Merge pull request #250 from sartography/206-extend-study-access
206 extend study access
This commit is contained in:
Dan Funk
GitHub
commit
3e0541fa15
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@ -6,7 +6,8 @@ from sqlalchemy.exc import IntegrityError
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from crc import session
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from crc.api.common import ApiError, ApiErrorSchema
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from crc.models.protocol_builder import ProtocolBuilderStatus
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from crc.models.study import Study, StudyEvent, StudyEventType, StudyModel, StudySchema, StudyForUpdateSchema, StudyStatus
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from crc.models.study import Study, StudyEvent, StudyEventType, StudyModel, StudySchema, StudyForUpdateSchema, \
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StudyStatus
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from crc.services.study_service import StudyService
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from crc.services.user_service import UserService
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from crc.services.workflow_service import WorkflowService
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@ -35,6 +35,7 @@ class StudyEventType(enum.Enum):
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automatic = 'automatic'
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class StudyModel(db.Model):
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__tablename__ = 'study'
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id = db.Column(db.Integer, primary_key=True)
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@ -51,7 +52,7 @@ class StudyModel(db.Model):
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requirements = db.Column(db.ARRAY(db.Integer), nullable=True)
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on_hold = db.Column(db.Boolean, default=False)
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enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
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# events = db.relationship("TaskEventModel")
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#events = db.relationship("TaskEventModel")
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events_history = db.relationship("StudyEvent", cascade="all, delete, delete-orphan")
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def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
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@ -63,6 +64,21 @@ class StudyModel(db.Model):
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self.irb_status = IrbStatus.incomplete_in_protocol_builder
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class StudyAssociated(db.Model):
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"""
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This model allows us to associate people with a study, and optionally
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give them edit access. This allows us to create a table with PI, D_CH, etc.
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and give access to people other than the study owner.
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Task_Events will still work as they have previously
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"""
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__tablename__ = 'study_associated_user'
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id = db.Column(db.Integer, primary_key=True)
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study_id = db.Column(db.Integer, db.ForeignKey(StudyModel.id), nullable=False)
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uid = db.Column(db.String, db.ForeignKey('ldap_model.uid'), nullable=False)
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role = db.Column(db.String, nullable=True)
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send_email = db.Column(db.Boolean, nullable=True)
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access = db.Column(db.Boolean, nullable=True)
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class StudyEvent(db.Model):
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__tablename__ = 'study_event'
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id = db.Column(db.Integer, primary_key=True)
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@ -0,0 +1,31 @@
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from crc.api.common import ApiError
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from crc.scripts.script import Script
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from crc.services.study_service import StudyService
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class GetStudyAssociates(Script):
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def get_description(self):
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return """
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Returns person assocated with study or an error if one is not associated.
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example : get_study_associate('sbp3ey') => {'uid':'sbp3ey','role':'Unicorn Herder', 'send_email': False,
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'access':True}
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"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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if len(args)<1:
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return False
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return True
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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if len(args)<1:
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raise ApiError('no_user_id_specified', 'A uva uid is the sole argument to this function')
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if not isinstance(args[0],type('')):
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raise ApiError('argument_should_be_string', 'A uva uid is always a string, please check type')
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return StudyService.get_study_associate(study_id=study_id,uid=args[0])
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@ -0,0 +1,29 @@
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from crc.api.common import ApiError
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from crc.scripts.script import Script
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from crc.services.study_service import StudyService
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class GetStudyAssociates(Script):
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argument_error_message = "You must supply at least one argument to the " \
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"update_study_associates task, an array of objects in the form " \
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"{'uid':'someid', 'role': 'text', 'send_email: 'boolean', " \
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"'access':'boolean'} "
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def get_description(self):
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return """
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Returns all people associated with the study - Will always return the study owner as assocated
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example : get_study_associates() => [{'uid':'sbp3ey','role':'Unicorn Herder', 'send_email': False, 'access':True}]
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"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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return True
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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return StudyService.get_study_associates(study_id)
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@ -35,8 +35,17 @@ class Script(object):
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updating the task data.
