src/hg/hgSuggest/hgSuggest.c 1.3

Index: src/hg/hgSuggest/hgSuggest.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgSuggest/hgSuggest.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/hgSuggest/hgSuggest.c	10 Feb 2010 06:23:00 -0000	1.2
+++ src/hg/hgSuggest/hgSuggest.c	3 Mar 2010 23:52:24 -0000	1.3
@@ -1,80 +1,80 @@
 /* hgGeneSuggest - suggest a gene. */
 
 #include "common.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "cheapcgi.h"
 #include "dystring.h"
 
 static char const rcsid[] = "$Id$";
 
 static void fail(char *msg)
 {
 puts("Status: 400\n\n");
 puts(msg);
 exit(-1);
 }
 
 int main(int argc, char *argv[])
 {
 char *prefix = sqlEscapeString(cgiOptionalString("prefix"));
 char *database = sqlEscapeString(cgiOptionalString("db"));
 int exact = cgiOptionalInt("exact", 0);
 struct sqlConnection *conn;
 char query[2048];
 char **row;
 struct sqlResult *sr;
 int count = 0;
 boolean hasKnownCanonical;
 boolean hasRefSeq;
 struct dyString *str = newDyString(10000);
 char previous[256];
 
 if(prefix == NULL || database == NULL)
     fail("Missing prefix or database parameter");
 
 conn = hAllocConn(database);
 
 hasKnownCanonical = sqlTableExists(conn, "knownCanonical");
 hasRefSeq = sqlTableExists(conn, "refGene");
 if(!hasKnownCanonical && !hasRefSeq)
     fail("gene autosuggest is not supported for this assembly because it does not have a knownCanonical or a refGene table");
 
 puts("Content-Type:text/plain");
 puts("\n");
 
 dyStringPrintf(str, "[\n");
 if(exact)
     {
     if(hasKnownCanonical)
         safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol = '%s' order by x.geneSymbol, k2.txEnd - k2.txStart desc", prefix);
     else
         safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from refGene r where r.name2 = '%s' order by r.name2, r.txEnd - r.txStart desc", prefix);
     }
 else
     {
     // We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
     // Also note that we take advantage of the fact that searches are case-insensitive in mysql.
     // Some tables have duplicates (e.g. 2 TTn's in mm9 knownCanonical); currently the larger one wins.
     if(hasKnownCanonical)
         safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k2.txEnd - k2.txStart desc", prefix);
     else
         // arbitrarily prefer the longest isoform
         safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from refGene r where r.name2 LIKE '%s%%' order by r.name2, r.txEnd - r.txStart desc", prefix);
     }
 sr = sqlGetResult(conn, query);
 previous[0] = 0;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if(!previous[0] || !sameString(previous, row[0]))
         {
         count++;
         dyStringPrintf(str, "%s{\"value\": \"%s\", \"id\": \"%s:%d-%s\"}", count == 1 ? "" : ",\n",
                        row[0], row[1], atoi(row[2])+1, row[3]);
-        safef(previous, sizeof(previous), row[0]);
+        safef(previous, sizeof(previous), "%s", row[0]);
         }
     }
 dyStringPrintf(str, "\n]\n");
 puts(dyStringContents(str));
 return 0;
 }