5194786c88bd4ab5e802eec79089897461389fe9 hiram Fri Mar 22 14:52:22 2019 -0700 getting a little bit better refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 410a905..76c7c93 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -1,1236 +1,1302 @@ /* hubApi - access mechanism to hub data resources. */ #include "dataApi.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 */ /* Global only to this one source file */ -static boolean debug = FALSE; /* can be set in URL debug=1 */ +static boolean debug = TRUE; /* can be set in URL debug=1 */ 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 char *urlPrefix = ""; /* initalized to support self references */ 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("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; } #ifdef NOT static void showCounts(struct hash *countTracks) { if (countTracks->elCount) { hPrintf("
    • \n"); } } #endif 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); // char *compositeTrack = trackDbLocalSetting(tdb, "compositeTrack"); boolean compositeContainer = tdbIsComposite(tdb); boolean compositeView = tdbIsCompositeView(tdb); // char *superTrack = trackDbLocalSetting(tdb, "superTrack"); 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); // showCounts(countTracks); } -static void sampleUrl(struct trackHub *hub, char *db, struct trackDb *tdb, char *chrom, long long chromSize, char *errorString) +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); } 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) { if (tdb->parent) hPrintf("
  • %s : %s subtrack of parent: %s (sample getData)%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint); else hPrintf("
  • %s : %s (sample getData)%s
    • \n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint); } else { if (tdb->parent) hPrintf("
  • %s : %s subtrack of parent: %s (sample getData)%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, db, chrom, tdb->track, start, end, errorPrint); else hPrintf("
  • %s : %s (sample getData)%s
    • \n", tdb->track, tdb->type, urlPrefix, db, chrom, tdb->track, start, end, errorPrint); } } else if (hub) { if (tdb->parent) hPrintf("
  • %s : %s subtrack of parent: %s (sample getData)%s
    • \n", tdb->track, tdb->type, tdb->parent->track, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint); else hPrintf("
  • %s : %s (sample getData)%s
    • \n", tdb->track, tdb->type, urlPrefix, hub->url, genome, chrom, tdb->track, start, end, errorPrint); } else hPrintf("
  • %s : %s not db hub track ?
    • \n", tdb->track, tdb->type); } -static void showSubTracks(struct trackHub *hub, char *db, struct trackDb *tdb, struct hash *countTracks, - char *chromName, long long chromSize, char *errorString) -/* tdb has subtracks, show only subTracks, no details */ -{ -hPrintf("
    • \n"); + safef(countsMessage, sizeof(countsMessage), " : %ld chroms : %ld count ", chromCount, itemCount); } -static void trackSettings(struct trackDb *tdb, struct hash *countTracks) -/* process the settingsHash for a trackDb, recursive when subtracks */ -{ -hPrintf("
    • \n"); + if (startsWithWord("bigBed", 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 bbiBiggestChrom(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); bbiBiggestChrom(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; bbiBiggestChrom(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 hubSampleUrl(struct trackHub *hub, struct trackDb *tdb, - long chromCount, long itemCount, char *chromName, unsigned chromSize, - char *genome, char *errorString) +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 */ { -unsigned start = chromSize / 4; -unsigned end = start + 10000; -if (end > chromSize) - end = chromSize; - -char errorPrint[2048]; -errorPrint[0] = 0; - -if (isNotEmpty(errorString)) +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 hubSampleUrl(struct trackHub *hub, struct trackDb *tdb, - * long chromCount, long itemCount, char *chromName, unsigned chromSize, - * char *genome) - */ 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); -char *longName = NULL; -unsigned longSize = 0; 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)) - { - if (chromSize > 0) hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); - else - hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, 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) hPrintf("
  • %s : %s : superTrack child of parent: %s (sample getData)
    • \n", tdb->track, tdb->type, tdb->parent->track); else if (! depthSearch && bigDataUrl) { if (isSupportedType(tdb->type)) { - if (chromSize > 0) hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); - else - hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string); } - // hPrintf("
  • %s : %s : %s (maybe sample ?)
    • \n", tdb->track, tdb->type, bigDataUrl); } else { if (isSupportedType(tdb->type)) { - if (chromSize > 0) hubSampleUrl(hub, tdb, chromCount, itemCount, chromName, chromSize, genome, errors->string); - else - hubSampleUrl(hub, tdb, chromCount, itemCount, longName, longSize, genome, errors->string); } else hPrintf("
  • %s : %s (what is this)
    • \n", tdb->track, tdb->type); } } if (allTrackSettings) { hPrintf("
    • \n"); } else if (tdb->subtracks) { - showSubTracks(hub, db, tdb, countTracks, chromName, chromSize, errors->string); + 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, long long chromSize) + * 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"); // 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); 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) 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) /* 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); 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 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; } 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; unsigned chromSize = largestChrom(db, &chromName); hPrintf("

