e06aca36b8d5f820603188308c7bec8749427fe0
hiram
Wed Feb 6 14:32:14 2019 -0800
chrom list from specific track on ucsc database output and jsonErr output refs #18869
diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c
index c726cc7..40f8e25 100644
--- src/hg/hubApi/hubApi.c
+++ src/hg/hubApi/hubApi.c
@@ -583,35 +583,85 @@
/* output the dbDb SQL table */
{
struct dbDb *dbList = ucscDbDb();
struct dbDb *el;
jsonStartOutput(stdout);
printf("\"ucscGenomes\":[");
for ( el=dbList; el != NULL; el = el->next )
{
dbDbJsonOutput(el, stdout);
if (el->next)
printf(",");
}
printf("]}\n");
}
+static void jsonErrAbort(char *format, ...)
+/* Issue an error message in json format. */
+{
+char errMsg[2048];
+va_list args;
+va_start(args, format);
+vsnprintf(errMsg, sizeof(errMsg), format, args);
+fputc('{',stdout);
+jsonStringOut(stdout, "error", errMsg);
+fputc('}',stdout);
+}
+
static void chromInfoJsonOutput(char *db, FILE *f, char *track)
{
if (track)
{
-;
+ struct sqlConnection *conn = hAllocConn(db);
+ if (! sqlTableExists(conn, track))
+ jsonErrAbort("ERROR: endpoint: /list/chromosomes?db=%&table=%s ERROR table does not exist", db, track);
+ if (sqlColumnExists(conn, track, "chrom"))
+ {
+ jsonStartOutput(f);
+ jsonStringOut(f, "genome", db);
+ fputc(',',f);
+ jsonStringOut(f, "track", track);
+ fputc(',',f);
+ struct slPair *list = NULL;
+ char query[2048];
+ sqlSafef(query, sizeof(query), "select distinct chrom from %s", track);
+ struct sqlResult *sr = sqlGetResult(conn, query);
+ char **row;
+ while ((row = sqlNextRow(sr)) != NULL)
+ {
+ int size = hChromSize(db, row[0]);
+ slAddHead(&list, slPairNew(row[0], intToPt(size)));
+ }
+ sqlFreeResult(&sr);
+ slPairIntSort(&list);
+ slReverse(&list);
+ jsonInteger(f, "chromCount", slCount(list));
+ fputc(',',f);
+ struct slPair *el = list;
+ for ( ; el != NULL; el = el->next )
+ {
+ jsonInteger(f, el->name, ptToInt(el->val));
+ if (el->next)
+ fputc(',',f);
+ }
+ fputc('}',f);
+ }
+ else
+ {
+ jsonErrAbort("ERROR: table '%s' is not a position table, no chromosomes for genome: '%s'", track, db);
+ }
+ hFreeConn(&conn);
}
else
{
struct chromInfo *ciList = createChromInfoList(NULL, db);
struct chromInfo *el = ciList;
jsonStartOutput(f);
jsonStringOut(f, "genome", db);
fputc(',',f);
jsonInteger(f, "chromCount", slCount(ciList));
fputc(',',f);
for ( ; el != NULL; el = el->next )
{
jsonInteger(f, el->chrom, el->size);
if (el->next)
fputc(',',f);
@@ -650,143 +700,139 @@
fprintf(f, "]}\n");
} /* static void trackDbJsonOutput(char *db, FILE *f) */
#define MAX_PATH_INFO 32
static void apiList(char *words[MAX_PATH_INFO])
/* 'list' function words[1] is the subCommand */
{
if (sameWord("publicHubs", words[1]))
jsonPublicHubs();
else if (sameWord("ucscGenomes", words[1]))
jsonDbDb();
else if (sameWord("hubGenomes", words[1]))
{
char *hubUrl = cgiOptionalString("hubUrl");
if (isEmpty(hubUrl))
- errAbort("# must supply hubUrl='http:...' some URL to a hub for /list/genomes\n");
+ jsonErrAbort("ERROR: must supply hubUrl='http:...' some URL to a hub for /list/genomes\n");
struct trackHub *hub = trackHubOpen(hubUrl, "");
if (hub->genomeList)
{
jsonStartOutput(stdout);
jsonStringOut(stdout, "hubUrl", hubUrl);
fputc(',',stdout);
printf("\"genomes\":[");
struct slName *theList = genomeList(hub, NULL, NULL);
slNameSort(&theList);
struct slName *el = theList;
for ( ; el ; el = el->next )
{
