class ReferenceSequence(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_referencesequence'
id = db.Column(db.Integer, primary_key=True)
data_set_sample_sequences = db.relationship('DataSetSampleSequence',
backref='referencesequence',
lazy='select')
data_set_sample_sequences_pm = db.relationship('DataSetSampleSequencePM',
backref='referencesequence',
lazy='select')
name = db.Column(db.String(30), default='noName')
has_name = db.Column(db.Boolean, default=False)
clade = db.Column(db.String(30))
accession = db.Column(db.String(50), nullable=True)
sequence = db.Column(db.String(500), nullable=False)
def __str__(self):
if self.has_name:
return self.name
else:
return f'{self.id}_{self.clade}'
def __repr__(self):
if self.has_name:
return self.name
else:
return f'{self.id}_{self.clade}'
class DataSetSample(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_datasetsample'
id = db.Column(db.Integer, primary_key=True)
data_submission_from_id = db.Column(db.Integer,
db.ForeignKey('dbApp_dataset.id'),
nullable=False)
clade_collections = db.relationship('CladeCollection',
backref='dataset_sample')
data_set_sample_sequences = db.relationship('DataSetSampleSequence',
backref='datasetsample')
data_set_sample_sequences_pm = db.relationship('DataSetSampleSequencePM',
backref='datasetsample')
name = db.Column(db.String(200), nullable=False)
# This is the absolute number of sequences after make.contigs
num_contigs = db.Column(db.Integer, default=0)
# store the aboslute number of sequences after inital mothur QC i.e. before tax and size screening
post_qc_absolute_num_seqs = db.Column(db.Integer, default=0)
# This is the unique number of sequences after inital mothur QC i.e. before tax and size screening
post_qc_unique_num_seqs = db.Column(db.Integer, default=0)
# Absolute number of sequences after sequencing QC and screening for Symbiodinium (i.e. Symbiodinium only)
absolute_num_sym_seqs = db.Column(db.Integer, default=0)
# Same as above but the number of unique seqs
unique_num_sym_seqs = db.Column(db.Integer, default=0)
# store the abosolute number of sequenes that were not considered Symbiodinium
non_sym_absolute_num_seqs = db.Column(db.Integer, default=0)
# This is the number of unique sequences that were not considered Symbiodinium
non_sym_unique_num_seqs = db.Column(db.Integer, default=0)
# store the abosulte number of sequences that were lost during the size selection
size_violation_absolute = db.Column(db.Integer, default=0)
# store the unique number of sequences that were lost during the size screening
size_violation_unique = db.Column(db.Integer, default=0)
# store the number of absolute sequences remaining after MED
post_med_absolute = db.Column(db.Integer, default=0)
# store the number of unique sequences remaining after MED (nodes)
post_med_unique = db.Column(db.Integer, default=0)
error_in_processing = db.Column(db.Boolean, default=False)
error_reason = db.Column(db.String(100), nullable=False)
cladal_seq_totals = db.Column(db.String(5000), nullable=False)
# Meta data for the sample
sample_type = db.Column(db.String(50), nullable=False)
host_phylum = db.Column(db.String(50), nullable=False)
host_class = db.Column(db.String(50), nullable=False)
host_order = db.Column(db.String(50), nullable=False)
host_family = db.Column(db.String(50), nullable=False)
host_genus = db.Column(db.String(50), nullable=False)
host_species = db.Column(db.String(50), nullable=False)
collection_latitude = db.Column(db.Numeric(11, 8), nullable=False)
collection_longitude = db.Column(db.Numeric(11, 8), nullable=False)
# do not use the django date field as this causes problems when trying to dump and load the database
collection_date = db.Column(db.String(40), nullable=False)
# store a string rather than a number as this may be given as a range e.g. 6 - 12
collection_date = db.Column(db.String(40), nullable=False)
def __str__(self):
return self.name
def __repr__(self):
return f'<DataSetSample {self.name}>'
class Study(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_study'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(100), index=True, unique=True, nullable=False)
title = db.Column(db.String(250), nullable=True)
is_published = db.Column(db.Boolean, default=False)
location = db.Column(db.String(50), nullable=True)
run_type = db.Column(db.String(50), default='remote')
