8715d83d38d8bb18adfdd9ce05771b4cede85407 angie Fri Dec 5 09:52:07 2014 -0800 Moved some hgTables code that had been copied into a couple differentplaces into a new lib module, cartTrackDb. hgGenome/import.c has code that is fairly similar but that also needs to filter out custom tracks that were generated by hgGenome. diff --git src/hg/hgVai/libifyMe.c src/hg/hgVai/libifyMe.c index 8baf084..8db79a6 100644 --- src/hg/hgVai/libifyMe.c +++ src/hg/hgVai/libifyMe.c @@ -68,222 +68,30 @@ if (range[0] != 0) isSingle = searchPosition(range, cart, cartVar); else cartSetString(cart, cartVar, hDefaultPos(db)); return isSingle; } void nbSpaces(int count) /* Print some non-breaking spaces. */ { int i; for (i=0; i<count; ++i) printf(" "); } -//#*** --------------------- almost verbatim from hgTables/custom.c (+ globals) ------------------------- -static struct customTrack *getCustomTracks(char *database, struct cart *cart) -/* Get custom track list. */ -{ -static struct slName *browserLines = NULL; -static struct customTrack *theCtList = NULL; -if (theCtList == NULL) - theCtList = customTracksParseCart(database, cart, &browserLines, NULL); -return theCtList; -} -//#*** --------------------- end verbatim from hgTables/custom.c ------------------------- - -boolean hasCustomTracks(struct cart *cart) -/* Return TRUE if cart has custom tracks for the current db. */ -{ -char *db = cartString(cart, "db"); -struct customTrack *ctList = getCustomTracks(db, cart); -return (ctList != NULL); -} - -//#*** libify to hg/lib/wikiTrack.c -//#*** should it sort trackDb, or leave that to the caller? -void wikiTrackDb(struct trackDb **list) -/* create a trackDb entry for the wiki track */ -{ -struct trackDb *tdb; - -AllocVar(tdb); -tdb->track = WIKI_TRACK_TABLE; -tdb->table = WIKI_TRACK_TABLE; -tdb->shortLabel = WIKI_TRACK_LABEL; -tdb->longLabel = WIKI_TRACK_LONGLABEL; -tdb->visibility = tvFull; -tdb->priority = WIKI_TRACK_PRIORITY; - -tdb->html = hFileContentsOrWarning(hHelpFile(tdb->track)); -tdb->type = "none"; -tdb->grp = "map"; -tdb->canPack = FALSE; - -slAddHead(list, tdb); -slSort(list, trackDbCmp); -} - -static struct trackDb *getFullTrackList(struct cart *cart, struct hubConnectStatus *hubList, - struct grp **pHubGroups) -/* Get all tracks including custom tracks if any. *pHubGroups is reversed. */ -{ -char *db = cartString(cart, "db"); -struct trackDb *list = hTrackDb(db); -struct customTrack *ctList, *ct; - -/* exclude any track with a 'tableBrowser off' setting */ -//#*** NOTE: this only scans top-level tdb's, and would miss a setting applied -//#*** only to lower levels. So far we have not encountered such a track. -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 (tbOff == NULL || !startsWithWord("off", tbOff)) - slAddHead(&newList, tdb); - } -slReverse(&newList); -list = newList; - -/* add wikiTrack if enabled */ -if (wikiTrackEnabled(db, NULL)) - wikiTrackDb(&list); - -/* Add hub tracks. */ -struct trackDb *hubTrackList = hubCollectTracks(db, pHubGroups); -if (hubTrackList != NULL) - list = slCat(list, hubTrackList); - -/* Add custom tracks to list */ -ctList = getCustomTracks(db, cart); -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 *groupsInDb = newHash(0); -struct trackDb *track; - -/* Stream through track list building up hash of active groups. */ -for (track = trackList; track != NULL; track = track->next) - hashStoreName(groupsInTrackList, track->grp); - -/* 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(groupsInDb, 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 (sameString(groupList->name, "user")) - addAfter = groupList; - -/* Add in groups from hubs. *pHubGrpList is reversed, so we add at head to restore order. */ -for (group = slPopHead(pHubGrpList); group != NULL; group = slPopHead(pHubGrpList)) - { - /* check to see if we're inserting hubs rather than - * adding them to the front of the list */ - if (addAfter != NULL) - { - group->next = addAfter->next; - addAfter->next = group; - } - else - slAddHead(&groupList, group); - hashAdd(groupsInDb, group->name, group); - } - -/* Do some error checking for tracks with group names that are - * not in db. Just warn about them. */ -for (track = trackList; track != NULL; track = track->next) - { - if (!hashLookup(groupsInDb, 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(&groupsInDb); -return groupList; -} - -void initGroupsTracksTables(struct cart *cart, - struct trackDb **retFullTrackList, struct grp **retFullGroupList) -/* Get lists of all tracks and of groups that actually have tracks in them. */ -{ -static boolean inited = FALSE; -static struct trackDb *fullTrackList = NULL; -static struct grp *fullGroupList = NULL; -if (! inited) - { - struct hubConnectStatus *hubList = hubConnectStatusListFromCart(cart); - struct grp *hubGrpList = NULL; - fullTrackList = getFullTrackList(cart, hubList, &hubGrpList); - char *db= cartString(cart, "db"); - fullGroupList = makeGroupList(db, fullTrackList, &hubGrpList, FALSE); - inited = TRUE; - } -if (retFullTrackList != NULL) - *retFullTrackList = fullTrackList; -if (retFullGroupList != NULL) - *retFullGroupList = fullGroupList; -} - //#*** duplicated in hgVarAnnoGrator and annoGratorTester struct annoAssembly *getAnnoAssembly(char *db) /* Make annoAssembly for db. */ { static struct annoAssembly *aa = NULL; if (aa == NULL) { char *nibOrTwoBitDir = hDbDbNibPath(db); if (nibOrTwoBitDir == NULL) errAbort("Can't find .2bit for db '%s'", db); char twoBitPath[HDB_MAX_PATH_STRING]; safef(twoBitPath, sizeof(twoBitPath), "%s/%s.2bit", nibOrTwoBitDir, db); char *path = hReplaceGbdb(twoBitPath); aa = annoAssemblyNew(db, path); freeMem(path);