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cr-connect-workflow
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Merge branch 'dev' into feature/parallel_multiinstance_tasks

This commit is contained in:
Dan Funk 2020-06-25 23:20:38 -04:00
parent c3ceda4c2f da530c13a4
commit 150117587e
41 changed files with 776 additions and 350 deletions
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3
Pipfile
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@ -24,6 +24,8 @@ flask-restful = "*"
gunicorn = "*"
httpretty = "*"
ldap3 = "*"
lxml = "*"
markdown = "*"
marshmallow = "*"
marshmallow-enum = "*"
marshmallow-sqlalchemy = "*"
@ -42,7 +44,6 @@ webtest = "*"
werkzeug = "*"
xlrd = "*"
xlsxwriter = "*"
lxml = "*"
[requires]
python_version = "3.7"

136
Pipfile.lock generated
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"sha256:ed375a79f06cad285166e5be74745df1ed6845c5624aafadec4b7a29c25866ef",
"sha256:f35248f7e0d63b234a109dd72fbfb4b5cb6cb6840b221d0df0ecbf54ab087654",
"sha256:f502ef245c492b391e0e23e94cba030ab91722dcc56963c85bfd7f3441ea2bbe",
"sha256:fe01bac7226499aedf472c62fa3b85b2c619365f3f14dd222ffe4f3aa91e5f98"
"sha256:0942a3a0df3f6131580eddd26d99071b48cfe5aaf3eab2783076fbc5a1c1882e",
"sha256:0ec575db1b54909750332c2e335c2bb11257883914a03bc5a3306a4488ecc772",
"sha256:109581ccc8915001e8037b73c29590e78ce74be49ca0a3630a23831f9e3ed6c7",
"sha256:16593fd748944726540cd20f7e83afec816c2ac96b082e26ae226e8f7e9688cf",
"sha256:427273b08efc16a85aa2b39892817e78e3ed074fcb89b2a51c4979bae7e7ba98",
"sha256:50c4ee32f0e1581828843267d8de35c3298e86ceecd5e9017dc45788be70a864",
"sha256:512a85c3c8c3995cc91af3e90f38f460da5d3cade8dc3a229c8e0879037547c9",
"sha256:57aa843b783179ab72e863512e14bdcba186641daf69e4e3a5761d705dcc35b1",
"sha256:621f58cd921cd71ba6215c42954ffaa8a918eecd8c535d97befa1a8acad986dd",
"sha256:6ac2558631a81b85e7fb7a44e5035347938b0a73f5fdc27a8566777d0792a6a4",
"sha256:716754d0b5490bdcf68e1e4925edc02ac07209883314ad01a137642ddb2056f1",
"sha256:736d41cfebedecc6f159fc4ac0769dc89528a989471dc1d378ba07d29a60ba1c",
"sha256:8619b86cb68b185a778635be5b3e6018623c0761dde4df2f112896424aa27bd8",
"sha256:87fad64529cde4f1914a5b9c383628e1a8f9e3930304c09cf22c2ae118a1280e",
"sha256:89494df7f93b1836cae210c42864b292f9b31eeabca4810193761990dc689cce",
"sha256:8cac7bb373a5f1423e28de3fd5fc8063b9c8ffe8957dc1b1a59cb90453db6da1",
"sha256:8fd452dc3d49b3cc54483e033de6c006c304432e6f84b74d7b2c68afa2569ae5",
"sha256:adad60eea2c4c2a1875eb6305a0b6e61a83163f8e233586a4d6a55221ef984fe",
"sha256:c26f95e7609b821b5f08a72dab929baa0d685406b953efd7c89423a511d5c413",
"sha256:cbe1324ef52ff26ccde2cb84b8593c8bf930069dfc06c1e616f1bfd4e47f48a3",
"sha256:d05c4adae06bd0c7f696ae3ec8d993ed8ffcc4e11a76b1b35a5af8a099bd2284",
"sha256:d98bc827a1293ae767c8f2f18be3bb5151fd37ddcd7da2a5f9581baeeb7a3fa1",
"sha256:da2fb75f64792c1fc64c82313a00c728a7c301efe6a60b7a9fe35b16b4368ce7",
"sha256:e4624d7edb2576cd72bb83636cd71c8ce544d8e272f308bd80885056972ca299",
"sha256:e89e0d9e106f8a9180a4ca92a6adde60c58b1b0299e1b43bd5e0312f535fbf33",
