2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8
lrnassar
  Wed Jul 8 13:53:54 2026 -0700
Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840

Extends #37840 to same-CGI links that omitted db= and relied on the cart db,
which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi
adds db to the superTrack member list, container-configure, description,
sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds
the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt,
hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain,
hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq,
refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links.
The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb=
params are left untouched.

diff --git src/hg/hgc/cgapSageClick.c src/hg/hgc/cgapSageClick.c
index 53f79f50773..f7d1e456ddd 100644
--- src/hg/hgc/cgapSageClick.c
+++ src/hg/hgc/cgapSageClick.c
@@ -1,221 +1,221 @@
 /* Handle details page for CGAP SAGE track. */
 
 /* 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 "cart.h"
 #include "hgc.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "web.h"
 #include "cgapSage/cgapSage.h"
 #include "cgapSage/cgapSageLib.h"
 
 static struct cgapSage *cgapSageTagLoad(struct sqlConnection *conn, struct trackDb *tdb)
 /* Return the positional info (bed) with the list of libs/measurements. */
 {
 struct cgapSage *tag = NULL;
 struct sqlResult *sr;
 char **row;
 char *chrom = cgiString("c");
 int start = cgiInt("o");
 int end = cgiUsualInt("t", 0);
 char *tagName = cgiString("i");
 int rowOffset;
 char extraWhere[128];
 if (tagName == NULL)
     errAbort("Missing tag sequence in click for cgapSage track.");
 sqlSafef(extraWhere, sizeof(extraWhere), "name=\'%s\'", tagName);
 sr = hOrderedRangeQuery(conn, tdb->table, chrom, start, end,
 			extraWhere, &rowOffset);
 row = sqlNextRow(sr);
 if (row != NULL)
     tag = cgapSageLoad(row+rowOffset);
 sqlFreeResult(&sr);
 return tag;
 }
 
 static struct cgapSageLib *loadLibTable(struct sqlConnection *conn)
 /* Just load up the whole cgapSageLib table. */
 {
 struct cgapSageLib *libs = NULL;
 char query[256];
 sqlSafef(query, sizeof(query), "select * from cgapSageLib");
 libs = cgapSageLibLoadByQuery(conn, query);
 return libs;
 }
 
 static struct hash *getLibHash(struct sqlConnection *conn)
 /* Hash up a loaded cgapSageLib table. */
 {
 struct hash *hash = newHash(9);
 struct cgapSageLib *libs = loadLibTable(conn);
 struct cgapSageLib *lib;
 for (lib = libs; lib != NULL; lib = lib->next)
     {
     char s[16];
     safef(s, sizeof(s), "%d", lib->libId);
     hashAdd(hash, s, lib);
     }
 return hash;
 }
 
 static void printCgapSageHeader(struct cgapSage *tag)
 /* Print basic information about the tag at the top. */
 {
 printf("<B>Tag sequence</B>: %s<BR>\n", tag->name);
 printf("<B>Position:</B> "
        "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
        hgTracksPathAndSettings(), database, tag->chrom, tag->chromStart+1, tag->chromEnd, tag->chrom, tag->chromStart+1, tag->chromEnd);
 printf("<B>Strand:</B> %c<BR>\n", tag->strand[0]);
 if (tag->numSnps > 0)
     {
     int i;
     printf("<B>Number of SNPs associated with tag</B>: %d<BR>\n", tag->numSnps);
     printf("<B>SNPs associated with tag</B>: ");
     for (i = 0; i < tag->numSnps-1; i++)
 	printf("%s, ", tag->snps[i]);
     printf("%s<BR>\n", tag->snps[i]);
     }
 }
 
 static void stringCellLabelVal(char *label, char *val, boolean newRow)
 /* print label and value as adjacent cells  */
 {
 if (val && !sameString(val, ""))
     {
     webPrintLabelCell(label);
     webPrintLinkCell(val);
     if (newRow)
 	webPrintLinkTableNewRow();
     }
 }
 
 static void intCellLabelVal(char *label, int val, boolean newRow)
 /* much like stringCellLabelVal, but allowing numbers. */
 {
 char buf[32];
 safef(buf, sizeof(buf), "%d", val);
 stringCellLabelVal(label, buf, newRow);
 }
 
 static void printCgapLibSection(struct hash *libHash, char *libId)
 /* Print a section about a library. */
 {
 struct cgapSageLib *lib = hashMustFindVal(libHash, libId);
 webNewSection("CGAP Library Information");
 webPrintLinkTableStart();
 stringCellLabelVal("Library Name", lib->newLibName, TRUE);
 stringCellLabelVal("Old Library Name", lib->oldLibName, TRUE);
 intCellLabelVal("Total tags in library", lib->totalTags, TRUE);
 intCellLabelVal("Unique tags in library", lib->uniqueTags, TRUE);
 stringCellLabelVal("Organ/tissue", lib->tissue, TRUE);
 stringCellLabelVal("Tissue preparation", lib->tissuePrep, TRUE);
 stringCellLabelVal("Cell type", lib->cellType, TRUE);
 stringCellLabelVal("Keywords", lib->keywords, TRUE);
 stringCellLabelVal("Age", lib->age, TRUE);
 stringCellLabelVal("Mutations", lib->mutations, TRUE);
 stringCellLabelVal("Other information", lib->otherInfo, TRUE);
 stringCellLabelVal("Tagging enzyme", lib->tagEnzyme, TRUE);
 stringCellLabelVal("Anchoring enzyme", lib->anchorEnzyme, TRUE);
 stringCellLabelVal("Tissue or cell line supplier", lib->cellSupplier, TRUE);
 stringCellLabelVal("Library producer", lib->libProducer, TRUE);
 stringCellLabelVal("Laboratory", lib->laboratory, TRUE);
 stringCellLabelVal("References", lib->refs, FALSE);
 webPrintLinkTableEnd();
 }
 
