a623f8b7d5f5d7ad88a33e7a0cba4a91f76800ac hiram Tue Feb 26 17:53:14 2019 -0800 catch up list functions to recent revisions to getting trackDb refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 45a44b1..77d64ed 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -1,789 +1,792 @@ /* 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 */ 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 int publicHubCmpCase(const void *va, const void *vb) /* Compare two slNames, 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); } static struct hubPublic *hubPublicLoad(char **row) /* Load a hubPublic from row fetched with select * from hubPublic * from database. Dispose of this with hubPublicFree(). */ { struct hubPublic *ret; AllocVar(ret); 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]); ret->descriptionUrl = cloneString(row[6]); return ret; } struct hubPublic *hubPublicLoadAll() /* 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(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(countTracks); while ((hel = hashNext(&hc)) != NULL) hPrintf(" <li>%d - %s</li>\n", ptToInt(hel->val), hel->name); hPrintf(" </ul>\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 trackSettings(struct trackDb *tdb, struct hash *countTracks) /* process the settingsHash for a trackDb, recursive when subtracks */ { hPrintf(" <ul>\n"); // if (tdb->children) haven't yet seen a track with children ? // hPrintf(" <li>%s: has children</li>\n", tdb->track); // else // hPrintf(" <li>%s: NO children</li>\n", tdb->track); 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)) hPrintf(" <li>%s : <empty></li>\n", hel->name); else hPrintf(" <li>%s : '%s'</li>\n", hel->name, (char *)hel->val); } if (tdb->subtracks) { struct trackDb *tdbEl = tdb->subtracks; hPrintf(" <li>has %d subtrack(s)</li>\n", slCount(tdb->subtracks)); for (tdbEl = tdb->subtracks; tdbEl; tdbEl = tdbEl->next) { hPrintf("<li>subtrack: %s of parent: %s : type: '%s'</li>\n", tdbEl->track, tdbEl->parent->track, tdbEl->type); hashCountTrack(tdbEl, countTracks); trackSettings(tdbEl, countTracks); } } hPrintf(" </ul>\n"); } static int bbiBriefMeasure(char *type, char *bigDataUrl, char *bigDataIndex, long *chromCount, long *itemCount, struct dyString *errors) /* check a bigDataUrl to find chrom count and item count */ { 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); 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; 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 countOneTdb(struct trackDb *tdb, char *bigDataIndex, struct hash *countTracks) { 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 (depthSearch && bigDataUrl) { long chromCount = 0; long itemCount = 0; struct dyString *errors = newDyString(1024); int retVal = bbiBriefMeasure(tdb->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors); if (retVal) { hPrintf(" <li>%s : %s : <font color='red'>ERROR: %s</font></li>\n", tdb->track, tdb->type, errors->string); } else { if (startsWithWord("bigBed", tdb->type)) hPrintf(" <li>%s : %s : %ld chroms : %ld item count</li>\n", tdb->track, tdb->type, chromCount, itemCount); else if (startsWithWord("bigWig", tdb->type)) hPrintf(" <li>%s : %s : %ld chroms : %ld bases covered</li>\n", tdb->track, tdb->type, chromCount, itemCount); else hPrintf(" <li>%s : %s : %ld chroms : %ld count</li>\n", tdb->track, tdb->type, chromCount, itemCount); } } else { if (compositeContainer) hPrintf(" <li>%s : %s : composite track container</li>\n", tdb->track, tdb->type); else if (compositeView) - hPrintf(" <li>%s : %s : composite view</li>\n", tdb->track, tdb->type); + hPrintf(" <li>%s : %s : composite view of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track); else if (superChild) - hPrintf(" <li>%s : %s : superTrack child</li>\n", tdb->track, tdb->type); + hPrintf(" <li>%s : %s : superTrack child of parent: %s</li>\n", tdb->track, tdb->type, tdb->parent->track); else if (! depthSearch) hPrintf(" <li>%s : %s : %s</li>\n", tdb->track, tdb->type, bigDataUrl); else hPrintf(" <li>%s : %s</li>\n", tdb->track, tdb->type); } if (allTrackSettings) { hPrintf(" <ul>\n"); trackSettings(tdb, countTracks); /* show all settings */ hPrintf(" </ul>\n"); } return; } /* static void countOneTdb(struct trackDb *tdb, * char *bigDataIndex, struct hash *countTracks) */ static void hubTrackList(struct trackDb *topTrackDb, struct trackHubGenome *genome) /* process the track list in a hub to show all tracks */ { if (topTrackDb) { struct hash *countTracks = hashNew(0); hPrintf(" <ul>\n"); struct trackDb *tdb = NULL; for ( tdb = topTrackDb; tdb; tdb = tdb->next ) { char *bigDataIndex = NULL; char *relIdxUrl = trackDbSetting(topTrackDb, "bigDataIndex"); if (relIdxUrl != NULL) bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl); countOneTdb(tdb, bigDataIndex, countTracks); if (timeOutReached()) break; } /* for ( tdb = topTrackDb; tdb; tdb = tdb->next ) */ hPrintf(" <li>%d different track types</li>\n", countTracks->elCount); /* add this single genome count to the overall multi-genome counts */ if (countTracks->elCount) { hPrintf(" <ol>\n"); struct hashEl *hel, *helList = hashElListHash(countTracks); slSort(&helList, hashElCmpIntValDesc); for (hel = helList; hel; hel = hel->next) { int prevCount = ptToInt(hashFindVal(trackCounter, hel->name)); if (differentStringNullOk("track count", hel->name)) totalTracks += ptToInt(hel->val); hashReplace(trackCounter, hel->name, intToPt(prevCount + ptToInt(hel->val))); hPrintf(" <li>%d - %s</li>\n", ptToInt(hel->val), hel->name); } hPrintf(" </ol>\n"); } hPrintf(" </ul>\n"); } else hPrintf(" <li>no trackTopDb</li>\n"); } /* static struct trackDb *hubTrackList() */ -static void assemblySettings(struct trackHubGenome *genome) +static struct trackDb *assemblySettings(struct trackHubGenome *genome) /* display all the assembly 'settingsHash' */ { struct trackDb *tdb = trackHubTracksForGenome(genome->trackHub, genome); tdb = trackDbLinkUpGenerations(tdb); hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(genome->settingsHash); while ((hel = hashNext(&hc)) != NULL) { hPrintf(" <li>%s : %s</li>\n", hel->name, (char *)hel->val); if (sameWord("trackDb", hel->name)) /* examine the trackDb structure */ { hubTrackList(tdb, genome); } if (timeOutReached()) break; } hPrintf(" </ul>\n"); +return tdb; } struct slName *genomeList(struct trackHub *hubTop, struct trackDb **dbTrackList, char *selectGenome) /* follow the pointers from the trackHub to trackHubGenome and around * in a circle from one to the other to find all hub resources * return slName list of the genomes in this track hub * optionally, return the trackList from this hub for the specified genome */ { struct slName *retList = NULL; long totalAssemblyCount = 0; struct trackHubGenome *genome = hubTop->genomeList; hPrintf("<h4>genome sequences (and tracks) present in this track hub</h4>\n"); hPrintf("<ul>\n"); long lastTime = clock1000(); for ( ; genome; genome = genome->next ) { if (selectGenome) /* is only one genome requested ? */ { if ( differentStringNullOk(selectGenome, genome->name) ) continue; } ++totalAssemblyCount; struct slName *el = slNameNew(genome->name); slAddHead(&retList, el); if (genome->organism) { hPrintf("<li>%s - %s - %s</li>\n", genome->organism, genome->name, genome->description); } else { /* can there be a description when organism is empty ? */ hPrintf("<li>%s</li>\n", genome->name); } - assemblySettings(genome); + struct trackDb *tdb = assemblySettings(genome); + if (dbTrackList) + *dbTrackList = tdb; if (measureTiming) { long thisTime = clock1000(); hPrintf("<em>processing time %s: %ld millis</em><br>\n", genome->name, thisTime - lastTime); } if (timeOutReached()) break; } if (trackCounter->elCount) { hPrintf(" <li>total genome assembly count: %ld</li>\n", totalAssemblyCount); hPrintf(" <li>%ld total tracks counted, %d different track types:</li>\n", totalTracks, trackCounter->elCount); hPrintf(" <ol>\n"); struct hashEl *hel, *helList = hashElListHash(trackCounter); slSort(&helList, hashElCmpIntValDesc); for (hel = helList; hel; hel = hel->next) { hPrintf(" <li>%d - %s - total</li>\n", ptToInt(hel->val), hel->name); } hPrintf(" </ol>\n"); } hPrintf("</ul>\n"); return retList; } /* static struct slName *genomeList () */ 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 void apiFunctionSwitch(char *pathInfo) /* given a pathInfo string: /command/subCommand/etc... * parse that and decide on which function to acll */ { 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) apiErrAbort("unknown endpoint command: '/%s'", pathInfo); struct hashEl *hel = hashLookup(apiFunctionHash, words[0]); if (hel == NULL) apiErrAbort("no such command: '%s' for endpoint '/%s'", words[0], pathInfo); void (*apiFunction)(char **) = hel->val; // void (*apiFunction)(char **) = hashMustFindVal(apiFunctionHash, words[0]); (*apiFunction)(words); } /* static void apiFunctionSwitch(char *pathInfo) */ static void tracksForUcscDb(char *db) /* scan the specified database for all tracks */ { struct hash *countTracks = hashNew(0); hPrintf("<p>Tracks in UCSC genome: '%s'<br>\n", db); struct trackDb *tdbList = hTrackDb(db); struct trackDb *tdb; hPrintf("<ul>\n"); for (tdb = tdbList; tdb != NULL; tdb = tdb->next ) { countOneTdb(tdb, NULL, countTracks); if (timeOutReached()) break; } int trackCount = ptToInt(hashFindVal(countTracks, "track count")); hPrintf(" <li>%d total tracks counted, %d different track types</li>\n", trackCount, countTracks->elCount); if (countTracks->elCount) { hPrintf(" <ol>\n"); struct hashEl *hel, *helList = hashElListHash(countTracks); slSort(&helList, hashElCmpIntValDesc); for (hel = helList; hel; hel = hel->next) { hPrintf(" <li>%d - %s</li>\n", ptToInt(hel->val), hel->name); } hPrintf(" </ol>\n"); } hPrintf("</ul>\n"); hPrintf("</p>\n"); } // static void tracksForUcscDb(char * db) static void showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb) { hPrintf("<h2>Example URLs to return json data structures:</h2>\n"); hPrintf("<ol>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/publicHubs' target=_blank>list public hubs</a> <em>/cgi-bin/hubApi/list/publicHubs</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/ucscGenomes' target=_blank>list database genomes</a> <em>/cgi-bin/hubApi/list/ucscGenomes</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/list/hubGenomes?hubUrl=%s' target=_blank>list genomes from specified hub</a> <em>/cgi-bin/hubApi/list/hubGenomes?hubUrl=%s</em></li>\n", url, url); hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?hubUrl=%s&hubUrl=%s&genome=%s' target=_blank>list tracks from specified hub and genome</a> <em>/cgi-bin/hubApi/list/tracks?hubUrl=%s&genome=%s</em></li>\n", url, url, hubGenome->name, url, hubGenome->name); hPrintf("<li><a href='/cgi-bin/hubApi/list/tracks?db=%s' target=_blank>list tracks from specified UCSC database</a> <em>/cgi-bin/hubApi/list/tracks?db=%s</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/list/chromosomes?db=%s' target=_blank>list chromosomes from specified UCSC database</a> <em>/cgi-bin/hubApi/list/chromosomes?db=%s</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/list/chromosomes?db=%s&track=gap' target=_blank>list chromosomes from specified track from UCSC databaset</a> <em>/cgi-bin/hubApi/list/chromosomes?db=%s&track=gap</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM' target=_blank>get sequence from specified database and chromosome</a> <em>/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128' target=_blank>get sequence from specified database, chromosome with start,end coordinates</a> <em>/cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&track=gold' target=_blank>get entire track data from specified database and track name (gold == Assembly)</a> <em>/cgi-bin/hubApi/getData/track?db=%s&track=gold</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold' target=_blank>get track data from specified database, chromosome and track name (gold == Assembly)</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148' target=_blank>get track data from specified database, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?db=%s&chrom=chr1&track=gold&start=107680&end=186148</em></li>\n", ucscDb, ucscDb); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved' target=_blank>get entire track data from specified hub and track name</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_' target=_blank>get track data from specified hub, chromosome and track name (full chromosome)</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base_' target=_blank>get all track data from specified hub and track name</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base</em></li>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base_&start=143600&end=143685' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base&start=143600&end=143685</em></li>\n"); hPrintf("</ol>\n"); hPrintf("<h2>Example URLs to generate errors:</h2>\n"); hPrintf("<li><a href='/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681' target=_blank>get track data from specified hub, chromosome, track name, start and end coordinates</a> <em>/cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681</em></li>\n"); hPrintf("<ol>\n"); hPrintf("</ol>\n"); } /* static void showExamples() */ static void showCartDump() /* for information purposes only during development, will become obsolete */ { hPrintf("<h4>cart dump</h4>"); hPrintf("<pre>\n"); cartDump(cart); hPrintf("</pre>\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); char *docRoot = cfgOptionDefault("browser.documentRoot", DOCUMENT_ROOT); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); char *pathInfo = getenv("PATH_INFO"); if (isNotEmpty(pathInfo)) { puts("Content-Type:application/json"); puts("\n"); /* skip the first leading slash to simplify chopByChar parsing */ pathInfo += 1; setupFunctionHash(); apiFunctionSwitch(pathInfo); return; } puts("Content-Type:text/html"); puts("\n"); (void) hubPublicLoadAll(); 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 = errCatchTrackHubOpen(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; showExamples(urlInput, hubGenome, ucscDb); showCartDump(); 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)); 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. */ static char *excludeVars[] = {"Submit", "submit", 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; }