"sha256:f11c2437fb5f812d020932119ba02d9e2bc29a6eca01a055233a8b449e3e1e7d",
"sha256:f57be5673e12763dd400fea568608700a63ce1c6bd5bdbc3cc3a2c5fdb045274",
"sha256:fc728ece3d5c772c196fd338a99798e7efac7a04f9cb6416299a3638ee9a94cd"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.3.17"
"version": "==1.3.18"
},
"swagger-ui-bundle": {
"hashes": [
@ -968,7 +927,6 @@
"sha256:3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527",
"sha256:88206b0eb87e6d677d424843ac5209e3fb9d0190d0ee169599165ec25e9d9115"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
"version": "==1.25.9"
},
"vine": {
@ -976,7 +934,6 @@
"sha256:133ee6d7a9016f177ddeaf191c1f58421a1dcc6ee9a42c58b34bed40e1d2cd87",
"sha256:ea4947cc56d1fd6f2095c8d543ee25dad966f78692528e68b4fada11ba3f98af"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.3.0"
},
"waitress": {
@ -984,7 +941,6 @@
"sha256:1bb436508a7487ac6cb097ae7a7fe5413aefca610550baf58f0940e51ecfb261",
"sha256:3d633e78149eb83b60a07dfabb35579c29aac2d24bb803c18b26fb2ab1a584db"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==1.4.4"
},
"webob": {
@ -992,7 +948,6 @@
"sha256:a3c89a8e9ba0aeb17382836cdb73c516d0ecf6630ec40ec28288f3ed459ce87b",
"sha256:aa3a917ed752ba3e0b242234b2a373f9c4e2a75d35291dcbe977649bd21fd108"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.8.6"
},
"webtest": {
@ -1039,7 +994,6 @@
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
],
"markers": "python_version >= '3.6'",
"version": "==3.1.0"
}
},
@ -1049,7 +1003,6 @@
"sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c",
"sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==19.3.0"
},
"coverage": {
@ -1102,7 +1055,6 @@
"sha256:68c70cc7167bdf5c7c9d8f6954a7837089c6a36bf565383919bb595efb8a17e5",
"sha256:b78134b2063dd214000685165d81c154522c3ee0a1c0d4d113c80361c234c5a2"
],
"markers": "python_version >= '3.5'",
"version": "==8.4.0"
},
"packaging": {
@ -1110,7 +1062,6 @@
"sha256:4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8",
"sha256:998416ba6962ae7fbd6596850b80e17859a5753ba17c32284f67bfff33784181"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==20.4"
},
"pbr": {
@ -1126,7 +1077,6 @@
"sha256:15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0",
"sha256:966c145cd83c96502c3c3868f50408687b38434af77734af1e9ca461a4081d2d"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==0.13.1"
},
"py": {
@ -1134,7 +1084,6 @@
"sha256:366389d1db726cd2fcfc79732e75410e5fe4d31db13692115529d34069a043c2",
"sha256:9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.9.0"
},
"pyparsing": {
@ -1142,7 +1091,6 @@
"sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1",
"sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
],
"markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.4.7"
},
"pytest": {
@ -1158,7 +1106,6 @@
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.15.0"
},
"wcwidth": {
@ -1173,7 +1120,6 @@
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
],
"markers": "python_version >= '3.6'",
"version": "==3.1.0"
}
}