 static void tagTableRow(struct cgapSage *tag, unsigned libId, 
         unsigned freq, double tagTpm, 
 	struct hash *libHash, char *clickedLibId, char *clickedTissue) 
 /* Print one of the rows in the tag information section table.  */
 {
 struct cgapSageLib *lib;
 char s[256];
 safef(s, sizeof(s), "%d", libId);
 lib = (struct cgapSageLib *)hashFindVal(libHash, s);
 if ((clickedLibId && sameString(s, clickedLibId)) ||
     (clickedTissue && sameString(clickedTissue, lib->tissue)))
     {
     safef(s, sizeof(s), "<B>%d</B>", libId);
     webPrintLinkCell(s);
-    safef(s, sizeof(s), "<A HREF=\"%s&o=%d&t=%d&c=%s&g=cgapSage&i=%s&lib=%d\"><B>%s</B></A>", 
-	  hgcPathAndSettings(), tag->chromStart, tag->chromEnd, tag->chrom, tag->name, libId,
+    safef(s, sizeof(s), "<A HREF=\"%s&db=%s&o=%d&t=%d&c=%s&g=cgapSage&i=%s&lib=%d\"><B>%s</B></A>", 
+	  hgcPathAndSettings(), database, tag->chromStart, tag->chromEnd, tag->chrom, tag->name, libId,
 	  lib->newLibName);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "<B>%s</B>", lib->tissue);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "<B>%d</B>", freq);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "<B>%d</B>", lib->totalTags);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "<B>%.3f</B>", tagTpm);
     webPrintLinkCell(s);
     }
 else
     {
     safef(s, sizeof(s), "%d", libId);
     webPrintLinkCell(s);  
-    safef(s, sizeof(s), "<A HREF=\"%s&o=%d&t=%d&c=%s&g=cgapSage&i=%s&lib=%d\">%s</A>", hgcPathAndSettings(), 
-	  tag->chromStart, tag->chromEnd, tag->chrom, tag->name, libId,
+    safef(s, sizeof(s), "<A HREF=\"%s&db=%s&o=%d&t=%d&c=%s&g=cgapSage&i=%s&lib=%d\">%s</A>", hgcPathAndSettings(), 
+	  database, tag->chromStart, tag->chromEnd, tag->chrom, tag->name, libId,
 	  lib->newLibName);
     webPrintLinkCell(s);
     webPrintLinkCell(lib->tissue);
     safef(s, sizeof(s), "%d", freq);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "%d", lib->totalTags);
     webPrintLinkCell(s);
     safef(s, sizeof(s), "%.3f", tagTpm);
     webPrintLinkCell(s);
     }
 }
 
 static void printCgapTagSection(struct cgapSage *tag, struct hash *libHash)
 /* Print section with frequency and TPM info for all the libs with the tag. */
 {
 int i;
 int N = tag->numLibs;
 char *libId = cgiUsualString("lib", NULL);
 char *tissue = cgiUsualString("tiss", NULL);
 /* char *libSex = cgapSageLibSex(lib->sex); */
 webNewSection("Libraries With Selected SAGE Tag");
 webPrintLinkTableStart();
 webPrintLabelCell("Library ID");
 webPrintLabelCell("Library Name");
 webPrintLabelCell("Tissue");
 webPrintLabelCell("Tag Frequency");
 webPrintLabelCell("Total Tags in Library");
 webPrintLabelCell("Tags Per Million");
 
 webPrintLinkTableNewRow();
 for (i = 0; i < N-1; i++)
     {
     tagTableRow(tag, tag->libIds[i], tag->freqs[i], tag->tagTpms[i], libHash, libId, tissue);
     webPrintLinkTableNewRow();
     }
 tagTableRow(tag, tag->libIds[N-1], tag->freqs[N-1], tag->tagTpms[N-1], libHash, libId, tissue);
 webPrintLinkTableEnd();
 }
 
 void doCgapSage(struct trackDb *tdb, char *itemName)
 /* CGAP SAGE details. */
 {
 struct sqlConnection *conn = hAllocConn(database);
 struct cgapSage *tag = cgapSageTagLoad(conn, tdb);
 struct hash *libHash = getLibHash(conn);
 char *libId = cgiUsualString("lib", NULL);
 genericHeader(tdb, NULL);
 /* Print out tag information. */
 printCgapSageHeader(tag);
 if (libId)
     {
     printCgapLibSection(libHash, libId);
     }
 printCgapTagSection(tag, libHash);
 webNewSection("Track Details");
 printTrackHtml(tdb);
 cgapSageFree(&tag);
 hFreeConn(&conn);
 hashFreeWithVals(&libHash, cgapSageLibFree);
 }