0dbf3efc8d7c425510c124204883708273691ec8
hiram
  Tue Mar 19 13:36:44 2019 -0700
correctly listing full set of tracks for a hub or database with all attributes refs #18869

diff --git src/hg/hubApi/list.c src/hg/hubApi/list.c
index 5ee114d..b464631 100644
--- src/hg/hubApi/list.c
+++ src/hg/hubApi/list.c
@@ -1,348 +1,384 @@
 /* manage endpoint /list/ functions */
 
 #include "dataApi.h"
 
 static void hubPublicJsonData(struct jsonWrite *jw, struct hubPublic *el,
   int columnCount, char **columnNames)
 /* Print array data for one row from hubPublic table, order here
  * must be same as was stated in the columnName header element
  * This code should be in hg/lib/hubPublic.c (which does not exist)
  */
 {
 int i = 0;
 jsonWriteObjectStart(jw, NULL);
 jsonWriteString(jw, columnNames[i++], el->hubUrl);
 jsonWriteString(jw, columnNames[i++], el->shortLabel);
 jsonWriteString(jw, columnNames[i++], el->longLabel);
 jsonWriteString(jw, columnNames[i++], el->registrationTime);
 jsonWriteNumber(jw, columnNames[i++], (long long)el->dbCount);
 jsonWriteString(jw, columnNames[i++], el->dbList);
 jsonWriteString(jw, columnNames[i++], el->descriptionUrl);
 jsonWriteObjectEnd(jw);
 #ifdef NOT
 jsonWriteListStart(jw, NULL);
 jsonWriteString(jw, NULL, el->hubUrl);
 jsonWriteString(jw, NULL, el->shortLabel);
 jsonWriteString(jw, NULL, el->longLabel);
 jsonWriteString(jw, NULL, el->registrationTime);
 jsonWriteNumber(jw, NULL, (long long)el->dbCount);
 jsonWriteString(jw, NULL, el->dbList);
 jsonWriteString(jw, NULL, el->descriptionUrl);
 jsonWriteListEnd(jw);
 #endif
 }
 
 static void jsonPublicHubs()
 /* output the hubPublic SQL table */
 {
 struct sqlConnection *conn = hConnectCentral();
 char *dataTime = sqlTableUpdate(conn, hubPublicTableName());
 time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
 replaceChar(dataTime, ' ', 'T');	/* ISO 8601 */
 struct hubPublic *el = hubPublicLoadAll();
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "dataTime", dataTime);
 jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
 freeMem(dataTime);
 // redundant: jsonWriteString(jw, "tableName", hubPublicTableName());
 char **columnNames = NULL;
 char **columnTypes = NULL;
 int columnCount = tableColumns(conn, jw, hubPublicTableName(), &columnNames, &columnTypes);
 jsonWriteListStart(jw, "publicHubs");
 for ( ; el != NULL; el = el->next )
     {
     hubPublicJsonData(jw, el, columnCount, columnNames);
     }
 jsonWriteListEnd(jw);
 jsonWriteObjectEnd(jw);
 fputs(jw->dy->string,stdout);
 hDisconnectCentral(&conn);
 }
 
