3589900a038034a6c2112c308946f67889c11170
braney
  Fri May 15 11:40:30 2020 -0700
fix URL to Comparative Toxicogenomics Database

diff --git src/hg/hgGene/ctd.c src/hg/hgGene/ctd.c
index 25129ab..c638e16 100644
--- src/hg/hgGene/ctd.c
+++ src/hg/hgGene/ctd.c
@@ -1,145 +1,145 @@
 /* ctd - do CTD section. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "spDb.h"
 #include "hgGene.h"
 #include "hdb.h"
 #include "net.h"
 
 
 static boolean ctdExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if CTD database exists and it has an entry with the gene symbol */
 {
 char query[1024];
 char *geneSymbol;
 if (isRgdGene(conn))
     {
     if (sqlTableExists(conn, "rgdGene2Xref") == FALSE) return FALSE;
     }
 else
     {
     if (sqlTableExists(conn, "kgXref") == FALSE) return FALSE;
     }
 
 if (sqlTableExists(conn, "hgFixed.ctdSorted") == TRUE)
     {
     if (isRgdGene(conn))
 	{
 	sqlSafef(query, sizeof(query), "select ChemicalId from rgdGene2Xref x, hgFixed.ctdSorted c"
 	" where x.info=c.GeneSymbol and infoType = 'Name' and rgdGeneId='%s' limit 1", geneId);
 	geneSymbol = sqlQuickString(conn, query);
 	}
     else
         {
 	sqlSafef(query, sizeof(query), "select ChemicalId from kgXref x, hgFixed.ctdSorted c"
 	" where x.geneSymbol=c.GeneSymbol and kgId='%s' limit 1", geneId);
 	geneSymbol = sqlQuickString(conn, query);
 	}
 
     if (geneSymbol != NULL) return(TRUE);
     }
 return(FALSE);
 }
 
 static void ctdPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out CTD section. */
 {
 char query[256];
 struct sqlResult *sr;
 char **row;
 char *chemId, *chemName;
 int chemCnt;
 int first = 1;
 boolean showCompleteCtdList;
 struct dyString *currentCgiUrl;
 
 showCompleteCtdList = FALSE;
 if (cgiOptionalString("showAllCtdRef") != NULL)
     {
     if (sameWord(cgiOptionalString("showAllCtdRef"), "Y") ||
 	sameWord(cgiOptionalString("showAllCtdRef"), "y") )
 	{
 	showCompleteCtdList = TRUE;
 	}
     cartRemove(cart, "showAllCtdRef");
     }
 currentCgiUrl = cgiUrlString();
     
 /* List chemicals related to this gene */
 if (isRgdGene(conn))
     {
     sqlSafef(query, sizeof(query),
           "select ChemicalId, ChemicalName from rgdGene2Xref x, hgFixed.ctdSorted c where x.info=c.GeneSymbol and rgdGeneId='%s' and infoType='Name'", 
 	  geneId);
     }
 else
     {
     sqlSafef(query, sizeof(query),
           "select ChemicalId, ChemicalName from kgXref x, hgFixed.ctdSorted c where x.geneSymbol=c.GeneSymbol and kgId='%s'", 
 	  geneId);
     }
 
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
     
 chemCnt = 0;
 while (row != NULL) 
     {
     chemId   = cloneString(row[0]);
     chemName = cloneString(row[1]);
    
     if (first)
     	{
 	printf("<B>The following chemicals interact with this gene</B>\n");
 	printf("<UL>");
 	first = 0;
 	}
     
-    printf("<LI><A HREF=\"http://ctd.mdibl.org/detail.go?type=chem&acc=%s\" target=_blank>", 
+    printf("<LI><A HREF=\"http://ctdbase.org/detail.go?type=chem&acc=%s\" target=_blank>", 
     	   chemId);
     printf("%s</A>\n", chemId);
     printf("%s\n", chemName);
     printf("</LI>");	
     chemCnt++;
     row = sqlNextRow(sr);
     /* Initially, just show no more than 10 items */
     if ((!showCompleteCtdList) && (chemCnt >= 10) && (row != NULL))
 	{
 	chemCnt++;
 	break;
 	}
     }
 sqlFreeResult(&sr);
 
 if (!first) printf("</UL>");
 
 /* Offer user the option to see the complete list */
 if ((!showCompleteCtdList) && chemCnt > 10)
     {
     printf("<B>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; more ...  </B>");
     printf("<A HREF=\"%s?showAllCtdRef=Y&%s&#35;ctd\">click here to view the complete list</A> " 
 	   ,"hgGene", currentCgiUrl->string);
     }
 
 return;
 }
 
 struct section *ctdSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create CTD section. */
 {
 struct section *section = sectionNew(sectionRa, "ctd");
 section->exists = ctdExists;
 section->print = ctdPrint;
 return section;
 }