class TableIgvGermline(pssql.Model):
__bind_key__ = 'curation'
__tablename__ = "table_igv_germline"
id = pssql.Column(pssql.Integer, primary_key=True, nullable=False)
PROJECT_ID = pssql.Column(pssql.String, nullable=False)
SDID = pssql.Column(pssql.String, nullable=False)
CAPTURE_ID = pssql.Column(pssql.String, nullable=False)
CHROM = pssql.Column(pssql.String)
START = pssql.Column(pssql.String)
END = pssql.Column(pssql.String)
REF = pssql.Column(pssql.String)
ALT = pssql.Column(pssql.String)
CALL = pssql.Column(pssql.String)
TAG = pssql.Column(pssql.String)
NOTES = pssql.Column(pssql.String)
GENE = pssql.Column(pssql.String)
IMPACT = pssql.Column(pssql.String)
CONSEQUENCE = pssql.Column(pssql.String)
HGVSp = pssql.Column(pssql.String)
N_DP = pssql.Column(pssql.String)
N_ALT = pssql.Column(pssql.String)
N_VAF = pssql.Column(pssql.String)
CLIN_SIG = pssql.Column(pssql.String)
gnomAD = pssql.Column(pssql.String)
BRCAEx = pssql.Column(pssql.String)
OncoKB = pssql.Column(pssql.String)
def __init__(self, row_dict):
self.PROJECT_ID = row_dict.get('PROJECT_ID', None)
self.SDID = row_dict.get('SDID', None)
self.CAPTURE_ID = row_dict.get('CAPTURE_ID', None)
self.CHROM = row_dict.get('CHROM', None)
self.START = row_dict.get('START', None)
self.END = row_dict.get('END', None)
self.REF = row_dict.get('REF', None)
self.ALT = row_dict.get('ALT', None)
self.CALL = row_dict.get('CALL', None)
self.TAG = row_dict.get('TAG', None)
self.NOTES = row_dict.get('NOTES', None)
self.GENE = row_dict.get('GENE', None)
self.IMPACT = row_dict.get('IMPACT', None)
self.CONSEQUENCE = row_dict.get('CONSEQUENCE', None)
self.HGVSp = row_dict.get('HGVSp', None)
self.N_DP = row_dict.get('N_DP', None)
self.N_ALT = row_dict.get('N_ALT', None)
self.N_VAF = row_dict.get('N_VAF', None)
self.CLIN_SIG = row_dict.get('CLIN_SIG', None)
self.gnomAD = row_dict.get('gnomAD', None)
self.BRCAEx = row_dict.get('BRCAEx', None)
self.OncoKB = row_dict.get('OncoKB', None)
def __repr__(self):
return "<TableIgvGermline (id='%s', projectid='%s', sdid='%s', captureid='%s')>" % (
self.id, self.PROJECT_ID, self.SDID, self.CAPTURE_ID)
class ProbioBloodReferral(pssql.Model):
__tablename__ = "probio_bloodreferrals"
crid = pssql.Column(pssql.Integer, primary_key=True, nullable=False)
pnr = pssql.Column(pssql.String, nullable=False)
rid = pssql.Column(pssql.String, nullable=False)
datum = pssql.Column(pssql.Date, nullable=False)
tid = pssql.Column(pssql.String, nullable=False)
sign = pssql.Column(pssql.Integer)
countyletter = pssql.Column(pssql.String, nullable=False)
new = pssql.Column(pssql.String, nullable=False)
progression = pssql.Column(pssql.String, nullable=False)
follow_up = pssql.Column(pssql.String, nullable=False)
cf_dna1 = pssql.Column(pssql.String, nullable=False)
cf_dna2 = pssql.Column(pssql.String, nullable=False)
cf_dna3 = pssql.Column(pssql.String, nullable=False)
kommentar = pssql.Column(pssql.String, nullable=False)
filnamn = pssql.Column(pssql.String, nullable=False)
def __repr__(self):
return "<ProbioReferral (crid='%s', pnr='%s', rid='%s', date='%s', filename='%s')>" % (
self.crid, self.pnr, self.rid, self.datum, self.filnamn)
class PSFFBloodReferral(pssql.Model):
