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/visiGene/hgVisiGene/probePage.c src/hg/visiGene/hgVisiGene/probePage.c
index 6c132367289..906608f8af4 100644
--- src/hg/visiGene/hgVisiGene/probePage.c
+++ src/hg/visiGene/hgVisiGene/probePage.c
@@ -1,224 +1,231 @@
 /* probePage - put up page of info on probe. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "cart.h"
 #include "htmshell.h"
 #include "dnautil.h"
 #include "web.h"
 #include "hdb.h"
+#include "hubConnect.h"
 #include "visiGene.h"
 #include "hgVisiGene.h"
 #include "probePage.h"
 
 static char *orgName(struct sqlConnection *conn, int taxon)
 /* Return organism name associated with taxon. */
 {
 char *binomial;
 char query[256];
 sqlSafef(query, sizeof(query), 
 	"select binomial from uniProt.taxon where id=%d", taxon);
 binomial = sqlQuickString(conn, query);
 return shortOrgName(binomial);
 }
 
 static void labeledText(char *label, char *text)
 /* Print out labeled text */
 {
 printf("<B>%s</B>: %s ", label, naForEmpty(text));
 }
 
 static void labeledResult(char *label, struct sqlConnection *conn, char *query)
 /* Put up labeled query result. */
 {
 labeledText(label, sqlQuickString(conn, query));
 }
 
 static void rnaProbeInfo(struct sqlConnection *conn, int probeId)
 /* Print out info on RNA/DNA based probe */
 {
 char query[256];
 char *seq;
 printf("<BR>\n");
 sqlSafef(query, sizeof(query), 
     "select fPrimer from probe where id=%d", probeId);
 labeledResult("forward primer", conn, query);
 printf("<BR>\n");
 sqlSafef(query, sizeof(query), 
     "select rPrimer from probe where id=%d", probeId);
 labeledResult("reverse primer", conn, query);
 printf("<BR>\n");
 sqlSafef(query, sizeof(query),
     "select seq from probe where id=%d", probeId);
 seq = naForEmpty(sqlQuickString(conn, query));
 printf("<BR><B>sequence:</B>\n");
 if (sameWord(seq, "n/a"))
    printf("%s<BR>", seq);
 else
     {
     printf("<TT><PRE>");
     writeSeqWithBreaks(stdout, seq, strlen(seq), 60);
     printf("</PRE></TT>");
     }
 }
 
 static void bacProbeInfo(struct sqlConnection *conn, int probeId, int taxon)
 /* Print out information about BAC probe. */
 {
 char query[256];
 int bacId;
 char *name = NULL;
 char *genomeDb = hDbForTaxon(taxon);
 boolean gotMapping = FALSE;
 
+/* hDbForTaxon may return a curated hub (GenArk) assembly with no real SQL
+ * database; genomeDb is passed to sqlConnect() below, which would abort on a
+ * hub db name.  Treat it as no usable native db. */
+if (genomeDb != NULL && hubConnectIsCurated(genomeDb))
+    genomeDb = NULL;
+
 /* Start new line. */
 printf("<BR>\n");
 
 /* Lookup bacId and print name associated with it. */
 sqlSafef(query, sizeof(query), "select bac from probe where id=%d", probeId);
 bacId = sqlQuickNum(conn, query);
 if (bacId != 0)
     {
     sqlSafef(query, sizeof(query), "select name from bac where id=%d", bacId);
     name = sqlQuickString(conn, query);
     }
 
 /* Find where bac lands in genome and print hyperlink to genome browser. */
 if (genomeDb != NULL && name != NULL && name[0] != 0)
     {
     struct sqlConnection *gConn = sqlConnect(genomeDb);
     if (sqlTableExists(gConn, "bacEndPairs"))
         {
 	char query[256];
 	int count;
 	sqlSafef(query, sizeof(query), 
 	    "select count(*) from bacEndPairs where name = '%s'", name);
 	count = sqlQuickNum(gConn, query);
 	if (count > 0)
 	    gotMapping = TRUE;
 	}
     sqlDisconnect(&gConn);
     }
 
