be persevered and you will need to click the Save button on each step to proceed.
When your Research Ramp-up Plan is complete and ready to submit for review and approval, click the Continue button below.</bpmn:documentation>
<bpmn:incoming>Flow_0aqgwvu</bpmn:incoming>
<bpmn:outgoing>Flow_1e2qi9s</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:userTask id="Activity_SharedSpaceInfo" name="Enter Shared Space" camunda:formKey="Space Involved in this Request">
<bpmn:documentation>#### Space used by {{ PIComputingID.label }} and shared with other PIs. If all space is exclusive and not shared with one or more other investigators, Click Save to skip this section and proceed to the next section.</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="SharedSpaceBuilding" label="Building Name" type="autocomplete">
<camunda:properties>
<camunda:property id="description" value="Select the building where this shared lab space is housed." />
<camunda:property id="spreadsheet.name" value="BuildingList.xls" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Building Name" />
<camunda:property id="repeat" value="Shared" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="SharedSpaceRoomID" label="Shared Space Room ID" type="string">
<camunda:properties>
<camunda:property id="repeat" value="Shared" />
<camunda:property id="description" value="Enter the room number or other unique identifier" />
<camunda:property id="hide_expression" value="model.SharedSpaceBuilding === &#34;Other&#34;" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="ShareSpaceRoomIDBuilding" label="Room No, and Building Name" type="string">
<camunda:properties>
<camunda:property id="description" value="Enter the Room No and Building of your shared space." />
<camunda:property id="hide_expression" value="model.SharedSpaceBuilding !== &#34;Other&#34; | model.SharedSpaceBuilding === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="SharedSpaceAMComputingID" label="Area Monitor" type="autocomplete">
<camunda:properties>
<camunda:property id="ldap.lookup" value="true" />
<camunda:property id="placeholder" value="wxy0z or Smith" />
<camunda:property id="description" value="Enter Area Monitor&#39;s Computing ID or last name and select Area Monitor. Leave blank if not known." />
<camunda:property id="repeat" value="Shared" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="SharedSpaceSqFt" label="Space square Feet" type="long">
<camunda:properties>
<camunda:property id="repeat" value="Shared" />
<camunda:property id="description" value="Enter the number of square feet in this space." />
</camunda:properties>
</camunda:formField>
<camunda:formField id="SharedSpacePercentUsable" label="Percent of Space Usable By Personnel" type="long">
<camunda:properties>
<camunda:property id="repeat" value="Shared" />
<camunda:property id="description" value="If known, enter a number between 1 &#38; 100 which indicates the approximate percent of the total space personnel will work in and move around in during the workday." />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="min" config="1" />
<camunda:constraint name="max" config="100" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="SharedSpaceMaxPersonnel" label="Maximum Number of Personnel Occupying Space" type="long">
<camunda:properties>
<camunda:property id="description" value="Enter the maximum number of personnel, including yourself, who will occupy this space." />
<camunda:property id="repeat" value="Shared" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="SharedSpacePI" label="Shared Space PI(s)" type="textarea">
<camunda:properties>
<camunda:property id="description" value="For each PI you share this space with, enter their Name, School, Department and Email Address." />
<camunda:property id="rows" value="5" />
<camunda:property id="repeat" value="Shared" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_19xeq76</bpmn:incoming>
<bpmn:outgoing>Flow_16342pm</bpmn:outgoing>
</bpmn:userTask>
<bpmn:parallelGateway id="Gateway_0frfdnc">
<bpmn:incoming>Flow_1v7r1tg</bpmn:incoming>
<bpmn:outgoing>Flow_19xeq76</bpmn:outgoing>
<bpmn:outgoing>Flow_0qf2y84</bpmn:outgoing>
<bpmn:outgoing>Flow_15zy1q7</bpmn:outgoing>
<bpmn:outgoing>Flow_0ya8hw8</bpmn:outgoing>
</bpmn:parallelGateway>
<bpmn:parallelGateway id="Gateway_1vj4zd3">
<bpmn:incoming>Flow_0tk64b6</bpmn:incoming>
<bpmn:incoming>Flow_12ie6w0</bpmn:incoming>
<bpmn:incoming>Flow_0zz2hbq</bpmn:incoming>
<bpmn:incoming>Flow_16342pm</bpmn:incoming>
<bpmn:outgoing>Flow_1eiud85</bpmn:outgoing>
</bpmn:parallelGateway>
<bpmn:sequenceFlow id="Flow_19xeq76" sourceRef="Gateway_0frfdnc" targetRef="Activity_SharedSpaceInfo" />
<bpmn:sequenceFlow id="Flow_16342pm" sourceRef="Activity_SharedSpaceInfo" targetRef="Gateway_1vj4zd3" />
<bpmn:sequenceFlow id="Flow_16y8glw" sourceRef="Activity-PI_Info" targetRef="Activity_1u58hox" />
<bpmn:sequenceFlow id="Flow_0qf2y84" sourceRef="Gateway_0frfdnc" targetRef="Activity_ExclusiveSpace" />
<bpmn:sequenceFlow id="Flow_0tk64b6" sourceRef="Activity_ExclusiveSpace" targetRef="Gateway_1vj4zd3" />
<bpmn:userTask id="Activity_ExclusiveSpace" name="Enter Exclusive Space" camunda:formKey="ExclusiveSpace">
<bpmn:documentation>#### Space managed exclusively by {{ PIComputingID.label }}
Submit one entry for each space the PI is the exclusive investigator. If all space is shared with one or more other investigators, Click Save to skip this section and proceed to the Shared Space section.</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="ExclusiveSpaceBuilding" label="Room No. &#38; Building Name" type="autocomplete">
<camunda:properties>
<camunda:property id="description" value="Type key word to find the building in which the lab is located." />
<camunda:property id="spreadsheet.name" value="BuildingList.xls" />
<camunda:property id="spreadsheet.value.column" value="Value" />
<camunda:property id="spreadsheet.label.column" value="Building Name" />
<camunda:property id="repeat" value="Exclusive" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="ExclusiveSpaceRoomID" label="Exclusive Space Room ID" type="string">
<camunda:properties>
<camunda:property id="hide_expression" value="model.ExclusiveSpaceBuilding === &#34;Other&#34;" />
<camunda:property id="repeat" value="Exclusive" />
<camunda:property id="description" value="Enter the room number or other unique identifier" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="ExclusiveSpaceRoomIDBuilding" label="Room No, and Building Name" type="string">
<camunda:properties>
<camunda:property id="description" value="Enter the Room No and Building of your exclusive space." />
<camunda:property id="hide_expression" value="model.ExclusiveSpaceBuilding !== &#34;Other&#34; | model.ExclusiveSpaceBuilding === null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="ExclusiveSpaceType" label="Space Room Type" type="enum">
<camunda:properties>
<camunda:property id="repeat" value="Exclusive" />
<camunda:property id="enum_type" value="radio" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
<camunda:value id="Lab" name="Lab" />
<camunda:value id="Office" name="Office" />
</camunda:formField>
<camunda:formField id="ExclusiveSpaceAMComputingID" label="Area Monitor" type="autocomplete">
<camunda:properties>
<camunda:property id="ldap.lookup" value="true" />
<camunda:property id="description" value="Enter Area Monitor&#39;s Computing ID or last name and select Area Monitor. Leave blank if not known." />
<camunda:property id="repeat" value="Exclusive" />
<camunda:property id="placeholder" value="wxy0z or Smith" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="ExclusiveSpaceSqFt" label="Space Square Feet" type="long">
<camunda:properties>
<camunda:property id="repeat" value="Exclusive" />
<camunda:property id="description" value="Enter the number of square feet in this space." />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="ExclusiveSpacePercentUsable" label="Percent of Space Usable By Personnel" type="long">
<camunda:properties>
<camunda:property id="repeat" value="Exclusive" />
<camunda:property id="description" value="If known, enter a number between 1 &#38; 100 which indicates the approximate percent of the total space personnel will work in and move around in during the workday." />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="min" config="1" />
<camunda:constraint name="max" config="100" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="ExclusiveSpaceMaxPersonnel" label="Maximum Number of Personnel Occupying Space" type="long">
<camunda:properties>
<camunda:property id="description" value="Enter the maximum number of personnel, including yourself, who will occupy this space." />
<camunda:property id="repeat" value="Exclusive" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0qf2y84</bpmn:incoming>
<bpmn:outgoing>Flow_0tk64b6</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_15zy1q7" sourceRef="Gateway_0frfdnc" targetRef="UserTask_CoreResource" />
<bpmn:sequenceFlow id="Flow_12ie6w0" sourceRef="UserTask_CoreResource" targetRef="Gateway_1vj4zd3" />
<bpmn:sequenceFlow id="Flow_0ya8hw8" sourceRef="Gateway_0frfdnc" targetRef="Activity_nonUVASpaces" />
<bpmn:userTask id="Activity_nonUVASpaces" name="Enter non-UVA Spaces" camunda:formKey="nonUVA Spaces">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="isNonUVASpaces" label="non-UVA Spaces?" type="boolean">
<camunda:properties>
<camunda:property id="description" value="Does any of your research occur in non-UVA spaces? (For example, field stations or UVA leased buildings off Grounds) " />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="NonUVASpaces" label="Where?" type="textarea">
<camunda:properties>
<camunda:property id="description" value="Does any of your research occur in non-UVA spaces? (For example, field stations or UVA leased buildings off Grounds) " />
<camunda:property id="hide_expression" value="!model.isNonUVASpaces | model.isNonUVASpaces == null" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0ya8hw8</bpmn:incoming>
<bpmn:outgoing>Flow_0zz2hbq</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_0zz2hbq" sourceRef="Activity_nonUVASpaces" targetRef="Gateway_1vj4zd3" />
<bpmn:sequenceFlow id="Flow_1eiud85" sourceRef="Gateway_1vj4zd3" targetRef="Personnel" />
<bpmn:sequenceFlow id="Flow_1nbjr72" sourceRef="Personnel" targetRef="Gateway_18jn18b" />
<bpmn:userTask id="Activity_DistanceReq" name="Enter Distancing Requirements" camunda:formKey="Distancing Requirements">
<bpmn:documentation>#### Distancing requirements:
Maintain social distancing by designing space between people to be at least 9 feet during prolonged work which will be accomplished by restricting the number of people in the lab to a density of ~250 sq. ft. /person in lab areas. When moving around, a minimum of 6 feet social distancing is required. Ideally only one person per lab bench and not more than one person can work at the same time in the same bay.</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="CIDR_TotalSqFt" label="What is the total square footage of your lab?" type="long">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="CIDR_MaxPersonnel" label="How many personnel will be using the lab at any one time, at a maximum?" type="long">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0p2r1bo</bpmn:incoming>
<bpmn:outgoing>Flow_0tz5c2v</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_0p2r1bo" sourceRef="Gateway_18jn18b" targetRef="Activity_DistanceReq" />
<bpmn:parallelGateway id="Gateway_18jn18b">
<bpmn:incoming>Flow_1nbjr72</bpmn:incoming>
<bpmn:outgoing>Flow_0p2r1bo</bpmn:outgoing>
<bpmn:outgoing>Flow_0mkh1wn</bpmn:outgoing>
<bpmn:outgoing>Flow_1yqkpgu</bpmn:outgoing>
<bpmn:outgoing>Flow_1c6m5wv</bpmn:outgoing>
</bpmn:parallelGateway>
<bpmn:sequenceFlow id="Flow_0mkh1wn" sourceRef="Gateway_18jn18b" targetRef="Activity_PWA" />
<bpmn:userTask id="Activity_PWA" name="Enter Physical Work Arrangements" camunda:formKey="Physical Work Arrangements">
<bpmn:documentation>Describe physical work arrangements for each lab. Show schematic of the lab and space organization to meet the distancing guidelines (see key safety expectations for ramp-up).
- Show gross dimensions, location of desks, and equipment in blocks (not details) that show available space for work and foot traffic.
- Indicate total square footage for every lab/space that you are requesting adding personnel to in this application. If you would like help obtaining a floor plan for your lab, your department or deans office can help. You can also create a hand drawing/block diagram of your space and the location of objects on a graph paper.
- Upload your physical layout and workspace organization in the form of a jpg image or a pdf file. This can be hand-drawn or actual floor plans.
- Show and/or describe designated work location for each member (during their shift) in the lab when multiple members are present at a time to meet the distancing guidelines.
- Provide a foot traffic plan (on the schematic) to indicate how people can move around while maintaining distancing requirements. This can be a freeform sketch on your floor plan showing where foot traffic can occur in your lab, and conditions, if any, to ensure distancing at all times. (e.g., direction to walk around a lab bench, rules for using shared equipment located in the lab, certain areas of lab prohibited from access, etc.).
- Provide your initial weekly laboratory schedule (see excel template) for all members that you are requesting access for, indicating all shifts as necessary. If schedule changes, please submit your revised schedule through the web portal.</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="PWADescribe" label="Describe" type="textarea">
<camunda:properties>
<camunda:property id="rows" value="10" />
<camunda:property id="autosize" value="true" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="PWAFiles" label="Upload supporting files" type="files" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0mkh1wn</bpmn:incoming>
<bpmn:outgoing>Flow_0zrsh65</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_1yqkpgu" sourceRef="Gateway_18jn18b" targetRef="Activity_HSR" />
<bpmn:userTask id="Activity_HSR" name="Enter Health Safety Requirements" camunda:formKey="Lab Plan">
<bpmn:documentation>#### Health Safety Requirements:
Use the EHS [Lab Safety Plan During COVID 19 template](https://www.google.com/url?q=http://ehs.virginia.edu/files/Lab-Safety-Plan-During-COVID-19.docx&amp;source=gmail&amp;ust=1590687968958000&amp;usg=AFQjCNE83uGDFtxGkKaxjuXGhTocu-FDmw) to create and upload a copy of your laboratory policy statement to all members which includes at a minimum the following details:
- Laboratory face covering rules, use of other PPE use as required
- Adherence to individual schedules, check-in, check out requirements
- Completion of online EHS safety training requirement
- Health self-attestation requirement
- Sanitizing procedures including frequency and type of disinfectants to use
- Where and how to obtain PPE including face covering</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="LabPlan" label="Upload Lab Plan" type="files" />
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_1yqkpgu</bpmn:incoming>
<bpmn:outgoing>Flow_1ox5nv6</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_1c6m5wv" sourceRef="Gateway_18jn18b" targetRef="Activity_OtherReq" />
<bpmn:userTask id="Activity_OtherReq" name="Enter Other Requirements" camunda:formKey="Other Requirements">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="isAnimalResearch" label="Will you be using animals in your research? " type="boolean">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="isAnimalResearchCoordinated" label="Have you coordinated with the vivarium manager to meet your needs?" type="boolean">
<camunda:properties>
