download: fix dgidb in gene downloader

opencb · Dec 31, 2023 · 1629ad4 · 1629ad4
1 parent 73c4939
commit 1629ad4
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/cellbase-core/src/main/resources/configuration.yml b/cellbase-core/src/main/resources/configuration.yml
@@ -157,14 +157,15 @@ download:
       - all_gene_disease_associations.tsv.gz
       - readme.txt
   dgidb:
-    host: https://dgidb.org/data/monthly_tsvs/2021-Jan/interactions.tsv
+    host: https://old.dgidb.org/data/monthly_tsvs/2022-Feb/interactions.tsv
+    version: "2022-02-01"
   cadd:
     host: https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/whole_genome_SNVs.tsv.gz
   reactome:
     host: http://www.reactome.org/download/current/biopax.zip
   gnomadConstraints:
     host: https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz
-    version: 2.1.1
+    version: "2.1.1"
   hpoObo:
     host: http://purl.obolibrary.org/obo/hp.obo
   goObo:

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/GeneBuilder.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/GeneBuilder.java
@@ -90,7 +90,7 @@ public GeneBuilder(Path geneDirectoryPath, Path genomeSequenceFastaFile, Species
                        boolean flexibleGTFParsing, CellBaseSerializer serializer) throws CellBaseException {
         this(null, geneDirectoryPath.resolve("description.txt"),
                 geneDirectoryPath.resolve("xrefs.txt"),
-                geneDirectoryPath.resolve("hgnc_complete_set_2022-01-01.txt"),
+                geneDirectoryPath.resolve("hgnc_complete_set_2023-11-01.txt"),
                 geneDirectoryPath.resolve("MANE.GRCh38.v1.1.summary.txt.gz"),
                 geneDirectoryPath.resolve("list_LRGs_transcripts_xrefs.txt"),
                 geneDirectoryPath.resolve("idmapping_selected.tab.gz"),