Added resources and scripts

bin/ebnf_to_parsers.py-fixme

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+
+######################
+TODO Copied here from BEL module - needs to be re-worked to operate in bel_specifications repository
+######################
+
+
+Usage: python yaml_to_ebnf.py <version> <path to output .ebnf file>
+
+Use this script to convert the user defined YAML file to two other files:
+    - an EBNF file used by Tatsu to compile into a parser (syntax)
+"""
+
+import click
+import tatsu
+import glob
+import os
+
+root_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+
+
+@click.command()
+@click.option('--parser_fn', help='Specify resulting BEL Parser filename')
+@click.option('--ebnf_fn', help='Specify EBNF input filename')
+def main(ebnf_fn, parser_fn):
+    """Create BEL Parser file from EBNF file
+
+    If you do not specify any options, then this will process all of the BEL EBNF
+    files in bel/lang/versions into EBNF files
+    """
+    if ebnf_fn:
+        files = glob.glob(f'{root_dir}/{ebnf_fn}')
+    else:
+        files = glob.glob(f'{root_dir}/bel/lang/versions/bel_v*ebnf')
+
+    for fn in files:
+        if parser_fn is None:
+            parser_fn = fn.replace('bel_v', 'parser_v').replace('ebnf', 'py')
+
+        with open(fn, 'r') as f:
+            grammar = f.read()
+
+        print('Creating Parser:', parser_fn)
+        parser = tatsu.to_python_sourcecode(grammar, filename=parser_fn)
+        with open(parser_fn, 'wt') as f:
+            f.write(parser)
+
+
+if __name__ == '__main__':
+    main()

bin/make_test_parser.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+
+
+# non-version specific variables ---------------------------------------------------------------------------------------
+
+EBNF_TEMPLATE_FILE="dev/bel.ebnf.j2"
+SCRIPT_TO_TEST_PARSER="dev/parser_testing.py"
+YAML_TO_EBNF_SCRIPT="dev/yaml_to_ebnf.py"
+MULTIPLE_TEST_STATEMENTS="test/bel2_test_statements.txt"
+SINGLE_TEST_STATEMENT="test/bel2_test_statement.txt"
+
+
+# versions -------------------------------------------------------------------------------------------------------------
+
+VERSIONS=(2_0_0 2_0_1)
+
+
+# build all versions ---------------------------------------------------------------------------------------------------
+
+for v in "${VERSIONS[@]}"
+do
+
+    EBNF_SYNTAX_FILE="bel/lang/versions/bel_v$v.ebnf"
+    PARSER_PY_FILE="bel/lang/versions/parser_v$v.py"
+    YAML_FILE_NAME="bel/lang/versions/bel_v$v.yaml"
+
+    printf "\nBUILDING VERSION %s ********************************************************\n\n" "$v"
+
+    if [[ ! -f ${YAML_FILE_NAME} ]] ; then
+        printf "ERROR: %s does not exist! Exiting.\n" "${YAML_FILE_NAME}"
+        exit
+    fi
+
+    printf "1. Generating syntax EBNF file from YAML...\n"
+
+    python yaml_to_ebnf.py "$YAML_FILE_NAME" "$EBNF_TEMPLATE_FILE" "$EBNF_SYNTAX_FILE"
+
+    printf "2. Generated in %s.\n" "$EBNF_SYNTAX_FILE"
+    printf "3. Generating parser file from syntax EBNF file...\n"
+
+    python -m tatsu --generate-parser --outfile "$PARSER_PY_FILE" "$EBNF_SYNTAX_FILE"
+
+    printf "4. Generated in %s.\n" "$PARSER_PY_FILE"
+    printf "5. Complete!\n\n\n"
+
+done
+
+
+# testing --------------------------------------------------------------------------------------------------------------
+# python "$SCRIPT_TO_TEST_PARSER" "$SINGLE_TEST_STATEMENT"
+# python "$SCRIPT_TO_TEST_PARSER" "$MULTIPLE_TEST_STATEMENTS"