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"""
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def make_closure(subclass,task,study_id,workflow_id):
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"""
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yes - this is black magic
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Essentially, we want to build a list of all of the submodules (i.e. email, user_data_get, etc)
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and a function that is assocated with them.
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This basically creates an Instance of the class and returns a function that calls do_task
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on the instance of that class.
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the next for x in range, then grabs the name of the module and associates it with the function
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that we created.
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"""
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instance = subclass()
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return lambda *a : subclass.do_task(instance,task,study_id,workflow_id,*a)
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return lambda *ar,**kw: subclass.do_task(instance,task,study_id,workflow_id,*ar,**kw)
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execlist = {}
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subclasses = Script.get_all_subclasses()
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for x in range(len(subclasses)):
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@ -59,7 +68,7 @@ class Script(object):
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def make_closure_validate(subclass,task,study_id,workflow_id):
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instance = subclass()
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return lambda *a : subclass.do_task_validate_only(instance,task,study_id,workflow_id,*a)
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return lambda *a, **b: subclass.do_task_validate_only(instance,task,study_id,workflow_id,*a,**b)
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execlist = {}
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subclasses = Script.get_all_subclasses()
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for x in range(len(subclasses)):
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@ -4,7 +4,7 @@ from crc.scripts.script import Script
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class StudyDataSet(Script,DataStoreBase):
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def get_description(self):
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return """Sets study data from the data store."""
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return """Sets study data from the data store. Takes two positional arguments key and value"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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self.set_validate_common(study_id,
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@ -0,0 +1,38 @@
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from crc.api.common import ApiError
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from crc.scripts.script import Script
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from crc.services.study_service import StudyService
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class UpdateStudyAssociates(Script):
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argument_error_message = "You must supply at least one argument to the " \
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"update_study_associates task, an array of objects in the form " \
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"{'uid':'someid', 'role': 'text', 'send_email: 'boolean', " \
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"'access':'boolean'} "
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def get_description(self):
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return """
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Allows you to associate other users with a study - only 'uid' is a required keyword argument
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An empty list will delete the existing Associated list (except owner)
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The UID will be validated vs ldap and will raise an error if the uva_uid is not found. This will replace any
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association already in place for this user.
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example : update_study_associate(uid='sbp3ey',role='Unicorn Herder',send_email=False, access=True)
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"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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if kwargs.get('uid') is None:
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raise ApiError('uid_is_required_argument','a valid keyword argument of uid is required, it should be the '
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'uva uid for this user')
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return True
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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return StudyService.update_study_associate(study_id=study_id,**kwargs)
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@ -0,0 +1,45 @@
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from crc.api.common import ApiError
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from crc.scripts.script import Script
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from crc.services.study_service import StudyService
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class UpdateStudyAssociates(Script):
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argument_error_message = "You must supply at least one argument to the " \
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"update_study_associates task, an array of objects in the form " \
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"{'uid':'someid', 'role': 'text', 'send_email: 'boolean', " \
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"'access':'boolean'} "
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def get_description(self):
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return """
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Allows you to associate other users with a study - only 'uid' is required in the
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incoming dictionary, but will be useless without other information - all values will default to
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false or blank
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An empty list will delete the existing Associated list (except owner)
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Each UID will be validated vs ldap and will raise an error if the uva_uid is not found. This supplied list will replace
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any
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associations already in place.
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example : update_study_associates([{'uid':'sbp3ey','role':'Unicorn Herder', 'send_email': False, 'access':True}])
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"""
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def validate_arg(self,arg):
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if not isinstance(arg,list):
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raise ApiError("invalid parameter", "This function is expecting a list of dictionaries")
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if not len(arg) > 0 and not isinstance(arg[0],dict):
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raise ApiError("invalid paramemter","This function is expecting a list of dictionaries")
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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items = args[0]
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self.validate_arg(items)
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return all([x.get('uid',False) for x in items])
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def do_task(self, task, study_id, workflow_id, *args, **kwargs):
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access_list = args[0]
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self.validate_arg(access_list)
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return StudyService.update_study_associates(study_id,access_list)
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@ -6,7 +6,7 @@ from crc.scripts.script import Script
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class UserDataGet(Script, DataStoreBase):
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def get_description(self):
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return """Gets user data from the data store."""
