src/hg/hgSuggest/hgSuggest.c 1.1

Index: src/hg/hgSuggest/hgSuggest.c
===================================================================
RCS file: src/hg/hgSuggest/hgSuggest.c
diff -N src/hg/hgSuggest/hgSuggest.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/hgSuggest/hgSuggest.c	9 Feb 2010 08:41:02 -0000	1.1
@@ -0,0 +1,68 @@
+/* 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 = cgiOptionalString("prefix");
+    char *database = cgiOptionalString("db");
+    struct sqlConnection *conn;
+    char query[2048];
+    char **row;
+    struct sqlResult *sr;
+    int count = 0;
+    boolean hasKnownCanonical;
+    boolean hasRefSeq;
+    struct dyString *str = newDyString(1000);
+    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");
+    // 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);
+    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]);
+            }
+        }
+    dyStringPrintf(str, "\n]\n");
+    puts(dyStringContents(str));
+    return 0;
+}