static void wikiTrackMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) /* create a special map box item with different i=hgcClickName and * pop-up statusLine with the item name */ { char *userName; /* already been determined to be enabled by getting here, need to verify * userName vs editors and vs owner */ (void) wikiTrackEnabled(database, &userName); char *hgcClickName = tg->mapItemName(tg, item); char *statusLine = tg->itemName(tg, item); boolean editor = isWikiEditor(userName); struct wikiTrack *wikiItem = NULL; boolean enableHgcClick = FALSE; /* allow hgc click (i.e. delete privs) if the following are true 1. this is the item 0 "add new item" 2. logged into the wiki 3. user is an editor or user is the owner */ if (differentWord("0", hgcClickName)) wikiItem = findWikiItemId(hgcClickName); else enableHgcClick = TRUE; /* item 0 "add new item" must go to hgc */ if (wikiItem) { if (isNotEmpty(userName) && sameWord(userName, wikiItem->owner)) enableHgcClick = TRUE; /* owner has delete privls */ if (editor) enableHgcClick = TRUE; /* editors have delete privls */ } if (enableHgcClick) { mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track, hgcClickName, statusLine, NULL, FALSE, NULL ); } else { /* go directly to the wiki description */ char *directUrl = wikiUrl(wikiItem); mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track, hgcClickName, statusLine, directUrl, FALSE, NULL); freeMem(directUrl); } }
void addWikiTrack(struct track **pGroupList) /* Add wiki track and append to group list. */ { if (wikiTrackEnabled(database, NULL)) { struct track *tg = trackNew(); static char longLabel[80]; struct trackDb *tdb; struct sqlConnection *wikiConn = wikiConnect(); if (! sqlTableExists(wikiConn,WIKI_TRACK_TABLE)) errAbort("loadWikiTrack configuration error, set wikiTrack.URL in hg.conf"); linkedFeaturesMethods(tg); AllocVar(tdb); tg->track = WIKI_TRACK_TABLE; tg->table = WIKI_TRACK_TABLE; tg->canPack = TRUE; tg->visibility = tvHide; tg->hasUi = TRUE; tg->shortLabel = cloneString(WIKI_TRACK_LABEL); safef(longLabel, sizeof(longLabel), WIKI_TRACK_LONGLABEL); tg->longLabel = longLabel; tg->loadItems = wikiTrackLoadItems; tg->itemName = linkedFeaturesName; tg->mapItemName = wikiTrackMapItemName; tg->mapItem = wikiTrackMapItem; tg->priority = WIKI_TRACK_PRIORITY; tg->defaultPriority = WIKI_TRACK_PRIORITY; tg->groupName = cloneString("map"); tg->defaultGroupName = cloneString("map"); tg->exonArrows = TRUE; tg->nextItemButtonable = TRUE; tdb->track = cloneString(tg->track); tdb->canPack = tg->canPack; tdb->table = cloneString(tg->table); tdb->shortLabel = cloneString(tg->shortLabel); tdb->longLabel = cloneString(tg->longLabel); tdb->useScore = 1; tdb->grp = cloneString(tg->groupName); tdb->priority = tg->priority; trackDbPolish(tdb); tg->tdb = tdb; slAddHead(pGroupList, tg); wikiDisconnect(&wikiConn); } }
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)) slAddHead(&forbiddenTrackList, 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 link *getLinkList(struct sqlConnection *conn, char *raFile) /* Get list of links - starting with everything in .ra file, * and making sure any associated tables and databases exist. */ { struct hash *ra, *raList = readRa(raFile, NULL); struct link *linkList = NULL, *link; for (ra = raList; ra != NULL; ra = ra->next) { if (linkOptionalField(ra, "hide") == NULL) { if (checkDatabases(linkOptionalField(ra, "databases")) && sqlTablesExist(conn, linkOptionalField(ra, "tables"))) { /* only include the wikiTrack if it is enabled */ if (sameWord(linkRequiredField(ra, "name"), "wikiTrack") && ! wikiTrackEnabled(database, NULL)) continue; AllocVar(link); link->priority = atof(linkRequiredField(ra, "priority")); link->name = linkRequiredField(ra, "name"); link->shortLabel = linkRequiredField(ra, "shortLabel"); link->idSql = linkRequiredField(ra, "idSql"); link->nameSql = linkOptionalField(ra, "nameSql"); link->nameFormat = linkOptionalField(ra, "nameFormat"); link->url = linkRequiredField(ra, "url"); link->useHgsid = (linkOptionalField(ra, "hgsid") != NULL); link->useDb = (linkOptionalField(ra, "dbInUrl") != NULL); link->preCutAt = linkOptionalField(ra, "preCutAt"); link->postCutAt = linkOptionalField(ra, "postCutAt"); slAddHead(&linkList, link); } } } slSort(&linkList, linkCmpPriority); return linkList; }
static void wikiTrackLoadItems(struct track *tg) /* Load the items from the wikiTrack table */ { struct bed *bed; struct sqlConnection *wikiConn = wikiConnect(); struct sqlResult *sr; char **row; int rowOffset; char where[256]; struct linkedFeatures *lfList = NULL, *lf; int scoreMin = 0; int scoreMax = 99999; safef(where, ArraySize(where), "db='%s'", database); sr = hRangeQuery(wikiConn, tg->table, chromName, winStart, winEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { struct wikiTrack *item = wikiTrackLoad(row); AllocVar(bed); bed->chrom = cloneString(item->chrom); bed->chromStart = item->chromStart; bed->chromEnd = item->chromEnd; bed->name = cloneString(item->name); bed->score = item->score; safecpy(bed->strand, sizeof(bed->strand), item->strand); bed->thickStart = item->chromStart; bed->thickEnd = item->chromEnd; bed->itemRgb = hexToDecimal(item->color); bed8To12(bed); lf = lfFromBedExtra(bed, scoreMin, scoreMax); lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ lf->filterColor=bed->itemRgb; /* overload itemAttr fields to be able to pass id to hgc click box */ struct itemAttr *id; AllocVar(id); id->chromStart = item->id; lf->itemAttr = id; slAddHead(&lfList, lf); wikiTrackFree(&item); } sqlFreeResult(&sr); wikiDisconnect(&wikiConn); slSort(&lfList, linkedFeaturesCmp); /* read-only option 2012-06-25 */ if ((! wikiTrackReadOnly()) && wikiTrackEnabled(database, NULL)) { // add special item to allow creation of new entries AllocVar(bed); bed->chrom = chromName; bed->chromStart = winStart; bed->chromEnd = winEnd; bed->name = cloneString("Make new entry"); bed->score = 100; bed->strand[0] = ' '; /* no barbs when strand is unknown */ bed->thickStart = winStart; bed->thickEnd = winEnd; bed->itemRgb = 0xcc0000; bed8To12(bed); lf = lfFromBedExtra(bed, scoreMin, scoreMax); lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ lf->filterColor=bed->itemRgb; slAddHead(&lfList, lf); } tg->items = lfList; } /* static void wikiTrackLoadItems(struct track *tg) */