article_url = db.Column(db.String(250), nullable=True)
display_online = db.Column(db.Boolean, default=False)
data_url = db.Column(db.String(250), nullable=True)
data_explorer = db.Column(db.Boolean, default=False)
analysis = db.Column(db.Boolean, default=True)
author_list_string = db.Column(db.String(500))
additional_markers = db.Column(db.String(200))
creation_time_stamp = db.Column(db.String(100),
default=set_creation_time_stamp_default)
data_set_samples = db.relationship('DataSetSample',
secondary=Study__DataSetSample,
lazy='dynamic',
backref=db.backref('studies',
lazy='dynamic'))
# num_samples = self.get_num_samples()
def __str__(self):
return self.name
def __repr__(self):
return f'<Study {self.name}>'
def get_num_samples(self):
return len(list(self.data_set_samples))
class CladeCollection(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_cladecollection'
id = db.Column(db.Integer, primary_key=True)
data_set_sample_from_id = db.Column(
db.Integer, db.ForeignKey('dbApp_datasetsample.id'), nullable=False)
analysis_types = db.relationship('AnalysisType',
secondary=cladeCollectionType,
backref=db.backref('clade_collections'))
data_set_sample_sequences = db.relationship('DataSetSampleSequence',
backref='cladecollection')
# data_set_sample_from = models.ForeignKey(DataSetSample, on_delete=models.CASCADE, null=True)
clade = db.Column(db.String(1), nullable=False)
# the method below to get the footprint of the clade_collection_object is incredibly slow.
# Hopefully a much faster way will be to store the ID's of the refseqs that make up the footprint
# I will therefore store the reference uids in the field below
footprint = db.Column(db.String(100000), nullable=False)
def __str__(self):
return self.datasetsample.name
class DataAnalysis(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_dataanalysis'
id = db.Column(db.Integer, primary_key=True)
analysis_types = db.relationship('AnalysisType', backref='data_analysis')
# This will be a jsoned list of uids of the dataSubmissions that are included in this analysis
list_of_data_set_uids = db.Column(db.String(500), nullable=True)
# within_clade_cutoff = models.FloatField(default=0.04)
within_clade_cutoff = db.Column(db.Float(), nullable=False)
name = db.Column(db.String(500), nullable=True)
# name = models.CharField(max_length=100, null=True)
# description = models.CharField(max_length=5000, null=True)
description = db.Column(db.String(5000), nullable=True)
time_stamp = db.Column(db.String(100), nullable=False)
submitting_user = db.Column(db.String(100), nullable=False)
submitting_user_email = db.Column(db.String(100), nullable=False)
analysis_complete_time_stamp = db.Column(db.String(100), nullable=False)
class SPDataSet(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_dataset'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(30), nullable=False)
reference_fasta_database_used = db.Column(db.String(60), nullable=False)
submitting_user = db.Column(db.String(100), nullable=False)
submitting_user_email = db.Column(db.String(100), nullable=False)
working_directory = db.Column(db.String(300), nullable=False)
time_stamp = db.Column(db.String(100), nullable=False)
loading_complete_time_stamp = db.Column(db.String(100), nullable=False)
data_set_samples = db.relationship('DataSetSample', backref='dataset')
def __str__(self):
return self.name
def __repr__(self):
return f'<SPDataSet {self.name}>'
class SPUser(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_user'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(100), index=True, unique=True, nullable=False)
studies = db.relationship('Study',
secondary=SPUser__Study,
lazy='dynamic',
backref=db.backref('users', lazy='dynamic'))
# This is set to False when User is created. Upon upload to symportal.org
# a user that matches this name will be searched for in the app.db database.
# If no matching user if found, an error will be thrown. If a user is found,
# This value will be set to true, and the ID of the User in the app.db database
# will be stored in app_db_key below.
# The id of this object will also be stored in the app.db User object that matches
app_db_key_is_set = db.Column(db.Boolean, default=False)
app_db_key_id = db.Column(db.Integer, nullable=True)
def __repr__(self):
return f'<SPUser {self.name}>'