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 printCladeOrgDbTree(struct jsonWrite *jw)
/* Print out the tree of clades, organisms and dbs as JSON. Each node has value and label
* for menu options; clade nodes and org nodes also have children and default. */
{
jsonWriteListStart(jw, "cladeOrgDb");
struct slPair *clade, *cladeOptions = hGetCladeOptions();
struct dbDb *centralDbDbList = hDbDbList();
for (clade = cladeOptions; clade != NULL; clade = clade->next)
{
jsonWriteObjectStart(jw, NULL);
jsonWriteValueLabel(jw, clade->name, clade->val);
jsonWriteListStart(jw, "children");
struct slPair *org, *orgOptions = hGetGenomeOptionsForClade(clade->name);
for (org = orgOptions; org != NULL; org = org->next)
{
jsonWriteObjectStart(jw, NULL);
jsonWriteValueLabel(jw, org->name, org->val);
jsonWriteListStart(jw, "children");
struct dbDb *dbDb, *dbDbList;
if (isHubTrack(org->name))
dbDbList = trackHubGetDbDbs(clade->name);
else
dbDbList = centralDbDbList;
for (dbDb = dbDbList; dbDb != NULL; dbDb = dbDb->next)
{
if (sameString(org->name, dbDb->genome))
{
jsonWriteObjectStart(jw, NULL);
jsonWriteValueLabel(jw, dbDb->name, dbDb->description);
jsonWriteString(jw, "defaultPos", dbDb->defaultPos);
jsonWriteObjectEnd(jw);
}
}
jsonWriteListEnd(jw); // children (dbs)
jsonWriteString(jw, "default", trimSpaces(hDefaultDbForGenome(org->name)));
jsonWriteObjectEnd(jw); // org
}
jsonWriteListEnd(jw); // children (orgs)
jsonWriteString(jw, "default", trimSpaces(hDefaultGenomeForClade(clade->name)));
jsonWriteObjectEnd(jw); // clade
}
jsonWriteListEnd(jw);
}
static boolean writeGroupedTrack(struct jsonWrite *jw, char *name, char *label,
struct hash *fieldHash, struct hash *excludeTypesHash,
int maxDepth, struct slRef *tdbRefList)
/* If tdbRefList is empty after excluding tracks/views/subtracks whose types are
* in excludeTypesHash, then return FALSE and write nothing. Otherwise write a group
* and its tracks/views/subtracks and return TRUE. */
{
// Make a new jsonWrite object in case this group turns out to have no children after filtering.
struct jsonWrite *jwNew = jsonWriteNew();
jsonWriteObjectStart(jwNew, NULL);
jsonWriteString(jwNew, "name", name);
jsonWriteString(jwNew, "label", label);
jsonWriteListStart(jwNew, "tracks");
boolean gotSomething = FALSE;
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *tdb = tdbRef->val;
// First see if there are any tracks to show for this group:
struct jsonWrite *jwTrack = rTdbToJw(tdb, fieldHash, excludeTypesHash, 1, maxDepth);
if (jwTrack)
{
gotSomething = TRUE;
jsonWriteAppend(jwNew, NULL, jwTrack);
jsonWriteFree(&jwTrack);
}
}
if (gotSomething)
{
// Group has at least one track, so append it to jw.
jsonWriteListEnd(jwNew);
jsonWriteObjectEnd(jwNew);
jsonWriteAppend(jw, NULL, jwNew);
}
jsonWriteFree(&jwNew);
return gotSomething;
}
void suggestAltOrPatch(char *database, char *term)
/* Print out a Javascript list of objects describing alternate haplotype or fix patch sequences
* from database that match term. */
{
struct jsonWrite *jw = jsonWriteNew();
jsonWriteListStart(jw, NULL);
struct sqlConnection *conn = hAllocConn(database);
// First, search for prefix matches
struct slName *fixMatches = queryAltFixNames(conn, "fixLocations", term, "alt", TRUE);
struct slName *altMatches = queryAltFixNames(conn, "altLocations", term, "fix", TRUE);
// Add category labels only if we get both types of matches.
writeAltFixMatches(jw, fixMatches, altMatches ? "Fix Patches" : "");
writeAltFixMatches(jw, altMatches, fixMatches ? "Alt Patches" : "");
// If there are no prefix matches, look for partial matches
if (fixMatches == NULL && altMatches == NULL)
{
fixMatches = queryAltFixNames(conn, "fixLocations", term, "alt", FALSE);
altMatches = queryAltFixNames(conn, "altLocations", term, "fix", FALSE);
writeAltFixMatches(jw, fixMatches, altMatches ? "Fix Patches" : "");
writeAltFixMatches(jw, altMatches, fixMatches ? "Alt Patches" : "");
}
// If there are still no matches, try chromAlias.
