442377f11fc92393b84c1324bd2ca8cb5306372a kent Thu Oct 28 16:08:28 2010 -0700 Making hubs appear in group list. diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c index 23d5ac7..60a0982 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -101,30 +101,31 @@ boolean dragZooming = TRUE; struct hash *oldVars = NULL; boolean hideControls = FALSE; /* Hide all controls? */ boolean trackImgOnly = FALSE; /* caller wants just the track image and track table html */ boolean ideogramToo = FALSE; /* caller wants the ideoGram (when requesting just one track) */ /* Structure returned from findGenomePos. * We use this to to expand any tracks to full * that were found to contain the searched-upon * position string */ struct hgPositions *hgp = NULL; /* Other global variables. */ +struct trackHub *hubList = NULL; /* List of all relevant hubs. */ struct group *groupList = NULL; /* List of all tracks. */ char *browserName; /* Test or public browser */ char *organization; /* UCSC */ struct hash *trackHash = NULL; /* Hash of the tracks by their name. */ struct track *trackFindByName(struct track *tracks, char *trackName) /* find a track in tracks by name, recursively searching subtracks */ { struct track *track; for (track = tracks; track != NULL; track = track->next) { if (sameString(track->track, trackName)) return track; else if (track->subtracks != NULL) @@ -3312,81 +3313,82 @@ { if (wordCount != 3) errAbort("Expecting 3 words in pix line"); trackLayoutSetPicWidth(&tl, words[2]); } } } for (ct = ctList; ct != NULL; ct = ct->next) { hasCustomTracks = TRUE; tg = newCustomTrack(ct); slAddHead(pTrackList, tg); } } -void addTracksFromTrackHub(char *hubName, char *hubUrl, struct track **pTrackList) +void addTracksFromTrackHub(char *hubName, char *hubUrl, struct track **pTrackList, + struct trackHub **pHubList) /* Load up stuff from data hub and append to list. The hubUrl points to * a trackDb.ra format file. */ { -/* Squirrel away hub directory for later. */ -char hubDir[PATH_LEN]; -splitPath(hubUrl, hubDir, NULL, NULL); - /* Load trackDb.ra file and make it into proper trackDb tree */ struct trackHub *hub = trackHubOpen(hubUrl); +if (hub != NULL) + { struct trackHubGenome *hubGenome = trackHubFindGenome(hub, database); + hub->name = catTwoStrings("hub_", hubName); if (hubGenome != NULL) { struct trackDb *tdb, *tdbList = trackHubTracksForGenome(hub, hubGenome); uglyf("Got %d tracks from %s@%s<BR>\n", slCount(tdbList), hubName, hubUrl); trackDbAddTableField(tdbList); trackHubAddNamePrefix(hubName, tdbList); + trackHubAddGroupName(hub->name, tdbList); uglyf("added hub_%s_ prefix to track list<BR>\n", hubName); for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { trackDbFieldsFromSettings(tdb); trackDbPolish(tdb); } uglyf("polished tracks<BR>\n"); trackDbLinkUpGenerations(tdbList); uglyf("About to addTdbListToTrackList<BR>\n"); uglyOne = TRUE; addTdbListToTrackList(tdbList, NULL, pTrackList); - uglyf("Used to crash by here<BR>\n"); -#ifdef SOON -#endif /* SOON */ + if (tdbList != NULL) + slAddHead(pHubList, hub); } } +} -void loadTrackHubs(struct track **pTrackList) -/* Load up stuff from data hubs and append to list. */ +void loadTrackHubs(struct track **pTrackList, struct trackHub **pHubList) +/* Load up stuff from data hubs and append to lists. */ { char *trackHubs = cloneString(cartUsualString(cart, "trackHubs", NULL)); uglyf("trackHubs=%s\n<BR>\n", trackHubs); if (trackHubs == NULL) return; struct slPair *hubList = slPairFromString(trackHubs); uglyf("Got %d hubs<BR>\n", slCount(hubList)); struct slPair *hub; for (hub = hubList; hub != NULL; hub = hub->next) { - addTracksFromTrackHub(hub->name, hub->val, pTrackList); + addTracksFromTrackHub(hub->name, hub->val, pTrackList, pHubList); } slPairFreeValsAndList(&hubList); } boolean restrictionEnzymesOk() /* Check to see if it's OK to do restriction enzymes. */ { return (hTableExists("hgFixed", "cutters") && hTableExists("hgFixed", "rebaseRefs") && hTableExists("hgFixed", "rebaseCompanies")); } void fr2ScaffoldEnsemblLink(char *archive) /* print out Ensembl link to appropriate scaffold there */ { @@ -3759,69 +3761,88 @@ /* Determine if any member tracks are visible -- currently * recording this in the parent's visibility setting */ { tdb->visibility = tvDense; } boolean superTrackHasVisibleMembers(struct trackDb *tdb) /* Determine if any member tracks are visible -- currently * recording this in the parent's visibility setting */ { if (!tdbIsSuper(tdb)) return FALSE; return (tdb->visibility != tvHide); } -static void groupTracks(struct track **pTrackList, struct group **pGroupList, - int vis) +static void groupTracks(struct trackHub *hubList, struct track **pTrackList, + struct group **pGroupList, int vis) /* Make up groups and assign tracks to groups. * If vis is -1, restore default groups to tracks. */ { struct group *unknown = NULL; struct group *group, *list = NULL; struct hash *hash = newHash(8); struct track *track; struct trackRef *tr; struct grp* grps = hLoadGrps(database); struct grp *grp; +float maxPriority = 0; /* build group objects from database. */ for (grp = grps; grp != NULL; grp = grp->next) { /* deal with group reordering */ float priority = grp->priority; + if (priority > maxPriority) maxPriority = priority; if (withPriorityOverride) { char cartVar[512]; safef(cartVar, sizeof(cartVar), "%s.priority",grp->name); if (vis != -1) priority = (float)cartUsualDouble(cart, cartVar, grp->priority); if (priority == grp->priority) cartRemove(cart, cartVar); } /* create group object; add to list and hash */ AllocVar(group); group->name = cloneString(grp->name); group->label = cloneString(grp->label); group->defaultPriority = grp->priority; group->priority = priority; group->defaultIsClosed = grp->defaultIsClosed; slAddHead(&list, group); hashAdd(hash, grp->name, group); } grpFreeList(&grps); +/* build group objects from hub */ + { + uglyf("Got %d hubs, making groups from them<BR>\n", slCount(hubList)); + struct trackHub *hub; + for (hub = hubList; hub != NULL; hub = hub->next) + { + AllocVar(group); + group->name = cloneString(hub->name); + group->label = cloneString(hub->shortLabel); + group->defaultPriority = group->priority = maxPriority; + maxPriority += 1; + slAddHead(&list, group); + hashAdd(hash, group->name, group); + uglyf("group name %s, label %s, priority %f<BR>\n", group->name, group->label, group->priority); + } + } + /* Loop through tracks and fill in their groups. * If necessary make up an unknown group. */ for (track = *pTrackList; track != NULL; track = track->next) { /* handle track reordering feature -- change group assigned to track */ if (withPriorityOverride) { char *groupName = NULL; char cartVar[256]; /* belt and suspenders -- accomodate inconsistent track/trackDb * creation. Note -- with code cleanup, these default variables * could be retired, and the tdb versions used as defaults */ if (!track->defaultGroupName) { @@ -3860,30 +3881,31 @@ /* remove cart variables that are the same as the trackDb settings */ /* UGLY - add me back when tdb->priority is no longer pre-clobbered by cart var value if (priority == track->defaultPriority) cartRemove(cart, cartVar); */ track->priority = priority; } /* assign group object to track */ if (track->groupName == NULL) group = NULL; else group = hashFindVal(hash, track->groupName); if (group == NULL) { + uglyf("missing group for %s %s<BR>\n", track->track, track->tdb->grp); if (unknown == NULL) { AllocVar(unknown); unknown->name = cloneString("other"); unknown->label = cloneString("other"); unknown->priority = 1000000; slAddHead(&list, unknown); } group = unknown; } track->group = group; } /* Sort tracks by combined group/track priority, and * then add references to track to group. */ @@ -4044,35 +4066,34 @@ struct track *track, *trackList = NULL; registerTrackHandlers(); /* Load regular tracks, blatted tracks, and custom tracks. * Best to load custom last. */ loadFromTrackDb(&trackList); if (pcrResultParseCart(database, cart, NULL, NULL, NULL)) slSafeAddHead(&trackList, pcrResultTg()); if (userSeqString != NULL) slSafeAddHead(&trackList, userPslTg()); slSafeAddHead(&trackList, oligoMatchTg()); if (restrictionEnzymesOk()) { slSafeAddHead(&trackList, cuttersTg()); } if (wikiTrackEnabled(database, NULL)) addWikiTrack(&trackList); -loadTrackHubs(&trackList); -#ifdef SOON -#endif /* SOON */ +loadTrackHubs(&trackList, &hubList); +slReverse(&hubList); loadCustomTracks(&trackList); -groupTracks(&trackList, pGroupList, vis); +groupTracks(hubList, &trackList, pGroupList, vis); setSearchedTrackToPackOrFull(trackList); if (cgiOptionalString( "hideTracks")) changeTrackVis(groupList, NULL, tvHide); /* Get visibility values if any from ui. */ for (track = trackList; track != NULL; track = track->next) { char *s = cartOptionalString(cart, track->track); if (cgiOptionalString("hideTracks")) { s = cgiOptionalString(track->track); if (s != NULL && (hTvFromString(s) != track->tdb->visibility)) { cartSetString(cart, track->track, s); }