<camunda:property id="hide_expression" value="!model.isAnimalResearch | model.isAnimalResearch == null" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="isHumanSubjects" label="Does your research involve human subjects? " type="boolean">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="IRBApprovalRelevantNumbers" label="List IRB Approval Relevant Numbers" type="textarea">
<camunda:properties>
<camunda:property id="rows" value="5" />
<camunda:property id="hide_expression" value="!model.isHumanSubjects | model.isHumanSubjects == null" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="isNecessarySupplies" label="Do you have the necessary materials, supplies, cleaning supplies and PPE for your laboratory?" type="boolean">
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
<camunda:formField id="SupplyList" label="List your needs" type="textarea">
<camunda:properties>
<camunda:property id="hide_expression" value="model.isNecessarySupplies | model.isNecessarySupplies == null" />
<camunda:property id="rows" value="5" />
</camunda:properties>
<camunda:validation>
<camunda:constraint name="required" config="true" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_1c6m5wv</bpmn:incoming>
<bpmn:outgoing>Flow_0qbi47d</bpmn:outgoing>
</bpmn:userTask>
<bpmn:manualTask id="Activity_SubmitPlan" name="Acknowledge Plan Submission">
<bpmn:documentation>#### By submitting this request, you understand that every member listed in this form for on Grounds laboratory access will:
- Complete online COVID awareness &amp; precaution training module (link forthcoming-May 25)
- Complete daily health acknowledgement form signed (electronically) –email generated daily to those listed on your plan for access to on Grounds lab/research space
- Fill out daily work attendance log for all lab members following your school process to check-in and out of work each day.</bpmn:documentation>
<bpmn:incoming>Flow_08njvvi</bpmn:incoming>
<bpmn:outgoing>Flow_0j4rs82</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:sequenceFlow id="Flow_0zrsh65" sourceRef="Activity_PWA" targetRef="Gateway_0sijkgx" />
<bpmn:sequenceFlow id="Flow_0tz5c2v" sourceRef="Activity_DistanceReq" targetRef="Gateway_0sijkgx" />
<bpmn:sequenceFlow id="Flow_1ox5nv6" sourceRef="Activity_HSR" targetRef="Gateway_0sijkgx" />
<bpmn:sequenceFlow id="Flow_0qbi47d" sourceRef="Activity_OtherReq" targetRef="Gateway_0sijkgx" />
<bpmn:sequenceFlow id="Flow_06873ag" sourceRef="Gateway_0sijkgx" targetRef="Activity_1tub2mc" />
<bpmn:parallelGateway id="Gateway_0sijkgx">
<bpmn:incoming>Flow_0zrsh65</bpmn:incoming>
<bpmn:incoming>Flow_0tz5c2v</bpmn:incoming>
<bpmn:incoming>Flow_1ox5nv6</bpmn:incoming>
<bpmn:incoming>Flow_0qbi47d</bpmn:incoming>
<bpmn:outgoing>Flow_06873ag</bpmn:outgoing>
</bpmn:parallelGateway>
<bpmn:scriptTask id="Activity_1tub2mc" name="Generate RRP">
<bpmn:incoming>Flow_06873ag</bpmn:incoming>
<bpmn:outgoing>Flow_0aqgwvu</bpmn:outgoing>
<bpmn:script>CompleteTemplate ResearchRampUpPlan.docx RESEARCH_RAMPUP</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_0aqgwvu" sourceRef="Activity_1tub2mc" targetRef="Activity_AcknowledgePlanReview" />
<bpmn:sequenceFlow id="Flow_0j4rs82" sourceRef="Activity_SubmitPlan" targetRef="Activity_0absozl" />
<bpmn:sequenceFlow id="Flow_07ge8uf" sourceRef="Activity_0absozl" targetRef="Activity_RequestStatus" />
<bpmn:sequenceFlow id="Flow_1ufh44h" sourceRef="Activity_RequestStatus" targetRef="Activity_AreaMonitorNotification" />
<bpmn:userTask id="Activity_RequestStatus" name="Check-on Request Status" camunda:formKey="Rquest Status">
<bpmn:documentation>#### Approval Process
The Research Ramp-up Plan and associated documents will be reviewed by{{ " " + ApprvlApprvrName1 }}{{ '.' if ApprvlApprvrName2 == 'n/a' else ' and ' + ApprvlApprvrName2 + '.' }} While waiting for approval, be sure that all required training has been completed and supplies secured. When the approval email notification is received, confirming the three questions below will allow you to proceed.
If a rejection notification is received, go back to the first step that needs to be addressed and step through each subsequent form from that point.</bpmn:documentation>
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="ApprovalReceived" label="Please Confirm:" type="enum">
<camunda:properties>
<camunda:property id="enum_type" value="checkbox" />
</camunda:properties>
<camunda:value id="ApprovalNotificationReceived" name="Approval Notification Received?" />
</camunda:formField>
<camunda:formField id="RequiredTraining" label="Please Confirm:" type="enum">
<camunda:properties>
<camunda:property id="enum_type" value="checkbox" />
</camunda:properties>
<camunda:value id="AllRequiredTraining" name="All Required Training Completed?" />
</camunda:formField>
<camunda:formField id="NeededSupplies" label="Please Confirm&#34;" type="enum">
<camunda:properties>
<camunda:property id="enum_type" value="checkbox" />
</camunda:properties>
<camunda:value id="NeededSupplies" name="All Needed Supplies Secured?" />
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_07ge8uf</bpmn:incoming>
<bpmn:outgoing>Flow_1ufh44h</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_05w8yd6" sourceRef="Activity_WhatNext" targetRef="EndEvent_09wp7av" />
<bpmn:sequenceFlow id="Flow_08njvvi" sourceRef="Activity_ApprovalInfo" targetRef="Activity_SubmitPlan" />
<bpmn:businessRuleTask id="Activity_ApprovalInfo" name="Assign Approval Info" camunda:decisionRef="Decision_ApprovalInfo">
<bpmn:incoming>Flow_1e2qi9s</bpmn:incoming>
<bpmn:outgoing>Flow_08njvvi</bpmn:outgoing>
</bpmn:businessRuleTask>
<bpmn:manualTask id="Activity_WhatNext" name="Review What&#39;s Next?">
<bpmn:documentation>### Stay Here, In Case Something Changes
If anything changes in the Research Ramp-up Plan submitted, click **Start over** at the top of the menu and step through each form, updating as needed. Data will be preserved, so if no changes are needed on a specific form, click Save and proceed.
If notification is received that the Research Ramp-up Plan approval process is no longer required, click Continue to close out the workflow process.</bpmn:documentation>
<bpmn:incoming>Flow_0cpmvcw</bpmn:incoming>
<bpmn:outgoing>Flow_05w8yd6</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:sequenceFlow id="Flow_0cpmvcw" sourceRef="Activity_AreaMonitorNotification" targetRef="Activity_WhatNext" />
<bpmn:manualTask id="Activity_AreaMonitorNotification" name="Send Area Monitor Notification">
<bpmn:documentation>#### Ready to Ramp-up Research
Notify the Area Monitor for
#### Exclusive Space Area Monitors
{% for es in exclusive %}
{{ es.ExclusiveSpaceAMComputingID.data.display_name }}
{% else %}
No exclusive space entered
{% endfor %}
#### Shared Space Area Monitors
{% for ss in shared %}
{{ ss.SharedSpaceAMComputingID.data.display_name }}
{% else %}
No shared space entered
{% endfor %}</bpmn:documentation>
<bpmn:incoming>Flow_1ufh44h</bpmn:incoming>
<bpmn:outgoing>Flow_0cpmvcw</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:scriptTask id="Activity_0absozl" name="Execute Plan Submission">
<bpmn:incoming>Flow_0j4rs82</bpmn:incoming>
<bpmn:outgoing>Flow_07ge8uf</bpmn:outgoing>
<bpmn:script>RequestApproval ApprvlApprvr1 ApprvlApprvr2</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1v7r1tg" sourceRef="Activity_1u58hox" targetRef="Gateway_0frfdnc" />
<bpmn:scriptTask id="Activity_1u58hox" name="Update Request">
<bpmn:incoming>Flow_16y8glw</bpmn:incoming>
<bpmn:outgoing>Flow_1v7r1tg</bpmn:outgoing>
<bpmn:script>UpdateStudy title:PIComputingID.label pi:PIComputingID.value</bpmn:script>
</bpmn:scriptTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0ssahs9">
<bpmndi:BPMNEdge id="Flow_1v7r1tg_di" bpmnElement="Flow_1v7r1tg">
<di:waypoint x="630" y="307" />
<di:waypoint x="685" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0cpmvcw_di" bpmnElement="Flow_0cpmvcw">
<di:waypoint x="2470" y="307" />
<di:waypoint x="2520" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_08njvvi_di" bpmnElement="Flow_08njvvi">
<di:waypoint x="1900" y="307" />
<di:waypoint x="1930" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_05w8yd6_di" bpmnElement="Flow_05w8yd6">
<di:waypoint x="2620" y="307" />
<di:waypoint x="2692" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1ufh44h_di" bpmnElement="Flow_1ufh44h">
<di:waypoint x="2330" y="307" />
<di:waypoint x="2370" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_07ge8uf_di" bpmnElement="Flow_07ge8uf">
<di:waypoint x="2180" y="307" />
<di:waypoint x="2230" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0j4rs82_di" bpmnElement="Flow_0j4rs82">
<di:waypoint x="2030" y="307" />
<di:waypoint x="2080" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0aqgwvu_di" bpmnElement="Flow_0aqgwvu">
<di:waypoint x="1640" y="307" />
<di:waypoint x="1670" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_06873ag_di" bpmnElement="Flow_06873ag">
<di:waypoint x="1495" y="307" />
<di:waypoint x="1540" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0qbi47d_di" bpmnElement="Flow_0qbi47d">
<di:waypoint x="1400" y="510" />
<di:waypoint x="1470" y="510" />
<di:waypoint x="1470" y="332" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1ox5nv6_di" bpmnElement="Flow_1ox5nv6">
<di:waypoint x="1400" y="380" />
<di:waypoint x="1470" y="380" />
<di:waypoint x="1470" y="332" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0tz5c2v_di" bpmnElement="Flow_0tz5c2v">
<di:waypoint x="1400" y="120" />
<di:waypoint x="1470" y="120" />
<di:waypoint x="1470" y="282" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0zrsh65_di" bpmnElement="Flow_0zrsh65">
<di:waypoint x="1400" y="240" />
<di:waypoint x="1470" y="240" />
<di:waypoint x="1470" y="282" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1c6m5wv_di" bpmnElement="Flow_1c6m5wv">
<di:waypoint x="1230" y="332" />
<di:waypoint x="1230" y="510" />
<di:waypoint x="1300" y="510" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1yqkpgu_di" bpmnElement="Flow_1yqkpgu">
<di:waypoint x="1230" y="332" />
<di:waypoint x="1230" y="380" />
<di:waypoint x="1300" y="380" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0mkh1wn_di" bpmnElement="Flow_0mkh1wn">
<di:waypoint x="1230" y="282" />
<di:waypoint x="1230" y="240" />
<di:waypoint x="1300" y="240" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0p2r1bo_di" bpmnElement="Flow_0p2r1bo">
<di:waypoint x="1230" y="282" />
<di:waypoint x="1230" y="120" />
<di:waypoint x="1300" y="120" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1nbjr72_di" bpmnElement="Flow_1nbjr72">
<di:waypoint x="1150" y="307" />
<di:waypoint x="1205" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1eiud85_di" bpmnElement="Flow_1eiud85">
<di:waypoint x="995" y="307" />
<di:waypoint x="1050" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0zz2hbq_di" bpmnElement="Flow_0zz2hbq">
<di:waypoint x="890" y="510" />
<di:waypoint x="970" y="510" />
<di:waypoint x="970" y="332" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0ya8hw8_di" bpmnElement="Flow_0ya8hw8">
<di:waypoint x="710" y="332" />
<di:waypoint x="710" y="510" />
<di:waypoint x="790" y="510" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_12ie6w0_di" bpmnElement="Flow_12ie6w0">
<di:waypoint x="890" y="370" />
<di:waypoint x="970" y="370" />
<di:waypoint x="970" y="332" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_15zy1q7_di" bpmnElement="Flow_15zy1q7">
<di:waypoint x="710" y="332" />
<di:waypoint x="710" y="370" />
<di:waypoint x="790" y="370" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0tk64b6_di" bpmnElement="Flow_0tk64b6">
<di:waypoint x="890" y="110" />
<di:waypoint x="970" y="110" />
<di:waypoint x="970" y="282" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0qf2y84_di" bpmnElement="Flow_0qf2y84">
<di:waypoint x="710" y="282" />
<di:waypoint x="710" y="110" />
<di:waypoint x="790" y="110" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_16y8glw_di" bpmnElement="Flow_16y8glw">
<di:waypoint x="480" y="307" />
<di:waypoint x="530" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_16342pm_di" bpmnElement="Flow_16342pm">
<di:waypoint x="890" y="240" />
<di:waypoint x="970" y="240" />
<di:waypoint x="970" y="282" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_19xeq76_di" bpmnElement="Flow_19xeq76">
<di:waypoint x="710" y="282" />
<di:waypoint x="710" y="240" />
<di:waypoint x="790" y="240" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1e2qi9s_di" bpmnElement="Flow_1e2qi9s">
<di:waypoint x="1770" y="307" />
<di:waypoint x="1800" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_05ja25w_di" bpmnElement="SequenceFlow_05ja25w">
<di:waypoint x="168" y="307" />
<di:waypoint x="230" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0h50bp3_di" bpmnElement="SequenceFlow_0h50bp3">
<di:waypoint x="330" y="307" />
<di:waypoint x="380" y="307" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="132" y="289" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ManualTask_1ofy9yz_di" bpmnElement="ManualTask_Instructions">
<dc:Bounds x="230" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_0xdpoxl_di" bpmnElement="Activity-PI_Info">
<dc:Bounds x="380" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_0ecab9j_di" bpmnElement="Personnel">
<dc:Bounds x="1050" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_0l8vxty_di" bpmnElement="UserTask_CoreResource">
<dc:Bounds x="790" y="330" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_09wp7av_di" bpmnElement="EndEvent_09wp7av">
<dc:Bounds x="2692" y="289" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1mg5lp9_di" bpmnElement="Activity_AcknowledgePlanReview">
<dc:Bounds x="1670" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1xgrlzr_di" bpmnElement="Activity_SharedSpaceInfo">
<dc:Bounds x="790" y="200" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_0tn2il3_di" bpmnElement="Gateway_0frfdnc">
<dc:Bounds x="685" y="282" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_1o1fcbg_di" bpmnElement="Gateway_1vj4zd3">
<dc:Bounds x="945" y="282" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1jefdme_di" bpmnElement="Activity_ExclusiveSpace">
<dc:Bounds x="790" y="70" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0ysw6zo_di" bpmnElement="Activity_nonUVASpaces">
<dc:Bounds x="790" y="470" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1xag6qb_di" bpmnElement="Activity_DistanceReq">
<dc:Bounds x="1300" y="80" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_0yof76x_di" bpmnElement="Gateway_18jn18b">
<dc:Bounds x="1205" y="282" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_166b0qq_di" bpmnElement="Activity_PWA">
<dc:Bounds x="1300" y="200" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0byj9mp_di" bpmnElement="Activity_HSR">
<dc:Bounds x="1300" y="340" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0j0p13i_di" bpmnElement="Activity_OtherReq">
<dc:Bounds x="1300" y="470" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1h30fo8_di" bpmnElement="Activity_SubmitPlan">
<dc:Bounds x="1930" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_03lxnzh_di" bpmnElement="Gateway_0sijkgx">
<dc:Bounds x="1445" y="282" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_117owwi_di" bpmnElement="Activity_1tub2mc">
<dc:Bounds x="1540" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0fxf44t_di" bpmnElement="Activity_RequestStatus">
<dc:Bounds x="2230" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_080o38p_di" bpmnElement="Activity_ApprovalInfo">
<dc:Bounds x="1800" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0wuukfn_di" bpmnElement="Activity_WhatNext">
<dc:Bounds x="2520" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0js9ww9_di" bpmnElement="Activity_AreaMonitorNotification">
<dc:Bounds x="2370" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0wnn9de_di" bpmnElement="Activity_0absozl">
<dc:Bounds x="2080" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_0f0ak6p_di" bpmnElement="Activity_1u58hox">
<dc:Bounds x="530" y="267" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

