sartography
/
cr-connect-workflow
mirror of https://github.com/sartography/cr-connect-workflow.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Check Study Associates Endpoint

This commit is contained in:
nilez 2021-08-16 09:32:02 -04:00
parent cdf454b705 4a2581e938
commit f8dd4c3eb9
25 changed files with 350 additions and 156 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.gitignore vendored Normal file → Executable file
View File

@ -14,7 +14,7 @@ local.properties
.settings/
.loadpath
.recommenders
.vscode/
# External tool builders
.externalToolBuilders/

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:

12
crc/api/file.py Normal file → Executable file
View File

@ -71,9 +71,9 @@ def get_reference_file(name):
file_data = FileService.get_reference_file_data(name)
return send_file(
io.BytesIO(file_data.data),
attachment_filename=file_data.file_model.name,
download_name=file_data.file_model.name,
mimetype=file_data.file_model.content_type,
cache_timeout=-1 # Don't cache these files on the browser.
max_age=-1 # Don't cache these files on the browser.
)
@ -120,9 +120,9 @@ def get_file_data(file_id, version=None):
raise ApiError('no_such_file', 'The file id you provided does not exist')
return send_file(
io.BytesIO(file_data.data),
attachment_filename=file_data.file_model.name,
download_name=file_data.file_model.name,
mimetype=file_data.file_model.content_type,
cache_timeout=-1, # Don't cache these files on the browser.
max_age=-1, # Don't cache these files on the browser.
last_modified=file_data.date_created
)
@ -135,9 +135,9 @@ def get_file_data_link(file_id, auth_token, version=None):
raise ApiError('no_such_file', 'The file id you provided does not exist')
return send_file(
io.BytesIO(file_data.data),
attachment_filename=file_data.file_model.name,
download_name=file_data.file_model.name,
mimetype=file_data.file_model.content_type,
cache_timeout=-1, # Don't cache these files on the browser.
max_age=-1, # Don't cache these files on the browser.
last_modified=file_data.date_created,
as_attachment = True
)

12
crc/api/study.py Normal file → Executable file
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)
@ -95,6 +99,12 @@ def user_studies():
user = UserService.current_user(allow_admin_impersonate=True)
StudyService.synch_with_protocol_builder_if_enabled(user)
studies = StudyService().get_studies_for_user(user)
if len(studies) == 0:
studies = StudyService().get_studies_for_user(user, include_invalid=True)
if len(studies) > 0:
message = f"All studies associated with User: {user.display_name} failed study validation"
raise ApiError(code="study_integrity_error", message=message)
results = StudySchema(many=True).dump(studies)
return results

4
crc/api/tools.py Normal file → Executable file
View File

@ -43,9 +43,9 @@ def render_docx():
return send_file(
io.BytesIO(target_stream.read()),
as_attachment=True,
attachment_filename="output.docx",
download_name="output.docx",
mimetype="application/octet-stream",
cache_timeout=-1 # Don't cache these files on the browser.
max_age=-1 # Don't cache these files on the browser.
)
except ValueError as e:
raise ApiError(code="undefined_field", message=str(e))

7
crc/models/study.py Normal file → Executable file
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 Normal file → Executable file
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 Normal file → Executable file
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 Normal file → Executable file
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))

115
crc/services/study_service.py Normal file → Executable file
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
@ -41,17 +42,17 @@ class StudyService(object):
return True
return False
def get_studies_for_user(self, user):
def get_studies_for_user(self, user, include_invalid=False):
"""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))
if include_invalid or self._is_valid_study(study_model.id):
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

