6eacdcdb29afdeefa7ba7a5ec1e52e13e86680f9 hiram Wed Apr 10 14:45:45 2019 -0700 better layout for selection menus and now returning errors properly refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 40b1708..a81f253 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -1,1385 +1,1432 @@ /* hubApi - access mechanism to hub data resources. */ #include "dataApi.h" #include "botDelay.h" #include "jsHelper.h" /* +------------------+------------------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +------------------+------------------+------+-----+---------+-------+ | hubUrl | longblob | NO | PRI | NULL | | | shortLabel | varchar(255) | NO | | NULL | | | longLabel | varchar(255) | NO | | NULL | | | registrationTime | varchar(255) | NO | | NULL | | | dbCount | int(10) unsigned | NO | | NULL | | | dbList | blob | YES | | NULL | | | descriptionUrl | longblob | YES | | NULL | | +------------------+------------------+------+-----+---------+-------+ */ /* Global Variables for all modules */ int maxItemsOutput = 1000; /* can be set in URL maxItemsOutput=N */ static int maxItemLimit = 1000000; /* maximum of 1,000,000 items returned */ /* for debugging purpose, current bot delay value */ int botDelay = 0; boolean debug = FALSE; /* can be set in URL debug=1, to turn off: debug=0 */ #define delayFraction 0.03 /* default is to list all trackDb entries, composite containers too. * This option will limit to only the actual track entries with data */ boolean trackLeavesOnly = FALSE; /* set by CGI parameter 'trackLeavesOnly' */ /* Global only to this one source file */ 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 *defaultHubUrl = " http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt"; 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 char *urlPrefix = ""; /* initalized to support self references */ + + /* supportedTypes will be initialized to a known supported set */ static struct slName *supportedTypes = NULL; - /* will be initialized to a known supported set */ + static void initSupportedTypes() /* initalize the list of supported track types */ { struct slName *el = newSlName("bed"); slAddHead(&supportedTypes, el); el = newSlName("wig"); slAddHead(&supportedTypes, el); el = newSlName("broadPeak"); slAddHead(&supportedTypes, el); el = newSlName("narrowPeak"); slAddHead(&supportedTypes, el); el = newSlName("bigBed"); slAddHead(&supportedTypes, el); el = newSlName("bigWig"); slAddHead(&supportedTypes, el); el = newSlName("bigNarrowPeak"); slAddHead(&supportedTypes, el); el = newSlName("bigGenePred"); slAddHead(&supportedTypes, el); el = newSlName("genePred"); slAddHead(&supportedTypes, el); el = newSlName("psl"); slAddHead(&supportedTypes, el); el = newSlName("rmsk"); slAddHead(&supportedTypes, el); el = newSlName("bigPsl"); slAddHead(&supportedTypes, el); // el = newSlName("bigBarChart"); // slAddHead(&supportedTypes, el); // el = newSlName("bigInteract"); // slAddHead(&supportedTypes, el); // el = newSlName("bigMaf"); // slAddHead(&supportedTypes, el); // el = newSlName("bigChain"); // slAddHead(&supportedTypes, el); slNameSort(&supportedTypes); } static boolean isSupportedType(char *type) /* is given type in the supportedTypes list ? */ { boolean ret = FALSE; if (startsWith("wigMaf", type)) /* not wigMaf at this time */ return ret; struct slName *el; for (el = supportedTypes; el; el = el->next) { if (startsWith(el->name, type)) { ret = TRUE; break; } } return ret; } static int publicHubCmpCase(const void *va, const void *vb) /* Compare two shortLabels, ignore case. */ { const struct hubPublic *a = *((struct hubPublic **)va); const struct hubPublic *b = *((struct hubPublic **)vb); return strcasecmp(a->shortLabel, b->shortLabel); } static void publicHubSortCase(struct hubPublic **pList) /* Sort slName list, ignore case. */ { slSort(pList, publicHubCmpCase); } struct hubPublic *hubPublicDbLoadAll() /* read entire hubPublic table in hgcentral and return resulting list */ { char query[1024]; struct hubPublic *list = NULL; struct sqlConnection *conn = hConnectCentral(); 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 ) { shortLabels[i++] = el->shortLabel; ++publicHubCount; } return list; } static boolean timeOutReached() /* see if the timeout has been reached to determine if an exit * is appropriate at this time */ { long nowTime = clock1000(); timedOut = FALSE; if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds)) timedOut= TRUE; return timedOut; } static void hashCountTrack(struct trackDb *tdb, struct hash *countTracks) /* this is counting up track types into the hash countTracks */ { char *stripType = cloneString(tdb->type); if (startsWith("chain ", tdb->type)) stripType = cloneString("chain"); else if (startsWith("netAlign ", tdb->type)) stripType = cloneString("netAlign"); else if (startsWith("genePred ", tdb->type)) stripType = cloneString("genePred"); else if (startsWith("bigWig ", tdb->type)) stripType = cloneString("bigWig"); else if (startsWith("wigMaf ", tdb->type)) stripType = cloneString("wigMaf"); else if (startsWith("wig ", tdb->type)) stripType = cloneString("wig"); else stripType = cloneString(tdb->type); boolean compositeContainer = tdbIsComposite(tdb); boolean compositeView = tdbIsCompositeView(tdb); boolean superChild = tdbIsSuperTrackChild(tdb); if (compositeContainer) hashIncInt(countTracks, "composite container"); else if (compositeView) hashIncInt(countTracks, "composite view"); else if (superChild) { hashIncInt(countTracks, "superTrack child"); hashIncInt(countTracks, stripType); hashIncInt(countTracks, "track count"); } else if (isEmpty(tdb->type)) hashIncInt(countTracks, "no type specified"); else { hashIncInt(countTracks, stripType); hashIncInt(countTracks, "track count"); } freeMem(stripType); } static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, unsigned chromSize, char *errorString) /* print out a sample getData URL */ { char errorPrint[2048]; errorPrint[0] = 0; if (isNotEmpty(errorString)) { safef(errorPrint, sizeof(errorPrint), " ERROR: %s", errorString); } boolean superChild = tdbIsSuperTrackChild(tdb); unsigned start = chromSize / 4; unsigned end = start + 10000; if (end > chromSize) end = chromSize; char *genome = NULL; if (hub) genome = hub->genomeList->name; if (db) { if (hub) { char urlReference[2048]; - safef(urlReference, sizeof(urlReference), " (sample getData)%s\n", urlPrefix, hub->url, genome, tdb->track, chrom, start, end, errorPrint); + safef(urlReference, sizeof(urlReference), " (sample data)%s\n", urlPrefix, hub->url, genome, tdb->track, chrom, start, end, errorPrint); if (tdb->parent) hPrintf("
  • %s: %s subtrack of parent: %s%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlReference); else hPrintf("
  • %s: %s%s
    • \n", tdb->track, tdb->type, urlReference); } else { char urlReference[2048]; - safef(urlReference, sizeof(urlReference), " (sample getData)%s\n", urlPrefix, db, chrom, tdb->track, start, end, errorPrint); + safef(urlReference, sizeof(urlReference), " (sample data)%s\n", urlPrefix, db, chrom, tdb->track, start, end, errorPrint); if (superChild) hPrintf("
  • %s: %s superTrack child of parent: %s%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlReference); else if (tdb->parent) hPrintf("
  • %s: %s subtrack of parent: %s%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlReference); else hPrintf("
  • %s: %s%s
    • \n", tdb->track, tdb->type, urlReference ); } } else if (hub) { char urlReference[2048]; - safef(urlReference, sizeof(urlReference), " (sample getData)%s\n", urlPrefix, hub->url, genome, tdb->track, chrom, start, end, errorPrint); + safef(urlReference, sizeof(urlReference), " (sample data)%s\n", urlPrefix, hub->url, genome, tdb->track, chrom, start, end, errorPrint); if (tdb->parent) hPrintf("
  • %s: %s subtrack of parent: %s%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlReference); else hPrintf("
  • %s: %s%s
    • \n", tdb->track, tdb->type, urlReference); } else hPrintf("
  • %s : %s not db hub track ?
    • \n", tdb->track, tdb->type); } static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb, long chromCount, long itemCount, char *chromName, unsigned chromSize, char *genome, char *errorString) { unsigned start = chromSize / 4; unsigned end = start + 10000; if (end > chromSize) end = chromSize; char errorPrint[2048]; errorPrint[0] = 0; if (isNotEmpty(errorString)) { safef(errorPrint, sizeof(errorPrint), " : ERROR: %s", errorString); } char countsMessage[512]; countsMessage[0] = 0; if (chromCount > 0 || itemCount > 0) { if (allowedBigBedType(tdb->type)) safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld item count ", chromCount, itemCount); else if (startsWithWord("bigWig", tdb->type)) safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld bases covered ", chromCount, itemCount); else safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld count ", chromCount, itemCount); } if (isSupportedType(tdb->type)) { char urlReference[2048]; - safef(urlReference, sizeof(urlReference), "(sample getData)%s\n", urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint); + safef(urlReference, sizeof(urlReference), "(sample data)%s\n", urlPrefix, hub->url, genome, tdb->track, chromName, start, end, errorPrint); if (allowedBigBedType(tdb->type)) hPrintf("
  • %s: %s%s%s
    • \n", tdb->track, tdb->type, countsMessage, urlReference); else if (startsWithWord("bigWig", tdb->type)) hPrintf("
  • %s: %s%s%s
    • \n", tdb->track, tdb->type, countsMessage, urlReference); else hPrintf("
  • %s: %s%s%s
    • \n", tdb->track, tdb->type, countsMessage, urlReference); } else { if (allowedBigBedType(tdb->type)) hPrintf("
  • %s: %s%s
    • \n", tdb->track, tdb->type, countsMessage); else if (startsWithWord("bigWig", tdb->type)) hPrintf("
  • %s: %s%s
    • \n", tdb->track, tdb->type, countsMessage); else hPrintf("
  • %s: %s%s
