Mercurial > repos > iuc > sqlite_to_tabular
diff load_db.py @ 9:4678715f7147 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
| author | iuc |
|---|---|
| date | Sat, 12 Sep 2020 01:22:24 +0000 |
| parents | b722161a845a |
| children | dfe38b7c34ed |
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--- a/load_db.py Thu Jan 23 07:36:57 2020 -0500 +++ b/load_db.py Sat Sep 12 01:22:24 2020 +0000 @@ -176,7 +176,7 @@ def get_column_def(file_path, table_name, skip=0, comment_char='#', - column_names=None, max_lines=100, load_named_columns=False, + column_names=None, max_lines=1000, load_named_columns=False, firstlinenames=False, filters=None): col_pref = ['TEXT', 'REAL', 'INTEGER', None] col_types = [] @@ -272,8 +272,26 @@ 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), + print('Load %s Failed line: %d err: %s' % (file_path, linenum, e), file=sys.stderr) + for i, val in enumerate(fields): + try: + col_func[i](val) + except Exception: + colType = getValueType(val) + col_func[i] = float if colType == 'REAL' else int if colType == 'INTEGER' else str + print('Changing %s from %s to %s' % (col_names[i], col_types[i], colType), + file=sys.stderr) + col_types[i] = colType + vals = [col_func[i](x) + if x else None for i, x in enumerate(fields)] + print('%s %s' % (insert_stmt, vals), + file=sys.stderr) + try: + c.execute(insert_stmt, vals) + except Exception as e: + print('Insert %s line: %d Failed err: %s' % (file_path, linenum, e), + file=sys.stderr) conn.commit() c.close() for i, index in enumerate(unique_indexes):