7c3b34b1f68877584541e8c0806caf609e923cc8 braney Sat Jul 25 12:49:32 2020 -0700 get gtex to work with known databases diff --git src/hg/hgc/gtexClick.c src/hg/hgc/gtexClick.c index 5886fd5..f7dc159 100644 --- src/hg/hgc/gtexClick.c +++ src/hg/hgc/gtexClick.c @@ -71,31 +71,32 @@ if (sameString(database, "hg38")) { char *geneId = cloneString(gtexGene->geneId); chopSuffix(geneId); sqlSafef(query, sizeof(query), "SELECT kgXref.description FROM kgXref, knownCanonical WHERE " "knownCanonical.protein LIKE '%%%s%%' AND " "knownCanonical.transcript=kgXref.kgID", geneId); } else { sqlSafef(query, sizeof(query), "SELECT kgXref.description FROM kgXref WHERE geneSymbol='%s'", gtexGene->name); } -struct sqlConnection *conn = hAllocConn(database); +char *knownDatabase = hdbDefaultKnownDb(database); +struct sqlConnection *conn = hAllocConn(knownDatabase); char *desc = sqlQuickString(conn, query); hFreeConn(&conn); return desc; } void doGtexGeneExpr(struct trackDb *tdb, char *item) /* Details of GTEx gene expression item */ { int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); struct gtexGeneBed *gtexGene = getGtexGene(item, seqName, start, end, tdb->table); if (gtexGene == NULL) errAbort("Can't find gene %s in GTEx gene table %s\n", item, tdb->table); char *version = gtexVersion(tdb->table);