8aba55de743fd795f8c26d730567ff8a359254e8 hiram Tue Feb 5 15:58:07 2019 -0800 beginning to show everything about a track in ucsc database refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 8264495..3c81333 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -55,30 +55,31 @@ 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 char *defaultHub = "Plants"; +static char *defaultDb = "ce11"; 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) /* output one json string: "tag":"value" appropriately quoted and encoded */ @@ -536,47 +537,55 @@ 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 */ +static struct dbDb *ucscDbDb() +/* return the dbDb table as an slList */ { 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); +return dbList; +} + +static void jsonDbDb() +/* output the dbDb SQL table */ +{ +struct dbDb *dbList = ucscDbDb(); +struct dbDb *el; printf("{\"source\":\"UCSantaCruz\",\"ucscGenomes\":["); for ( el=dbList; el != NULL; el = el->next ) { dbDbJsonOutput(el, stdout); if (el->next) printf(","); } printf("]}\n"); } static void trackDbJsonOutput(char *db, FILE *f) /* return track list from specified UCSC database name */ { struct trackDb *tdbList = hTrackDb(db); struct trackDb *el; @@ -700,30 +709,46 @@ { 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"); void (*apiFunction)(char **) = hashMustFindVal(apiFunctionHash, words[0]); (*apiFunction)(words); +} /* static void apiFunctionSwitch(char *pathInfo) */ + +static void tracksForUcscDb(char * ucscDb) +{ +hPrintf("<p>Tracks in UCSC genome: '%s'<br>\n", ucscDb); +struct trackDb *tdbList = hTrackDb(ucscDb); +struct trackDb *track; +hPrintf("<ul>\n"); +for (track = tdbList; track != NULL; track = track->next ) + { + hPrintf("<li>%s</li>\n", track->track); + if (allTrackSettings) + trackSettings(track); /* show all settings */ + } +hPrintf("</ul>\n"); +hPrintf("</p>\n"); } static void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { // struct hubPublic *hubList = hubPublicLoadAll(); publicHubList = hubPublicLoadAll(); cart = theCart; measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming")); measureTiming = TRUE; char *database = NULL; char *genome = NULL; getDbAndGenome(cart, &database, &genome, oldVars); initGenbankTableNames(database); @@ -734,110 +759,142 @@ if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); char *pathInfo = getenv("PATH_INFO"); if (isNotEmpty(pathInfo)) { /* skip the first leading slash to simplify chopByChar parsing */ pathInfo += 1; setupFunctionHash(); apiFunctionSwitch(pathInfo); return; } +struct dbDb *dbList = ucscDbDb(); +char **ucscDbList = NULL; +int listSize = slCount(dbList); +AllocArray(ucscDbList, listSize); +struct dbDb *el = dbList; +int ucscDataBaseCount = 0; +int maxDbNameWidth = 0; +for ( ; el != NULL; el = el->next ) + { + ucscDbList[ucscDataBaseCount++] = el->name; + if (strlen(el->name) > maxDbNameWidth) + maxDbNameWidth = strlen(el->name); + } +maxDbNameWidth += 1; + cartWebStart(cart, database, "access mechanism to hub data resources"); char *goOtherHub = cartUsualString(cart, "goOtherHub", defaultHub); +char *goUcscDb = cartUsualString(cart, "goUcscDb", ""); char *otherHubUrl = cartUsualString(cart, "urlHub", defaultHub); char *goPublicHub = cartUsualString(cart, "goPublicHub", defaultHub); char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub); char *urlDropDown = urlFromShortLabel(hubDropDown); +char *ucscDb = cartUsualString(cart, "ucscGenomes", defaultDb); char *urlInput = urlDropDown; /* assume public hub */ if (sameWord("go", goOtherHub)) /* requested other hub URL */ urlInput = otherHubUrl; long lastTime = clock1000(); struct trackHub *hub = trackHubOpen(urlInput, ""); if (measureTiming) { long thisTime = clock1000(); hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime); } +hPrintf("<h3>ucscDb: '%s'</h2>\n", ucscDb); + struct trackHubGenome *hubGenome = hub->genomeList; hPrintf("<h2>Example URLs to