50bf71bc5c57303fb4d7225283f48cd13ba41bcf
angie
  Wed Nov 18 23:20:57 2015 -0800
Change to interface of annoStreamDbNew: instead of making the caller
pass in an asObject, the caller may now pass in a parsed JSON config
object (or NULL).  annoStreamDbNew will use this config object to
determine whether related tables need to be joined with the track table,
and produce its own asObj.  It doesn't actually do that yet -- this
is just an interface change that will enable it to do so.
refs #15544

diff --git src/hg/lib/hAnno.c src/hg/lib/hAnno.c
index b4d2953..8f1ba9e 100644
--- src/hg/lib/hAnno.c
+++ src/hg/lib/hAnno.c
@@ -150,31 +150,32 @@
 static boolean dbTableMatchesAutoSql(char *db, char *table, struct asObject *asObj)
 /* Return true if table exists and its fields match the columns of asObj. */
 {
 boolean matches = FALSE;
 struct sqlConnection *conn = hAllocConn(db);
 if (sqlTableExists(conn, table))
     {
     struct sqlFieldInfo *fieldList = sqlFieldInfoGet(conn, table);
     matches = columnsMatch(asObj, fieldList);
     }
 hFreeConn(&conn);
 return matches;
 }
 
 struct annoStreamer *hAnnoStreamerFromTrackDb(struct annoAssembly *assembly, char *selTable,
-                                              struct trackDb *tdb, char *chrom, int maxOutRows)
+                                              struct trackDb *tdb, char *chrom, int maxOutRows,
+                                              struct jsonElement *config)
 /* 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;
     }
 if (startsWithWord("wig", tdb->type))
     streamer = annoStreamWigDbNew(dataDb, dbTable, assembly, maxOutRows);
@@ -209,67 +210,63 @@
     char *inputsTable = trackDbSetting(tdb, "inputTrackTable");
     streamer = annoStreamDbFactorSourceNew(dataDb, tdb->track, sourceTable, inputsTable, assembly,
 					   maxOutRows);
     }
 else if (sameString("knownGene", tdb->track))
     {
     struct sqlConnection *conn = hAllocConn(dataDb);
     if (sqlTableExists(conn, "knownGene") && sqlTableExists(conn, "kgXref"))
         streamer = annoStreamDbKnownGeneNew(dataDb, assembly, maxOutRows);
     hFreeConn(&conn);
     }
 else if (trackHubDatabase(db))
     errAbort("Unrecognized type '%s' for hub track '%s'", tdb->type, tdb->track);
 if (streamer == NULL)
     {
-    char maybeSplitTable[HDB_MAX_TABLE_STRING];
-    if (!hFindSplitTable(dataDb, chrom, dbTable, maybeSplitTable, NULL))
-        errAbort("hAnnoStreamerFromTrackDb: can't find table (or split table) for '%s.%s'",
-                 dataDb, dbTable);
-    struct asObject *asObj = hAnnoGetAutoSqlForDbTable(dataDb, maybeSplitTable, tdb, TRUE);
-    streamer = annoStreamDbNew(dataDb, maybeSplitTable, assembly, asObj, maxOutRows);
+    streamer = annoStreamDbNew(dataDb, dbTable, assembly, maxOutRows, config);
     }
 return streamer;
 }
 
 struct annoGrator *hAnnoGratorFromBigFileUrl(char *fileOrUrl, struct annoAssembly *assembly,
                                              int maxOutRows, enum annoGratorOverlap overlapRule)
 /* Determine what kind of big data file/url we have and make streamer & grator for it. */
 {
 struct annoStreamer *streamer = NULL;
 struct annoGrator *grator = NULL;
 char *type = customTrackTypeFromBigFile(fileOrUrl);
 if (sameString(type, "bigBed") || sameString("bigGenePred", type))
     streamer = annoStreamBigBedNew(fileOrUrl, assembly, maxOutRows);
 else if (sameString(type, "vcfTabix"))
     streamer = annoStreamVcfNew(fileOrUrl, TRUE, assembly, maxOutRows);
 else if (sameString(type, "bigWig"))
     grator = annoGrateBigWigNew(fileOrUrl, assembly, agwmAverage);
 else if (sameString(type, "bam"))
     errAbort("Sorry, BAM is not yet supported");
 else
     errAbort("Unrecognized bigData type %s of file or url '%s'", type, fileOrUrl);
 if (grator == NULL)
     grator = annoGratorNew(streamer);
 grator->setOverlapRule(grator, overlapRule);
 return grator;
 }
 
 struct annoGrator *hAnnoGratorFromTrackDb(struct annoAssembly *assembly, char *selTable,
                                           struct trackDb *tdb, char *chrom, int maxOutRows,
                                           struct asObject *primaryAsObj,
-                                          enum annoGratorOverlap overlapRule)
+                                          enum annoGratorOverlap overlapRule,
+                                          struct jsonElement *config)
 /* Figure out the source and type of data, make an annoStreamer & wrap in annoGrator.
  * If not NULL, primaryAsObj is used to determine whether we can make an annoGratorGpVar. */
 {
 struct annoGrator *grator = NULL;
 boolean primaryIsVariants = (primaryAsObj != NULL &&
                              (asObjectsMatch(primaryAsObj, pgSnpAsObj()) ||
                               asObjectsMatch(primaryAsObj, vcfAsObj())));
 char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl");
 if (bigDataUrl != NULL)
     {
     if (primaryIsVariants && sameString("bigGenePred", tdb->type))
         {
         struct annoStreamer *streamer = annoStreamBigBedNew(bigDataUrl, assembly, maxOutRows);
         grator = annoGratorGpVarNew(streamer);
         }
@@ -285,31 +282,31 @@
         dbTable = trackDbSetting(tdb, "dbTableName");
         if (dbTable != NULL)
             // This is really a database table, not a bigDataUrl CT.
             dataDb = CUSTOM_TRASH;
         }
     grator = annoGrateWigDbNew(dataDb, dbTable, assembly, agwmAverage, maxOutRows);
     }
 else if (startsWithWord("bigWig", tdb->type))
     {
     char *fileOrUrl = getBigDataFileName(assembly->name, tdb, tdb->table, chrom);
     grator = annoGrateBigWigNew(fileOrUrl, assembly, agwmAverage);
     }
 else
     {
     struct annoStreamer *streamer = hAnnoStreamerFromTrackDb(assembly, selTable, tdb, chrom,
-                                                             maxOutRows);
+                                                             maxOutRows, config);
     if (primaryIsVariants &&
         (asColumnNamesMatchFirstN(streamer->asObj, genePredAsObj(), 10) ||
          asObjectsMatch(streamer->asObj, bigGenePredAsObj())))
 	grator = annoGratorGpVarNew(streamer);
     else
 	grator = annoGratorNew(streamer);
     }
 grator->setOverlapRule(grator, overlapRule);
 return grator;
 }
 
 static struct asObject *getAutoSqlForType(char *db, char *chrom, struct trackDb *tdb)
 /* Return an asObject for tdb->type if recognized as a hub or custom track type. */
 {
 struct asObject * asObj = NULL;