class Taxa(db.Model):
__tablename__ = 'taxa'
id = db.Column(BIGINT, primary_key=True)
tax_rank = db.Column(VARCHAR(128), default=True, nullable=True)
tax_name = db.Column(VARCHAR(128), default=True, nullable=True)
tax_color = db.Column(VARCHAR(12), default=True, nullable=True)
parent = db.Column(BIGINT, default=True, nullable=True)
superkingdom = db.Column(BIGINT, default=True, nullable=True)
reads = db.Column(BIGINT, default=0, nullable=False)
results_taxoncount = db.relationship('ResultsTaxoncount', backref='taxa')
taxon_infos = db.relationship('TaxonInfo', uselist=False, backref='taxa')
def __init__(self, tax_rank, tax_name, tax_color, parent, superkingdom,
reads):
self.tax_rank = tax_rank
self.tax_name = tax_name
self.tax_color = tax_color
self.parent = parent
self.superkingdom = superkingdom
self.reads = reads
def __repr__(self):
return '<id {}>'.format(self.id)
class Experiments(db.Model):
__tablename__ = 'experiments'
id = db.Column(BIGINT, primary_key = True)
name = db.Column(VARCHAR(64), default = True, nullable = False)
color = db.Column(VARCHAR(6), default = True, nullable = False)
description = db.Column(TEXT, default = True, nullable = False)
instructions = db.Column(TEXT)
spare_answer_id = db.Column(BIGINT, default = True, nullable = True)
tag = db.Column(VARCHAR(10), default = True, nullable = True)
deliver_data = db.Column(SMALLINT, default = 0, nullable = False)
samples = db.relationship('Samples', backref='experiments')
kit_types_questions = db.relationship('KitTypesQuestions', secondary=kit_types_questions_X_experiments,
backref=db.backref('experiments', lazy='dynamic'))
def __init__(self, name, color, description, instructions, spare_answer_id, tag, deliver_data):
self.name = name
self.color = color
self.description = description
self.instructions = instructions
self.spare_answer_id = spare_answer_id
self.tag = tag
self.deliver_data = deliver_data
def __repr__(self):
return '<id {}>'.format(self.id)
class KitTypesQuestions(db.Model):
__tablename__ = 'kit_types_questions'
id = db.Column(BIGINT, primary_key=True)
kit_type = db.Column(BIGINT, db.ForeignKey('kit_types.id'), nullable=False)
question_text = db.Column(TEXT, nullable=False)
question_type = db.Column(INTEGER, default=True, nullable=True)
question_order = db.Column(INTEGER, nullable=False)
page = db.Column(INTEGER, default=True, nullable=True)
show_number = db.Column(SMALLINT, default=1, nullable=False)
requiredFilterPermission = db.Column(INTEGER, default=15, nullable=False)
kit_types_questions_answer_options = db.relationship(
'KitTypesQuestionsAnswerOptions', backref='kit_types_questions')
def __init__(self, kit_type, question_text, question_type, question_order,
page, show_number, requiredFilterPermission):
self.kit_type = kit_type
self.question_text = question_text
self.question_type = question_type
self.question_order = question_order
self.page = page
self.show_number = show_number
self.requiredFilterPermission = requiredFilterPermission
def __repr__(self):
return '<id {}>'.format(self.id)
class Kits(db.Model):
__tablename__ = 'kits'
id = db.Column(BIGINT, primary_key=True)
user = db.Column(BIGINT, db.ForeignKey('users.id'), nullable=False)
mailinglabel = db.Column(BIGINT, default=0, nullable=True)
record_created = db.Column(TIMESTAMP,
default=func.current_timestamp(),
nullable=False)
assembled = db.Column(TIMESTAMP)
registered = db.Column(TIMESTAMP)
barcode = db.Column(VARCHAR(9), default=True, nullable=True)
order_id = db.Column(BIGINT, default=0, nullable=True)
kit_type = db.Column(BIGINT, db.ForeignKey('kit_types.id'), nullable=False)
survey_page = db.Column(INTEGER, default=0, nullable=False)
survey_completed = db.Column(TIMESTAMP)
registration_override = db.Column(INTEGER, default=0, nullable=False)
tubesReceived = db.Column(TIMESTAMP)
processed = db.Column(TIMESTAMP)
analyzed = db.Column(TIMESTAMP)
last_reminder = db.Column(TIMESTAMP)
samples = db.relationship('Samples', backref='kits')
kit_types_questions_answers = db.relationship('KitTypesQuestionsAnswers',
backref='kits')
def __init__(self, user, mailinglabel, assembled, registered, barcode,
order_id, kit_type, survey_page, survey_completed,
registration_override, tubesReceived, processed, analyzed,
last_reminder):
self.user = user
self.mailinglabel = mailinglabel
self.assembled = assembled
self.registered = registered
self.barcode = barcode
self.order_id = order_id
self.kit_type = kit_type
self.survey_page = survey_page
self.survey_completed = survey_completed
self.registration_override = registration_override
self.tubesReceived = tubesReceived
self.processed = processed
self.analyzed = analyzed
self.last_reminder = last_reminder
def __repr__(self):
return '<id {}>'.format(self.id)
class User(db.Model, UserMixin):
__tablename__ = 'user'
id = db.Column(BIGINT, primary_key=True)
email = db.Column(VARCHAR(255), unique=True)
