Replace message on ParseException.

Increment version number.

Author: donkirkby

README.md

@@ -91,11 +91,14 @@ The `vcf` module has basic helper functions for construction lists of mutation
 calls:
 
 ```
-from pyvdrm.vcf import call_mutations
+from pyvdrm.vcf import VariantCalls
 from pyvdrm.asi2 import ASI2
 
-ref = "APITAYAQQTRGLLGCIITSLTGRD"
-sample = "APITAYAQQTRGLLTCIITSLTGRD"
+calls = VariantCalls(reference="APITAYAQQTRGLLGCIITSLTGRD",
+                     sample=   "APITAYAQQTRGLLTCIITSLTGRD")
+# mutation G15T ------------------------------^
 
-score = rule(call_mutations(ref, sample))
+rule = ASI2('SCORE FROM ( G15T => 5 )')
+score = rule(calls)
+print(score)  # => 5
 ```

pyvdrm/asi2.py

@@ -4,7 +4,7 @@
 
 from functools import reduce, total_ordering
 from pyparsing import (Literal, nums, Word, Forward, Optional, Regex,
-                       infixNotation, delimitedList, opAssoc)
+                       infixNotation, delimitedList, opAssoc, ParseException)
 from pyvdrm.drm import AsiExpr, AsiBinaryExpr, AsiUnaryExpr, DRMParser
 from pyvdrm.vcf import MutationSet
 
@@ -299,4 +299,8 @@ def parser(self, rule):
 
         statement = booleancondition | scorecondition
 
-        return statement.parseString(rule)
+        try:
+            return statement.parseString(rule)
+        except ParseException as ex:
+            ex.msg = 'Error in ASI2: ' + ex.markInputline()
+            raise

pyvdrm/hcvr.py

@@ -4,7 +4,7 @@
 
 from functools import reduce, total_ordering
 from pyparsing import (Literal, nums, Word, Forward, Optional, Regex,
-                       infixNotation, delimitedList, opAssoc, alphas)
+                       infixNotation, delimitedList, opAssoc, alphas, ParseException)
 from pyvdrm.drm import AsiExpr, AsiBinaryExpr, AsiUnaryExpr, DRMParser
 from pyvdrm.vcf import MutationSet
 
@@ -329,4 +329,8 @@ def parser(self, rule):
 
         statement = booleancondition | scorecondition
 
-        return statement.parseString(rule)
+        try:
+            return statement.parseString(rule)
+        except ParseException as ex:
+            ex.msg = 'Error in HCVR: ' + ex.markInputline()
+            raise

pyvdrm/tests/test_asi2.py

@@ -1,4 +1,7 @@
 import unittest
+
+from pyparsing import ParseException
+
 from pyvdrm.asi2 import ASI2, AsiMutations, Score
 from pyvdrm.vcf import Mutation, MutationSet, VariantCalls
 
@@ -99,6 +102,29 @@ def test_score_from_exactly(self):
         score = rule(VariantCalls("2T 7Y 1G"))
         self.assertEqual(0, score)
 
+    def test_parse_exception(self):
+        expected_error_message = (
+            "Error in ASI2: SCORE FROM ( 10R => 2>!<;0 ) (at char 21), (line:1, col:22)")
+
+        with self.assertRaises(ParseException) as context:
+            ASI2("SCORE FROM ( 10R => 2;0 )")
+
+        self.assertEqual(expected_error_message, str(context.exception))
+
+    def test_parse_exception_multiline(self):
+        rule = """\
+SCORE FROM (
+    10R => 2;0
+)
+"""
+        expected_error_message = (
+            "Error in ASI2: 10R => 2>!<;0 (at char 25), (line:2, col:13)")
+
+        with self.assertRaises(ParseException) as context:
+            ASI2(rule)
+
+        self.assertEqual(expected_error_message, str(context.exception))
+
 
 class TestActualRules(unittest.TestCase):
     def test_hivdb_rules_parse(self):

pyvdrm/tests/test_hcvr.py

@@ -1,5 +1,7 @@
-import sys
 import unittest
+
+from pyparsing import ParseException
+
 from pyvdrm.hcvr import HCVR, AsiMutations, Score
 from pyvdrm.vcf import Mutation, MutationSet, VariantCalls
 
@@ -120,6 +122,30 @@ def test_score_comment(self):
         self.assertEqual(result.score, 3)
         self.assertTrue("flag1 with_space" in result.flags)
 
+    def test_parse_exception(self):
+        expected_error_message = (
+            "Error in HCVR: SCORE FROM ( 10R => 2>!<;0 ) (at char 21), (line:1, col:22)")
+
+        with self.assertRaises(ParseException) as context:
+            HCVR("SCORE FROM ( 10R => 2;0 )")
+
+        self.assertEqual(expected_error_message, str(context.exception))
+
+    def test_parse_exception_multiline(self):
+        rule = """\
+SCORE FROM (
+    10R => 2;0
+)
+"""
+        expected_error_message = (
+            "Error in HCVR: 10R => 2>!<;0 (at char 25), (line:2, col:13)")
+
+        with self.assertRaises(ParseException) as context:
+            HCVR(rule)
+
+        self.assertEqual(expected_error_message, str(context.exception))
+
+
 class TestActualRules(unittest.TestCase):
     def test_hivdb_rules_parse(self):
         for line in open("pyvdrm/tests/HIVDB.rules"):
@@ -210,5 +236,6 @@ def test_true_positive(self):
         expected_repr = "[Mutation('Q54H'), Mutation('444H')]"
         self.assertEqual(expected_repr, repr(sorted(dtree.residues)))
 
+
 if __name__ == '__main__':
     unittest.main()

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='pyvdrm',
-    version='0.1.1',
+    version='0.2.0',
     description='',
 
     url='',