galaxy/tools/stats/filtering.py

#!/usr/bin/env python
# This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties.
# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
from __future__ import (
    division,
    print_function,
)

import json
import re
import sys
from ast import (
    Module,
    parse,
    walk,
)

AST_NODE_TYPE_WHITELIST = [
    "Expr",
    "Load",
    "Str",
    "Num",
    "BoolOp",
    "Compare",
    "And",
    "Eq",
    "NotEq",
    "Or",
    "GtE",
    "LtE",
    "Lt",
    "Gt",
    "BinOp",
    "Add",
    "Div",
    "Sub",
    "Mult",
    "Mod",
    "Pow",
    "LShift",
    "GShift",
    "BitAnd",
    "BitOr",
    "BitXor",
    "UnaryOp",
    "Invert",
    "Not",
    "UAdd",
    "USub",
    "NotIn",
    "In",
    "Is",
    "IsNot",
    "List",
    "Index",
    "Subscript",
    "Constant",
    # Further checks
    "Name",
    "Call",
    "Attribute",
]


BUILTIN_AND_MATH_FUNCTIONS = "abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor".split(
    "|"
)
STRING_AND_LIST_METHODS = [name for name in dir("") + dir([]) if not name.startswith("_")]
VALID_FUNCTIONS = BUILTIN_AND_MATH_FUNCTIONS + STRING_AND_LIST_METHODS


def __check_name(ast_node):
    name = ast_node.id
    if re.match(r"^c\d+$", name):
        return True
    return name in VALID_FUNCTIONS


def __check_attribute(ast_node):
    attribute_name = ast_node.attr
    if attribute_name not in STRING_AND_LIST_METHODS:
        return False
    return True


def __check_call(ast_node):
    # If we are calling a function or method, it better be a math,
    # string or list function.
    ast_func = ast_node.func
    ast_func_class = ast_func.__class__.__name__
    if ast_func_class == "Name":
        if ast_func.id not in BUILTIN_AND_MATH_FUNCTIONS:
            return False
    elif ast_func_class == "Attribute":
        if not __check_attribute(ast_func):
            return False
    else:
        return False

    return True


def check_expression(text):
    """

    >>> check_expression("c1=='chr1' and c3-c2>=2000 and c6=='+'")
    True
    >>> check_expression("eval('1+1')")
    False
    >>> check_expression("import sys")
    False
    >>> check_expression("[].__str__")
    False
    >>> check_expression("__builtins__")
    False
    >>> check_expression("'x' in globals")
    False
    >>> check_expression("'x' in [1,2,3]")
    True
    >>> check_expression("c3=='chr1' and c5>5")
    True
    >>> check_expression("c3=='chr1' and c5>-5 and c5<+5")  # Unary +/-
    True
    >>> check_expression("c3=='chr1' and d5>5")  # Invalid d5 reference
    False
    >>> check_expression("c3=='chr1' and c5>5 or exec")
    False
    >>> check_expression("type(c1) != type(1)")
    True
    >>> check_expression("c1.split(',')[1] == '1'")
    True
    >>> check_expression("exec 1")
    False
    >>> check_expression("str(c2) in [\\\"a\\\",\\\"b\\\"]")
    True
    """
    try:
        module = parse(text)
    except SyntaxError:
        return False

    if not isinstance(module, Module):
        return False
    statements = module.body
    if not len(statements) == 1:
        return False
    expression = statements[0]
    if expression.__class__.__name__ != "Expr":
        return False

    for ast_node in walk(expression):
        ast_node_class = ast_node.__class__.__name__

        # Toss out everything that is not a "simple" expression,
        # imports, error handling, etc...
        if ast_node_class not in AST_NODE_TYPE_WHITELIST:
            return False

        # White-list more potentially dangerous types AST elements.
        if ast_node_class == "Name":
            # In order to prevent loading 'exec', 'eval', etc...
            # put string restriction on names allowed.
            if not __check_name(ast_node):
                return False
        # Check only valid, white-listed functions are called.
        elif ast_node_class == "Call":
            if not __check_call(ast_node):
                return False
        # Check only valid, white-listed attributes are accessed
        elif ast_node_class == "Attribute":
            if not __check_attribute(ast_node):
                return False

    return True


def get_operands(filter_condition):
    # Note that the order of all_operators is important
    items_to_strip = [
        "+",
        "-",
        "**",
        "*",
        "//",
        "/",
        "%",
        "<<",
        ">>",
        "&",
        "|",
        "^",
        "~",
        "<=",
        "<",
        ">=",
        ">",
        "==",
        "!=",
        "<>",
        " and ",
        " or ",
        " not ",
        " is ",
        " is not ",
        " in ",
        " not in ",
    ]
    for item in items_to_strip:
        if filter_condition.find(item) >= 0:
            filter_condition = filter_condition.replace(item, " ")
    operands = set(filter_condition.split(" "))
    return operands


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


in_fname = sys.argv[1]
out_fname = sys.argv[2]
with open(sys.argv[3]) as f:
    inputs = json.load(f)
cond_text = inputs["cond"]
try:
    in_columns = int(sys.argv[4])
    assert sys.argv[5]  # check to see that the column types variable isn't null
    in_column_types = sys.argv[5].split(",")
except Exception:
    stop_err("Data does not appear to be tabular.  This tool can only be used with tab-delimited data.")
num_header_lines = int(sys.argv[6])

# Unescape if input has been escaped
mapped_str = {
    "__lt__": "<",
    "__le__": "<=",
    "__eq__": "==",
    "__ne__": "!=",
    "__gt__": ">",
    "__ge__": ">=",
    "__sq__": "'",
    "__dq__": '"',
    "__ob__": "[",
    "__cb__": "]",
}
for key, value in mapped_str.items():
    cond_text = cond_text.replace(key, value)

# Attempt to determine if the condition includes executable stuff and, if so, exit
secured = dir()
operands = get_operands(cond_text)
for operand in operands:
    try:
        check = int(operand)
    except ValueError:
        if operand in secured:
            stop_err("Illegal value '%s' in condition '%s'" % (operand, cond_text))

if not check_expression(cond_text):
    stop_err("Illegal/invalid in condition '%s'" % (cond_text))

# Work out which columns are used in the filter (save using 1 based counting)
used_cols = sorted({int(match.group()[1:]) for match in re.finditer(r"c(\d)+", cond_text)})
largest_col_index = max(used_cols)

# Prepare the column variable names and wrappers for column data types. Only
# cast columns used in the filter.
cols, type_casts = [], []
for col in range(1, largest_col_index + 1):
    col_name = "c%d" % col
    cols.append(col_name)
    col_type = in_column_types[col - 1]
    if col in used_cols:
        type_cast = "%s(%s)" % (col_type, col_name)
    else:
        # If we don't use this column, don't cast it.
        # Otherwise we get errors on things like optional integer columns.
        type_cast = col_name
    type_casts.append(type_cast)

col_str = ", ".join(cols)  # 'c1, c2, c3, c4'
type_cast_str = ", ".join(type_casts)  # 'str(c1), int(c2), int(c3), str(c4)'
assign = "%s, = line.split( '\\t' )[:%i]" % (col_str, largest_col_index)
wrap = "%s = %s" % (col_str, type_cast_str)
skipped_lines = 0
invalid_lines = 0
first_invalid_line = 0
invalid_line = None
lines_kept = 0
total_lines = 0
out = open(out_fname, "w")

# Read and filter input file, skipping invalid lines
code = """
for i, line in enumerate( open( in_fname ) ):
    total_lines += 1
    line = line.rstrip( '\\r\\n' )

    if i < num_header_lines:
        lines_kept += 1
        print( line, file=out )
        continue

    if not line or line.startswith( '#' ):
        skipped_lines += 1
        continue
    try:
        %s
        %s
        if %s:
            lines_kept += 1
            print( line, file=out )
    except Exception:
        invalid_lines += 1
        if not invalid_line:
            first_invalid_line = i + 1
            invalid_line = line
""" % (
    assign,
    wrap,
    cond_text,
)
valid_filter = True
try:
    exec(code)
except Exception as e:
    out.close()
    if str(e).startswith("invalid syntax"):
        valid_filter = False
        stop_err('Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % cond_text)
    else:
        stop_err(str(e))

if valid_filter:
    out.close()
    valid_lines = total_lines - skipped_lines
    print("Filtering with %s, " % cond_text)
    if valid_lines > 0:
        print(
            "kept %4.2f%% of %d valid lines (%d total lines)."
            % (100.0 * lines_kept / valid_lines, valid_lines, total_lines)
        )
    else:
        print(
            'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.'
            % cond_text
        )
    if invalid_lines:
        print(
            'Skipped %d invalid line(s) starting at line #%d: "%s"' % (invalid_lines, first_invalid_line, invalid_line)
        )
    if skipped_lines:
        print("Skipped %i comment (starting with #) or blank line(s)" % skipped_lines)