 /* Print out BAC name, hyperlinked to genome browser if possible. */
 printf("<B>BAC name:</B> ");
 if (gotMapping)
     {
     printf("<A HREF=\"");
     printf("../cgi-bin/hgTracks?db=%s&position=%s", genomeDb, name);
     printf("\">");
     }
 printf("%s", naForEmpty(name));
 if (gotMapping)
    printf("</A>");
 }
 
 static void antibodyProbeInfo(struct sqlConnection *conn, 
     int probeId, int submissionSourceId)
 /* Print out info on antibody based probe */
 {
 char query[256];
 int abId;
 int taxon;
 char *species = "n/a";
 char *abUrl = NULL;
 
 /* Lookup antibody id and taxon. */
 sqlSafef(query, sizeof(query), "select antibody from probe where id=%d", 
 	probeId);
 abId = sqlQuickNum(conn, query);
 sqlSafef(query, sizeof(query), "select taxon from antibody where id=%d", abId);
 taxon = sqlQuickNum(conn, query);
 
 sqlSafef(query, sizeof(query), "select name from antibody where id=%d", abId);
 labeledResult("name", conn, query);
 if (taxon != 0)
     species = orgName(conn, taxon);
 labeledText("species", species);
 printf("<BR>\n");
 sqlSafef(query, sizeof(query), "select description from antibody where id=%d", abId);
 labeledResult("description", conn, query);
 printf("<BR>\n");
 
 sqlSafef(query, sizeof(query), "select abUrl from submissionSource where id=%d", submissionSourceId);
 abUrl = sqlQuickString(conn, query);
 if (abUrl != NULL && abUrl[0] != 0)
     {
     char *abSubmitId = NULL;
     sqlSafef(query, sizeof(query), "select abSubmitId from antibodySource"
 	" where antibody=%d and submissionSource=%d", abId, submissionSourceId);
     abSubmitId = sqlQuickString(conn, query);
     if (abSubmitId != NULL && abSubmitId[0] != 0)
 	{
 	printf("<B>source:</B> ");
 	printf("<A HREF=\"");
 	printf(abUrl, abSubmitId);
 	printf("\" target=_blank>%s</A> ", "MGI");
 	freez(&abSubmitId);
 	}
     }
 
 freez(&abUrl);
 }
 
 void probePage(struct sqlConnection *conn, int probeId, int submissionSourceId)
 /* Put up a page of info on probe. */
 {
 char query[256];
 int geneId, taxon;
 char *probeType;
 
 webStartWrapperDetailedNoArgs(cart, NULL, "", "Probe Information",
         FALSE, FALSE, FALSE, TRUE);
 
 /* Get gene ID. */
 sqlSafef(query, sizeof(query), "select gene from probe where id=%d", probeId);
 geneId = sqlQuickNum(conn, query);
 
 /* Print gene symbol. */
 sqlSafef(query, sizeof(query), "select name from gene where id=%d", geneId);
 labeledResult("gene symbol", conn, query);
 
 /* Print organism. */
 sqlSafef(query, sizeof(query), "select taxon from gene where id=%d", geneId);
 taxon = sqlQuickNum(conn, query);
 labeledText("organism", orgName(conn, taxon));
 
 /* Print synonyms if any. */
 sqlSafef(query, sizeof(query), 
 	"select name from geneSynonym where gene=%d", geneId);
 printf("<B>synonyms: </B> %s<BR>\n", 
 	makeCommaSpacedList(sqlQuickList(conn, query)));
 
 /* Print refSeq, genbank, uniProt */
 sqlSafef(query, sizeof(query), "select refSeq from gene where id=%d", geneId);
 labeledResult("RefSeq", conn, query);
 sqlSafef(query, sizeof(query), "select genbank from gene where id=%d", geneId);
 labeledResult("GenBank", conn, query);
 sqlSafef(query, sizeof(query), "select uniProt from gene where id=%d", geneId);
 labeledResult("UniProt", conn, query);
 
 /* Now print probe information. */
 sqlSafef(query, sizeof(query),
 	"select probeType.name from probe,probeType "
 	"where probe.id = %d and probe.probeType = probeType.id"
 	, probeId);
 probeType = sqlQuickString(conn, query);
 labeledText("probe type", probeType);
 if (sameWord(probeType, "antibody"))
     antibodyProbeInfo(conn, probeId, submissionSourceId);
 else if (sameWord(probeType, "BAC"))
     bacProbeInfo(conn, probeId, taxon);
 else
     rnaProbeInfo(conn, probeId);
 
 webEnd();
 }