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cr-connect-workflow
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Merge pull request #347 from sartography/bug/pi_name_missing_246 

Bug/pi name missing 246
This commit is contained in:
Dan Funk 2021-08-10 16:29:09 -04:00 committed by GitHub
parent cdf454b705 848c2e622f
commit fd468f1013
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10 changed files with 140 additions and 107 deletions
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41
crc/api.yml Normal file → Executable file
View File

@ -190,8 +190,8 @@ paths:
/workflow_sync/{workflow_spec_id}/spec:
parameters:
- name: workflow_spec_id
required: true
in: path
required: true
description: The unique id of an existing workflow specification to modify.
schema:
type: string
@ -394,6 +394,30 @@ paths:
application/json:
schema:
$ref: "#/components/schemas/Study"
/study/{study_id}/associates:
parameters:
- name: study_id
in: path
required: true
description: The id of the study for which associates should be returned.
schema:
type: integer
format: int32
get:
operationId: crc.api.study.get_study_associates
summary: Provides a list of associates for a particular study
tags:
- Studies
responses:
'200':
description: list of Study Associate Objects
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/StudyAssociate"
/workflow-specification:
get:
operationId: crc.api.workflow.all_specifications
@ -561,7 +585,7 @@ paths:
- name: test_until
in: query
required: false
description: Optional name of task to stop validating at
description: Optional name of task to stop validating at
schema:
type: string
get:
@ -1607,6 +1631,17 @@ components:
type: string
x-nullable: true
example: "27b-6-1212"
StudyAssociate:
properties:
uid:
type: string
example: "dhf8r"
access:
type: boolean
example: False
role:
type: string
example: "TODO"
DocumentDirectory:
properties:
level:
@ -1727,7 +1762,7 @@ components:
example: "random_fact"
x-nullable: true
file:
type: string
type: string
Workflow:
properties:
id:

6
crc/api/study.py
View File

@ -7,7 +7,7 @@ from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import Study, StudyEvent, StudyEventType, StudyModel, StudySchema, StudyForUpdateSchema, \
StudyStatus
StudyStatus, StudyAssociatedSchema
from crc.services.study_service import StudyService
from crc.services.user_service import UserService
from crc.services.workflow_service import WorkflowService
@ -81,6 +81,10 @@ def get_study(study_id, update_status=False):
return StudySchema().dump(study)
def get_study_associates(study_id):
return StudyAssociatedSchema(many=True).dump(StudyService.get_study_associates(study_id))
def delete_study(study_id):
try:
StudyService.delete_study(study_id)

7
crc/models/study.py
View File

@ -80,6 +80,13 @@ class StudyAssociated(db.Model):
send_email = db.Column(db.Boolean, nullable=True)
access = db.Column(db.Boolean, nullable=True)
class StudyAssociatedSchema(ma.Schema):
class Meta:
fields=['uid', 'role', 'send_email', 'access']
model = StudyAssociated
unknown = INCLUDE
class StudyEvent(db.Model):
__tablename__ = 'study_event'
id = db.Column(db.Integer, primary_key=True)

4
crc/scripts/email.py
View File

@ -114,7 +114,7 @@ email (subject="My Subject", recipients=["dhf8r@virginia.edu", pi.email], cc='as
associated_emails = []
associates = StudyService.get_study_associates(study_id)
for associate in associates:
if associate['send_email'] is True:
user_info = LdapService.user_info(associate['uid'])
if associate.send_email is True:
user_info = LdapService.user_info(associate.uid)
associated_emails.append(user_info.email_address)
return associated_emails

11
crc/scripts/get_study_associate.py
View File

@ -1,24 +1,24 @@
from crc.api.common import ApiError
from crc.models.study import StudyAssociatedSchema
from crc.scripts.script import Script
from crc.services.study_service import StudyService
class GetStudyAssociates(Script):
class GetStudyAssociate(Script):
def get_description(self):
return """
Returns people associated with a study or an error if one is not associated.
Returns how a single person is associated with a study and what access they need,
or raises an error if the person is not associated with the study.
example : get_study_associate('sbp3ey') => {'uid':'sbp3ey','role':'Unicorn Herder', 'send_email': False,
'access':True}
"""
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
if len(args) < 1:
raise ApiError('no_user_id_specified', 'A uva uid is the sole argument to this function')
return {'uid': 'sbp3ey', 'role': 'Unicorn Herder', 'send_email': False, 'access': True}
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
@ -26,4 +26,5 @@ example : get_study_associate('sbp3ey') => {'uid':'sbp3ey','role':'Unicorn Herde
raise ApiError('no_user_id_specified', 'A uva uid is the sole argument to this function')
if not isinstance(args[0], str):
raise ApiError('argument_should_be_string', 'A uva uid is always a string, please check type')
return StudyService.get_study_associate(study_id=study_id, uid=args[0])
associate = StudyService.get_study_associate(study_id=study_id, uid=args[0])
return StudyAssociatedSchema().dump(associate)

