c74baf995ca1b7d3de1b1af4b125afa4c9d39b39 angie Wed Jun 22 08:55:07 2016 -0700 Yet another case of assuming a mysql db, which breaks track hubs. refs #17582 MLQ and probably a follow-up patch request. diff --git src/hg/lib/cartTrackDb.c src/hg/lib/cartTrackDb.c index 984fce9..3efab84 100644 --- src/hg/lib/cartTrackDb.c +++ src/hg/lib/cartTrackDb.c @@ -1,425 +1,428 @@ /* 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 slRef *accessControlTrackRefList = 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) || startsWithWord("noGenome", tbOff))) { slAddHead(&accessControlTrackRefList, slRefNew(tdb)); if (! startsWithWord("off", tbOff)) slAddHead(&newList, 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) { newGrp->next = addAfter->next; addAfter->next = newGrp; } else 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; } struct accessControl /* Restricted permission settings for a table */ { struct slName *hostList; // List of hosts that are allowed to view this table boolean isNoGenome; // True if it's OK for position range but not genome-wide query }; void accessControlAddHost(struct accessControl *ac, char *host) /* Alloc an slName for host (unless NULL or empty) and add it to ac->hostList. */ { if (isNotEmpty(host)) slAddHead(&ac->hostList, slNameNew(host)); } struct accessControl *accessControlNew(char *host, boolean isNoGenome) /* Alloc, init & return accessControl. */ { struct accessControl *ac; AllocVar(ac); accessControlAddHost(ac, host); ac->isNoGenome = isNoGenome; return ac; } static void acHashAddOneTable(struct hash *acHash, char *table, char *host, boolean isNoGenome) /* If table is already in acHash, update its accessControl fields; otherwise store a * new accessControl for table. */ { struct hashEl *hel = hashLookup(acHash, table); if (hel == NULL) { struct accessControl *ac = accessControlNew(host, isNoGenome); hashAdd(acHash, table, ac); } else { struct accessControl *ac = hel->val; ac->isNoGenome = isNoGenome; accessControlAddHost(ac, host); } } static struct hash *accessControlInit(char *db) /* Return a hash associating restricted table/track names in the given db/conn * with virtual hosts -- hash is empty if there is no tableAccessControl table and no * accessControlTrackRefList (see getFullTrackList). */ { struct hash *acHash = hashNew(0); +if (! trackHubDatabase(db)) + { struct sqlConnection *conn = hAllocConn(db); 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) acHashAddOneTable(acHash, row[0], chopAtFirstDot(row[1]), FALSE); sqlFreeResult(&sr); } + hFreeConn(&conn); + } struct slRef *tdbRef; for (tdbRef = accessControlTrackRefList; tdbRef != NULL; tdbRef = tdbRef->next) { struct trackDb *tdb = tdbRef->val; char *tbOff = cloneString(trackDbSetting(tdb, "tableBrowser")); if (isEmpty(tbOff)) errAbort("accessControlInit bug: tdb for %s does not have tableBrowser setting", tdb->track); // First word is "off" or "noGenome": char *type = nextWord(&tbOff); boolean isNoGenome = sameString(type, "noGenome"); // Add track table to acHash: acHashAddOneTable(acHash, tdb->table, NULL, isNoGenome); // Remaining words are additional table names to add: char *tbl; while ((tbl = nextWord(&tbOff)) != NULL) acHashAddOneTable(acHash, tbl, NULL, isNoGenome); } -hFreeConn(&conn); return acHash; } static struct hash *getCachedAcHash(char *db) /* Returns a hash that maps table names to accessControl, creating it if necessary. */ { static struct hash *dbToAcHash = NULL; if (dbToAcHash == NULL) dbToAcHash = hashNew(0); struct hash *acHash = hashFindVal(dbToAcHash, db); if (acHash == NULL) { acHash = accessControlInit(db); hashAdd(dbToAcHash, db, acHash); } return acHash; } static char *getCachedCurrentHost() /* Return the current host name chopped at the first '.' or NULL if not in the CGI environment. */ { static char *currentHost = NULL; if (currentHost == NULL) { currentHost = cloneString(cgiServerName()); if (currentHost == NULL) return NULL; else chopAtFirstDot(currentHost); } return currentHost; } 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. */ { if (!useAC) return FALSE; struct hash *acHash = getCachedAcHash(db); struct accessControl *ac = hashFindVal(acHash, table); if (ac == NULL) return FALSE; if (ac->isNoGenome && ac->hostList == NULL) return FALSE; char *currentHost = getCachedCurrentHost(); if (currentHost == NULL) warn("accessControl: unable to determine current host"); return (! slNameInList(ac->hostList, currentHost)); } boolean cartTrackDbIsNoGenome(char *db, char *table) /* Return TRUE if range queries, but not genome-queries, are permitted for this table. */ { struct hash *acHash = getCachedAcHash(db); struct accessControl *ac = hashFindVal(acHash, table); return (ac != NULL && ac->isNoGenome); } 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; }