26
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@ -0,0 +1,26 @@
<?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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="empty_workflow" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
<bpmn:endEvent id="EndEvent_0q4qzl9">
<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
</bpmn:endEvent>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="empty_workflow">
<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
<di:waypoint x="238" y="117" />
<di:waypoint x="432" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
<dc:Bounds x="432" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="202" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

81
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@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1x1akiz" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<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_1x1akiz" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_0quormc" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_17znkku</bpmn:outgoing>
@ -16,10 +16,9 @@
</camunda:formField>
<camunda:formField id="FormField_FromOSP" label="From OSP" type="autocomplete">
<camunda:properties>
<camunda:property id="enum.options.file" value="sponsors.xls" />
<camunda:property id="enum.options.value.column" value="CUSTOMER_NUMBER" />
<camunda:property id="enum.options.label.column" value="CUSTOMER_NAME" />
<camunda:property id="enum.options.lookup" value="True" />
<camunda:property id="spreadsheet.name" value="sponsors.xls" />
<camunda:property id="spreadsheet.value.column" value="CUSTOMER_NUMBER" />
<camunda:property id="spreadsheet.label.column" value="CUSTOMER_NAME" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="FormField_Type" label="Select all that apply:" type="enum">
@ -70,51 +69,51 @@
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0quormc">
<bpmndi:BPMNEdge id="SequenceFlow_1n3utyf_di" bpmnElement="SequenceFlow_1n3utyf">
<di:waypoint x="430" y="40" />
<di:waypoint x="490" y="40" />
<di:waypoint x="490" y="92" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_17znkku_di" bpmnElement="SequenceFlow_17znkku">
<di:waypoint x="188" y="117" />
<di:waypoint x="235" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_13604n2_di" bpmnElement="Flow_13604n2">
<di:waypoint x="260" y="92" />
<di:waypoint x="260" y="40" />
<di:waypoint x="330" y="40" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_030v94s_di" bpmnElement="Flow_030v94s">
<di:waypoint x="515" y="117" />
<di:waypoint x="552" y="117" />
<bpmndi:BPMNEdge id="Flow_1l3gw28_di" bpmnElement="Flow_1l3gw28">
<di:waypoint x="430" y="280" />
<di:waypoint x="490" y="280" />
<di:waypoint x="490" y="222" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0hdjgx6_di" bpmnElement="Flow_0hdjgx6">
<di:waypoint x="260" y="142" />
<di:waypoint x="260" y="200" />
<di:waypoint x="330" y="200" />
<di:waypoint x="260" y="222" />
<di:waypoint x="260" y="280" />
<di:waypoint x="330" y="280" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1l3gw28_di" bpmnElement="Flow_1l3gw28">
<di:waypoint x="430" y="200" />
<di:waypoint x="490" y="200" />
<di:waypoint x="490" y="142" />
<bpmndi:BPMNEdge id="Flow_030v94s_di" bpmnElement="Flow_030v94s">
<di:waypoint x="515" y="197" />
<di:waypoint x="552" y="197" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="EndEvent_19upzzo_di" bpmnElement="EndEvent_19upzzo">
<dc:Bounds x="552" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_1s4ro2h_di" bpmnElement="Gateway_0bgimhg">
<dc:Bounds x="235" y="92" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_1kowkjp_di" bpmnElement="Gateway_1924s77">
<dc:Bounds x="465" y="92" width="50" height="50" />
<bpmndi:BPMNEdge id="Flow_13604n2_di" bpmnElement="Flow_13604n2">
<di:waypoint x="260" y="172" />
<di:waypoint x="260" y="120" />
<di:waypoint x="330" y="120" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1n3utyf_di" bpmnElement="SequenceFlow_1n3utyf">
<di:waypoint x="430" y="120" />
<di:waypoint x="490" y="120" />
<di:waypoint x="490" y="172" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_17znkku_di" bpmnElement="SequenceFlow_17znkku">
<di:waypoint x="188" y="197" />
<di:waypoint x="235" y="197" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="152" y="179" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_15oiwqt_di" bpmnElement="Task_14cuhvm">
<dc:Bounds x="330" y="0" width="100" height="80" />
<dc:Bounds x="330" y="80" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_19upzzo_di" bpmnElement="EndEvent_19upzzo">
<dc:Bounds x="552" y="179" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1oeywwl_di" bpmnElement="Activity_0xxhfyh">
<dc:Bounds x="330" y="160" width="100" height="80" />
<dc:Bounds x="330" y="240" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="152" y="99" width="36" height="36" />
<bpmndi:BPMNShape id="Gateway_1s4ro2h_di" bpmnElement="Gateway_0bgimhg">
<dc:Bounds x="235" y="172" width="50" height="50" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Gateway_1kowkjp_di" bpmnElement="Gateway_1924s77">
<dc:Bounds x="465" y="172" width="50" height="50" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>

BIN
crc/static/reference/rrt_documents.xlsx Normal file
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Binary file not shown.

15
crconnect.wsgi Normal file
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@ -0,0 +1,15 @@
python_home = '/usr/local/envs/crcpython3'
import os
import sys
# Calculate path to site-packages directory.
python_version = '.'.join(map(str, sys.version_info[:2]))
site_packages = python_home + '/lib/python%s/site-packages' % python_version
# Add the site-packages directory.
site.addsitedir(site_packages)
from crc import app as application

90
deploy/requirements.txt Normal file
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@ -0,0 +1,90 @@
alabaster==0.7.12
alembic==1.4.2
amqp==2.5.2
aniso8601==8.0.0
attrs==19.3.0
babel==2.8.0
bcrypt==3.1.7
beautifulsoup4==4.9.1
billiard==3.6.3.0
blinker==1.4
celery==4.4.2
certifi==2020.4.5.1
cffi==1.14.0
chardet==3.0.4
click==7.1.2
clickclick==1.2.2
commonmark==0.9.1
configparser==5.0.0
connexion==2.7.0
coverage==5.1
docutils==0.16
docxtpl==0.9.2
et-xmlfile==1.0.1
flask==1.1.2
flask-bcrypt==0.7.1
flask-cors==3.0.8
flask-marshmallow==0.12.0
flask-migrate==2.5.3
flask-restful==0.3.8
flask-sqlalchemy==2.4.1
flask-sso==0.4.0
future==0.18.2
httpretty==1.0.2
idna==2.9
imagesize==1.2.0
importlib-metadata==1.6.0
inflection==0.4.0
itsdangerous==1.1.0
jdcal==1.4.1
jinja2==2.11.2
jsonschema==3.2.0
kombu==4.6.8
ldap3==2.7
lxml==4.5.1
mako==1.1.2
markupsafe==1.1.1
marshmallow==3.6.0
marshmallow-enum==1.5.1
marshmallow-sqlalchemy==0.23.0
numpy==1.18.4
openapi-spec-validator==0.2.8
openpyxl==3.0.3
packaging==20.4
pandas==1.0.3
psycopg2-binary==2.8.5
pyasn1==0.4.8
pycparser==2.20
pygments==2.6.1
pyjwt==1.7.1
pyparsing==2.4.7
pyrsistent==0.16.0
python-dateutil==2.8.1
python-docx==0.8.10
python-editor==1.0.4
pytz==2020.1
pyyaml==5.3.1
recommonmark==0.6.0
requests==2.23.0
six==1.14.0
snowballstemmer==2.0.0
soupsieve==2.0.1
sphinx==3.0.3
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==1.0.3
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.4
spiffworkflow
sqlalchemy==1.3.17
swagger-ui-bundle==0.0.6
urllib3==1.25.9
vine==1.3.0
waitress==1.4.3
webob==1.8.6
webtest==2.0.35
werkzeug==1.0.1
xlrd==1.2.0
xlsxwriter==1.2.8
zipp==3.1.0