4
crc/scripts/get_study_associates.py
View File

@ -1,4 +1,5 @@
from crc.api.common import ApiError
from crc.models.study import StudyAssociatedSchema
from crc.scripts.script import Script
from crc.services.study_service import StudyService
@ -26,7 +27,6 @@ example : get_study_associates() => [{'uid':'sbp3ey','role':'Unicorn Herder', 's
return study_associates
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
return StudyService.get_study_associates(study_id)
return StudyAssociatedSchema(many=True).dump(StudyService.get_study_associates(study_id))

111
crc/services/study_service.py
View File

@ -16,10 +16,11 @@ from crc.models.data_store import DataStoreModel
from crc.models.email import EmailModel
from crc.models.file import FileModel, File
from crc.models.ldap import LdapSchema
from crc.models.protocol_builder import ProtocolBuilderStudy
from crc.models.study import StudyModel, Study, StudyStatus, Category, \
WorkflowMetadata, StudyEventType, StudyEvent, IrbStatus, StudyAssociated
from crc.models.task_event import TaskEventModel
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata, StudyEventType, StudyEvent, \
IrbStatus, StudyAssociated, StudyAssociatedSchema
from crc.models.task_event import TaskEventModel, TaskEvent
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
WorkflowStatus, WorkflowSpecDependencyFile
from crc.services.document_service import DocumentService
@ -43,15 +44,15 @@ class StudyService(object):
def get_studies_for_user(self, user):
"""Returns a list of all studies for the given user."""
associated = session.query(StudyAssociated).filter_by(uid=user.uid,access=True).all()
associated = session.query(StudyAssociated).filter_by(uid=user.uid, access=True).all()
associated_studies = [x.study_id for x in associated]
db_studies = session.query(StudyModel).filter((StudyModel.user_uid==user.uid)|
db_studies = session.query(StudyModel).filter((StudyModel.user_uid == user.uid) |
(StudyModel.id.in_(associated_studies))).all()
studies = []
for study_model in db_studies:
if self._is_valid_study(study_model.id):
studies.append(StudyService.get_study(study_model.id, study_model,do_status=False))
studies.append(StudyService.get_study(study_model.id, study_model, do_status=False))
return studies
@staticmethod
@ -75,8 +76,8 @@ class StudyService(object):
study = Study.from_model(study_model)
study.create_user_display = LdapService.user_info(study.user_uid).display_name
last_event: TaskEventModel = session.query(TaskEventModel)\
.filter_by(study_id=study_id,action='COMPLETE')\
last_event: TaskEventModel = session.query(TaskEventModel) \
.filter_by(study_id=study_id, action='COMPLETE') \
.order_by(TaskEventModel.date.desc()).first()
if last_event is None:
study.last_activity_user = 'Not Started'
@ -108,9 +109,9 @@ class StudyService(object):
return study
@staticmethod
def get_study_associate(study_id = None, uid=None):
def get_study_associate(study_id=None, uid=None):
"""
gets all associated people for a study from the database
gets details on how one uid is related to a study, returns a StudyAssociated model
"""
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
@ -118,23 +119,18 @@ class StudyService(object):
raise ApiError('study_not_found', 'No study found with id = %d' % study_id)
if uid is None:
raise ApiError('uid not specified','A valid uva uid is required for this function')
raise ApiError('uid not specified', 'A valid uva uid is required for this function')
if uid == study.user_uid:
return {'uid': ownerid, 'role': 'owner', 'send_email': True, 'access': True}
return StudyAssociated(uid=uid, role='owner', send_email=True, access=True)
person = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(
StudyAssociated.uid == uid)).first()
if person:
newAssociate = {'uid':person.uid}
newAssociate['role'] = person.role
newAssociate['send_email'] = person.send_email
newAssociate['access'] = person.access
return newAssociate
raise ApiError('uid_not_associated_with_study',"user id %s was not associated with study number %d"%(uid,
study_id))
people = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id) &
(StudyAssociated.uid == uid)).first()
if people:
return people
else:
raise ApiError('uid_not_associated_with_study', "user id %s was not associated with study number %d" % (uid,
study_id))
@staticmethod
def get_study_associates(study_id):
@ -144,22 +140,15 @@ class StudyService(object):
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
if study is None:
raise ApiError('study_not_found','No study found with id = %d'%study_id)
ownerid = study.user_uid
people_list = [{'uid':ownerid,'role':'owner','send_email':True,'access':True}]
people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id)
for person in people:
newAssociate = {'uid':person.uid}
newAssociate['role'] = person.role
newAssociate['send_email'] = person.send_email
newAssociate['access'] = person.access
people_list.append(newAssociate)
return people_list