1
config/default.py
View File

@ -46,6 +46,7 @@ LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
# Email configuration
DEFAULT_SENDER = 'askresearch@virginia.edu'
FALLBACK_EMAILS = ['askresearch@virginia.edu', 'sartographysupport@googlegroups.com']
MAIL_DEBUG = environ.get('MAIL_DEBUG', default=True)
MAIL_SERVER = environ.get('MAIL_SERVER', default='smtp.mailtrap.io')

5
crc/__init__.py
View File

@ -34,6 +34,9 @@ db = SQLAlchemy(app)
session = db.session
""":type: sqlalchemy.orm.Session"""
# Mail settings
mail = Mail(app)
migrate = Migrate(app, db)
ma = Marshmallow(app)
@ -58,8 +61,6 @@ if app.config['ENABLE_SENTRY']:
# Jinja environment definition, used to render mail templates
template_dir = os.getcwd() + '/crc/static/templates/mails'
env = Environment(loader=FileSystemLoader(template_dir))
# Mail settings
mail = Mail(app)
print('=== USING THESE CONFIG SETTINGS: ===')
print('APPLICATION_ROOT = ', app.config['APPLICATION_ROOT'])

15
crc/api.yml
View File

@ -923,6 +923,21 @@ paths:
application/json:
schema:
type: object
/health_attesting:
get:
operationId: crc.api.approval.get_health_attesting_csv
summary: Returns a CSV file with health attesting records
tags:
- Approvals
responses:
'200':
description: A CSV file
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
components:
securitySchemes:
jwt:

76
crc/api/approval.py
View File

@ -1,9 +1,11 @@
import csv
import io
import json
import pickle
from base64 import b64decode
from datetime import datetime
from flask import g
from flask import g, make_response
from crc import db, session
from crc.api.common import ApiError
@ -88,71 +90,25 @@ def get_approvals_for_study(study_id=None):
return results
def get_health_attesting_csv():
records = ApprovalService.get_health_attesting_records()
si = io.StringIO()
cw = csv.writer(si)
cw.writerows(records)
output = make_response(si.getvalue())
output.headers["Content-Disposition"] = "attachment; filename=health_attesting.csv"
output.headers["Content-type"] = "text/csv"
return output
# ----- Begin descent into madness ---- #
def get_csv():
"""A damn lie, it's a json file. A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
man to do just about anything"""
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
output = []
errors = []
for approval in approvals:
try:
if approval.status != ApprovalStatus.APPROVED.value:
continue
for related_approval in approval.related_approvals:
if related_approval.status != ApprovalStatus.APPROVED.value:
continue
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
data = json.loads(workflow.bpmn_workflow_json)
last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
personnel = extract_value(last_task, 'personnel')
training_val = extract_value(last_task, 'RequiredTraining')
pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
review_complete = 'AllRequiredTraining' in training_val
pi_uid = workflow.study.primary_investigator_id
pi_details = LdapService.user_info(pi_uid)
details = []
details.append(pi_details)
for person in personnel:
uid = person['PersonnelComputingID']['value']
details.append(LdapService.user_info(uid))
content = ApprovalService.get_not_really_csv_content()
for person in details:
record = {
"study_id": approval.study_id,
"pi_uid": pi_details.uid,
"pi": pi_details.display_name,
"name": person.display_name,
"uid": person.uid,
"email": person.email_address,
"supervisor": "",
"review_complete": review_complete,
}
# We only know the PI's supervisor.
if person.uid == pi_details.uid:
record["supervisor"] = pi_supervisor
return content
output.append(record)
except Exception as e:
errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
return {"results": output, "errors": errors }
def extract_value(task, key):
if key in task['data']:
return pickle.loads(b64decode(task['data'][key]['__bytes__']))
else:
return ""
def find_task(uuid, task):
if task['id']['__uuid__'] == uuid:
return task
for child in task['children']:
task = find_task(uuid, child)
if task:
return task
# ----- come back to the world of the living ---- #

4
crc/api/tools.py
View File

@ -14,7 +14,7 @@ from crc.services.mails import send_test_email
def render_markdown(data, template):
"""
Provides a quick way to very that a Jinja markdown template will work properly on a given json
Provides a quick way to very that a Jinja markdown template will work properly on a given json
data structure. Useful for folks that are building these markdown templates.
"""
try:
@ -65,4 +65,4 @@ def send_email(address):
"""Just sends a quick test email to assure the system is working."""
if not address:
address = "dan@sartography.com"
return send_test_email(address, [address])
return send_test_email(address, [address])

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

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

3
crc/models/ldap.py
View File

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

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

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

2
crc/scripts/fact_service.py
View File

@ -5,7 +5,7 @@ from crc.scripts.script import Script
class FactService(Script):
def get_description(self):
return """Just your basic class that can pull in data from a few api endpoints and
return """Just your basic class that can pull in data from a few api endpoints and
do a basic task."""
def get_cat(self):

128
crc/services/approval_service.py
View File

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

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

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

2
crc/services/file_service.py
View File

@ -58,7 +58,7 @@ class FileService(object):
"irb_docunents.xslx reference file. This code is not found in that file '%s'" % irb_doc_code)
"""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
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)\