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

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

    \n"); } // static void tracksForUcscDb(char * db) static void introductionText() /* output explanation text */ { char *scriptUri = getenv("SCRIPT_URI"); hPrintf("

    JSON data API interface to U.C. Santa Cruz genome browser data

    \n"); hPrintf("

    Data access URL: %s

    \n", scriptUri); hPrintf("

    Endpoint functions:

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

    Parameters to endpoint functions:

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

    Supported track types, at this time, for getData functions:

    \n"); hPrintf("\n"); } 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 showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb) { hPrintf("

    Example URLs to return json data structures:

    \n"); hPrintf("

    listing functions

    \n"); hPrintf("
      \n"); hPrintf("
    1. list public hubs %s/list/publicHubs
      2. \n", urlPrefix, urlPrefix); hPrintf("
    2. list database genomes %s/list/ucscGenomes
      3. \n", urlPrefix, urlPrefix); hPrintf("
    3. list genomes from specified hub %s/list/hubGenomes?hubUrl=%s
      4. \n", urlPrefix, url, urlPrefix, url); hPrintf("
    4. list tracks from specified hub and genome %s/list/tracks?hubUrl=%s&genome=%s
      5. \n", urlPrefix, url, hubGenome->name, urlPrefix, url, hubGenome->name); hPrintf("
    5. list tracks from specified UCSC database %s/list/tracks?db=%s
      6. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    6. list chromosomes from specified UCSC database %s/list/chromosomes?db=%s
      7. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    7. list chromosomes from specified track from UCSC databaset %s/list/chromosomes?db=%s&track=gold
      8. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    \n"); hPrintf("

    getData functions

    \n"); hPrintf("
      \n"); hPrintf("
    1. get sequence from specified database and chromosome %s/getData/sequence?db=%s&chrom=chrM
      2. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    2. get sequence from specified database, chromosome with start,end coordinates %s/getData/sequence?db=%s&chrom=chrM&start=0&end=128
      3. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    3. get entire track data from specified database and track name (gold == Assembly) %s/getData/track?db=%s&track=gold
      4. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    4. get track data from specified database, chromosome and track name (gold == Assembly) %s/getData/track?db=%s&chrom=chrM&track=gold
      5. \n", urlPrefix, ucscDb, urlPrefix, ucscDb); hPrintf("
    5. get track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148
      6. \n", urlPrefix, defaultDb, urlPrefix, defaultDb); hPrintf("
    6. get entire track data from specified hub and track name %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved
      7. \n", urlPrefix, urlPrefix); hPrintf("
    7. get track data from specified hub, chromosome and track name (full chromosome) %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_
      8. \n", urlPrefix, urlPrefix); hPrintf("
    8. get track data from specified hub, chromosome, track name, start and end coordinates %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681
      9. \n", urlPrefix, urlPrefix); hPrintf("
    9. get all track data from specified hub and track name %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base
      10. \n", urlPrefix, urlPrefix); hPrintf("
    10. get track data from specified hub, chromosome, track name, start and end coordinates %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base&start=143600&end=143685
      11. \n", urlPrefix, urlPrefix); hPrintf("
    11. get bigWig track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148
      12. \n", urlPrefix, defaultDb, urlPrefix, defaultDb); hPrintf("
    12. get bigBed track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chrII&track=ncbiRefSeqOther&start=14334626&end=14979625
      13. \n", urlPrefix, defaultDb, urlPrefix, defaultDb); hPrintf("
    13. get narrowPeak track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chr1&track=wgEncodeAwgDnaseDuke8988tUniPk&start=14334626&end=14979625
      14. \n", urlPrefix, "hg19", urlPrefix, "hg19"); hPrintf("
    14. get broadPeak track data from specified database, chromosome, track name, start and end coordinates %s/getData/track?db=%s&chrom=chr1&track=wgEncodeBroadHistoneOsteoP300kat3bPk&start=14334626&end=14979625
      15. \n", urlPrefix, "hg19", urlPrefix, "hg19"); hPrintf("
    \n"); hPrintf("

    Example URLs to generate errors:

    \n"); hPrintf("
      \n"); hPrintf("
    1. get track data from specified hub, chromosome, track name, start and end coordinates %s/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681
      2. \n", urlPrefix, urlPrefix); hPrintf("
    \n"); } /* static void showExamples() */ static void showCartDump() /* for information purposes only during development, will become obsolete */ { hPrintf("

    cart dump

    "); hPrintf("
    \n");
 cartDump(cart);
 hPrintf("
    \n"); } 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(); /* global variable for all workers to honor this limit */ maxItemsOutput = cartUsualInt(cart, "maxItemsOutput", maxItemsOutput); +if (maxItemsOutput > maxItemLimit) /* safety check */ + maxItemsOutput = maxItemLimit; +if (maxItemsOutput < 1) /* safety check */ + maxItemsOutput = 1; 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(); puts("Content-Type:application/json"); puts("\n"); void (*apiFunction)(char **) = hel->val; (*apiFunction)(words); return; } else commandError = TRUE; } 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; cartWebStart(cart, database, "UCSC JSON API interface"); if (debug) { hPrintf("\n"); } 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; else if (isEmpty(otherHubUrl)) otherHubUrl = urlInput; 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) +if (measureTiming || debug) { long thisTime = clock1000(); if (debug) hPrintf("hub open time: %ld millis
    \n", thisTime - lastTime); } // hPrintf("

    ucscDb: '%s'

    \n", ucscDb); struct trackHubGenome *hubGenome = hub->genomeList; introductionText(); showExamples(urlInput, hubGenome, ucscDb); if (debug) showCartDump(); hPrintf("

    Explore hub or database assemblies and tracks

    \n"); // hPrintf("
    \n\n", "../cgi-bin/hubApi"); hPrintf("\n\n", urlPrefix); #ifdef NOT if (isEmpty(urlPrefix)) { char *scriptUri = getenv("SCRIPT_URI"); hPrintf("\n\n", scriptUri); } else hPrintf("\n\n", urlPrefix); #endif 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("ucscGenomes", "ucscGenomes", 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 : %s
    \n", allTrackSettings ? "TRUE" : "FALSE"); hPrintf("
    \n
    \n"); hPrintf("

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

    Examine %s at: %s

    \n", sameWord("go",goPublicHub) ? "public hub" : "other hub", urlInput); hPrintf("\n"); genomeList(hub); } if (timedOut) hPrintf("

    Reached time out %ld seconds

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

    \n"); 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", "ucscGenomes", "publicHubs", NULL,}; int main(int argc, char *argv[]) /* Process command line. */ { enteredMainTime = clock1000(); cgiSpoof(&argc, argv); measureTiming = TRUE; verboseTimeInit(); trackCounter = hashNew(0); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }