Mercurial > repos > iuc > query_tabular
view query_db.py @ 13:cf34c344508d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
author | iuc |
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date | Thu, 19 Aug 2021 19:40:53 +0000 |
parents | 623f3eb7aa48 |
children |
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#!/usr/bin/env python from __future__ import print_function import math import re import sqlite3 as sqlite import sys TABLE_QUERY = \ """ SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name """ def msg(e): print(e, file=sys.stderr) 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 math_acos(x): try: return math.acos(x) except ValueError as ve: msg('acos(%s): %s' % (x, ve)) return None def math_acosh(x): try: return math.acosh(x) except ValueError as ve: msg(f'acosh({x}): {ve}') return None def math_asin(x): try: return math.asin(x) except ValueError as ve: msg(f'asin({x}): {ve}') return None def math_asinh(x): try: return math.asinh(x) except ValueError as ve: msg(f'asinh({x}): {ve}') return None def math_atan(x): try: return math.atan(x) except ValueError as ve: msg(f'atan({x}): {ve}') return None def math_atanh(x): try: return math.atanh(x) except ValueError as ve: msg(f'atanh({x}): {ve}') return None def math_atan2(x, y): try: return math.atan2(x, y) except ValueError as ve: msg(f'atan2({x}, {y}): {ve}') return None def math_ceil(x): try: return math.ceil(x) except ValueError as ve: msg(f'ceil({x}): {ve}') return None def math_cos(x): try: return math.cos(x) except ValueError as ve: msg(f'cos({x}): {ve}') return None def math_cosh(x): try: return math.cosh(x) except ValueError as ve: msg(f'cosh({x}): {ve}') return None def math_degrees(x): try: return math.degrees(x) except ValueError as ve: msg(f'degrees({x}): {ve}') return None def math_exp(x): try: return math.exp(x) except ValueError as ve: msg(f'exp({x}): {ve}') return None def math_expm1(x): try: return math.expm1(x) except ValueError as ve: msg(f'expm1({x}): {ve}') return None def math_fabs(x): try: return math.fabs(x) except ValueError as ve: msg(f'fabs({x}): {ve}') return None def math_floor(x): try: return math.floor(x) except ValueError as ve: msg(f'floor({x}): {ve}') return None def math_fmod(x, y): try: return math.fmod(x, y) except ValueError as ve: msg(f'fmod({x}, {y}): {ve}') return None def math_blog(b, x): try: return math.log(b, x) except ValueError as ve: msg(f'log({b}, {x}): {ve}') return None def math_log(x): try: return math.log(x) except ValueError as ve: msg(f'log({x}): {ve}') return None def math_log10(x): try: return math.log10(x) except ValueError as ve: msg(f'log10({x}): {ve}') return None def math_log1p(x): try: return math.log1p(x) except ValueError as ve: msg(f'log1p({x}): {ve}') return None def math_log2(x): try: return math.log2(x) except ValueError as ve: msg(f'log2({x}): {ve}') return None def math_mod(x, y): try: return x % y except ValueError as ve: msg(f'mod({x}, {y}): {ve}') return None def math_pow(x, y): try: return math.pow(x, y) except ValueError as ve: msg(f'pow({x}, {y}): {ve}') return None def math_radians(x): try: return math.radians(x) except ValueError as ve: msg(f'radians({x}): {ve}') return None def math_sin(x): try: return math.sin(x) except ValueError as ve: msg(f'sin({x}): {ve}') return None def math_sinh(x): try: return math.sinh(x) except ValueError as ve: msg(f'sinh({x}): {ve}') return None def math_sqrt(x): try: return math.sqrt(x) except ValueError as ve: msg(f'sqrt({x}): {ve}') return None def math_tan(x): try: return math.tan(x) except ValueError as ve: msg(f'tan({x}): {ve}') return None def math_tanh(x): try: return math.tanh(x) except ValueError as ve: msg(f'tanh({x}): {ve}') return None def math_trunc(x): try: return math.trunc(x) except ValueError as ve: msg(f'trunc({x}): {ve}') return None def get_connection(sqlitedb_path, addfunctions=True): sqlite.enable_callback_tracebacks(addfunctions) 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) conn.create_function("acos", 1, math_acos) conn.create_function("acosh", 1, math_acosh) conn.create_function("asin", 1, math_asin) conn.create_function("asinh", 1, math_asinh) conn.create_function("atan", 1, math_atan) conn.create_function("atanh", 1, math_atanh) conn.create_function("atan2", 2, math_atan2) conn.create_function("ceil", 1, math_ceil) conn.create_function("cos", 1, math_cos) conn.create_function("cosh", 1, math_cosh) conn.create_function("degrees", 1, math_degrees) conn.create_function("exp", 1, math_exp) conn.create_function("expm1", 1, math_expm1) conn.create_function("fabs", 1, math_fabs) conn.create_function("floor", 1, math_floor) conn.create_function("fmod", 2, math_fmod) conn.create_function("log", 1, math_log) conn.create_function("log", 2, math_blog) conn.create_function("log10", 1, math_log10) conn.create_function("log2", 1, math_log2) conn.create_function("log1p", 1, math_log1p) conn.create_function("mod", 2, math_mod) conn.create_function("pow", 2, math_pow) conn.create_function("radians", 1, math_radians) conn.create_function("sin", 1, math_sin) conn.create_function("sinh", 1, math_sinh) conn.create_function("sqrt", 1, math_sqrt) conn.create_function("tan", 1, math_tan) conn.create_function("tanh", 1, math_tanh) conn.create_function("trunc", 1, math_trunc) 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('describe_tables Error: %s' % (e)) exit(0) def run_query(conn, query, outputFile, no_header=False, comment_char='#'): cur = conn.cursor() results = cur.execute(query) if outputFile is not None: 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])) else: conn.commit() return results