diff query_db.py @ 0:6fbd9d25ceef draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/query_db.py	Tue Jul 18 09:06:47 2017 -0400
@@ -0,0 +1,67 @@
+#!/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):
+    cur = conn.cursor()
+    results = cur.execute(query)
+    if not no_header:
+        outputFile.write("#%s\n" % '\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]))