class Role(db.Model, RoleMixin):
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(80), unique=True)
description = db.Column(db.String(250))
def __repr__(self):
return ('%s' % (self.name))
class SampleName(db.Model):
id = db.Column(db.Integer, primary_key=True)
sam_accession_no = db.Column(db.String(1000))
sam_record_title = db.Column(db.String(1000))
sam_url = db.Column(db.String(1000))
genotype_description_id = db.Column(
db.Integer, db.ForeignKey('genotype_description.id'))
genotype_description = db.relationship('GenotypeDescription',
backref='sample_names')
class AttachedFile(db.Model):
id = db.Column(db.Integer, primary_key=True)
filename = db.Column(db.String(1000))
notes_id = db.Column(db.Integer, db.ForeignKey('notes_entry.id'))
notes_entry = db.relationship('NotesEntry', backref='attached_files')
gene_description_id = db.Column(db.Integer,
db.ForeignKey('gene_description.id'))
gene_description = db.relationship('GeneDescription',
backref='attached_files')
novel_vdjbase_id = db.Column(db.Integer, db.ForeignKey('novel_vdjbase.id'))
novel_vdjbase = db.relationship('NovelVdjbase', backref='attached_files')
class JournalEntry(db.Model):
id = db.Column(db.Integer, primary_key=True)
date = db.Column(db.DateTime)
author = db.Column(db.String(255))
type = db.Column(db.String(255))
title = db.Column(db.String(1000))
body = db.Column(db.Text())
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref='journal_entries')
gene_description_id = db.Column(db.Integer,
db.ForeignKey('gene_description.id'))
gene_description = db.relationship('GeneDescription',
backref='journal_entries')
germline_set_id = db.Column(db.Integer, db.ForeignKey('germline_set.id'))
germline_set = db.relationship('GermlineSet', backref='journal_entries')
parent_id = db.Column(db.Integer, db.ForeignKey('journal_entry.id'))
children = db.relationship('JournalEntry',
backref=backref('parent', remote_side=[id]))
class InferenceTool(db.Model, InferenceToolMixin):
id = db.Column(db.Integer, primary_key=True)
tool_settings_name = db.Column(db.String(1000))
tool_name = db.Column(db.String(1000))
tool_version = db.Column(db.String(1000))
tool_starting_database = db.Column(db.Text())
tool_settings = db.Column(db.Text())
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref='inference_tools')
class PubId(db.Model):
id = db.Column(db.Integer, primary_key=True)
pubmed_id = db.Column(db.String(1000))
pub_title = db.Column(db.Text())
pub_authors = db.Column(db.Text())
repertoire_id = db.Column(db.Integer, db.ForeignKey('repertoire.id'))
repertoire = db.relationship('Repertoire', backref='pub_ids')
sequence_id = db.Column(db.Integer, db.ForeignKey('gene_description.id'))
gene_description = db.relationship('GeneDescription', backref='pub_ids')
germline_set_id = db.Column(db.Integer, db.ForeignKey('germline_set.id'))
germline_set = db.relationship('GermlineSet', backref='pub_ids')
class Acknowledgements(db.Model):
id = db.Column(db.Integer, primary_key=True)
ack_name = db.Column(db.String(1000))
ack_institution_name = db.Column(db.String(1000))
ack_ORCID_id = db.Column(db.String(255))
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref='acknowledgements')
description_id = db.Column(db.Integer,
db.ForeignKey('gene_description.id'))
gene_description = db.relationship('GeneDescription',
backref='acknowledgements')
germline_set_id = db.Column(db.Integer, db.ForeignKey('germline_set.id'))
germline_set = db.relationship('GermlineSet', backref='acknowledgements')
class User(db.Model, UserMixin):
id = db.Column(db.Integer, primary_key=True)
email = db.Column(db.String(255), unique=True)
password = db.Column(db.String(255))
name = db.Column(db.String(255))
address = db.Column(db.String(250))
accepted_terms = db.Column(db.Boolean)
reduce_emails = db.Column(db.Boolean)
active = db.Column(db.Boolean())
confirmed_at = db.Column(db.DateTime())
roles = db.relationship('Role',
secondary=roles_users,
backref=db.backref('users', lazy='dynamic'))
delegated_submissions = db.relationship('Submission',
secondary=roles_submissions,
backref=db.backref('delegates',
lazy='dynamic'))
def __repr__(self):
return ('%s' % (self.email))
class DupeGeneNote(db.Model):
