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Merge branch 'rrt/dev' into rrt/testing

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This commit is contained in:
Aaron Louie 2020-06-07 19:57:09 -04:00
commit af1c848f65
10 changed files with 201 additions and 59 deletions
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56
Pipfile.lock generated
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2
config/default.py
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@ -42,7 +42,7 @@ PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL +
PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/') # No trailing slash or http://
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=3))
LDAP_TIMEOUT_SEC = int(environ.get('LDAP_TIMEOUT_SEC', default=1))
# Email configuration
FALLBACK_EMAILS = ['askresearch@virginia.edu', 'sartographysupport@googlegroups.com']

6
crc/__init__.py
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@ -81,3 +81,9 @@ def load_example_rrt_data():
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
ExampleDataLoader().load_rrt()
@app.cli.command()
def clear_db():
"""Load example data into the database."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()

58
crc/api.yml
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@ -806,14 +806,42 @@ paths:
type: array
items:
$ref: "#/components/schemas/Script"
/approval:
/approval-counts:
parameters:
- name: everything
- name: as_user
in: query
required: false
description: If set to true, returns all the approvals known to the system.
description: If provided, returns the approval counts for that user.
schema:
type: boolean
type: string
get:
operationId: crc.api.approval.get_approval_counts
summary: Provides counts for approvals by status for the given user, or all users if no user is provided
tags:
- Approvals
responses:
'200':
description: An dictionary of Approval Statuses and the counts for each
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/ApprovalCounts"
/approval:
parameters:
- name: status
in: query
required: false
description: If provided, returns just approvals for the given status.
schema:
type: string
- name: as_user
in: query
required: false
description: If provided, returns the approval results as they would appear for that user.
schema:
type: string
get:
operationId: crc.api.approval.get_approvals
summary: Provides a list of workflows approvals
@ -1280,4 +1308,26 @@ components:
type: number
format: integer
example: 5
ApprovalCounts:
properties:
PENDING:
type: number
format: integer
example: 5
APPROVED:
type: number
format: integer
example: 5
DECLINED:
type: number
format: integer
example: 5
CANCELED:
type: number
format: integer
example: 5
AWAITING:
type: number
format: integer
example: 5

67
crc/api/approval.py
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@ -13,11 +13,63 @@ from crc.services.approval_service import ApprovalService
from crc.services.ldap_service import LdapService
def get_approvals(everything=False):
if everything:
approvals = ApprovalService.get_all_approvals(include_cancelled=True)
else:
approvals = ApprovalService.get_approvals_per_user(g.user.uid, include_cancelled=False)
# Returns counts of approvals in each status group assigned to the given user.
# The goal is to return results as quickly as possible.
def get_approval_counts(as_user=None):
uid = as_user or g.user.uid
db_user_approvals = db.session.query(ApprovalModel)\
.filter_by(approver_uid=uid)\
.filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
.all()
study_ids = [a.study_id for a in db_user_approvals]
print('study_ids', study_ids)
db_other_approvals = db.session.query(ApprovalModel)\
.filter(ApprovalModel.study_id.in_(study_ids))\
.filter(ApprovalModel.approver_uid != uid)\
.filter(ApprovalModel.status != ApprovalStatus.CANCELED.name)\
.all()
# Make a dict of the other approvals where the key is the study id and the value is the approval
# TODO: This won't work if there are more than 2 approvals with the same study_id
other_approvals = {}
for approval in db_other_approvals:
other_approvals[approval.study_id] = approval
counts = {}
for status in ApprovalStatus:
counts[status.name] = 0
for approval in db_user_approvals:
# Check if another approval has the same study id
if approval.study_id in other_approvals:
other_approval = other_approvals[approval.study_id]
# Other approval takes precedence over this one
if other_approval.id < approval.id:
if other_approval.status == ApprovalStatus.PENDING.name:
counts[ApprovalStatus.AWAITING.name] += 1
elif other_approval.status == ApprovalStatus.DECLINED.name:
counts[ApprovalStatus.DECLINED.name] += 1
elif other_approval.status == ApprovalStatus.CANCELED.name:
counts[ApprovalStatus.CANCELED.name] += 1
elif other_approval.status == ApprovalStatus.APPROVED.name:
counts[approval.status] += 1
else:
counts[approval.status] += 1
return counts
def get_approvals(status=None, as_user=None):
#status = ApprovalStatus.PENDING.value
user = g.user.uid
if as_user:
user = as_user
approvals = ApprovalService.get_approvals_per_user(user, status,
include_cancelled=False)
results = ApprovalSchema(many=True).dump(approvals)
return results
@ -29,7 +81,7 @@ def get_approvals_for_study(study_id=None):
return results
# ----- Being decent into madness ---- #
# ----- 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"""
@ -79,12 +131,14 @@ def get_csv():
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
@ -94,6 +148,7 @@ def find_task(uuid, task):
return task
# ----- come back to the world of the living ---- #
def update_approval(approval_id, body):
if approval_id is None:
raise ApiError('unknown_approval', 'Please provide a valid Approval ID.')

