static void getGeneSuggestTrack(struct cartJson *cj, struct hash *paramHash)
/* Get the gene track used by hgSuggest for db (defaulting to cart db), or null if
* there is none for this assembly. */
{
char *db = cartJsonOptionalParam(paramHash, "db");
printGeneSuggestTrack(cj, db);
}
static void getHasCustomTracks(struct cartJson *cj, struct hash *paramHash)
/* Tell whether cart has custom tracks for db. If db param is NULL, use db from cart. */
{
char *db = cartJsonOptionalParam(paramHash, "db");
if (db == NULL)
db = cartString(cj->cart, "db");
jsonWriteBoolean(cj->jw, "hasCustomTracks", customTracksExistDb(cj->cart, db, NULL));
}
static void setDb(struct cartJson *cj, struct hash *paramHash)
/* Set taxId and genome according to db and return the info we'll need to fill in
* the findPosition section. */
{
char *db = cartJsonRequiredParam(paramHash, "db", cj->jw, "setDb");
char *hubUrl = cartJsonOptionalParam(paramHash, "hubUrl");
int taxId = hTaxId(db);
writeFindPositionInfo(cj->jw, db, taxId, hubUrl, hDefaultPos(db));
cartSetString(cart, "db", db);
cartSetString(cart, "position", hDefaultPos(db));
}
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 getStaticHtml(struct cartJson *cj, struct hash *paramHash)
/* Read HTML text from a relative path under browser.documentRoot and
* write it as an encoded JSON string */
{
char *tag = cartJsonOptionalParam(paramHash, "tag");
if (isEmpty(tag))
tag = "html";
char *file = cartJsonRequiredParam(paramHash, "file", cj->jw, "getStaticHtml");
char *html = hFileContentsOrWarning(file);
//#*** TODO: move jsonStringEscape inside jsonWriteString
char *encoded = jsonStringEscape(html);
jsonWriteString(cj->jw, tag, encoded);
}
static void getAssemblyInfo(struct cartJson *cj, struct hash *paramHash)
/* Return useful things from dbDb (or track hub) and assembly description html (possibly NULL).
* If db param is NULL, use db from cart. */
{
char *db = cartJsonOptionalParam(paramHash, "db");
if (db == NULL)
db = cartString(cj->cart, "db");
jsonWriteString(cj->jw, "db", db);
jsonWriteString(cj->jw, "commonName", hGenome(db));
jsonWriteString(cj->jw, "scientificName", hScientificName(db));
jsonWriteString(cj->jw, "dbLabel", hFreezeDate(db));
//#*** TODO: move jsonStringEscape inside jsonWriteString
jsonWriteString(cj->jw, "assemblyDescription", jsonStringEscape(hAssemblyDescription(db)));
}
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 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));
}
}
void cartJsonGetGroupedTrackDb(struct cartJson *cj, struct hash *paramHash)
/* Translate trackDb list (only a subset of the fields) into JSON array of track group objects;
* each group contains an array of track objects that may have subtracks. Send it in a wrapper
* object that includes the database from which it was taken; it's possible that by the time
* this reaches the client, the user might have switched to a new db. */
{
struct jsonWrite *jw = cj->jw;
struct trackDb *fullTrackList = NULL;
struct grp *fullGroupList = NULL;
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
cartTrackDbInit(cj->cart, &fullTrackList, &fullGroupList, /* useAccessControl=*/TRUE);
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
warn("%s", errCatch->message->string);
jsonWriteObjectStart(jw, "groupedTrackDb");
jsonWriteString(jw, "db", cartString(cj->cart, "db"));
jsonWriteListStart(jw, "groupedTrackDb");
jsonWriteListEnd(jw);
jsonWriteObjectEnd(jw);
return;
}
errCatchFree(&errCatch);
struct hash *groupedTrackRefList = hashTracksByGroup(fullTrackList);
// If the optional param 'fields' is given, hash the field names that should be returned.
char *fields = cartJsonOptionalParam(paramHash, "fields");
struct hash *fieldHash = hashFromCommaString(fields);
char *excludeTypes = cartJsonOptionalParam(paramHash, "excludeTypes");
struct hash *excludeTypesHash = hashFromCommaString(excludeTypes);
// Also check for optional parameter 'maxDepth':
int maxDepth = -1;
char *maxDepthStr = cartJsonOptionalParam(paramHash, "maxDepth");
if (isNotEmpty(maxDepthStr))
maxDepth = atoi(maxDepthStr);
jsonWriteObjectStart(jw, "groupedTrackDb");
jsonWriteString(jw, "db", cartString(cj->cart, "db"));
jsonWriteListStart(jw, "groupedTrackDb");
int nonEmptyGroupCount = 0;
struct grp *grp;
for (grp = fullGroupList; grp != NULL; grp = grp->next)
{
struct slRef *tdbRefList = hashFindVal(groupedTrackRefList, grp->name);
if (writeGroupedTrack(jw, grp->name, grp->label, fieldHash, excludeTypesHash,
maxDepth, tdbRefList))
{
nonEmptyGroupCount++;
}
}
if (nonEmptyGroupCount == 0)
{
// Catch-all for assembly hubs that don't declare groups for their tracks: add All Tracks
struct slRef *allTracks = sortedAllTracks(fullTrackList);
(void)writeGroupedTrack(jw, "allTracks", "All Tracks", fieldHash, excludeTypesHash,
maxDepth, allTracks);
}
jsonWriteListEnd(jw);
jsonWriteObjectEnd(jw);
}
