Mercurial > repos > iuc > query_tabular
diff query_tabular.py @ 4:973f03d82c86 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
author | iuc |
---|---|
date | Thu, 03 May 2018 10:16:38 -0400 |
parents | 1ea4e668bf73 |
children |
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--- a/query_tabular.py Mon Nov 06 23:20:29 2017 -0500 +++ b/query_tabular.py Thu May 03 10:16:38 2018 -0400 @@ -59,6 +59,9 @@ help='comment character to prefix column header line') parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results') + parser.add_option('-d', '--debug', dest='debug', default=False, + action='store_true', + help='Output info to stderr') (options, args) = parser.parse_args() # determine output destination @@ -109,9 +112,35 @@ try: with open(options.jsonfile) as fh: tdef = json.load(fh) + if options.debug: + print('JSON: %s' % tdef, file=sys.stderr) if 'tables' in tdef: for ti, table in enumerate(tdef['tables']): _create_table(ti, table) + if 'sql_stmts' in tdef: + for si, stmt in enumerate(tdef['sql_stmts']): + rowcount = run_query(get_connection(options.sqlitedb), stmt, None) + if options.debug: + print('\nDB modification: %s \nrowcount: %s' % + (stmt, rowcount), file=sys.stderr) + if 'queries' in tdef: + for qi, qstmt in enumerate(tdef['queries']): + if 'header' in qstmt: + no_header = False + comment_char = qstmt['header'] + else: + no_header = True + comment_char = None + with open(qstmt['result_file'], 'w') as fh: + query = qstmt['query'] + rowcount = run_query(get_connection(options.sqlitedb), + query, + fh, + no_header=no_header, + comment_char=comment_char) + if options.debug: + print('\nSQL: %s \nrowcount: %s' % + (query, rowcount), file=sys.stderr) except Exception as e: exit('Error: %s' % (e)) @@ -131,9 +160,13 @@ exit('Error: %s' % (e)) else: try: - run_query(get_connection(options.sqlitedb), query, outputFile, - no_header=options.no_header, - comment_char=options.comment_char) + rowcount = run_query(get_connection(options.sqlitedb), + query, outputFile, + no_header=options.no_header, + comment_char=options.comment_char) + if options.debug: + print('\nSQL: %s \nrowcount: %s' % + (query, rowcount), file=sys.stderr) except Exception as e: exit('Error: %s' % (e))