class DemographicsRequestColumn(db.Model):
id = db.Column(db.Integer, primary_key=True)
demographics_request_id = db.Column(db.Integer,
db.ForeignKey(DemographicsRequest.id))
demographics_request = db.relationship(
DemographicsRequest,
foreign_keys=[demographics_request_id],
backref=db.backref("columns"))
name = db.Column(db.String(500))
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(
User, foreign_keys=[last_updated_by_user_id])
def __lt__(self, other):
return self.name < other.name
def __repr__(self):
fields = '; '.join([
f'{key}="{value}"' for key, value in self.__dict__.items()
if key[0] != '_'
])
return f'[{type(self).__name__}({fields})]'
class LegacyId(db.Model):
id = db.Column(db.Integer, primary_key=True)
legacy_id_provider_id = db.Column(db.Integer,
db.ForeignKey(LegacyIdProvider.id))
legacy_id_provider = db.relationship(LegacyIdProvider)
number = db.Column(db.Integer, nullable=False)
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
def __repr__(self):
return str(self.__class__) + ": " + str(self.__dict__)
def __str__(self):
return self.prefix + self.zero_filled_number
@property
def barcode(self):
return '{}{}'.format(
self.legacy_id_provider.prefix,
str(self.number).zfill(
self.legacy_id_provider.number_fixed_length),
)
class TaskFile(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
filename = db.Column(db.UnicodeText())
local_filepath = db.Column(db.UnicodeText())
task_id = db.Column(db.Integer, db.ForeignKey(Task.id))
task = db.relationship(Task,
backref=backref('files',
cascade='all, delete-orphan'))
field_id = db.Column(db.Integer, db.ForeignKey(Field.id))
field = db.relationship(Field, lazy="joined")
def set_filename_and_save(self, file):
self.filename = file.filename
local_filepath = self._new_local_filepath(
filename=file.filename,
parent=str(self.task.id),
)
self.local_filepath = str(local_filepath)
local_filepath.parent.mkdir(parents=True, exist_ok=True)
file.save(local_filepath)
def _new_local_filepath(self, filename, parent=None):
result = pathlib.Path(current_app.config["FILE_UPLOAD_DIRECTORY"])
if parent:
result = result.joinpath(secure_filename(parent))
result = result.joinpath(
secure_filename("{}_{}".format(uuid.uuid1().hex, filename)))
return result
class Organisation(db.Model, CommonMixin):
CARDIOVASCULAR = 'BRC Cardiovascular Theme'
LIFESTYLE = 'BRC Lifestyle Theme'
PRECICION = 'BRC Precision Medicine Theme'
RESPIRATORY = 'BRC Respiratory Theme'
LDC = 'Leicester Diabetes Centre'
PRC = 'Patient Recruitment Centre'
RandI = 'R&I'
OTHER = 'Other - please specify'
all_organisations = [
CARDIOVASCULAR, LIFESTYLE, PRECICION, RESPIRATORY, LDC, PRC, RandI,
OTHER
]
id = db.Column(db.Integer(), primary_key=True)
name = db.Column(db.String(255))
@classmethod
def get_organisation(cls, name):
return Organisation.query.filter_by(name=name).one()
@classmethod
def get_other(cls):
return cls.get_organisation(Organisation.OTHER)
class BlindingSet(db.Model):
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(100), nullable=False)
study_id = db.Column(db.Integer, db.ForeignKey(Study.id), nullable=False)
study = db.relationship(Study, backref=db.backref("blinding_sets"))
def __repr__(self):
return self.name
def __lt__(self, other):
return self.name < other.name
def get_blind_ids(self, unblind_id, user):
result = []
for bt in self.blinding_types:
blind_id = bt.get_blind_id(unblind_id, user)
if blind_id:
result.append(blind_id)
return result
def get_unblind_id(self, blind_id):
for bt in self.blinding_types:
unblind_id = bt.get_unblind_id(blind_id)
if unblind_id:
return unblind_id
class TaskAssignedUser(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
task_id = db.Column(db.Integer, db.ForeignKey(Task.id), nullable=False)
