def glue_in_gene_names(three_counts_table, gene_table, target_dataset,
output_table, do_replace, sql_dict, do_batch):
sql = glue_in_gene_names_sql(three_counts_table, gene_table, sql_dict)
print(sql)
return generic_bq_harness(sql, target_dataset, output_table, do_batch,
do_replace)
def extract_aligned_file_data(release_table, program_name, sql_dict,
target_dataset, dest_table, do_batch):
sql = extract_alignment_file_data_sql(release_table, program_name,
sql_dict)
print(sql)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def build_final_table(pdc_meta_aliquot_table, pdc_quant_aliquot_table,
pdc_meta_cases_table, gdc_case_data_table,
target_dataset, dest_table, do_batch):
sql = build_final_table_sql(pdc_meta_aliquot_table,
pdc_quant_aliquot_table, pdc_meta_cases_table,
gdc_case_data_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def join_with_aliquot_table(cnv_table, aliquot_table, target_dataset,
dest_table, do_batch):
sql = merge_bq_sql(cnv_table, aliquot_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def extract_other_file_data(release_table, program_name, sql_dict, barcode,
target_dataset, dest_table, do_batch):
sql = extract_other_file_data_sql(release_table, program_name, sql_dict,
barcode)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def attach_barcodes(temp_table, aliquot_table, target_dataset, dest_table,
do_batch, program, case_table):
sql = attach_barcodes_sql(temp_table, aliquot_table, program, case_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def build_file_map(mani_table, target_dataset, dest_table, do_batch):
sql = file_map_sql(mani_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def install_uris(union_table, mapping_table, target_dataset, dest_table,
do_batch):
sql = install_uris_sql(union_table, mapping_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def import_radiology(r14_table, target_dataset, dest_table, do_batch):
sql = import_radiology_sql(r14_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def extract_clinbio_file_data(release_table, program_name, target_dataset,
dest_table, do_batch):
sql = extract_file_data_sql_clinbio(release_table, program_name)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def extract_active_aliquot_file_data(release_table, program_name,
target_dataset, dest_table, do_batch):
sql = extract_active_aliquot_file_data_sql(release_table, program_name)
print(sql)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def build_union(table_list, target_dataset, dest_table, do_batch):
sql = union_sql(table_list)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def extract_aliquot_barcodes(release_table, aliquot_2_case_table, program_name,
target_dataset, dest_table, do_batch):
sql = aliquot_barcodes_sql(release_table, aliquot_2_case_table,
program_name)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def prepare_aliquot_without_map(release_table, case_table, program_name,
target_dataset, dest_table, do_batch):
sql = aliquot_barcodes_without_map_sql(release_table, case_table,
program_name)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def repair_slide_file_data(case_table, broken_table, target_dataset,
dest_table, do_batch):
sql = repair_missing_case_data_sql_slides(case_table, broken_table)
print(sql)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def extract_slide_barcodes(release_table, slide_2_case_table, program_name,
target_dataset, dest_table, do_batch):
sql = slide_barcodes_sql_archive(release_table, slide_2_case_table,
program_name)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def build_union(slide_table, align_table, clin_table, target_dataset,
dest_table, do_batch):
sql = union_sql(slide_table, align_table, clin_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def attach_barcodes(step2_table, aliquot_table, case_table, target_dataset,
output_table, do_replace, do_batch):
sql = attach_barcodes_sql(step2_table, aliquot_table, case_table)
return generic_bq_harness(sql, target_dataset, output_table, do_batch,
do_replace)
def extract_aligned_file_data(release_table, program_name, target_dataset,
dest_table, do_batch):
sql = extract_file_data_sql_archived_aligned(release_table, program_name)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def merge_counts_and_metadata(step3_table, counts_table, target_dataset,
output_table, do_replace, sql_dict, do_batch):
sql = glue_counts_and_metadata_sql(step3_table, counts_table, sql_dict)
return generic_bq_harness(sql, target_dataset, output_table, do_batch,
do_replace)
def attach_aliquot_ids(maf_table, file_table, target_dataset, dest_table,
do_batch):
sql = attach_aliquot_ids_sql(maf_table, file_table)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def all_counts_to_one_table(target_dataset, output_table, do_replace, sql_dict,
do_batch):
sql = join_three_sql(None, None, sql_dict)
return generic_bq_harness(sql, target_dataset, output_table, do_batch,
do_replace)
def final_merge(maf_table, barcode_table, target_dataset, dest_table, do_batch,
program):
sql = final_join_sql(maf_table, barcode_table, program)
return generic_bq_harness(sql, target_dataset, dest_table, do_batch, True)
def extract_platform_for_files(step2_table, file_table, target_dataset,
output_table, do_replace, sql_dict, do_batch):
sql = extract_platform_for_files_sql(step2_table, file_table, sql_dict)
return generic_bq_harness(sql, target_dataset, output_table, do_batch,
do_replace)