a4234f184e880692939c7dfe967d1d3b220399e6
angie
  Wed Sep 26 12:25:10 2018 -0700
In multi-region alt/fix autocomplete, escape search terms in the same way for chromAlias search as for {alt,fix}SeqLiftOverPsl.  refs #18544

diff --git src/hg/hgSuggest/hgSuggest.c src/hg/hgSuggest/hgSuggest.c
index 1e710fb..97a3a18 100644
--- src/hg/hgSuggest/hgSuggest.c
+++ src/hg/hgSuggest/hgSuggest.c
@@ -83,81 +83,86 @@
         dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
                        "\"id\": \"%s:%d-%s\", "
                        "\"geneSymbol\": \"%s\", "
                        "\"internalId\": \"%s\"}",
                        count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
                        row[1], atoi(row[2])+1, row[3],
                        jsonStringEscape(row[0]),
                        jsonStringEscape(row[4]));
         }
     }
 hFreeConn(&conn);
 dyStringPrintf(str, "\n]\n");
 puts(dyStringContents(str));
 }
 
-struct slName *queryQNames(struct sqlConnection *conn, char *table, char *term, boolean prefixOnly)
-/* If table exists, return qNames in table that match term, otherwise NULL.  Exclude items whose
- * tName contains '_' so the mappings between _alt and _fix sequences don't sneak into the wrong
- * category's results. */
-{
-struct slName *names = NULL;
-if (sqlTableExists(conn, table))
+char *escapeAltFixTerm(char *term)
+/* Special tweaks for SQL search of alt/fix terms that may include '.' and '_' characters. */
 {
 // If there is a ".", make it into a single-character wildcard so that "GL383518.1"
 // can match "chr1_GL383518v1_alt".
 char termCpy[strlen(term)+1];
 safecpy(termCpy, sizeof termCpy, term);
 subChar(termCpy, '.', '?');
 // Escape '_' because that is an important character in alt/fix sequence names, and support
 // wildcards:
-    char *escapedTerm = sqlLikeFromWild(termCpy);
+return sqlLikeFromWild(termCpy);
+}
+
+struct slName *queryQNames(struct sqlConnection *conn, char *table, char *term, boolean prefixOnly)
+/* If table exists, return qNames in table that match term, otherwise NULL.  Exclude items whose
+ * tName contains '_' so the mappings between _alt and _fix sequences don't sneak into the wrong
+ * category's results. */
+{
+struct slName *names = NULL;
+if (sqlTableExists(conn, table))
+    {
     char query[2048];
     sqlSafef(query, sizeof query, "select distinct(qName) from %s where qName like '%s%s%%' "
              "and tName not rlike '.*_.*' order by qName",
-             table, (prefixOnly ? "" : "%"), escapedTerm);
+             table, (prefixOnly ? "" : "%"), escapeAltFixTerm(term));
     names = sqlQuickList(conn, query);
     }
 return names;
 }
 
 void writeAltFixMatches(struct jsonWrite *jw, struct slName *matches, char *category)
 /* Append JSON objects containing alt or fix patch sequence names & optional category. */
 {
 struct slName *match;
 for (match = matches; match != NULL; match = match->next)
     {
     if (strchr(match->name, '_'))
         {
         jsonWriteObjectStart(jw, NULL);
         jsonWriteString(jw, "value", match->name);
         if (isNotEmpty(category))
             jsonWriteString(jw, "category", category);
         jsonWriteObjectEnd(jw);
         }
     }
 }
 
 struct slPair *queryChromAlias(struct sqlConnection *conn, char *term, boolean prefixOnly)
 /* Search chromAlias for prefix matches for term. */
 {
 struct slPair *matches = NULL;
 if (sqlTableExists(conn, "chromAlias"))
     {
     char query[1024];
     sqlSafef(query, sizeof query, "select chrom, alias from chromAlias where alias like '%s%s%%' "
-             "order by chrom", (prefixOnly ? "" : "%"), term);
+             "order by chrom", (prefixOnly ? "" : "%"), escapeAltFixTerm(term));
     matches = sqlQuickPairList(conn, query);
     }
 return matches;
 }
 
 void writeValLabelMatches(struct jsonWrite *jw, struct slPair *matches, char *category)
 /* Append JSON objects containing alt/fix seqs with extra label info & optional category. */
 {
 struct slPair *match;
 for (match = matches; match != NULL; match = match->next)
     {
     char *seqName = match->name;
     if (strchr(seqName, '_') && !endsWith(seqName, "_random") && !startsWith("chrUn", seqName))
         {
         jsonWriteObjectStart(jw, NULL);