void addVersion(boolean strict, char *database, char *dirName, char *raName,
struct hash *uniqHash,
struct hash *htmlHash,
struct hgFindSpec **pSpecList)
/* Read in specs from raName and add them to list/database if new. */
{
struct hgFindSpec *hfsList = NULL, *hfs = NULL;
struct hgFindSpec *hfsNext = NULL;
hfsList = hgFindSpecFromRa(database, raName, NULL);
/* prune records of the incorrect release */
hfsList = pruneRelease(hfsList);
if (strict)
{
for (hfs = hfsList; hfs != NULL; hfs = hfsNext)
{
hfsNext = hfs->next;
if (! hTableOrSplitExists(database, hfs->searchTable))
{
if (verboseLevel() > 1)
printf("%s missing\n", hfs->searchTable);
slRemoveEl(&hfsList, hfs);
}
else if (hfs->xrefTable[0] != 0)
{
// Use sqlTableExists because xrefTable might be $db.$table,
// not supported by hTableExists / hTableOrSplitExists
// NOTE hfs->xrefTable can sometimes contain a comma-separated table list,
// rather than just a single table.
struct sqlConnection *conn = hAllocConn(database);
char *tables = replaceChars(hfs->xrefTable, ",", " ");
boolean exists = sqlTablesExist(conn, tables);
hFreeConn(&conn);
freeMem(tables);
if (! exists)
{
if (verboseLevel() > 1)
printf("%s (xref) missing\n", hfs->xrefTable);
slRemoveEl(&hfsList, hfs);
}
}
}
}
for (hfs = hfsList; hfs != NULL; hfs = hfsNext)
{
hfsNext = hfs->next;
if (! hashLookup(uniqHash, hfs->searchName))
{
hashAdd(uniqHash, hfs->searchName, hfs);
slAddHead(pSpecList, hfs);
}
}
}
static boolean canIntersect(char *db, char *table)
/* Return true if table exists and is positional. */
{
if (isCustomTrack(table) && ctLookupName(table) != NULL)
return TRUE;
if (sameWord(table, WIKI_TRACK_TABLE))
return TRUE;
if (hTableOrSplitExists(db, table))
return isPositional(db, table);
return FALSE;
}
boolean canIntersect(char *db, char *table)
/* Return true if table exists and is positional. */
{
if (isCustomTrack(table) && ctLookupName(table) != NULL)
return TRUE;
if (isBamTable(table))
return TRUE;
if (isBigWigTable(table))
return TRUE;
if (isBigBed(database, table, curTrack, ctLookupName))
return TRUE;
if (isVcfTable(table, NULL))
return TRUE;
if (isHubTrack(table))
return TRUE;
if (sameWord(table, WIKI_TRACK_TABLE))
return TRUE;
if (hTableOrSplitExists(db, table))
return isPositional(db, table);
return FALSE;
}
static struct trackDb *pruneStrict(struct trackDb *tdbList, char *db)
/* Remove tracks without data. For parent tracks data in any child is sufficient to keep
* them alive. */
{
struct trackDb *newList = NULL, *tdb, *next;
for (tdb = tdbList; tdb != NULL; tdb = next)
{
next = tdb->next;
verbose(3,"pruneStrict checking track: '%s'\n", tdb->track);
if (tdb->subtracks != NULL)
{
tdb->subtracks = pruneStrict(tdb->subtracks, db);
}
if (tdb->subtracks != NULL)
{
slAddHead(&newList, tdb);
}
else if (hTableOrSplitExists(db, tdb->table))
{
slAddHead(&newList, tdb);
}
else if (tdbIsDownloadsOnly(tdb))
{
slAddHead(&newList, tdb);
}
// We will allow these at some point, but currently(10/10/2011) the table browser still chokes.
//else if (trackDbSetting(tdb, "bigDataUrl") != NULL)
// {
// slAddHead(&newList, tdb);
// }
else
verbose(3,"pruneStrict removing track: '%s' no table %s\n", tdb->track, tdb->table);
}
slReverse(&newList);
return newList;
}