raise ApiError('study_not_found', 'No study found with id = %d' % study_id)
people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).all()
owner = StudyAssociated(uid=study.user_uid, role='owner', send_email=True, access=True)
people.append(owner)
return people
@staticmethod
def update_study_associates(study_id,associates):
def update_study_associates(study_id, associates):
"""
updates the list of associates in the database for a study_id and a list
of dicts that contains associates
@ -168,20 +157,19 @@ class StudyService(object):
raise ApiError('study_id not specified', "This function requires the study_id parameter")
for person in associates:
if not LdapService.user_exists(person.get('uid','impossible_uid')):
if person.get('uid','impossible_uid') == 'impossible_uid':
raise ApiError('associate with no uid','One of the associates passed as a parameter doesnt have '
if not LdapService.user_exists(person.get('uid', 'impossible_uid')):
if person.get('uid', 'impossible_uid') == 'impossible_uid':
raise ApiError('associate with no uid', 'One of the associates passed as a parameter doesnt have '
'a uid specified')
raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to "
"%s, but that user was not found in "
"ldap "
"- please check to ensure it is a "
"valid uva uid"%person.get('uid'))
raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap', "You are trying to grant access to "
"%s, but that user was not found in "
"ldap "
"- please check to ensure it is a "
"valid uva uid" % person.get('uid'))
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
if study is None:
raise ApiError('study_id not found', "A study with id# %d was not found"%study_id)
raise ApiError('study_id not found', "A study with id# %d was not found" % study_id)
db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).delete()
for person in associates:
@ -190,27 +178,27 @@ class StudyService(object):
newAssociate.uid = person['uid']
newAssociate.role = person.get('role', None)
newAssociate.send_email = person.get('send_email', False)
newAssociate.access = person.get('access',False)
newAssociate.access = person.get('access', False)
session.add(newAssociate)
session.commit()
@staticmethod
def update_study_associate(study_id=None,uid=None,role="",send_email=False,access=False):
def update_study_associate(study_id=None, uid=None, role="", send_email=False, access=False):
if study_id is None:
raise ApiError('study_id not specified', "This function requires the study_id parameter")
if uid is None:
raise ApiError('uid not specified', "This function requires a uva uid parameter")
if not LdapService.user_exists(uid):
raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to "
"%s but they were not found in ldap "
"- please check to ensure it is a "
"valid uva uid"%uid)
raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap', "You are trying to grant access to "
"%s but they were not found in ldap "
"- please check to ensure it is a "
"valid uva uid" % uid)
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
if study is None:
raise ApiError('study_id not found', "A study with id# %d was not found"%study_id)
db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(StudyAssociated.uid ==
uid) ).delete()
raise ApiError('study_id not found', "A study with id# %d was not found" % study_id)
db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id) & (StudyAssociated.uid ==
uid)).delete()
newAssociate = StudyAssociated()
newAssociate.study_id = study_id
@ -222,7 +210,6 @@ class StudyService(object):
session.commit()
return True
@staticmethod
def delete_study(study_id):
session.query(TaskEventModel).filter_by(study_id=study_id).delete()
@ -305,18 +292,18 @@ class StudyService(object):
# when we run tests - it doesn't look like the user is available
# so we return a bogus token
token = 'not_available'
if hasattr(flask.g,'user'):
if hasattr(flask.g, 'user'):
token = flask.g.user.encode_auth_token()
for file in doc_files:
file_data = {'file_id': file.id,
'name': file.name,
'url': app.config['APPLICATION_ROOT']+
'url': app.config['APPLICATION_ROOT'] +
'file/' + str(file.id) +
'/download?auth_token='+
'/download?auth_token=' +
urllib.parse.quote_plus(token),
'workflow_id': file.workflow_id
}
data = db.session.query(DataStoreModel).filter(DataStoreModel.file_id==file.id).all()
data = db.session.query(DataStoreModel).filter(DataStoreModel.file_id == file.id).all()
data_store_data = {}
for d in data:
data_store_data[d.key] = d.value

2
crc/services/workflow_service.py
View File

@ -770,7 +770,7 @@ class WorkflowService(object):
else:
if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
associated = StudyService.get_study_associates(processor.workflow_model.study.id)
return [user['uid'] for user in associated if user['access']]
return [user.uid for user in associated if user.access]
if spiff_task.task_spec.lane not in spiff_task.data:
return [] # No users are assignable to the task at this moment
lane_users = spiff_task.data[spiff_task.task_spec.lane]

