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 DataSetSampleSequencePM(db.Model):
# this is the pre-MED version of the DataSetSampleSequence object
# its purpose is to keep track of the
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_datasetsamplesequencepm'
id = db.Column(db.Integer, primary_key=True)
# FKeys
data_set_sample_from_id = db.Column(
db.Integer, db.ForeignKey('dbApp_datasetsample.id'))
reference_sequence_of_id = db.Column(
db.Integer, db.ForeignKey('dbApp_referencesequence.id'))
abundance = db.Column(db.Integer, default=0)
def __str__(self):
if self.referencesequence.has_name:
return self.referncesequence.name
else:
return 'ID=' + str(self.id)
class DataSetSampleSequence(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_datasetsamplesequence'
id = db.Column(db.Integer, primary_key=True)
# FKeys
data_set_sample_from_id = db.Column(
db.Integer, db.ForeignKey('dbApp_datasetsample.id'))
clade_collection_found_in_id = db.Column(
db.Integer, db.ForeignKey('dbApp_cladecollection.id'))
reference_sequence_of_id = db.Column(
db.Integer, db.ForeignKey('dbApp_referencesequence.id'))
abundance = db.Column(db.Integer, default=0)
def __str__(self):
if self.referencesequence.has_name:
return self.referencesequence.name
else:
return 'ID=' + str(self.id)
class AnalysisType(db.Model):
__bind_key__ = 'symportal_database'
__tablename__ = 'dbApp_analysistype'
id = db.Column(db.Integer, primary_key=True)
data_analysis_from_id = db.Column(db.Integer,
db.ForeignKey('dbApp_dataanalysis.id'),
nullable=False)
# This should be a frozen set of referenceSequences
# As this is not possible in a django field or jsonable
# I will instead make it a string of reference sequence uids
# I will make set and get methods for the footprint
# This will be a list of refSeqs that make up the footprint in order of their abundance when type first defined
# This is a commar separated string of the uids of the ref seqs that define the type
ordered_footprint_list = db.Column(db.String(200), nullable=True)
# Same for listOfMajs
# set() of refseqs that are Majs in each of the CCs this type was initially identified in.
# Note that this is therefore in no particular order
majority_reference_sequence_set = db.Column(db.String(40), nullable=True)
list_of_clade_collections = db.Column(db.String(100000), nullable=True)
# This is a 2D list, a list for each clade collection in order of the listofCladeCollections
# Within each list the absolute abundances of the defining seqs in order of ordered_footprint_list
footprint_sequence_abundances = db.Column(db.String(100000), nullable=True)
# Same as above but the proportion of the seqs to each other in the cladecollection.
footprint_sequence_ratios = db.Column(db.String(100000), nullable=True)
clade = db.Column(db.String(1), nullable=False)
co_dominant = db.Column(db.Boolean, default=False)
name = db.Column(db.String(1000), nullable=True)
# The list of speceis that this type is associated with
species = db.Column(db.String(200), nullable=True)
# this list will keep track of which of the defining intras of this type are 'unlocked' i.e. at least one
# of the instances of that intra were found at <5%. We will use this list to the 'artefact type creation'
# This artefact_intras will hold a char string of comma separated ints that represent the id's of the
# refseqs that are unlocked
artefact_intras = db.Column(db.String(5000), default='')
def get_ratio_list(self):
return json.loads(self.footprint_sequence_ratios)
# def get_clade_collections(self):
# uids_for_query = [int(x) for x in self.list_of_clade_collections.split(',')]
# cc_objs_list = []
# for uid_list in general.chunks(uids_for_query):
# cc_objs_list.extend(list(CladeCollection.objects.filter(id__in=uid_list)))
# return cc_objs_list
def __str__(self):
return self.name
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
from werkzeug.security import generate_password_hash, check_password_hash
from flask_login import UserMixin
from sp_app import login
@login.user_loader
def load_user(id):
return User.query.get(int(id))
cladeCollectionType = db.Table(
'dbApp_cladecollectiontype',
db.Column('id', db.Integer, primary_key=True),
db.Column('analysis_type_of_id',
db.Integer,
db.ForeignKey('dbApp_analysistype.id'),
primary_key=True),
db.Column('clade_collection_found_in_id',
db.Integer,
db.ForeignKey('dbApp_cladecollection.id'),
primary_key=True),
info={'bind_key': 'symportal_database'})
Study__DataSetSample = db.Table('dbApp_study_data_set_samples',
db.Column('id', db.Integer, primary_key=True),
db.Column(
'datasetsample_id',
db.Integer,
db.ForeignKey('dbApp_datasetsample.id'),
primary_key=True),
db.Column('study_id',