Only Use FastaSeqFetchers if Data is Available

Author: bencap

src/mavedb/deps.py

@@ -19,11 +19,24 @@ def get_db() -> Generator:
 
 
 def hgvs_data_provider() -> RESTDataProvider:
-    grch38_fetcher = FastaSeqFetcher("/data/GCF_000001405.39_GRCh38.p13_genomic.fna.gz")
-    grch37_fetcher = FastaSeqFetcher("/data/GCF_000001405.25_GRCh37.p13_genomic.fna.gz")
-
     # Prioritize fetching from SeqRepo, then GRCh38, then GRCh37.
-    seqfetcher = ChainedSeqFetcher(SeqFetcher(), grch38_fetcher, grch37_fetcher)
+    seqfetcher = ChainedSeqFetcher(SeqFetcher())
+
+    # Attempt to resolve FASTA Seq fetchers from data files, but don't fail if neither file is
+    # available. This way, we at least retain some ability to resolve sequences if we don't have
+    # FASTA file access and we are able to run our test suite without needing access to large genomic
+    # files.
+    try:
+        grch38_fetcher = FastaSeqFetcher("/data/GCF_000001405.39_GRCh38.p13_genomic.fna.gz")
+        seqfetcher.seq_fetchers.append(grch38_fetcher)
+    except OSError:
+        pass
+
+    try:
+        grch37_fetcher = FastaSeqFetcher("/data/GCF_000001405.25_GRCh37.p13_genomic.fna.gz")
+        seqfetcher.seq_fetchers.append(grch37_fetcher)
+    except OSError:
+        pass
 
     return RESTDataProvider(seqfetcher=seqfetcher)