 static void dbDbJsonData(struct jsonWrite *jw, struct dbDb *el, int columnCount,
   char **columnNames)
 /* Print out dbDb table element in JSON format.
  * must be same as was stated in the columnName header element
  * This code should be over in hg/lib/dbDb.c
  */
 {
 int i = 0;
 jsonWriteObjectStart(jw, el->name);
 i++;
 // redundant: jsonWriteString(jw, NULL, el->name);
 jsonWriteString(jw, columnNames[i++], el->description);
 jsonWriteString(jw, columnNames[i++], el->nibPath);
 jsonWriteString(jw, columnNames[i++], el->organism);
 jsonWriteString(jw, columnNames[i++], el->defaultPos);
 jsonWriteNumber(jw, columnNames[i++], (long long)el->active);
 jsonWriteNumber(jw, columnNames[i++], (long long)el->orderKey);
 jsonWriteString(jw, columnNames[i++], el->genome);
 jsonWriteString(jw, columnNames[i++], el->scientificName);
 jsonWriteString(jw, columnNames[i++], el->htmlPath);
 jsonWriteNumber(jw, columnNames[i++], (long long)el->hgNearOk);
 jsonWriteNumber(jw, columnNames[i++], (long long)el->hgPbOk);
 jsonWriteString(jw, columnNames[i++], el->sourceName);
 jsonWriteNumber(jw, columnNames[i++], (long long)el->taxId);
 jsonWriteObjectEnd(jw);
 #ifdef NOT
 jsonWriteListStart(jw, NULL);
 jsonWriteString(jw, NULL, el->name);
 jsonWriteString(jw, NULL, el->description);
 jsonWriteString(jw, NULL, el->nibPath);
 jsonWriteString(jw, NULL, el->organism);
 jsonWriteString(jw, NULL, el->defaultPos);
 jsonWriteNumber(jw, NULL, (long long)el->active);
 jsonWriteNumber(jw, NULL, (long long)el->orderKey);
 jsonWriteString(jw, NULL, el->genome);
 jsonWriteString(jw, NULL, el->scientificName);
 jsonWriteString(jw, NULL, el->htmlPath);
 jsonWriteNumber(jw, NULL, (long long)el->hgNearOk);
 jsonWriteNumber(jw, NULL, (long long)el->hgPbOk);
 jsonWriteString(jw, NULL, el->sourceName);
 jsonWriteNumber(jw, NULL, (long long)el->taxId);
 jsonWriteListEnd(jw);
 #endif
 }
 
 static void jsonDbDb()
 /* output the dbDb SQL table */
 {
 struct sqlConnection *conn = hConnectCentral();
 char *dataTime = sqlTableUpdate(conn, "dbDb");
 time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
 replaceChar(dataTime, ' ', 'T');	/* ISO 8601 */
 struct dbDb *dbList = ucscDbDb();
 struct dbDb *el;
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "dataTime", dataTime);
 jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
 freeMem(dataTime);
 // not needed: jsonWriteString(jw, "tableName", "dbDb");
 char **columnNames = NULL;
 char **columnTypes = NULL;
 int columnCount = tableColumns(conn, jw, "dbDb", &columnNames, &columnTypes);
 if (columnCount)
     {
     }
 // jsonWriteListStart(jw, "ucscGenomes");
 jsonWriteObjectStart(jw, "ucscGenomes");
 for ( el=dbList; el != NULL; el = el->next )
     {
     dbDbJsonData(jw, el, columnCount, columnNames);
     }
 // jsonWriteListEnd(jw);
 jsonWriteObjectEnd(jw);
 jsonWriteObjectEnd(jw);
 fputs(jw->dy->string,stdout);
 hDisconnectCentral(&conn);
 }
 
 static void chromInfoJsonOutput(FILE *f, char *db)
 /* for given db, if there is a track, list the chromosomes in that track,
  * for no track, simply list the chromosomes in the sequence
  */
 {
 char *table = cgiOptionalString("track");
 struct sqlConnection *conn = hAllocConn(db);
 /* in trackDb language: track == table */
 if (table)
     {
     if (! sqlTableExists(conn, table))
 	apiErrAbort("can not find specified 'track=%s' for endpoint: /list/chromosomes?db=%s&track=%s", table, db, table);
     if (sqlColumnExists(conn, table, "chrom"))
 	{
 	char *dataTime = sqlTableUpdate(conn, table);
 	time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
 	replaceChar(dataTime, ' ', 'T');	/* ISO 8601 */
         struct jsonWrite *jw = apiStartOutput();
 	jsonWriteString(jw, "genome", db);
 	jsonWriteString(jw, "track", table);
 	jsonWriteString(jw, "dataTime", dataTime);
 	jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
 	freeMem(dataTime);
         struct slPair *list = NULL;
 	char query[2048];
         sqlSafef(query, sizeof(query), "select distinct chrom from %s", table);
 	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);
         jsonWriteNumber(jw, "chromCount", (long long)slCount(list));
 	jsonWriteObjectStart(jw, "chromosomes");
         struct slPair *el = list;
         for ( ; el != NULL; el = el->next )
             jsonWriteNumber(jw, el->name, (long long)ptToInt(el->val));
 	jsonWriteObjectEnd(jw);	/* chromosomes */
         jsonWriteObjectEnd(jw);	/* top level */
         fputs(jw->dy->string,stdout);
 	}
     else
 	apiErrAbort("track '%s' is not a position track, request table without chrom specification, genome: '%s'", table, db);
     }
 else
     {
     char *dataTime = sqlTableUpdate(conn, "chromInfo");
     time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
     replaceChar(dataTime, ' ', 'T');	/* ISO 8601 */
     struct chromInfo *ciList = createChromInfoList(NULL, db);
     struct chromInfo *el = ciList;
     struct jsonWrite *jw = apiStartOutput();
     jsonWriteString(jw, "genome", db);
     jsonWriteString(jw, "dataTime", dataTime);
     jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
     freeMem(dataTime);
     jsonWriteNumber(jw, "chromCount", (long long)slCount(ciList));
     jsonWriteObjectStart(jw, "chromosomes");
     for ( ; el != NULL; el = el->next )
 	{
         jsonWriteNumber(jw, el->chrom, (long long)el->size);
 	}
     jsonWriteObjectEnd(jw);	/* chromosomes */
     jsonWriteObjectEnd(jw);	/* top level */
     fputs(jw->dy->string,stdout);
     }
 hFreeConn(&conn);
 }
 
