cc5381e539ecba5b07109b194acf1d76b0c8f641
braney
  Thu Jul 23 06:22:48 2026 -0700
Guard hDbForTaxon() callers against curated hub (GenArk) db names. hDbForTaxon() can now return a GenArk-only assembly with no real SQL database, which would abort in sqlConnect()/"use <db>"/cross-db sqlTableExists(). Treat a hubConnectIsCurated() db as no usable native db in uniProtAccToDb(), bacProbeInfo(), and getKnownGeneUrl(). refs #37909

diff --git src/hg/hgLinkIn/handlerList.c src/hg/hgLinkIn/handlerList.c
index 2e5901a628d..3911b4b98da 100644
--- src/hg/hgLinkIn/handlerList.c
+++ src/hg/hgLinkIn/handlerList.c
@@ -1,214 +1,220 @@
 /* Copyright (C) 2017 The Regents of the University of California
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 /* handlerList - a list of handler functions for translating identifiers
  * from different external databases to browser positions.  Used by
  * linkInHandlers.c. */
 
 #include "common.h"
 #include "hdb.h"
+#include "hubConnect.h"
 #include "jksql.h"
 #include "handlerList.h"
 
 /********************************************
  *      UniProtKB Handler
  *******************************************/
 
 /* Databases whose IDs we can link to using the position parameter.  ... this varies by database,
  * so be restrictive.  Ordered by preference. */
 /* 1 = EMBL, 2 = RefSeq, */
 #define UniProtExtRefSeqId 2
 #define UniProtExtEMBLId 1
 
 /*
  * +---------+--------------+----+-----+------+--+
  * |     acc |     char(12) | NO | MUL | NULL |  |
  * |   extDb |      int(11) | NO |     | NULL |  |
  * | extAcc1 | varchar(255) | NO | MUL | NULL |  |
  * | extAcc2 | varchar(255) | NO |     | NULL |  |
  * | extAcc3 | varchar(255) | NO |     | NULL |  |
  * +---------+--------------+----+-----+------+--+
  *
  * Looks like UniProt marks the end of the IDs list on
  * each line with a '-'.  Supplementary material may follow
  * in the extra field(s), e.g.
  * P01892  1       M86404  -       NOT_ANNOTATED_CDS
  */
 
 
 void addIdsToList(struct slName **listPtr, char **ids, int count)
 /* Given a list of alternate identifiers taken from the uniProt
  * table, add them to the supplied list.  The identifiers list is
  * terminated with a '-' */
 {
 int i=0;
 for (i=0; i<count; i++)
     {
     if (sameString(ids[i], "-"))
         break;
     slNameStore(listPtr, ids[i]);
     }
 }
 
 
 char *uniProtAccToDb(char *id, struct sqlConnection *conn)
 /* Searches the uniProt database (which conn must be connected to)
  * for the given identifier and returns the name of the database
  * that is most relevant.  This is usually the default assembly
  * for the genome that the identifier is on. */
 {
 char *db = NULL;
 char query[4096];
 sqlSafef(query, sizeof(query), "select taxon from accToTaxon where acc = '%s'", id);
 int taxon = sqlQuickNum(conn, query);
 if (taxon != 0)
     db = hDbForTaxon(taxon);
+/* hDbForTaxon may return a curated hub (GenArk) assembly with no real SQL
+ * database.  This handler issues "use <db>" and queries native tables, so a
+ * hub db name would abort.  Treat it as no usable native db. */
+if (db != NULL && hubConnectIsCurated(db))
+    db = NULL;
 return db;
 }
 
 
 struct linkInResult *getEmblList(char *db, struct slName *emblNames, struct sqlConnection *conn)
 /* Given a connection to a genome database (e.g., hg19), the name of that database, and
  * a list of identifiers, search for any EMBL mRNA names that we have positions for.
  * Return a list of matching positions. */
 {
 struct linkInResult *results = NULL;
 bool hasMRna = sqlTableExists(conn, "all_mrna");
 if (!hasMRna)
     return NULL;
 struct dyString *query = dyStringNew(0);
 sqlDyStringPrintf(query, "select tName, tStart, tEnd from all_mrna where qName in (");
 struct slName *thisName = emblNames;
 bool firstName = TRUE;
 while (thisName != NULL)
     {
     if (firstName)
         {
         sqlDyStringPrintf(query, "'%s'", thisName->name);
         firstName = FALSE;
         }
     else
         sqlDyStringPrintf(query, ",'%s'", thisName->name);
     thisName = thisName->next;
     }
 sqlDyStringPrintf(query, ")");
 struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
 char **row = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct linkInResult *newResult = NULL;
     AllocVar(newResult);
     newResult->db = cloneString(db);
     char position[4096];
     safef(position, sizeof(position), "%s:%s-%s", row[0], row[1], row[2]);
     newResult->position = cloneString(position);
     newResult->trackToView = cloneString("all_mrna");
     slAddHead(&results, newResult);
     }
 slReverse(&results);
 sqlFreeResult(&sr);
 return results;
 }
 
