Mercurial > repos > iuc > filter_tabular

comparison query_db.py @ 0:6fbd9d25ceef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author iuc
date Tue, 18 Jul 2017 09:06:47 -0400
parents
children cd2a99849f8b
comparison
equal deleted inserted replaced
-1:000000000000 0:6fbd9d25ceef
1 #!/usr/bin/env python
2
3 from __future__ import print_function
4
5 import re
6 import sqlite3 as sqlite
7 import sys
8
9
10 TABLE_QUERY = \
11 """
12 SELECT name, sql
13 FROM sqlite_master
14 WHERE type='table'
15 ORDER BY name
16 """
17
18
19 def regex_match(expr, item):
20 return re.match(expr, item) is not None
21
22
23 def regex_search(expr, item):
24 return re.search(expr, item) is not None
25
26
27 def regex_sub(expr, replace, item):
28 return re.sub(expr, replace, item)
29
30
31 def get_connection(sqlitedb_path, addfunctions=True):
32 conn = sqlite.connect(sqlitedb_path)
33 if addfunctions:
34 conn.create_function("re_match", 2, regex_match)
35 conn.create_function("re_search", 2, regex_search)
36 conn.create_function("re_sub", 3, regex_sub)
37 return conn
38
39
40 def describe_tables(conn, outputFile):
41 try:
42 c = conn.cursor()
43 tables_query = TABLE_QUERY
44 rslt = c.execute(tables_query).fetchall()
45 for table, sql in rslt:
46 print("Table %s:" % table, file=outputFile)
47 try:
48 col_query = 'SELECT * FROM %s LIMIT 0' % table
49 cur = conn.cursor().execute(col_query)
50 cols = [col[0] for col in cur.description]
51 print(" Columns: %s" % cols, file=outputFile)
52 except Exception as exc:
53 print("Warning: %s" % exc, file=sys.stderr)
54 except Exception as e:
55 exit('Error: %s' % (e))
56 exit(0)
57
58
59 def run_query(conn, query, outputFile, no_header=False):
60 cur = conn.cursor()
61 results = cur.execute(query)
62 if not no_header:
63 outputFile.write("#%s\n" % '\t'.join(
64 [str(col[0]) for col in cur.description]))
65 for i, row in enumerate(results):
66 outputFile.write("%s\n" % '\t'.join(
67 [str(val) if val is not None else '' for val in row]))