    • \n", tdb->track, tdb->type, countsMessage); } } /* static void hubSampleUrl(struct trackHub *hub, struct trackDb *tdb, * long chromCount, long itemCount, char *chromName, unsigned chromSize, * char *genome) */ static void bbiLargestChrom(struct bbiChromInfo *chromList, char **chromName, unsigned *chromSize) /* find largest chromosome name and size in the chromList */ { if (chromName && chromSize) { *chromSize = 0; char *returnName = NULL; struct bbiChromInfo *el; for (el = chromList; el; el = el->next) { if (el->size > *chromSize) { *chromSize = el->size; returnName = el->name; } } if (chromSize > 0) *chromName = cloneString(returnName); } } static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors, char **chromName, unsigned *chromSize) /* check a bigDataUrl to find chrom count and item count, return * name of largest chrom and its size */ { int retVal = 0; *chromCount = 0; *itemCount = 0; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { if (startsWithWord("bigNarrowPeak", type) || startsWithWord("bigBed", type) || startsWithWord("bigGenePred", type) || startsWithWord("bigPsl", type) || startsWithWord("bigChain", type) || startsWithWord("bigMaf", type) || startsWithWord("bigBarChart", type) || startsWithWord("bigInteract", type)) { struct bbiFile *bbi = NULL; bbi = bigBedFileOpen(bigDataUrl); struct bbiChromInfo *chromList = bbiChromList(bbi); *chromCount = slCount(chromList); *itemCount = bigBedItemCount(bbi); bbiLargestChrom(chromList, chromName, chromSize); bbiChromInfoFreeList(&chromList); bbiFileClose(&bbi); } else if (startsWithWord("bigWig", type)) { struct bbiFile *bwf = bigWigFileOpen(bigDataUrl); struct bbiChromInfo *chromList = bbiChromList(bwf); struct bbiSummaryElement sum = bbiTotalSummary(bwf); *chromCount = slCount(chromList); *itemCount = sum.validCount; bbiLargestChrom(chromList, chromName, chromSize); bbiChromInfoFreeList(&chromList); bbiFileClose(&bwf); } else if (startsWithWord("vcfTabix", type)) { struct vcfFile *vcf = vcfTabixFileAndIndexMayOpen(bigDataUrl, bigDataIndex, NULL, 0, 0, 1, 1); if (vcf == NULL) { dyStringPrintf(errors, "Could not open %s and/or its tabix index (.tbi) file. See http://genome.ucsc.edu/goldenPath/help/vcf.html", bigDataUrl); retVal = 1; } else vcfFileFree(&vcf); } else if (startsWithWord("bam", type)) { bamFileAndIndexMustExist(bigDataUrl, bigDataIndex); } else if (startsWithWord("longTabix", type)) { struct bedTabixFile *btf = bedTabixFileMayOpen(bigDataUrl, NULL, 0, 0); if (btf == NULL) { dyStringPrintf(errors, "Couldn't open %s and/or its tabix index (.tbi) file.", bigDataUrl); retVal = 1; } else bedTabixFileClose(&btf); } #ifdef USE_HAL else if (startsWithWord("halSnake", type)) { char *errString; int handle = halOpenLOD(bigDataUrl, &errString); if (handle < 0) { dyStringPrintf(errors, "HAL open error: %s", errString); retVal = 1; } if (halClose(handle, &errString) < 0) { dyStringPrintf(errors, "HAL close error: %s", errString); retVal = 1; } } #endif else { dyStringPrintf(errors, "unrecognized type %s", type); retVal = 1; } } errCatchEnd(errCatch); if (errCatch->gotError) { retVal = 1; dyStringPrintf(errors, "%s", errCatch->message->string); } errCatchFree(&errCatch); return retVal; } /* static int bbiBriefMeasure() */ static void hubSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks, long chromCount, long itemCount, char *chromName, unsigned chromSize, char *genome, char *errorString) /* tdb has subtracks, show only subTracks, no details */ { hPrintf("
    • \n"); } /* hubSubTracks() */ static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks, char *chromName, unsigned chromSize, char *errorString) /* tdb has subtracks, show only subTracks, no details */ { hPrintf("
    • \n"); } static void trackSettings(struct trackDb *tdb, struct hash *countTracks) /* process the settingsHash for a trackDb, recursive when subtracks */ { hPrintf("
    • \n"); } static void hubCountOneTdb(struct trackHub *hub, char *db, struct trackDb *tdb, char *bigDataIndex, struct hash *countTracks, char *chromName, unsigned chromSize, char *genome) { char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); -// char *compositeTrack = trackDbSetting(tdb, "compositeTrack"); boolean compositeContainer = tdbIsComposite(tdb); boolean compositeView = tdbIsCompositeView(tdb); -// char *superTrack = trackDbSetting(tdb, "superTrack"); boolean superChild = tdbIsSuperTrackChild(tdb); boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); hashCountTrack(tdb, countTracks); long chromCount = 0; long itemCount = 0; struct dyString *errors = newDyString(1024); /* if given a chromSize, it belongs to a UCSC db and this is *not* an * assembly hub, otherwise, look up a chrom and size in the bbi file */ if (! (compositeContainer || compositeView) ) { if (chromSize < 1 || depthSearch) { char *longName = NULL; unsigned longSize = 0; (void) bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors, &longName, &longSize); chromSize = longSize; chromName = longName; } } if (depthSearch && bigDataUrl) { if (isSupportedType(tdb->type)) hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); } else { if (compositeContainer) hPrintf("
