5f810f9181ad6941961257f9dca2cedc9857969f
angie
  Wed Mar 11 01:01:35 2015 -0700
Fixing a few cases of assuming the database is in mysql (could be assembly hub!).

diff --git src/hg/lib/hAnno.c src/hg/lib/hAnno.c
index 419ff0f..6e7fd7e 100644
--- src/hg/lib/hAnno.c
+++ src/hg/lib/hAnno.c
@@ -1,57 +1,67 @@
 /* hAnno -- helpers for creating anno{Streamers,Grators,Formatters,Queries} */
 
 #include "common.h"
 #include "hAnno.h"
 #include "basicBed.h"
 #include "customTrack.h"
 #include "grp.h"
 #include "hdb.h"
 #include "hubConnect.h"
 #include "hui.h"
 #include "jksql.h"
 #include "pgSnp.h"
+#include "trackHub.h"
 #include "vcf.h"
 #include "annoGratorQuery.h"
 #include "annoGratorGpVar.h"
 #include "annoStreamBigBed.h"
 #include "annoStreamBigWig.h"
 #include "annoStreamDb.h"
 #include "annoStreamDbFactorSource.h"
 #include "annoStreamTab.h"
 #include "annoStreamVcf.h"
 #include "annoStreamWig.h"
 #include "annoGrateWigDb.h"
 #include "annoFormatTab.h"
 #include "annoFormatVep.h"
 
 //#*** duplicated in hgVarAnnoGrator and annoGratorTester
 struct annoAssembly *hAnnoGetAssembly(char *db)
 /* Make annoAssembly for db. */
 {
 static struct annoAssembly *aa = NULL;
 if (aa == NULL)
     {
+    if (trackHubDatabase(db))
+        {
+        struct trackHubGenome *thg = trackHubGetGenome(db);
+        char *url = thg->twoBitPath;
+        aa = annoAssemblyNew(db, url);
+        }
+    else
+        {
         char *nibOrTwoBitDir = hDbDbNibPath(db);
         if (nibOrTwoBitDir == NULL)
             errAbort("Can't find .2bit for db '%s'", db);
         char twoBitPath[HDB_MAX_PATH_STRING];
         safef(twoBitPath, sizeof(twoBitPath), "%s/%s.2bit", nibOrTwoBitDir, db);
         char *path = hReplaceGbdb(twoBitPath);
         aa = annoAssemblyNew(db, path);
         freeMem(path);
         }
+    }
 return aa;
 }
 
 static boolean columnsMatch(struct asObject *asObj, struct sqlFieldInfo *fieldList)
 /* Return TRUE if asObj's column names match the given SQL fields. */
 {
 if (asObj == NULL)
     return FALSE;
 struct sqlFieldInfo *firstRealField = fieldList;
 if (sameString("bin", fieldList->field) && differentString("bin", asObj->columnList->name))
     firstRealField = fieldList->next;
 boolean columnsMatch = TRUE;
 struct sqlFieldInfo *field = firstRealField;
 struct asColumn *asCol = asObj->columnList;
 for (;  field != NULL && asCol != NULL;  field = field->next, asCol = asCol->next)
@@ -108,35 +118,42 @@
 if (tdb != NULL)
     {
     struct sqlConnection *connDb = hAllocConn(dataDb);
     asObj = asForTdb(connDb, tdb);
     hFreeConn(&connDb);
     }
 if (columnsMatch(asObj, fieldList))
     return asObj;
 else
     return asObjectFromFields(dbTable, fieldList, skipBin);
 }
 
 static char *getBigDataFileName(char *db, struct trackDb *tdb, char *selTable, char *chrom)
 /* Get fileName from bigBed/bigWig/BAM/VCF database table, or bigDataUrl from custom track. */
 {
+if (trackHubDatabase(db))
+    {
+    return trackDbSetting(tdb, "bigDataUrl");
+    }
+else
+    {
     struct sqlConnection *conn = hAllocConn(db);
     char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, selTable, chrom);
     hFreeConn(&conn);
     return fileOrUrl;
     }
+}
 
 struct annoStreamer *hAnnoStreamerFromTrackDb(struct annoAssembly *assembly, char *selTable,
                                               struct trackDb *tdb, char *chrom, int maxOutRows)
 /* Figure out the source and type of data and make an annoStreamer. */
 {
 struct annoStreamer *streamer = NULL;
 char *db = assembly->name, *dataDb = db, *dbTable = selTable;
 if (chrom == NULL)
     chrom = hDefaultChrom(db);
 if (isCustomTrack(selTable))
     {
     dbTable = trackDbSetting(tdb, "dbTableName");
     if (dbTable != NULL)
 	// This is really a database table, not a bigDataUrl CT.
 	dataDb = CUSTOM_TRASH;