| Previous changeset 1:dddadbbac949 (2019-08-30) Next changeset 3:60ff16842fcd (2019-10-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09" |
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modified:
scripts/safety.py scripts/table_compute.py table_compute.xml |
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| diff -r dddadbbac949 -r 02c3e335a695 scripts/safety.py --- a/scripts/safety.py Fri Aug 30 05:28:18 2019 -0400 +++ b/scripts/safety.py Fri Sep 13 14:54:41 2019 -0400 |
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| @@ -11,7 +11,6 @@ '(', ')', 'if', 'else', 'or', 'and', 'not', 'in', '+', '-', '*', '/', '%', ',', '!=', '==', '>', '>=', '<', '<=', 'min', 'max', 'sum', - 'str', 'int', 'float' ) __allowed_ref_types = { 'pd.DataFrame': { @@ -177,12 +176,13 @@ # ['vec.median', '(', ')', '+', 'vec.sum', '(', ')'] tokens = [ e for e in re.split( - r'("[a-zA-Z%0-9_.]+"|[a-zA-Z0-9_.]+|[^a-zA-Z0-9_.() ]+|[()])', self.expr + r'([a-zA-Z0-9_.]+|[^a-zA-Z0-9_.() ]+|[()])', self.expr ) if e.strip() ] # 2. Subtract allowed standard tokens rem = [e for e in tokens if e not in self.__allowed_tokens] + # 3. Subtract allowed qualified objects from allowed modules # and whitelisted references and their attributes rem2 = [] @@ -194,32 +194,18 @@ if len(parts) == 2: if parts[0] in self.these: parts[0] = '_this' - elif parts[0] == "": - # e.g. '.T' gives ['','.T'] - # Here we assume that the blank part[0] refers to the - # self.ref_type (e.g. "pd.DataFrame"), and that - # the second part is a function of that type. - if parts[1] in self.allowed_qualified['_this']: - continue - if parts[0] in self.allowed_qualified: if parts[1] in self.allowed_qualified[parts[0]]: continue - rem2.append(e) - # Debug - # for x in (tokens, rem, rem2):print(x) - # 4. Assert that rest are real numbers or strings e = '' for e in rem2: try: _ = float(e) except ValueError: - # e.g. '"TEXT"' is okay. - if not(e[0] == '"' and e[-1] == '"'): - safe = False - break + safe = False + break return safe, e |
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| diff -r dddadbbac949 -r 02c3e335a695 scripts/table_compute.py --- a/scripts/table_compute.py Fri Aug 30 05:28:18 2019 -0400 +++ b/scripts/table_compute.py Fri Sep 13 14:54:41 2019 -0400 |
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| @@ -4,7 +4,7 @@ """ -__version__ = "0.9.1" +__version__ = "0.9.2" import csv import math @@ -265,7 +265,12 @@ mode = params["element_mode"] if mode == "replace": replacement_val = params["element_replace"] - out_table = data.mask(bool_mat, replacement_val) + out_table = data.mask( + bool_mat, + data.where(bool_mat).applymap( + lambda x: replacement_val.format(elem=x) + ) + ) elif mode == "modify": mod_op = Utils.getOneValueMathOp(params["element_modify_op"]) out_table = data.mask( @@ -300,7 +305,9 @@ elif user_mode_single == "fulltable": general_mode = params["mode"] - if general_mode == "melt": + if general_mode == "transpose": + out_table = data.T + elif general_mode == "melt": melt_ids = params["MELT"]["melt_ids"] melt_values = params["MELT"]["melt_values"] |
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| diff -r dddadbbac949 -r 02c3e335a695 table_compute.xml --- a/table_compute.xml Fri Aug 30 05:28:18 2019 -0400 +++ b/table_compute.xml Fri Sep 13 14:54:41 2019 -0400 |
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| b'@@ -1,7 +1,7 @@\n <tool id="table_compute" name="Table Compute" version="@VERSION@">\n <description>computes operations on table data</description>\n <macros>\n- <token name="@VERSION@">0.9.1</token>\n+ <token name="@VERSION@">0.9.2</token>\n <token name="@COPEN@"><![CDATA[<code>]]></token>\n <token name="@CCLOSE@"><![CDATA[</code>]]></token>\n <import>allowed_functions.xml</import>\n@@ -23,7 +23,7 @@\n <sanitizer sanitize="false" />\n </macro>\n <macro name="validator_functiondef">\n- <validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters \'_ !-+=/*%.<>()\'">^[\'"\\w !\\-+=/*%,.<>()]+$</validator>\n+ <validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters _ !-+=/*%.<>()">^[\\w !\\-+=/*%,.<>()]+$</validator>\n <sanitizer sanitize="false" />\n </macro>\n <!-- macro for main input tests -->\n@@ -51,8 +51,9 @@\n <yield />\n <conditional name="user" >\n <param name="mode" value="element" />\n- <param name="element_op" value="gt" />\n- <param name="element_value" value="0" />\n+ <conditional name="elem_val">\n+ <param name="element_op" value="None" />\n+ </conditional>\n <conditional name="element" >\n <param name="mode" value="custom" />\n <param name="custom_expr" value="-math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5" />\n@@ -133,6 +134,7 @@\n }\n \n #if str($singtabop.use_type) == "single":\n+ #set $op_mode = str($singtabop.user.mode)\n Data = {\n "tables": [\n {\n@@ -159,12 +161,12 @@\n }\n ],\n "params": {\n- "user_mode_single": \'$singtabop.user.mode.value\',\n- #if $singtabop.user.mode.value == \'precision\':\n+ "user_mode_single": \'$op_mode\',\n+ #if $op_mode == \'precision\':\n ## Literally do nothing, the user just sets the precision slider\n ## at the top default level\n }\n- #elif $singtabop.user.mode.value == \'select\':\n+ #elif $op_mode == \'select\':\n "select_cols_unique": #echo \'select_cols_keepdupe\' in str($singtabop.user.select_keepdupe)#,\n "select_rows_unique": #echo \'select_rows_keepdupe\' in str($singtabop.user.select_keepdupe)#,\n #if $singtabop.user.select_cols_wanted:\n@@ -178,24 +180,25 @@\n "select_rows_wanted": None,\n #end if\n }\n- #elif $singtabop.user.mode.value == \'filtersumval\':\n- "filtersumval_mode": \'$singtabop.user.filtersumval_mode.use.value\',\n- "filtersumval_axis": $singtabop.user.axis.value,\n- #if $singtabop.user.filtersumval_mode.use.value == \'operation\':\n- "filtersumval_compare": \'$singtabop.user.filtersumval_mode.compare_op.value\',\n- "filtersumval_op": \'$singtabop.user.filtersumval_mode.operation.value\',\n+ #elif $op_mode == \'filtersumval\':\n+ #set $filter_type = str($singtabop.user.filtersumval_mode.use)\n+ "filtersumval_mode": \'$filter_type\',\n+ "filtersumval_axis": $singtabop.user.axis,\n+ #if $filter_type == \'operation\':\n+ "filtersumval_compare": \'$singtabop.user.filtersumval_mode.compare_op\',\n+ "filtersumval_op": \'$singtabop.user.filtersumval_mode.operation\',\n "filtersumval_against": $singtabop.user.filtersumval_mode.against,\n "filtersumval_minmatch": None,\n- #elif $singtabop.user.filtersumval_mode.use.value == \'element\':\n+ #elif $filter_type == \'element\':\n "filtersumval_compare": None,\n- "filtersumval_op": \'$singtabop.user.filtersumval_mode.operation.value\',\n+ "filtersumval_op": \'$singtabop.user.filtersumval_mode.operation\',\n ## against could be string or float, so we parse this in the code\n "filtersumval_against": \'$singtabop.user.filtersumv'..b'9;ab" />\n+ <not_has_text text="g3	ab" />\n+ <not_has_text text="g4	ab" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1" expect_failure="true">\n+ <!-- Test 41: Test safety of custom expression free text\n+ Tries to escape/reenter config file quoting.\n+\n+ This test is expected to fail if either\n+ - a validator disallows the use of single quotes or\n+ - the single quotes get sanitized (which is unlikely to result in a\n+ valid expression); note that in this situation, it cannot be\n+ guaranteed that the single quote sanitization is safe with\n+ *every* input\n+\n+ If the test succeeds unexpectedly, this shows that Python\n+ has performed string concatenation upon importing the config file\n+ resulting in each element of the test table being retained.\n+ -->\n+ <conditional name="singtabop" >\n+ <param name="use_type" value="single" />\n+ <param name="input" value="examples.4.tsv" />\n+ <param name="col_row_names" value="has_col_names,has_row_names" />\n+ <conditional name="user" >\n+ <param name="mode" value="element" />\n+ <conditional name="element" >\n+ <param name="mode" value="custom" />\n+ <param name="custom_expr" value="el\'+\'em" />\n+ </conditional>\n+ <conditional name="elem_val" >\n+ <param name="element_op" value="All" />\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ </test>\n </tests>\n <help><![CDATA[\n This tool computes table expressions on the element, row, and column basis. It can sub-select,\n duplicate, as well as perform general and custom expressions on rows, columns or elements.\n \n-Only a single operation can be performed on the data. Multiple operations can be performed by\n-chaining successive runs of this tool. This is to provide a more transparent workflow for complex operations.\n+.. class:: infomark\n+\n+ Only a single operation can be performed on the data. Multiple operations\n+ can be performed by chaining successive runs of this tool. This is to\n+ provide a more transparent workflow for complex operations.\n \n \n \n@@ -1582,6 +1609,14 @@\n \n table1 / min(np.max(np.max(table2)), np.max(np.max(table3)))\n \n+.. class:: infomark\n+\n+ Complex operations (like ones that would benefit from specifying nested\n+ attributes) can often be broken into subsequent runs ot the tool, in\n+ which the first run generates an intermediate table representing the result\n+ of the "inner" operation that the second run can then use as input to\n+ perform the "outer" operation.\n+\n Also note that, currently `min()`, `max()` and `sum()` are the only built-in\n Python functions that can be used inside expressions. If you want to use\n additional functions, these have to be qualified functions from the `math`,\n@@ -1702,11 +1737,17 @@\n \n * *Type of table operation* \xe2\x86\x92 **Manipulate selected table elements**\n \n- * *Operation to perform* \xe2\x86\x92 **Custom**\n+ * *Operation to perform* \xe2\x86\x92 **Replace values**\n+\n+ * *Replacement value* \xe2\x86\x92 ::\n+\n+ chr{elem:.0f}\n \n- * *Custom Expression* \xe2\x86\x92 ::\n-\n- "chr%.f" % elem\n+ Here, the placeholder ``{elem}`` lets us refer to each element\'s\n+ current value, while the ``:.0f`` part is a format specifier that makes\n+ sure numbers are printed without decimals (for a complete description of\n+ the available syntax see the\n+ `Python Format Specification Mini-Language <https://docs.python.org/3/library/string.html#formatspec>`_).\n \n * *Operate on elements* \xe2\x86\x92 **Specific Rows and/or Columns**\n * *List of columns to select* \xe2\x86\x92 "2"\n' |