744c81420cd907aa74e69a6cd8b3617609368aeb braney Thu Apr 14 16:34:19 2011 -0700 take out no longer valid assertion diff --git src/hg/lib/hubConnect.c src/hg/lib/hubConnect.c index 4c9d923..3df3634 100644 --- src/hg/lib/hubConnect.c +++ src/hg/lib/hubConnect.c @@ -1,359 +1,357 @@ /* 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, ' '); } static struct hubConnectStatus *hubConnectStatusForIdDb(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. */ /* If the id is negative, then the hub is private and the number is the * offset into the private hubfile in the trash */ { 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; } boolean hubWriteToFile(FILE *f, struct hubConnectStatus *el) /* write out a hubConnectStatus structure to a file */ { char sep = '\t'; char lastSep = '\n'; fprintf(f, "%d", el->id); fputc(sep,f); fprintf(f, "%s", el->shortLabel); fputc(sep,f); fprintf(f, "%s", el->longLabel); fputc(sep,f); fprintf(f, "%s", el->hubUrl); fputc(sep,f); fprintf(f, "%s", el->errorMessage); fputc(sep,f); fprintf(f, "%u", el->dbCount); fputc(sep,f); int ii; for(ii=0; ii < el->dbCount; ii++) { fprintf(f, "%s", el->dbArray[ii]); if (ii != el->dbCount - 1) fprintf(f, ","); } fputc(lastSep,f); return TRUE; } static struct hubConnectStatus *readHubFromFile(struct lineFile *lf) { struct hubConnectStatus *hub = NULL; char *row[5]; int count; if ((count = lineFileChopTab(lf, row)) != ArraySize(row)) errAbort("expect %d fields on line %d in %s, got %d\n",(int)ArraySize(row),lf->lineIx, lf->fileName, count); AllocVar(hub); hub->id = sqlSigned(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[4]); //int sizeOne; //sqlStringDynamicArray(row[5], &hub->dbArray, &sizeOne); //assert(sizeOne == hub->dbCount); return hub; } #define HUBFILE_CART_NAME "hghub_file" char *hubFileVar() /* return the name of the cart variable that holds the name of the * file in trash that has private hubs */ { return HUBFILE_CART_NAME; } struct hubConnectStatus *hubConnectStatusForIdFile(struct cart *cart, int id) /* id is offset into the private hubfile in the trash */ { struct hubConnectStatus *hub = NULL; char *fileVar = hubFileVar(); char *hubFileName = cartOptionalString(cart, fileVar); struct lineFile *lf = lineFileOpen(hubFileName, TRUE); int lineSize; char *line; int count = id; while(--count) if (lineFileNext(lf, &line, &lineSize) == FALSE) errAbort("not enough lines in %s to find line number %d\n", lf->fileName, id); hub = readHubFromFile(lf); return hub; } struct hubConnectStatus *hubConnectStatusForId(struct cart *cart, 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. */ /* If the id is negative, then the hub is private and the number is the * offset into the private hubfile in the trash */ { struct hubConnectStatus *hub = NULL; if (id < 0) hub = hubConnectStatusForIdFile(cart, -id); else hub = hubConnectStatusForIdDb(conn, id); 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 = sqlSigned(name->name); hub = hubConnectStatusForId(cart, 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(struct cart *cart, 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(cart, 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(struct cart *cart, 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(cart, 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; }