533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/lib/cartTrackDb.c src/hg/lib/cartTrackDb.c deleted file mode 100644 index 702d4d8..0000000 --- src/hg/lib/cartTrackDb.c +++ /dev/null @@ -1,447 +0,0 @@ -/* 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); - -/* 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); - -/* 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 custom tracks at head of list -struct customTrack *ctList, *ct; -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; - -/* Do some error checking for tracks with group names that are not in database. - * Warnings at this stage mess up CGIs that may produce text output like hgTables & hgIntegrator, - * so don't warn, just put CTs in group user and others in group x. */ -groupsAll = hLoadGrps(db); -if (!trackHubDatabase(db)) - { - struct hash *allGroups = hashNew(0); - for (group = groupsAll; group != NULL; group = group->next) - hashAdd(allGroups, group->name, group); - for (track = trackList; track != NULL; track = track->next) - { - /* If track isn't in a track up, and has a group we don't know about, change it to one we do. */ - if (!startsWith("hub_", track->grp) && !hashLookup(allGroups, track->grp)) - { - fprintf(stderr, "Track %s has group %s, which isn't in grp table\n", - track->table, track->grp); - if (isCustomTrack(track->track)) - track->grp = cloneString("user"); - else - track->grp = cloneString("x"); - } - } - hashFree(&allGroups); - } - -/* 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. */ -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); - } - -/* 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); - } -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; - -/* suppress for parent tracks -- only the subtracks have tables */ -if (track->subtracks == NULL) - { - name = slNameNew(trackTable); - slAddHead(&nameList, name); - hashAdd(uniqHash, trackTable, NULL); - } -addTablesAccordingToTrackType(db, &nameList, uniqHash, track); -if (useJoiner) - { - if (allJoiner == NULL) - allJoiner = joinerRead("all.joiner"); - struct slName *joinedList = NULL, *t; - for (t = nameList; t != NULL; t = t->next) - { - struct joinerPair *jpList, *jp; - jpList = joinerRelate(allJoiner, db, t->name, db); - 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(&joinedList, name); - } - } - } - slNameSort(&joinedList); - nameList = slCat(nameList, joinedList); - } -hashFree(&uniqHash); -return nameList; -}