Mercurial > repos > iuc > table_compute

annotate scripts/safety.py @ 1:dddadbbac949 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
author iuc
date Fri, 30 Aug 2019 05:28:18 -0400
parents 1b0f96ed73f2
children 02c3e335a695
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1 import re
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
2
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
4 class Safety():
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
5 """
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
6 Class to safely evaluate mathematical expression on single
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
7 or table data
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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8 """
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
10 __allowed_tokens = (
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
11 '(', ')', 'if', 'else', 'or', 'and', 'not', 'in',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
12 '+', '-', '*', '/', '%', ',', '!=', '==', '>', '>=', '<', '<=',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
13 'min', 'max', 'sum',
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
14 'str', 'int', 'float'
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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15 )
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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16 __allowed_ref_types = {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
17 'pd.DataFrame': {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
18 'abs', 'add', 'agg', 'aggregate', 'align', 'all', 'any', 'append',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
19 'apply', 'applymap', 'as_matrix', 'asfreq', 'at', 'axes', 'bool',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
20 'clip', 'clip_lower', 'clip_upper', 'columns', 'combine',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
21 'compound', 'corr', 'count', 'cov', 'cummax', 'cummin', 'cumprod',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
22 'cumsum', 'describe', 'div', 'divide', 'dot', 'drop',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
23 'drop_duplicates', 'droplevel', 'dropna', 'duplicated', 'empty',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
24 'eq', 'equals', 'expanding', 'ffill', 'fillna', 'filter', 'first',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
25 'first_valid_index', 'floordiv', 'ge', 'groupby', 'gt', 'head',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
26 'iat', 'iloc', 'index', 'insert', 'interpolate', 'isin', 'isna',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
27 'isnull', 'items', 'iteritems', 'iterrows', 'itertuples', 'ix',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
28 'join', 'keys', 'kurt', 'kurtosis', 'last', 'last_valid_index',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
29 'le', 'loc', 'lookup', 'lt', 'mad', 'mask', 'max', 'mean',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
30 'median', 'melt', 'merge', 'min', 'mod', 'mode', 'mul', 'multiply',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
31 'ndim', 'ne', 'nlargest', 'notna', 'notnull', 'nsmallest',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
32 'nunique', 'pct_change', 'pivot', 'pivot_table', 'pop', 'pow',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
33 'prod', 'product', 'quantile', 'radd', 'rank', 'rdiv', 'replace',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
34 'resample', 'rfloordiv', 'rmod', 'rmul', 'rolling', 'round',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
35 'rpow', 'rsub', 'rtruediv', 'sample', 'select',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
36 'sem', 'shape', 'shift', 'size', 'skew', 'slice_shift',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
37 'squeeze', 'stack', 'std', 'sub', 'subtract', 'sum', 'swapaxes',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
38 'swaplevel', 'T', 'tail', 'take', 'transform', 'transpose',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
39 'truediv', 'truncate', 'tshift', 'unstack', 'var', 'where',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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40 },
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
41 'pd.Series': {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
42 'abs', 'add', 'agg', 'aggregate', 'align', 'all', 'any', 'append',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
43 'apply', 'argsort', 'as_matrix', 'asfreq', 'asof', 'astype', 'at',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
44 'at_time', 'autocorr', 'axes', 'between', 'between_time', 'bfill',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
45 'bool', 'cat', 'clip', 'clip_lower', 'clip_upper', 'combine',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
46 'combine_first', 'compound', 'corr', 'count', 'cov', 'cummax',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
47 'cummin', 'cumprod', 'cumsum', 'describe', 'diff', 'div', 'divide',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
48 'divmod', 'dot', 'drop', 'drop_duplicates', 'droplevel', 'dropna',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
49 'dt', 'dtype', 'dtypes', 'duplicated', 'empty', 'eq', 'equals',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
50 'ewm', 'expanding', 'factorize', 'ffill', 'fillna', 'filter',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
51 'first', 'first_valid_index', 'flags', 'floordiv', 'ge', 'groupby',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
52 'gt', 'hasnans', 'head', 'iat', 'idxmax', 'idxmin', 'iloc', 'imag',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
53 'index', 'interpolate', 'is_monotonic', 'is_monotonic_decreasing',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
54 'is_monotonic_increasing', 'is_unique', 'isin', 'isna', 'isnull',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
55 'item', 'items', 'iteritems', 'ix', 'keys', 'kurt', 'kurtosis',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
56 'last', 'last_valid_index', 'le', 'loc', 'lt', 'mad', 'map',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
57 'mask', 'max', 'mean', 'median', 'min', 'mod', 'mode', 'mul',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
58 'multiply', 'name', 'ndim', 'ne', 'nlargest', 'nonzero', 'notna',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
59 'notnull', 'nsmallest', 'nunique', 'pct_change', 'pop', 'pow',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
60 'prod', 'product', 'ptp', 'quantile', 'radd', 'rank', 'rdiv',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
61 'rdivmod', 'real', 'repeat', 'replace', 'resample', 'rfloordiv',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
62 'rmod', 'rmul', 'rolling', 'round', 'rpow', 'rsub', 'rtruediv',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
63 'sample', 'searchsorted', 'select', 'sem', 'shape', 'shift',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
64 'size', 'skew', 'slice_shift', 'sort_index', 'sort_values',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
