d48f39fe56017d31ed77b0d389542ada8ff6277a
angie
  Tue Apr 26 14:07:58 2016 -0700
Add geneSymbol to the JSON results so it can be used in place of the verbose item value.

diff --git src/hg/hgSuggest/hgSuggest.c src/hg/hgSuggest/hgSuggest.c
index e6114ee..681aa89 100644
--- src/hg/hgSuggest/hgSuggest.c
+++ src/hg/hgSuggest/hgSuggest.c
@@ -1,97 +1,103 @@
 /* hgGeneSuggest - suggest a gene. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "cheapcgi.h"
 #include "htmshell.h"
 #include "dystring.h"
 #include "jsonParse.h"
 #include "suggest.h"
 #include "genbank.h"
 
 
 int main(int argc, char *argv[])
 {
 long enteredMainTime = clock1000();
 
 cgiSpoof(&argc, argv);
 char *prefix = cgiOptionalString("prefix");
 char *database = cgiOptionalString("db");
 
 initGenbankTableNames(database);
 
 int exact = cgiOptionalInt("exact", 0);
 struct sqlConnection *conn;
 char query[2048];
 char **row;
 struct sqlResult *sr;
 int count = 0;
 boolean hasKnownCanonical;
 struct dyString *str = newDyString(10000);
 char *table;
 
 pushAbortHandler(htmlVaBadRequestAbort);
 if(prefix == NULL || database == NULL)
     errAbort("%s", "Missing prefix and/or db CGI parameter");
 
 conn = hAllocConn(database);
 table = connGeneSuggestTable(conn);
 if(table == NULL)
     errAbort("gene autosuggest is not supported for db '%s'", database);
 popAbortHandler();
 
 hasKnownCanonical = sameString(table, "knownCanonical");
 
 puts("Content-Type:text/plain");
 puts("\n");
 
 dyStringPrintf(str, "[\n");
 
 if(exact)
     {
     // NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
     if(hasKnownCanonical)
         sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
               "from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
               "and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
     else
         sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
               "from %s r, %s g, %s d where r.name2 = '%s' and g.acc = r.name "
               "and g.description = d.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, gbCdnaInfoTable, descriptionTable, 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.
     // Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
     // 3 POU5F1's in hg19); we return all of them (#5962).
     if(hasKnownCanonical)
         sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
               "from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
               "and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
     else
         sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
               "from %s r, %s g, %s d where r.name2 LIKE '%s%%' and g.acc = r.name "
               "and g.description = d.id order by r.name2, r.chrom, r.txStart", table, gbCdnaInfoTable, descriptionTable, prefix);
     }
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     // ignore funny chroms (e.g. _hap chroms. See redmine #4257.
     if(!strchr(row[1], '_'))
         {
         count++;
-        dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", \"id\": \"%s:%d-%s\", \"internalId\": \"%s\"}", count == 1 ? "" : ",\n",
-                       row[0], jsonStringEscape(row[5]), row[1], atoi(row[2])+1, row[3], jsonStringEscape(row[4]));
+        dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
+                       "\"id\": \"%s:%d-%s\", "
+                       "\"geneSymbol\": \"%s\", "
+                       "\"internalId\": \"%s\"}",
+                       count == 1 ? "" : ",\n", row[0], jsonStringEscape(row[5]),
+                       row[1], atoi(row[2])+1, row[3],
+                       jsonStringEscape(row[0]),
+                       jsonStringEscape(row[4]));
         }
     }
 
 dyStringPrintf(str, "\n]\n");
 puts(dyStringContents(str));
 cgiExitTime("hgSuggest", enteredMainTime);
 return 0;
 }