void doSummaryStatsWikiTrack(struct sqlConnection *conn)
/* Put up page showing summary stats for wikiTrack. */
{
struct sqlConnection *wikiConn = wikiConnect();
doSummaryStatsBed(wikiConn);
wikiDisconnect(&wikiConn);
}
struct bed *wikiTrackGetBedRange(char *table, char *chromName,
int start, int end)
/* fetch wiki track items as simple bed 3 list in given range */
{
struct bed *bed, *bedList = NULL;
struct sqlConnection *wikiConn = wikiConnect();
struct sqlResult *sr;
char **row;
char where[256];
int rowOffset;
safef(where, ArraySize(where), "db='%s'", database);
sr = hRangeQuery(wikiConn, table, chromName, start, end, 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;
slAddHead(&bedList, bed);
wikiTrackFree(&item);
}
sqlFreeResult(&sr);
wikiDisconnect(&wikiConn);
return bedList;
}
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 void wikiTrackFilteredBedOnRegion(
struct region *region, /* Region to get data from. */
struct hash *idHash, /* Hash of identifiers or NULL */
struct bedFilter *bf, /* Filter or NULL */
struct lm *lm, /* Local memory pool. */
struct bed **pBedList /* Output get's appended to this list */
)
/* Get the wikiTrack items passing filter on a single region. */
{
struct bed *bed;
int fieldCount = 6;
char query[512];
int rowOffset;
char **row;
struct sqlConnection *wikiConn = wikiConnect();
struct sqlResult *sr = NULL;
char where[512];
char *filter = filterClause(wikiDbName(), WIKI_TRACK_TABLE, region->chrom, NULL);
if (filter)
sqlSafefFrag(where, sizeof(where), "db='%s' AND %-s", database, filter);
else
sqlSafefFrag(where, sizeof(where), "db='%s'", database);
sqlSafef(query, sizeof(query), "select * from %s", WIKI_TRACK_TABLE);
sr = hRangeQuery(wikiConn, WIKI_TRACK_TABLE, region->chrom,
region->start, region->end, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
if ((idHash == NULL || hashLookup(idHash, bed->name)) &&
(bf == NULL || bedFilterOne(bf, bed)))
{
struct bed *copy = lmCloneBed(bed, lm);
slAddHead(pBedList, copy);
}
}
sqlFreeResult(&sr);
wikiDisconnect(&wikiConn);
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
static struct hash *getAllPossibleIds(struct sqlConnection *conn,
struct lm *lm, char *idField, char *extraWhere)
/* If curTable is a custom track or bigFile, return NULL. Otherwise,
* make a hash of all identifiers in curTable (and alias tables if specified)
* so that we can check the validity of pasted/uploaded identifiers. */
{
if (isCustomTrack(curTable) || isBamTable(curTable) || isVcfTable(curTable, NULL) ||
isBigBed(database, curTable, curTrack, ctLookupName))
return NULL;
struct hash *matchHash = hashNew(20);
struct slName *tableList;
char *xrefTable = NULL, *xrefIdField = NULL, *aliasField = NULL;
struct sqlConnection *alternateConn = conn;
if (sameWord(curTable, WIKI_TRACK_TABLE))
alternateConn = wikiConnect();
if (sameWord(curTable, WIKI_TRACK_TABLE))
tableList = slNameNew(WIKI_TRACK_TABLE);
else if (strchr(curTable, '.'))
tableList = slNameNew(curTable);
else
tableList = hSplitTableNames(database, curTable);
if (idField != NULL)
addPrimaryIdsToHash(alternateConn, matchHash, idField, tableList, lm, extraWhere);
getXrefInfo(alternateConn, &xrefTable, &xrefIdField, &aliasField);
if (xrefTable != NULL)
{
addXrefIdsToHash(alternateConn, matchHash, idField,
xrefTable, xrefIdField, aliasField, lm, extraWhere);
}
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
return matchHash;
}
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) */