id = db.Column(db.Integer, primary_key=True)
date = db.Column(db.DateTime)
author = db.Column(db.String(255))
body = db.Column(db.Text())
gene_description_id = db.Column(db.Integer,
db.ForeignKey('gene_description.id'))
gene_description = db.relationship('GeneDescription', backref='dupe_notes')
genotype_id = db.Column(db.Integer, db.ForeignKey('genotype.id'))
genotype = db.relationship('Genotype', backref='dupe_notes')
class NotesEntry(db.Model):
id = db.Column(db.Integer, primary_key=True)
notes_text = db.Column(db.Text())
notes_attachment_filename = db.Column(db.String(1000))
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref = 'notes_entries')
germline_set_id = db.Column(db.Integer, db.ForeignKey('germline_set.id'))
germline_set = db.relationship('GermlineSet', backref = 'notes_entries')
novel_vdjbase_id = db.Column(db.Integer, db.ForeignKey('novel_vdjbase.id'))
novel_vdjbase = db.relationship('NovelVdjbase', backref = 'notes_entries')
class RecordSet(db.Model):
id = db.Column(db.Integer, primary_key=True)
rec_accession_no = db.Column(db.String(1000))
rec_record_title = db.Column(db.String(1000))
rec_url = db.Column(db.String(1000))
inferred_sequence_id = db.Column(db.Integer,
db.ForeignKey('inferred_sequence.id'))
inferred_sequence = db.relationship('InferredSequence',
backref='record_set')
genotype_description_id = db.Column(
db.Integer, db.ForeignKey('genotype_description.id'))
genotype_description = db.relationship('GenotypeDescription',
backref='record_set')
class Repertoire(db.Model, RepertoireMixin):
id = db.Column(db.Integer, primary_key=True)
repository_name = db.Column(db.String(1000))
rep_accession_no = db.Column(db.String(1000))
rep_title = db.Column(db.String(1000))
dataset_url = db.Column(db.String(500))
miairr_compliant = db.Column(db.String(255))
miairr_link = db.Column(db.String(500))
sequencing_platform = db.Column(db.String(1000))
read_length = db.Column(db.String(1000))
primers_overlapping = db.Column(db.String(255))
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref='repertoire')
class Committee(db.Model):
id = db.Column(db.Integer, primary_key=True)
committee = db.Column(db.String(80), unique=True)
species = db.Column(db.String(80), unique=True)
loci = db.Column(db.String(80))
sequence_types = db.Column(db.String(80))
class NovelVdjbase(db.Model):
id = db.Column(db.Integer, primary_key=True)
vdjbase_name = db.Column(db.String(1000))
species = db.Column(db.String(50))
locus = db.Column(db.String(255))
subject_count = db.Column(db.Integer)
j_haplotypes = db.Column(db.Integer)
d_haplotypes = db.Column(db.Integer)
hetero_alleleic_j_haplotypes = db.Column(db.Integer)
status = db.Column(db.String(255))
sequence = db.Column(db.String(1000))
example = db.Column(db.String(50))
first_seen = db.Column(db.DateTime)
last_seen = db.Column(db.DateTime)
last_updated = db.Column(db.DateTime)
updated_by = db.Column(db.String(50))
# Copyright William Lees
#
# This source code, and any executable file compiled or derived from it, is governed by the European Union Public License v. 1.2,
# the English version of which is available here: https://perma.cc/DK5U-NDVE
#
# ORM definitions for user management
from head import db
from flask_security import UserMixin, RoleMixin
roles_users = db.Table(
'roles_users', db.Column('user_id', db.Integer(),
db.ForeignKey('user.id')),
db.Column('role_id', db.Integer(), db.ForeignKey('role.id')))
class Role(db.Model, RoleMixin):
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(80), unique=True)
description = db.Column(db.String(250))
def __repr__(self):
return ('%s' % (self.name))
roles_submissions = db.Table(
'roles_submissions',
db.Column('user_id', db.Integer(), db.ForeignKey('user.id')),
db.Column('submission_id', db.Integer(), db.ForeignKey('submission.id')))
class GenotypeDescription(db.Model, GenotypeDescriptionMixin):
id = db.Column(db.Integer, primary_key=True)
genotype_name = db.Column(db.String(1000))
genotype_subject_id = db.Column(db.String(1000))
genotype_biosample_ids = db.Column(db.String(255))
genotype_run_ids = db.Column(db.String(1000))
gen_ncbi_hash = db.Column(db.String(1000))
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref='genotype_descriptions')
