Multiple repeats syntax

massql/msql.ebnf

@@ -142,7 +142,9 @@ factor: floating
     | "aminoaciddelta(" aminoacids ")"
     | peptidefunction
     | "(" numericalexpression ")"
+    | multiplefunction
 peptidefunction: "peptide(" peptide "," "charge=" peptidecharge "," "ion=" peptideion ")"
+multiplefunction: "multiple(mz=" factor "," "min=" multiplenumber "," "max=" multiplenumber ")"
 multiply: "*"
 divide: "/"
 plus: "+"
@@ -154,6 +156,8 @@ peptide: /[A-Z][A-Z]*/
 peptidecharge: /[1-9]/
 peptideion: /[A-Za-z]/
 
+multiplenumber: /[1-9][0-9]*/
+
 // Boiler Plate
 %import common.ESCAPED_STRING   -> STRING
 %import common.SIGNED_NUMBER    -> NUMBER

massql/msql_parser.py

@@ -116,6 +116,18 @@ def mobilityfunction(self, items):
 
    def mobilityrange(self, items):
       return "mobilityrange"
+
+   def multiplenumber(self, items):
+      return int(items[0])
+
+   def multiplefunction(self, items):
+      multiple_repeater_dict = {}
+      multiple_repeater_dict["type"] = "multiple"
+      multiple_repeater_dict["mz"] = items[0]
+      multiple_repeater_dict["min"] = items[1]
+      multiple_repeater_dict["max"] = items[2]
+
+      return multiple_repeater_dict
 
    def qualifier(self, items):
       if len(items) == 1 and items[0] == "qualifierintensityreference":
@@ -375,12 +387,26 @@ def numericalexpression(self, items):
          return items[0]
 
       has_variable = _has_variable(items)
+      has_multiple = _has_multiple(items)
 
       string_items = [str(item) for item in items]
       full_expression = "".join(string_items)
 
       if has_variable:
          return full_expression
+
+      if has_multiple:
+         # then we are going to expand this into an OR query         
+         mz = items[-1]["mz"]
+         min_value = items[-1]["min"]
+         max_value = items[-1]["max"]
+
+         all_mz_values = []
+         for i in range(min_value, max_value+1):
+            actual_mz = mz*i
+            all_mz_values.append(actual_mz)
+
+         return all_mz_values
 
       # Calculating the expression
       calculated_value = math_parser.parse(full_expression).evaluate({})
@@ -429,8 +455,6 @@ def peptidefunction(self, items):
       exact_mass = mass.calculate_mass(sequence=items[0], ion_type=items[2].lower(), charge=int(items[1]))
       return exact_mass
 
-
-
    def string(self, s):
       (s,) = s
       return s[1:-1]
@@ -450,6 +474,15 @@ def _has_variable(items):
 
    return False 
 
+def _has_multiple(items):
+   for item in items:
+      if isinstance(item, dict):
+         if "type" in item:
+            if item["type"] == "multiple":
+               return True
+
+   return False
+
 def _visualize_parse(input_query, path_to_grammar=None, output_filename="parse.png"):
    if path_to_grammar is None:
       path_to_grammar = os.path.join(os.path.dirname(__file__), "msql.ebnf")

tests/test_parse.py

@@ -229,13 +229,21 @@ def test_or_cardinality():
     print(parsed_output)
 
 
+def test_repeat_parse():
+    query = """
+        QUERY scaninfo(MS2DATA) WHERE MS2PROD=(formula(C3H5O2C2H6) + multiple(mz=formula(CH2),min=2, max=60) )
+    """
 
+    parsed_output = msql_parser.parse_msql(query)
+    print(parsed_output)
 
 
 
 def main():
+    test_repeat_parse()
+    #test_ms1_multiple_or_with_variable()
     #test_xrange_parse()
-    test_parse()
+    #test_parse()
     #test_comment_parse()
     #test_number_expression_parse()
     #test_formula_expression_parse()