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)