19
crc/services/workflow_service.py Normal file → Executable file
View File

@ -1,3 +1,4 @@
import copy
import string
from datetime import datetime
import random
@ -312,7 +313,7 @@ class WorkflowService(object):
data = {}
if field.has_property(Task.FIELD_PROP_FILE_DATA) and \
field.get_property(Task.FIELD_PROP_FILE_DATA) in data and \
field.id in data:
field.id in data and data[field.id]:
file_id = data[field.get_property(Task.FIELD_PROP_FILE_DATA)]["id"]
if field.type == 'enum':
data_args = (field.id, data[field.id]['label'])
@ -325,10 +326,19 @@ class WorkflowService(object):
expression = field.get_property(property_name)
data = task.data
if field.has_property(Task.FIELD_PROP_REPEAT):
# Then you must evaluate the expression based on the data within the group only.
# Then you must evaluate the expression based on the data within the group, if that data exists.
# There may not be data available in the group, if no groups where added
group = field.get_property(Task.FIELD_PROP_REPEAT)
if group in task.data:
# Here we must make the current group data top level (as it would be in a repeat section) but
# make all other top level task data available as well.
new_data = copy.deepcopy(task.data)
del(new_data[group])
data = task.data[group][0]
data.update(new_data)
else:
return None # We may not have enough information to process this
try:
return task.workflow.script_engine.eval(expression, data)
except Exception as e:
@ -770,7 +780,8 @@ 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]
@ -780,7 +791,7 @@ class WorkflowService(object):
lane_uids = []
for user in lane_users:
if isinstance(user, dict):
if 'value' in user and user['value'] is not None:
if user.get("value"):
lane_uids.append(user['value'])
else:
raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user dict must have a key called 'value' with the user's uid in it." %

87
tests/data/hidden_file_data_field/hidden_file_data_field.bpmn Normal file
View File

@ -0,0 +1,87 @@
<?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_ef382ee" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
<bpmn:process id="Process_eea3627" name="Test Empty Hidden Field" isExecutable="true">
<bpmn:startEvent id="StartEvent_1">
<bpmn:outgoing>Flow_0eg42kv</bpmn:outgoing>
</bpmn:startEvent>
<bpmn:userTask id="Activity_FileUpload" name="File Upload" camunda:formKey="UploadFile">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="UploadFile" label="Select File" type="file" />
<camunda:formField id="Name" label="Enter Name" type="string">
<camunda:properties>
<camunda:property id="file_data" value="UploadFile" />
</camunda:properties>
</camunda:formField>
<camunda:formField id="ExtraField" label="Could Be Hidden" type="string" defaultValue="Extra Field String">
<camunda:properties>
<camunda:property id="hide_expression" value="hide_field" />
<camunda:property id="file_data" value="UploadFile" />
</camunda:properties>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_074gk91</bpmn:incoming>
<bpmn:outgoing>Flow_1gseke4</bpmn:outgoing>
</bpmn:userTask>
<bpmn:sequenceFlow id="Flow_0eg42kv" sourceRef="StartEvent_1" targetRef="Activity_AddData" />
<bpmn:sequenceFlow id="Flow_074gk91" sourceRef="Activity_AddData" targetRef="Activity_FileUpload" />
<bpmn:sequenceFlow id="Flow_1gseke4" sourceRef="Activity_FileUpload" targetRef="Activity_ViewData" />
<bpmn:endEvent id="Event_0qcduja">
<bpmn:incoming>Flow_04ozqju</bpmn:incoming>
</bpmn:endEvent>
<bpmn:sequenceFlow id="Flow_04ozqju" sourceRef="Activity_ViewData" targetRef="Event_0qcduja" />
<bpmn:manualTask id="Activity_ViewData" name="View Data">
<bpmn:incoming>Flow_1gseke4</bpmn:incoming>
<bpmn:outgoing>Flow_04ozqju</bpmn:outgoing>
</bpmn:manualTask>
<bpmn:userTask id="Activity_AddData" name="Add Data" camunda:formKey="HideData">
<bpmn:extensionElements>
<camunda:formData>
<camunda:formField id="hide_field" label="Hide Field?" type="boolean">
<camunda:validation>
<camunda:constraint name="required" config="True" />
</camunda:validation>
</camunda:formField>
</camunda:formData>
</bpmn:extensionElements>
<bpmn:incoming>Flow_0eg42kv</bpmn:incoming>
<bpmn:outgoing>Flow_074gk91</bpmn:outgoing>
</bpmn:userTask>
</bpmn:process>
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_eea3627">
<bpmndi:BPMNEdge id="Flow_04ozqju_di" bpmnElement="Flow_04ozqju">
<di:waypoint x="690" y="117" />
<di:waypoint x="752" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_1gseke4_di" bpmnElement="Flow_1gseke4">
<di:waypoint x="530" y="117" />
<di:waypoint x="590" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_074gk91_di" bpmnElement="Flow_074gk91">
<di:waypoint x="370" y="117" />
<di:waypoint x="430" y="117" />
</bpmndi:BPMNEdge>
<bpmndi:BPMNEdge id="Flow_0eg42kv_di" bpmnElement="Flow_0eg42kv">
<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="Activity_0zui1g5_di" bpmnElement="Activity_FileUpload">
<dc:Bounds x="430" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Event_0qcduja_di" bpmnElement="Event_0qcduja">
<dc:Bounds x="752" y="99" width="36" height="36" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="Activity_1fkiik9_di" bpmnElement="Activity_ViewData">
<dc:Bounds x="590" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
<bpmndi:BPMNShape id="UserTask_0wc78yf_di" bpmnElement="Activity_AddData">
<dc:Bounds x="270" y="77" width="100" height="80" />
</bpmndi:BPMNShape>
</bpmndi:BPMNPlane>
</bpmndi:BPMNDiagram>
</bpmn:definitions>

