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/hgTables/hgTables.c src/hg/hgTables/hgTables.c index 43f4451..5dbf879 100644 --- src/hg/hgTables/hgTables.c +++ src/hg/hgTables/hgTables.c @@ -1,28 +1,29 @@ /* hgTables - Main and utility functions for table browser. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "memalloc.h" #include "obscure.h" #include "htmshell.h" #include "cheapcgi.h" #include "cart.h" +#include "cartTrackDb.h" #include "textOut.h" #include "jksql.h" #include "hdb.h" #include "web.h" #include "hui.h" #include "hCommon.h" #include "hgColors.h" #include "trackDb.h" #include "botDelay.h" #include "grp.h" #include "customTrack.h" #include "pipeline.h" #include "hgFind.h" #include "hgTables.h" #include "joiner.h" @@ -47,51 +48,40 @@ " hgTables XXX\n" "options:\n" " -xxx=XXX\n" ); } /* Global variables. */ struct cart *cart; /* This holds cgi and other variables between clicks. */ struct hash *oldVars; /* The cart before new cgi stuff added. */ char *genome; /* Name of genome - mouse, human, etc. */ char *database; /* Current genome database - hg17, mm5, etc. */ char *freezeName; /* Date of assembly. */ struct grp *fullGroupList; /* List of all groups. */ struct grp *curGroup; /* Currently selected group. */ struct trackDb *fullTrackList; /* List of all tracks in database. */ -struct hash *fullTrackHash; /* Hash of all tracks in fullTrackList keyed by ->track field. */ -#ifdef UNUSED -struct hash *fullTrackAndSubtrackHash; /* All tracks and subtracks keyed by tdb->track field. */ -#endif /* UNUSED */ struct hash *fullTableToTdbHash; /* All tracks and subtracks keyed by tdb->table field. */ -struct trackDb *forbiddenTrackList; /* List of tracks with 'tableBrowser off' setting. */ struct trackDb *curTrack; /* Currently selected track. */ char *curTable; /* Currently selected table. */ struct joiner *allJoiner; /* Info on how to join tables. */ static struct pipeline *compressPipeline = (struct pipeline *)NULL; char *gsTemp = NULL; int saveStdout = -1; -boolean allowAllTables(void) -/* determine if all tables should is allowed by configuration */ -{ -return !cfgOptionBooleanDefault("hgta.disableAllTables", FALSE); -} - /* --------------- HTML Helpers ----------------- */ void hPrintSpaces(int count) /* Print a number of non-breaking spaces. */ { int i; for (i=0; i<count; ++i) hPrintf(" "); } static void stripHtmlTags(char *text) /* remove HTML tags from text string, replacing in place by moving * the text up to take their place */ { @@ -262,75 +252,30 @@ void dbOverrideFromTable(char buf[256], char **pDb, char **pTable) /* If *pTable includes database, overrider *pDb with it, using * buf to hold string. */ { char *s; safef(buf, 256, "%s", *pTable); s = strchr(buf, '.'); if (s != NULL) { *pDb = buf; *s++ = 0; *pTable = s; } } -static struct trackDb *getFullTrackList(struct grp **pHubGroups) -{ -struct trackDb *list = hTrackDb(database); -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 (tbOff != NULL && startsWithWord("off", tbOff)) - slAddHead(&forbiddenTrackList, tdb); - else - slAddHead(&newList, tdb); - } -slReverse(&newList); -list = newList; - -/* add wikiTrack if enabled */ -if (wikiTrackEnabled(database, NULL)) - wikiTrackDb(&list); - -struct trackDb *tdbList = hubCollectTracks(database, pHubGroups); -list = slCat(list, tdbList); - -/* Create dummy group for custom tracks if any. Add custom tracks to list */ -ctList = getCustomTracks(); -for (ct = ctList; ct != NULL; ct = ct->next) - { - slAddHead(&list, ct->tdb); - } - -return list; -} - boolean fullGenomeRegion() /* Return TRUE if region is full genome. */ { char *regionType = cartUsualString(cart, hgtaRegionType, "genome"); return sameString(regionType, "genome"); } static int regionCmp(const void *va, const void *vb) /* Compare to sort based on chrom,start */ { const struct region *a = *((struct region **)va); const struct region *b = *((struct region **)vb); int dif; dif = chrStrippedCmp(a->chrom, b->chrom); if (dif == 0) @@ -904,248 +849,65 @@ } if (track == NULL) { if (group == NULL || sameString(group->name, "all")) track = trackList; else { for (track = trackList; track != NULL; track = track->next) if (sameString(track->grp, group->name)) break; } } return track; } -struct grp *makeGroupList(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(database); -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 */ - if (addAfter != NULL) - { - group->next = addAfter->next; - addAfter->next = group; - } - else - slAddHead(&groupList, group); - hashAdd(groupsInDatabase, group->name, group); - } - -/* Do some error checking for tracks with group names that are - * not in database. Just warn about them. */ -if (!trackHubDatabase(database)) - 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; -} - static struct grp *findGroup(struct grp *groupList, char *name) /* Return named group in list, or NULL if not found. */ { struct grp *group; for (group = groupList; group != NULL; group = group->next) if (sameString(name, group->name)) return group; return NULL; } struct grp *findSelectedGroup(struct grp *groupList, char *cgiVar) /* Find user-selected group if possible. If not then * go to various levels of defaults. */ { char *defaultGroup = "genes"; char *name = cartUsualString(cart, cgiVar, defaultGroup); struct grp *group = findGroup(groupList, name); if (group == NULL) group = findGroup(groupList, defaultGroup); if (group == NULL) group = groupList; return group; } - -static void addTablesAccordingToTrackType(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(database, 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 *tablesForTrack(struct trackDb *track, boolean useJoiner) -/* Return list of all tables associated with track. */ -{ -struct hash *uniqHash = newHash(8); -struct slName *name, *nameList = NULL; -char *trackTable = track->table; - -hashAdd(uniqHash, trackTable, NULL); -if (useJoiner) - { - struct joinerPair *jpList, *jp; - jpList = joinerRelate(allJoiner, database, trackTable); - for (jp = jpList; jp != NULL; jp = jp->next) - { - struct joinerDtf *dtf = jp->b; - if (accessControlDenied(dtf->database, dtf->table)) - continue; - char buf[256]; - char *s; - if (sameString(dtf->database, database)) - 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(&nameList, uniqHash, track); -hashFree(&uniqHash); -return nameList; -} - static char *findSelectedTable(struct trackDb *track, char *var) /* Find selected table. Default to main track table if none * found. */ { if (track == NULL) return cartString(cart, var); else if (isCustomTrack(track->table)) return track->table; else { - struct slName *tableList = tablesForTrack(track, TRUE); + struct slName *tableList = cartTrackDbTablesForTrack(database, track, TRUE); char *table = cartUsualString(cart, var, tableList->name); if (slNameInList(tableList, table)) return table; return tableList->name; } } void addWhereClause(struct dyString *query, boolean *gotWhere) /* Add where clause to query. If already have a where clause * add 'and' to it. */ { if (*gotWhere) { @@ -1939,54 +1701,39 @@ char *excludeVars[] = {"Submit", "submit", NULL}; static void rAddTablesToHash(struct trackDb *tdbList, struct hash *hash) /* Add tracks in list to hash, keyed by tdb->table*/ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { hashAdd(hash, tdb->table, tdb); if (tdb->subtracks) rAddTablesToHash(tdb->subtracks, hash); } } -static struct hash *hashTrackList(struct trackDb *tdbList) -/* Return hash full of trackDb's from list, keyed by tdb->track */ -{ -struct hash *hash = hashNew(0); -struct trackDb *tdb; -for (tdb = tdbList; tdb != NULL; tdb = tdb->next) - { - hashAdd(hash, tdb->track, tdb); - } -return hash; -} - void initGroupsTracksTables() /* Get list of groups that actually have something in them, prepare hashes * containing all tracks and all tables. Set global variables that correspond * to the group, track, and table specified in the cart. */ { -struct grp *hubGrpList = NULL; -fullTrackList = getFullTrackList( &hubGrpList); -fullTrackHash = hashTrackList(fullTrackList); +cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE); fullTableToTdbHash = hashNew(0); rAddTablesToHash(fullTrackList, fullTableToTdbHash); curTrack = findSelectedTrack(fullTrackList, NULL, hgtaTrack); -fullGroupList = makeGroupList(fullTrackList, &hubGrpList, allowAllTables()); // if there isn't a current track, then use the default group if (curTrack != NULL) curGroup = findSelectedGroup(fullGroupList, hgtaGroup); else curGroup = fullGroupList; if (sameString(curGroup->name, "allTables")) curTrack = NULL; curTable = findSelectedTable(curTrack, hgtaTable); if (curTrack == NULL) { struct trackDb *tdb = hTrackDbForTrack(database, curTable); struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb); if (cTdb) curTrack = cTdb;