Any python module for customized BNF parser?

Question

friends.

I have a 'make'-like style file needed to be parsed. The grammar is something like:

samtools=/path/to/samtools
picard=/path/to/picard

task1: 
    des: description
    path: /path/to/task1
    para: [$global.samtools,
           $args.input,
           $path
          ]

task2: task1

Where $global contains the variables defined in a global scope. $path is a 'local' variable. $args contains the key/pair values passed in by users.

I would like to parse this file by some python libraries. Better to return some parse tree. If there are some errors, better to report them. I found this one: CodeTalker and yeanpypa. Can they be used in this case? Any other recommendations?

score 6 · Accepted Answer · answered Jun 13 '12 at 08:45

I had to guess what your makefile structure allows based on your example, but this should get you close:

from pyparsing import *
# elements of the makefile are delimited by line, so we must
# define skippable whitespace to include just spaces and tabs
ParserElement.setDefaultWhitespaceChars(' \t')
NL = LineEnd().suppress()

EQ,COLON,LBRACK,RBRACK = map(Suppress, "=:[]")
identifier = Word(alphas+'_', alphanums)

symbol_assignment = Group(identifier("name") + EQ + empty + 
                          restOfLine("value"))("symbol_assignment")
symbol_ref = Word("$",alphanums+"_.")

def only_column_one(s,l,t):
    if col(l,s) != 1:
        raise ParseException(s,l,"not in column 1")
# task identifiers have to start in column 1
task_identifier = identifier.copy().setParseAction(only_column_one)

task_description = "des:" + empty + restOfLine("des")
task_path = "path:" + empty + restOfLine("path")
task_para_body = delimitedList(symbol_ref)
task_para = "para:" + LBRACK + task_para_body("para") + RBRACK
task_para.ignore(NL)
task_definition = Group(task_identifier("target") + COLON + 
        Optional(delimitedList(identifier))("deps") + NL +
        (
        Optional(task_description + NL) & 
        Optional(task_path + NL) & 
        Optional(task_para + NL)
        )
    )("task_definition")

makefile_parser = ZeroOrMore(
    symbol_assignment |
    task_definition |
    NL
    )


if __name__ == "__main__":
    test = """\
samtools=/path/to/samtools
picard=/path/to/picard

task1:  
    des: description 
    path: /path/to/task1 
    para: [$global.samtools, 
           $args.input, 
           $path 
          ] 

task2: task1 
"""

# dump out what we parsed, including results names
for element in makefile_parser.parseString(test):
    print element.getName()
    print element.dump()
    print

Prints:

symbol_assignment
['samtools', '/path/to/samtools']
- name: samtools
- value: /path/to/samtools

symbol_assignment
['picard', '/path/to/picard']
- name: picard
- value: /path/to/picard

task_definition
['task1', 'des:', 'description ', 'path:', '/path/to/task1 ', 'para:', 
 '$global.samtools', '$args.input', '$path']
- des: description 
- para: ['$global.samtools', '$args.input', '$path']
- path: /path/to/task1 
- target: task1

task_definition
['task2', 'task1']
- deps: ['task1']
- target: task2

The dump() output shows you what names you can use to get at the fields within the parsed elements, or to distinguish what kind of element you have. dump() is a handy, generic tool to output whatever pyparsing has parsed. Here is some code that is more specific to your particular parser, showing how to use the field names as either dotted object references (element.target, element.deps, element.name, etc.) or dict-style references (element[key]):

for element in makefile_parser.parseString(test):
    if element.getName() == 'task_definition':
        print "TASK:", element.target,
        if element.deps:
            print "DEPS:(" + ','.join(element.deps) + ")"
        else:
            print
        for key in ('des', 'path', 'para'):
            if key in element:
                print " ", key.upper()+":", element[key]

    elif element.getName() == 'symbol_assignment':
        print "SYM:", element.name, "->", element.value

prints:

SYM: samtools -> /path/to/samtools
SYM: picard -> /path/to/picard
TASK: task1
  DES: description 
  PATH: /path/to/task1 
  PARA: ['$global.samtools', '$args.input', '$path']
TASK: task2 DEPS:(task1)

score 3 · Answer 2 · answered Jun 13 '12 at 05:17

3

I've used pyparsing in the past and been immensely pleased with it (q.v., the pyparsing project site).

answered Jun 13 '12 at 05:17

Greg E.

2,722
1
16
22

Your link is dead. (Which is also the reason an answer should consist of more than just a link.) – zrajm Jan 04 '19 at 12:00
The `pyparsing' module can be found at [pyparsing](https://pythonhosted.org/pyparsing/pyparsing-module.html) as of 2021-01. – D McKeon Jan 29 '21 at 16:41

Any python module for customized BNF parser?

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