def get_expression_from_run( run_id, pathway, by_rank ): res = RunGPUDiracModel.get( run_id, timestamp ) config = json.loads(base64.b64decode( res.config )) net_table = config['network_config']['network_table'] net_source_id = config['network_config']['network_source'] source_dataframe = config['dest_data']['dataframe_file'] metadata_file = config['dest_data']['meta_file'] source_bucket = config['dest_data']['working_bucket'] app_path = '/home/sgeadmin/.local/lib/python2.7/site-packages/tcdiracweb-0.1.0-py2.7.egg/tcdiracweb' data_path = 'static/data' args = (net_table, net_source_id, source_dataframe, metadata_file, app_path, source_bucket, data_path) tsv = TSVGen( * args ) return t.genNetworkGeneExpTables( pathway, by_rank=by_rank )
def dumpExpression(): runs = {} ignore = ['black_6_go_wt_v_q111'] for item in RunGPUDiracModel.scan(): if item.run_id not in ignore: runs[item.run_id] = json.loads(base64.b64decode( item.config )) for k in runs.keys(): net_table = runs[k]['network_config']['network_table'] net_source_id = runs[k]['network_config']['network_source'] source_dataframe = runs[k]['dest_data']['dataframe_file'] metadata_file = runs[k]['dest_data']['meta_file'] source_bucket = runs[k]['dest_data']['working_bucket'] app_path = '/home/sgeadmin/.local/lib/python2.7/site-packages/tcdiracweb-0.1.0-py2.7.egg/tcdiracweb' data_path = 'static/data' runs['tsvargs'] = (net_table, net_source_id, source_dataframe, metadata_file, app_path, source_bucket, data_path) runs['sig_nets'] = get_sig(k) t = TSVGen( *runs['tsvargs'] ) for pw in runs['sig_nets']: for rank in [True,False]: for j in [True,False]: print t.genNetworkGeneExpTables(pw, by_rank=rank) return print pw