__tablename__ = "psff_bloodreferrals"
crid = pssql.Column(pssql.Integer, primary_key=True, nullable=False)
rid = pssql.Column(pssql.String, nullable=False)
datum = pssql.Column(pssql.Date, nullable=False)
tid = pssql.Column(pssql.String, nullable=False)
sign = pssql.Column(pssql.Integer)
blood1 = pssql.Column(pssql.String, nullable=False)
blood2 = pssql.Column(pssql.String, nullable=False)
blood3 = pssql.Column(pssql.String, nullable=False)
blood4 = pssql.Column(pssql.String, nullable=False)
comment = pssql.Column(pssql.String, nullable=False)
filnamn = pssql.Column(pssql.String, nullable=False)
cdk = pssql.Column(pssql.String, nullable=False)
def __repr__(self):
return "<PSFFReferral (cdk='%s', rid='%s', date='%s', filename='%s')>" % (
self.cdk, self.rid, self.datum, self.filnamn)
class TableSVS(pssql.Model):
__bind_key__ = 'curation'
__tablename__ = "table_svs"
id = pssql.Column(pssql.Integer, primary_key=True, nullable=False)
PROJECT_ID = pssql.Column(pssql.String, nullable=False)
SDID = pssql.Column(pssql.String, nullable=False)
CAPTURE_ID = pssql.Column(pssql.String, nullable=False)
CHROM_A = pssql.Column(pssql.String)
START_A = pssql.Column(pssql.String)
END_A = pssql.Column(pssql.String)
CHROM_B = pssql.Column(pssql.String)
START_B = pssql.Column(pssql.String)
END_B = pssql.Column(pssql.String)
SVTYPE = pssql.Column(pssql.String)
SV_LENGTH = pssql.Column(pssql.String)
SUPPORT_READS = pssql.Column(pssql.String)
TOOL = pssql.Column(pssql.String)
SAMPLE = pssql.Column(pssql.String)
GENE_A = pssql.Column(pssql.String)
IN_DESIGN_A = pssql.Column(pssql.String)
GENE_B = pssql.Column(pssql.String)
IN_DESIGN_B = pssql.Column(pssql.String)
GENE_A_GENE_B_sorted = pssql.Column('GENE_A-GENE_B-sorted', pssql.String)
CALL = pssql.Column(pssql.String)
TYPE = pssql.Column(pssql.String)
SECONDHIT = pssql.Column(pssql.String)
COMMENT = pssql.Column(pssql.String)
def __init__(self, row_dict):
self.PROJECT_ID = row_dict.get('PROJECT_ID', None)
self.SDID = row_dict.get('SDID', None)
self.CAPTURE_ID = row_dict.get('CAPTURE_ID', None)
self.CHROM_A = row_dict.get('CHROM_A', None)
self.START_A = row_dict.get('START_A', None)
self.END_A = row_dict.get('END_A', None)
self.CHROM_B = row_dict.get('CHROM_B', None)
self.START_B = row_dict.get('START_B', None)
self.END_B = row_dict.get('END_B', None)
self.SVTYPE = row_dict.get('SVTYPE', None)
self.SV_LENGTH = row_dict.get('SV_LENGTH', None)
self.SUPPORT_READS = row_dict.get('SUPPORT_READS', None)
self.TOOL = row_dict.get('TOOL', None)
self.SAMPLE = row_dict.get('SAMPLE', None)
self.GENE_A = row_dict.get('GENE_A', None)
self.IN_DESIGN_A = row_dict.get('IN_DESIGN_A', None)
self.GENE_B = row_dict.get('GENE_B', None)
self.IN_DESIGN_B = row_dict.get('IN_DESIGN_B', None)
self.GENE_A_GENE_B_sorted = row_dict.get('GENE_A-GENE_B-sorted', None)
self.CALL = row_dict.get('CALL', None)
self.TYPE = row_dict.get('TYPE', None)
self.SECONDHIT = row_dict.get('SECONDHIT', None)
self.COMMENT = row_dict.get('COMMENT', None)
def __repr__(self):
return "<TableIgvSomatic (id='%s', projectid='%s', sdid='%s', captureid='%s')>" % (
self.id, self.PROJECT_ID, self.SDID, self.CAPTURE_ID)
class TableProbioSummary(pssql.Model):