  • %s: %s : composite track container has %d subtracks
    • \n", tdb->track, tdb->type, slCount(tdb->subtracks)); else if (compositeView) hPrintf("
  • %s: %s : composite view of parent: %s
    • \n", tdb->track, tdb->type, tdb->parent->track); else if (superChild) { if (isSupportedType(tdb->type)) hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); else hPrintf("
  • %s: %s : superTrack child of parent: %s
    • \n", tdb->track, tdb->type, tdb->parent->track); } else if (! depthSearch && bigDataUrl) { if (isSupportedType(tdb->type)) { hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); } } else { if (isSupportedType(tdb->type)) { hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); } else hPrintf("
  • %s: %s (what is this)
    • \n", tdb->track, tdb->type); } } if (allTrackSettings) { hPrintf("
    • \n"); } else if (tdb->subtracks) { hubSubTracks(hub, db, tdb, countTracks, chromCount, itemCount, chromName, chromSize, genome, errors->string); } return; } /* static void hubCountOneTdb(char *db, struct trackDb *tdb, * char *bigDataIndex, struct hash *countTracks, * char *chromName, unsigned chromSize) */ static void countOneTdb(char *db, struct trackDb *tdb, struct hash *countTracks, char *chromName, unsigned chromSize, char *errorString) /* for this tdb in this db, count it up and provide a sample */ { char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); boolean compositeContainer = tdbIsComposite(tdb); boolean compositeView = tdbIsCompositeView(tdb); boolean superChild = tdbIsSuperTrackChild(tdb); boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); hashCountTrack(tdb, countTracks); if (compositeContainer) hPrintf("
  • %s: %s : composite track container has %d subtracks
    • \n", tdb->track, tdb->type, slCount(tdb->subtracks)); else if (compositeView) hPrintf("
  • %s: %s : composite view of parent: %s
    • \n", tdb->track, tdb->type, tdb->parent->track); else if (superChild) { if (isSupportedType(tdb->type)) sampleUrl(NULL, db, tdb, chromName, chromSize, errorString); else hPrintf("
  • %s: %s : superTrack child of parent: %s
    • \n", tdb->track, tdb->type, tdb->parent->track); } else if (! depthSearch && bigDataUrl) hPrintf("
  • %s: %s : %s
    • \n", tdb->track, tdb->type, bigDataUrl); else { if (isSupportedType(tdb->type)) sampleUrl(NULL, db, tdb, chromName, chromSize, errorString); else hPrintf("
  • %s: %s
    • \n", tdb->track, tdb->type); } if (allTrackSettings) { hPrintf("
    • \n"); } else if (tdb->subtracks) { showSubTracks(NULL, db, tdb, countTracks, chromName, chromSize, NULL); } return; } /* static void countOneTdb(char *db, struct trackDb *tdb, * struct hash *countTracks, char *chromName, * unsigned chromSize) */ static unsigned largestChrom(char *db, char **nameReturn, int *chromCount) /* return the length and get the chrom name for the largest chrom * from chromInfo table. For use is sample getData URLs */ { char query[1024]; struct sqlConnection *conn = hAllocConn(db); sqlSafef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit 1"); struct sqlResult *sr = sqlGetResult(conn, query); char **row = sqlNextRow(sr); unsigned length = 0; if (row) { *nameReturn = cloneString(row[0]); length = sqlLongLong(row[1]); } sqlFreeResult(&sr); if (chromCount) { sqlSafef(query, sizeof(query), "select count(*) from chromInfo"); *chromCount = sqlQuickNum(conn, query); } hFreeConn(&conn); return length; } static void hubTrackList(struct trackHub *hub, struct trackDb *topTrackDb, struct trackHubGenome *genome) /* process the track list in a hub to show all tracks */ { hPrintf("
    • \n"); } /* static struct trackDb *hubTrackList() */ static void hubAssemblySettings(struct trackHub *hub, struct trackHubGenome *genome) /* display all the assembly 'settingsHash' */ { struct trackDb *tdb = obtainTdb(genome, NULL); hPrintf("
    • \n"); } static unsigned largestChromInfo(struct chromInfo *ci, char **chromName) /* find largest chrom in this chromInfo, return name and size */ { unsigned size = 0; char *name = NULL; struct chromInfo *el; for (el = ci; el; el = el->next) { if (el->size > size) { size = el->size; name = el->chrom; } } if (chromName) *chromName = name; return size; } static void hubInfo(char *tag, char *val) /* print one list element with the given tag and value, show * if not value present */ { if (isNotEmpty(val)) hPrintf("
  • %s: '%s'
    • \n", tag, val); else hPrintf("
  • %s: <empty>
    • \n", tag); } static void genomeList(struct trackHub *hubTop) /* follow the pointers from the trackHub to trackHubGenome and around * in a circle from one to the other to find all hub resources */ { long totalAssemblyCount = 0; struct trackHubGenome *genome = hubTop->genomeList; hPrintf("

