int hubCheckGenome(struct trackHub *hub, struct trackHubGenome *genome,
struct trackHubCheckOptions *options, struct dyString *errors)
/* Check out genome within hub. */
{
struct errCatch *errCatch = errCatchNew();
struct trackDb *tdbList = NULL;
int retVal = 0;
if (errCatchStart(errCatch))
{
tdbList = trackHubTracksForGenome(hub, genome);
tdbList = trackDbLinkUpGenerations(tdbList);
tdbList = trackDbPolishAfterLinkup(tdbList, genome->name);
trackHubPolishTrackNames(hub, tdbList);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
retVal = 1;
dyStringPrintf(errors, "%s", errCatch->message->string);
}
if (errCatch->gotWarning && !errCatch->gotError)
dyStringPrintf(errors, "%s", errCatch->message->string);
errCatchFree(&errCatch);
verbose(2, "%d tracks in %s\n", slCount(tdbList), genome->name);
struct trackDb *tdb;
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
retVal |= hubCheckTrack(hub, genome, tdb, options, errors);
}
return retVal;
}
static struct trackDb *buildTrackDb(char *org, char *database, char *hgRoot, boolean strict)
/* Build trackDb objects from files. */
{
struct hash *trackHash = newHash(0);
char rootDir[PATH_LEN], orgDir[PATH_LEN], asmDir[PATH_LEN];
/* Create track list from hgRoot and hgRoot/org and hgRoot/org/assembly
* ra format database. */
safef(rootDir, sizeof(rootDir), "%s", hgRoot);
safef(orgDir, sizeof(orgDir), "%s/%s", hgRoot, org);
safef(asmDir, sizeof(asmDir), "%s/%s/%s", hgRoot, org, database);
/* Must call these top-down.
* Also prunes things not in our release. */
layerOnRa(strict, database, rootDir, trackHash, TRUE);
layerOnRa(strict, database, orgDir, trackHash, FALSE);
layerOnRa(strict, database, asmDir, trackHash, FALSE);
/* Represent hash as list */
struct trackDb *tdbList = trackDbListFromHash(trackHash);
trackDbAddTableField(tdbList);
/* Get rid of orphans with no parent of the correct release. */
tdbList = pruneOrphans(tdbList, trackHash);
/* After this the hash is no longer needed, so get rid of it. */
hashFree(&trackHash);
/* Read in HTML bits onto what remains. */
layerOnHtml(asmDir, tdbList, database);
layerOnHtml(orgDir, tdbList, database);
layerOnHtml(rootDir, tdbList, database);
/* Set up parent/subtracks pointers. */
tdbList = trackDbLinkUpGenerations(tdbList);
rSetTrackDbFields(tdbList);
/* Fill in any additional missing info from defaults. */
rPolish(tdbList);
polishSupers(tdbList);
/* Optionally check for tables/tracks that actually exist and get rid of ones that don't. */
if (strict)
tdbList = pruneStrict(tdbList, database);
tdbList = pruneEmptyContainers(tdbList);
checkSubGroups(database,tdbList,strict);
trackDbPrioritizeContainerItems(tdbList);
return tdbList;
}
struct trackDb *hubAddTracks(struct hubConnectStatus *hub, char *database)
/* Load up stuff from data hub and append to list. The hubUrl points to
* a trackDb.ra format file. */
{
/* Load trackDb.ra file and make it into proper trackDb tree */
struct trackDb *tdbList = NULL;
struct trackHub *trackHub = hub->trackHub;
if (trackHub != NULL)
{
struct trackHubGenome *hubGenome = trackHubFindGenome(trackHub, database);
if (hubGenome != NULL)
{
tdbList = trackHubTracksForGenome(trackHub, hubGenome);
tdbList = trackDbLinkUpGenerations(tdbList);
tdbList = trackDbPolishAfterLinkup(tdbList, database);
trackDbPrioritizeContainerItems(tdbList);
trackHubPolishTrackNames(trackHub, tdbList);
}
}
return tdbList;
}
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. */
{
unsigned hubId = hubIdFromTrackName(trackName);
struct hubConnectStatus *hub = hubFromId(hubId);
struct trackHubGenome *hubGenome = trackHubFindGenome(hub->trackHub, database);
struct trackDb *tdbList = trackHubTracksForGenome(hub->trackHub, hubGenome);
tdbList = trackDbLinkUpGenerations(tdbList);
tdbList = trackDbPolishAfterLinkup(tdbList, database);
trackDbPrioritizeContainerItems(tdbList);
trackHubPolishTrackNames(hub->trackHub, tdbList);
char *fixTrackName = cloneString(trackName);
trackHubFixName(fixTrackName);
rAddTrackListToHash(trackHash, tdbList, NULL, FALSE);
if (pTdbList != NULL)
*pTdbList = slCat(*pTdbList, tdbList);
struct trackDb *tdb = hashFindVal(trackHash, fixTrackName);
if (tdb == NULL)
// superTracks aren't in the hash... look in tdbList
tdb = findSuperTrack(tdbList, fixTrackName);
if (tdb == NULL)
errAbort("Can't find track %s in %s", fixTrackName, hub->trackHub->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)
trackHubAddDescription(hubGenome->trackDbFile, parent);
return tdb;
}