if (fixMatches == NULL && altMatches == NULL)
{
struct slPair *aliasMatches = queryChromAlias(conn, term, TRUE);
writeValLabelMatches(jw, aliasMatches, "");
if (aliasMatches == NULL)
{
struct slPair *aliasMatches = queryChromAlias(conn, term, FALSE);
writeValLabelMatches(jw, aliasMatches, "");
}
}
hFreeConn(&conn);
jsonWriteListEnd(jw);
puts(jw->dy->string);
jsonWriteFree(&jw);
}
static void lookupTerm()
/* Look for matches to term in hgcentral and print as JSON for autocomplete if found. */
{
char *term = getSearchTermUpperCase();
// Write JSON response with list of matches
puts("Content-Type:text/javascript\n");
struct dbDb *dbDbList = hDbDbList();
struct dbDbMatch *matchList = searchDbDb(dbDbList, term);
struct aHubMatch *aHubMatchList = searchPublicHubs(dbDbList, term);
struct jsonWrite *jw = jsonWriteNew();
jsonWriteListStart(jw, NULL);
// Write out JSON for dbDb matches, if any; add category if we found assembly hub matches too.
char *category = aHubMatchList ? "UCSC databases" : NULL;
struct dbDbMatch *match;
for (match = matchList; match != NULL; match = match->next)
writeDbDbMatch(jw, match, term, category);
// Write out assembly hub matches, if any.
writeAssemblyHubMatches(jw, aHubMatchList);
jsonWriteListEnd(jw);
puts(jw->dy->string);
jsonWriteFree(&jw);
}
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
}
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);
}
static struct jsonWrite *rTdbToJw(struct trackDb *tdb, struct hash *fieldHash,
struct hash *excludeTypesHash, int depth, int maxDepth)
/* Recursively build and return a new jsonWrite object with JSON for tdb and its children,
* or NULL if tdb or all children have been filtered out by excludeTypesHash.
* If excludeTypesHash is non-NULL, omit any tracks/views/subtracks with type in excludeTypesHash.
* If fieldHash is non-NULL, include only the field names indexed in fieldHash. */
{
if (maxDepth >= 0 && depth > maxDepth)
return NULL;
boolean doSubtracks = (tdb->subtracks && fieldOk("subtracks", fieldHash));
// If excludeTypesHash is given and tdb is a leaf track/subtrack, look up the first word
// of tdb->type in excludeTypesHash; if found, return NULL.
if (excludeTypesHash && !doSubtracks)
{
char typeCopy[PATH_LEN];
safecpy(typeCopy, sizeof(typeCopy), tdb->type);
if (hashLookup(excludeTypesHash, firstWordInLine(typeCopy)))
return NULL;
}
boolean gotSomething = !doSubtracks;
struct jsonWrite *jwNew = jsonWriteNew();
jsonWriteObjectStart(jwNew, NULL);
writeTdbSimple(jwNew, tdb, fieldHash);
if (tdb->parent && fieldOk("parent", fieldHash))
{
// We can't link to an object in JSON and better not recurse here or else infinite loop.
if (tdbIsSuperTrackChild(tdb))
{
// Supertracks have been omitted from fullTrackList, so add the supertrack object's
// non-parent/child info here.
jsonWriteObjectStart(jwNew, "parent");
writeTdbSimple(jwNew, tdb->parent, fieldHash);
jsonWriteObjectEnd(jwNew);
}
else
// Just the name so we don't have infinite loops.
jsonWriteString(jwNew, "parent", tdb->parent->track);
}
if (doSubtracks)
{
jsonWriteListStart(jwNew, "subtracks");
slSort(&tdb->subtracks, trackDbViewCmp);
struct trackDb *subTdb;
for (subTdb = tdb->subtracks; subTdb != NULL; subTdb = subTdb->next)
{
struct jsonWrite *jwSub = rTdbToJw(subTdb, fieldHash, excludeTypesHash, depth+1, maxDepth);
if (jwSub)
{
gotSomething = TRUE;
jsonWriteAppend(jwNew, NULL, jwSub);
jsonWriteFree(&jwSub);
}
}
jsonWriteListEnd(jwNew);
}
jsonWriteObjectEnd(jwNew);
if (! gotSomething)
// All children were excluded; clean up and null out jwNew.
jsonWriteFree(&jwNew);
return jwNew;
}
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;
}