4
deploy/update_requirements.sh Executable file
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@ -0,0 +1,4 @@
jq -r '.default
| to_entries[]
| .key + .value.version' \
../Pipfile.lock > requirements.txt

27
docker_run.sh
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@ -1,23 +1,30 @@
#!/bin/bash
# run migrations
export FLASK_APP=./crc/__init__.py
for entry in ./instance/* ; do
echo "$entry"
cat $entry
done
export FLASK_APP=/app/crc/__init__.py
if [ "$DOWNGRADE_DB" = "true" ]; then
echo 'Downgrading...'
echo 'Downgrading database...'
pipenv run flask db downgrade
fi
pipenv run flask db upgrade
if [ "$UPGRADE_DB" = "true" ]; then
echo 'Upgrading database...'
pipenv run flask db upgrade
fi
if [ "$RESET_DB" = "true" ]; then
echo 'Resetting database...'
echo 'Resetting database and seeding it with example CR Connect data...'
pipenv run flask load-example-data
fi
pipenv run python ./run.py
if [ "$RESET_DB_RRT" = "true" ]; then
echo 'Resetting database and seeding it with example RRT data...'
pipenv run flask load-example-rrt-data
fi
if [ "$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

70
example_data.py
View File

@ -14,7 +14,8 @@ class ExampleDataLoader:
session.flush() # Clear out any transactions before deleting it all to avoid spurious errors.
for table in reversed(db.metadata.sorted_tables):
session.execute(table.delete())
session.flush()
session.commit()
session.flush()
def load_all(self):
@ -191,8 +192,68 @@ class ExampleDataLoader:
category_id=None,
master_spec=True)
def load_rrt(self):
file_path = os.path.join(app.root_path, 'static', 'reference', 'rrt_documents.xlsx')
file = open(file_path, "rb")
FileService.add_reference_file(FileService.DOCUMENT_LIST,
binary_data=file.read(),
content_type=CONTENT_TYPES['xls'])
file.close()
def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False, category_id=None, display_order=None):
category = WorkflowSpecCategoryModel(
id=0,
name='research_rampup_category',
display_name='Research Ramp-up Category',
display_order=0
)
db.session.add(category)
db.session.commit()
self.create_spec(id="rrt_top_level_workflow",
name="rrt_top_level_workflow",
display_name="Top Level Workflow",
description="Does nothing, we don't use the master workflow here.",
category_id=None,
master_spec=True)
self.create_spec(id="research_rampup",
name="research_rampup",
display_name="Research Ramp-up Toolkit",
description="Process for creating a new research ramp-up request.",
category_id=0,
master_spec=False)
def load_test_data(self):
self.load_reference_documents()
category = WorkflowSpecCategoryModel(
id=0,
name='test_category',
display_name='Test Category',
display_order=0
)
db.session.add(category)
db.session.commit()
self.create_spec(id="empty_workflow",
name="empty_workflow",
display_name="Top Level Workflow",
description="Does nothing, we don't use the master workflow here.",
category_id=None,
master_spec=True,
from_tests = True)
self.create_spec(id="random_fact",
name="random_fact",
display_name="Random Fact",
description="The workflow for a Random Fact.",
category_id=0,
master_spec=False,
from_tests=True)
def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False,
category_id=None, display_order=None, from_tests=False):
"""Assumes that a directory exists in static/bpmn with the same name as the given id.
further assumes that the [id].bpmn is the primary file for the workflow.
returns an array of data models to be added to the database."""
@ -207,8 +268,11 @@ class ExampleDataLoader:
display_order=display_order)
db.session.add(spec)
db.session.commit()
if not filepath:
if not filepath and not from_tests:
filepath = os.path.join(app.root_path, 'static', 'bpmn', id, "*")
if not filepath and from_tests:
filepath = os.path.join(app.root_path, '..', 'tests', 'data', id, "*")
files = glob.glob(filepath)
for file_path in files:
noise, file_extension = os.path.splitext(file_path)

34
migrations/versions/23c62c933848_.py Normal file
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@ -0,0 +1,34 @@
"""empty message
Revision ID: 23c62c933848
Revises: 9b43e725f39c
Create Date: 2020-05-28 10:30:49.409760
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '23c62c933848'
down_revision = '9b43e725f39c'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_constraint('file_study_id_fkey', 'file', type_='foreignkey')
op.drop_column('file', 'task_id')
op.drop_column('file', 'study_id')
op.drop_column('file', 'form_field_key')
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('file', sa.Column('form_field_key', sa.VARCHAR(), autoincrement=False, nullable=True))
op.add_column('file', sa.Column('study_id', sa.INTEGER(), autoincrement=False, nullable=True))
op.add_column('file', sa.Column('task_id', sa.VARCHAR(), autoincrement=False, nullable=True))
op.create_foreign_key('file_study_id_fkey', 'file', 'study', ['study_id'], ['id'])
# ### end Alembic commands ###

36
migrations/versions/5064b72284b7_.py Normal file
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@ -0,0 +1,36 @@
"""empty message
Revision ID: 5064b72284b7
Revises: bec71f7dc652
Create Date: 2020-05-28 23:54:45.623361
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '5064b72284b7'
down_revision = 'bec71f7dc652'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('lookup_file', sa.Column('field_id', sa.String(), nullable=True))
op.add_column('lookup_file', sa.Column('is_ldap', sa.Boolean(), nullable=True))
op.add_column('lookup_file', sa.Column('workflow_spec_id', sa.String(), nullable=True))
op.drop_column('lookup_file', 'value_column')
op.drop_column('lookup_file', 'label_column')
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('lookup_file', sa.Column('label_column', sa.VARCHAR(), autoincrement=False, nullable=True))
op.add_column('lookup_file', sa.Column('value_column', sa.VARCHAR(), autoincrement=False, nullable=True))
op.drop_column('lookup_file', 'workflow_spec_id')
op.drop_column('lookup_file', 'is_ldap')
op.drop_column('lookup_file', 'field_id')
# ### end Alembic commands ###

39
migrations/versions/55c6cd407d89_.py Normal file
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@ -0,0 +1,39 @@
"""empty message
Revision ID: 55c6cd407d89
Revises: cc4bccc5e5a8
Create Date: 2020-05-22 22:02:46.650170
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '55c6cd407d89'
down_revision = 'cc4bccc5e5a8'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('approval',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('study_id', sa.Integer(), nullable=False),
sa.Column('workflow_id', sa.Integer(), nullable=False),
sa.Column('workflow_version', sa.String(), nullable=True),
sa.Column('approver_uid', sa.String(), nullable=True),
sa.Column('status', sa.String(), nullable=True),
sa.Column('message', sa.String(), nullable=True),
sa.ForeignKeyConstraint(['study_id'], ['study.id'], ),
sa.ForeignKeyConstraint(['workflow_id'], ['workflow.id'], ),
sa.PrimaryKeyConstraint('id')
)
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('approval')
# ### end Alembic commands ###

44
migrations/versions/9b43e725f39c_.py Normal file
View File

@ -0,0 +1,44 @@
"""empty message
Revision ID: 9b43e725f39c
Revises: 55c6cd407d89
Create Date: 2020-05-25 23:09:14.761831
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '9b43e725f39c'
down_revision = '55c6cd407d89'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('approval_file',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('file_id', sa.Integer(), nullable=False),
sa.Column('approval_id', sa.Integer(), nullable=False),
sa.Column('file_version', sa.Integer(), nullable=False),
sa.ForeignKeyConstraint(['approval_id'], ['approval.id'], ),
sa.ForeignKeyConstraint(['file_id'], ['file.id'], ),
sa.PrimaryKeyConstraint('id')
)
op.add_column('approval', sa.Column('date_created', sa.DateTime(timezone=True), nullable=True))
op.add_column('approval', sa.Column('version', sa.Integer(), nullable=True))
op.add_column('approval', sa.Column('workflow_hash', sa.String(), nullable=True))
op.drop_column('approval', 'workflow_version')
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('approval', sa.Column('workflow_version', sa.VARCHAR(), autoincrement=False, nullable=True))
op.drop_column('approval', 'workflow_hash')
op.drop_column('approval', 'version')
op.drop_column('approval', 'date_created')
op.drop_table('approval_file')
# ### end Alembic commands ###

63
migrations/versions/bec71f7dc652_.py Normal file
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@ -0,0 +1,63 @@
"""empty message
Revision ID: bec71f7dc652
Revises: 23c62c933848
Create Date: 2020-05-28 20:08:45.891406
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision = 'bec71f7dc652'
down_revision = '23c62c933848'
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('workflow_spec_dependency_file',
sa.Column('file_data_id', sa.Integer(), nullable=False),
sa.Column('workflow_id', sa.Integer(), nullable=False),
sa.ForeignKeyConstraint(['file_data_id'], ['file_data.id'], ),
sa.ForeignKeyConstraint(['workflow_id'], ['workflow.id'], ),
sa.PrimaryKeyConstraint('file_data_id', 'workflow_id')
)
op.drop_column('approval', 'workflow_hash')
op.execute(
"""
delete from approval_file;
delete from approval;
"""
)
op.add_column('approval_file', sa.Column('file_data_id', sa.Integer(), nullable=False))
op.drop_constraint('approval_file_file_id_fkey', 'approval_file', type_='foreignkey')
op.create_foreign_key(None, 'approval_file', 'file_data', ['file_data_id'], ['id'])
op.drop_column('approval_file', 'id')
op.drop_column('approval_file', 'file_version')
op.drop_column('approval_file', 'file_id')
op.drop_column('file', 'latest_version')
op.add_column('file_data', sa.Column('date_created', sa.DateTime(timezone=True), nullable=True))
op.drop_column('file_data', 'last_updated')
op.drop_column('workflow', 'spec_version')
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.add_column('workflow', sa.Column('spec_version', sa.VARCHAR(), autoincrement=False, nullable=True))
op.add_column('file_data', sa.Column('last_updated', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True))
op.drop_column('file_data', 'date_created')
op.add_column('file', sa.Column('latest_version', sa.INTEGER(), autoincrement=False, nullable=True))
op.add_column('approval_file', sa.Column('file_id', sa.INTEGER(), autoincrement=False, nullable=False))
op.add_column('approval_file', sa.Column('file_version', sa.INTEGER(), autoincrement=False, nullable=False))
op.add_column('approval_file', sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False))
op.drop_constraint(None, 'approval_file', type_='foreignkey')
op.create_foreign_key('approval_file_file_id_fkey', 'approval_file', 'file', ['file_id'], ['id'])
op.drop_column('approval_file', 'file_data_id')
op.add_column('approval', sa.Column('workflow_hash', sa.VARCHAR(), autoincrement=False, nullable=True))
op.drop_table('workflow_spec_dependency_file')
# ### end Alembic commands ###

5
setup.cfg Normal file
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@ -0,0 +1,5 @@
[metadata]
name = crc
[files]
packages = crc

3
setup.py Normal file
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@ -0,0 +1,3 @@
from setuptools import setup
setup(setup_requires=["pbr"], pbr=True)

