static void listAssemblyHubs(struct jsonWrite *jw)
/* Write out JSON describing assembly hubs (not track-only hubs) connected in the cart. */
{
jsonWriteListStart(jw, "hubs");
struct hubConnectStatus *status, *statusList = hubConnectStatusListFromCart(cart);
for (status = statusList; status != NULL; status = status->next)
{
struct trackHub *hub = status->trackHub;
if (hub == NULL)
continue;
int assemblyCount = trackHubCountAssemblies(hub);
if (assemblyCount > 0)
{
jsonWriteObjectStart(jw, NULL);
jsonWriteString(jw, "name", hub->name);
jsonWriteString(jw, "shortLabel", hub->shortLabel);
jsonWriteString(jw, "longLabel", hub->longLabel);
jsonWriteString(jw, "defaultDb", trackHubDefaultAssembly(hub));
jsonWriteString(jw, "hubUrl", status->hubUrl);
jsonWriteNumber(jw, "assemblyCount", assemblyCount);
jsonWriteString(jw, "errorMessage", status->errorMessage);
// We might be able to do better than this for taxId, for example if defaultDb is local
// or if hub genomes ever specify taxId...
jsonWriteNumber(jw, "taxId", 0);
jsonWriteObjectEnd(jw);
}
}
jsonWriteListEnd(jw);
}
static void printActiveGenomes()
/* Print out JSON for an object mapping each genome that has at least one db with active=1
* to its taxId. */
{
struct jsonWrite *jw = jsonWriteNew();
jsonWriteObjectStart(jw, NULL);
struct sqlConnection *conn = hConnectCentral();
// Join with defaultDb because in rare cases, different taxIds (species vs. subspecies)
// may be used for different assemblies of the same species. Using defaultDb means that
// we send a taxId consistent with the taxId of the assembly that we'll change to when
// the species is selected from the tree.
char *query = NOSQLINJ "select dbDb.genome, taxId, dbDb.name from dbDb, defaultDb "
"where defaultDb.name = dbDb.name and active = 1 "
"and taxId > 1;"; // filter out experimental hgwdev-only stuff with invalid taxIds
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *genome = row[0], *db = row[2];
int taxId = atoi(row[1]);
if (hDbExists(db))
jsonWriteNumber(jw, genome, taxId);
}
hDisconnectCentral(&conn);
jsonWriteObjectEnd(jw);
puts(jw->dy->string);
jsonWriteFree(&jw);
}
static void writeDbDbMatch(struct jsonWrite *jw, struct dbDbMatch *match, char *term,
char *category)
/* Write out the JSON encoding of a match in dbDb. */
{
struct dbDb *dbDb = match->dbDb;
jsonWriteObjectStart(jw, NULL);
jsonWriteString(jw, "genome", dbDb->genome);
// label includes <b> tag to highlight the match for term.
char label[PATH_LEN*4];
// value is placed in the input box when user selects the item.
char value[PATH_LEN*4];
if (match->type == ddmtSciName)
{
safef(value, sizeof(value), "%s (%s)", dbDb->scientificName, dbDb->genome);
char *bolded = boldTerm(dbDb->scientificName, term, match->offset, match->type);
safef(label, sizeof(label), "%s (%s)", bolded, dbDb->genome);
freeMem(bolded);
}
else if (match->type == ddmtGenome)
{
safecpy(value, sizeof(value), dbDb->genome);
char *bolded = boldTerm(dbDb->genome, term, match->offset, match->type);
safecpy(label, sizeof(label), bolded);
freeMem(bolded);
}
else if (match->type == ddmtDb)
{
safecpy(value, sizeof(value), dbDb->name);
char *bolded = boldTerm(dbDb->name, term, match->offset, match->type);
safef(label, sizeof(label), "%s (%s %s)",
bolded, dbDb->genome, dbDb->description);
freeMem(bolded);
jsonWriteString(jw, "db", dbDb->name);
}
else if (match->type == ddmtDescription)
{
safef(value, sizeof(value), "%s (%s %s)",
dbDb->name, dbDb->genome, dbDb->description);
char *bolded = boldTerm(dbDb->description, term, match->offset, match->type);
safef(label, sizeof(label), "%s (%s %s)",
dbDb->name, dbDb->genome, bolded);
freeMem(bolded);
jsonWriteString(jw, "db", dbDb->name);
}
else
errAbort("writeDbDbMatch: unrecognized dbDbMatchType value %d (db %s, term %s)",
match->type, dbDb->name, term);
jsonWriteString(jw, "label", label);
jsonWriteString(jw, "value", value);
jsonWriteNumber(jw, "taxId", dbDb->taxId);
if (isNotEmpty(category))
jsonWriteString(jw, "category", category);
jsonWriteObjectEnd(jw);
}
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);
}
}
static void getUiState(struct cartJson *cj, struct hash *paramHash)
/* Write out JSON for hgGateway.js's uiState object using current cart settings. */
{
char *db = cartUsualString(cj->cart, "db", hDefaultDb());
char *position = cartUsualString(cart, "position", hDefaultPos(db));
char *hubUrl = NULL;
if (trackHubDatabase(db))
{
struct trackHub *hub = hubConnectGetHubForDb(db);
hubUrl = hub->url;
}
writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position);
// If cart already has a pix setting, pass that along; otherwise the JS will
// set pix according to web browser window width.
int pix = cartUsualInt(cj->cart, "pix", 0);
if (pix)
jsonWriteNumber(cj->jw, "pix", pix);
}
struct jsonWrite *jsonForStep(struct sqlConnection *conn, struct eapStep *step)
/* Convert an eapStep to json. See step.json in same directory as the .c file.
* for an example. */
{
struct jsonWrite *jw = jsonWriteNew();
jsonWriteObjectStart(jw);
/* Write name and description. */
jsonWriteString(jw, "name", step->name);
jsonWriteString(jw, "description", step->description);
/* Write version */
struct eapStepVersion *ver = eapStepVersionLatest(conn, step->name);
jsonWriteNumber(jw, "version", ver->version);
/* Write software */
jsonWriteListStart(jw, "software");
char query[512];
sqlSafef(query, sizeof(query), "select * from eapStepSoftware where step='%s'", step->name);
struct eapStepSoftware *ss, *ssList = eapStepSoftwareLoadByQuery(conn, query);
boolean isFirst = TRUE;
struct dyString *dy = jw->dy;
for (ss = ssList; ss != NULL; ss = ss->next)
{
struct eapSoftware *software = eapSoftwareLoadByName(conn, ss->software);
assert(software != NULL);
if (software->metaUuid)
{
if (!isFirst)
{
dyStringAppendC(dy, ',');
dyStringAppendC(dy, '\n');
}
isFirst = FALSE;
dyStringAppendC(dy, '"');
dyStringPrintf(dy, "/software/%s/", software->metaUuid);
dyStringAppendC(dy, '"');
}
}
if (!isFirst)
dyStringAppendC(dy, '\n');
jsonWriteListEnd(jw);
/* Done with writing software list */
/* Write input list */
jsonWriteListStart(jw, "inputs");
int i;
for (i=0; i<step->inCount; ++i)
{
jsonWriteObjectStart(jw);
jsonWriteString(jw, "format", step->inputFormats[i]);
jsonWriteString(jw, "name", step->inputTypes[i]);
jsonWriteString(jw, "description", step->inputDescriptions[i]);
jsonWriteObjectEnd(jw);
}
jsonWriteListEnd(jw);
/* Write output list */
jsonWriteListStart(jw, "outputs");
for (i=0; i<step->outCount; ++i)
{
jsonWriteObjectStart(jw);
jsonWriteString(jw, "format", step->outputFormats[i]);
jsonWriteString(jw, "name", step->outputTypes[i]);
jsonWriteString(jw, "description", step->outputDescriptions[i]);
jsonWriteObjectEnd(jw);
}
jsonWriteListEnd(jw);
jsonWriteObjectEnd(jw);
return jw;
}