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return """Gets user data from the data store - takes only one argument 'key' """
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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self.do_task(task, study_id, workflow_id, *args, **kwargs)
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@ -6,7 +6,9 @@ from crc.scripts.script import Script
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class UserDataSet(Script,DataStoreBase):
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def get_description(self):
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return """Sets user data to the data store."""
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return """Sets user data to the data store these are positional arguments key and value.
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example: user_data_set('mykey','myvalue')
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"""
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def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
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self.set_validate_common(None,
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@ -48,6 +48,13 @@ class LdapService(object):
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LdapService.conn = conn
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return LdapService.conn
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@staticmethod
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def user_exists(uva_uid):
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try:
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x = LdapService.user_info(uva_uid)
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except:
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return False
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return True
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@staticmethod
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def user_info(uva_uid):
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@ -13,7 +13,7 @@ from crc.models.file import FileDataModel, FileModel, FileModelSchema, File, Loo
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from crc.models.ldap import LdapSchema
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from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
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from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata, StudyEventType, StudyEvent, \
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IrbStatus
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IrbStatus, StudyAssociated
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from crc.models.task_event import TaskEventModel, TaskEvent
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
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WorkflowStatus, WorkflowSpecDependencyFile
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@ -29,7 +29,11 @@ class StudyService(object):
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@staticmethod
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def get_studies_for_user(user):
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"""Returns a list of all studies for the given user."""
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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associated = session.query(StudyAssociated).filter_by(uid=user.uid,access=True).all()
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associated_studies = [x.study_id for x in associated]
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db_studies = session.query(StudyModel).filter((StudyModel.user_uid==user.uid)|
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(StudyModel.id.in_(associated_studies))).all()
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studies = []
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for study_model in db_studies:
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studies.append(StudyService.get_study(study_model.id, study_model))
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@ -86,6 +90,122 @@ class StudyService(object):
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return study
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@staticmethod
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def get_study_associate(study_id = None, uid=None):
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"""
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gets all associated people for a study from the database
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"""
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_not_found', 'No study found with id = %d' % study_id)
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if uid is None:
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raise ApiError('uid not specified','A valid uva uid is required for this function')
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if uid == study.user_uid:
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return {'uid': ownerid, 'role': 'owner', 'send_email': True, 'access': True}
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person = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(
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StudyAssociated.uid == uid)).first()
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if person:
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newAssociate = {'uid':person.uid}
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newAssociate['role'] = person.role
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newAssociate['send_email'] = person.send_email
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newAssociate['access'] = person.access
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return newAssociate
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raise ApiError('uid_not_associated_with_study',"user id %s was not associated with study number %d"%(uid,
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study_id))
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@staticmethod
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def get_study_associates(study_id):
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"""
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gets all associated people for a study from the database
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"""
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_not_found','No study found with id = %d'%study_id)
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ownerid = study.user_uid
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people_list = [{'uid':ownerid,'role':'owner','send_email':True,'access':True}]
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people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id)
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for person in people:
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newAssociate = {'uid':person.uid}
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newAssociate['role'] = person.role
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newAssociate['send_email'] = person.send_email
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newAssociate['access'] = person.access
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people_list.append(newAssociate)
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return people_list
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@staticmethod
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def update_study_associates(study_id,associates):
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"""
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updates the list of associates in the database for a study_id and a list
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of dicts that contains associates
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"""
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if study_id is None:
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raise ApiError('study_id not specified', "This function requires the study_id parameter")
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for person in associates:
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if not LdapService.user_exists(person.get('uid','impossible_uid')):
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if person.get('uid','impossible_uid') == 'impossible_uid':
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raise ApiError('associate with no uid','One of the associates passed as a parameter doesnt have '
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'a uid specified')
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raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to "
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"%s, but that user was not found in "
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"ldap "
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"- please check to ensure it is a "
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"valid uva uid"%person.get('uid'))
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_id not found', "A study with id# %d was not found"%study_id)
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db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).delete()
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for person in associates:
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newAssociate = StudyAssociated()
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newAssociate.study_id = study_id
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newAssociate.uid = person['uid']
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newAssociate.role = person.get('role', None)
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newAssociate.send_email = person.get('send_email', False)
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newAssociate.access = person.get('access',False)
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session.add(newAssociate)
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session.commit()
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@staticmethod
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def update_study_associate(study_id=None,uid=None,role="",send_email=False,access=False):
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if study_id is None:
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raise ApiError('study_id not specified', "This function requires the study_id parameter")
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if uid is None:
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raise ApiError('uid not specified', "This function requires a uva uid parameter")
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if not LdapService.user_exists(uid):
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raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to "
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"%s but they were not found in ldap "
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"- please check to ensure it is a "
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"valid uva uid"%uid)
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_id not found', "A study with id# %d was not found"%study_id)
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db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(StudyAssociated.uid ==
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uid) ).delete()