73
tests/base_test.py
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@ -1,7 +1,12 @@
# Set environment variable to testing before loading.
# IMPORTANT - Environment must be loaded before app, models, etc....
import json
import os
from sqlalchemy import Sequence
os.environ["TESTING"] = "true"
import json
import unittest
import urllib.parse
import datetime
@ -10,10 +15,6 @@ from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudyModel
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
os.environ["TESTING"] = "true"
from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel
from crc.models.user import UserModel
@ -21,10 +22,9 @@ from crc.models.user import UserModel
from crc import app, db, session
from example_data import ExampleDataLoader
# UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
# import logging
# logging.basicConfig()
# logging.getLogger('sqlalchemy.engine').setLevel(logging.INFO)
#UNCOMMENT THIS FOR DEBUGGING SQL ALCHEMY QUERIES
import logging
logging.basicConfig()
class BaseTest(unittest.TestCase):
@ -32,6 +32,10 @@ class BaseTest(unittest.TestCase):
efficiently when we have a database in place.
"""
if not app.config['TESTING']:
raise (Exception("INVALID TEST CONFIGURATION. This is almost always in import order issue."
"The first class to import in each test should be the base_test.py file."))
auths = {}
test_uid = "dhf8r"
@ -83,7 +87,7 @@ class BaseTest(unittest.TestCase):
@classmethod
def tearDownClass(cls):
cls.ctx.pop()
session.remove()
db.drop_all()
pass
def setUp(self):
@ -97,12 +101,10 @@ class BaseTest(unittest.TestCase):
def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):
if user is None:
uid = self.test_uid
user_info = {'uid': self.test_uid, 'first_name': 'Daniel', 'last_name': 'Funk',
'email_address': 'dhf8r@virginia.edu'}
user_info = {'uid': self.test_uid}
else:
uid = user.uid
user_info = {'uid': user.uid, 'first_name': user.first_name, 'last_name': user.last_name,
'email_address': user.email_address}
user_info = {'uid': user.uid}
query_string = self.user_info_to_query_string(user_info, redirect_url)
rv = self.app.get("/v1.0/sso_backdoor%s" % query_string, follow_redirects=False)
@ -113,10 +115,17 @@ class BaseTest(unittest.TestCase):
self.assertIsNotNone(user_model.display_name)
return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode())
def load_example_data(self):
def load_example_data(self, use_crc_data=False):
"""use_crc_data will cause this to load the mammoth collection of documents
we built up developing crc, otherwise it depends on a small setup for
running tests."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_all()
if(use_crc_data):
ExampleDataLoader().load_all()
else:
ExampleDataLoader().load_test_data()
for user_json in self.users:
db.session.add(UserModel(**user_json))
@ -125,6 +134,7 @@ class BaseTest(unittest.TestCase):
study_model = StudyModel(**study_json)
db.session.add(study_model)
StudyService._add_all_workflow_specs_to_study(study_model)
db.session.execute(Sequence(StudyModel.__tablename__ + '_id_seq'))
db.session.commit()
db.session.flush()
@ -149,7 +159,7 @@ class BaseTest(unittest.TestCase):
def load_test_spec(dir_name, master_spec=False, category_id=None):
"""Loads a spec into the database based on a directory in /tests/data"""
if session.query(WorkflowSpecModel).filter_by(id=dir_name).count() > 0:
return
return session.query(WorkflowSpecModel).filter_by(id=dir_name).first()
filepath = os.path.join(app.root_path, '..', 'tests', 'data', dir_name, "*")
return ExampleDataLoader().create_spec(id=dir_name, name=dir_name, filepath=filepath, master_spec=master_spec,
category_id=category_id)
@ -187,7 +197,7 @@ class BaseTest(unittest.TestCase):
for key, value in items:
query_string_list.append('%s=%s' % (key, urllib.parse.quote(value)))
query_string_list.append('redirect_url=%s' % redirect_url)
query_string_list.append('redirect=%s' % redirect_url)
return '?%s' % '&'.join(query_string_list)
@ -203,10 +213,31 @@ class BaseTest(unittest.TestCase):
content_type = CONTENT_TYPES[file_extension[1:]]
file_service.update_file(file_model, data, content_type)
def create_user(self, uid="dhf8r", email="daniel.h.funk@gmail.com", display_name="Hoopy Frood"):
user = session.query(UserModel).filter(UserModel.uid == uid).first()
if user is None:
user = UserModel(uid=uid, email_address=email, display_name=display_name)
db.session.add(user)
db.session.commit()
return user
def create_study(self, uid="dhf8r", title="Beer conception in the bipedal software engineer"):
study = session.query(StudyModel).first()
if study is None:
user = self.create_user(uid=uid)
study = StudyModel(title=title, protocol_builder_status=ProtocolBuilderStatus.ACTIVE,
user_uid=user.uid)
db.session.add(study)
db.session.commit()
return study
def create_workflow(self, workflow_name, study=None, category_id=None):
if study == None:
study = session.query(StudyModel).first()
spec = self.load_test_spec(workflow_name, category_id=category_id)
db.session.flush()
spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()
if spec is None:
spec = self.load_test_spec(workflow_name, category_id=category_id)
if study is None:
study = self.create_study()
workflow_model = StudyService._create_workflow_model(study, spec)
return workflow_model

30
tests/data/docx/docx.bpmn
View File

@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_96a17d9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_96a17d9" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_93a29b3" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0637d8i</bpmn:outgoing>
@ -27,7 +27,7 @@
</bpmn:extensionElements>
<bpmn:incoming>SequenceFlow_1i7hk1a</bpmn:incoming>
<bpmn:outgoing>SequenceFlow_11c35oq</bpmn:outgoing>
<bpmn:script>CompleteTemplate Letter.docx AncillaryDocument.CoCApplication</bpmn:script>
<bpmn:script>CompleteTemplate Letter.docx AD_CoCApp</bpmn:script>
</bpmn:scriptTask>
<bpmn:endEvent id="EndEvent_0evb22x">
<bpmn:incoming>SequenceFlow_11c35oq</bpmn:incoming>
@ -36,30 +36,30 @@
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_93a29b3">
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_0637d8i_di" bpmnElement="SequenceFlow_0637d8i">
<di:waypoint x="215" y="117" />
<di:waypoint x="265" y="117" />
<bpmndi:BPMNEdge id="SequenceFlow_11c35oq_di" bpmnElement="SequenceFlow_11c35oq">
<di:waypoint x="565" y="117" />
<di:waypoint x="665" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="UserTask_02o51o8_di" bpmnElement="task_gather_information">
<dc:Bounds x="265" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_1i7hk1a_di" bpmnElement="SequenceFlow_1i7hk1a">
<di:waypoint x="365" y="117" />
<di:waypoint x="465" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_0637d8i_di" bpmnElement="SequenceFlow_0637d8i">
<di:waypoint x="215" y="117" />
<di:waypoint x="265" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_02o51o8_di" bpmnElement="task_gather_information">
<dc:Bounds x="265" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_0xjh8x4_di" bpmnElement="task_generate_document">
<dc:Bounds x="465" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0evb22x_di" bpmnElement="EndEvent_0evb22x">
<dc:Bounds x="665" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="SequenceFlow_11c35oq_di" bpmnElement="SequenceFlow_11c35oq">
<di:waypoint x="565" y="117" />
<di:waypoint x="665" y="117" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

26
tests/data/empty_workflow/empty_workflow.bpmn Normal file
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@ -0,0 +1,26 @@
<?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:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1v1rp1q" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="empty_workflow" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_0lvudp8</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:sequenceFlow id="SequenceFlow_0lvudp8" sourceRef="StartEvent_1" targetRef="EndEvent_0q4qzl9" />
<bpmn:endEvent id="EndEvent_0q4qzl9">
<bpmn:incoming>SequenceFlow_0lvudp8</bpmn:incoming>
</bpmn:endEvent>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="empty_workflow">
<bpmndi:BPMNEdge id="SequenceFlow_0lvudp8_di" bpmnElement="SequenceFlow_0lvudp8">
<di:waypoint x="215" y="117" />
<di:waypoint x="432" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
<dc:Bounds x="179" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0q4qzl9_di" bpmnElement="EndEvent_0q4qzl9">
<dc:Bounds x="432" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

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113
tests/test_approvals_api.py Normal file
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@ -0,0 +1,113 @@
import json
from tests.base_test import BaseTest
from crc import app, db, session
from crc.models.approval import ApprovalModel, ApprovalSchema, ApprovalStatus
APPROVAL_PAYLOAD = {
'id': None,
'approver': {
'uid': 'bgb22',
'display_name': 'Billy Bob (bgb22)',
'title': 'E42:He\'s a hoopy frood',
'department': 'E0:EN-Eng Study of Parallel Universes'
},
'title': 'El Study',
'status': 'DECLINED',
'version': 1,
'message': 'Incorrect documents',
'associated_files': [
{
'id': 42,
'name': 'File 1',
'content_type': 'document'
},
{
'id': 43,
'name': 'File 2',
'content_type': 'document'
}
],
'workflow_id': 1,
'study_id': 1
}
class TestApprovals(BaseTest):
def setUp(self):
"""Initial setup shared by all TestApprovals tests"""
self.load_example_data()
self.study = self.create_study()
self.workflow = self.create_workflow('random_fact')
# TODO: Move to base_test as a helper
self.approval = ApprovalModel(
study=self.study,
workflow=self.workflow,
approver_uid='arc93',
status=ApprovalStatus.WAITING.value,
version=1
)
session.add(self.approval)
self.approval_2 = ApprovalModel(
study=self.study,
workflow=self.workflow,
approver_uid='dhf8r',
status=ApprovalStatus.WAITING.value,
version=1
)
session.add(self.approval_2)
session.commit()
def test_list_approvals_per_approver(self):
"""Only approvals associated with approver should be returned"""
approver_uid = self.approval_2.approver_uid
rv = self.app.get(f'/v1.0/approval?approver_uid={approver_uid}', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
# Stored approvals are 2
approvals_count = ApprovalModel.query.count()
self.assertEqual(approvals_count, 2)
# but Dan's approvals should be only 1
self.assertEqual(len(response), 1)
# Confirm approver UID matches returned payload
approval = ApprovalSchema().load(response[0])
self.assertEqual(approval.approver['uid'], approver_uid)
def test_list_approvals_per_admin(self):
"""All approvals will be returned"""
rv = self.app.get('/v1.0/approval', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
# Returned approvals should match what's in the db
approvals_count = ApprovalModel.query.count()
response_count = len(response)
self.assertEqual(approvals_count, response_count)
def test_update_approval(self):
"""Approval status will be updated"""
approval_id = self.approval.id
data = dict(APPROVAL_PAYLOAD)
data['id'] = approval_id
self.assertEqual(self.approval.status, ApprovalStatus.WAITING.value)
rv = self.app.put(f'/v1.0/approval/{approval_id}',
content_type="application/json",
headers=self.logged_in_headers(),
data=json.dumps(data))
self.assert_success(rv)
session.refresh(self.approval)
# Updated record should now have the data sent to the endpoint
self.assertEqual(self.approval.message, data['message'])
self.assertEqual(self.approval.status, ApprovalStatus.DECLINED.value)

59
tests/test_approvals_service.py Normal file
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@ -0,0 +1,59 @@
from tests.base_test import BaseTest
from crc import db
from crc.models.approval import ApprovalModel
from crc.services.approval_service import ApprovalService
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
class TestApprovalsService(BaseTest):
def test_create_approval_record(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
self.assertEquals(1, db.session.query(ApprovalModel).count())
model = db.session.query(ApprovalModel).first()
self.assertEquals(workflow.study_id, model.study_id)
self.assertEquals(workflow.id, model.workflow_id)
self.assertEquals("dhf8r", model.approver_uid)
self.assertEquals(1, model.version)
def test_new_requests_dont_add_if_approval_exists_for_current_workflow(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
self.assertEquals(1, db.session.query(ApprovalModel).count())
model = db.session.query(ApprovalModel).first()
self.assertEquals(1, model.version)
def test_new_approval_requests_after_file_modification_create_new_requests(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")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
self.assertEquals(2, db.session.query(ApprovalModel).count())
models = db.session.query(ApprovalModel).order_by(ApprovalModel.version).all()
self.assertEquals(1, models[0].version)
self.assertEquals(2, models[1].version)

27
tests/test_authentication.py
View File

@ -1,6 +1,7 @@
from tests.base_test import BaseTest
from crc import db
from crc.models.user import UserModel
from tests.base_test import BaseTest
class TestAuthentication(BaseTest):
@ -12,8 +13,8 @@ class TestAuthentication(BaseTest):
self.assertTrue(isinstance(auth_token, bytes))
self.assertEqual("dhf8r", user.decode_auth_token(auth_token).get("sub"))
def test_auth_creates_user(self):
new_uid = 'czn1z';
def test_backdoor_auth_creates_user(self):
new_uid = 'lb3dp' ## Assure this user id is in the fake responses from ldap.
self.load_example_data()
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
self.assertIsNone(user)
@ -37,6 +38,23 @@ class TestAuthentication(BaseTest):
self.assertTrue(rv_2.status_code == 302)
self.assertTrue(str.startswith(rv_2.location, redirect_url))
def test_normal_auth_creates_user(self):
new_uid = 'lb3dp' # This user is in the test ldap system.
self.load_example_data()
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
self.assertIsNone(user)
redirect_url = 'http://worlds.best.website/admin'
headers = dict(Uid=new_uid)
rv = self.app.get('v1.0/login', follow_redirects=False, headers=headers)
self.assert_success(rv)
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
self.assertIsNotNone(user)
self.assertEquals(new_uid, user.uid)
self.assertEquals("Laura Barnes", user.display_name)
self.assertEquals("lb3dp@virginia.edu", user.email_address)
self.assertEquals("E0:Associate Professor of Systems and Information Engineering", user.title)
def test_current_user_status(self):
self.load_example_data()
rv = self.app.get('/v1.0/user')
@ -45,6 +63,7 @@ class TestAuthentication(BaseTest):
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers())
self.assert_success(rv)
user = UserModel(uid="ajl2j", first_name='Aaron', last_name='Louie', email_address='ajl2j@virginia.edu')
# User must exist in the mock ldap responses.
user = UserModel(uid="dhf8r", first_name='Dan', last_name='Funk', email_address='dhf8r@virginia.edu')
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers(user, redirect_url='http://omg.edu/lolwut'))
self.assert_success(rv)

73
tests/test_file_service.py Normal file
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@ -0,0 +1,73 @@
from tests.base_test import BaseTest
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
class TestFileService(BaseTest):
"""Largely tested via the test_file_api, and time is tight, but adding new tests here."""
def test_add_file_from_task_increments_version_and_replaces_on_subsequent_add(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code=irb_code)
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_data))
self.assertEquals(2, file_data[0].version)
def test_add_file_from_form_increments_version_and_replaces_on_subsequent_add_with_same_name(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_data))
self.assertEquals(2, file_data[0].version)
def test_add_file_from_form_allows_multiple_files_with_different_names(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png", content_type="text",
binary_data=b'1234')
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="a_different_thing.png", content_type="text",
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(2, len(file_models))

