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 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 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 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 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 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 User(BaseUser):
__table_args__ = {'extend_existing': True}
studies = db.relationship("Study",
secondary=users_studies,
backref=db.backref("users", lazy="joined"))
def __str__(self):
return 'user'
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 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 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 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 DemographicsRequestDataMessage(db.Model):
id = db.Column(db.Integer, primary_key=True)
demographics_request_data_id = db.Column(
db.Integer, db.ForeignKey(DemographicsRequestData.id))
demographics_request_data = db.relationship(DemographicsRequestData,
backref=db.backref("messages"))
type = db.Column(db.String)
source = db.Column(db.String)
scope = db.Column(db.String)
message = db.Column(db.String)
created_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
@property
def is_error(self):
return self.type == 'error'
class BlindingType(db.Model):
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(100), nullable=False)
blinding_set_id = db.Column(db.Integer,
db.ForeignKey(BlindingSet.id),
nullable=False)
blinding_set = db.relationship(BlindingSet,
backref=db.backref("blinding_types"))
pseudo_random_id_provider_id = db.Column(db.Integer,
db.ForeignKey(
PseudoRandomIdProvider.id),
nullable=False)
pseudo_random_id_provider = db.relationship(PseudoRandomIdProvider)
deleted = db.Column(db.Boolean, nullable=False, default=False)
duplicate_number = db.Column(db.Integer, default=0, nullable=False)
def __repr__(self):
return self.name
def __lt__(self, other):
return self.name < other.name
def get_blind_id(self, unblind_id, user):
blinding = (Blinding.query.filter_by(
blinding_type_id=self.id).filter_by(unblind_id=unblind_id).first())
if not blinding:
pseudo_random_id = self.pseudo_random_id_provider.allocate_id(user)
blinding = Blinding(
unblind_id=unblind_id,
blinding_type=self,
pseudo_random_id=pseudo_random_id,
last_updated_by_user=user,
)
return blinding
def get_unblind_id(self, blind_id):
blinding = (Blinding.query.filter_by(
blinding_type_id=self.id).join(PseudoRandomId).filter_by(
full_code=blind_id).first())
return blinding
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 DemographicsRequestData(db.Model):
id = db.Column(db.Integer, primary_key=True)
demographics_request_id = db.Column(db.Integer,
db.ForeignKey(DemographicsRequest.id))
row_number = db.Column(db.Integer, nullable=False)
demographics_request = db.relationship(DemographicsRequest,
backref=db.backref("data"))
response = db.relationship("DemographicsRequestDataResponse",
uselist=False,
back_populates="demographics_request_data")
pmi_data = db.relationship("DemographicsRequestPmiData",
uselist=False,
back_populates="demographics_request_data")
nhs_number = db.Column(db.String)
uhl_system_number = db.Column(db.String)
family_name = db.Column(db.String)
given_name = db.Column(db.String)
gender = db.Column(db.String)
dob = db.Column(db.String)
postcode = db.Column(db.String)
created_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
processed_datetime = db.Column(db.DateTime)
pmi_pre_processed_datetime = db.Column(db.DateTime)
pmi_post_processed_datetime = db.Column(db.DateTime)
@property
def processed(self):
return self.processed_datetime is not None
@property
def pmi_pre_processed(self):
return self.pmi_pre_processed_datetime is not None
@property
def pmi_post_processed(self):
return self.pmi_post_processed_datetime is not None
@property
def has_error(self):
return any(m.is_error for m in self.messages)
@property
def has_error(self):
return any(m.is_error for m in self.messages)
@property
def confidence(self):
if self.response is None:
return 0
parts = []
if self.nhs_number:
parts.append(similarity(self.nhs_number, self.response.nhs_number))
if self.family_name:
parts.append(similarity(self.family_name, self.response.lastname))
if self.given_name:
parts.append(similarity(self.given_name, self.response.forename))
if self.postcode:
parts.append(similarity(self.postcode, self.response.postcode))
return round(sum(parts) / len(parts), 2)
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 DemographicsRequest(db.Model):
id = db.Column(db.Integer, primary_key=True)
created_datetime = db.Column(db.DateTime,
nullable=False,
default=datetime.utcnow)
filename = db.Column(db.String(500))
extension = db.Column(db.String(100), nullable=False)
owner_user_id = db.Column(db.Integer, db.ForeignKey(User.id))
owner = db.relationship(User,
foreign_keys=[owner_user_id],
backref=db.backref("demographic_requests"))
submitted_datetime = db.Column(db.DateTime)
deleted_datetime = db.Column(db.DateTime)
paused_datetime = db.Column(db.DateTime)
data_extracted_datetime = db.Column(db.DateTime)
pmi_data_pre_completed_datetime = db.Column(db.DateTime)
pmi_data_post_completed_datetime = db.Column(db.DateTime)
lookup_completed_datetime = db.Column(db.DateTime)
result_created_datetime = db.Column(db.DateTime)
result_downloaded_datetime = db.Column(db.DateTime)
error_datetime = db.Column(db.DateTime)
error_message = db.Column(db.Text)
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])
column_definition = db.relationship("DemographicsRequestColumnDefinition",
uselist=False,
back_populates="demographics_request")
skip_pmi = db.Column(db.Boolean, default=False)
__mapper_args__ = {
"polymorphic_on": extension,
}
@property
def filepath(self):
return os.path.join(
current_app.config["FILE_UPLOAD_DIRECTORY"],
secure_filename(
"{}_{}".format(self.last_updated_by_user.id,
self.last_updated_by_user.full_name)),
secure_filename("{}_{}".format(self.id, self.filename)),
)
@property
def result_filename(self):
return secure_filename("{}_result_{}".format(self.id, self.filename))
@property
def result_filepath(self):
return os.path.join(
current_app.config["FILE_UPLOAD_DIRECTORY"],
secure_filename(
"{}_{}".format(self.last_updated_by_user.id,
self.last_updated_by_user.full_name)),
self.result_filename,
)
def __lt__(self, other):
return self.created_datetime < other.created_datetime
@property
def data_extracted(self):
return self.data_extracted_datetime is not None
@property
def paused(self):
return self.paused_datetime is not None
@property
def columns_defined(self):
return self.column_definition and self.column_definition.is_valid
@property
def awaiting_submission(self):
return self.columns_defined and self.submitted_datetime is None
@property
def submitted(self):
return self.submitted_datetime is not None
@property
def deleted(self):
return self.deleted_datetime is not None
@property
def result_created(self):
return self.result_created_datetime is not None
@property
def pmi_data_pre_completed(self):
return self.pmi_data_pre_completed_datetime is not None
@property
def pmi_data_post_completed(self):
return self.pmi_data_post_completed_datetime is not None
@property
def result_downloaded(self):
return self.result_downloaded_datetime is not None
@property
def lookup_completed(self):
return self.lookup_completed_datetime is not None
@property
def in_error(self):
return self.error_datetime is not None
@property
def requires_column_definition(self):
return not self.deleted and not self.submitted and not self.in_error
@property
def requires_submission(self):
return not self.deleted and self.awaiting_submission and not self.in_error
@property
def can_be_resubmitted(self):
return not self.deleted and self.submitted and not self.result_created and not self.in_error
@property
def can_be_paused(self):
return not self.deleted and self.submitted and not self.result_created and not self.paused and not self.in_error
@property
def can_be_downloaded(self):
return not self.deleted and self.result_created and not self.in_error
@property
def can_be_deleted(self):
return not self.deleted
@property
def status(self):
if self.deleted:
return 'Deleted'
elif self.in_error:
return 'Error'
elif self.paused:
return 'Paused'
if not self.columns_defined:
return 'Uploaded'
elif not self.submitted:
return 'Awaiting Submission'
elif not self.data_extracted:
return f'Extracting Data'
elif not self.pmi_data_pre_completed and not self.skip_pmi:
return f'Fetching PMI details {self.prepmi_count} of {self.data_count} before spine lookup'
elif not self.lookup_completed:
return f'Fetching Demographics {self.fetched_count} of {self.data_count}'
elif not self.pmi_data_post_completed and not self.skip_pmi:
return f'Fetching PMI details {self.postpmi_count} of {self.data_count} after spine lookup'
elif not self.result_created:
return 'Processing Demographics'
elif not self.result_downloaded:
return 'Ready to Download'
else:
return 'Downloaded'
@property
def data_count(self):
return DemographicsRequestData.query.filter(
DemographicsRequestData.demographics_request_id ==
self.id).count()
@property
def fetched_count(self):
return DemographicsRequestData.query.filter(
DemographicsRequestData.demographics_request_id == self.id).filter(
DemographicsRequestData.processed_datetime.isnot(
None)).count()
@property
def prepmi_count(self):
return DemographicsRequestData.query.filter(
DemographicsRequestData.demographics_request_id == self.id).filter(
DemographicsRequestData.pmi_pre_processed_datetime.isnot(
None)).count()
@property
def postpmi_count(self):
return DemographicsRequestData.query.filter(
DemographicsRequestData.demographics_request_id == self.id).filter(
DemographicsRequestData.pmi_post_processed_datetime.isnot(
None)).count()
def get_most_likely_uhl_system_number_column_id(self):
return self._get_most_likely_column_id('(uhl|\bs).*(number|no|)')
def get_most_likely_nhs_number_column_id(self):
return self._get_most_likely_column_id('nhs.*(number|no|)')
def get_most_likely_family_name_column_id(self):
return self._get_most_likely_column_id('(surname|(family|last).*name)')
def get_most_likely_given_name_column_id(self):
return self._get_most_likely_column_id('(first|given|fore).*name|name')
def get_most_likely_gender_column_id(self):
return self._get_most_likely_column_id('(gender|sex)')
def get_most_likely_dob_column_id(self):
return self._get_most_likely_column_id('(dob|date.*birth|birth.*date)')
def get_most_likely_postcode_column_id(self):
return self._get_most_likely_column_id('(post.*code)')
def _get_most_likely_column_id(self, regular_expression):
repat = re.compile(regular_expression, re.IGNORECASE)
ids = (c.id for c in self.columns if re.search(repat, c.name))
return next(ids, 0)
def set_error(self, message):
self.error_datetime = datetime.utcnow()
self.error_message = message