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newAssociate = StudyAssociated()
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newAssociate.study_id = study_id
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newAssociate.uid = uid
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newAssociate.role = role
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newAssociate.send_email = send_email
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newAssociate.access = access
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session.add(newAssociate)
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session.commit()
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return True
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@staticmethod
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def delete_study(study_id):
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session.query(TaskEventModel).filter_by(study_id=study_id).delete()
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@ -649,8 +649,8 @@ class WorkflowService(object):
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@staticmethod
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def get_users_assigned_to_task(processor, spiff_task) -> List[str]:
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||||
if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
|
||||
return [processor.workflow_model.study.user_uid]
|
||||
# todo: return a list of all users that can edit the study by default
|
||||
associated = StudyService.get_study_associates(processor.workflow_model.study.id)
|
||||
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]
|
||||
|
|
|
|||
|
|
@ -0,0 +1,38 @@
|
|||
"""empty message
|
||||
|
||||
Revision ID: cb892916166a
|
||||
Revises: ff29528a9909
|
||||
Create Date: 2021-02-24 12:16:45.779821
|
||||
|
||||
"""
|
||||
from alembic import op
|
||||
import sqlalchemy as sa
|
||||
|
||||
|
||||
# revision identifiers, used by Alembic.
|
||||
revision = 'cb892916166a'
|
||||
down_revision = 'ff29528a9909'
|
||||
branch_labels = None
|
||||
depends_on = None
|
||||
|
||||
|
||||
def upgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.create_table('study_associated_user',
|
||||
sa.Column('id', sa.Integer(), nullable=False),
|
||||
sa.Column('study_id', sa.Integer(), nullable=False),
|
||||
sa.Column('uid', sa.String(), nullable=False),
|
||||
sa.Column('role', sa.String(), nullable=True),
|
||||
sa.Column('send_email', sa.Boolean(), nullable=True),
|
||||
sa.Column('access', sa.Boolean(), nullable=True),
|
||||
sa.ForeignKeyConstraint(['study_id'], ['study.id'], ),
|
||||
sa.ForeignKeyConstraint(['uid'], ['ldap_model.uid'], ),
|
||||
sa.PrimaryKeyConstraint('id')
|
||||
)
|
||||
# ### end Alembic commands ###
|
||||
|
||||
|
||||
def downgrade():
|
||||
# ### commands auto generated by Alembic - please adjust! ###
|
||||
op.drop_table('study_associated_user')
|
||||
# ### end Alembic commands ###
|
||||
|
|
@ -0,0 +1,93 @@
|
|||
<?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="3.7.0">
|
||||
<bpmn:process id="Process_0exnnpv" isExecutable="true">
|
||||
<bpmn:startEvent id="StartEvent_1">
|
||||
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
|
||||
</bpmn:startEvent>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
|
||||
<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
|
||||
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
|
||||
<bpmn:script>sponsors = study_info('sponsors')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="Activity_0cm6tn2" />
|
||||
<bpmn:sequenceFlow id="Flow_09cika8" sourceRef="Activity_0cm6tn2" targetRef="Activity_14td33q" />
|
||||
<bpmn:scriptTask id="Activity_0cm6tn2" name="setval">
|
||||
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_09cika8</bpmn:outgoing>
|
||||
<bpmn:script>update_study_associate(uid='lb3dp',role='SuperDude',send_email=False,access=True)</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:scriptTask id="Activity_0d8iftx" name="getval2">
|
||||
<bpmn:incoming>Flow_1vlh6s0</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0cttkwp</bpmn:outgoing>
|
||||
<bpmn:script>out3 = get_study_associates()
|
||||
out4 = get_study_associate('lb3dp')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:endEvent id="Event_0c8gcuh">
|
||||
<bpmn:incoming>Flow_0cttkwp</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:sequenceFlow id="Flow_0cttkwp" sourceRef="Activity_0d8iftx" targetRef="Event_0c8gcuh" />
|
||||
<bpmn:scriptTask id="Activity_0run091" name="setval - 2">
|
||||
<bpmn:incoming>Flow_14n3ixy</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_1vlh6s0</bpmn:outgoing>
|
||||
<bpmn:script>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" />
|
||||
<bpmn:scriptTask id="Activity_14td33q" name="getval">
|
||||
<bpmn:incoming>Flow_09cika8</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_14n3ixy</bpmn:outgoing>
|
||||
<bpmn:script>out = get_study_associates()
|
||||
out2 = get_study_associate('lb3dp')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="Flow_14n3ixy" sourceRef="Activity_14td33q" targetRef="Activity_0run091" />
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
|
||||
<di:waypoint x="370" y="117" />
|
||||
<di:waypoint x="440" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
|
||||
<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="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>
|
||||
<bpmndi:BPMNShape id="Activity_0cq37mm_di" bpmnElement="Activity_0d8iftx">
|
||||
<dc:Bounds x="900" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<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>
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
<?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="3.7.0">
|
||||
<bpmn:process id="Process_0exnnpv" isExecutable="true">
|
||||