65 'squeeze', 'std', 'sub', 'subtract', 'sum', 'swapaxes',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
66 'swaplevel', 'T', 'tail', 'take', 'transform', 'transpose',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
67 'truediv', 'truncate', 'tshift', 'unique', 'unstack',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
68 'value_counts', 'var', 'where', 'xs',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
69 },
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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70 }
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
71
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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72 __allowed_qualified = {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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73 # allowed numpy functionality
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
74 'np': {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
75 'abs', 'add', 'all', 'any', 'append', 'array', 'bool', 'ceil',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
76 'complex', 'cos', 'cosh', 'cov', 'cumprod', 'cumsum', 'degrees',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
77 'divide', 'divmod', 'dot', 'e', 'empty', 'exp', 'float', 'floor',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
78 'hypot', 'inf', 'int', 'isfinite', 'isin', 'isinf', 'isnan', 'log',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
79 'log10', 'log2', 'max', 'mean', 'median', 'min', 'mod', 'multiply',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
80 'nan', 'ndim', 'pi', 'product', 'quantile', 'radians', 'rank',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
81 'remainder', 'round', 'sin', 'sinh', 'size', 'sqrt', 'squeeze',
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iuc
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82 'stack', 'std', 'str', 'subtract', 'sum', 'swapaxes', 'take',
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iuc
parents:
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83 'tan', 'tanh', 'transpose', 'unique', 'var', 'where',
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iuc
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84 },
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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85 # allowed math functionality
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iuc
parents:
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86 'math': {
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87 'acos', 'acosh', 'asin', 'asinh', 'atan', 'atan2', 'atanh', 'ceil',
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88 'copysign', 'cos', 'cosh', 'degrees', 'e', 'erf', 'erfc', 'exp',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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89 'expm1', 'fabs', 'factorial', 'floor', 'fmod', 'frexp', 'fsum',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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90 'gamma', 'gcd', 'hypot', 'inf', 'isclose', 'isfinite', 'isinf',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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91 'isnan', 'ldexp', 'lgamma', 'log', 'log10', 'log1p', 'log2',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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92 'modf', 'nan', 'pi', 'pow', 'radians', 'remainder', 'sin', 'sinh',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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93 'sqrt', 'tan', 'tanh', 'tau', 'trunc',
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iuc
parents:
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94 },
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iuc
parents:
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95 # allowed pd functionality
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96 'pd': {
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97 'DataFrame', 'array', 'concat', 'cut', 'date_range', 'factorize',
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98 'interval_range', 'isna', 'isnull', 'melt', 'merge', 'notna',
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99 'notnull', 'period_range', 'pivot', 'pivot_table', 'unique',
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iuc
parents:
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100 'value_counts', 'wide_to_long',
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101 },
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iuc
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102 }
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103
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104 def __init__(self, expression,
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105 ref_whitelist=None, ref_type=None,
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106 custom_qualified=None):
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107 self.allowed_qualified = self.__allowed_qualified.copy()
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108 if ref_whitelist is None:
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109 self.these = []
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110 else:
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111 self.these = ref_whitelist
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112 if ref_type is None or ref_type not in self.__allowed_ref_types:
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113 self.allowed_qualified['_this'] = set()
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114 else:
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115 self.allowed_qualified[
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116 '_this'
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117 ] = self.__allowed_ref_types[ref_type]
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118 if custom_qualified is not None:
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119 self.allowed_qualified.update(custom_qualified)
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120 self.expr = expression
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121 self.__assertSafe()
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122
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123 def generateFunction(self):
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124 "Generates a function to be evaluated outside the class"
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125 cust_fun = "def fun(%s):\n\treturn(%s)" % (self.these[0], self.expr)
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126 return cust_fun
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127
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128 def __assertSafe(self):
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129 indeed, problematic_token = self.__isSafeStatement()
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130 if not indeed:
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131 self.detailedExcuse(problematic_token)
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132 raise ValueError("Custom Expression is not safe.")
