Updated EBNF creation scripts for bel_spec refactor

belbio · Jan 20, 2018 · b8d7784 · b8d7784
1 parent 492fdc2
commit b8d7784
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/bel/lang/versions/bel_v2_0_0.ebnf b/bel/lang/versions/bel_v2_0_0.ebnf
@@ -6,7 +6,7 @@
 ##############
 
 # BEL VERSION: 2.0.0
-# EBNF CREATION TIMESTAMP: December 29, 2017 - 10:50:19PM
+# EBNF CREATION TIMESTAMP: January 19, 2018 - 07:20:38PM
 
 #########################
 #  GRAMMAR DEFINITIONS  #
@@ -22,7 +22,7 @@ enclosed_statement = function_open bel_statement:bel_statement function_close ;
 
 function = function:funcs function_open function_args:f_args function_close ;
 funcs =
-    'cellSurfaceExpression' | 'compositeAbundance' | 'biologicalProcess' | 'microRNAAbundance' | 'complexAbundance' | 'proteinAbundance' | 'cellSecretion' | 'geneAbundance' | 'translocation' | 'rnaAbundance' | 'degradation' | 'abundance' | 'composite' | 'pathology' | 'activity' | 'reaction' | 'complex' | 'surf' | 'list' | 'list' | 'path' | 'tloc' | 'act' | 'sec' | 'deg' | 'rxn' | 'bp' | 'a' | 'g' | 'm' | 'p' | 'r' ;
+    'cellSurfaceExpression' | 'compositeAbundance' | 'biologicalProcess' | 'microRNAAbundance' | 'complexAbundance' | 'proteinAbundance' | 'cellSecretion' | 'geneAbundance' | 'translocation' | 'rnaAbundance' | 'degradation' | 'abundance' | 'composite' | 'pathology' | 'activity' | 'reaction' | 'complex' | 'list' | 'list' | 'path' | 'surf' | 'tloc' | 'act' | 'deg' | 'rxn' | 'sec' | 'bp' | 'a' | 'g' | 'm' | 'p' | 'r' ;
 
 f_args = ','.{(function | modifier_function | namespace_arg | string_arg)}* ;
 

diff --git a/bel/lang/versions/parser_v2_0_0.py b/bel/lang/versions/parser_v2_0_0.py
@@ -171,24 +171,24 @@ def _funcs_(self):  # noqa
                 self._token('reaction')
             with self._option():
                 self._token('complex')
-            with self._option():
-                self._token('surf')
             with self._option():
                 self._token('list')
             with self._option():
                 self._token('list')
             with self._option():
                 self._token('path')
+            with self._option():
+                self._token('surf')
             with self._option():
                 self._token('tloc')
             with self._option():
                 self._token('act')
-            with self._option():
-                self._token('sec')
             with self._option():
                 self._token('deg')
             with self._option():
                 self._token('rxn')
+            with self._option():
+                self._token('sec')
             with self._option():
                 self._token('bp')
             with self._option():

diff --git a/bin/yaml_to_ebnf.py b/bin/yaml_to_ebnf.py
@@ -35,9 +35,11 @@ def render_ebnf(tmpl_fn, bel_version, created_time, bel_spec):
     template = env.get_template(tmpl_basename)  # get the template
 
     # replace template placeholders with appropriate variables
-    ebnf = template.render(functions=sorted(specs['function_list'], key=len, reverse=True),
-                           m_functions=sorted(specs['modifier_list'], key=len, reverse=True),
-                           relations=sorted(specs['relation_list'], key=len, reverse=True),
+    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)