2a1b2c58c1fbc54cb24b1476670557fdfdfef187 braney Tue Aug 16 19:20:29 2011 -0700 cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255 diff --git src/hg/lib/hubConnect.c src/hg/lib/hubConnect.c index ddc82ee..510a5f9 100644 --- src/hg/lib/hubConnect.c +++ src/hg/lib/hubConnect.c @@ -1,573 +1,572 @@ /* 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" #include "errCatch.h" #include "obscure.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, hubPublicTableName); 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. */ { struct hubConnectStatus *hub = NULL; char query[1024]; safef(query, sizeof(query), "select id,shortLabel,longLabel,hubUrl,errorMessage,dbCount,dbList,status from %s where id=%d", hubStatusTableName, 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); hub->status = sqlUnsigned(row[7]); } sqlFreeResult(&sr); return hub; } boolean isHubUnlisted(struct hubConnectStatus *hub) /* Return TRUE if it's an unlisted hub */ { return (hub->status & HUB_UNLISTED); } -struct hubConnectStatus *hubConnectStatusForId(struct cart *cart, struct sqlConnection *conn, int id) +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. */ /* 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; hub = hubConnectStatusForIdDb(conn, id); return hub; } struct hubConnectStatus *hubConnectStatusListFromCartAll(struct cart *cart) /* Return list of all track hubs that are referenced by cart. */ { struct hubConnectStatus *hubList = NULL, *hub; struct slPair *pair, *pairList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix); struct sqlConnection *conn = hConnectCentral(); for (pair = pairList; pair != NULL; pair = pair->next) { int id = hubIdFromCartName(pair->name); - hub = hubConnectStatusForId(cart, conn, id); + hub = hubConnectStatusForId(conn, id); if (hub != NULL) { slAddHead(&hubList, hub); } } slFreeList(&pairList); hDisconnectCentral(&conn); slReverse(&hubList); return hubList; } 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); + hub = hubConnectStatusForId(conn, id); if (hub != NULL) { slAddHead(&hubList, hub); } } slFreeList(&nameList); hDisconnectCentral(&conn); slReverse(&hubList); return hubList; } int hubIdFromCartName(char *cartName) /* Given something like "hgHubConnect.hub.123" return 123 */ { assert(startsWith("hgHubConnect.hub.", cartName)); char *ptr1 = strchr(cartName, '.'); char *ptr2 = strchr(ptr1 + 1, '.'); return sqlUnsigned(ptr2+1); } -int hubIdFromTrackName(char *trackName) +unsigned hubIdFromTrackName(char *trackName) /* Given something like "hub_123_myWig" return 123 */ { assert(startsWith("hub_", trackName)); char *ptr1 = trackName; ptr1 += 4; char *ptr2 = strchr(ptr1, '_'); if (ptr2 == NULL) errAbort("hub track %s not in correct format\n", trackName); char save = *ptr2; *ptr2 = 0; unsigned val = sqlUnsigned(ptr1); *ptr2 = save; return val; } 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; trackName = strchr(trackName, '_'); assert(trackName != NULL); return trackName + 1; } -struct trackHub *trackHubFromId(struct cart *cart, unsigned hubId) +struct trackHub *trackHubFromId(unsigned 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); +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_%u", 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) +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(cart, hubId); +unsigned 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; } static void enterHubInStatus(struct trackHub *tHub, boolean unlisted) /* put the hub status in the hubStatus table */ { struct sqlConnection *conn = hConnectCentral(); /* calculate dbList */ struct dyString *dy = newDyString(1024); struct hashEl *hel; struct hashCookie cookie = hashFirst(tHub->genomeHash); int dbCount = 0; while ((hel = hashNext(&cookie)) != NULL) { dbCount++; dyStringPrintf(dy,"%s,", hel->name); } char query[512]; safef(query, sizeof(query), "insert into %s (hubUrl,status,shortLabel, longLabel, dbList, dbCount) values (\"%s\",%d,\"%s\",\"%s\", \"%s\", %d)", hubStatusTableName, tHub->url, unlisted ? 1 : 0, tHub->shortLabel, tHub->longLabel, dy->string, dbCount); sqlUpdate(conn, query); hDisconnectCentral(&conn); } static unsigned getHubId(char *url, char **errorMessage) /* find id for url in hubStatus table */ { struct sqlConnection *conn = hConnectCentral(); char query[512]; char **row; boolean foundOne = FALSE; int id = 0; safef(query, sizeof(query), "select id,errorMessage from %s where hubUrl = \"%s\"", hubStatusTableName, url); struct sqlResult *sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { if (foundOne) errAbort("more than one line in %s with hubUrl %s\n", hubStatusTableName, url); foundOne = TRUE; char *thisId = row[0], *thisError = row[1]; if (!isEmpty(thisError)) *errorMessage = cloneString(thisError); id = sqlUnsigned(thisId); } sqlFreeResult(&sr); hDisconnectCentral(&conn); return id; } static boolean hubHasDatabase(unsigned id, char *database) /* check to see if hub specified by id supports database */ { struct sqlConnection *conn = hConnectCentral(); char query[512]; safef(query, sizeof(query), "select dbList from %s where id=%d", hubStatusTableName, id); char *dbList = sqlQuickString(conn, query); boolean gotIt = FALSE; if (nameInCommaList(database, dbList)) gotIt = TRUE; hDisconnectCentral(&conn); freeMem(dbList); return gotIt; } static boolean fetchHub(char *database, char *url, boolean unlisted) { struct errCatch *errCatch = errCatchNew(); struct trackHub *tHub = NULL; boolean gotWarning = FALSE; unsigned id = 0; if (errCatchStart(errCatch)) tHub = trackHubOpen(url, "1"); // open hub.. it'll get renamed later errCatchEnd(errCatch); if (errCatch->gotError) { gotWarning = TRUE; warn("%s", errCatch->message->string); } errCatchFree(&errCatch); if (gotWarning) { return 0; } if (hashLookup(tHub->genomeHash, database) != NULL) { enterHubInStatus(tHub, unlisted); } else { warn("requested hub at %s does not have data for %s\n", url, database); return 0; } trackHubClose(&tHub); char *errorMessage = NULL; id = getHubId(url, &errorMessage); return id; } static void getAndSetHubStatus(char *database, struct cart *cart, char *url, boolean set, boolean unlisted) { char *errorMessage = NULL; unsigned id; if ((id = getHubId(url, &errorMessage)) == 0) { if ((id = fetchHub(database, url, unlisted)) == 0) return; } else if (!hubHasDatabase(id, database)) { warn("requested hub at %s does not have data for %s\n", url, database); return; } char hubName[32]; safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id); if (set) cartSetString(cart, hubName, "1"); } unsigned hubFindOrAddUrlInStatusTable(char *database, struct cart *cart, char *url, char **errorMessage) /* find this url in the status table, and return its id and errorMessage (if an errorMessage exists) */ { int id = 0; *errorMessage = NULL; if ((id = getHubId(url, errorMessage)) > 0) return id; getAndSetHubStatus(database, cart, url, FALSE, FALSE); if ((id = getHubId(url, errorMessage)) == 0) errAbort("inserted new hubUrl %s, but cannot find it", url); return id; } boolean hubCheckForNew(char *database, struct cart *cart) /* see if the user just typed in a new hub url, return TRUE if so */ { char *url = cartOptionalString(cart, hgHubDataText); if (url != NULL) { trimSpaces(url); getAndSetHubStatus(database, cart, url, TRUE, TRUE); cartRemove(cart, hgHubDataText); return TRUE; } return FALSE; } unsigned hubResetError(char *url) /* clear the error for this url in the hubStatus table,return the id */ { struct sqlConnection *conn = hConnectCentral(); char query[512]; safef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", hubStatusTableName, url); unsigned id = sqlQuickNum(conn, query); if (id == 0) errAbort("could not find url %s in status table (%s)\n", url, hubStatusTableName); safef(query, sizeof(query), "update %s set errorMessage=\"\" where hubUrl = \"%s\"", hubStatusTableName, url); sqlUpdate(conn, query); hDisconnectCentral(&conn); return id; } unsigned hubClearStatus(char *url) /* drop the information about this url from the hubStatus table */ { struct sqlConnection *conn = hConnectCentral(); char query[512]; safef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", hubStatusTableName, url); unsigned id = sqlQuickNum(conn, query); if (id == 0) errAbort("could not find url %s in status table (%s)\n", url, hubStatusTableName); safef(query, sizeof(query), "delete from %s where hubUrl = \"%s\"", hubStatusTableName, url); sqlUpdate(conn, query); hDisconnectCentral(&conn); return id; } void hubDisconnect(struct cart *cart, char *url) /* drop the information about this url from the hubStatus table, and * the cart variable the references this hub */ { /* clear the hubStatus table */ unsigned id = hubClearStatus(url); /* remove the cart variable */ char buffer[1024]; safef(buffer, sizeof buffer, "hgHubConnect.hub.%d", id); cartRemove(cart, buffer); } void hubSetErrorMessage(char *errorMessage, unsigned id) /* set the error message in the hubStatus table */ { struct sqlConnection *conn = hConnectCentral(); char query[256]; if (errorMessage != NULL) { safef(query, sizeof(query), "update %s set errorMessage=\"%s\", lastNotOkTime=now() where id=%d", hubStatusTableName, errorMessage, id); } else { safef(query, sizeof(query), "update %s set errorMessage=\"\", lastOkTime=now() where id=%d", hubStatusTableName, id); } sqlUpdate(conn, query); hDisconnectCentral(&conn); }