7c3b34b1f68877584541e8c0806caf609e923cc8 braney Sat Jul 25 12:49:32 2020 -0700 get gtex to work with known databases diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c index dfb2bc5..dd5ea00 100644 --- src/hg/hgTracks/gtexTracks.c +++ src/hg/hgTracks/gtexTracks.c @@ -486,31 +486,32 @@ else if (extras->labelStyle == LABEL_BOTH) { char buf[256]; safef(buf, sizeof(buf), "%s/%s", geneBed->name, geneBed->geneId); geneInfo->label = cloneString(buf); } else geneInfo->label = ""; // get description geneInfo->geneModel = hashFindVal(modelHash, geneBed->geneId); // sometimes this is missing, hash returns NULL. do we check? // NOTE: Consider loading all gene descriptions to save queries char query[256]; sqlSafef(query, sizeof(query), "select kgXref.description from kgXref where geneSymbol='%s'", geneBed->name); - struct sqlConnection *conn = hAllocConn(database); + char *knownDatabase = hdbDefaultKnownDb(database); + struct sqlConnection *conn = hAllocConn(knownDatabase); char *desc = sqlQuickString(conn, query); hFreeConn(&conn); if (desc) { // hg38 known genes has extra detail about source; strip it char *fromDetail = strstrNoCase(desc, "(from"); if (fromDetail) *fromDetail = 0; if (strlen(desc) > MAX_DESC) strcpy(desc+MAX_DESC, "..."); // also strip 'homo sapiens' prefix #define SPECIES_PREFIX "Homo sapiens " if (startsWith(SPECIES_PREFIX, desc)) desc += strlen(SPECIES_PREFIX); geneInfo->description = desc;