Pydantic models for OBX Segments

Pydantic models for OBX Segments

Author: katie-perry

pyproject.toml

@@ -34,7 +34,8 @@ dependencies = [
   "ga4gh.cat_vrs~=0.7.1",
   "ga4gh.va_spec~=0.4.2",
   "ga4gh.vrs==2.1.3",
-  "pyyaml ~= 6.0"
+  "pyyaml ~= 6.0",
+  "pydantic==2.*"
 ]
 description = "biocommons.example package (namespaced)"
 dynamic = ["version"]

src/biocommons/models.py

@@ -1 +1,68 @@
+from pydantic import BaseModel
+
 """A file for models used in the converter tool"""
+
+class OBXSegmentBase(BaseModel):
+    """Common OBX fields (1..5 without the value)."""
+      
+    line_number: int                                     # OBX-2
+
+    variant_identifier_line: str                         # OBX-5  
+
+
+class OBXSegmentST(OBXSegmentBase):
+    '''A class representing a segment with a string type'''
+
+    observation_type: str = "ST"
+
+    value: str
+
+
+class OBXSegmentCWE(OBXSegmentBase):
+    '''A class representing a segment with a codeable concept type'''
+
+    observation_type: str = "CWE"
+
+    code: str 
+
+    coding_system: str
+
+    label: str
+
+
+class OBXSegmentNM(OBXSegmentBase): 
+    '''A class representing a segment with a numeric type'''
+
+    observation_type: str = "NM"
+
+    value: float
+
+
+class OBXSegmentNR(OBXSegmentBase): 
+    '''A class representing a segment with a numeric range type'''
+    
+    observation_type: str = "NR"
+
+    lower_bound: float
+
+    upper_bound: float
+
+
+class OBXSegmentGroup(BaseModel):
+    '''A class representing one or more segments that have the same type and segment identifier (e.g., the Discrete Genetic Variant lines)'''
+
+    segments: list[OBXSegmentBase]
+
+    segment_type:  str = "OBX"                           # OBX-1
+
+    observation_type: str                                # OBX-3
+
+    variant_type: int = 2                                # OBX-5
+
+    variant_identifier: str                              # OBX-5
+
+    segment_identifier: str                              # OBX-3.1
+
+    segment_name: str                                    # OBX 3.2
+
+    segment_identifier_system: str                       # OBX 3.3