78dfd4b6e906a962da40780c799f92bb7ea1b3c1
kent
  Wed Jan 12 15:47:29 2011 -0800
Starting to integrate data hub into table browser.  Still problems, so effectively is commented out at the moment.
diff --git src/hg/lib/hubConnect.c src/hg/lib/hubConnect.c
index a1d1222..6194a40 100644
--- src/hg/lib/hubConnect.c
+++ src/hg/lib/hubConnect.c
@@ -1,188 +1,188 @@
 /* hubConnect - stuff to manage connections to track hubs.  Most of this is mediated through
  * the hubConnect table in the hgCentral database.  Here there are routines to translate between
  * hub symbolic names and hub URLs,  to see if a hub is up or down or sideways (up but badly
  * formatted) etc.  Note that there is no C structure corresponding to a row in the hubConnect 
  * table by design.  We just want field-by-field access to this. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "dystring.h"
 #include "sqlNum.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "hui.h"
 
 
 boolean isHubTrack(char *trackName)
 /* Return TRUE if it's a hub track. */
 {
 return startsWith(hubTrackPrefix, trackName);
 }
 
 boolean hubConnectTableExists()
 /* Return TRUE if the hubConnect table exists. */
 {
 struct sqlConnection *conn = hConnectCentral();
 boolean exists = sqlTableExists(conn, hubConnectTableName);
 hDisconnectCentral(&conn);
 return exists;
 }
 
 void hubConnectStatusFree(struct hubConnectStatus **pHub)
 /* Free hubConnectStatus */
 {
 struct hubConnectStatus *hub = *pHub;
 if (hub != NULL)
     {
     freeMem(hub->shortLabel);
     freeMem(hub->longLabel);
     freeMem(hub->hubUrl);
     freeMem(hub->errorMessage);
     if (hub->dbArray)
         {
 	freeMem(hub->dbArray[0]);
 	freeMem(hub->dbArray);
 	}
     freez(pHub);
     }
 }
 
 void hubConnectStatusFreeList(struct hubConnectStatus **pList)
 /* Free a list of dynamically allocated hubConnectStatus's */
 {
 struct hubConnectStatus *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hubConnectStatusFree(&el);
     }
 *pList = NULL;
 }
 
 static void hubConnectRemakeTrackHubVar(struct cart *cart)
 /* Remake trackHub cart variable if need be from various check box vars. */
 {
 if (cartVarExists(cart, hgHubConnectRemakeTrackHub))
     {
     struct slPair *hubVarList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
     int prefixLength = strlen(hgHubConnectHubVarPrefix);
     struct dyString *trackHubs = dyStringNew(0);
     struct slPair *hubVar;
     boolean firstOne = TRUE;
     for (hubVar = hubVarList; hubVar != NULL; hubVar = hubVar->next)
         {
 	if (cartBoolean(cart, hubVar->name))
 	    {
 	    if (firstOne)
 		firstOne = FALSE;
 	    else
 		dyStringAppendC(trackHubs, ' ');
 	    dyStringAppend(trackHubs, hubVar->name + prefixLength);
 	    }
 	}
     slPairFreeList(&hubVarList);
     cartSetString(cart, hubConnectTrackHubsVarName, trackHubs->string);
     dyStringFree(&trackHubs);
     cartRemove(cart, hgHubConnectRemakeTrackHub);
     }
 }
 
 struct slName *hubConnectHubsInCart(struct cart *cart)
 /* Return list of track hub ids that are turned on. */
 {
 hubConnectRemakeTrackHubVar(cart);
 char *trackHubString = cartOptionalString(cart, hubConnectTrackHubsVarName);
 return slNameListFromString(trackHubString, ' ');
 }
 
 struct hubConnectStatus *hubConnectStatusForId(struct sqlConnection *conn, int id)
 /* Given a hub ID return associated status. Returns NULL if no such hub.  If hub
  * exists but has problems will return with errorMessage field filled in. */
 {
 struct hubConnectStatus *hub = NULL;
 char query[1024];
 safef(query, sizeof(query), 
     "select id,shortLabel,longLabel,hubUrl,errorMessage,dbCount,dbList from %s where id=%d",
     hubConnectTableName, id);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = sqlNextRow(sr);
 if (row != NULL)
     {
     AllocVar(hub);
     hub->id = sqlUnsigned(row[0]);
     hub->shortLabel = cloneString(row[1]);
     hub->longLabel = cloneString(row[2]);
     hub->hubUrl = cloneString(row[3]);
     hub->errorMessage = cloneString(row[4]);
     hub->dbCount = sqlUnsigned(row[5]);
     int sizeOne;
     sqlStringDynamicArray(row[6], &hub->dbArray, &sizeOne);
     assert(sizeOne == hub->dbCount);
     }
 sqlFreeResult(&sr);
 return hub;
 }
 
-struct hubConnectStatus *hubConnectStatusFromCart(struct cart *cart)
+struct hubConnectStatus *hubConnectStatusListFromCart(struct cart *cart)
 /* Return list of track hubs that are turned on by user in cart. */
 {
 struct hubConnectStatus *hubList = NULL, *hub;
 struct slName *name, *nameList = hubConnectHubsInCart(cart);
 struct sqlConnection *conn = hConnectCentral();
 for (name = nameList; name != NULL; name = name->next)
     {
     int id = sqlUnsigned(name->name);
     hub = hubConnectStatusForId(conn, id);
     if (hub != NULL)
         slAddHead(&hubList, hub);
     }
 slFreeList(&nameList);
 hDisconnectCentral(&conn);
 slReverse(&hubList);
 return hubList;
 }
 
 int hubIdFromTrackName(char *trackName)
 /* Given something like "hub_123_myWig" return 123 */
 {
 assert(startsWith("hub_", trackName));
 trackName += 4;
 assert(isdigit(trackName[0]));
 return atoi(trackName);
 }
 
 struct trackDb *hubConnectAddHubForTrackAndFindTdb(char *database, 
 	char *trackName, struct trackDb **pTdbList, struct hash *trackHash)
 /* Go find hub for trackName (which will begin with hub_), and load the tracks
  * for it, appending to end of list and adding to trackHash.  Return the
  * trackDb associated with trackName.  */
 {
 int hubId = hubIdFromTrackName(trackName);
 struct sqlConnection *conn = hConnectCentral();
 struct hubConnectStatus *hubStatus = hubConnectStatusForId(conn, hubId);
 hDisconnectCentral(&conn);
 if (hubStatus == NULL)
     errAbort("The hubId %d was not found", hubId);
 if (!isEmpty(hubStatus->errorMessage))
     errAbort("Hub %s at %s has the error: %s", hubStatus->shortLabel, 
 	    hubStatus->hubUrl, hubStatus->errorMessage);
 char hubName[16];
 safef(hubName, sizeof(hubName), "%d", hubId);
 struct trackHub *hub = trackHubOpen(hubStatus->hubUrl, hubName);
 struct trackHubGenome *hubGenome = trackHubFindGenome(hub, database);
 struct trackDb *tdbList = trackHubTracksForGenome(hub, hubGenome);
 tdbList = trackDbLinkUpGenerations(tdbList);
 tdbList = trackDbPolishAfterLinkup(tdbList, database);
 rAddTrackListToHash(trackHash, tdbList, NULL, FALSE);
 if (pTdbList != NULL)
     *pTdbList = slCat(*pTdbList, tdbList);
 struct trackDb *tdb = hashFindVal(trackHash, trackName);
 if (tdb == NULL)
     errAbort("Can't find track %s in %s", trackName, hubStatus->hubUrl);
 return tdb;
 }