002a02e0a481cb3f1f06c7f848adfdc7940844cf hiram Tue Feb 5 11:24:36 2019 -0800 return dbDb contents /list/ucscGenomes function refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 9ae29b3..c74b89a 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -52,32 +52,32 @@ char *longLabel; /* Hub long label. */ char *registrationTime; /* Time first registered */ unsigned dbCount; /* Number of databases hub has data for. */ char *dbList; /* Comma separated list of databases. */ char *descriptionUrl; /* URL to description HTML */ }; /* Global Variables */ static struct cart *cart; /* CGI and other variables */ static struct hash *oldVars = NULL; static struct hash *trackCounter = NULL; static long totalTracks = 0; static boolean measureTiming = FALSE; /* set by CGI parameters */ static boolean allTrackSettings = FALSE; /* checkbox setting */ static char **shortLabels = NULL; /* public hub short labels in array */ +struct hubPublic *publicHubList = NULL; static int publicHubCount = 0; -static struct hubPublic *publicHubList = NULL; static char *defaultHub = "Plants"; static long enteredMainTime = 0; /* will become = clock1000() on entry */ /* to allow calculation of when to bail out, taking too long */ static long timeOutSeconds = 100; static boolean timedOut = FALSE; /* ######################################################################### */ static void jsonInteger(FILE *f, char *tag, int value) /* output one json interger: "tag":value appropriately quoted and encoded */ { fprintf(f,"\"%s\":%d",tag, value); } static void jsonStringOut(FILE *f, char *tag, char *value) @@ -136,36 +136,35 @@ ret->hubUrl = cloneString(row[0]); ret->shortLabel = cloneString(row[1]); ret->longLabel = cloneString(row[2]); ret->registrationTime = cloneString(row[3]); ret->dbCount = sqlUnsigned(row[4]); ret->dbList = cloneString(row[5]); // if (row[6]) ret->descriptionUrl = cloneString(row[6]); // else // ret->descriptionUrl = cloneString(""); return ret; } static struct hubPublic *hubPublicLoadAll() { +char query[1024]; struct hubPublic *list = NULL; struct sqlConnection *conn = hConnectCentral(); -// Build a query to find all public hub URL's -struct dyString *query = sqlDyStringCreate("select * from %s", - hubPublicTableName()); -struct sqlResult *sr = sqlGetResult(conn, query->string); +sqlSafef(query, sizeof(query), "select * from %s", hubPublicTableName()); +struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct hubPublic *el = hubPublicLoad(row); slAddHead(&list, el); } sqlFreeResult(&sr); hDisconnectCentral(&conn); publicHubSortCase(&list); int listSize = slCount(list); AllocArray(shortLabels, listSize); struct hubPublic *el = list; int i = 0; for ( ; el != NULL; el = el->next ) { @@ -481,59 +480,131 @@ static char *urlFromShortLabel(char *shortLabel) { char hubUrl[1024]; char query[1024]; struct sqlConnection *conn = hConnectCentral(); // Build a query to select the hubUrl for the given shortLabel sqlSafef(query, sizeof(query), "select hubUrl from %s where shortLabel='%s'", hubPublicTableName(), shortLabel); if (! sqlQuickQuery(conn, query, hubUrl, sizeof(hubUrl))) hubUrl[0] = 0; hDisconnectCentral(&conn); return cloneString(hubUrl); } +static void dbDbJsonOutput(struct dbDb *el, FILE *f) +/* Print out hubPublic element in JSON format. */ +{ +fputc('{',f); +jsonStringOut(f, "name", el->name); +fputc(',',f); +jsonStringOut(f, "description", el->description); +fputc(',',f); +jsonStringOut(f, "nibPath", el->nibPath); +fputc(',',f); +jsonStringOut(f, "organism", el->organism); +fputc(',',f); +jsonStringOut(f, "defaultPos", el->defaultPos); +fputc(',',f); +jsonInteger(f, "active", el->active); +fputc(',',f); +jsonInteger(f, "orderKey", el->orderKey); +fputc(',',f); +jsonStringOut(f, "genome", el->genome); +fputc(',',f); +jsonStringOut(f, "scientificName", el->scientificName); +fputc(',',f); +jsonStringOut(f, "htmlPath", el->htmlPath); +fputc(',',f); +jsonInteger(f, "hgNearOk", el->hgNearOk); +fputc(',',f); +jsonInteger(f, "hgPbOk", el->hgPbOk); +fputc(',',f); +jsonStringOut(f, "sourceName", el->sourceName); +fputc(',',f); +jsonInteger(f, "taxId", el->taxId); +fputc('}',f); +} + static void jsonPublicHubs() +/* output the hubPublic SQL table */ { struct hubPublic *el = publicHubList; -printf("{\"publicHubs\":["); +printf("{\"source\":\"UCSantaCruz\",\"publicHubs\":["); for ( ; el != NULL; el = el->next ) { hubPublicJsonOutput(el, stdout); if (el->next) printf(","); } printf("]}\n"); } +static int dbDbCmpName(const void *va, const void *vb) +/* Compare two dbDb elements: name, ignore case. */ +{ +const struct dbDb *a = *((struct dbDb **)va); +const struct dbDb *b = *((struct dbDb **)vb); +return strcasecmp(a->name, b->name); +} + +static void jsonDbDb() +/* output the dbDb SQL table */ +{ +char query[1024]; +struct sqlConnection *conn = hConnectCentral(); +sqlSafef(query, sizeof(query), "select * from dbDb"); +struct dbDb *dbList = NULL, *el = NULL; +struct sqlResult *sr = sqlGetResult(conn, query); +char **row; +while ((row = sqlNextRow(sr)) != NULL) + { + el = dbDbLoad(row); + slAddHead(&dbList, el); + } +sqlFreeResult(&sr); +hDisconnectCentral(&conn); +slSort(&dbList, dbDbCmpName); +printf("{\"source\":\"UCSantaCruz\",\"ucscGenomes\":["); +for ( el=dbList; el != NULL; el = el->next ) + { + dbDbJsonOutput(el, stdout); + if (el->next) + printf(","); + } +printf("]}\n"); +} + #define MAX_PATH_INFO 32 static void apiList(char *words[MAX_PATH_INFO]) /* 'list' function */ { if (sameWord("publicHubs", words[1])) jsonPublicHubs(); +else if (sameWord("ucscGenomes", words[1])) + jsonDbDb(); else if (sameWord("genomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); if (isEmpty(hubUrl)) errAbort("# must supply hubUrl='http:...' some URL to a hub for /list/genomes\n"); struct trackHub *hub = trackHubOpen(hubUrl, ""); if (hub->genomeList) { - fputc('{',stdout); + printf("{\"source\":\"UCSantaCruz\","); 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"); @@ -544,31 +615,31 @@ char *hubUrl = cgiOptionalString("hubUrl"); char *genome = cgiOptionalString("genome"); 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"); } struct trackHub *hub = trackHubOpen(hubUrl, ""); if (hub->genomeList) { struct slName *dbTrackList = NULL; (void) genomeList(hub, &dbTrackList, genome); - fputc('{',stdout); + printf("{\"source\":\"UCSantaCruz\","); jsonStringOut(stdout, "hubUrl", hubUrl); fputc(',',stdout); jsonStringOut(stdout, "genome", genome); fputc(',',stdout); printf("\"tracks\":["); slNameSort(&dbTrackList); struct slName *el = dbTrackList; for ( ; el ; el = el->next ) { char *a = jsonStringEscape(el->name); printf("\"%s\"", a); freeMem(a); if (el->next) fputc(',',stdout); } @@ -656,32 +727,33 @@ urlInput = otherHubUrl; long lastTime = clock1000(); struct trackHub *hub = trackHubOpen(urlInput, ""); if (measureTiming) { long thisTime = clock1000(); hPrintf("hub open time: %ld millis
\n", thisTime - lastTime); } struct trackHubGenome *hubGenome = hub->genomeList; hPrintf("

Example URLs to return json data structures:

\n"); hPrintf("\n"); hPrintf("

cart dump

"); hPrintf("
\n");
 cartDump(cart);
 hPrintf("
\n"); hPrintf("
\n\n", "../cgi-bin/hubApi"); hPrintf("Select public hub: "); #define JBUFSIZE 2048 char javascript[JBUFSIZE]; struct slPair *events = NULL; safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;"); slPairAdd(&events, "focus", cloneString(javascript));