static void writeFindPositionInfo(struct jsonWrite *jw, char *db, int taxId, char *hubUrl,
char *position)
/* Write JSON for the info needed to populate the 'Find Position' section. */
{
char *genome = hGenome(db);
if (isEmpty(genome))
{
jsonWriteStringf(jw, "error", "No genome for db '%s'", db);
}
else
{
jsonWriteString(jw, "db", db);
jsonWriteNumber(jw, "taxId", taxId);
jsonWriteString(jw, "genome", genome);
struct slPair *dbOptions = NULL;
char genomeLabel[PATH_LEN*4];
if (isNotEmpty(hubUrl))
{
struct trackHub *hub = hubConnectGetHub(hubUrl);
if (hub == NULL)
{
jsonWriteStringf(jw, "error", "Can't connect to hub at '%s'", hubUrl);
return;
}
struct dbDb *dbDbList = trackHubGetDbDbs(hub->name);
dbOptions = trackHubDbDbToValueLabel(dbDbList);
safecpy(genomeLabel, sizeof(genomeLabel), hub->shortLabel);
jsonWriteString(jw, "hubUrl", hubUrl);
}
else
{
dbOptions = hGetDbOptionsForGenome(genome);
safecpy(genomeLabel, sizeof(genomeLabel), genome);
}
jsonWriteValueLabelList(jw, "dbOptions", dbOptions);
jsonWriteString(jw, "genomeLabel", genomeLabel);
jsonWriteString(jw, "position", position);
char *suggestTrack = NULL;
if (! trackHubDatabase(db))
suggestTrack = assemblyGeneSuggestTrack(db);
jsonWriteString(jw, "suggestTrack", suggestTrack);
char *description = maybeGetDescriptionText(db);
//#*** TODO: move jsonStringEscape inside jsonWriteString
char *encoded = jsonStringEscape(description);
jsonWriteString(jw, "description", encoded);
listAssemblyHubs(jw);
}
}
char *cartJsonRequiredParam(struct hash *paramHash, char *name, struct jsonWrite *jw, char *context)
/* Convenience function for a CartJsonHandler function: Look up name in paramHash.
* If found, return the string contained in its jsonElement value.
* If not, write an error message (using context) and return NULL. */
{
char *param = cartJsonOptionalParam(paramHash, name);
if (param == NULL)
jsonWriteStringf(jw, "error",
"%s: required param %s is missing", context, name);
return param;
}
static void setHubDb(struct cartJson *cj, struct hash *paramHash)
/* Set db and genome according to hubUrl (and/or db and hub) and return the info we'll need
* to fill in the findPosition section. */
{
char *hubUrl = cartJsonRequiredParam(paramHash, "hubUrl", cj->jw, "setHubDb");
char *taxIdStr = cartJsonOptionalParam(paramHash, "taxId");
int taxId = taxIdStr ? atoi(taxIdStr) : -1;
// cart's db was already set by magic handling of hub CGI variables sent along
// with this command.
char *db = cartString(cart, "db");
if (isEmpty(db))
jsonWriteStringf(cj->jw, "error", "No db for hubUrl '%s'", hubUrl);
else
writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db));
}
static void doOneCommand(struct cartJson *cj, char *command,
struct jsonElement *paramObject)
/* Dispatch command by name, checking for required parameters. */
{
CartJsonHandler *handler = hashFindVal(cj->handlerHash, command);
if (handler)
{
struct hash *paramHash = jsonObjectVal(paramObject, command);
handler(cj, paramHash);
}
else
{
jsonWriteStringf(cj->jw, "error",
"cartJson: unrecognized command '%s'\"", command);
return;
}
}
static void setTaxId(struct cartJson *cj, struct hash *paramHash)
/* Set db and genome according to taxId (and/or db) and return the info we'll need
* to fill in the findPosition section. */
{
char *taxIdStr = cartJsonRequiredParam(paramHash, "taxId", cj->jw, "setTaxId");
char *db = cartJsonOptionalParam(paramHash, "db");
int taxId = atoi(taxIdStr);
if (isEmpty(db))
db = hDbForTaxon(taxId);
if (isEmpty(db))
jsonWriteStringf(cj->jw, "error", "No db for taxId '%s'", taxIdStr);
else
{
writeFindPositionInfo(cj->jw, db, taxId, NULL, hDefaultPos(db));
cartSetString(cart, "db", db);
cartSetString(cart, "position", hDefaultPos(db));
}
}
static void hgPositionsJson(struct jsonWrite *jw, char *db, struct hgPositions *hgp, struct cart *cart)
/* Write out JSON description of multiple position matches. */
{
struct hgPosTable *table;
jsonWriteListStart(jw, "positionMatches");
struct trackDb *tdbList = NULL;
for (table = hgp->tableList; table != NULL; table = table->next)
{
if (table->posList != NULL)
{
char *tableName = table->name;
// clear the tdb cache if this track is a hub track
if (isHubTrack(tableName))
tdbList = NULL;
struct trackDb *tdb = tdbForTrack(db, tableName, &tdbList);
if (!tdb && startsWith("all_", tableName))
tdb = tdbForTrack(db, tableName+strlen("all_"), &tdbList);
if (!tdb)
errAbort("no track for table \"%s\" found via a findSpec", tableName);
char *trackName = tdb->track;
jsonWriteObjectStart(jw, NULL);
jsonWriteString(jw, "name", table->name);
jsonWriteString(jw, "trackName", trackName);
jsonWriteString(jw, "description", table->description);
jsonWriteString(jw, "vis", hCarefulTrackOpenVis(db, trackName));
jsonWriteListStart(jw, "matches");
struct hgPos *pos;
for (pos = table->posList; pos != NULL; pos = pos->next)
{
char *encMatches = cgiEncode(pos->browserName);
jsonWriteObjectStart(jw, NULL); // begin one match
if (pos->chrom != NULL)
jsonWriteStringf(jw, "position", "%s:%d-%d",
pos->chrom, pos->chromStart+1, pos->chromEnd);
else
// GenBank results set position to GB accession instead of chr:s-e position.
