Mercurial > repos > iuc > sqlite_to_tabular
view query_db.py @ 2:150765965caa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
author | iuc |
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date | Mon, 23 Oct 2017 13:27:54 -0400 |
parents | c1b700bc0150 |
children | 6e72fd26a9d3 |
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#!/usr/bin/env python from __future__ import print_function import re import sqlite3 as sqlite import sys TABLE_QUERY = \ """ SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name """ def regex_match(expr, item): return re.match(expr, item) is not None def regex_search(expr, item): return re.search(expr, item) is not None def regex_sub(expr, replace, item): return re.sub(expr, replace, item) def get_connection(sqlitedb_path, addfunctions=True): conn = sqlite.connect(sqlitedb_path) if addfunctions: conn.create_function("re_match", 2, regex_match) conn.create_function("re_search", 2, regex_search) conn.create_function("re_sub", 3, regex_sub) return conn def describe_tables(conn, outputFile): try: c = conn.cursor() tables_query = TABLE_QUERY rslt = c.execute(tables_query).fetchall() for table, sql in rslt: print("Table %s:" % table, file=outputFile) try: col_query = 'SELECT * FROM %s LIMIT 0' % table cur = conn.cursor().execute(col_query) cols = [col[0] for col in cur.description] print(" Columns: %s" % cols, file=outputFile) except Exception as exc: print("Warning: %s" % exc, file=sys.stderr) except Exception as e: exit('Error: %s' % (e)) exit(0) def run_query(conn, query, outputFile, no_header=False, comment_char='#'): cur = conn.cursor() results = cur.execute(query) if not no_header: outputFile.write("%s%s\n" % (comment_char, '\t'.join( [str(col[0]) for col in cur.description]))) for i, row in enumerate(results): outputFile.write("%s\n" % '\t'.join( [str(val) if val is not None else '' for val in row]))