add reference record class

cmat/clinvar_xml_io/clinvar_dataset.py

@@ -3,7 +3,7 @@
 import re
 from datetime import date
 
-from cmat.clinvar_xml_io.clinvar_record import ClinVarRecord
+from cmat.clinvar_xml_io.clinvar_reference_record import ClinVarReferenceRecord
 from cmat.clinvar_xml_io.xml_parsing import iterate_rcv_from_xml, parse_header_attributes
 
 logger = logging.getLogger(__name__)
@@ -20,7 +20,7 @@ def __init__(self, clinvar_xml):
 
     def __iter__(self):
         for rcv in iterate_rcv_from_xml(self.clinvar_xml):
-            yield ClinVarRecord(rcv, self.xsd_version)
+            yield ClinVarReferenceRecord(rcv, self.xsd_version)
 
     def get_xsd_version(self):
         # For format, see https://github.com/ncbi/clinvar/blob/master/FTPSiteXsdChanges.md

cmat/clinvar_xml_io/clinvar_record.py

@@ -4,7 +4,7 @@
 from functools import cached_property
 from xml.dom import minidom
 
-from cmat.clinvar_xml_io.clinical_classification import ClinicalClassification, MultipleClinicalClassificationsError
+from cmat.clinvar_xml_io.clinical_classification import MultipleClinicalClassificationsError
 from cmat.clinvar_xml_io.clinvar_measure import ClinVarRecordMeasure
 from cmat.clinvar_xml_io.clinvar_trait import ClinVarTrait
 from cmat.clinvar_xml_io.xml_parsing import find_elements, find_optional_unique_element, \
@@ -15,10 +15,10 @@
 
 
 class ClinVarRecord:
-    """Instances of this class hold data on individual ClinVar records. See also:
-    * /data-exploration/clinvar-variant-types/README.md for the in-depth explanation of ClinVar data model;
-    * Issue https://github.com/EBIvariation/eva-opentargets/issues/127 for the most recent discussions on changing
-      support of different ClinVar record types."""
+    """
+    Base class for both reference and submitted records in ClinVar. See also:
+    /data-exploration/clinvar-variant-types/README.md for the in-depth explanation of ClinVar data model
+    """
 
     # Some allele origin terms in ClinVar are essentially conveying lack of information and are thus not useful.
     NONSPECIFIC_ALLELE_ORIGINS = {'unknown', 'not provided', 'not applicable', 'tested-inconclusive', 'not-reported'}
@@ -62,13 +62,15 @@ def accession(self):
 
     @property
     def last_updated_date(self):
-        """This tracks the latest update date, counting even minor technical updates."""
-        return self.record_xml.attrib['DateLastUpdated']
+        """This tracks the latest update date, counting even minor technical updates.
+        Appears differently in reference and submitted records."""
+        raise NotImplementedError
 
     @property
     def created_date(self):
-        """This tracks the date the record was first made public on ClinVar."""
-        return self.record_xml.attrib['DateCreated']
+        """This tracks the date the record was first made public on ClinVar.
+        Appears differently in reference and submitted records."""
+        raise NotImplementedError
 
     @property
     def mode_of_inheritance(self):
@@ -111,15 +113,7 @@ def valid_allele_origins(self):
     @cached_property
     def clinical_classifications(self):
         """List of clinical classifications (Germline, Somatic, or Oncogenecity)"""
-        clinical_classifications = []
-        if self.xsd_version < 2:
-            # V1 only ever has a single clinical classification / clinical significance
-            clinical_classifications.append(
-                ClinicalClassification(find_mandatory_unique_element(self.record_xml, './ClinicalSignificance'), self))
-        else:
-            for clin_class in find_elements(self.record_xml, './Classifications/*'):
-                clinical_classifications.append(ClinicalClassification(clin_class, self))
-        return clinical_classifications
+        raise NotImplementedError
 
     # The following properties are maintained for backwards compatibility, but are only present for a ClinVarRecord
     # if there is exactly one ClinicalClassification for the record.

cmat/clinvar_xml_io/clinvar_reference_record.py

@@ -0,0 +1,41 @@
+import logging
+from functools import cached_property
+
+from cmat.clinvar_xml_io.clinical_classification import ClinicalClassification
+
+from cmat.clinvar_xml_io.clinvar_record import ClinVarRecord
+from cmat.clinvar_xml_io.xml_parsing import find_mandatory_unique_element, find_elements
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+
+class ClinVarReferenceRecord(ClinVarRecord):
+    """Reference records (RCVs) summarise information from submitted records (SCVs) and include additional annotations
+    and cross-references supplied by ClinVar."""
+
+    def __init__(self, record_xml, xsd_version):
+        super().__init__(record_xml, xsd_version)
+
+    def __str__(self):
+        return f'ClinVarReferenceRecord object with accession {self.accession}'
+
+    @property
+    def last_updated_date(self):
+        return self.record_xml.attrib['DateLastUpdated']
+
+    @property
+    def created_date(self):
+        return self.record_xml.attrib['DateCreated']
+
+    @cached_property
+    def clinical_classifications(self):
+        clinical_classifications = []
+        if self.xsd_version < 2:
+            # V1 only ever has a single clinical classification / clinical significance
+            clinical_classifications.append(
+                ClinicalClassification(find_mandatory_unique_element(self.record_xml, './ClinicalSignificance'), self))
+        else:
+            for clin_class in find_elements(self.record_xml, './Classifications/*'):
+                clinical_classifications.append(ClinicalClassification(clin_class, self))
+        return clinical_classifications

cmat/clinvar_xml_io/clinvar_submitted_record.py

@@ -32,12 +32,10 @@ def submission_date(self):
 
     @property
     def last_updated_date(self):
-        """Overrides parent definition, in SCV this date is in the accession element"""
         return find_mandatory_unique_element(self.record_xml, './ClinVarAccession').attrib['DateUpdated']
 
     @property
     def created_date(self):
-        """Overrides parent definition, in SCV this date is in the accession element"""
         return find_mandatory_unique_element(self.record_xml, './ClinVarAccession').attrib['DateCreated']
 
     @property

data-exploration/drug-response/drug-response-background-trait.ipynb

@@ -3087,4 +3087,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

tests/clinvar_xml_io/test_clinvar_record.py

@@ -35,6 +35,8 @@ def test_multiple_clinical_classifications_record():
 
 
 class TestClinvarRecord:
+    """Tests base class as well as reference record"""
+
     @classmethod
     def setup_class(cls):
         input_file = os.path.join(resources_dir, 'clinvar_dataset_v2.xml.gz')