| Previous changeset 11:bce29ec10b78 (2021-02-12) Next changeset 13:c29d2f80a066 (2021-08-19) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4fd70e184fca17ad430c30eb286127c4a198ef11" |
|
modified:
macros.xml query_db.py sqlite_to_tabular.xml |
|
added:
test-data/math_input.tsv test-data/math_output.tsv |
| b |
| diff -r bce29ec10b78 -r 575cd6cd537c macros.xml --- a/macros.xml Fri Feb 12 21:20:55 2021 +0000 +++ b/macros.xml Sat Jun 19 14:16:32 2021 +0000 |
| b |
| @@ -383,6 +383,7 @@ =========== ========== ========== ===================== ========== ============ + Regular_expression_ functions are included for: :: @@ -423,7 +424,33 @@ James Smith 20/10/80 =========== ========== ========== -.. _Regular_expression: https://docs.python.org/release/2.7/library/re.html + Math_ functions *( python math library: https://docs.python.org/3.6/library/math.html )*: + + acos(x), acosh(x), asin(x), asinh(x), atan(x), atanh(x), atan2(x, y), ceil(x), cos(x), cosh(x), degrees(x), exp(x), expm1(x), fabs(x), floor(x), fmod(x, y), log(b,x), log(x), log10(x), log1p(x), log2(x), mod(x, y), pow(x, y), radians(x), sin(x), sinh(x), sqrt(x), tan(x), tanh(x), trunc(x) + + + :: + + Query: + + SELECT SaleAmount, floor(SaleAmount) as "dollars" + FROM sales + + Results: + + ============ ======== + SaleAmount dollars + ============ ======== + 100.22 100 + 99.95 99 + 122.95 122 + 100.00 100 + 555.55 555 + ============ ======== + + +.. _Regular_expression: https://docs.python.org/3.9/library/re.html +.. _Math: https://docs.python.org/3.9/library/math.html .. _SQLite: http://www.sqlite.org/index.html .. _SQLite_functions: http://www.sqlite.org/docs.html |
| b |
| diff -r bce29ec10b78 -r 575cd6cd537c query_db.py --- a/query_db.py Fri Feb 12 21:20:55 2021 +0000 +++ b/query_db.py Sat Jun 19 14:16:32 2021 +0000 |
| b |
| @@ -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 |
| b |
| diff -r bce29ec10b78 -r 575cd6cd537c sqlite_to_tabular.xml --- a/sqlite_to_tabular.xml Fri Feb 12 21:20:55 2021 +0000 +++ b/sqlite_to_tabular.xml Sat Jun 19 14:16:32 2021 +0000 |
| b |
| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="sqlite_to_tabular" name="SQLite to tabular" version="2.0.1"> +<tool id="sqlite_to_tabular" name="SQLite to tabular" version="3.2.0"> <description>for SQL query</description> <macros> |
| b |
| diff -r bce29ec10b78 -r 575cd6cd537c test-data/math_input.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/math_input.tsv Sat Jun 19 14:16:32 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +-2 -2.222 +-1 -1.999 +0 0 +1 1.0 +2 2.22 +3 3.33333 +4 4.00444 +5 5.555 |
| b |
| diff -r bce29ec10b78 -r 575cd6cd537c test-data/math_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/math_output.tsv Sat Jun 19 14:16:32 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +#c1 c2 trunc(c2) floor(c2) ceil(c2) abs(c1) fabs(c2) mod(c1,2) fmod(c2, 1.5) sqrt(c1) sqrt(c2) degrees(c1) radians(c1) log(c1) log10(c1) pow(c1,2) exp(c2) exp(c1) cos(c1) sin(c1) tan(c1) cosh(c1) sinh(c1) tanh(c1) acos(c1) asin(c1) acosh(c1) asinh(c1) +-2 -2.222 -2 -3 -2 2 2.222 0 -0.722 -114.59155902616465 -0.03490658503988659 4.0 0.10839210768078596 0.1353352832366127 -0.4161468365471424 -0.9092974268256817 2.185039863261519 3.7621956910836314 -3.6268604078470186 -0.9640275800758169 -1.4436354751788103 +-1 -1.999 -1 -2 -1 1 1.999 1 -0.4990000000000001 -57.29577951308232 -0.017453292519943295 1.0 0.13547068621005243 0.36787944117144233 0.5403023058681398 -0.8414709848078965 -1.557407724654902 1.5430806348152437 -1.1752011936438014 -0.7615941559557649 3.141592653589793 -1.5707963267948966 -0.881373587019543 +0 0.0 0 0 0 0 0.0 0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 1.0 0.0 0.0 1.5707963267948966 0.0 0.0 +1 1.0 1 1 1 1 1.0 1 1.0 1.0 1.0 57.29577951308232 0.017453292519943295 0.0 0.0 1.0 2.718281828459045 2.718281828459045 0.5403023058681398 0.8414709848078965 1.557407724654902 1.5430806348152437 1.1752011936438014 0.7615941559557649 0.0 1.5707963267948966 0.0 0.881373587019543 +2 2.22 2 2 3 2 2.22 0 0.7200000000000002 1.4142135623730951 1.489966442575134 114.59155902616465 0.03490658503988659 0.6931471805599453 0.3010299956639812 4.0 9.207330865882252 7.38905609893065 -0.4161468365471424 0.9092974268256817 -2.185039863261519 3.7621956910836314 3.6268604078470186 0.9640275800758169 1.3169578969248166 1.4436354751788103 +3 3.33333 3 3 4 3 3.33333 1 0.3333300000000001 1.7320508075688772 1.8257409454793962 171.88733853924697 0.05235987755982989 1.0986122886681098 0.47712125471966244 9.0 28.03153145593222 20.085536923187668 -0.9899924966004454 0.1411200080598672 -0.1425465430742778 10.067661995777765 10.017874927409903 0.9950547536867305 1.762747174039086 1.8184464592320668 +4 4.00444 4 4 5 4 4.00444 0 1.0044399999999998 2.0 2.0011096921458353 229.1831180523293 0.06981317007977318 1.3862943611198906 0.6020599913279624 16.0 54.84110477970282 54.598150033144236 -0.6536436208636119 -0.7568024953079282 1.1578212823495775 27.308232836016487 27.289917197127753 0.999329299739067 2.0634370688955608 2.0947125472611012 +5 5.555 5 5 6 5 5.555 1 1.0549999999999997 2.23606797749979 2.356904749878535 286.4788975654116 0.08726646259971647 1.6094379124341003 0.6989700043360189 25.0 258.52696452057376 148.4131591025766 0.2836621854632263 -0.9589242746631385 -3.380515006246585 74.20994852478785 74.20321057778875 0.9999092042625951 2.2924316695611777 2.3124383412727525 |