    genome sequences (and tracks) present in this track hub

    \n"); if (NULL == genome) { hPrintf("

    odd error, can not find a gnomeList ? at url: '%s'

    \n", hubTop->url); return; } + +// testing /list/tracks?db=ce11 +// testing /list/tracks? hubUrl genome=_araTha1 + hPrintf("\n"); } /* static void genomeList (hubTop) */ static char *urlFromShortLabel(char *shortLabel) /* this is not a fair way to get the URL since shortLabel's are not * necessarily unique. This is temporary. TBD: need to always use URL * and then get the 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 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); } 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 struct hash *apiFunctionHash = NULL; static void setupFunctionHash() /* initialize the apiFunctionHash */ { if (apiFunctionHash) return; /* already done */ apiFunctionHash = hashNew(0); hashAdd(apiFunctionHash, "list", &apiList); hashAdd(apiFunctionHash, "getData", &apiGetData); } static struct hashEl *parsePathInfo(char *pathInfo, char *words[MAX_PATH_INFO]) /* given a pathInfo string: /command/subCommand/etc... * parse that and return a function pointer and the parsed words * Returns NULL if not recognized */ { char *tmp = cloneString(pathInfo); /* skip the first leading slash to simplify chopByChar parsing */ tmp += 1; int wordCount = chopByChar(tmp, '/', words, MAX_PATH_INFO); if (wordCount < 1) return NULL; struct hashEl *hel = hashLookup(apiFunctionHash, words[0]); return hel; } static void tracksForUcscDb(char *db) /* scan the specified database for all tracks */ { struct hash *countTracks = hashNew(0); char *chromName = NULL; int chromCount = 0; unsigned chromSize = largestChrom(db, &chromName, &chromCount); char countString[64]; sprintLongWithCommas(countString, chromCount); char sizeString[64]; sprintLongWithCommas(sizeString, chromSize); hPrintf("

    Tracks in UCSC genome: '%s', chrom count: %s, longest chrom: %s : %s

    \n", db, countString, chromName, sizeString); + +char urlReference[2048]; +safef(urlReference, sizeof(urlReference), " JSON output: list tracks", urlPrefix, db); +hPrintf("

    %s

    \n", urlReference); + struct trackDb *tdbList = obtainTdb(NULL, db); struct trackDb *tdb; hPrintf("\n"); hPrintf("