task = db.relationship(Task, backref="assigned_user_history")
user_id = db.Column(db.Integer, db.ForeignKey(User.id), nullable=False)
user = db.relationship(User)
notes = db.Column(db.String(255))
class ApiKey(db.Model):
id = db.Column(db.Integer, primary_key=True)
key = db.Column(GUID, nullable=False, default=uuid.uuid4)
user_id = db.Column(db.Integer, db.ForeignKey(User.id), nullable=False)
user = db.relationship(User, backref=db.backref("api_key", uselist=False))
def __repr__(self):
return f'API Key for User {self.user.full_name}'
class FieldGroup(db.Model):
id = db.Column(db.Integer(), primary_key=True)
name = db.Column(db.String)
def __str__(self):
return self.name
def get_field_for_field_name(self, field_name):
return {f.field_name: f for f in self.fields}.get(field_name)
class AbstractSection(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
publication_id = db.Column(db.Integer(), db.ForeignKey(Publication.id))
publication = db.relationship(Publication,
lazy="joined",
backref='abstracts')
label = db.Column(db.String(200))
text = db.Column(db.UnicodeText())
class LabelPack(db.Model):
id = db.Column(db.Integer, primary_key=True)
type = db.Column(db.String(100), nullable=False)
study_id = db.Column(db.Integer, db.ForeignKey(Study.id))
study = db.relationship(Study, backref=db.backref("label_packs"))
__mapper_args__ = {
"polymorphic_identity": "Pack",
"polymorphic_on": type,
}
def user_defined_participant_id(self):
return False
def allow_batch_printing(self):
return True
@property
def name(self):
return re.sub('([a-z])([A-Z])', r'\1 \2', self.__class__.__name__)
def print(self, count):
for _ in range(count):
current_app.logger.info(
f'Printing label for study {self.study.name}')
self._do_print()
db.session.commit()
time.sleep(current_app.config['PRINTING_SET_SLEEP'])
def save_participant_id(self, participant_id):
pit = ParticipantIdentifierType.get_study_participant_id()
pi = ParticipantIdentifier.query.filter_by(
participant_identifier_type_id=pit.id,
identifier=participant_id,
).one_or_none()
if pi is None:
db.session.add(
ParticipantIdentifier(
participant_identifier_type_id=pit.id,
identifier=participant_id,
last_updated_by_user_id=current_user.id,
))
def _do_print(self, participant_id=None):
pass
def __repr__(self):
return self.name
def __lt__(self, other):
return self.name < other.name
class StudyParticipant(db.Model):
id = db.Column(db.Integer, primary_key=True)
study_id = db.Column(db.Integer, db.ForeignKey(Study.id), nullable=False)
study = db.relationship(Study, backref=db.backref("participants"))
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
class TaskStatus(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
task_id = db.Column(db.Integer, db.ForeignKey(Task.id), nullable=False)
task = db.relationship(Task, backref="status_history")
notes = db.Column(db.String(255))
task_status_type_id = db.Column(db.Integer,
db.ForeignKey(TaskStatusType.id),
nullable=False)
task_status_type = db.relationship(TaskStatusType,
backref="assigned_tasks")
class UploadData(db.Model):
id = db.Column(db.Integer(), primary_key=True)
upload_id = db.Column(db.Integer(), db.ForeignKey(Upload.id))
upload = db.relationship(Upload, backref=db.backref("data"))
field_id = db.Column(db.Integer(), db.ForeignKey(Field.id))
field = db.relationship(Field)
value = db.Column(db.String)
def __repr__(self):
items = ("%s = %r" % (k, v) for k, v in self.__dict__.items())
return "<%s: {%s}>" % (self.__class__.__name__, ', '.join(items))
class Publication(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
pm_id = db.Column(db.Integer())
journal = db.Column(db.String(200))
published_date = db.Column(db.Date)
title = db.Column(db.UnicodeText())
academics = db.relationship("Academic",
secondary=academics_publications,
collection_class=set,
backref=db.backref("publications",
lazy="joined"))
class BioresourceId(db.Model):
id = db.Column(db.Integer, primary_key=True)
bioresource_id_provider_id = db.Column(
db.Integer, db.ForeignKey(BioresourceIdProvider.id))
bioresource_id_provider = db.relationship(BioresourceIdProvider)
number = db.Column(db.Integer, nullable=False)
check_character = db.Column(db.String(1), nullable=False)
legacy_number = db.Column(db.Integer)
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
def __repr__(self):
return str(self.__class__) + ": " + str(self.__dict__)
def __str__(self):
return self.full_code
@property
def full_code(self):
return self.bioresource_id_provider.prefix + str(
self.number) + self.check_character
@property
def barcode(self):
return self.full_code
class Study(db.Model):
id = db.Column(db.Integer, primary_key=True)
edge_id = db.Column(db.Integer, nullable=True)
name = db.Column(db.String(50), nullable=False)
def __str__(self):
return self.name or ""
def get_blind_ids(self, unblind_id, user):
result = []
for bs in self.blinding_sets:
for bt in [t for t in bs.blinding_types if not t.deleted]:
blind_id = bt.get_blind_id(unblind_id, user)
if blind_id:
result.append(blind_id)
return result
class TaskData(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
value = db.Column(db.UnicodeText())
task_id = db.Column(db.Integer, db.ForeignKey(Task.id))
task = db.relationship(Task,
backref=backref('data',
cascade='all, delete-orphan'))
field_id = db.Column(db.Integer, db.ForeignKey(Field.id))
field = db.relationship(Field, lazy="joined")
@property
def formated_value(self):
return self.field.format_value(self.value)
@property
def data_value(self):
return self.field.data_value(self.value)
class LabelParticipantIdentifierSource(ParticipantIdentifierSource):
__tablename__ = 'label_participant_identifier_source'
id = db.Column(db.Integer,
db.ForeignKey('participant_identifier_source.id'),
primary_key=True)
__mapper_args__ = {
'polymorphic_identity': 'label_participant_identifier_source',
}
class Task(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
name = db.Column(db.String(255))
organisation_id = db.Column(db.Integer, db.ForeignKey(Organisation.id))
organisation = db.relationship(Organisation,
lazy="joined",
backref='tasks')
organisation_description = db.Column(db.String(255))
service_id = db.Column(db.Integer, db.ForeignKey(Service.id))
service = db.relationship(Service, lazy="joined", backref='tasks')
requestor_id = db.Column(db.Integer,
db.ForeignKey(User.id),
nullable=False)
requestor = db.relationship(User,
lazy="joined",
backref='tasks',
foreign_keys=[requestor_id])
current_status_type_id = db.Column(db.Integer,
db.ForeignKey(TaskStatusType.id),
nullable=False)
current_status_type = db.relationship(TaskStatusType)
current_assigned_user_id = db.Column(db.Integer,
db.ForeignKey(User.id),
nullable=True)
current_assigned_user = db.relationship(
User, foreign_keys=[current_assigned_user_id])
@property
def long_name(self):
return "{}: {}".format(self.service.name, self.name)
@property
def total_todos(self):
return len(self.todos)
@property
def required_todos(self):
return len([t for t in self.todos if t.is_required])
@property
def complete_todos(self):
return len([t for t in self.todos if t.is_complete])
@property
def notification_email_addresses(self):
return self.service.notification_email_addresses + [
self.requestor.email
]
def get_data_for_task_id(self, field_id):
return next((t for t in self.data if t.field_id == field_id), None)
class Site(db.Model):
LBRC = "Leicester Biomedical Research Centre"
id = db.Column(db.Integer(), primary_key=True)
name = db.Column(db.String(255))
number = db.Column(db.String(20))
date_created = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
def __str__(self):
return self.name
@property
def name_and_number(self):
number_portion = ""
if self.number:
number_portion = " ({})".format(self.number)
return self.name + number_portion
class Blinding(db.Model):
id = db.Column(db.Integer, primary_key=True)
unblind_id = db.Column(db.String(100), nullable=False)
blinding_type_id = db.Column(db.Integer,
db.ForeignKey(BlindingType.id),
nullable=False)
blinding_type = db.relationship(BlindingType,
backref=db.backref("blindings"))
pseudo_random_id_id = db.Column(db.Integer,
db.ForeignKey(PseudoRandomId.id),
nullable=False)
pseudo_random_id = db.relationship(PseudoRandomId)
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
def __repr__(self):
return '; '.join([
self.blinding_type.name,
self.unblind_id,
self.pseudo_random_id.full_code,
])
def __lt__(self, other):
return self.name < other.name
class ToDo(AuditMixin, CommonMixin, db.Model):
OUTSTANDING = 'Outstanding'
COMPLETED = 'Completed'
NOT_REQUIRED = 'Not Required'
_status_map = {
-1: NOT_REQUIRED,
0: OUTSTANDING,
1: COMPLETED,
}
@staticmethod
def get_status_code_from_name(name):
return {v: k for k, v in ToDo._status_map.items()}[name]
id = db.Column(db.Integer(), primary_key=True)
task_id = db.Column(db.Integer, db.ForeignKey(Task.id))
task = db.relationship(Task, backref='todos')
description = db.Column(db.UnicodeText())
status = db.Column(db.Integer,
db.CheckConstraint("status IN (-1, 0, 1)"),
nullable=False,
default=0)
@property
def status_name(self):
return ToDo._status_map[self.status]
@property
def is_outstanding(self):
return self.status == 0
@property
def is_required(self):
return self.status > -1
@property
def is_complete(self):
return self.status == 1
class ParticipantIdentifierSource(db.Model):
__tablename__ = 'participant_identifier_source'
id = db.Column(db.Integer, primary_key=True)
linked_minimum_patient_identifier_source_id = db.Column(
db.Integer,
db.ForeignKey("participant_identifier_source.id"),
nullable=True)
type = db.Column(db.String(100), nullable=False)
study_id = db.Column(db.Integer, db.ForeignKey(Study.id), nullable=True)
study = db.relationship(
Study, backref=db.backref("participant_identifier_sources"))
__mapper_args__ = {
'polymorphic_identity': 'participant_identifier_source',
'polymorphic_on': type,
}
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
identifiers = db.relationship(
"ParticipantIdentifier",
secondary=participant_identifiers__participant_identifier_sources,
back_populates="sources",
collection_class=set)
def __str__(self):
return f"{self.type.name}: {self.identifier}"
class Academic(AuditMixin, CommonMixin, db.Model):
id = db.Column(db.Integer(), primary_key=True)
google_scholar_id = db.Column(db.String(255))
name = db.Column(db.String(500))
affiliation = db.Column(db.String(500))
cited_by = db.Column(db.Integer)
h_index = db.Column(db.Integer)
i10_index = db.Column(db.Integer)
is_updating = db.Column(db.Boolean)
@property
def pubmed_name(self):
firstname, *_, lastname = self.name.split()
return f'{lastname} {firstname[0]}'
class ParticipantIdentifierType(db.Model):
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(100), nullable=False)
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
def __str__(self):
return self.name
@staticmethod
def get_type(type_name):
return ParticipantIdentifierType.query.filter_by(
name=type_name, ).one_or_none()
@staticmethod
def get_study_participant_id():
return ParticipantIdentifierType.get_type(
ParticipantIdentifierTypeName.STUDY_PARTICIPANT_ID)
class ParticipantIdentifier(db.Model):
__tablename__ = 'participant_identifier'
id = db.Column(db.Integer, primary_key=True)
identifier = db.Column(db.String(100), nullable=False)
participant_identifier_type_id = db.Column(
db.Integer, db.ForeignKey(ParticipantIdentifierType.id))
participant_identifier_type = db.relationship(ParticipantIdentifierType)
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
sources = db.relationship(
"ParticipantIdentifierSource",
secondary=participant_identifiers__participant_identifier_sources,
back_populates="identifiers",
collection_class=set)
def __str__(self):
return f"{self.type.name}: {self.identifier}"
class Study(db.Model):
id = db.Column(db.Integer(), primary_key=True)
name = db.Column(db.String(100))
date_created = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
allow_duplicate_study_number = db.Column(db.Boolean,
nullable=False,
default=False)
allow_empty_study_number = db.Column(db.Boolean,
nullable=False,
default=False)
study_number_format = db.Column(db.String(50))
study_number_name = db.Column(db.String(100))
field_group_id = db.Column(db.Integer(), db.ForeignKey(FieldGroup.id))
field_group = db.relationship(FieldGroup, backref=db.backref("study"))
owners = db.relationship(
User,
secondary=studies_owners,
backref=db.backref("owned_studies", lazy="dynamic"),
)
collaborators = db.relationship(
User,
secondary=studies_collaborators,
backref=db.backref("collaborator_studies", lazy="dynamic"),
)
def __str__(self):
return self.name
@property
def upload_count(self):
return len([u for u in self.uploads if not u.deleted])
def upload_count_for_user(self, user):
return len(
[u for u in self.uploads if not u.deleted and u.uploader == user])
@property
def outstanding_upload_count(self):
return len(
[u for u in self.uploads if not u.deleted and not u.completed])
def get_study_number_name(self):
return self.study_number_name or 'Study Number'
class Upload(db.Model):
id = db.Column(db.Integer(), primary_key=True)
study_id = db.Column(db.Integer(), db.ForeignKey(Study.id))
study_number = db.Column(db.String(20))
uploader_id = db.Column(db.Integer(), db.ForeignKey(User.id))
date_created = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
study = db.relationship(Study, backref=db.backref("uploads"))
uploader = db.relationship(User)
completed = db.Column(db.Boolean, default=0)
deleted = db.Column(db.Boolean, default=0)
class UploadFile(db.Model):
id = db.Column(db.Integer(), primary_key=True)
upload_id = db.Column(db.Integer(), db.ForeignKey(Upload.id))
upload = db.relationship(Upload, backref=db.backref("files"))
field_id = db.Column(db.Integer(), db.ForeignKey(Field.id))
field = db.relationship(Field)
filename = db.Column(db.String(500))
def get_download_filename(self):
if len(self.field.download_filename_format or '') == 0:
return self.filename
else:
return self.field.download_filename_format.format(
file=self) + os.path.splitext(self.filename)[-1]
def filepath(self):
return os.path.join(
secure_filename("{}_{}".format(self.upload.study.id,
self.upload.study.name)),
secure_filename("{}_{}_{}".format(self.id,
self.upload.study_number,
self.filename)),
)
class PseudoRandomId(db.Model):
id = db.Column(db.Integer, primary_key=True)
pseudo_random_id_provider_id = db.Column(
db.Integer, db.ForeignKey(PseudoRandomIdProvider.id))
pseudo_random_id_provider = db.relationship(PseudoRandomIdProvider)
ordinal = db.Column(db.Integer, nullable=False)
unique_code = db.Column(db.Integer, nullable=False)
check_character = db.Column(db.String(1), nullable=False)
full_code = db.Column(db.String(20), nullable=False)
last_updated_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
last_updated_by_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
last_updated_by_user = db.relationship(User)
@property
def barcode(self):
return self.full_code