36
tests/data/study_sponsors_associate/study_sponsors_associate.bpmn Normal file → Executable file
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>

2
tests/files/test_file_service.py Normal file → Executable file
View File

@ -72,7 +72,7 @@ class TestFileService(BaseTest):
file_data = FileService.get_workflow_data_files(workflow_id=workflow.id)
self.assertEqual(1, len(file_data))
self.assertEqual(2, file_data[0].version)
self.assertEquals(4, file_data[0].size) # File dat size is included.
self.assertEqual(4, file_data[0].size) # File dat size is included.
def test_add_file_from_form_increments_version_and_replaces_on_subsequent_add_with_same_name(self):
self.load_example_data()

2
tests/files/test_files_api.py Normal file → Executable file
View File

@ -191,7 +191,7 @@ class TestFilesApi(BaseTest):
rv = self.app.post('/v1.0/file?workflow_spec_id=%s' % spec.id, data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
file_json = json.loads(rv.get_data(as_text=True))
self.assertEquals(80, file_json['size'])
self.assertEqual(80, file_json['size'])
data['file'] = io.BytesIO(self.minimal_bpmn("efghijk")), 'my_new_file.bpmn'
rv = self.app.put('/v1.0/file/%i/data' % file_json['id'], data=data, follow_redirects=True,

27
tests/study/test_study_associate_script.py Normal file → Executable file
View File

@ -53,20 +53,19 @@ 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.assertEquals(3, len(data['sponsors']))
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.assertEqual(3, len(data['sponsors']))
@patch('crc.services.protocol_builder.requests.get')

6
tests/study/test_study_data_store_script.py Normal file → Executable file
View File

@ -50,6 +50,6 @@ class TestSudySponsorsScript(BaseTest):
data = processor.next_task().data
self.assertIn('sponsors', data)
self.assertIn('out', data)
self.assertEquals('empty', data['empty'])
self.assertEquals('newval', data['out'])
self.assertEquals(3, len(data['sponsors']))
self.assertEqual('empty', data['empty'])
self.assertEqual('newval', data['out'])
self.assertEqual(3, len(data['sponsors']))

25
tests/study/test_study_details_documents.py Normal file → Executable file
View File

@ -1,4 +1,3 @@
from SpiffWorkflow.bpmn.PythonScriptEngine import Box
from tests.base_test import BaseTest
@ -56,7 +55,6 @@ class TestStudyDetailsDocumentsScript(BaseTest):
@patch('crc.services.protocol_builder.requests.get')
def test_no_validation_error_when_correct_file_exists(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('required_docs.json')
@ -105,15 +103,15 @@ class TestStudyDetailsDocumentsScript(BaseTest):
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file = FileService.add_workflow_file(workflow_id=workflow_model.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
FileDataSet().do_task(task, study.id, workflow_model.id, key="ginger", value="doodle", file_id=file.id)
docs = StudyInfo().do_task(task, study.id, workflow_model.id, "documents")
self.assertTrue(isinstance(docs, Box))
self.assertEquals(1, len(docs.UVACompl_PRCAppr.files))
self.assertEquals("doodle", docs.UVACompl_PRCAppr.files[0].data_store.ginger)
self.assertEqual(1, len(docs.UVACompl_PRCAppr.files))
self.assertEqual("doodle", docs.UVACompl_PRCAppr.files[0].data_store.ginger)
@patch('crc.services.protocol_builder.requests.get')
def test_file_data_set_changes_irb_code(self, mock_get):
@ -126,16 +124,15 @@ class TestStudyDetailsDocumentsScript(BaseTest):
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file = FileService.add_workflow_file(workflow_id=workflow_model.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
FileDataSet().do_task(task, study.id, workflow_model.id, key="irb_code", value="Study_App_Doc", file_id=file.id)
docs = StudyInfo().do_task(task, study.id, workflow_model.id, "documents")
self.assertTrue(isinstance(docs, Box))
self.assertEquals(1, len(docs.Study_App_Doc.files))
self.assertEquals("Study_App_Doc", docs.Study_App_Doc.files[0].data_store.irb_code)
self.assertEqual(1, len(docs.Study_App_Doc.files))
self.assertEqual("Study_App_Doc", docs.Study_App_Doc.files[0].data_store.irb_code)
@patch('crc.services.protocol_builder.requests.get')
def test_file_data_set_invalid_irb_code_fails(self, mock_get):
@ -148,10 +145,10 @@ class TestStudyDetailsDocumentsScript(BaseTest):
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file = FileService.add_workflow_file(workflow_id=workflow_model.id,
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
name="anything.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
with self.assertRaises(ApiError):
FileDataSet().do_task(task, study.id, workflow_model.id, key="irb_code", value="My_Pretty_Pony",
file_id=file.id)
file_id=file.id)

2
tests/study/test_study_sponsors_script.py Normal file → Executable file
View File

@ -45,4 +45,4 @@ class TestSudySponsorsScript(BaseTest):
self.assertTrue(processor.bpmn_workflow.is_completed())
data = processor.next_task().data
self.assertIn('sponsors', data)
self.assertEquals(3, len(data['sponsors']))
self.assertEqual(3, len(data['sponsors']))

16
tests/test_document_directories.py Normal file → Executable file
View File

@ -28,11 +28,11 @@ class TestDocumentDirectories(BaseTest):
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
print(json_data)
self.assertEquals(2, len(json_data))
self.assertEquals('UVA Compliance', json_data[0]['level'])
self.assertEquals('PRC Approval', json_data[0]['children'][0]['level'])
self.assertEquals('something.png', json_data[0]['children'][0]['children'][0]['file']['name'])
self.assertEquals('Study', json_data[1]['level'])
self.assertEquals('Application', json_data[1]['children'][0]['level'])
self.assertEquals('Document', json_data[1]['children'][0]['children'][0]['level'])
self.assertEquals('anything.png', json_data[1]['children'][0]['children'][0]['children'][0]['file']['name'])
self.assertEqual(2, len(json_data))
self.assertEqual('UVA Compliance', json_data[0]['level'])
self.assertEqual('PRC Approval', json_data[0]['children'][0]['level'])
self.assertEqual('something.png', json_data[0]['children'][0]['children'][0]['file']['name'])
self.assertEqual('Study', json_data[1]['level'])
self.assertEqual('Application', json_data[1]['children'][0]['level'])
self.assertEqual('Document', json_data[1]['children'][0]['children'][0]['level'])
self.assertEqual('anything.png', json_data[1]['children'][0]['children'][0]['children'][0]['file']['name'])

2
tests/test_multi_instance_tasks_api.py Normal file → Executable file
View File

@ -106,6 +106,6 @@ class TestMultiinstanceTasksApi(BaseTest):
self.assertEqual(WorkflowStatus.complete, workflow.status)
data = workflow.next_task.data
for key in data["StudyInfo"]["investigators"]:
self.assertEquals("dhf8r@virginia.edu", data["StudyInfo"]["investigators"][key]['email'])
self.assertEqual("dhf8r@virginia.edu", data["StudyInfo"]["investigators"][key]['email'])

4
tests/test_wait_event.py Normal file → Executable file
View File

@ -40,7 +40,7 @@ class TestTimerEvent(BaseTest):
with self.assertLogs('crc', level='ERROR') as cm:
WorkflowService.do_waiting()
self.assertEqual(1, len(cm.output))
self.assertRegexpMatches(cm.output[0], f"workflow #%i" % workflow.id)
self.assertRegexpMatches(cm.output[0], f"study #%i" % workflow.study_id)
self.assertRegex(cm.output[0], f"workflow #%i" % workflow.id)
self.assertRegex(cm.output[0], f"study #%i" % workflow.study_id)
self.assertTrue(wf.status == WorkflowStatus.waiting)

4
tests/workflow/test_workflow_enum_empty_list.py Normal file → Executable file
View File

@ -24,5 +24,5 @@ class TestEmptyEnumList(BaseTest):
service = WorkflowService()
checkbox_enum_field = task.task_spec.form.fields[0]
radio_enum_field = task.task_spec.form.fields[1]
self.assertEquals([], service.get_default_value(checkbox_enum_field, task))
self.assertEquals({'label': None, 'value': None}, service.get_default_value(radio_enum_field, task))
self.assertEqual([], service.get_default_value(checkbox_enum_field, task))
self.assertEqual({'label': None, 'value': None}, service.get_default_value(radio_enum_field, task))

60
tests/workflow/test_workflow_hidden_file_data_field.py Normal file
View File

@ -0,0 +1,60 @@
from tests.base_test import BaseTest
from io import BytesIO
import json
class TestHiddenFileDataField(BaseTest):
def test_hidden_file_data_field(self):
self.load_example_data()
workflow = self.create_workflow('hidden_file_data_field')
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
self.complete_form(workflow, task, {'hide_field': True})
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
data = {'file': (BytesIO(b"abcdef"), 'test_file.txt')}
rv = self.app.post('/v1.0/file?study_id=%i&workflow_id=%s&task_id=%s&form_field_key=%s' %
(workflow.study_id, workflow.id, task.id, 'Study_App_Doc'), data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
file_id = json.loads(rv.get_data())['id']
self.complete_form(workflow, task, {'UploadFile': {'id': file_id},
'Name': 'Some Name String'})
workflow_api = self.get_workflow_api(workflow)
new_task = workflow_api.next_task
self.assertEqual('Activity_ViewData', new_task.name)
self.assertEqual('Some Name String', new_task.data['Name'])
self.assertNotIn('ExtraField', new_task.data)
def test_not_hidden_file_data_field(self):
self.load_example_data()
workflow = self.create_workflow('hidden_file_data_field')
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
self.complete_form(workflow, task, {'hide_field': False})
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
data = {'file': (BytesIO(b"abcdef"), 'test_file.txt')}
rv = self.app.post('/v1.0/file?study_id=%i&workflow_id=%s&task_id=%s&form_field_key=%s' %
(workflow.study_id, workflow.id, task.id, 'Study_App_Doc'), data=data, follow_redirects=True,
content_type='multipart/form-data', headers=self.logged_in_headers())
self.assert_success(rv)
file_id = json.loads(rv.get_data())['id']
self.complete_form(workflow, task, {'UploadFile': {'id': file_id},
'Name': 'Some Name String',
'ExtraField': 'Some Extra String'})
workflow_api = self.get_workflow_api(workflow)
new_task = workflow_api.next_task
self.assertEqual('Activity_ViewData', new_task.name)
self.assertEqual('Some Name String', new_task.data['Name'])
self.assertIn('ExtraField', new_task.data)
self.assertEqual('Some Extra String', new_task.data['ExtraField'])

2
tests/workflow/test_workflow_spec_validation_api.py Normal file → Executable file
View File

@ -145,5 +145,5 @@ class TestWorkflowSpecValidation(BaseTest):
final_data = WorkflowService.test_spec(spec_model.id, required_only=True)
self.assertIsNotNone(final_data)
self.assertIn('enum_with_default', final_data)
self.assertEquals('maybe', final_data['enum_with_default']['value'])
self.assertEqual('maybe', final_data['enum_with_default']['value'])