94041c12e043016875ebd340568bda0ccaf122f6
lrnassar
  Wed Jul 8 13:53:22 2026 -0700
Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840

Completes the incomplete work from #26892: links from the browser to a different
CGI omitted db=, so the target CGI fell back to the cart's db (often wrong),
producing "Can't find <track> in track database <db>" errors and broken shared
links. Adds the current-assembly db to link builders across hgTracks
(chromGraphTrack, expRatioTracks, config ruler and per-track configure links,
variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the
barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi
group-configure link.

diff --git src/hg/hgGene/pseudoGene.c src/hg/hgGene/pseudoGene.c
index 3926510fae1..5b49b9e1c4f 100644
--- src/hg/hgGene/pseudoGene.c
+++ src/hg/hgGene/pseudoGene.c
@@ -1,119 +1,119 @@
 /* pseudoGene descriptions. */
 
 /* 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 "linefile.h"
 #include "dystring.h"
 #include "spDb.h"
 #include "hdb.h"
 #include "web.h"
 #include "genePred.h"
 #include "bed.h"
 #include "hgGene.h"
 #include "genbank.h"
 
 
 static boolean pseudoGeneExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if mrna  on this one. */
 {
 boolean result;
 
 result = FALSE;
 if (hTableExists(sqlGetDatabase(conn), "ucscRetroInfo"))
     {
     struct sqlResult *sr;
     char **row;
     char query[255];
     sqlSafef(query, sizeof(query),
           "select name from ucscRetroInfo where name='%s' or kgName='%s' or refseq='%s'",
 	  geneId, geneId, geneId);
     sr = sqlGetResult(conn, query);
     if ((row = sqlNextRow(sr)) != NULL) 
     	{
 	result = TRUE;
 	}
 	
     sqlFreeResult(&sr);
     }
 return(result);
 }
 
 static void pseudoGenePrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out mrna descriptions annotations. */
 {
 struct sqlResult *sr;
 char **row;
 char condStr[255];
 char *descID, *desc;    
 char *emptyStr;
 char query[255];
 char *name, *chrom, *chromStart, *chromEnd, *refseq, *rtype;
 int  score;
 
 webPrintLinkTableStart();
 webPrintLabelCell("Retro Id");
 webPrintLabelCell("Type");
 webPrintLabelCell("Score ");
 webPrintLabelCell("Genome Location");
 webPrintLabelCell("Description");
 hPrintf("</TR>\n<TR>");
 emptyStr = cloneString("");
 sqlSafef(query, sizeof(query),
       "select distinct name, chrom, chromStart, chromEnd, refseq, type, score from ucscRetroInfo where name='%s' or kgName='%s' or refseq='%s'",
       geneId, geneId, geneId);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL) 
     {
     name 	= row[0];
     chrom	= row[1];
     chromStart  = row[2];
     chromEnd	= row[3];
     refseq	= row[4];
     rtype	= row[5];
     score	= sqlUnsigned(row[6]);
    
     desc = emptyStr;
     sqlSafef(condStr, sizeof(condStr), "acc='%s'", refseq);
     descID= sqlGetField(database, gbCdnaInfoTable, "description", condStr);
     if (descID != NULL)
     	{
     	sqlSafef(condStr, sizeof(condStr), "id=%s", descID);
     	desc = sqlGetField(database, descriptionTable, "name", condStr);
 	if (desc == NULL) desc = emptyStr;
 	}
    	
     webPrintLinkCellStart();
-    hPrintf("<A HREF=\"hgc?g=ucscRetroAli&i=%s\">%s</A>", name, name);
+    hPrintf("<A HREF=\"hgc?db=%s&g=ucscRetroAli&i=%s\">%s</A>", database, name, name);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("%s ", rtype);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("%d ", score);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("<A HREF=\"hgTracks?position=%s:%s-%s&ucscRetroAli=pack&hgFind.matches=%s,\">%s:%s-%s</A>",
            chrom, chromStart, chromEnd, name, chrom, chromStart, chromEnd);
     webPrintLinkCellEnd();
     webPrintLinkCellStart();
     hPrintf("%s\n", desc);
     webPrintLinkCellEnd();
     hPrintf("</TR>\n<TR>");
     }
 sqlFreeResult(&sr);
 }
 
 struct section *pseudoGeneSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create pseudoGene section. */
 {
 struct section *section = sectionNew(sectionRa, "pseudoGene");
 section->exists = pseudoGeneExists;
 section->print = pseudoGenePrint;
 return section;
 }