return json data structures:</h2>\n"); hPrintf("<ul>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/publicHubs'>list public hubs</a> <em>/cgi-bin/hubApi/list/publicHubs</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/ucscGenomes'>list database genomes</a> <em>/cgi-bin/hubApi/list/ucscGenomes</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/genomes?hubUrl=%s'>list genomes from specified hub</a> <em>/cgi-bin/hubApi/list/genomes?hubUrl='%s'</em></li>\n", urlInput, urlInput); hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?hubUrl=%s&genome=%s'>list tracks from specified hub and genome</a> <em>/cgi-bin/hubApi/list/tracks?hubUrl='%s&genome=%s'</em></li>\n", urlInput, hubGenome->name, urlInput, hubGenome->name); -hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?db=%s'>list tracks from specified UCSC database</a> <em>/cgi-bin/hubApi/list/tracks?db='%s'</em></li>\n", "ce11", "ce11"); +hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?db=%s'>list tracks from specified UCSC database</a> <em>/cgi-bin/hubApi/list/tracks?db='%s'</em></li>\n", ucscDb, ucscDb); hPrintf("</ul>\n"); hPrintf("<h4>cart dump</h4>"); hPrintf("<pre>\n"); cartDump(cart); hPrintf("</pre>\n"); hPrintf("<form action='%s' name='hubApiUrl' id='hubApiUrl' method='GET'>\n\n", "../cgi-bin/hubApi"); hPrintf("<b>Select public hub: </b>"); #define JBUFSIZE 2048 +#define SMALLBUF 256 char javascript[JBUFSIZE]; struct slPair *events = NULL; safef(javascript, sizeof(javascript), "this.lastIndex=this.selectedIndex;"); slPairAdd(&events, "focus", cloneString(javascript)); -#define SMALLBUF 256 -// char class[SMALLBUF]; -// safef(class, sizeof(class), "viewDD normalText %s", "class"); cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs", shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events); hWrites(" "); hButton("goPublicHub", "go"); hPrintf("<br>Or, enter a hub URL: "); hPrintf("<input type='text' name='urlHub' id='urlHub' size='60' value='%s'>\n", urlInput); hWrites(" "); hButton("goOtherHub", "go"); +hPrintf("<br>Or, select a UCSC database name: "); +maxDbNameWidth *= 9; // 9 should be font width here +char widthPx[SMALLBUF]; +safef(widthPx, sizeof(widthPx), "width: %dpx", maxDbNameWidth); +cgiMakeDropListClassWithIdStyleAndJavascript("ucscGenomes", "ucscGenomes", + ucscDbList, ucscDataBaseCount, ucscDb, NULL, widthPx, events); +hWrites(" "); +hButton("goUcscDb", "go"); + boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); hPrintf("<br>\n "); hCheckBox("depthSearch", cartUsualBoolean(cart, "depthSearch", FALSE)); hPrintf(" perform full bbi file measurement : %s (will time out if taking longer than %ld seconds)<br>\n", depthSearch ? "TRUE" : "FALSE", timeOutSeconds); hPrintf("\n "); allTrackSettings = cartUsualBoolean(cart, "allTrackSettings", FALSE); hCheckBox("allTrackSettings", allTrackSettings); hPrintf(" display all track settings for each track : %s<br>\n", allTrackSettings ? "TRUE" : "FALSE"); - hPrintf("<br>\n</form>\n"); +if (sameWord("go", goUcscDb)) /* requested UCSC db track list */ + { + tracksForUcscDb(ucscDb); + } +else + { hPrintf("<p>URL: %s - %s<br>\n", urlInput, sameWord("go",goPublicHub) ? "public hub" : "other hub"); hPrintf("name: %s<br>\n", hub->shortLabel); hPrintf("description: %s<br>\n", hub->longLabel); hPrintf("default db: '%s'<br>\n", isEmpty(hub->defaultDb) ? "(none available)" : hub->defaultDb); printf("docRoot:'%s'<br>\n", docRoot); if (hub->genomeList) (void) genomeList(hub, NULL, NULL); /* ignore returned list */ - hPrintf("</p>\n"); + } + if (timedOut) hPrintf("<h1>Reached time out %ld seconds</h1>", timeOutSeconds); if (measureTiming) hPrintf("<em>Overall total time: %ld millis</em><br>\n", clock1000() - enteredMainTime); cartWebEnd(); } /* void doMiddle(struct cart *theCart) */ /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = {"Submit", "submit", NULL,}; int main(int argc, char *argv[]) /* Process command line. */