36
tests/data/study_sponsors_associate/study_sponsors_associate.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:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_0kmksnn" 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:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
<bpmn:process id="Process_0exnnpv" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
@ -32,7 +32,7 @@ out4 = get_study_associate('lb3dp')</bpmn:script>
<bpmn:outgoing>Flow_1vlh6s0</bpmn:outgoing>
<bpmn:script>uids = []
for assoc in out:
uids.append(assoc['uid'])
uids.append(assoc.uid)
update_study_associates([{'uid':'lb3dp','role':'SuperGal','send_email':False,'access':True}])</bpmn:script>
</bpmn:scriptTask>
<bpmn:sequenceFlow id="Flow_1vlh6s0" sourceRef="Activity_0run091" targetRef="Activity_0d8iftx" />
@ -46,6 +46,22 @@ out2 = get_study_associate('lb3dp')</bpmn:script>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
<bpmndi:BPMNEdge id="Flow_14n3ixy_di" bpmnElement="Flow_14n3ixy">
<di:waypoint x="680" y="117" />
<di:waypoint x="750" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1vlh6s0_di" bpmnElement="Flow_1vlh6s0">
<di:waypoint x="850" y="117" />
<di:waypoint x="900" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0cttkwp_di" bpmnElement="Flow_0cttkwp">
<di:waypoint x="1000" y="117" />
<di:waypoint x="1042" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_09cika8_di" bpmnElement="Flow_09cika8">
<di:waypoint x="540" y="117" />
<di:waypoint x="580" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
<di:waypoint x="370" y="117" />
<di:waypoint x="440" y="117" />
@ -60,10 +76,6 @@ out2 = get_study_associate('lb3dp')</bpmn:script>
<bpmndi:BPMNShape id="ScriptTask_1mp6xid_di" bpmnElement="Task_Script_Load_Study_Sponsors">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_09cika8_di" bpmnElement="Flow_09cika8">
<di:waypoint x="540" y="117" />
<di:waypoint x="580" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="Activity_0wnwluq_di" bpmnElement="Activity_0cm6tn2">
<dc:Bounds x="440" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
@ -73,24 +85,12 @@ out2 = get_study_associate('lb3dp')</bpmn:script>
<bpmndi:BPMNShape id="Event_0c8gcuh_di" bpmnElement="Event_0c8gcuh">
<dc:Bounds x="1042" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_0cttkwp_di" bpmnElement="Flow_0cttkwp">
<di:waypoint x="1000" y="117" />
<di:waypoint x="1042" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="Activity_0run091_di" bpmnElement="Activity_0run091">
<dc:Bounds x="750" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_1vlh6s0_di" bpmnElement="Flow_1vlh6s0">
<di:waypoint x="850" y="117" />
<di:waypoint x="900" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNShape id="Activity_14td33q_di" bpmnElement="Activity_14td33q">
<dc:Bounds x="580" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNEdge id="Flow_14n3ixy_di" bpmnElement="Flow_14n3ixy">
<di:waypoint x="680" y="117" />
<di:waypoint x="750" y="117" />
</bpmndi:BPMNEdge>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

25
tests/study/test_study_associate_script.py
View File

@ -53,19 +53,18 @@ class TestSudySponsorsScript(BaseTest):
self.assertIn('sponsors', data)
self.assertIn('out', data)
print(data['out'])
self.assertEquals([{'uid': 'dhf8r', 'role': 'owner', 'send_email': True, 'access': True},
{'uid': 'lb3dp', 'role': 'SuperDude', 'send_email': False, 'access': True}]
, data['out'])
self.assertEquals({'uid': 'lb3dp', 'role': 'SuperDude', 'send_email': False, 'access': True}
, data['out2'])
self.assertEquals([{'uid': 'dhf8r', 'role': 'owner', 'send_email': True, 'access': True},
{'uid': 'lb3dp', 'role': 'SuperGal', 'send_email': False, 'access': True}]
, data['out3'])
self.assertEquals({'uid': 'lb3dp', 'role': 'SuperGal', 'send_email': False, 'access': True}
, data['out4'])
self.assertDictEqual({'uid': 'dhf8r', 'role': 'owner', 'send_email': True, 'access': True},
data['out'][1])
self.assertDictEqual({'uid': 'lb3dp', 'role': 'SuperDude', 'send_email': False, 'access': True},
data['out'][0])
self.assertDictEqual({'uid': 'lb3dp', 'role': 'SuperDude', 'send_email': False, 'access': True},
data['out2'])
self.assertDictEqual({'uid': 'dhf8r', 'role': 'owner', 'send_email': True, 'access': True},
data['out3'][1])
self.assertDictEqual({'uid': 'lb3dp', 'role': 'SuperGal', 'send_email': False, 'access': True},
data['out3'][0])
self.assertDictEqual({'uid': 'lb3dp', 'role': 'SuperGal', 'send_email': False, 'access': True},
data['out4'])
self.assertEquals(3, len(data['sponsors']))