-static void recursiveTrackList(struct jsonWrite *jw, struct trackDb *tdb, char *type)
-/* output trackDb tags, recursive when composite track */
+static void recursiveTrackList(struct jsonWrite *jw, struct trackDb *tdb)
+/* output trackDb tags only for real tracks, not containers,
+ * recursive when subtracks exist
+ */
 {
-jsonWriteListStart(jw, type);
-struct trackDb *el = NULL;
-for (el = tdb; el != NULL; el = el->next )
+if (! ( tdbIsComposite(tdb) || tdbIsCompositeView(tdb) ) )
     {
-    jsonWriteObjectStart(jw, NULL);
-    jsonWriteString(jw, "track", el->track);
-    jsonWriteString(jw, "shortLabel", el->shortLabel);
-    jsonWriteString(jw, "type", el->type);
-    jsonWriteString(jw, "longLabel", el->longLabel);
-    if (el->parent)
-        jsonWriteString(jw, "parent", el->parent->track);
-    if (el->subtracks)
-	recursiveTrackList(jw, el->subtracks, "subtracks");
+    jsonWriteObjectStart(jw, tdb->track);
+    jsonWriteString(jw, "shortLabel", tdb->shortLabel);
+    jsonWriteString(jw, "type", tdb->type);
+    jsonWriteString(jw, "longLabel", tdb->longLabel);
+    if (tdb->parent)
+	jsonWriteString(jw, "parent", tdb->parent->track);
+    if (tdb->settingsHash)
+	{
+	jsonWriteString(jw, "hasSettingsHash", "TRUE");
+	struct hashEl *hel;
+	struct hashCookie hc = hashFirst(tdb->settingsHash);
+	while ((hel = hashNext(&hc)) != NULL)
+	    {
+	    if (sameWord("track", hel->name))
+		continue;	// already output in header
+	    if (isEmpty((char *)hel->val))
+		jsonWriteString(jw, hel->name, "empty");
+	    else
+		jsonWriteString(jw, hel->name, (char *)hel->val);
+	    }
+	}
     jsonWriteObjectEnd(jw);
     }
-jsonWriteListEnd(jw);
+
+if (tdb->subtracks)
+    {
+    struct trackDb *el = NULL;
+    for (el = tdb->subtracks; el != NULL; el = el->next )
+	{
+	recursiveTrackList(jw, el);
+	}
+    }
 }	/*	static void recursiveTrackList()	*/
 
 static int trackDbTrackCmp(const void *va, const void *vb)
 /* Compare to sort based on 'track' name; use shortLabel as secondary sort key.
  * Note: parallel code to hgTracks.c:tgCmpPriority */
 {
 const struct trackDb *a = *((struct trackDb **)va);
 const struct trackDb *b = *((struct trackDb **)vb);
 int dif = strcmp(a->track, b->track);
 if (dif < 0)
    return -1;
 else if (dif == 0.0)
    return strcasecmp(a->shortLabel, b->shortLabel);
 else
    return 1;
 }
 
