d6ffdf62df145a1e6dca3359a1f2a0a7a7bfeed0
max
  Tue May 14 16:06:02 2013 -0700
trying to work around some sort of bug in mysql 5.6, see rm #10688
diff --git src/hg/hgc/pubs.c src/hg/hgc/pubs.c
index 96d5c45..7f1db3b 100644
--- src/hg/hgc/pubs.c
+++ src/hg/hgc/pubs.c
@@ -674,34 +674,39 @@
 
 web2ImgLink(yifPageUrl, clickedFileUrl, "Image from YIF", 600, 10, 10); 
 
 web2EndSection();
 }
 
 static bool printSeqSection(char *articleId, char *title, bool showDesc, struct sqlConnection *conn, struct hash* clickedSeqs, bool isClickedSection, bool fasta, char *pslTable, char *articleTable)
 /* print a section with a table of sequences, show only sequences with IDs in hash,
  * There are two sections, respective sequences are shown depending on isClickedSection and clickedSeqs 
  *   - seqs that were clicked on (isClickedSection=True) -> show only seqs in clickedSeqs
  *   - other seqs (isClickedSection=False) -> show all other seqs
  * 
  * */
 {
 // get data from mysql
+char* oldQuery = "SELECT fileDesc, snippet, locations, annotId, sequence, \"\" FROM %s WHERE articleId='%s'";
+char* newQuery = "SELECT fileDesc, snippet, locations, annotId, sequence, fileUrl FROM %s WHERE articleId='%s'";
+
+char* queryTemplate = oldQuery;
+if (hHasField("hgFixed", pubsSequenceTable, "fileUrl"))
+    queryTemplate = newQuery;
+
 char query[4096];
-safef(query, sizeof(query), 
-"SELECT fileDesc, snippet, locations, annotId, sequence, fileUrl "
-"FROM %s WHERE articleId='%s';", pubsSequenceTable, articleId);
+safef(query, sizeof(query), queryTemplate, pubsSequenceTable, articleId);
 if (pubsDebug)
     puts(query);
 struct sqlResult *sr = sqlGetResult(conn, query);
 
 // construct title for section
 char *otherFormat = NULL;
 if (fasta)
     otherFormat = "table";
 else
     otherFormat = "fasta";
 
 char fullTitle[5000];
 safef(fullTitle, sizeof(fullTitle), 
 "%s&nbsp;<A HREF=\"../cgi-bin/hgc?%s&o=%s&t=%s&g=%s&i=%s&fasta=%d\"><SMALL>(%s format)</SMALL></A>\n", 
 title, cartSidUrlString(cart), cgiOptionalString("o"), cgiOptionalString("t"), cgiString("g"), cgiString("i"),