diff query_db.py @ 12:575cd6cd537c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11"

--- a/query_db.py	Fri Feb 12 21:20:55 2021 +0000
+++ b/query_db.py	Sat Jun 19 14:16:32 2021 +0000
@@ -2,6 +2,7 @@
 
 from __future__ import print_function
 
+import math
 import re
 import sqlite3 as sqlite
 import sys
@@ -16,6 +17,10 @@
     """
 
 
+def msg(e):
+    print(e, file=sys.stderr)
+
+
 def regex_match(expr, item):
     return re.match(expr, item) is not None
 
@@ -28,12 +33,283 @@
     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