    \n"); } // static void tracksForUcscDb(char * db) static void initUrlPrefix() /* set up urlPrefix for self referenes */ { char *httpHost = getenv("HTTP_HOST"); if (isEmpty(httpHost)) urlPrefix = ""; else { if (! startsWith("hgwdev-api", httpHost)) { if (startsWith("hgwdev",httpHost) || startsWith("genome-test", httpHost)) { urlPrefix = "../cgi-bin/hubApi"; } } } } static void showCartDump() /* for information purposes only during development, will become obsolete */ { hPrintf("

    cart dump

    "); hPrintf("
    \n");
 cartDump(cart);
 hPrintf("
    \n"); } static void sendJsonHogMessage(char *hogHost) { -apiErrAbort("Your host, %s, has been sending too many requests lately and is " +apiErrAbort(429, "Too Many Requests", "Your host, %s, has been sending too many requests lately and is " "unfairly loading our site, impacting performance for other users. " "Please contact genome@soe.ucsc.edu to ask that your site " "be reenabled. Also, please consider downloading sequence and/or " "annotations in bulk -- see http://genome.ucsc.edu/downloads.html.", hogHost); } static void sendHogMessage(char *hogHost) { +puts("Content-Type:text/html"); +puts("Status: 429 Too Many Requests"); +puts("Retry-After: 30"); +puts("\n"); + hPrintf("\n"); hPrintf("\n"); hPrintf("\n"); hPrintf("\n"); hPrintf("Status 459 Too Many Requests\n"); hPrintf("

    Status 459 Too many Requests

    \n"); hPrintf("Your host, %s, has been sending too many requests lately and is " "unfairly loading our site, impacting performance for other users. " "Please contact genome@soe.ucsc.edu to ask that your site " "be reenabled. Also, please consider downloading sequence and/or " "annotations in bulk -- see http://genome.ucsc.edu/downloads.html.", hogHost); hPrintf("