password = db.Column(VARCHAR(255))
active = db.Column(BOOLEAN)
confirmed_at = db.Column(TIMESTAMP, default = func.current_timestamp())
#Optional/Additional fields for Registration
first_name = db.Column(VARCHAR(255))
last_name = db.Column(VARCHAR(255))
admin = db.Column(BOOLEAN, default = False)
last_login_at = db.Column(TIMESTAMP)
current_login_at = db.Column(TIMESTAMP)
last_login_ip = db.Column(TEXT)
current_login_ip = db.Column(TEXT)
login_count = db.Column(BIGINT)
user_survey = db.relationship('UserSurvey', backref='users')
roles = db.relationship('Role', secondary=roles_users,
backref=db.backref('users', lazy='dynamic'))
class Samples(db.Model):
__tablename__ = 'samples'
id = db.Column(BIGINT, primary_key = True)
vial_barcode = db.Column(VARCHAR(32), default = True, nullable = True)
experiment = db.Column(BIGINT, db.ForeignKey('experiments.id'), nullable = False)
assigned_kit = db.Column(TIMESTAMP)
kit = db.Column(BIGINT, db.ForeignKey('kits.id'), nullable = False)
assigned_vial = db.Column(TIMESTAMP)
created = db.Column(TIMESTAMP, default = func.current_timestamp())
processed = db.Column(TIMESTAMP)
received = db.Column(TIMESTAMP)
analyzed = db.Column(TIMESTAMP)
query_exclude = db.Column(INTEGER, default = 0, nullable = False)
collected = db.Column(TIMESTAMP)
sequencing_revision = db.Column(BIGINT, nullable = False)
lab_sample_loading = db.relationship('LabSampleLoading', backref='samples')
results_taxoncount = db.relationship('ResultsTaxoncount', uselist=False, backref='samples')
def __init__(self, vial_barcode, experiment, assigned_kit, kit, assigned_vial,
processed, received, analyzed, query_exclude, collected,
sequencing_revision):
self.vial_barcode = vial_barcode
self.experiment = experiment
self.assigned_kit = assigned_kit
self.kit = kit
self.assigned_vial = assigned_vial
self.processed = processed
self.received = received
self.analyzed = analyzed
self.query_exclude = query_exclude
self.collected = collected
self.sequencing_revision = sequencing_revision
def __repr__(self):
return '<id {}>'.format(self.id)
class Users(db.Model):
__tablename__ = 'users'
id = db.Column(BIGINT, primary_key=True)
facebook_id = db.Column(BIGINT, default = True, nullable = True)
username = db.Column(VARCHAR(128), default = True, nullable = True)
email = db.Column(VARCHAR(196), default = True, nullable = True)
password = db.Column(VARCHAR(256), default = True, nullable = True)
confirmed_at = db.Column(TIMESTAMP, default = func.current_timestamp())
name_first = db.Column(VARCHAR(128), default = True, nullable = False)
name_last = db.Column(VARCHAR(128), default = True, nullable = False)
induction_completed = db.Column(INTEGER, default = 0)
adminlevel = db.Column(INTEGER, default = 0)
outbound_last_identify = db.Column(TIMESTAMP)
serviceConsent = db.Column(INTEGER, default = True, nullable = True)
sitever = db.Column(BIGINT, default = 0)
firstrunwarning = db.Column(INTEGER, default = 0)
displayname = db.Column(VARCHAR(64), default = True, nullable = True)
consentonfile = db.Column(BOOLEAN, default = 0)
mailinglist_invite = db.Column(TIMESTAMP)
active = db.Column(BOOLEAN)
kits = db.relationship('Kits', backref='users')
def __init__(self, facebook_id, username, email, password, name_first, name_last, induction_completed,
adminlevel, outbound_last_identify, serviceConsent, sitever, firstrunwarning, displayname,
consentonfile, mailinglist_invite):
self.facebook_id = facebook_id
self.username = username
self.email = email
self.password = password
self.name_first = name_first
self.name_last = name_last
self.induction_completed = induction_completed
self.adminlevel = adminlevel
self.outbound_last_identify = outbound_last_identify
self.serviceConsent = serviceConsent
self.sitever = sitever
self.firstrunwarning = firstrunwarning
self.displayname = displayname
self.consentonfile = consentonfile
self.mailinglist_invite = mailinglist_invite
def __repr__(self):
return '<id {}>'.format(self.id)
class KitTypesQuestionsAnswerOptions(db.Model):
__tablename__ = 'kit_types_questions_answer_options'
id = db.Column(BIGINT, primary_key = True)
kit_type_question = db.Column(BIGINT, db.ForeignKey('kit_types_questions.id'), nullable = False)
answer_text = db.Column(VARCHAR(256), nullable = False)
answer_tooltip = db.Column(VARCHAR(256), nullable = False)
answer_order = db.Column(INTEGER, default = True, nullable = True)
answer_validation = db.Column(TEXT)
kit_types_questions_answers = db.relationship('KitTypesQuestionsAnswers', backref='kit_types_questions_answer_options')
def __init__(self, kit_type_question, answer_text, answer_tooltip, answer_order,
answer_validation):
self.kit_type_question = kit_type_question
self.answer_text = answer_text
self.answer_tooltip = answer_tooltip
self.answer_order = answer_order
self.answer_validation = answer_validation
def __repr__(self):
return '<id {}>'.format(self.id)