inference_tool_id = db.Column(db.Integer,
db.ForeignKey('inference_tool.id'))
inference_tool = db.relationship('InferenceTool',
backref='genotype_descriptions')
locus = db.Column(db.String(255))
sequence_type = db.Column(db.String(255))
genotype_filename = db.Column(db.String(1000))
class Primer(db.Model):
id = db.Column(db.Integer, primary_key=True)
primer_name = db.Column(db.String(1000))
primer_seq = db.Column(db.String(1000))
primer_set_id = db.Column(db.Integer, db.ForeignKey('primer_set.id'))
primer_set = db.relationship('PrimerSet', backref='primers')
# ORM definitions for GeneDescription
# This file is automatically generated from the schema by schema/build_from_schema.py
from head import db
from db.userdb import User
from db.styled_table import *
from flask_table import Table, Col, LinkCol, create_table
from db.view_table import ViewCol
from sqlalchemy.orm import backref
inferred_sequences_gene_descriptions = db.Table('inferred_sequences_gene_descriptions',
db.Column('inferred_sequences_id', db.Integer(), db.ForeignKey('inferred_sequence.id')),
db.Column('gene_descriptions_id', db.Integer(), db.ForeignKey('gene_description.id')))
supporting_observations_supporting_gene_descriptions = db.Table('supporting_observations_supporting_gene_descriptions',
db.Column('supporting_observations_id', db.Integer(), db.ForeignKey('genotype.id')),
db.Column('supporting_gene_descriptions_id', db.Integer(), db.ForeignKey('gene_description.id')))
duplicate_sequences_published_duplicates = db.Table('duplicate_sequences_published_duplicates',
db.Column('duplicate_sequences_id', db.Integer(), db.ForeignKey('genotype.id')),
db.Column('published_duplicates_id', db.Integer(), db.ForeignKey('gene_description.id')))
from db._gene_description_db import *
class Submission(db.Model, SubmissionMixin):
id = db.Column(db.Integer, primary_key=True)
submission_id = db.Column(db.String(1000))
submission_date = db.Column(db.DateTime)
submission_status = db.Column(db.String(255))
public = db.Column(db.Boolean)
submitter_name = db.Column(db.String(1000))
submitter_address = db.Column(db.String(1000))
submitter_email = db.Column(db.String(255))
species = db.Column(db.String(255))
population_ethnicity = db.Column(db.String(1000))
owner_id = db.Column(db.Integer, db.ForeignKey('user.id'))
owner = db.relationship('User', backref='submissions')
class GeneDescription(db.Model, GeneDescriptionMixin):
id = db.Column(db.Integer, primary_key=True)
description_id = db.Column(db.String(50))
maintainer = db.Column(db.String(50))
lab_address = db.Column(db.String(1000))
release_version = db.Column(db.Integer)
release_date = db.Column(db.DateTime)
release_description = db.Column(db.Text())
imgt_name = db.Column(db.String(50))
sequence_name = db.Column(db.String(50))
alt_names = db.Column(db.String(1000))
chromosome = db.Column(db.Integer)
locus = db.Column(db.String(255))
sequence_type = db.Column(db.String(255))
functionality = db.Column(db.String(255))
inference_type = db.Column(db.String(255))
affirmation_level = db.Column(db.String(255))
species = db.Column(db.String(1000))
species_subgroup = db.Column(db.String(50))
species_subgroup_type = db.Column(db.String(255))
status = db.Column(db.String(255))
gene_subgroup = db.Column(db.String(50))
subgroup_designation = db.Column(db.String(50))
allele_designation = db.Column(db.String(50))
sequence = db.Column(db.Text())
coding_seq_imgt = db.Column(db.Text())
gene_start = db.Column(db.Integer)
gene_end = db.Column(db.Integer)
utr_5_prime_start = db.Column(db.Integer)
utr_5_prime_end = db.Column(db.Integer)
leader_1_start = db.Column(db.Integer)
leader_1_end = db.Column(db.Integer)
leader_2_start = db.Column(db.Integer)
leader_2_end = db.Column(db.Integer)
v_rs_start = db.Column(db.Integer)
v_rs_end = db.Column(db.Integer)
d_rs_3_prime_start = db.Column(db.Integer)
d_rs_3_prime_end = db.Column(db.Integer)
d_rs_5_prime_start = db.Column(db.Integer)
d_rs_5_prime_end = db.Column(db.Integer)
j_rs_start = db.Column(db.Integer)
j_rs_end = db.Column(db.Integer)
j_codon_frame = db.Column(db.String(255))
j_cdr3_end = db.Column(db.Integer)
paralogs = db.Column(db.String(1000))
notes = db.Column(db.Text())