151
crc/services/mails.py
View File

@ -3,13 +3,15 @@ import os
from flask import render_template, render_template_string
from flask_mail import Message
from crc.services.email_service import EmailService
# TODO: Extract common mailing code into its own function
def send_test_email(sender, recipients):
try:
msg = Message('Research Ramp-up Plan test',
sender=sender,
recipients=recipients)
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_approval_request_first_review.txt')
template_vars = {'primary_investigator': "test"}
@ -20,109 +22,84 @@ def send_test_email(sender, recipients):
except Exception as e:
return str(e)
def send_mail(subject, sender, recipients, content, content_html, study_id=None):
EmailService.add_email(subject=subject, sender=sender, recipients=recipients,
content=content, content_html=content_html, study_id=study_id)
def send_ramp_up_submission_email(sender, recipients, approver_1, approver_2=None):
try:
msg = Message('Research Ramp-up Plan Submitted',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_submission.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_submission.html')
msg.html = template.render(template_vars)
from crc import env
subject = 'Research Ramp-up Plan Submitted'
mail.send(msg)
except Exception as e:
return str(e)
template = env.get_template('ramp_up_submission.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
content = template.render(template_vars)
template = env.get_template('ramp_up_submission.html')
content_html = template.render(template_vars)
result = send_mail(subject, sender, recipients, content, content_html)
return result
def send_ramp_up_approval_request_email(sender, recipients, primary_investigator):
try:
msg = Message('Research Ramp-up Plan Approval Request',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_approval_request.txt')
template_vars = {'primary_investigator': primary_investigator}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approval_request.html')
msg.html = template.render(template_vars)
from crc import env
subject = 'Research Ramp-up Plan Approval Request'
mail.send(msg)
except Exception as e:
return str(e)
template = env.get_template('ramp_up_approval_request.txt')
template_vars = {'primary_investigator': primary_investigator}
content = template.render(template_vars)
template = env.get_template('ramp_up_approval_request.html')
content_html = template.render(template_vars)
result = send_mail(subject, sender, recipients, content, content_html)
return result
def send_ramp_up_approval_request_first_review_email(sender, recipients, primary_investigator):
try:
msg = Message('Research Ramp-up Plan Approval Request',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env, mail
template = env.get_template('ramp_up_approval_request_first_review.txt')
template_vars = {'primary_investigator': primary_investigator}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approval_request_first_review.html')
msg.html = template.render(template_vars)
from crc import env
subject = 'Research Ramp-up Plan Approval Request'
mail.send(msg)
except Exception as e:
return str(e)
template = env.get_template('ramp_up_approval_request_first_review.txt')
template_vars = {'primary_investigator': primary_investigator}
content = template.render(template_vars)
template = env.get_template('ramp_up_approval_request_first_review.html')
content_html = template.render(template_vars)
result = send_mail(subject, sender, recipients, content, content_html)
return result
def send_ramp_up_approved_email(sender, recipients, approver_1, approver_2=None):
try:
msg = Message('Research Ramp-up Plan Approved',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env
subject = 'Research Ramp-up Plan Approved'
from crc import env, mail
template = env.get_template('ramp_up_approved.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_approved.html')
msg.html = template.render(template_vars)
template = env.get_template('ramp_up_approved.txt')
template_vars = {'approver_1': approver_1, 'approver_2': approver_2}
content = template.render(template_vars)
template = env.get_template('ramp_up_approved.html')
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
def send_ramp_up_denied_email(sender, recipients, approver):
try:
msg = Message('Research Ramp-up Plan Denied',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env
subject = 'Research Ramp-up Plan Denied'
from crc import env, mail
template = env.get_template('ramp_up_denied.txt')
template_vars = {'approver': approver}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_denied.html')
msg.html = template.render(template_vars)
template = env.get_template('ramp_up_denied.txt')
template_vars = {'approver': approver}
content = template.render(template_vars)
template = env.get_template('ramp_up_denied.html')
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result
def send_ramp_up_denied_email_to_approver(sender, recipients, primary_investigator, approver_2):
try:
msg = Message('Research Ramp-up Plan Denied',
sender=sender,
recipients=recipients,
bcc=['rrt_emails@googlegroups.com'])
from crc import env
subject = 'Research Ramp-up Plan Denied'
from crc import env, mail
template = env.get_template('ramp_up_denied_first_approver.txt')
template_vars = {'primary_investigator': primary_investigator, 'approver_2': approver_2}
msg.body = template.render(template_vars)
template = env.get_template('ramp_up_denied_first_approver.html')
msg.html = template.render(template_vars)
template = env.get_template('ramp_up_denied_first_approver.txt')
template_vars = {'primary_investigator': primary_investigator, 'approver_2': approver_2}
content = template.render(template_vars)
template = env.get_template('ramp_up_denied_first_approver.html')
content_html = template.render(template_vars)
mail.send(msg)
except Exception as e:
return str(e)
result = send_mail(subject, sender, recipients, content, content_html)
return result

