Merge pull request #34 from VariantEffect/mavedb-dev

Release 2024.1.3

Author: bencap

src/dcd_mapping/annotate.py

@@ -306,22 +306,20 @@ def _annotate_haplotype_mapping(
     for allele in pre_mapped.members:
         allele.extensions = [_get_vrs_ref_allele_seq(allele, metadata, tx_results)]
 
-    # Determine reference sequence
-    if mapped_score.annotation_layer == AnnotationLayer.GENOMIC:
-        sequence_id = (
-            f"ga4gh:{post_mapped.members[0].location.sequenceReference.refgetAccession}"
-        )
-        accession = get_chromosome_identifier_from_vrs_id(sequence_id)
-        if accession is None:
-            raise ValueError
-        if accession.startswith("refseq:"):
-            accession = accession[7:]
-    else:
-        if tx_results is None:
-            raise ValueError  # impossible by definition
-        accession = tx_results.np
-
     if post_mapped:
+        # Determine reference sequence
+        if mapped_score.annotation_layer == AnnotationLayer.GENOMIC:
+            sequence_id = f"ga4gh:{post_mapped.members[0].location.sequenceReference.refgetAccession}"
+            accession = get_chromosome_identifier_from_vrs_id(sequence_id)
+            if accession is None:
+                raise ValueError
+            if accession.startswith("refseq:"):
+                accession = accession[7:]
+        else:
+            if tx_results is None:
+                raise ValueError  # impossible by definition
+            accession = tx_results.np
+
         sr = get_seqrepo()
         for allele in post_mapped.members:
             loc = allele.location

src/dcd_mapping/mavedb_data.py

@@ -14,6 +14,7 @@
 from typing import Any
 
 import requests
+from fastapi import HTTPException
 from pydantic import ValidationError
 
 from dcd_mapping.resource_utils import (
@@ -283,8 +284,17 @@ async def wrapper(*args, **kwargs) -> ScoresetMapping:  # noqa: ANN002
             # Set up metadata and scores for the current run. Now they will be accessible by these functions
             # without the need to download the data again.
             temp_dir_as_path = Path(temp_dir)
-            get_scoreset_metadata(urn, temp_dir_as_path)
-            get_scoreset_records(urn, silent, temp_dir_as_path)
+            try:
+                get_scoreset_metadata(urn, temp_dir_as_path)
+                get_scoreset_records(urn, silent, temp_dir_as_path)
+            except ScoresetNotSupportedError as e:
+                return ScoresetMapping(
+                    metadata=None,
+                    error_message=str(e).strip("'"),
+                )
+            except ResourceAcquisitionError as e:
+                msg = f"Unable to acquire resource from MaveDB: {e}"
+                raise HTTPException(status_code=500, detail=msg) from e
 
             # Pass the storage path of the temp directory to the wrapped function as a kwarg.
             kwargs["store_path"] = temp_dir_as_path

src/dcd_mapping/version.py

@@ -1,3 +1,3 @@
 """Provide dcd mapping version"""
 
-dcd_mapping_version = "2024.1.2"
+dcd_mapping_version = "2024.1.3"