<bpmn:startEvent id="StartEvent_1">
|
||||
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
|
||||
</bpmn:startEvent>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
|
||||
<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
|
||||
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
|
||||
<bpmn:script>sponsors = study_info('sponsors')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="Activity_0cm6tn2" />
|
||||
<bpmn:sequenceFlow id="Flow_09cika8" sourceRef="Activity_0cm6tn2" targetRef="Activity_0d8iftx" />
|
||||
<bpmn:scriptTask id="Activity_0cm6tn2" name="setval">
|
||||
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_09cika8</bpmn:outgoing>
|
||||
<bpmn:script>update_study_associate(uid='cah5us',role='SuperDude',send_email=False,access=True)</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:scriptTask id="Activity_0d8iftx" name="getval">
|
||||
<bpmn:incoming>Flow_09cika8</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0cttkwp</bpmn:outgoing>
|
||||
<bpmn:script>out = get_study_associates()
|
||||
out2 = get_study_associate('lb3dp')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:endEvent id="Event_0c8gcuh">
|
||||
<bpmn:incoming>Flow_0cttkwp</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:sequenceFlow id="Flow_0cttkwp" sourceRef="Activity_0d8iftx" targetRef="Event_0c8gcuh" />
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
|
||||
<di:waypoint x="370" y="117" />
|
||||
<di:waypoint x="440" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
|
||||
<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="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="600" 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>
|
||||
<bpmndi:BPMNShape id="Activity_0cq37mm_di" bpmnElement="Activity_0d8iftx">
|
||||
<dc:Bounds x="600" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Event_0c8gcuh_di" bpmnElement="Event_0c8gcuh">
|
||||
<dc:Bounds x="762" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="Flow_0cttkwp_di" bpmnElement="Flow_0cttkwp">
|
||||
<di:waypoint x="700" y="117" />
|
||||
<di:waypoint x="762" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
<?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="3.7.0">
|
||||
<bpmn:process id="Process_0exnnpv" isExecutable="true">
|
||||
<bpmn:startEvent id="StartEvent_1">
|
||||
<bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
|
||||
</bpmn:startEvent>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
|
||||
<bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
|
||||
<bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
|
||||
<bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
|
||||
<bpmn:script>sponsors = study_info('sponsors')</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="Activity_0cm6tn2" />
|
||||
<bpmn:sequenceFlow id="Flow_09cika8" sourceRef="Activity_0cm6tn2" targetRef="Activity_0s3e9zu" />
|
||||
<bpmn:scriptTask id="Activity_0cm6tn2" name="setval">
|
||||
<bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_09cika8</bpmn:outgoing>
|
||||
<bpmn:script>update_study_associate(uid='lb3dp',role='SuperGal',send_email=False,access=True)
|
||||
update_study_associate(uid='lje5u',role='SuperGal2',send_email=False,access=False)</bpmn:script>
|
||||
</bpmn:scriptTask>
|
||||
<bpmn:endEvent id="Event_0c8gcuh">
|
||||
<bpmn:incoming>Flow_0axwrzg</bpmn:incoming>
|
||||
</bpmn:endEvent>
|
||||
<bpmn:task id="Activity_0s3e9zu" name="Meaningless User Task">
|
||||
<bpmn:documentation>This should just leave us a task to complete after the update_study_assocate script</bpmn:documentation>
|
||||
<bpmn:incoming>Flow_09cika8</bpmn:incoming>
|
||||
<bpmn:outgoing>Flow_0axwrzg</bpmn:outgoing>
|
||||
</bpmn:task>
|
||||
<bpmn:sequenceFlow id="Flow_0axwrzg" sourceRef="Activity_0s3e9zu" targetRef="Event_0c8gcuh" />
|
||||
</bpmn:process>
|
||||
<bpmndi:BPMNDiagram id="BPMNDiagram_1">
|
||||
<bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
|
||||
<di:waypoint x="370" y="117" />
|
||||
<di:waypoint x="440" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
<bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
|
||||
<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="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="610" 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>
|
||||
<bpmndi:BPMNShape id="Event_0c8gcuh_di" bpmnElement="Event_0c8gcuh">
|
||||
<dc:Bounds x="1042" y="99" width="36" height="36" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNShape id="Activity_0s3e9zu_di" bpmnElement="Activity_0s3e9zu">
|
||||
<dc:Bounds x="610" y="77" width="100" height="80" />
|
||||
</bpmndi:BPMNShape>
|
||||
<bpmndi:BPMNEdge id="Flow_0axwrzg_di" bpmnElement="Flow_0axwrzg">
|
||||
<di:waypoint x="710" y="117" />
|
||||
<di:waypoint x="1042" y="117" />
|
||||
</bpmndi:BPMNEdge>
|
||||
</bpmndi:BPMNPlane>
|
||||
</bpmndi:BPMNDiagram>
|
||||
</bpmn:definitions>
|
||||
|
|
@ -0,0 +1,163 @@
|
|||
import json
|
||||
from unittest.mock import patch
|
||||
import flask
|
||||
|
||||
from crc.api.common import ApiError
|
||||
from crc.services.user_service import UserService
|
||||
from tests.base_test import BaseTest
|
||||
|
||||
from crc import session, app
|
||||
from crc.models.study import StudyModel
|
||||
from crc.models.user import UserModel
|
||||
from crc.api.study import user_studies
|
||||
from crc.services.study_service import StudyService
|
||||
from crc.services.workflow_processor import WorkflowProcessor
|
||||
from crc.services.workflow_service import WorkflowService
|
||||
|
||||
class TestSudySponsorsScript(BaseTest):
|
||||
test_uid = "dhf8r"
|
||||
test_study_id = 1
|
||||
|
||||
|
||||
def test_study_sponsors_script_validation(self):
|
||||
flask.g.user = UserModel(uid='dhf8r')
|
||||
self.load_example_data() # study_info script complains if irb_documents.xls is not loaded
|
||||
# during the validate phase I'm going to assume that we will never
|
||||
# have a case where irb_documents.xls is not loaded ??
|
||||
|
||||
self.load_test_spec("study_sponsors_associate")
|
||||
WorkflowService.test_spec("study_sponsors_associate") # This would raise errors if it didn't validate
|
||||
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_study_sponsors_script(self, mock_get):
|
||||
mock_get.return_value.ok = True
|
||||
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
|
||||
flask.g.user = UserModel(uid='dhf8r')
|
||||
app.config['PB_ENABLED'] = True
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("study_sponsors_associate")
|
||||
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
|
||||
WorkflowService.test_spec("study_sponsors_associate")
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.do_engine_steps()
|
||||
self.assertTrue(processor.bpmn_workflow.is_completed())
|
||||
data = processor.next_task().data
|
||||
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']))
|
||||
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_study_sponsors_script_fail(self, mock_get):
|
||||
mock_get.return_value.ok = True
|
||||
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
|
||||
flask.g.user = UserModel(uid='dhf8r')
|
||||
app.config['PB_ENABLED'] = True
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("study_sponsors_associate_fail")
|
||||
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
|
||||
WorkflowService.test_spec("study_sponsors_associate_fail")
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
with self.assertRaises(ApiError):
|
||||
processor.do_engine_steps()
|
||||
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_study_sponsors_script_primary_user(self, mock_get):
|
||||
mock_get.return_value.ok = True
|
||||
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
|
||||
flask.g.user = UserModel(uid='dhf8r')
|
||||
app.config['PB_ENABLED'] = True
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("study_sponsors_associate_switch_user")
|
||||
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
|
||||
WorkflowService.test_spec("study_sponsors_associate_switch_user")
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.do_engine_steps()
|
||||
tasks = processor.next_user_tasks()
|
||||
self.assertEqual(len(tasks),1)
|
||||
processor.complete_task(tasks[0])
|
||||
processor.do_engine_steps()
|
||||
self.assertTrue(processor.bpmn_workflow.is_completed())
|
||||
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_study_sponsors_script_valid_users(self, mock_get):
|
||||
mock_get.return_value.ok = True
|
||||
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
|
||||
flask.g.user = UserModel(uid='dhf8r')
|
||||
app.config['PB_ENABLED'] = True
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("study_sponsors_associate_switch_user")
|
||||
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
|
||||
WorkflowService.test_spec("study_sponsors_associate_switch_user")
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.do_engine_steps()
|
||||
tasks = processor.next_user_tasks()
|
||||
self.assertEqual(len(tasks),1)
|
||||
users = WorkflowService.get_users_assigned_to_task(processor,tasks[0])
|
||||
self.assertFalse('cah3us' in users)
|
||||
self.assertFalse('lje5u' in users)
|
||||
self.assertTrue('lb3dp' in users)
|
||||
self.assertTrue('dhf8r' in users)
|
||||
# the above should emulate what is going on when we determine if a user can
|
||||
# make changes to a study or not.
|
||||
# in theory all endpoints that need to be limited are calling the
|
||||
# WorkflowService.get_users_assigned_to_task function to determine
|
||||
# who is allowed access
|
||||
|
||||
|
||||
@patch('crc.services.protocol_builder.requests.get')
|
||||
def test_study_sponsors_script_ensure_access(self, mock_get):
|
||||
mock_get.return_value.ok = True
|
||||
mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
|
||||
flask.g.user = UserModel(uid='dhf8r')
|
||||
app.config['PB_ENABLED'] = True
|
||||
|
||||
self.load_example_data()
|
||||
self.create_reference_document()
|
||||
study = session.query(StudyModel).first()
|
||||
workflow_spec_model = self.load_test_spec("study_sponsors_associate_switch_user")
|
||||
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
|
||||
WorkflowService.test_spec("study_sponsors_associate_switch_user")
|
||||
processor = WorkflowProcessor(workflow_model)
|
||||
processor.do_engine_steps()
|
||||
# change user and make sure we can access the study
|
||||
flask.g.user = UserModel(uid='lb3dp')
|
||||
flask.g.token = 'my spiffy token'
|
||||
app.config['PB_ENABLED'] = False
|
||||
output = user_studies()
|
||||
self.assertEqual(output[0]['id'], 0)
|
||||
self.assertEqual(output[0]['user_uid'], 'dhf8r')
|
||||
flask.g.user = UserModel(uid='lje5u')
|
||||
flask.g.token = 'my spiffy token'
|
||||
app.config['PB_ENABLED'] = False
|
||||
output = user_studies()
|
||||
self.assertEqual(len(output),0)
|
||||
Loading…
Reference in New Issue