073f999294e187d3ced854717e467a17098972d7
hiram
  Wed Apr 9 13:21:13 2025 -0700
do not look for genome chrom names/sizes in a database when it is a GenArk hub refs #35479 #34043

diff --git src/hg/lib/hdb.c src/hg/lib/hdb.c
index 63391ad7021..be2d9ceb980 100644
--- src/hg/lib/hdb.c
+++ src/hg/lib/hdb.c
@@ -38,30 +38,31 @@
 #include "hubConnect.h"
 #include "customTrack.h"
 #include "hgFind.h"
 #endif /* GBROWSE */
 #include "hui.h"
 #include "trackHub.h"
 #include "net.h"
 #include "udc.h"
 #include "paraFetch.h"
 #include "regexHelper.h"
 #include "filePath.h"
 #include "wikiLink.h"
 #include "cheapcgi.h"
 #include "chromAlias.h"
 #include "asmEquivalent.h"
+#include "genark.h"
 
 
 #ifdef LOWELAB
 #define DEFAULT_PROTEINS "proteins060115"
 #define DEFAULT_GENOME "Pyrobaculum aerophilum"
 #else
 #define DEFAULT_PROTEINS "proteins"
 #define DEFAULT_GENOME "Human"
 #endif
 
 static struct sqlConnCache *hdbCc = NULL;  /* cache for primary database connection */
 static struct sqlConnCache *centralCc = NULL;
 static char *centralDb = NULL;
 static struct sqlConnCache *cartCc = NULL;  /* cache for cart; normally same as centralCc */
 static char *cartDb = NULL;
@@ -1393,31 +1394,31 @@
 	  touppers(seq->dna);
 	}
 return seq;
 }
 
 struct dnaSeq *hLoadChrom(char *db, char *chromName)
 /* Fetch entire chromosome into memory. */
 {
 int size = hChromSize(db, chromName);
 return hDnaFromSeq(db, chromName, 0, size, dnaLower);
 }
 
 struct slName *hAllChromNames(char *db)
 /* Get list of all chromosome names in database. */
 {
-if (trackHubDatabase(db) || hubConnectIsCurated(trackHubSkipHubName(db)))
+if (trackHubDatabase(db) || hubConnectIsCurated(trackHubSkipHubName(db)) || isGenArk(db))
     return trackHubAllChromNames(db);
 struct slName *list = NULL;
 struct sqlConnection *conn = hAllocConn(db);
 struct sqlResult *sr;
 char **row;
 
 char query[1024];
 sqlSafef(query, sizeof query, "select chrom from chromInfo");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct slName *el = slNameNew(row[0]);
     slAddHead(&list, el);
     }
 sqlFreeResult(&sr);