946812f7ebe9bd45e3e3fbaaa3db102e9696a973 braney Thu Mar 24 14:21:20 2011 -0700 add support for supertracks in hubs #3381 diff --git src/hg/lib/hubConnect.c src/hg/lib/hubConnect.c index 25dea75..d7baeb5 100644 --- src/hg/lib/hubConnect.c +++ src/hg/lib/hubConnect.c @@ -1,225 +1,254 @@ /* 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 "net.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 *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); } char *hubConnectSkipHubPrefix(char *trackName) /* Given something like "hub_123_myWig" return myWig. Don't free this, it's not allocated */ { assert(startsWith("hub_", trackName)); trackName += 4; assert(isdigit(trackName[0])); trackName = strchr(trackName, '_'); assert(trackName != NULL); return trackName + 1; } struct trackHub *trackHubFromId(int hubId) /* Given a hub ID number, return corresponding trackHub structure. * ErrAbort if there's a problem. */ { struct sqlConnection *conn = hConnectCentral(); struct hubConnectStatus *status = hubConnectStatusForId(conn, hubId); hDisconnectCentral(&conn); if (status == NULL) errAbort("The hubId %d was not found", hubId); if (!isEmpty(status->errorMessage)) errAbort("Hub %s at %s has the error: %s", status->shortLabel, status->hubUrl, status->errorMessage); char hubName[16]; safef(hubName, sizeof(hubName), "hub_%d", hubId); struct trackHub *hub = trackHubOpen(status->hubUrl, hubName); hubConnectStatusFree(&status); return hub; } +static struct trackDb *findSuperTrack(struct trackDb *tdbList, char *trackName) +/* discover any supertracks, and if there are some add them + * to the subtrack list of the supertrack */ +{ +struct trackDb *tdb; +struct trackDb *p = NULL; +struct trackDb *next; + +for(tdb = tdbList; tdb; tdb = next) + { + /* save away the next pointer becuase we may detach this node and + * add it to its supertrack parent */ + next = tdb->next; + if (tdb->parent != NULL && sameString(trackName, tdb->parent->track)) + { + /* found a supertrack with the right name, add this child */ + p = tdb->parent; + slAddHead(&p->subtracks, tdb); + } + } + +return p; +} + 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. This will also fill in the html fields, * but just for that track and it's parents. */ { int hubId = hubIdFromTrackName(trackName); struct trackHub *hub = trackHubFromId(hubId); 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) + // superTracks aren't in the hash... look in tdbList + tdb = findSuperTrack(tdbList, trackName); + +if (tdb == NULL) errAbort("Can't find track %s in %s", trackName, hub->url); /* Add html for track and parents. */ +/* Note: this does NOT add the HTML for supertrack kids */ struct trackDb *parent; for (parent = tdb; parent != NULL; parent = parent->parent) { char *simpleName = hubConnectSkipHubPrefix(tdb->track); char *url = trackHubRelativeUrl(hubGenome->trackDbFile, simpleName); char buffer[10*1024]; safef(buffer, sizeof buffer, "%s.html", url); parent->html = netReadTextFileIfExists(buffer); freez(&url); } trackHubClose(&hub); return tdb; }