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133
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iuc
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134 @staticmethod
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135 def detailedExcuse(word):
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136 "Gives a verbose statement for why users should not use some specific operators."
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137 mess = None
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138 if word == "for":
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139 mess = "for loops and comprehensions are not allowed. Use numpy or pandas table operations instead."
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140 elif word == ":":
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iuc
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141 mess = "Colons are not allowed. Use inline Python if/else statements."
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142 elif word == "=":
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143 mess = "Variable assignment is not allowed. Use object methods to substitute values."
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iuc
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144 elif word in ("[", "]"):
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iuc
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145 mess = "Direct indexing of arrays is not allowed. Use numpy or pandas functions/methods to address specific parts of tables."
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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146 else:
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iuc
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147 mess = "Not an allowed token in this operation"
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iuc
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148 print("( '%s' ) %s" % (word, mess))
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149
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150 def __isSafeStatement(self):
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iuc
parents:
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151 """
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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152 Determines if a user-expression is safe to evaluate.
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153
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154 To be considered safe an expression may contain only:
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iuc
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155 - standard Python operators and numbers
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156 - inline conditional expressions
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157 - select functions and objects
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parents:
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158 by default, these come from the math, numpy and pandas
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iuc
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159 libraries, and must be qualified with the modules' conventional
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parents:
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160 names math, np, pd; can be overridden at the instance level
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161 - references to a whitelist of objects (pd.DataFrames by default)
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parents:
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162 and their methods
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iuc
parents:
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163 """
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164
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165 safe = True
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iuc
parents:
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166 # examples of user-expressions
1
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parents: 0
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167 # '-math.log(1 - elem/4096) * 4096 if elem != 1 else elem - 0.5'
0
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168 # 'vec.median() + vec.sum()'
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169
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170 # 1. Break expressions into tokens
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171 # e.g.,
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172 # [
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173 # '-', 'math.log', '(', '1', '-', 'elem', '/', '4096', ')', '*',
1
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174 # '4096', 'if', 'elem', '!=', '1', 'else', 'elem', '-', '0.5'
0
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175 # ]
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176 # or
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177 # ['vec.median', '(', ')', '+', 'vec.sum', '(', ')']
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178 tokens = [
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179 e for e in re.split(
1
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180 r'("[a-zA-Z%0-9_.]+"|[a-zA-Z0-9_.]+|[^a-zA-Z0-9_.() ]+|[()])', self.expr
0
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181 ) if e.strip()
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182 ]
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183
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184 # 2. Subtract allowed standard tokens
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185 rem = [e for e in tokens if e not in self.__allowed_tokens]
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186 # 3. Subtract allowed qualified objects from allowed modules
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187 # and whitelisted references and their attributes
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188 rem2 = []
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189 for e in rem:
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190 parts = e.split('.')
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191 if len(parts) == 1:
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192 if parts[0] in self.these:
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193 continue
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194 if len(parts) == 2:
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195 if parts[0] in self.these:
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196 parts[0] = '_this'
1
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197 elif parts[0] == "":
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198 # e.g. '.T' gives ['','.T']
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199 # Here we assume that the blank part[0] refers to the
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200 # self.ref_type (e.g. "pd.DataFrame"), and that
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201 # the second part is a function of that type.
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202 if parts[1] in self.allowed_qualified['_this']:
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203 continue
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204
0
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205 if parts[0] in self.allowed_qualified:
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206 if parts[1] in self.allowed_qualified[parts[0]]:
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207 continue
1
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208
0
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209 rem2.append(e)
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210
1
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211 # Debug
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212 # for x in (tokens, rem, rem2):print(x)
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213
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214 # 4. Assert that rest are real numbers or strings
0
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215 e = ''
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216 for e in rem2:
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217 try:
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218 _ = float(e)
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219 except ValueError:
1
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220 # e.g. '"TEXT"' is okay.
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221 if not(e[0] == '"' and e[-1] == '"'):
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222 safe = False
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223 break
0
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224
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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225 return safe, e