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) */
