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);
}
struct jsonWrite *jsonForSoftware(struct eapSoftware *sw)
/* Return JSON text for software. This is something that looks
* like:
{
"name" : "macs2",
"title" : "macs2",
"url" : "https://github.com/taoliu/MACS/"
}
*/
{
struct jsonWrite *jw = jsonWriteNew(0);
jsonWriteObjectStart(jw);
jsonWriteString(jw, "name", sw->name);
jsonWriteString(jw, "title", sw->name);
jsonWriteString(jw, "url", sw->url);
jsonWriteObjectEnd(jw);
return jw;
}
struct jsonWrite *jsonForSwVersion(struct sqlConnection *conn, struct eapSwVersion *ver)
/* Construct JSON string describing ver. */
{
char query[256];
sqlSafef(query, sizeof(query), "select * from eapSoftware where name='%s'", ver->software);
struct eapSoftware *sw = eapSoftwareLoadByQuery(conn, query);
if (sw == NULL || isEmpty(sw->metaUuid))
{
verbose(2, "Skipping %s %s because %s has not been registered with metadatabase\n",
ver->software, ver->version, ver->software);
return NULL;
}
uglyf("sw id %u, softare %s, metaUuid %s\n", sw->id, sw->name, sw->metaUuid);
struct jsonWrite *jw = jsonWriteNew(0);
jsonWriteObjectStart(jw);
jsonWriteString(jw, "software", sw->metaUuid);
jsonWriteString(jw, "version", ver->version);
jsonWriteString(jw, "dcc_md5", ver->md5);
jsonWriteObjectEnd(jw);
return jw;
}
struct cartJson *cartJsonNew(struct cart *cart)
/* Allocate and return a cartJson object with default handlers.
* cart must have "db" set already. */
{
struct cartJson *cj;
AllocVar(cj);
cj->handlerHash = hashNew(0);
cj->jw = jsonWriteNew();
cj->cart = cart;
cartJsonRegisterHandler(cj, "getCladeOrgDbPos", getCladeOrgDbPos);
cartJsonRegisterHandler(cj, "changePosition", changePositionHandler);
cartJsonRegisterHandler(cj, "get", getVar);
cartJsonRegisterHandler(cj, "getGroupedTrackDb", cartJsonGetGroupedTrackDb);
cartJsonRegisterHandler(cj, "getAssemblyInfo", getAssemblyInfo);
cartJsonRegisterHandler(cj, "getGeneSuggestTrack", getGeneSuggestTrack);
cartJsonRegisterHandler(cj, "getHasCustomTracks", getHasCustomTracks);
cartJsonRegisterHandler(cj, "getIsSpecialHost", getIsSpecialHost);
cartJsonRegisterHandler(cj, "getHasHubTable", getHasHubTable);
cartJsonRegisterHandler(cj, "setIfUnset", setIfUnset);
cartJsonRegisterHandler(cj, "getStaticHtml", getStaticHtml);
return cj;
}
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 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;
}