3
crc/services/study_service.py
View File

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

8
crc/services/workflow_processor.py
View File

@ -1,5 +1,6 @@
import re
from lxml import etree
import shlex
from datetime import datetime
from typing import List
@ -13,7 +14,6 @@ from SpiffWorkflow.camunda.parser.CamundaParser import CamundaParser
from SpiffWorkflow.dmn.parser.BpmnDmnParser import BpmnDmnParser
from SpiffWorkflow.exceptions import WorkflowTaskExecException
from SpiffWorkflow.specs import WorkflowSpec
from sqlalchemy import desc
from crc import session
from crc.api.common import ApiError
@ -36,7 +36,9 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
This allows us to reference custom code from the BPMN diagram.
"""
commands = script.split(" ")
# Shlex splits the whole string while respecting double quoted strings within
commands = shlex.split(script)
printable_comms = commands
path_and_command = commands[0].rsplit(".", 1)
if len(path_and_command) == 1:
module_name = "crc.scripts." + self.camel_to_snake(path_and_command[0])
@ -60,7 +62,7 @@ class CustomBpmnScriptEngine(BpmnScriptEngine):
"does not properly implement the CRC Script class.",
task=task)
if task.workflow.data[WorkflowProcessor.VALIDATION_PROCESS_KEY]:
"""If this is running a validation, and not a normal process, then we want to
"""If this is running a validation, and not a normal process, then we want to
mimic running the script, but not make any external calls or database changes."""
klass().do_task_validate_only(task, study_id, workflow_id, *commands[1:])
else:

2
crc/services/workflow_service.py
View File

@ -39,7 +39,7 @@ class WorkflowService(object):
the workflow Processor should be hidden behind this service.
This will help maintain a structure that avoids circular dependencies.
But for now, this contains tools for converting spiff-workflow models into our
own API models with additional information and capabilities and
own API models with additional information and capabilities and
handles the testing of a workflow specification by completing it with
random selections, attempting to mimic a front end as much as possible. """

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

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

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

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

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

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

@ -57,6 +57,32 @@ class TestApprovalsService(BaseTest):
self.assertEqual(1, models[0].version)
self.assertEqual(2, models[1].version)
def test_get_health_attesting_records(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
records = ApprovalService.get_health_attesting_records()
self.assertEqual(len(records), 1)
def test_get_not_really_csv_content(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
records = ApprovalService.get_not_really_csv_content()
self.assertEqual(len(records), 2)
def test_new_approval_sends_proper_emails(self):
self.assertEqual(1, 1)

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

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

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

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

@ -175,9 +175,6 @@ Your random fact is:
<bpmndi:BPMNShape id="UserTask_186s7tw_di" bpmnElement="Task_User_Select_Type">
<dc:Bounds x="270" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
<dc:Bounds x="470" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="EndEvent_0u1cgrf_di" bpmnElement="EndEvent_0u1cgrf">
<dc:Bounds x="692" y="232" width="36" height="36" />
</bpmndi:BPMNShape>
@ -187,6 +184,9 @@ Your random fact is:
<bpmndi:BPMNShape id="TextAnnotation_1234e5n_di" bpmnElement="TextAnnotation_1234e5n">
<dc:Bounds x="570" y="120" width="100" height="68" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="ScriptTask_10keafb_di" bpmnElement="Task_Get_Fact_From_API">
<dc:Bounds x="470" y="210" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Association_1cfasjp_di" bpmnElement="Association_1cfasjp">
<di:waypoint x="344" y="210" />
<di:waypoint x="359" y="184" />

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

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

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

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

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

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

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

@ -61,14 +61,14 @@ class TestFileService(BaseTest):
# Archive the file
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(1, len(file_models))
self.assertEqual(1, len(file_models))
file_model = file_models[0]
file_model.archived = True
db.session.add(file_model)
# Assure that the file no longer comes back.
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEquals(0, len(file_models))
self.assertEqual(0, len(file_models))
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,

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

@ -91,7 +91,6 @@ class TestFilesApi(BaseTest):
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
def test_archive_file_no_longer_shows_up(self):
self.load_example_data()
self.create_reference_document()
@ -109,21 +108,16 @@ class TestFilesApi(BaseTest):
self.assert_success(rv)
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEquals(1, len(json.loads(rv.get_data(as_text=True))))
self.assertEqual(1, len(json.loads(rv.get_data(as_text=True))))
file_model = db.session.query(FileModel).filter(FileModel.workflow_id == workflow.id).all()
self.assertEquals(1, len(file_model))
self.assertEqual(1, len(file_model))
file_model[0].archived = True
db.session.commit()
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id, headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEquals(0, len(json.loads(rv.get_data(as_text=True))))
self.assertEqual(0, len(json.loads(rv.get_data(as_text=True))))
def test_set_reference_file(self):
file_name = "irb_document_types.xls"
@ -285,8 +279,8 @@ class TestFilesApi(BaseTest):
.filter(ApprovalModel.status == ApprovalStatus.PENDING.value)\
.filter(ApprovalModel.study_id == workflow.study_id).all()
self.assertEquals(1, len(approvals))
self.assertEquals(1, len(approvals[0].approval_files))
self.assertEqual(1, len(approvals))
self.assertEqual(1, len(approvals[0].approval_files))
def test_change_primary_bpmn(self):

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

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

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

55
tests/test_mails.py
View File

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

32
tests/test_tasks_api.py
View File

@ -47,7 +47,7 @@ class TestTasksApi(BaseTest):
# The total number of tasks may change over time, as users move through gateways
# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
self.assertIsNotNone(workflow.total_tasks)
self.assertEquals(prev_completed_task_count + 1, workflow.completed_tasks)
self.assertEqual(prev_completed_task_count + 1, workflow.completed_tasks)
# Assure a record exists in the Task Events
task_events = session.query(TaskEventModel) \
.filter_by(workflow_id=workflow.id) \
@ -56,25 +56,25 @@ class TestTasksApi(BaseTest):
self.assertGreater(len(task_events), 0)
event = task_events[0]
self.assertIsNotNone(event.study_id)
self.assertEquals("dhf8r", event.user_uid)
self.assertEquals(workflow.id, event.workflow_id)
self.assertEquals(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEquals(workflow.spec_version, event.spec_version)
self.assertEquals(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEquals(task_in.id, task_id)
self.assertEquals(task_in.name, event.task_name)
self.assertEquals(task_in.title, event.task_title)
self.assertEquals(task_in.type, event.task_type)
self.assertEquals("COMPLETED", event.task_state)
self.assertEqual("dhf8r", event.user_uid)
self.assertEqual(workflow.id, event.workflow_id)
self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEqual(workflow.spec_version, event.spec_version)
self.assertEqual(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEqual(task_in.id, task_id)
self.assertEqual(task_in.name, event.task_name)
self.assertEqual(task_in.title, event.task_title)
self.assertEqual(task_in.type, event.task_type)
self.assertEqual("COMPLETED", event.task_state)
# Not sure what vodoo is happening inside of marshmallow to get me in this state.
if isinstance(task_in.multi_instance_type, MultiInstanceType):
self.assertEquals(task_in.multi_instance_type.value, event.mi_type)
self.assertEqual(task_in.multi_instance_type.value, event.mi_type)
else:
self.assertEquals(task_in.multi_instance_type, event.mi_type)
self.assertEqual(task_in.multi_instance_type, event.mi_type)
self.assertEquals(task_in.multi_instance_count, event.mi_count)
self.assertEquals(task_in.multi_instance_index, event.mi_index)
self.assertEquals(task_in.process_name, event.process_name)
self.assertEqual(task_in.multi_instance_count, event.mi_count)
self.assertEqual(task_in.multi_instance_index, event.mi_index)
self.assertEqual(task_in.process_name, event.process_name)
self.assertIsNotNone(event.date)
# Assure that there is data in the form_data

0
tests/test_workflow_processor.py → tests/workflow/test_workflow_processor.py
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0
tests/test_workflow_processor_multi_instance.py → tests/workflow/test_workflow_processor_multi_instance.py
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0
tests/test_workflow_service.py → tests/workflow/test_workflow_service.py
View File

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

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