Resolve String Error Code Usages

PiperOrigin-RevId: 392461789

Author: Genomics team in Google Brain

Diff for: nucleus/io/python/bed_reader_wrap_test.py

@@ -66,11 +66,8 @@ def test_bed_iterate(self):
       self.assertEqual(zactual[0], self.first)
 
   def test_from_file_raises_with_missing_bed(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'NOT_FOUND: Could not open missing.bed'):
-    with self.assertRaisesRegexp(ValueError,
-                                   'Could not open missing.bed'):
+    # TODO(b/196638558): OpError exception not propagated.
+    with self.assertRaisesRegexp(ValueError, 'Could not open missing.bed'):
       bed_reader.BedReader.from_file('missing.bed', self.options)
 
   def test_ops_on_closed_reader_raise(self):

Diff for: nucleus/io/python/fastq_reader_wrap_test.py

@@ -42,11 +42,8 @@ def test_fastq_iterate(self, filename):
       self.assertEqual(test_utils.iterable_len(iterable), 4)
 
   def test_from_file_raises_with_missing_fastq(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'NOT_FOUND: Could not open missing.fastq'):
-    with self.assertRaisesRegexp(ValueError,
-                                 'Could not open missing.fastq'):
+    # TODO(b/196638558): OpError exception not propagated.
+    with self.assertRaisesRegexp(ValueError, 'Could not open missing.fastq'):
       fastq_reader.FastqReader.from_file('missing.fastq', self.options)
 
   def test_ops_on_closed_reader_raise(self):

Diff for: nucleus/io/python/gff_reader_wrap_test.py

@@ -61,11 +61,8 @@ def test_gff_iterate(self, test_features_gff_filename):
       self.assertEqual(actual[1], self.second)
 
   def test_from_file_raises_with_missing_gff(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'NOT_FOUND: Could not open missing.gff'):
-    with self.assertRaisesRegexp(ValueError,
-                                 'Could not open missing.gff'):
+    # TODO(b/196638558): OpError exception not propagated.
+    with self.assertRaisesRegexp(ValueError, 'Could not open missing.gff'):
       gff_reader.GffReader.from_file('missing.gff', self.options)
 
   def test_ops_on_closed_reader_raise(self):

Diff for: nucleus/io/python/reference_wrap_test.py

@@ -66,13 +66,9 @@ def test_from_file_raises_with_missing_inputs(self, fasta_filename,
                                                 fai_filename):
     fasta = test_utils.genomics_core_testdata(fasta_filename)
     fai = test_utils.genomics_core_testdata(fai_filename)
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(
-    #     ValueError,
-    #     'NOT_FOUND: could not load fasta and/or fai for fasta ' + fasta):
+    # TODO(b/196638558): OpError exception not propagated.
     with self.assertRaisesRegexp(
-        ValueError,
-        'could not load fasta and/or fai for fasta ' + fasta):
+        ValueError, 'could not load fasta and/or fai for fasta ' + fasta):
       reference.IndexedFastaReader.from_file(fasta, fai,
                                              fasta_pb2.FastaReaderOptions())
 

Diff for: nucleus/io/python/sam_reader_wrap_test.py

@@ -130,11 +130,8 @@ def test_context_manager(self):
         self.assertIsInstance(query_iterable2, clif_postproc.WrappedCppIterable)
 
   def test_from_file_raises_with_missing_bam(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegex(ValueError,
-    #                             'NOT_FOUND: Could not open missing.bam'):
-    with self.assertRaisesRegex(ValueError,
-                                'Could not open missing.bam'):
+    # TODO(b/196638558): OpError exception not propagated.
+    with self.assertRaisesRegex(ValueError, 'Could not open missing.bam'):
       sam_reader.SamReader.from_file(
           reads_path='missing.bam', ref_path='', options=self.options)
 

Diff for: nucleus/io/python/vcf_reader_wrap_test.py

@@ -191,11 +191,8 @@ def test_vcf_from_string_raises_on_bad_input(self):
       self.samples_reader.from_string('BAD NOT A VCF RECORD\n;;')
 
   def test_from_file_raises_with_missing_source(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'NOT_FOUND: Could not open missing.vcf'):
-    with self.assertRaisesRegexp(ValueError,
-                               'Could not open missing.vcf'):
+    # TODO(b/196638558): OpError exception not propagated.
+    with self.assertRaisesRegexp(ValueError, 'Could not open missing.vcf'):
       vcf_reader.VcfReader.from_file('missing.vcf', self.options)
 
   def test_ops_on_closed_reader_raise(self):

Diff for: nucleus/vendor/python/statusor_examples_test.py

@@ -26,8 +26,7 @@ def test_make_int_ok(self):
     self.assertEqual(statusor_examples.MakeIntOK(), 42)
 
   def test_make_int_fail(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError, 'INVALID_ARGUMENT: MakeIntFail'):
+    # TODO(b/196638558): OpError exception not propagated.
     with self.assertRaisesRegexp(ValueError, 'MakeIntFail'):
       statusor_examples.MakeIntFail()
 
@@ -39,39 +38,32 @@ def test_make_str_ok(self):
   #   self.assertEqual(statusor_examples.MakeStrOKStrippedType(), 'hello')
 
   def test_make_str_fail(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError, 'INVALID_ARGUMENT: MakeStrFail'):
+    # TODO(b/196638558): OpError exception not propagated.
     with self.assertRaisesRegexp(ValueError, 'MakeStrFail'):
       statusor_examples.MakeStrFail()
 
   def test_make_int_unique_ptr_ok(self):
     self.assertEqual(statusor_examples.MakeIntUniquePtrOK(), 421)
 
   def test_make_int_unique_ptr_fail(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'INVALID_ARGUMENT: MakeIntUniquePtrFail'):
+    # TODO(b/196638558): OpError exception not propagated.
     with self.assertRaisesRegexp(ValueError, 'MakeIntUniquePtrFail'):
       statusor_examples.MakeIntUniquePtrFail()
 
   def test_make_int_vector_ok(self):
     self.assertEqual(statusor_examples.MakeIntVectorOK(), [1, 2, 42])
 
   def test_make_int_vector_fail(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'INVALID_ARGUMENT: MakeIntVectorFail'):
+    # TODO(b/196638558): OpError exception not propagated.
     with self.assertRaisesRegexp(ValueError, 'MakeIntVectorFail'):
       statusor_examples.MakeIntVectorFail()
 
   def test_returning_status_ok_returns_none(self):
     self.assertEqual(statusor_examples.FuncReturningStatusOK(), None)
 
   def test_returning_status_fail_raises(self):
-    # TODO(b/194924033): Swap statement after error code string is updated
-    # with self.assertRaisesRegexp(ValueError,
-    #                              'INVALID_ARGUMENT: FuncReturningStatusFail'):
-    with self.assertRaisesRegexp(ValueError,'FuncReturningStatusFail'):
+    # TODO(b/196638558): OpError exception not propagated.
+    with self.assertRaisesRegexp(ValueError, 'FuncReturningStatusFail'):
       statusor_examples.FuncReturningStatusFail()