bb1de08ea64e41b63cb861913f65712c29607e11
angie
  Fri Sep 22 15:51:49 2017 -0700
Updating urls for MGI ID.

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index f0c9bcf..2bba36b 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -11535,31 +11535,31 @@
            rl->locusLinkId);
     printf("%d</A><BR>\n", rl->locusLinkId);
 
     if ( (strstr(database, "mm") != NULL) && hTableExists(database, "MGIid"))
         {
         char *mgiID;
 	sqlSafef(query, sizeof(query), "select MGIid from MGIid where LLid = '%d';",
 		rl->locusLinkId);
 
 	sr = sqlGetResult(conn, query);
 	if ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    printf("<B>Mouse Genome Informatics:</B> ");
 	    mgiID = cloneString(row[0]);
 
-	    printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID);
+	    printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID);
 	    }
 	else
 	    {
 	    /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree
 	     * with Locuslink on seq to gene association.
 	     * Thus, not finding a MGIid even if a LocusLink ID
 	     * exists is always a possibility. */
 	    }
 	sqlFreeResult(&sr);
 	}
     }
 if (!startsWith("Worm", organism))
     {
     if (startsWith("dm", database))
 	{
@@ -11593,31 +11593,31 @@
     {
     struct jaxOrtholog jo;
     char * sqlRlName = rl->name;
 
     /* Make sure to escape single quotes for DB parseability */
     if (strchr(rl->name, '\''))
         {
         sqlRlName = replaceChars(rl->name, "'", "''");
         }
     sqlSafef(query, sizeof(query), "select * from jaxOrtholog where humanSymbol='%s'", sqlRlName);
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	jaxOrthologStaticLoad(row, &jo);
 	printf("<B>MGI Mouse Ortholog:</B> ");
-	printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" target=_BLANK>", jo.mgiId);
+	printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" target=_BLANK>", jo.mgiId);
 	printf("%s</A><BR>\n", jo.mouseSymbol);
 	}
     sqlFreeResult(&sr);
     }
 if (startsWith("hg", database))
     {
     printf("\n");
     printf("<B>AceView:</B> ");
     printf("<A HREF = \"https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s\" TARGET=_blank>",
 	   rl->name);
     printf("%s</A><BR>\n", rl->name);
     }
 prGRShortRefGene(rl->name);
 
 }
@@ -11672,31 +11672,31 @@
            rl->locusLinkId);
     printf("%d</A><BR>\n", rl->locusLinkId);
 
     if ( (strstr(database, "mm") != NULL) && hTableExists(database, "MGIid"))
         {
         char *mgiID;
 	sqlSafef(query, sizeof(query), "select MGIid from MGIid where LLid = '%d';",
 		rl->locusLinkId);
 
 	sr = sqlGetResult(conn, query);
 	if ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    printf("<B>Mouse Genome Informatics:</B> ");
 	    mgiID = cloneString(row[0]);
 
-	    printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID);
+	    printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID);
 	    }
 	else
 	    {
 	    /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree
 	     * with Locuslink on seq to gene association.
 	     * Thus, not finding a MGIid even if a LocusLink ID
 	     * exists is always a possibility. */
 	    }
 	sqlFreeResult(&sr);
 	}
     }
 }
 
 void doKnownGene(struct trackDb *tdb, char *rnaName)
 /* Process click on a known gene. */
@@ -14793,33 +14793,33 @@
     sqlFreeResult(&sr);
     sqlSafef(query, sizeof query, "SELECT * FROM stsInfoMouse WHERE identNo = '%d'", stsRow.identNo);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
 	{
 	infoRow = stsInfoMouseLoad(row);
 	printf("<TABLE>\n");
 	printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName);
 	printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1);
 	printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end);
 	printf("</TABLE>\n");
 	htmlHorizontalLine();
 	printf("<TABLE>\n");
         printf("<TR><TH ALIGN=left>MGI Marker ID:</TH><TD><B>MGI:</B>");
-	printf("<A HREF = \"http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIMarkerID, infoRow->MGIMarkerID);
+	printf("<A HREF = \"http://www.informatics.jax.org/marker/MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIMarkerID, infoRow->MGIMarkerID);
         printf("<TR><TH ALIGN=left>MGI Probe ID:</TH><TD><B>MGI:</B>");
-	printf("<A HREF = \"http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIPrimerID, infoRow->MGIPrimerID);
+	printf("<A HREF = \"http://www.informatics.jax.org/marker/MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIPrimerID, infoRow->MGIPrimerID);
 	printf("</TABLE>\n");
 	htmlHorizontalLine();
 	/* Print out primer information */
 	printf("<TABLE>\n");
 	printf("<TR><TH ALIGN=left>Left Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer1);
 	printf("<TR><TH ALIGN=left>Right Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer2);
 	printf("<TR><TH ALIGN=left>Distance:</TH><TD>%s bps</TD></TR>\n",infoRow->distance);
 	printf("</TABLE>\n");
 	htmlHorizontalLine();
 	/* Print out information from genetic maps for this marker */
         printf("<H3>Genetic Map Position</H3>\n");
 	printf("<TABLE>\n");
 	printf("<TH>&nbsp</TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n");
         printf("<TH ALIGN=left>&nbsp</TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n",
                infoRow->stsMarkerName, infoRow->Chr, infoRow->geneticPos);
@@ -18810,31 +18810,31 @@
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char query[256];
 char **row;
 int start = cartInt(cart, "o");
 struct jaxQTL3 *jaxQTL;
 
 genericHeader(tdb, item);
 sqlSafef(query, sizeof query, "select * from jaxQTL3 where name = '%s' and chrom = '%s' and chromStart = %d",
         item, seqName, start);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     jaxQTL = jaxQTL3Load(row);
     printf("<B>Jax/MGI Link: </B>");
-    printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\">%s</a><BR>\n",
+    printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/marker/%s\">%s</a><BR>\n",
            jaxQTL->mgiID, jaxQTL->mgiID);
     printf("<B>QTL:</B> %s<BR>\n", jaxQTL->name);
     printf("<B>Description:</B> %s <BR>\n", jaxQTL->description);
 
     if (!sameWord("", jaxQTL->flank1))
         {
         printf("<B>Flank Marker 1: </B>");
 	printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->flank1);
 	printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->flank1);
         }
     if (!sameWord("", jaxQTL->marker))
         {
 	printf("<B>Peak Marker: </B>");
 	printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->marker);
 	printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->marker);