31
tests/test_files_api.py
View File

@ -1,15 +1,14 @@
import io
import json
from datetime import datetime
from unittest.mock import patch
from tests.base_test import BaseTest
from crc import session
from crc.models.file import FileModel, FileType, FileModelSchema, FileDataModel
from crc.models.file import FileModel, FileType, FileSchema, FileModelSchema
from crc.models.workflow import WorkflowSpecModel
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
from example_data import ExampleDataLoader
from tests.base_test import BaseTest
class TestFilesApi(BaseTest):
@ -20,7 +19,7 @@ class TestFilesApi(BaseTest):
return (minimal_dbpm % content).encode()
def test_list_files_for_workflow_spec(self):
self.load_example_data()
self.load_example_data(use_crc_data=True)
spec_id = 'core_info'
spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
rv = self.app.get('/v1.0/file?workflow_spec_id=%s' % spec_id,
@ -166,17 +165,16 @@ class TestFilesApi(BaseTest):
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(2, file.latest_version)
self.assertEqual(FileType.bpmn, file.type)
self.assertEqual("application/octet-stream", file.content_type)
file_json = json.loads(rv.get_data(as_text=True))
self.assertEqual(2, file_json['latest_version'])
self.assertEqual(FileType.bpmn.value, file_json['type'])
self.assertEqual("application/octet-stream", file_json['content_type'])
self.assertEqual(spec.id, file.workflow_spec_id)
# Assure it is updated in the database and properly persisted.
file_model = session.query(FileModel).filter(FileModel.id == file.id).first()
self.assertEqual(2, file_model.latest_version)
file_data = FileService.get_file_data(file_model.id)
self.assertEqual(2, file_data.version)
rv = self.app.get('/v1.0/file/%i/data' % file.id, headers=self.logged_in_headers())
self.assert_success(rv)
@ -193,16 +191,13 @@ class TestFilesApi(BaseTest):
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(1, file.latest_version)
self.assertEqual(1, json_data['latest_version'])
data['file'] = io.BytesIO(self.minimal_bpmn("abcdef")), 'my_new_file.bpmn'
rv = self.app.put('/v1.0/file/%i/data' % file.id, data=data, follow_redirects=True,
rv = self.app.put('/v1.0/file/%i/data' % json_data['id'], data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(1, file.latest_version)
self.assertEqual(1, json_data['latest_version'])
def test_get_file(self):
self.load_example_data()

2
tests/test_ldap_service.py
View File

@ -21,7 +21,7 @@ class TestLdapService(BaseTest):
self.assertEqual("lb3dp", user_info.uid)
self.assertEqual("Laura Barnes", user_info.display_name)
self.assertEqual("Laura", user_info.given_name)
self.assertEqual("lb3dp@virginia.edu", user_info.email)
self.assertEqual("lb3dp@virginia.edu", user_info.email_address)
self.assertEqual("+1 (434) 924-1723", user_info.telephone_number)
self.assertEqual("E0:Associate Professor of Systems and Information Engineering", user_info.title)
self.assertEqual("E0:EN-Eng Sys and Environment", user_info.department)

113
tests/test_lookup_service.py
View File

@ -1,79 +1,128 @@
from crc import session
from crc.models.file import FileDataModel, FileModel, LookupFileModel, LookupDataModel
import os
from tests.base_test import BaseTest
from crc.services.file_service import FileService
from crc.api.common import ApiError
from crc import session, app
from crc.models.file import FileDataModel, FileModel, LookupFileModel, LookupDataModel, CONTENT_TYPES
from crc.services.lookup_service import LookupService
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
class TestLookupService(BaseTest):
def test_create_lookup_file_multiple_times_does_not_update_database(self):
spec = self.load_test_spec('enum_options_from_file')
def test_lookup_returns_good_error_on_bad_field(self):
spec = BaseTest.load_test_spec('enum_options_with_search')
workflow = self.create_workflow('enum_options_with_search')
file_model = session.query(FileModel).filter(FileModel.name == "customer_list.xls").first()
file_data_model = session.query(FileDataModel).filter(FileDataModel.file_model == file_model).first()
LookupService.get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
LookupService.get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
LookupService.get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
with self.assertRaises(ApiError):
LookupService.lookup(workflow, "not_the_right_field", "sam", limit=10)
def test_lookup_table_is_not_created_more_than_once(self):
spec = BaseTest.load_test_spec('enum_options_with_search')
workflow = self.create_workflow('enum_options_with_search')
LookupService.lookup(workflow, "sponsor", "sam", limit=10)
LookupService.lookup(workflow, "sponsor", "something", limit=10)
LookupService.lookup(workflow, "sponsor", "blah", limit=10)
lookup_records = session.query(LookupFileModel).all()
self.assertIsNotNone(lookup_records)
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(19, len(lookup_data))
# Using the same table with different lookup lable or value, does create additional records.
LookupService.get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NAME", "CUSTOMER_NUMBER")
self.assertEquals(28, len(lookup_data))
def test_updates_to_file_cause_lookup_rebuild(self):
spec = BaseTest.load_test_spec('enum_options_with_search')
workflow = self.create_workflow('enum_options_with_search')
file_model = session.query(FileModel).filter(FileModel.name == "sponsors.xls").first()
LookupService.lookup(workflow, "sponsor", "sam", limit=10)
lookup_records = session.query(LookupFileModel).all()
self.assertIsNotNone(lookup_records)
self.assertEqual(2, len(lookup_records))
FileService.delete_file(file_model.id) ## Assure we can delete the file.
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(28, len(lookup_data))
# Update the workflow specification file.
file_path = os.path.join(app.root_path, '..', 'tests', 'data',
'enum_options_with_search', 'sponsors_modified.xls')
file = open(file_path, 'rb')
FileService.update_file(file_model, file.read(), CONTENT_TYPES['xls'])
file.close()
# restart the workflow, so it can pick up the changes.
WorkflowProcessor(workflow, soft_reset=True)
LookupService.lookup(workflow, "sponsor", "sam", limit=10)
lookup_records = session.query(LookupFileModel).all()
lookup_record = lookup_records[0]
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(4, len(lookup_data))
def test_some_full_text_queries(self):
self.load_test_spec('enum_options_from_file')
file_model = session.query(FileModel).filter(FileModel.name == "customer_list.xls").first()
self.assertIsNotNone(file_model)
file_data_model = session.query(FileDataModel).filter(FileDataModel.file_model == file_model).first()
lookup_table = LookupService.get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
spec = BaseTest.load_test_spec('enum_options_from_file')
workflow = self.create_workflow('enum_options_from_file')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
results = LookupService._run_lookup_query(lookup_table, "medicines", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "", limit=10)
self.assertEquals(10, len(results), "Blank queries return everything, to the limit")
results = LookupService.lookup(workflow, "AllTheNames", "medicines", limit=10)
self.assertEquals(1, len(results), "words in the middle of label are detected.")
self.assertEquals("The Medicines Company", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "", limit=10)
self.assertEquals(10, len(results), "Blank queries return everything, to the limit")
results = LookupService._run_lookup_query(lookup_table, "UVA", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "UVA", limit=10)
self.assertEquals(1, len(results), "Beginning of label is found.")
self.assertEquals("UVA - INTERNAL - GM USE ONLY", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "uva", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "uva", limit=10)
self.assertEquals(1, len(results), "case does not matter.")
self.assertEquals("UVA - INTERNAL - GM USE ONLY", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "medici", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "medici", limit=10)
self.assertEquals(1, len(results), "partial words are picked up.")
self.assertEquals("The Medicines Company", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "Genetics Savings", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "Genetics Savings", limit=10)
self.assertEquals(1, len(results), "multiple terms are picked up..")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "Genetics Sav", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "Genetics Sav", limit=10)
self.assertEquals(1, len(results), "prefix queries still work with partial terms")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "Gen Sav", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "Gen Sav", limit=10)
self.assertEquals(1, len(results), "prefix queries still work with ALL the partial terms")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService._run_lookup_query(lookup_table, "Inc", limit=10)
results = LookupService.lookup(workflow, "AllTheNames", "Inc", limit=10)
self.assertEquals(7, len(results), "short terms get multiple correct results.")
self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)
results = LookupService.lookup(workflow, "AllTheNames", "reaction design", limit=10)
self.assertEquals(5, len(results), "all results come back for two terms.")
self.assertEquals("Reaction Design", results[0].label, "Exact matches come first.")
results = LookupService.lookup(workflow, "AllTheNames", "1 Something", limit=10)
self.assertEquals("1 Something", results[0].label, "Exact matches are prefered")
results = LookupService.lookup(workflow, "AllTheNames", "1 (!-Something", limit=10)
self.assertEquals("1 Something", results[0].label, "special characters don't flake out")
# 1018 10000 Something Industry
# 1019 1000 Something Industry
# 1020 1 Something Industry
# 1021 10 Something Industry
# 1022 10000 Something Industry
# Fixme: Stop words are taken into account on the query side, and haven't found a fix yet.
#results = WorkflowService.run_lookup_query(lookup_table.id, "in", limit=10)
#self.assertEquals(7, len(results), "stop words are not removed.")
#self.assertEquals("Genetics Savings & Clone, Inc.", results[0].label)

7
tests/test_protocol_builder.py
View File

@ -1,7 +1,8 @@
from unittest.mock import patch
from crc.services.protocol_builder import ProtocolBuilderService
from crc import app
from tests.base_test import BaseTest
from crc.services.protocol_builder import ProtocolBuilderService
class TestProtocolBuilder(BaseTest):
@ -10,6 +11,7 @@ class TestProtocolBuilder(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_get_studies(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('user_studies.json')
response = ProtocolBuilderService.get_studies(self.test_uid)
@ -17,6 +19,7 @@ class TestProtocolBuilder(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_get_investigators(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
response = ProtocolBuilderService.get_investigators(self.test_study_id)
@ -28,6 +31,7 @@ class TestProtocolBuilder(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_get_required_docs(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('required_docs.json')
response = ProtocolBuilderService.get_required_docs(self.test_study_id)
@ -37,6 +41,7 @@ class TestProtocolBuilder(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_get_details(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('study_details.json')
response = ProtocolBuilderService.get_study_details(self.test_study_id)

52
tests/test_request_approval_script.py Normal file
View File

@ -0,0 +1,52 @@
from crc.services.file_service import FileService
from tests.base_test import BaseTest
from crc.scripts.request_approval import RequestApproval
from crc.services.workflow_processor import WorkflowProcessor
from crc.api.common import ApiError
from crc import db
from crc.models.approval import ApprovalModel
class TestRequestApprovalScript(BaseTest):
def test_do_task(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code="UVACompl_PRCAppr",
name="anything.png", content_type="text",
binary_data=b'1234')
script = RequestApproval()
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
self.assertEquals(2, db.session.query(ApprovalModel).count())
def test_do_task_with_incorrect_argument(self):
"""This script should raise an error if it can't figure out the approvers."""
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"approvals": {'dhf8r':["invalid"], 'lb3dp':"invalid"}}
script = RequestApproval()
with self.assertRaises(ApiError):
script.do_task(task, workflow.study_id, workflow.id, "approvals")
def test_do_task_validate_only(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
script = RequestApproval()
script.do_task_validate_only(task, workflow.study_id, workflow.id, "study.approval1")
self.assertEquals(0, db.session.query(ApprovalModel).count())

