7f396ae51fb175f8a7785556f329d3391596b4b0 braney Mon Feb 23 16:07:03 2015 -0800 fix duplicated lines in group menu bug #14878 diff --git src/hg/lib/cartTrackDb.c src/hg/lib/cartTrackDb.c index b8cbf71..eb18344 100644 --- src/hg/lib/cartTrackDb.c +++ src/hg/lib/cartTrackDb.c @@ -1,380 +1,381 @@ /* cartTrackDb - Combine custom tracks, hub tracks & hTrackDb to get unified groups/tracks/tables */ #include "common.h" #include "cartTrackDb.h" #include "cheapcgi.h" #include "customTrack.h" #include "hash.h" #include "hCommon.h" #include "hdb.h" #include "hgConfig.h" #include "hgMaf.h" #include "hubConnect.h" #include "joiner.h" #include "trackHub.h" #include "wikiTrack.h" /* Static globals */ static boolean useAC = FALSE; static struct trackDb *forbiddenTrackList = NULL; static struct trackDb *getFullTrackList(struct cart *cart, char *db, struct grp **pHubGroups) { struct trackDb *list = hTrackDb(db); struct customTrack *ctList, *ct; /* exclude any track with a 'tableBrowser off' setting */ struct trackDb *tdb, *nextTdb, *newList = NULL; for (tdb = list; tdb != NULL; tdb = nextTdb) { nextTdb = tdb->next; if (tdbIsDownloadsOnly(tdb) || tdb->table == NULL) { //freeMem(tdb); // should not free tdb's. // While hdb.c should and says it does cache the tdbList, it doesn't. // The most notable reason that the tdbs are not cached is this hgTables CGI !!! // It needs to be rewritten to make tdbRef structures for the lists it creates here! continue; } char *tbOff = trackDbSetting(tdb, "tableBrowser"); if (useAC && tbOff != NULL && startsWithWord("off", tbOff)) slAddHead(&forbiddenTrackList, tdb); else slAddHead(&newList, tdb); } slReverse(&newList); list = newList; /* add wikiTrack if enabled */ if (wikiTrackEnabled(db, NULL)) slAddHead(&list, wikiTrackDb()); slSort(&list, trackDbCmp); // Add hub tracks at head of list struct trackDb *hubTdbList = hubCollectTracks(db, pHubGroups); list = slCat(list, hubTdbList); // Add custom tracks at head of list ctList = customTracksParseCart(db, cart, NULL, NULL); for (ct = ctList; ct != NULL; ct = ct->next) { slAddHead(&list, ct->tdb); } return list; } static struct grp *makeGroupList(char *db, struct trackDb *trackList, struct grp **pHubGrpList, boolean allTablesOk) /* Get list of groups that actually have something in them. */ { struct grp *groupsAll, *groupList = NULL, *group; struct hash *groupsInTrackList = newHash(0); struct hash *groupsInDatabase = newHash(0); struct trackDb *track; /* Stream through track list building up hash of active groups. */ for (track = trackList; track != NULL; track = track->next) { if (!hashLookup(groupsInTrackList,track->grp)) hashAdd(groupsInTrackList, track->grp, NULL); } /* Scan through group table, putting in ones where we have data. */ groupsAll = hLoadGrps(db); for (group = slPopHead(&groupsAll); group != NULL; group = slPopHead(&groupsAll)) { if (hashLookup(groupsInTrackList, group->name)) { slAddTail(&groupList, group); hashAdd(groupsInDatabase, group->name, group); } else grpFree(&group); } /* if we have custom tracks, we want to add the track hubs * after that group */ struct grp *addAfter = NULL; if ((groupList != NULL) && sameString(groupList->name, "user")) addAfter = groupList; /* Add in groups from hubs. */ for (group = slPopHead(pHubGrpList); group != NULL; group = slPopHead(pHubGrpList)) { // if the group isn't represented in any track, don't add it to list if (!hashLookup(groupsInTrackList,group->name)) continue; /* check to see if we're inserting hubs rather than * adding them to the front of the list */ + struct grp *newGrp = grpDup(group); if (addAfter != NULL) { - group->next = addAfter->next; - addAfter->next = group; + newGrp->next = addAfter->next; + addAfter->next = newGrp; } else - slAddHead(&groupList, group); - hashAdd(groupsInDatabase, group->name, group); + slAddHead(&groupList, newGrp); + hashAdd(groupsInDatabase, newGrp->name, newGrp); } /* Do some error checking for tracks with group names that are * not in database. Just warn about them. */ if (!trackHubDatabase(db)) for (track = trackList; track != NULL; track = track->next) { if (!hashLookup(groupsInDatabase, track->grp)) warn("Track %s has group %s, which isn't in grp table", track->table, track->grp); } /* Create dummy group for all tracks. */ AllocVar(group); group->name = cloneString("allTracks"); group->label = cloneString("All Tracks"); slAddTail(&groupList, group); /* Create another dummy group for all tables. */ if (allTablesOk) { AllocVar(group); group->name = cloneString("allTables"); group->label = cloneString("All Tables"); slAddTail(&groupList, group); } hashFree(&groupsInTrackList); hashFree(&groupsInDatabase); return groupList; } void cartTrackDbInit(struct cart *cart, struct trackDb **retFullTrackList, struct grp **retFullGroupList, boolean useAccessControl) /* Get lists of all tracks and of groups that actually have tracks in them. * If useAccessControl, exclude tracks with 'tableBrowser off' nor tables listed * in the table tableAccessControl. */ { char *db = cartString(cart, "db"); useAC = useAccessControl; struct grp *hubGrpList = NULL; struct trackDb *fullTrackList = getFullTrackList(cart, db, &hubGrpList); boolean allTablesOk = hAllowAllTables() && !trackHubDatabase(db); struct grp *fullGroupList = makeGroupList(db, fullTrackList, &hubGrpList, allTablesOk); if (retFullTrackList != NULL) *retFullTrackList = fullTrackList; if (retFullGroupList != NULL) *retFullGroupList = fullGroupList; } static char *chopAtFirstDot(char *string) /* Terminate string at first '.' if found. Return string for convenience. */ { char *ptr = strchr(string, '.'); if (ptr != NULL) *ptr = '\0'; return string; } static void hashAddSlName(struct hash *hash, char *key, char *val) /* If key is already in hash, add an slName for val to the head of the list; * otherwise just store key -> slName for val. */ { struct slName *sln = slNameNew(val); struct hashEl *hel = hashLookup(hash, key); if (hel == NULL) hashAdd(hash, key, sln); else slAddHead(&(hel->val), sln); } static struct hash *accessControlInit(struct sqlConnection *conn) /* Return a hash associating restricted table/track names in the given db/conn * with virtual hosts, or NULL if there is no tableAccessControl table and no * forbiddenTrackList (see getFullTrackList). */ { struct hash *acHash = NULL; if (sqlTableExists(conn, "tableAccessControl")) { struct sqlResult *sr = NULL; char **row = NULL; acHash = newHash(0); sr = sqlGetResult(conn, "NOSQLINJ select name,host from tableAccessControl"); while ((row = sqlNextRow(sr)) != NULL) hashAddSlName(acHash, row[0], chopAtFirstDot(row[1])); sqlFreeResult(&sr); } if (forbiddenTrackList != NULL) { if (acHash == NULL) acHash = newHash(0); struct trackDb *tdb; for (tdb = forbiddenTrackList; tdb != NULL; tdb = tdb->next) { char *tbOff = cloneString(trackDbSetting(tdb, "tableBrowser")); if (isEmpty(tbOff)) errAbort("bug: tdb for %s is in forbiddenTrackList without 'tableBrowser off' setting", tdb->track); hashAddSlName(acHash, tdb->table, "-"); // skip "off" and look for additional table names: nextWord(&tbOff); char *tbl; while ((tbl = nextWord(&tbOff)) != NULL) hashAddSlName(acHash, tbl, "-"); } } return acHash; } boolean cartTrackDbIsAccessDenied(char *db, char *table) /* Return TRUE if useAccessControl=TRUE was passed to cartTrackDbInit and * if access to table is denied (at least on this host) by 'tableBrowser off' * or by the tableAccessControl table. */ { static char *currentHost = NULL; static struct hash *dbToAcHash = NULL; if (!useAC) return FALSE; struct slName *enabledHosts = NULL; struct slName *sln = NULL; if (dbToAcHash == NULL) dbToAcHash = hashNew(0); struct hash *acHash = hashFindVal(dbToAcHash, db); if (acHash == NULL) { struct sqlConnection *conn = hAllocConn(db); acHash = accessControlInit(conn); hFreeConn(&conn); hashAdd(dbToAcHash, db, acHash); } if (acHash == NULL) return FALSE; enabledHosts = (struct slName *)hashFindVal(acHash, table); if (enabledHosts == NULL) return FALSE; if (currentHost == NULL) { currentHost = cloneString(cgiServerName()); if (currentHost == NULL) { warn("accessControl: unable to determine current host"); return FALSE; } else chopAtFirstDot(currentHost); } for (sln = enabledHosts; sln != NULL; sln = sln->next) { if (sameString(currentHost, sln->name)) return FALSE; } return TRUE; } static void addTablesAccordingToTrackType(char *db, struct slName **pList, struct hash *uniqHash, struct trackDb *track) /* Parse out track->type and if necessary add some tables from it. */ { struct slName *name; char *trackDupe = cloneString(track->type); if (trackDupe != NULL && trackDupe[0] != 0) { char *s = trackDupe; char *type = nextWord(&s); if (sameString(type, "wigMaf")) { static char *wigMafAssociates[] = {"frames", "summary"}; int i; for (i=0; i<ArraySize(wigMafAssociates); ++i) { char *setting = wigMafAssociates[i]; char *table = trackDbSetting(track, setting); if (table != NULL) { name = slNameNew(table); slAddHead(pList, name); hashAdd(uniqHash, table, NULL); } } /* include conservation wiggle tables */ struct consWiggle *wig, *wiggles = wigMafWiggles(db, track); slReverse(&wiggles); for (wig = wiggles; wig != NULL; wig = wig->next) { name = slNameNew(wig->table); slAddHead(pList, name); hashAdd(uniqHash, wig->table, NULL); } } if (track->subtracks) { struct slName *subList = NULL; struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks); slSort(&tdbRefList, trackDbRefCmp); struct slRef *tdbRef; for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *subTdb = tdbRef->val; name = slNameNew(subTdb->table); slAddTail(&subList, name); hashAdd(uniqHash, subTdb->table, NULL); } pList = slCat(pList, subList); } } freez(&trackDupe); } struct slName *cartTrackDbTablesForTrack(char *db, struct trackDb *track, boolean useJoiner) /* Return list of all tables associated with track. If useJoiner, the result can include * non-positional tables that are related to track by all.joiner. */ { static struct joiner *allJoiner = NULL; struct hash *uniqHash = newHash(8); struct slName *name, *nameList = NULL; char *trackTable = track->table; hashAdd(uniqHash, trackTable, NULL); if (useJoiner) { if (allJoiner == NULL) allJoiner = joinerRead("all.joiner"); struct joinerPair *jpList, *jp; jpList = joinerRelate(allJoiner, db, trackTable); for (jp = jpList; jp != NULL; jp = jp->next) { struct joinerDtf *dtf = jp->b; if (cartTrackDbIsAccessDenied(dtf->database, dtf->table)) continue; char buf[256]; char *s; if (sameString(dtf->database, db)) s = dtf->table; else { safef(buf, sizeof(buf), "%s.%s", dtf->database, dtf->table); s = buf; } if (!hashLookup(uniqHash, s)) { hashAdd(uniqHash, s, NULL); name = slNameNew(s); slAddHead(&nameList, name); } } slNameSort(&nameList); } /* suppress for parent tracks -- only the subtracks have tables */ if (track->subtracks == NULL) { name = slNameNew(trackTable); slAddHead(&nameList, name); } addTablesAccordingToTrackType(db, &nameList, uniqHash, track); hashFree(&uniqHash); return nameList; }