Fix branches in parsing GenomicInterpretation. Test parsing HGVS expr…

…ession.

src/genophenocorr/preprocessing/_phenopacket.py

@@ -47,7 +47,7 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC
         variant_descriptor = item.variant_interpretation.variation_descriptor
 
         vc = None
-        if variant_descriptor.vcf_record.IsInitialized():
+        if self._vcf_is_available(variant_descriptor.vcf_record):
             # We have a VCF record.
             contig = self._build.contig_by_name(variant_descriptor.vcf_record.chrom)
             start = int(variant_descriptor.vcf_record.pos) - 1
@@ -58,9 +58,10 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC
 
             region = GenomicRegion(contig, start, end, Strand.POSITIVE)
             vc = VariantCoordinates(region, ref, alt, change_length)
-        elif variant_descriptor.variation.IsInitialized():
+        elif self._cnv_is_available(variant_descriptor.variation):
             # We have a CNV.
-            seq_location = variant_descriptor.variation.copy_number.allele.sequence_location
+            variation = variant_descriptor.variation
+            seq_location = variation.copy_number.allele.sequence_location
             refseq_contig_name = seq_location.sequence_id.split(':')[1]
             contig = self._build.contig_by_name(refseq_contig_name)
 
@@ -69,7 +70,7 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC
             start = int(seq_location.sequence_interval.start_number.value) - 1
             end = int(seq_location.sequence_interval.end_number.value)
             ref = 'N'
-            number = int(variant_descriptor.variation.copy_number.number.value)
+            number = int(variation.copy_number.number.value)
             if number > 2:
                 alt = '<DUP>'
             else:
@@ -84,8 +85,8 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC
                 if expression.syntax == 'hgvs.c':
                     vc = self._hgvs_finder.find_coordinates(expression.value)
                     break
-        else:
-            # No way we can get something from this `GenomicInterpretation`!
+
+        if vc is None:
             raise ValueError('Expected a VCF record, a VRS CNV, or an expression with `hgvs.c` '
                              'but did not find one')
 
@@ -95,6 +96,25 @@ def find_coordinates(self, item: GenomicInterpretation) -> typing.Tuple[VariantC
 
         return vc, gt
 
+    @staticmethod
+    def _vcf_is_available(vcf_record) -> bool:
+        """
+        Check if we can parse data out of VCF record.
+        """
+        return (vcf_record.genome_assembly != ''
+                and vcf_record.chrom != ''
+                and vcf_record.pos >= 0
+                and vcf_record.ref != ''
+                and vcf_record.alt != '')
+
+    @staticmethod
+    def _cnv_is_available(variation):
+        seq_location = variation.copy_number.allele.sequence_location
+        return (seq_location.sequence_id != ''
+                and seq_location.sequence_interval.start_number.value >= 0
+                and seq_location.sequence_interval.end_number.value >= 0
+                and variation.copy_number.number.value != '')
+
     @staticmethod
     def _map_geno_genotype_label(genotype: str) -> Genotype:
         """

src/genophenocorr/preprocessing/_test_variant.py

@@ -7,36 +7,50 @@
 # pyright: reportGeneralTypeIssues=false
 from phenopackets import Phenopacket, GenomicInterpretation
 
-from genophenocorr.model.genome import GRCh38
+from genophenocorr.model.genome import GenomeBuild, GRCh38
 
+from ._api import VariantCoordinateFinder
 from ._phenopacket import PhenopacketVariantCoordinateFinder
 from ._protein import ProteinAnnotationCache, ProtCachingFunctionalAnnotator
 from ._uniprot import UniprotProteinMetadataService
 from ._variant import VariantAnnotationCache, VarCachingFunctionalAnnotator
 from ._vep import VepFunctionalAnnotator
+from ._vv import VVHgvsVariantCoordinateFinder
 
 
 @pytest.fixture
-def pp_vc_finder() -> PhenopacketVariantCoordinateFinder:
-    return PhenopacketVariantCoordinateFinder(GRCh38)
+def build() -> GenomeBuild:
+    return GRCh38
+
+
+@pytest.fixture
+def hgvs_vc_finder(build: GenomeBuild) -> VariantCoordinateFinder:
+    return VVHgvsVariantCoordinateFinder(build)
+
+
+@pytest.fixture
+def pp_vc_finder(build: GenomeBuild,
+                 hgvs_vc_finder: VariantCoordinateFinder) -> PhenopacketVariantCoordinateFinder:
+    return PhenopacketVariantCoordinateFinder(build, hgvs_vc_finder)
 
 
 @pytest.mark.parametrize("pp_path, expected",
                          [('test_data/deletion_test.json', '16_89284129_89284134_CTTTTT_C'),
-                          ('test_data/insertion_test.json', '16_89280829_89280830_C_CA'),
+                          ('test_data/insertion_test.json', '16_89280829_89280829_C_CA'),
                           ('test_data/missense_test.json', '16_89279135_89279135_G_C'),
-                          ('test_data/duplication_test.json', '16_89279850_89279851_G_GC'),
+                          ('test_data/missense_hgvs_test.json', '16_89279135_89279135_G_C'),
+                          ('test_data/duplication_test.json', '16_89279850_89279850_G_GC'),
                           ('test_data/delinsert_test.json', '16_89284601_89284602_GG_A'),
-                          ('test_data/CVDup_test.json', '16_89284524_89373231_DUP'),
-                          ('test_data/CVDel_test.json', '16_89217282_89506042_DEL')
+                          ('test_data/CVDup_test.json', '16_89284523_89373231_DUP'),
+                          ('test_data/CVDel_test.json', '16_89217281_89506042_DEL')
                           ])
 def test_find_coordinates(pp_path, expected, pp_vc_finder):
     fname = resource_filename(__name__, pp_path)
     gi = read_genomic_interpretation_json(fname)
 
     vc, gt = pp_vc_finder.find_coordinates(gi)
 
-    assert expected == vc.variant_key
+    assert vc.variant_key == expected
 
 
 def read_genomic_interpretation_json(fpath: str) -> GenomicInterpretation: