3d00d8348e1cb6eafec60cc3d7321f6de7e669be braney Mon Dec 12 13:09:49 2022 -0800 be smarter about showing the user error messages diff --git src/hg/lib/hubConnect.c src/hg/lib/hubConnect.c index 05ff98f..503a1e7 100644 --- src/hg/lib/hubConnect.c +++ src/hg/lib/hubConnect.c @@ -134,30 +134,31 @@ struct trackHubGenome *genomes = hub->genomeList; /* List of associated genomes. */ for(; genomes; genomes = genomes->next) if (sameString(genomes->name, database)) return TRUE; } return FALSE; } static struct trackHub *fetchHub(struct hubConnectStatus *hubStatus, char **errorMessage) { struct errCatch *errCatch = errCatchNew(); struct trackHub *tHub = NULL; boolean gotWarning = FALSE; char *url = hubStatus->hubUrl; +*errorMessage = NULL; char hubName[64]; safef(hubName, sizeof(hubName), "hub_%d", hubStatus->id); if (errCatchStart(errCatch)) tHub = trackHubOpen(url, cloneString(hubName)); // open hub errCatchEnd(errCatch); if (errCatch->gotError) { gotWarning = TRUE; *errorMessage = cloneString(errCatch->message->string); } errCatchFree(&errCatch); if (gotWarning) @@ -182,49 +183,50 @@ struct hubConnectStatus *hubConnectStatusForId(struct sqlConnection *conn, int id) { struct hubConnectStatus *hub = NULL; char query[1024]; sqlSafef(query, sizeof(query), "select hubUrl,status, errorMessage,lastNotOkTime, shortLabel from %s where id=%d", getHubStatusTableName(), id); struct sqlResult *sr = sqlGetResult(conn, query); char **row = sqlNextRow(sr); if (row != NULL) { AllocVar(hub); hub->id = id; hub->hubUrl = cloneString(row[0]); hub->status = sqlUnsigned(row[1]); hub->errorMessage = cloneString(row[2]); - char *shortLabel = row[4]; + hub->shortLabel = cloneString(row[4]); if (isEmpty(row[2]) || hubTimeToCheck(hub, row[3])) { char *errorMessage = NULL; hub->trackHub = fetchHub( hub, &errorMessage); if (hub->trackHub) hub->trackHub->hubStatus = hub; hub->errorMessage = cloneString(errorMessage); hubUpdateStatus( hub->errorMessage, hub); if (!isEmpty(hub->errorMessage)) { boolean isCollection = (strstr(hub->hubUrl, "hgComposite") != NULL); if (isCollection) warn("You created a <a href=\"/cgi-bin/hgCollection\"><b>Track " "Collection</b></a> that has expired and been removed. Track Collections " "expire 48 hours after their last use. <a href=\"/cgi-bin/hgSession\"><b>" "Save your session</b></a> to preserve collections long-term and to allow sharing."); - else - warn("Could not connect to hub \"%s\": %s", shortLabel, hub->errorMessage); + // commenting this out, but leaving it in the source because we might use it later. + //else + //warn("Could not connect to hub \"%s\": %s", hub->shortLabel, hub->errorMessage); } } } sqlFreeResult(&sr); 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) { @@ -505,30 +507,32 @@ errAbort("opened hub, but could not get it out of the hubStatus table"); } } /* allocate a hub */ struct hubConnectStatus *hub = NULL; AllocVar(hub); hub->id = id; hub->hubUrl = cloneString(url); /* new fetch the contents of the hub to fill in the status table */ struct trackHub *tHub = fetchHub( hub, &errorMessage); if (tHub != NULL) hub->trackHub = tHub; +if (errorMessage != NULL) + hub->errorMessage = cloneString(errorMessage); /* update the status table with the lastest label and database information */ hubUpdateStatus( errorMessage, hub); /* if we're turning on the hub, set the cart variable */ if (set) { char hubName[32]; safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id); cartSetString(cart, hubName, "1"); } return hub; } @@ -622,30 +626,32 @@ if ((wantFirstDb != NULL) && (hub->trackHub != NULL)) // choose the first db newDatabase = hub->trackHub->defaultDb; else if (assemblyDb != NULL) { // Check to see if the user specified an assembly within // an assembly hub. struct trackHub *trackHub = hub->trackHub; if (trackHub != NULL) { struct trackHubGenome *genomeList = trackHub->genomeList; for(; genomeList; genomeList = genomeList->next) { if (sameString(assemblyDb, hubConnectSkipHubPrefix(genomeList->name))) { + if (hub->errorMessage) + errAbort("Hub error: %s", hub->errorMessage); newDatabase = genomeList->name; break; } } } } } } cartRemove(cart, hgHubDataClearText); cartRemove(cart, hgHubDataText); cartRemove(cart, hgHubDoFirstDb); cartRemove(cart, hgHubGenome); return newDatabase; } @@ -786,31 +792,31 @@ if (doCache) trackDbHubCloneTdbListToSharedMem(hubGenome->trackDbFile, tdbList, memCheckPoint(), incFiles->string); } } return tdbList; } static struct grp *grpFromHub(struct hubConnectStatus *hub) /* Make up a grp structur from hub */ { struct grp *grp; AllocVar(grp); char name[16]; safef(name, sizeof(name), "hub_%d", hub->id); grp->name = cloneString(name); -grp->label = cloneString(hub->trackHub->shortLabel); +grp->label = cloneString(hub->shortLabel); return grp; } struct trackDb *hubCollectTracks( char *database, struct grp **pGroupList) /* Generate trackDb structures for all the tracks in attached hubs. * Make grp structures for each hub. Returned group list is reversed. */ { // return the cached copy if it exists static struct trackDb *hubTrackDbs; static struct grp *hubGroups; if (hubTrackDbs != NULL) { if (pGroupList != NULL) *pGroupList = hubGroups; @@ -833,30 +839,37 @@ errCatchEnd(errCatch); if (errCatch->gotError) { warn("%s", errCatch->message->string); hubUpdateStatus( errCatch->message->string, hub); } else { struct grp *grp = grpFromHub(hub); slAddHead(&hubGroups, grp); hubUpdateStatus(NULL, hub); } errCatchFree(&errCatch); } + else + { + /* create an empty group to hold the error message. */ + struct grp *grp = grpFromHub(hub); + grp->errMessage = hub->errorMessage; + slAddHead(&hubGroups, grp); + } } hubTrackDbs = tdbList; if (pGroupList != NULL) *pGroupList = hubGroups; return tdbList; } static struct hubConnectStatus *globalHubList; struct hubConnectStatus *hubConnectGetHubs() /* return the static global to the track data hubs */ { return globalHubList; } @@ -1005,31 +1018,36 @@ char *path = &dir[sizeof hubCuratedPrefix - 1]; char url[4096]; safef(url, sizeof url, "%s/%s/hub.txt", path, curatedHubPrefix); struct hubConnectStatus *status = getAndSetHubStatus( cart, url, TRUE); if (status && isEmpty(status->errorMessage)) { char buffer[4096]; safef(buffer, sizeof buffer, "hub_%d_%s", status->id, db); dbOveride = cloneString(buffer); return status->id; } else + { + if (!isEmpty(status->errorMessage)) + errAbort("Hub error: url %s: error %s.", url, status->errorMessage); + else errAbort("Cannot open hub %s.", url); + } } return 0; } char *hubConnectLoadHubs(struct cart *cart) /* load the track data hubs. Set a static global to remember them */ { int newCuratedHubId = 0; char *dbSpec = cartOptionalString(cart, "db"); char *curatedHubPrefix = cfgOption("curatedHubPrefix"); if (isEmpty(curatedHubPrefix)) curatedHubPrefix = "public"; if (dbSpec != NULL)