__bind_key__ = 'curation'
__tablename__ = "probio_summary"
id = pssql.Column(pssql.Integer, primary_key=True, nullable=False)
sample_id = pssql.Column(pssql.String)
capture_id = pssql.Column(pssql.String)
basic_qc = pssql.Column(pssql.String)
franken_plot = pssql.Column(pssql.String)
ploidy = pssql.Column(pssql.String)
ctdna_fraction = pssql.Column(pssql.String)
ctdna_param = pssql.Column(pssql.String)
ctdna_method = pssql.Column(pssql.String)
ctdna_category = pssql.Column(pssql.String)
study_code = pssql.Column(pssql.String)
study_site = pssql.Column(pssql.String)
somatic_mutations = pssql.Column(pssql.String)
germline_alterations = pssql.Column(pssql.String)
structural_variants = pssql.Column(pssql.String)
cnvs = pssql.Column(pssql.String)
comment_info = pssql.Column(pssql.String)
def __init__(self, row_dict):
self.id = row_dict.get('id', None)
self.sample_id = row_dict.get('sample_id', None)
self.capture_id = row_dict.get('capture_id', None)
self.basic_qc = row_dict.get('basic_qc', None)
self.franken_plot = row_dict.get('franken_plot', None)
self.ploidy = row_dict.get('ploidy', None)
self.ctdna_fraction = row_dict.get('ctdna_fraction', None)
self.ctdna_param = row_dict.get('ctdna_param', None)
self.ctdna_method = row_dict.get('ctdna_method', None)
self.ctdna_category = row_dict.get('ctdna_category', None)
self.study_code = row_dict.get('study_code', None)
self.study_site = row_dict.get('study_site', None)
self.somatic_mutations = row_dict.get('somatic_mutations', None)
self.germline_alterations = row_dict.get('germline_alterations', None)
self.structural_variants = row_dict.get('structural_variants', None)
self.cnvs = row_dict.get('cnvs', None)
self.comment_info = row_dict.get('comment_info', None)
def __repr__(self):
return "<TableProbioSummary (id='%s', sample_id='%s', capture_id='%s', basic_qc='%s')>" % (
self.id, self.sample_id, self.capture_id, self.basic_qc)
class TableIgvWarmspot(pssql.Model):
__bind_key__ = 'curation'
__tablename__ = "warmspots_table"
id = pssql.Column(pssql.Integer, primary_key=True, nullable=False)
gene = pssql.Column(pssql.String)
aapos = pssql.Column(pssql.String)
nmut = pssql.Column(pssql.String)
protmut = pssql.Column(pssql.String)
prot2mut = pssql.Column(pssql.String)
dnamut = pssql.Column(pssql.String)
canmut = pssql.Column(pssql.String)
conseqmut = pssql.Column(pssql.String)
transcript = pssql.Column(pssql.String)
dn_ds = pssql.Column(pssql.String)
community_notes = pssql.Column(pssql.String)
def __init__(self, row_dict):
self.id = row_dict.get('id', None)
self.gene = row_dict.get('gene', None)
self.aapos = row_dict.get('aapos', None)
self.nmut = row_dict.get('nmut', None)
self.protmut = row_dict.get('protmut', None)
self.prot2mut = row_dict.get('prot2mut', None)
self.dnamut = row_dict.get('dnamut', None)
self.canmut = row_dict.get('canmut', None)
self.conseqmut = row_dict.get('conseqmut', None)
self.transcript = row_dict.get('transcript', None)
self.dn_ds = row_dict.get('dn_ds', None)
self.community_notes = row_dict.get('community_notes', None)
def __repr__(self):
return "<TableIgvWarmspot (id='%s', gene='%s', protmut='%s', prot2mut='%s')>" % (
self.id, self.gene, self.protmut, self.prot2mut)