5
crc/models/approval.py
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@ -20,6 +20,9 @@ class ApprovalStatus(enum.Enum):
DECLINED = "DECLINED" # rejected by the reviewer
CANCELED = "CANCELED" # The document was replaced with a new version and this review is no longer needed.
# Used for overall status only, never set on a task.
AWAITING = "AWAITING" # awaiting another approval
class ApprovalFile(db.Model):
file_data_id = db.Column(db.Integer, db.ForeignKey(FileDataModel.id), primary_key=True)
@ -81,13 +84,13 @@ class Approval(object):
instance.associated_files = []
for approval_file in model.approval_files:
try:
# fixme: This is slow because we are doing a ton of queries to find the irb code.
extra_info = doc_dictionary[approval_file.file_data.file_model.irb_doc_code]
except:
extra_info = None
associated_file = {}
associated_file['id'] = approval_file.file_data.file_model.id
if extra_info:
irb_doc_code = approval_file.file_data.file_model.irb_doc_code
associated_file['name'] = '_'.join((extra_info['category1'],
approval_file.file_data.file_model.name))
associated_file['description'] = extra_info['description']

3
crc/scripts/request_approval.py
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@ -11,7 +11,8 @@ class RequestApproval(Script):
return """
Creates an approval request on this workflow, by the given approver_uid(s),"
Takes multiple arguments, which should point to data located in current task
or be quoted strings.
or be quoted strings. The order is important. Approvals will be processed
in this order.
Example:
RequestApproval approver1 "dhf8r"