    \n"); exit(0); } static void hogExit() /* bottleneck server requests exit */ { char *hogHost = getenv("REMOTE_ADDR"); char *pathInfo = getenv("PATH_INFO"); /* nothing on incoming path, then display the WEB page instead */ if (sameOk("/",pathInfo)) pathInfo = NULL; if (isNotEmpty(pathInfo)) { - puts("Content-Type:application/json"); - puts("Status: 459 Too Many Requests"); - /* maybe a Retry-After: 3600 statement here ? */ - puts("\n"); sendJsonHogMessage(hogHost); } else { - puts("Content-Type:text/html"); - puts("Status: 459 Too Many Requests"); - /* maybe a Retry-After: 3600 statement here ? */ - puts("\n"); sendHogMessage(hogHost); } +} /* static void hogExit() */ + +/* name of button group */ +#define RADIO_GROUP "selectRadio" +/* button functions */ +#define RADIO_PUBHUB "pubHub" +#define RADIO_OTHERHUB "otherHub" +#define RADIO_UCSCDB "ucscDb" + +static void selectionForm() +/* setup the selection pull-downs for source */ +{ +char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub); +char *urlDropDown = urlFromShortLabel(hubDropDown); +char *otherHubUrl = cartUsualString(cart, "urlHub", ""); +char *ucscDb = cartUsualString(cart, "ucscGenome", defaultDb); + +if (isEmpty(otherHubUrl)) + otherHubUrl = urlDropDown; + +char *radioOn = cartUsualString(cart, RADIO_GROUP, RADIO_PUBHUB); + +/* create border around table, but not inside the table with the data */ +hPrintf("\n"); +hPrintf("
    \n"); + +int maxDbNameWidth = 0; +struct dbDb *dbList = ucscDbDb(); +char **ucscDbList = NULL; +int listSize = slCount(dbList); +AllocArray(ucscDbList, listSize); +struct dbDb *el = dbList; +int ucscDataBaseCount = 0; +for ( ; el != NULL; el = el->next ) + { + ucscDbList[ucscDataBaseCount++] = el->name; + if (strlen(el->name) > maxDbNameWidth) + maxDbNameWidth = strlen(el->name); + } +maxDbNameWidth += 1; + +hPrintf("\n\n", urlPrefix); + +hWrites("\n"); + +hWrites("\n"); + +hWrites("\n"); + +allTrackSettings = cartUsualBoolean(cart, "allTrackSettings", FALSE); +hWrites("\n"); + + +trackLeavesOnly = cartUsualBoolean(cart, "trackLeavesOnly", trackLeavesOnly); +hWrites("\n"); + +/* go button at the bottom of the table */ +hWrites("\n"); + +hPrintf("\n"); +hPrintf("
    "); +jsMakeTrackingRadioButton(RADIO_GROUP, "typeOneJs", RADIO_PUBHUB, radioOn); +hWrites(""); +hWrites("Select public hub:"); +hWrites(""); + +#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)); + +cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs", + shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events); + +jsOnEventById("change", "publicHubs", "document.getElementById('"RADIO_GROUP"_"RADIO_PUBHUB"').checked=true;"); +hWrites("
    "); +jsMakeTrackingRadioButton(RADIO_GROUP, "typeOneJs", RADIO_OTHERHUB, radioOn); +hWrites(""); +hWrites("enter a hub URL:"); +hWrites(""); +hPrintf("\n", otherHubUrl); +jsOnEventById("change", "urlHub", "document.getElementById('"RADIO_GROUP"_"RADIO_OTHERHUB"').checked=true;"); +hWrites("
    "); +jsMakeTrackingRadioButton(RADIO_GROUP, "typeOneJs", RADIO_UCSCDB, radioOn); +hWrites(""); +hWrites("select a UCSC database name:"); +hWrites(""); +maxDbNameWidth *= 9; // 9 should be font width here +char widthPx[SMALLBUF]; +safef(widthPx, sizeof(widthPx), "width: %dpx", maxDbNameWidth); +cgiMakeDropListClassWithIdStyleAndJavascript("ucscGenome", "ucscGenome", + ucscDbList, ucscDataBaseCount, ucscDb, NULL, widthPx, events); +jsOnEventById("change", "ucscGenome", "document.getElementById('"RADIO_GROUP"_"RADIO_UCSCDB"').checked=true;"); +hWrites("
     display control:"); +hCheckBox("allTrackSettings", allTrackSettings); +hWrites(" display all track settings for each track"); +hWrites("
     JSON list output:"); +hCheckBox("trackLeavesOnly", trackLeavesOnly); +hWrites(" show only data tracks, do not show composite container information"); +hWrites("
     "); +hButton("sourceSelected", "go"); +hWrites("press 'go' after selections made
    \n"); +hPrintf("
    \n"); + +/* how does debug carry forward ? */ +// if (debug) +// cgiMakeHiddenVar("debug", "1"); } static void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { cart = theCart; measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming")); measureTiming = TRUE; char *database = NULL; char *genome = NULL; cgiVarSet("ignoreCookie", "1"); getDbAndGenome(cart, &database, &genome, oldVars); initGenbankTableNames(database); initSupportedTypes(); initUrlPrefix(); trackLeavesOnly = cartUsualBoolean(cart, "trackLeavesOnly", trackLeavesOnly); /* global variable for all workers to honor this limit */ maxItemsOutput = cartUsualInt(cart, "maxItemsOutput", maxItemsOutput); if (maxItemsOutput < 0) /* can use -1 to indicate as much as allowed */ maxItemsOutput = maxItemLimit; /* maxItemsOutput of 0 might be useful, to be seen, let it go through */ // if (maxItemsOutput < 1) /* safety check */ // maxItemsOutput = 1; if (maxItemsOutput > maxItemLimit) /* safety check */ maxItemsOutput = maxItemLimit; debug = cartUsualBoolean(cart, "debug", debug); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); char *pathInfo = getenv("PATH_INFO"); /* nothing on incoming path, then display the WEB page instead */ if (sameOk("/",pathInfo)) pathInfo = NULL; boolean commandError = FALSE; /*expect no more than MAX_PATH_INFO number of words*/ char *words[MAX_PATH_INFO]; if (isNotEmpty(pathInfo)) { setupFunctionHash(); struct hashEl *hel = parsePathInfo(pathInfo, words); /* verify valid API command */ if (hel) /* have valid command */ { hPrintDisable(); - /* could check botDelay here to see if 459 status is advised */ - puts("Content-Type:application/json"); - puts("\n"); void (*apiFunction)(char **) = hel->val; (*apiFunction)(words); return; } else commandError = TRUE; } -/* could check botDelay here to see if 459 status is advised */ -// puts("Content-Type:text/html"); -// puts("\n"); - (void) hubPublicDbLoadAll(); -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; - webStartJWest(cart, database, "UCSC JSON API interface"); // webStartGbNoBanner(cart, database, "UCSC JSON API interface"); // webStartGbOptionalBanner(cart, database, "UCSC JSON API interface", TRUE, FALSE); hPrintf("
    \n"); if (debug) { hPrintf("\n"); } -char *goOtherHub = cartUsualString(cart, "goOtherHub", ""); -char *goUcscDb = cartUsualString(cart, "goUcscDb", ""); char *otherHubUrl = cartUsualString(cart, "urlHub", ""); -char *goPublicHub = cartUsualString(cart, "goPublicHub", ""); char *hubDropDown = cartUsualString(cart, "publicHubs", defaultHub); char *urlDropDown = urlFromShortLabel(hubDropDown); char *ucscDb = cartUsualString(cart, "ucscGenome", defaultDb); +char *selectRadio = cartUsualString(cart, RADIO_GROUP, RADIO_PUBHUB); char *urlInput = urlDropDown; /* assume public hub */ if (debug) { hPrintf("\n"); } -if (sameWord("go", goOtherHub)) /* requested other hub URL */ - urlInput = otherHubUrl; -else if (isEmpty(otherHubUrl)) +if (isEmpty(otherHubUrl)) otherHubUrl = urlInput; +if (sameWord(RADIO_OTHERHUB, selectRadio)) /* requested other hub URL */ + urlInput = otherHubUrl; + if (commandError) { hPrintf("