bin/yaml_to_ebnf.py-fixme

@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+
+######################
+TODO Copied here from BEL module - needs to be re-worked to operate in bel_specifications repository
+######################
+
+
+Usage: python yaml_to_ebnf.py <version> <path to output .ebnf file>
+
+Use this script to convert the user defined YAML file to two other files:
+    - an EBNF file used by Tatsu to compile into a parser (syntax)
+"""
+
+import datetime
+import logging
+import glob
+import os.path
+import click
+from bel.lang.bel_specification import get_specification
+from jinja2 import Environment, FileSystemLoader
+
+log = logging.getLogger(__name__)
+
+root_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+tmpl_fn = 'bel.ebnf.j2'
+
+
+def render_ebnf(tmpl_fn, bel_version, created_time, bel_spec):
+
+    specs = get_specification(bel_version)
+
+    tmpl_dir = os.path.dirname(tmpl_fn)
+    tmpl_basename = os.path.basename(tmpl_fn)
+
+    bel_major_version = bel_version.split('.')[0]
+
+    env = Environment(loader=FileSystemLoader(tmpl_dir))  # create environment for template
+    template = env.get_template(tmpl_basename)  # get the template
+
+    # replace template placeholders with appropriate variables
+    functions_list = sorted(specs['functions']['primary']['list_short'] + specs['functions']['primary']['list_long'])
+    modifiers_list = sorted(specs['functions']['modifier']['list_short'] + specs['functions']['modifier']['list_long'])
+    ebnf = template.render(functions=sorted(functions_list, key=len, reverse=True),
+                           m_functions=sorted(modifiers_list, key=len, reverse=True),
+                           relations=sorted(specs['relations']['list'], key=len, reverse=True),
+                           bel_version=bel_version,
+                           bel_major_version=bel_major_version,
+                           created_time=created_time)
+
+    return ebnf
+
+
+def get_version(belspec_fn: str) -> str:
+    """Recover version number from belspec_fn"""
+
+    version = os.path.basename(belspec_fn).replace('bel_v', '').replace('.yaml', '').replace('_', '.')
+    return version
+
+
+def save_ebnf(ebnf_fn, ebnf):
+    with open(ebnf_fn, 'w') as f:
+        f.write(ebnf)
+
+
+@click.command()
+@click.option('--belspec_fn', help='BEL Language Specification filename')
+@click.option('--ebnf_fn', help='Specify EBNF filename')
+@click.option('--ebnf_tmpl_fn', default="./bel/lang/versions/bel.ebnf.j2", help='EBNF template filename')
+def main(belspec_fn, ebnf_fn, ebnf_tmpl_fn):
+    """Create EBNF files from BEL Specification yaml files and template
+
+    If you do not specify any options, then this will process all of the BEL Specification
+    files in bel/lang/versions into EBNF files
+    """
+    created_time = datetime.datetime.now().strftime('%B %d, %Y - %I:%M:%S%p')
+
+    if belspec_fn:
+        bel_version = get_version(belspec_fn)
+        if not ebnf_fn:
+            ebnf_fn = belspec_fn.replace('yaml', 'ebnf')
+            print(f'EBNF output file name is: {ebnf_fn}')
+
+        ebnf = render_ebnf(ebnf_tmpl_fn, bel_version, created_time, belspec_fn)
+        print(ebnf_fn)
+        save_ebnf(ebnf_fn, ebnf)
+
+    else:
+        files = glob.glob(f'{root_dir}/bel/lang/versions/bel_v*yaml')
+        for fn in files:
+            bel_version = get_version(fn)
+            bel_spec = get_specification(bel_version)
+            ebnf = render_ebnf(tmpl_fn, bel_version, created_time, bel_spec)
+            ebnf_fn = fn.replace('yaml', 'ebnf')
+            save_ebnf(ebnf_fn, ebnf)
+
+
+if __name__ == '__main__':
+    main()

resources/bel.ebnf.j2

@@ -0,0 +1,63 @@
+@@grammar::BEL
+@@parseinfo :: True
+
+##############
+#  METADATA  #
+##############
+
+# BEL VERSION: {{ bel_version }}
+# EBNF CREATION TIMESTAMP: {{ created_time }}
+
+#########################
+#  GRAMMAR DEFINITIONS  #
+#########################
+
+start = bel_statement $ ;
+bel_statement = subject:function ~ [relation:relation ~ object:obj] ;
+
+obj = (function | enclosed_statement) ;
+enclosed_statement = function_open bel_statement:bel_statement function_close ;
+
+##### FUNCTIONS #####
+
+function = function:funcs function_open function_args:f_args function_close ;
+funcs =
+    {% for function in functions %}'{{ function }}'{{ " | " if not loop.last }}{% endfor %} ;
+
+f_args = ','.{(function | modifier_function | namespace_arg | string_arg)}* ;
+
+##### MODIFIER FUNCTIONS #####
+
+modifier_function = modifier:m_funcs function_open modifier_args:m_args function_close ;
+m_funcs =
+    {% for modifier in m_functions %}'{{ modifier }}'{{ " | " if not loop.last }}{% endfor %} ;
+
+m_args = ','.{(function | namespace_arg | string_arg)}* ;
+
+##### RELATIONSHIPS #####
+
+relation = relations ;
+relations =
+    {% for relation in relations %}'{{ relation }}'{{ " | " if not loop.last }}{% endfor %} ;
+
+##### MISCELLANEOUS #####
+
+namespace_arg = ns_arg:full_nsv ;
+full_nsv = ns:ns_string ':' ns_value:(quoted_string | string) ;
+
+string_arg = str_arg:full_string ;
+full_string = (quoted_string | string) ;
+
+
+
+# quoted_string: Matches like any string but requires it to be in quotation marks.
+quoted_string = /\"(?:[^"\\]|\\.)*\"/ ;
+
+# string: Matches any char other than space, comma or ')'
+string = /[^\s\),]+/ ;
+
+# ns_string: Matches any capital letter or digit.
+ns_string = /[A-Z0-9]+/ ;
+
+function_open = '(' ;
+function_close = ')' ;