jsonWriteString(jw, "position", pos->name);
// this is magic to tell the browser to make the
// composite and this subTrack visible
if (tdb->parent)
{
if (tdbIsSuperTrackChild(tdb))
jsonWriteStringf(jw, "extraSel", "%s=show&", tdb->parent->track);
else
{
// tdb is a subtrack of a composite or a view
jsonWriteStringf(jw, "extraSel", "%s_sel=1&%s_sel=1&",
trackName, tdb->parent->track);
}
}
jsonWriteString(jw, "hgFindMatches", encMatches);
jsonWriteString(jw, "posName", htmlEncodeText(pos->name, FALSE));
if (pos->description)
{
stripString(pos->description, "\n");
jsonWriteString(jw, "description", stripAnchor(pos->description));
}
jsonWriteObjectEnd(jw); // end one match
}
jsonWriteListEnd(jw); // end matches
jsonWriteObjectEnd(jw); // end one table
}
}
jsonWriteListEnd(jw); // end positionMatches
}
static struct hgPositions *genomePosCJ(struct jsonWrite *jw,
char *db, char *spec, char **retChromName,
int *retWinStart, int *retWinEnd, struct cart *cart)
/* Search for positions in genome that match user query.
* Return an hgp unless there is a problem. hgp->singlePos will be set if a single
* position matched.
* Otherwise display list of positions, put # of positions in retWinStart,
* and return NULL. */
{
char *hgAppName = "cartJson";
struct hgPositions *hgp = NULL;
char *chrom = NULL;
int start = BIGNUM;
int end = 0;
char *terms[16];
int termCount = chopByChar(cloneString(spec), ';', terms, ArraySize(terms));
boolean multiTerm = (termCount > 1);
int i = 0;
for (i = 0; i < termCount; i++)
{
trimSpaces(terms[i]);
if (isEmpty(terms[i]))
continue;
hgp = hgPositionsFind(db, terms[i], "", hgAppName, cart, multiTerm);
if (hgp == NULL || hgp->posCount == 0)
{
jsonWriteStringf(jw, "error",
"Sorry, couldn't locate %s in genome database", htmlEncode(terms[i]));
if (multiTerm)
jsonWriteStringf(jw, "error",
"%s not uniquely determined -- can't do multi-position search.",
terms[i]);
*retWinStart = 0;
return NULL;
}
if (hgp->singlePos != NULL)
{
if (chrom != NULL && !sameString(chrom, hgp->singlePos->chrom))
{
jsonWriteStringf(jw, "error",
"Sites occur on different chromosomes: %s, %s.",
chrom, hgp->singlePos->chrom);
return NULL;
}
chrom = hgp->singlePos->chrom;
if (hgp->singlePos->chromStart < start)
start = hgp->singlePos->chromStart;
if (hgp->singlePos->chromEnd > end)
end = hgp->singlePos->chromEnd;
}
else
{
hgPositionsJson(jw, db, hgp, cart);
if (multiTerm && hgp->posCount != 1)
{
jsonWriteStringf(jw, "error",
"%s not uniquely determined (%d locations) -- "
"can't do multi-position search.",
terms[i], hgp->posCount);
return NULL;
}
break;
}
}
if (hgp != NULL)
{
*retChromName = chrom;
*retWinStart = start;
*retWinEnd = end;
}
return hgp;
}