68
tests/test_study_api.py
View File

@ -1,27 +1,25 @@
import json
from tests.base_test import BaseTest
from datetime import datetime, timezone
from unittest.mock import patch
from crc import session
from crc import session, app
from crc.models.protocol_builder import ProtocolBuilderStatus, \
ProtocolBuilderStudySchema
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel, StudySchema
from crc.models.workflow import WorkflowSpecModel, WorkflowModel, WorkflowSpecCategoryModel
from tests.base_test import BaseTest
from crc.services.protocol_builder import ProtocolBuilderService
class TestStudyApi(BaseTest):
TEST_STUDY = {
"id": 12345,
"title": "Phase III Trial of Genuine People Personalities (GPP) Autonomous Intelligent Emotional Agents "
"for Interstellar Spacecraft",
"last_updated": datetime.now(tz=timezone.utc),
"protocol_builder_status": ProtocolBuilderStatus.ACTIVE,
"primary_investigator_id": "tricia.marie.mcmillan@heartofgold.edu",
"sponsor": "Sirius Cybernetics Corporation",
"ind_number": "567890",
"primary_investigator_id": "tmm2x",
"user_uid": "dhf8r",
}
@ -38,35 +36,15 @@ class TestStudyApi(BaseTest):
study = session.query(StudyModel).first()
self.assertIsNotNone(study)
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies
def test_get_study(self, mock_studies, mock_details, mock_docs, mock_investigators):
def test_get_study(self):
"""Generic test, but pretty detailed, in that the study should return a categorized list of workflows
This starts with out loading the example data, to show that all the bases are covered from ground 0."""
# Mock Protocol Builder responses
studies_response = self.protocol_builder_response('user_studies.json')
mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response)
details_response = self.protocol_builder_response('study_details.json')
mock_details.return_value = json.loads(details_response)
docs_response = self.protocol_builder_response('required_docs.json')
mock_docs.return_value = json.loads(docs_response)
investigators_response = self.protocol_builder_response('investigators.json')
mock_investigators.return_value = json.loads(investigators_response)
"""NOTE: The protocol builder is not enabled or mocked out. As the master workflow (which is empty),
and the test workflow do not need it, and it is disabled in the configuration."""
self.load_example_data()
new_study = self.add_test_study()
new_study = session.query(StudyModel).filter_by(id=new_study["id"]).first()
# Add a category
new_category = WorkflowSpecCategoryModel(id=21, name="test_cat", display_name="Test Category", display_order=0)
session.add(new_category)
session.commit()
# Create a workflow specification
self.create_workflow("random_fact", study=new_study, category_id=new_category.id)
# Assure there is a master specification, and it has the lookup files it needs.
spec = self.load_test_spec("top_level_workflow", master_spec=True)
self.create_reference_document()
api_response = self.app.get('/v1.0/study/%i' % new_study.id,
headers=self.logged_in_headers(), content_type="application/json")
@ -75,13 +53,12 @@ class TestStudyApi(BaseTest):
self.assertEqual(study.title, self.TEST_STUDY['title'])
self.assertEqual(study.primary_investigator_id, self.TEST_STUDY['primary_investigator_id'])
self.assertEqual(study.sponsor, self.TEST_STUDY['sponsor'])
self.assertEqual(study.ind_number, self.TEST_STUDY['ind_number'])
self.assertEqual(study.user_uid, self.TEST_STUDY['user_uid'])
# Categories are read only, so switching to sub-scripting here.
category = [c for c in study.categories if c['name'] == "test_cat"][0]
self.assertEqual("test_cat", category['name'])
# This assumes there is one test category set up in the example data.
category = study.categories[0]
self.assertEqual("test_category", category['name'])
self.assertEqual("Test Category", category['display_name'])
self.assertEqual(1, len(category["workflows"]))
workflow = category["workflows"][0]
@ -94,7 +71,7 @@ class TestStudyApi(BaseTest):
def test_add_study(self):
self.load_example_data()
study = self.add_test_study()
db_study = session.query(StudyModel).filter_by(id=12345).first()
db_study = session.query(StudyModel).filter_by(id=study['id']).first()
self.assertIsNotNone(db_study)
self.assertEqual(study["title"], db_study.title)
self.assertEqual(study["primary_investigator_id"], db_study.primary_investigator_id)
@ -103,7 +80,7 @@ class TestStudyApi(BaseTest):
self.assertEqual(study["user_uid"], db_study.user_uid)
workflow_spec_count =session.query(WorkflowSpecModel).filter(WorkflowSpecModel.is_master_spec == False).count()
workflow_count = session.query(WorkflowModel).filter(WorkflowModel.study_id == 12345).count()
workflow_count = session.query(WorkflowModel).filter(WorkflowModel.study_id == study['id']).count()
error_count = len(study["errors"])
self.assertEqual(workflow_spec_count, workflow_count + error_count)
@ -126,6 +103,9 @@ class TestStudyApi(BaseTest):
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies
def test_get_all_studies(self, mock_studies, mock_details, mock_docs, mock_investigators):
# Enable the protocol builder for these tests, as the master_workflow and other workflows
# depend on using the PB for data.
app.config['PB_ENABLED'] = True
self.load_example_data()
s = StudyModel(
id=54321, # This matches one of the ids from the study_details_json data.
@ -208,6 +188,7 @@ class TestStudyApi(BaseTest):
self.assertEqual(study.sponsor, json_data['sponsor'])
self.assertEqual(study.ind_number, json_data['ind_number'])
def test_delete_study(self):
self.load_example_data()
study = session.query(StudyModel).first()
@ -216,20 +197,13 @@ class TestStudyApi(BaseTest):
def test_delete_study_with_workflow_and_status(self):
self.load_example_data()
study = session.query(StudyModel).first()
new_category = WorkflowSpecCategoryModel(id=21, name="test_cat", display_name="Test Category", display_order=0)
session.add(new_category)
session.commit()
# Create a workflow specification, and complete some stuff that would log stats
workflow = self.create_workflow("random_fact", study=study, category_id=new_category.id)
session.add(workflow)
session.commit()
stats2 = TaskEventModel(study_id=study.id, workflow_id=workflow.id, user_uid=self.users[0]['uid'])
workflow = session.query(WorkflowModel).first()
stats2 = TaskEventModel(study_id=workflow.study_id, workflow_id=workflow.id, user_uid=self.users[0]['uid'])
session.add(stats2)
session.commit()
rv = self.app.delete('/v1.0/study/%i' % study.id, headers=self.logged_in_headers())
rv = self.app.delete('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers())
self.assert_success(rv)
del_study = session.query(StudyModel).filter(StudyModel.id == study.id).first()
del_study = session.query(StudyModel).filter(StudyModel.id == workflow.study_id).first()
self.assertIsNone(del_study)

4
tests/test_study_details_documents.py
View File

@ -1,4 +1,5 @@
import json
from tests.base_test import BaseTest
from unittest.mock import patch
from crc import db, session
@ -10,7 +11,6 @@ from crc.scripts.study_info import StudyInfo
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from tests.base_test import BaseTest
class TestStudyDetailsDocumentsScript(BaseTest):
@ -63,7 +63,7 @@ class TestStudyDetailsDocumentsScript(BaseTest):
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
StudyInfo().do_task_validate_only(task, study.id, "documents")
StudyInfo().do_task_validate_only(task, study.id, workflow_model.id, "documents")
def test_load_lookup_data(self):
self.create_reference_document()

48
tests/test_study_service.py
View File

@ -2,7 +2,9 @@ import json
from datetime import datetime
from unittest.mock import patch
from crc import db
from tests.base_test import BaseTest
from crc import db, app
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import StudyModel
from crc.models.user import UserModel
@ -12,7 +14,6 @@ from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.services.workflow_processor import WorkflowProcessor
from example_data import ExampleDataLoader
from tests.base_test import BaseTest
class TestStudyService(BaseTest):
@ -57,7 +58,7 @@ class TestStudyService(BaseTest):
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
def test_total_tasks_updated(self, mock_docs):
"""Assure that as a users progress is available when getting a list of studies for that user."""
app.config['PB_ENABLED'] = True
docs_response = self.protocol_builder_response('required_docs.json')
mock_docs.return_value = json.loads(docs_response)
@ -73,7 +74,6 @@ class TestStudyService(BaseTest):
# workflow should not be started, and it should have 0 completed tasks, and 0 total tasks.
self.assertEqual(WorkflowStatus.not_started, workflow.status)
self.assertEqual(None, workflow.spec_version)
self.assertEqual(0, workflow.total_tasks)
self.assertEqual(0, workflow.completed_tasks)
@ -106,7 +106,7 @@ class TestStudyService(BaseTest):
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
def test_get_required_docs(self, mock_docs):
app.config['PB_ENABLED'] = True
# mock out the protocol builder
docs_response = self.protocol_builder_response('required_docs.json')
mock_docs.return_value = json.loads(docs_response)
@ -143,11 +143,9 @@ class TestStudyService(BaseTest):
# Add a document to the study with the correct code.
workflow = self.create_workflow('docx')
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_task_file(study_id=workflow.study_id, workflow_id=workflow.id,
workflow_spec_id=workflow.workflow_spec_id,
task_id="fakingthisout",
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
docs = StudyService().get_documents_status(workflow.study_id)
self.assertIsNotNone(docs)
@ -156,13 +154,31 @@ class TestStudyService(BaseTest):
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0])
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0]['file_id'])
self.assertEquals(workflow.id, docs["UVACompl_PRCAppr"]['files'][0]['workflow_id'])
self.assertEquals(workflow.workflow_spec_id, docs["UVACompl_PRCAppr"]['files'][0]['workflow_spec_id'])
# 'file_id': 123,
# 'task_id': 'abcdef14236890',
# 'workflow_id': 456,
# 'workflow_spec_id': 'irb_api_details',
# 'status': 'complete',
def test_get_all_studies(self):
user = self.create_user_with_study_and_workflow()
# Add a document to the study with the correct code.
workflow1 = self.create_workflow('docx')
workflow2 = self.create_workflow('empty_workflow')
# Add files to both workflows.
FileService.add_workflow_file(workflow_id=workflow1.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
FileService.add_workflow_file(workflow_id=workflow1.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code="AD_Consent_Model")
FileService.add_workflow_file(workflow_id=workflow2.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code="UVACompl_PRCAppr" )
studies = StudyService().get_all_studies_with_files()
self.assertEquals(1, len(studies))
self.assertEquals(3, len(studies[0].files))
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_docs
def test_get_personnel(self, mock_docs):

23
tests/test_tasks_api.py
View File

@ -3,13 +3,15 @@ import os
import random
from unittest.mock import patch
from tests.base_test import BaseTest
from crc import session, app
from crc.models.api_models import WorkflowApiSchema, MultiInstanceType, TaskSchema
from crc.models.file import FileModelSchema
from crc.models.stats import TaskEventModel
from crc.models.workflow import WorkflowStatus
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
class TestTasksApi(BaseTest):
@ -180,7 +182,6 @@ class TestTasksApi(BaseTest):
self.assertEquals("Task 2b", nav[5]['title'])
self.assertEquals("Task 3", nav[6]['title'])
def test_document_added_to_workflow_shows_up_in_file_list(self):
self.load_example_data()
self.create_reference_document()
@ -302,11 +303,16 @@ class TestTasksApi(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_multi_instance_task(self, mock_get):
self.load_example_data()
# Enable the protocol builder.
app.config['PB_ENABLED'] = True
# This depends on getting a list of investigators back from the protocol builder.
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
self.load_example_data()
workflow = self.create_workflow('multi_instance')
# get the first form in the two form workflow.
@ -328,8 +334,8 @@ class TestTasksApi(BaseTest):
workflow = self.get_workflow_api(workflow)
task = workflow.next_task
field_id = task.form['fields'][0]['id']
rv = self.app.get('/v1.0/workflow/%i/task/%s/lookup/%s?query=%s&limit=5' %
(workflow.id, task.id, field_id, 'c'), # All records with a word that starts with 'c'
rv = self.app.get('/v1.0/workflow/%i/lookup/%s?query=%s&limit=5' %
(workflow.id, field_id, 'c'), # All records with a word that starts with 'c'
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
@ -344,8 +350,8 @@ class TestTasksApi(BaseTest):
task = workflow.next_task
field_id = task.form['fields'][0]['id']
# lb3dp is a user record in the mock ldap responses for tests.
rv = self.app.get('/v1.0/workflow/%i/task/%s/lookup/%s?query=%s&limit=5' %
(workflow.id, task.id, field_id, 'lb3dp'),
rv = self.app.get('/v1.0/workflow/%s/lookup/%s?query=%s&limit=5' %
(workflow.id, field_id, 'lb3dp'),
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
@ -419,11 +425,12 @@ class TestTasksApi(BaseTest):
def test_parallel_multi_instance(self, mock_get):
# Assure we get nine investigators back from the API Call, as set in the investigators.json file.
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
self.load_example_data()
workflow = self.create_workflow('multi_instance_parallel')
workflow_api = self.get_workflow_api(workflow)

8
tests/test_tools_api.py
View File

@ -1,8 +1,8 @@
import json
import os
from crc import app
from tests.base_test import BaseTest
from crc import app
class TestStudyApi(BaseTest):
@ -22,11 +22,13 @@ class TestStudyApi(BaseTest):
{"option": "Address", "selected": False},
{"option": "Phone", "selected": True, "stored": ["Send or Transmit outside of UVA"]}]}
with open(filepath, 'rb') as f:
file_data = {'file': (f, 'my_new_file.bpmn')}
rv = self.app.put('/v1.0/render_docx?data=%s' % json.dumps(template_data),
file_data = {'file': (f, 'my_new_file.bpmn'), 'data': json.dumps(template_data)}
rv = self.app.put('/v1.0/render_docx',
data=file_data, follow_redirects=True,
content_type='multipart/form-data')
self.assert_success(rv)
self.assertIsNotNone(rv.data)
self.assertEquals('application/octet-stream', rv.content_type)
def test_list_scripts(self):
rv = self.app.get('/v1.0/list_scripts')

23
tests/test_update_study_script.py Normal file
View File

@ -0,0 +1,23 @@
from tests.base_test import BaseTest
from crc.scripts.update_study import UpdateStudy
from crc.services.workflow_processor import WorkflowProcessor
class TestUpdateStudyScript(BaseTest):
def test_do_task(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"details": {
"label": "My New Title",
"value": "dhf8r"}
}
script = UpdateStudy()
script.do_task(task, workflow.study_id, workflow.id, "title:details.label", "pi:details.value")
self.assertEquals("My New Title", workflow.study.title)
self.assertEquals("dhf8r", workflow.study.primary_investigator_id)