char *a = jsonStringEscape(el->name);
printf("\"%s\"", a);
freeMem(a);
if (el->next)
fputc(',',stdout);
}
printf("]}\n");
}
}
else if (sameWord("tracks", words[1]))
{
char *hubUrl = cgiOptionalString("hubUrl");
char *genome = cgiOptionalString("genome");
char *db = cgiOptionalString("db");
if (isEmpty(hubUrl) && isEmpty(db))
- {
- errAbort("# ERROR: must supply hubUrl or db name to return track list");
- }
+ jsonErrAbort("ERROR: must supply hubUrl or db name to return track list");
if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database
{
trackDbJsonOutput(db, stdout); // only need db for this function
return;
}
if (isEmpty(genome) || isEmpty(hubUrl))
{
if (isEmpty(genome))
warn("# must supply genome='someName' the name of a genome in a hub for /list/tracks\n");
if (isEmpty(hubUrl))
- warn("# must supply hubUrl='http:...' some URL to a hub for /list/genomes\n");
- errAbort("# ERROR exit");
+ jsonErrAbort("ERROR: must supply hubUrl='http:...' some URL to a hub for /list/genomes\n");
}
struct trackHub *hub = trackHubOpen(hubUrl, "");
if (hub->genomeList)
{
struct slName *dbTrackList = NULL;
(void) genomeList(hub, &dbTrackList, genome);
jsonStartOutput(stdout);
jsonStringOut(stdout, "hubUrl", hubUrl);
fputc(',',stdout);
jsonStringOut(stdout, "genome", genome);
fputc(',',stdout);
slNameSort(&dbTrackList);
struct slName *el = dbTrackList;
for ( ; el != NULL; el = el->next )
{
char *a = jsonStringEscape(el->name);
printf("\"%s\"", a);
freeMem(a);
if (el->next)
fputc(',',stdout);
}
printf("]}\n");
}
}
else if (sameWord("chromosomes", words[1]))
{
char *hubUrl = cgiOptionalString("hubUrl");
// char *genome = cgiOptionalString("genome");
char *db = cgiOptionalString("db");
if (isEmpty(hubUrl) && isEmpty(db))
- {
- errAbort("# ERROR: must supply hubUrl or db name to return chromosome list");
- }
+ jsonErrAbort("ERROR: must supply hubUrl or db name to return chromosome list");
+
if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database
{
chromListJsonOutput(db, stdout); // only need db for this function
return;
}
}
else
- errAbort("# ERROR: do not recognize endpoint '/list/%s' function\n", words[1]);
+ jsonErrAbort("ERROR: do not recognize endpoint '/list/%s' function\n", words[1]);
}
static struct hash *apiFunctionHash = NULL;
static void setupFunctionHash()
/* initialize the apiFunctionHash */
{
if (apiFunctionHash)
return;
apiFunctionHash = hashNew(0);
hashAdd(apiFunctionHash, "list", &apiList);
}
static void apiFunctionSwitch(char *pathInfo)
/* given a pathInfo string: /command/subCommand/etc...
* parse that and decide on which function to acll
*/
{
hPrintDisable(); /* turn off all normal HTML output, doing JSON output */
/* the leading slash has been removed from the pathInfo, therefore, the
* chop will have the first word in words[0]
*/
char *words[MAX_PATH_INFO];/*expect no more than MAX_PATH_INFO number of words*/
int wordCount = chopByChar(pathInfo, '/', words, ArraySize(words));
if (wordCount < 2)
- errAbort("ERROR: no commands found in path info\n");
+ jsonErrAbort("ERROR: no endpoint commands found ?\n");
void (*apiFunction)(char **) = hashMustFindVal(apiFunctionHash, words[0]);
(*apiFunction)(words);
} /* static void apiFunctionSwitch(char *pathInfo) */
static void tracksForUcscDb(char * ucscDb)
{
hPrintf("Tracks in UCSC genome: '%s'
\n", ucscDb);
struct trackDb *tdbList = hTrackDb(ucscDb);
struct trackDb *track;
hPrintf("