06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/hgGene/malaCards.c src/hg/hgGene/malaCards.c
index a4159d0..1543a53 100644
--- src/hg/hgGene/malaCards.c
+++ src/hg/hgGene/malaCards.c
@@ -1,94 +1,94 @@
 /* malaCards - do malaCards section. parts copied from gad.c */
 
 /* 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 malaCardsExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if malaCards table exists and it has an entry with the gene symbol */
 {
 char query[1024];
 char *geneSymbol;
 
 if (sqlTableExists(conn, "malacards") == TRUE)
     {
     sqlSafef(query, sizeof(query), "select k.geneSymbol from kgXref k, malacards m"
 	" where k.kgId='%s' and k.geneSymbol = m.geneSymbol", geneId);
     geneSymbol = sqlQuickString(conn, query);
     if (geneSymbol != NULL) return(TRUE);
     }
 return(FALSE);
 }
 static void malaCardsPrint(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Print out malaCards section. */
 {
 char query[1024];
 struct sqlResult *sr;
 char **row;
 char *itemName;
 
 sqlSafef(query, sizeof(query), "select k.geneSymbol from kgXref k, malacards m"
     " where k.kgId='%s' and k.geneSymbol = m.geneSymbol", geneId);
 itemName = sqlQuickString(conn, query);
 
 printf("<B>MalaCards Gene Search: ");
-printf("<A HREF='http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s' target=_blank>", itemName);
+printf("<A HREF='http://www.malacards.org/search/bySymbol/%s' target=_blank>", itemName);
 printf("%s</B></A>\n", itemName);
 
 /* List diseases associated with the gene */
 sqlSafef(query, sizeof(query),
 "select maladySymbol, urlSuffix, mainName, round(geneScore), isElite from malacards where geneSymbol='%s' order by geneScore desc",
 itemName);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 
 if (row != NULL) 
     printf("<BR><B>Diseases sorted by gene-association score:  </B>");
 
 int eliteCount = 0;
 
 while (row != NULL)
     {
     //char *maladySym = row[0];
     char *urlSuffix = row[1];
     char *mainName = row[2];
     char *score = row[3];
     char *isElite = row[4];
     char *isEliteChar = "";
     if (sameWord(isElite, "1"))
         {
         isEliteChar = "*";
         eliteCount += 1;
         }
 
     printf("<A HREF='http://www.malacards.org/card/%s' target=_blank>%s</a>%s (%s)",
         urlSuffix, mainName, isEliteChar, score);
     row = sqlNextRow(sr);
     if (row!=NULL)
         printf(", ");
     }
 if (eliteCount!=0)
     printf("<br><small>* = Manually curated disease association</small>");
 sqlFreeResult(&sr);
 }
 
 struct section *malaCardsSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create malaCards section. */
 {
 struct section *section = sectionNew(sectionRa, "malacards");
 section->exists = malaCardsExists;
 section->print = malaCardsPrint;
 return section;
 }