44
tests/test_workflow_processor.py
View File

@ -1,34 +1,31 @@
import json
import logging
import os
import json
import string
import random
from unittest.mock import patch
from SpiffWorkflow import Task as SpiffTask
from tests.base_test import BaseTest
from SpiffWorkflow.bpmn.specs.EndEvent import EndEvent
from SpiffWorkflow.camunda.specs.UserTask import Form, FormField
from SpiffWorkflow.specs import TaskSpec
from SpiffWorkflow.camunda.specs.UserTask import FormField
from crc import session, db, app
from crc.api.common import ApiError
from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
from crc.models.file import FileModel, FileDataModel
from crc.models.protocol_builder import ProtocolBuilderStudySchema
from crc.services.protocol_builder import ProtocolBuilderService
from crc.models.study import StudyModel
from crc.models.workflow import WorkflowSpecModel, WorkflowStatus, WorkflowModel
from crc.models.workflow import WorkflowSpecModel, WorkflowStatus
from crc.services.file_service import FileService
from crc.services.study_service import StudyService
from crc.models.protocol_builder import ProtocolBuilderStudySchema, ProtocolBuilderInvestigatorSchema, \
ProtocolBuilderRequiredDocumentSchema
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
class TestWorkflowProcessor(BaseTest):
def _populate_form_with_random_data(self, task):
api_task = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowProcessor.populate_form_with_random_data(task, api_task)
WorkflowService.populate_form_with_random_data(task, api_task)
def get_processor(self, study_model, spec_model):
workflow_model = StudyService._create_workflow_model(study_model, spec_model)
@ -226,10 +223,10 @@ class TestWorkflowProcessor(BaseTest):
self._populate_form_with_random_data(task)
processor.complete_task(task)
files = session.query(FileModel).filter_by(study_id=study.id, workflow_id=processor.get_workflow_id()).all()
files = session.query(FileModel).filter_by(workflow_id=processor.get_workflow_id()).all()
self.assertEqual(0, len(files))
processor.do_engine_steps()
files = session.query(FileModel).filter_by(study_id=study.id, workflow_id=processor.get_workflow_id()).all()
files = session.query(FileModel).filter_by(workflow_id=processor.get_workflow_id()).all()
self.assertEqual(1, len(files), "The task should create a new file.")
file_data = session.query(FileDataModel).filter(FileDataModel.file_model_id == files[0].id).first()
self.assertIsNotNone(file_data.data)
@ -257,12 +254,12 @@ class TestWorkflowProcessor(BaseTest):
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("decision_table")
processor = self.get_processor(study, workflow_spec_model)
self.assertTrue(processor.get_spec_version().startswith('v1.1'))
self.assertTrue(processor.get_version_string().startswith('v1.1'))
file_service = FileService()
file_service.add_workflow_spec_file(workflow_spec_model, "new_file.txt", "txt", b'blahblah')
processor = self.get_processor(study, workflow_spec_model)
self.assertTrue(processor.get_spec_version().startswith('v1.1.1'))
self.assertTrue(processor.get_version_string().startswith('v1.1.1'))
file_path = os.path.join(app.root_path, '..', 'tests', 'data', 'docx', 'docx.bpmn')
file = open(file_path, "rb")
@ -271,7 +268,7 @@ class TestWorkflowProcessor(BaseTest):
file_model = db.session.query(FileModel).filter(FileModel.name == "decision_table.bpmn").first()
file_service.update_file(file_model, data, "txt")
processor = self.get_processor(study, workflow_spec_model)
self.assertTrue(processor.get_spec_version().startswith('v2.1.1'))
self.assertTrue(processor.get_version_string().startswith('v2.1.1'))
def test_restart_workflow(self):
self.load_example_data()
@ -342,7 +339,7 @@ class TestWorkflowProcessor(BaseTest):
# Assure that creating a new processor doesn't cause any issues, and maintains the spec version.
processor.workflow_model.bpmn_workflow_json = processor.serialize()
processor2 = WorkflowProcessor(processor.workflow_model)
self.assertTrue(processor2.get_spec_version().startswith("v1 ")) # Still at version 1.
self.assertFalse(processor2.is_latest_spec) # Still at version 1.
# Do a hard reset, which should bring us back to the beginning, but retain the data.
processor3 = WorkflowProcessor(processor.workflow_model, hard_reset=True)
@ -352,16 +349,12 @@ class TestWorkflowProcessor(BaseTest):
self.assertEqual("New Step", processor3.next_task().task_spec.description)
self.assertEqual("blue", processor3.next_task().data["color"])
def test_get_latest_spec_version(self):
workflow_spec_model = self.load_test_spec("two_forms")
version = WorkflowProcessor.get_latest_version_string("two_forms")
self.assertTrue(version.startswith("v1 "))
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies')
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs')
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details')
def test_master_bpmn(self, mock_details, mock_required_docs, mock_investigators, mock_studies):
def test_master_bpmn_for_crc(self, mock_details, mock_required_docs, mock_investigators, mock_studies):
# Mock Protocol Builder response
studies_response = self.protocol_builder_response('user_studies.json')
@ -376,7 +369,8 @@ class TestWorkflowProcessor(BaseTest):
details_response = self.protocol_builder_response('study_details.json')
mock_details.return_value = json.loads(details_response)
self.load_example_data()
self.load_example_data(use_crc_data=True)
app.config['PB_ENABLED'] = True
study = session.query(StudyModel).first()
workflow_spec_model = db.session.query(WorkflowSpecModel).\

53
tests/test_workflow_service.py
View File

@ -1,10 +1,7 @@
from crc import session
from crc.models.file import FileDataModel, FileModel, LookupFileModel, LookupDataModel
from crc.services.file_service import FileService
from crc.services.lookup_service import LookupService
from tests.base_test import BaseTest
from crc.services.workflow_processor import WorkflowProcessor
from crc.services.workflow_service import WorkflowService
from tests.base_test import BaseTest
class TestWorkflowService(BaseTest):
@ -31,7 +28,7 @@ class TestWorkflowService(BaseTest):
* bullet one
* bullet two has {{replace_me}}
# other stuff.
# other stuff.
"""
expected = """
# Bigger Test
@ -39,7 +36,7 @@ class TestWorkflowService(BaseTest):
* bullet one
* bullet two has new_thing
# other stuff.
# other stuff.
"""
task.task_spec.documentation = documentation
result = WorkflowService._process_documentation(task)
@ -69,38 +66,16 @@ class TestWorkflowService(BaseTest):
task = processor.next_task()
WorkflowService.process_options(task, task.task_spec.form.fields[0])
options = task.task_spec.form.fields[0].options
self.assertEquals(19, len(options))
self.assertEquals(28, len(options))
self.assertEquals('1000', options[0]['id'])
self.assertEquals("UVA - INTERNAL - GM USE ONLY", options[0]['name'])
def test_create_lookup_file(self):
spec = self.load_test_spec('enum_options_from_file')
file_model = session.query(FileModel).filter(FileModel.name == "customer_list.xls").first()
file_data_model = session.query(FileDataModel).filter(FileDataModel.file_model == file_model).first()
LookupService.get_lookup_table_from_data_model(file_data_model, "CUSTOMER_NUMBER", "CUSTOMER_NAME")
lookup_records = session.query(LookupFileModel).all()
self.assertIsNotNone(lookup_records)
self.assertEqual(1, len(lookup_records))
lookup_record = lookup_records[0]
self.assertIsNotNone(lookup_record)
self.assertEquals("CUSTOMER_NUMBER", lookup_record.value_column)
self.assertEquals("CUSTOMER_NAME", lookup_record.label_column)
self.assertEquals("CUSTOMER_NAME", lookup_record.label_column)
lookup_data = session.query(LookupDataModel).filter(LookupDataModel.lookup_file_model == lookup_record).all()
self.assertEquals(19, len(lookup_data))
self.assertEquals("1000", lookup_data[0].value)
self.assertEquals("UVA - INTERNAL - GM USE ONLY", lookup_data[0].label)
# search_results = session.query(LookupDataModel).\
# filter(LookupDataModel.lookup_file_model_id == lookup_record.id).\
# filter(LookupDataModel.__ts_vector__.op('@@')(func.plainto_tsquery('INTERNAL'))).all()
search_results = LookupDataModel.query.filter(LookupDataModel.label.match("INTERNAL")).all()
self.assertEquals(1, len(search_results))
search_results = LookupDataModel.query.filter(LookupDataModel.label.match("internal")).all()
self.assertEquals(1, len(search_results))
# This query finds results where a word starts with "bio"
search_results = LookupDataModel.query.filter(LookupDataModel.label.match("bio:*")).all()
self.assertEquals(2, len(search_results))
def test_random_data_populate_form_on_auto_complete(self):
self.load_example_data()
workflow = self.create_workflow('enum_options_with_search')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, task_api)
self.assertTrue(isinstance(task.data["sponsor"], dict))

2
tests/test_workflow_spec_api.py
View File

@ -1,9 +1,9 @@
import json
from tests.base_test import BaseTest
from crc import session
from crc.models.file import FileModel
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
from tests.base_test import BaseTest
class TestWorkflowSpec(BaseTest):

35
tests/test_workflow_spec_validation_api.py
View File

@ -1,14 +1,14 @@
import json
import unittest
from unittest.mock import patch
from crc import session
from crc.api.common import ApiErrorSchema
from crc.models.file import FileModel
from crc.models.protocol_builder import ProtocolBuilderStudySchema
from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
from tests.base_test import BaseTest
from crc.services.protocol_builder import ProtocolBuilderService
from crc import session, app
from crc.api.common import ApiErrorSchema
from crc.models.protocol_builder import ProtocolBuilderStudySchema
from crc.models.workflow import WorkflowSpecModel
class TestWorkflowSpecValidation(BaseTest):
@ -20,22 +20,8 @@ class TestWorkflowSpecValidation(BaseTest):
json_data = json.loads(rv.get_data(as_text=True))
return ApiErrorSchema(many=True).load(json_data)
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators') # mock_studies
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies
def test_successful_validation_of_test_workflows(self, mock_studies, mock_details, mock_docs, mock_investigators):
# Mock Protocol Builder responses
studies_response = self.protocol_builder_response('user_studies.json')
mock_studies.return_value = ProtocolBuilderStudySchema(many=True).loads(studies_response)
details_response = self.protocol_builder_response('study_details.json')
mock_details.return_value = json.loads(details_response)
docs_response = self.protocol_builder_response('required_docs.json')
mock_docs.return_value = json.loads(docs_response)
investigators_response = self.protocol_builder_response('investigators.json')
mock_investigators.return_value = json.loads(investigators_response)
def test_successful_validation_of_test_workflows(self):
app.config['PB_ENABLED'] = False # Assure this is disabled.
self.assertEqual(0, len(self.validate_workflow("parallel_tasks")))
self.assertEqual(0, len(self.validate_workflow("decision_table")))
self.assertEqual(0, len(self.validate_workflow("docx")))
@ -49,7 +35,7 @@ class TestWorkflowSpecValidation(BaseTest):
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_required_docs') # mock_docs
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_study_details') # mock_details
@patch('crc.services.protocol_builder.ProtocolBuilderService.get_studies') # mock_studies
def test_successful_validation_of_auto_loaded_workflows(self, mock_studies, mock_details, mock_docs, mock_investigators):
def test_successful_validation_of_crc_workflows(self, mock_studies, mock_details, mock_docs, mock_investigators):
# Mock Protocol Builder responses
studies_response = self.protocol_builder_response('user_studies.json')
@ -61,7 +47,8 @@ class TestWorkflowSpecValidation(BaseTest):
investigators_response = self.protocol_builder_response('investigators.json')
mock_investigators.return_value = json.loads(investigators_response)
self.load_example_data()
self.load_example_data(use_crc_data=True)
app.config['PB_ENABLED'] = True
workflows = session.query(WorkflowSpecModel).all()
errors = []
for w in workflows:

23
wsgi.py Normal file
View File

@ -0,0 +1,23 @@
from werkzeug.exceptions import NotFound
from werkzeug.middleware.dispatcher import DispatcherMiddleware
from werkzeug.middleware.proxy_fix import ProxyFix
from crc import app
if __name__ == "__main__":
def no_app(environ, start_response):
return NotFound()(environ, start_response)
# Remove trailing slash, but add leading slash
base_url = '/' + app.config['APPLICATION_ROOT'].strip('/')
routes = {'/': app.wsgi_app}
if base_url != '/':
routes[base_url] = app.wsgi_app
app.wsgi_app = DispatcherMiddleware(no_app, routes)
app.wsgi_app = ProxyFix(app.wsgi_app)
flask_port = app.config['FLASK_PORT']
app.run(host='0.0.0.0', port=flask_port)