feat: add code for getting values needed for hl7 v2 from a va-spec statement

Author: katie-perry

src/biocommons/gks-conversion-tool/converter.py

@@ -1,11 +1,53 @@
-"""Converter for GKS <-> HL7"""
+"""Converter for GKS <-> HL7 v2"""
 
 import logging
+from ga4gh.va_spec.base.core import (
+    Statement,
+)
 
 _logger = logging.getLogger(__name__)
 
 
-def convert_gks_to_hl7(statement) -> dict:
-    """convert GKS to HL7"""
+def convert_gks_to_hl7_v2(statement: Statement) -> dict:
+    """convert GKS to HL7 v2"""
+    
+    proposition = statement.proposition
+    subject_variant = proposition.subjectVariant
+
+    # 504 - Variant Name
+    variant_name = subject_variant.name
+
+    # 505 - Discrete Genetic Variant
+    # wait for types and models for this
+
+    # 510 - Chromosome
+    members = subject_variant.members
+    genomic_allele = None
+    genomic_location = None
+    for allele in members:
+        # get member where the allele's location's sequence reference's moleculeType is genomic
+        genomic_location = allele.location
+        sequence_reference = genomic_location.sequenceReference
+        if sequence_reference.moleculeType == "genomic":
+            genomic_allele = allele
+            break
+    # get chromosome from allele
+    expressions = genomic_allele.expressions
+    expression = None
+    for expr in expressions:
+        if expr.get("syntax") == "hgvs.g":
+            expression = expr
+            break
+    g_dot_hgvs = expression.get("value")
+    g_dot_split = g_dot_hgvs.split(":", 2)
+    chromosome = g_dot_split[0]
+    g_dot = g_dot_split[1]
+
+    # 511 - Allele start/end
+    allele_start = genomic_location.start
+    allele_end = genomic_location.end
+
+    # TODO: finish tomorrow? :-)
+
 
     return {}