    ERROR: no such command: '%s/%s' for endpoint '%s'

    ", words[0], words[1], pathInfo); } long lastTime = clock1000(); struct trackHub *hub = errCatchTrackHubOpen(urlInput); if (measureTiming || debug) { long thisTime = clock1000(); if (debug) hPrintf("hub open time: %ld millis
    \n", thisTime - lastTime); } hPrintf("

    Please refer to API help documentation for more information about the JSON data API operation.

    \n"); hPrintf("

    See also: Track definition document for definitions of track settings.

    \n"); if (debug) showCartDump(); hPrintf("

    Explore hub or database assemblies and tracks

    \n"); +hPrintf("

    Select one of these three sources, and display options:

    \n"); -hPrintf("
    \n\n", urlPrefix); - -hPrintf("Select public hub: "); -#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)); - -cgiMakeDropListClassWithIdStyleAndJavascript("publicHubs", "publicHubs", - shortLabels, publicHubCount, hubDropDown, NULL, "width: 400px", events); - -hWrites(" "); -hButton("goPublicHub", "go"); - -hPrintf("
    Or, enter a hub URL: "); -hPrintf("\n", otherHubUrl); -hWrites(" "); -hButton("goOtherHub", "go"); - -hPrintf("
    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("ucscGenome", "ucscGenome", - ucscDbList, ucscDataBaseCount, ucscDb, NULL, widthPx, events); -hWrites(" "); -hButton("goUcscDb", "go"); - -// boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); -// hPrintf("
    \n  "); -// hCheckBox("depthSearch", cartUsualBoolean(cart, "depthSearch", FALSE)); -// hPrintf(" perform full bbi file measurement : %s (will time out if taking longer than %ld seconds)
    \n", depthSearch ? "TRUE" : "FALSE", timeOutSeconds); - -hPrintf("
    \n  "); - -allTrackSettings = cartUsualBoolean(cart, "allTrackSettings", FALSE); -hCheckBox("allTrackSettings", allTrackSettings); -hPrintf(" display all track settings for each track
    \n"); - -hPrintf("
    \n"); -// if (debug) -// cgiMakeHiddenVar("debug", "1"); -hPrintf("
    \n"); +selectionForm(); hPrintf("

    \n"); -if (sameWord("go", goUcscDb)) /* requested UCSC db track list */ +if (sameWord(RADIO_UCSCDB, selectRadio)) /* requested UCSC db track list */ { tracksForUcscDb(ucscDb); } else { - hPrintf("

    %s url: %s

    \n", sameWord("go",goPublicHub) ? "Public hub" : "Other hub", urlInput); + hPrintf("

    %s url: %s

    \n", sameWord(RADIO_PUBHUB,selectRadio) ? "Public hub" : "Other hub", urlInput); hPrintf("\n"); genomeList(hub); } if (timedOut) hPrintf("

    Reached time out %ld seconds

    ", timeOutSeconds); if (measureTiming || debug) hPrintf("Overall total time: %ld millis
    \n", clock1000() - enteredMainTime); hPrintf("

    \n"); hPrintf("
    \n"); webIncludeFile("inc/jWestFooter.html"); webEndJWest(); // cartWebEnd(); } /* void doMiddle(struct cart *theCart) */ /* Null terminated list of CGI Variables we don't want to save * permanently. */ -static char *excludeVars[] = {"Submit", "submit", "goOtherHub", "goPublicHub", "goUcscDb", "ucscGenome", "publicHubs", "clade", NULL,}; +static char *excludeVars[] = {"Submit", "submit", "sourceSelected", "selectRadio", "ucscGenome", "publicHubs", "clade", NULL,}; int main(int argc, char *argv[]) /* Process command line. */ { enteredMainTime = clock1000(); cgiSpoof(&argc, argv); measureTiming = TRUE; verboseTimeInit(); /* similar delay system as in DAS server */ botDelay = hgBotDelayTimeFrac(delayFraction); if (botDelay > 0) { if (botDelay > 2000) { hogExit(); return 0; } sleep1000(botDelay); } trackCounter = hashNew(0); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }