Mercurial > repos > iuc > query_tabular
view load_db.py @ 0:3708ff0198b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author | iuc |
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date | Tue, 18 Jul 2017 09:07:07 -0400 |
parents | |
children | 8a33b442ecd9 |
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#!/usr/bin/env python from __future__ import print_function import sys from filters import TabularReader def getValueType(val): if val or 0. == val: try: int(val) return 'INTEGER' except: try: float(val) return 'REAL' except: return 'TEXT' return None def get_column_def(file_path, table_name, skip=0, comment_char='#', column_names=None, max_lines=100, load_named_columns=False, filters=None): col_pref = ['TEXT', 'REAL', 'INTEGER', None] col_types = [] col_idx = None try: tr = TabularReader(file_path, skip=skip, comment_char=comment_char, col_idx=None, filters=filters) for linenum, fields in enumerate(tr): if linenum > max_lines: break try: while len(col_types) < len(fields): col_types.append(None) for i, val in enumerate(fields): colType = getValueType(val) if col_pref.index(colType) < col_pref.index(col_types[i]): col_types[i] = colType except Exception as e: print('Failed at line: %d err: %s' % (linenum, e), file=sys.stderr) except Exception as e: print('Failed: %s' % (e), file=sys.stderr) for i, col_type in enumerate(col_types): if not col_type: col_types[i] = 'TEXT' if column_names: col_names = [] if load_named_columns: col_idx = [] for i, cname in enumerate( [cn.strip() for cn in column_names.split(',')]): if cname != '': col_idx.append(i) col_names.append(cname) col_types = [col_types[i] for i in col_idx] else: col_names = ['c%d' % i for i in range(1, len(col_types) + 1)] for i, cname in enumerate( [cn.strip() for cn in column_names.split(',')]): if cname and i < len(col_names): col_names[i] = cname else: col_names = ['c%d' % i for i in range(1, len(col_types) + 1)] col_def = [] for i, col_name in enumerate(col_names): col_def.append('%s %s' % (col_names[i], col_types[i])) return col_names, col_types, col_def, col_idx def create_table(conn, file_path, table_name, skip=0, comment_char='#', pkey_autoincr=None, column_names=None, load_named_columns=False, filters=None, unique_indexes=[], indexes=[]): col_names, col_types, col_def, col_idx = \ get_column_def(file_path, table_name, skip=skip, comment_char=comment_char, column_names=column_names, load_named_columns=load_named_columns, filters=filters) col_func = [float if t == 'REAL' else int if t == 'INTEGER' else str for t in col_types] table_def = 'CREATE TABLE %s (\n %s%s\n);' % ( table_name, '%s INTEGER PRIMARY KEY AUTOINCREMENT,' % pkey_autoincr if pkey_autoincr else '', ', \n '.join(col_def)) # print >> sys.stdout, table_def insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % ( table_name, ','.join(col_names), ','.join(["?" for x in col_names])) # print >> sys.stdout, insert_stmt data_lines = 0 try: c = conn.cursor() c.execute(table_def) conn.commit() c.close() for i, index in enumerate(unique_indexes): index_name = 'idx_uniq_%s_%d' % (table_name, i) index_columns = index.split(',') create_index(conn, table_name, index_name, index_columns, unique=True) for i, index in enumerate(indexes): index_name = 'idx_%s_%d' % (table_name, i) index_columns = index.split(',') create_index(conn, table_name, index_name, index_columns) c = conn.cursor() tr = TabularReader(file_path, skip=skip, comment_char=comment_char, col_idx=col_idx, filters=filters) for linenum, fields in enumerate(tr): data_lines += 1 try: vals = [col_func[i](x) if x else None for i, x in enumerate(fields)] c.execute(insert_stmt, vals) except Exception as e: print('Failed at line: %d err: %s' % (linenum, e), file=sys.stderr) conn.commit() c.close() except Exception as e: exit('Error: %s' % (e)) def create_index(conn, table_name, index_name, index_columns, unique=False): index_def = "CREATE %s INDEX %s on %s(%s)" % ( 'UNIQUE' if unique else '', index_name, table_name, ','.join(index_columns)) c = conn.cursor() c.execute(index_def) conn.commit() c.close()