48
crc/services/approval_service.py
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@ -19,44 +19,70 @@ from crc.services.mails import (
send_ramp_up_denied_email_to_approver
)
class ApprovalService(object):
"""Provides common tools for working with an Approval"""
@staticmethod
def __one_approval_from_study(study, approver_uid = None, include_cancelled=True):
def __one_approval_from_study(study, approver_uid = None, status=None,
include_cancelled=True):
"""Returns one approval, with all additional approvals as 'related_approvals',
the main approval can be pinned to an approver with an optional argument.
Will return null if no approvals exist on the study."""
main_approval = None
related_approvals = []
query = db.session.query(ApprovalModel).\
filter(ApprovalModel.study_id == study.id)
query = db.session.query(ApprovalModel).filter(ApprovalModel.study_id == study.id)
if not include_cancelled:
query=query.filter(ApprovalModel.status != ApprovalStatus.CANCELED.value)
approvals = query.all() # All non-cancelled approvals.
approvals = query.all()
for approval_model in approvals:
if approval_model.approver_uid == approver_uid:
main_approval = Approval.from_model(approval_model)
main_approval = approval_model
else:
related_approvals.append(Approval.from_model(approval_model))
related_approvals.append(approval_model)
# IF WE ARE JUST RETURNING ALL OF THE APPROVALS PER STUDY
if not main_approval and len(related_approvals) > 0:
main_approval = related_approvals[0]
related_approvals = related_approvals[1:]
if len(related_approvals) > 0:
main_approval.related_approvals = related_approvals
if main_approval is not None: # May be null if the study has no approvals.
final_status = ApprovalService.__calculate_overall_approval_status(main_approval, related_approvals)
if status and final_status != status: return # Now that we are certain of the status, filter on it.
main_approval = Approval.from_model(main_approval)
main_approval.status = final_status
for ra in related_approvals:
main_approval.related_approvals.append(Approval.from_model(ra))
return main_approval
@staticmethod
def get_approvals_per_user(approver_uid, include_cancelled=False):
def __calculate_overall_approval_status(approval, related):
# In the case of pending approvals, check to see if there is a related approval
# that proceeds this approval - and if it is declined, or still pending, then change
# the state of the approval to be Declined, or Waiting respectively.
if approval.status == ApprovalStatus.PENDING.value:
for ra in related:
if ra.id < approval.id:
if ra.status == ApprovalStatus.DECLINED.value or ra.status == ApprovalStatus.CANCELED.value:
return ra.status # If any prior approval id declined or cancelled so is this approval.
elif ra.status == ApprovalStatus.PENDING.value:
return ApprovalStatus.AWAITING.value # if any prior approval is pending, then this is waiting.
return approval.status
else:
return approval.status
@staticmethod
def get_approvals_per_user(approver_uid, status=None, include_cancelled=False):
"""Returns a list of approval objects (not db models) for the given
approver. """
studies = db.session.query(StudyModel).join(ApprovalModel).\
filter(ApprovalModel.approver_uid == approver_uid).all()
approvals = []
for study in studies:
approval = ApprovalService.__one_approval_from_study(study, approver_uid, include_cancelled)
approval = ApprovalService.__one_approval_from_study(study, approver_uid,
status, include_cancelled)
if approval:
approvals.append(approval)
return approvals

4
crc/services/ldap_service.py
View File

@ -18,7 +18,7 @@ class LdapService(object):
user_or_last_name_search = "(&(objectclass=person)(|(uid=%s*)(sn=%s*)))"
cn_single_search = '(&(objectclass=person)(cn=%s*))'
cn_double_search = '(&(objectclass=person)(&(cn=%s*)(cn=*%s*)))'
temp_cache = {}
conn = None
@staticmethod
@ -43,6 +43,7 @@ class LdapService(object):
def user_info(uva_uid):
user_info = db.session.query(LdapModel).filter(LdapModel.uid == uva_uid).first()
if not user_info:
app.logger.info("No cache for " + uva_uid)
search_string = LdapService.uid_search_string % uva_uid
conn = LdapService.__get_conn()
conn.search(LdapService.search_base, search_string, attributes=LdapService.attributes)
@ -51,6 +52,7 @@ class LdapService(object):
entry = conn.entries[0]
user_info = LdapModel.from_entry(entry)
db.session.add(user_info)
db.session.commit()
return user_info
@staticmethod

11
tests/test_approvals_api.py
View File

@ -68,16 +68,15 @@ class TestApprovals(BaseTest):
approval = response[0]
self.assertEqual(approval['approver']['uid'], approver_uid)
def test_list_approvals_per_admin(self):
"""All approvals will be returned"""
rv = self.app.get('/v1.0/approval?everything=true', headers=self.logged_in_headers())
def test_list_approvals_as_user(self):
"""All approvals as different user"""
rv = self.app.get('/v1.0/approval?as_user=lb3dp', headers=self.logged_in_headers())
self.assert_success(rv)
response = json.loads(rv.get_data(as_text=True))
# Returned approvals should match what's in the db, we should get one approval back
# per study (2 studies), and that approval should have one related approval.
approvals_count = ApprovalModel.query.count()
# Returned approvals should match what's in the db for user ld3dp, we should get one
# approval back per study (2 studies), and that approval should have one related approval.
response_count = len(response)
self.assertEqual(2, response_count)