 static void trackDbJsonOutput(char *db, FILE *f)
 /* return track list from specified UCSC database name */
 {
 struct sqlConnection *conn = hAllocConn(db);
 char *dataTime = sqlTableUpdate(conn, "trackDb");
 time_t dataTimeStamp = sqlDateToUnixTime(dataTime);
 replaceChar(dataTime, ' ', 'T');	/* ISO 8601 */
 hFreeConn(&conn);
 struct trackDb *tdbList = obtainTdb(NULL, db);
 struct jsonWrite *jw = apiStartOutput();
 jsonWriteString(jw, "db", db);
 jsonWriteString(jw, "dataTime", dataTime);
 jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp);
 freeMem(dataTime);
-recursiveTrackList(jw, tdbList, "tracks");
+struct trackDb *el = NULL;
+for (el = tdbList; el != NULL; el = el->next )
+    {
+    recursiveTrackList(jw, el);
+    }
 jsonWriteObjectEnd(jw);
 fputs(jw->dy->string,stdout);
 }	/*	static void trackDbJsonOutput(char *db, FILE *f)	*/
 
 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))
 	apiErrAbort("must supply hubUrl='http:...' some URL to a hub for /list/hubGenomes");
 
     struct trackHub *hub = errCatchTrackHubOpen(hubUrl);
     if (hub->genomeList)
 	{
+	slNameSort((struct slName **)&hub->genomeList);
         struct jsonWrite *jw = apiStartOutput();
 	jsonWriteString(jw, "hubUrl", hubUrl);
-        jsonWriteListStart(jw, "genomes");
-	struct slName *theList = genomeList(hub, NULL, NULL);
-	slNameSort(&theList);
-	struct slName *el = theList;
-	for ( ; el ; el = el->next )
+        jsonWriteObjectStart(jw, "genomes");
+	struct trackHubGenome *el;
+        for ( el = hub->genomeList; el; el = el->next)
 	    {
-	    jsonWriteString(jw, NULL, el->name);
+	    jsonWriteObjectStart(jw, el->name);
+	    jsonWriteString(jw, "organism", el->organism);
+	    jsonWriteString(jw, "description", el->description);
+	    jsonWriteString(jw, "trackDbFile", el->trackDbFile);
+	    jsonWriteString(jw, "twoBitPath", el->twoBitPath);
+	    jsonWriteString(jw, "groups", el->groups);
+	    jsonWriteString(jw, "defaultPos", el->defaultPos);
+	    jsonWriteNumber(jw, "orderKey", el->orderKey);
+	    jsonWriteObjectEnd(jw);
 	    }
-	jsonWriteListEnd(jw);
+	jsonWriteObjectEnd(jw);
 	jsonWriteObjectEnd(jw);
         fputs(jw->dy->string,stdout);
 	}
     }
 else if (sameWord("tracks", words[1]))
     {
     char *hubUrl = cgiOptionalString("hubUrl");
     char *genome = cgiOptionalString("genome");
     char *db = cgiOptionalString("db");
     if (isEmpty(hubUrl) && isEmpty(db))
       apiErrAbort("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))
             apiErrAbort("ERROR: must supply hubUrl='http:...' some URL to a hub for /list/genomes");
 	}
     struct trackHub *hub = errCatchTrackHubOpen(hubUrl);
     if (hub->genomeList)
 	{
 	struct trackDb *tdbList = NULL;
 	(void) genomeList(hub, &tdbList, genome);
 	slSort(tdbList, trackDbTrackCmp);
         struct jsonWrite *jw = apiStartOutput();
 	jsonWriteString(jw, "hubUrl", hubUrl);
-	jsonWriteString(jw, "genome", genome);
-        recursiveTrackList(jw, tdbList, "tracks");
+	jsonWriteObjectStart(jw, genome);
+	struct trackDb *el = NULL;
+	for (el = tdbList; el != NULL; el = el->next )
+	    {
+	    recursiveTrackList(jw, el);
+	    }
+	jsonWriteObjectEnd(jw);
 	jsonWriteObjectEnd(jw);
         fputs(jw->dy->string,stdout);
 	}
     }
 else if (sameWord("chromosomes", words[1]))
     {
     char *hubUrl = cgiOptionalString("hubUrl");
 //    char *genome = cgiOptionalString("genome");
     char *db = cgiOptionalString("db");
     if (isEmpty(hubUrl) && isEmpty(db))
         apiErrAbort("ERROR: must supply hubUrl or db name to return chromosome list");
 
     if (isEmpty(hubUrl))	// missing hubUrl implies UCSC database
 	{
         chromInfoJsonOutput(stdout, db);
 	return;
 	}
     }
 else
     apiErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]);
 }	/*	void apiList(char *words[MAX_PATH_INFO])        */