 
 struct linkInResult *getRefGeneList(char *db, struct slName *refNames, struct sqlConnection *conn)
 /* Given a connection to a genome database (e.g., hg19), the name of that database, and
  * a list of identifiers, search for any RefSeq gene names that we have positions for.
  * Return a list of matching positions. */
 {
 struct linkInResult *results = NULL;
 bool hasNcbiRefGene = sqlTableExists(conn, "ncbiRefGene");
 bool hasRefGene = sqlTableExists(conn, "refGene");
 if (!hasNcbiRefGene && !hasRefGene)
     return NULL;
 struct dyString *query = dyStringNew(0);
 sqlDyStringPrintf(query, "select chrom, txStart, txEnd from %s where name in (",
         hasNcbiRefGene?"ncbiRefGene":"refGene");
 struct slName *thisName = refNames;
 bool firstName = TRUE;
 while (thisName != NULL)
     {
     if (firstName)
         {
         sqlDyStringPrintf(query, "'%s'", thisName->name);
         firstName = FALSE;
         }
     else
         sqlDyStringPrintf(query, ",'%s'", thisName->name);
     thisName = thisName->next;
     }
 sqlDyStringPrintf(query, ")");
 struct sqlResult *sr = sqlGetResult(conn, dyStringContents(query));
 char **row = NULL;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     struct linkInResult *newResult = NULL;
     AllocVar(newResult);
     newResult->db = cloneString(db);
     char position[4096];
     safef(position, sizeof(position), "%s:%s-%s", row[0], row[1], row[2]);
     newResult->position = cloneString(position);
     newResult->trackToView = cloneString(hasNcbiRefGene?"ncbiRefGene":"refGene");
     slAddHead(&results, newResult);
     }
 slReverse(&results);
 sqlFreeResult(&sr);
 return results;
 }
 
 
 struct linkInResult *uniProtHandler(struct sqlConnection *conn, char *id)
 /* Handler for translating a UniProtKB identifier to a genome assembly and
  * positions within that assembly.  Changes the database that conn
  * points to - first to uniProt, then to the relevant assembly.
  * Looks first for related RefSeq gene positions.  If none are found, will
  * then search for related mRNA positions. */
 {
 char query[8092], **row = NULL;
 struct slName *emblIdList = NULL, *refSeqIdList = NULL;
 
 sqlSafef(query, sizeof(query), "use uniProt");
 sqlUpdate(conn, query);
 char *db = uniProtAccToDb(id, conn);
 if (isEmpty(db))
     return NULL;
 
 sqlSafef(query, sizeof(query),
         "select extDb, extAcc1, extAcc2, extAcc3 from extDbRef where "
         "acc = '%s' and extDb in (%d, %d)", id, UniProtExtRefSeqId, UniProtExtEMBLId);
 /* Assemble resulting IDs into two lists; one for refSeq, and one for EMBL */
 struct sqlResult *sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     int extDbId = atoi(row[0]);
     switch(extDbId)
         {
         case UniProtExtEMBLId:
             addIdsToList(&emblIdList, &row[1], 3);
             break;
         case UniProtExtRefSeqId:
             addIdsToList(&refSeqIdList, &row[1], 3);
             break;
         default:
             errAbort("Got unexpected external database ID %d", extDbId);
         }
     }
 sqlFreeResult(&sr);
 
 sqlSafef(query, sizeof(query), "use %s", db);
 sqlUpdate(conn, query);
 struct linkInResult *searchResults = NULL;
 /* If there are any RefSeq IDs, and if they're in our database, use that */
 if (refSeqIdList != NULL)
     searchResults = getRefGeneList(db, refSeqIdList, conn);
 
 /* otherwise, hunt for any EMBL hits */
 if ((searchResults == NULL) && (emblIdList != NULL))
     searchResults = getEmblList(db, emblIdList, conn);
 
 return searchResults;
 }
 
 /***************************************
  *      End of UniProtKB handler
  **************************************/