initial checkin of changes for branch
This commit is contained in:
Kelly McDonald
parent
ff8a44a7b1
commit
3dbe39c6fe
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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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@ -34,6 +34,7 @@ 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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@ -50,7 +51,7 @@ 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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@ -62,6 +63,21 @@ 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([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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@ -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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@ -14,7 +14,7 @@ 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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@ -77,6 +77,120 @@ 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))
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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 assocated 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.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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db.session.add(newAssociate)
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db.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.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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db.session.add(newAssociate)
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db.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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