inferred_sequences = db.relationship('InferredSequence', secondary = inferred_sequences_gene_descriptions, backref = db.backref('gene_descriptions', lazy='dynamic'))
supporting_observations = db.relationship('Genotype', secondary = supporting_observations_supporting_gene_descriptions, backref = db.backref('supporting_gene_descriptions', lazy='dynamic'))
duplicate_sequences = db.relationship('Genotype', secondary = duplicate_sequences_published_duplicates, backref = db.backref('published_duplicates', lazy='dynamic'))
inferred_extension = db.Column(db.Boolean)
ext_3prime = db.Column(db.Text())
start_3prime_ext = db.Column(db.Integer)
end_3prime_ext = db.Column(db.Integer)
ext_5prime = db.Column(db.Text())
start_5prime_ext = db.Column(db.Integer)
end_5prime_ext = db.Column(db.Integer)
curational_tags = db.Column(db.String(255))
class PrimerSet(db.Model, PrimerSetMixin):
id = db.Column(db.Integer, primary_key=True)
primer_set_name = db.Column(db.String(1000))
primer_set_notes = db.Column(db.Text())
repertoire_id = db.Column(db.Integer, db.ForeignKey('repertoire.id'))
repertoire = db.relationship('Repertoire', backref='primer_sets')
class GenomicSupport(db.Model):
id = db.Column(db.Integer, primary_key=True)
sequence_type = db.Column(db.String(255))
sequence = db.Column(db.Text())
notes = db.Column(db.Text())
repository = db.Column(db.String(1000))
accession = db.Column(db.String(1000))
url = db.Column(db.String(1000))
patch_no = db.Column(db.String(1000))
gff_seqid = db.Column(db.String(1000))
sequence_start = db.Column(db.Integer)
sequence_end = db.Column(db.Integer)
sense = db.Column(db.String(255))
sequence_id = db.Column(db.Integer, db.ForeignKey('gene_description.id'))
gene_description = db.relationship('GeneDescription', backref = 'genomic_accessions')
class InferredSequence(db.Model, InferredSequenceMixin):
id = db.Column(db.Integer, primary_key=True)
sequence_id = db.Column(db.Integer, db.ForeignKey('genotype.id'))
sequence_details = db.relationship('Genotype', backref = 'inferred_sequences')
submission_id = db.Column(db.Integer, db.ForeignKey('submission.id'))
submission = db.relationship('Submission', backref = 'inferred_sequences')
genotype_id = db.Column(db.Integer, db.ForeignKey('genotype_description.id'))
genotype_description = db.relationship('GenotypeDescription', backref = 'inferred_sequences')
seq_accession_no = db.Column(db.String(1000))
seq_record_title = db.Column(db.String(1000))
ncbi_hash = db.Column(db.String(1000))
deposited_version = db.Column(db.String(1000))
run_ids = db.Column(db.String(1000))
inferred_extension = db.Column(db.Boolean)
ext_3prime = db.Column(db.Text())
start_3prime_ext = db.Column(db.Integer)
end_3prime_ext = db.Column(db.Integer)
ext_5prime = db.Column(db.Text())
start_5prime_ext = db.Column(db.Integer)
end_5prime_ext = db.Column(db.Integer)
class Genotype(db.Model, GenotypeMixin):
id = db.Column(db.Integer, primary_key=True)
sequence_id = db.Column(db.String(1000))
sequences = db.Column(db.Integer)
closest_reference = db.Column(db.String(1000))
closest_host = db.Column(db.String(1000))
nt_diff = db.Column(db.Integer)
nt_diff_host = db.Column(db.Integer)
nt_substitutions = db.Column(db.String(1000))
aa_diff = db.Column(db.Integer)
aa_substitutions = db.Column(db.String(1000))
unmutated_sequences = db.Column(db.Integer)
assigned_unmutated_frequency = db.Column(db.Numeric(precision=(12, 2)))
unmutated_umis = db.Column(db.Integer)
allelic_percentage = db.Column(db.Numeric(precision=(12, 2)))
unmutated_frequency = db.Column(db.Numeric(precision=(12, 2)))
unique_vs = db.Column(db.Integer)
unique_ds = db.Column(db.Integer)
unique_js = db.Column(db.Integer)
unique_cdr3s = db.Column(db.Integer)
unique_vs_unmutated = db.Column(db.Integer)
unique_ds_unmutated = db.Column(db.Integer)
unique_js_unmutated = db.Column(db.Integer)
unique_cdr3s_unmutated = db.Column(db.Integer)
haplotyping_gene = db.Column(db.String(1000))
haplotyping_ratio = db.Column(db.String(1000))
nt_sequence = db.Column(db.Text())
nt_sequence_gapped = db.Column(db.Text())
description_id = db.Column(db.Integer,
db.ForeignKey('genotype_description.id'))
genotype_description = db.relationship('GenotypeDescription',
backref='genotypes')
