8719bd3fc718d52ab67ce568131b5a97638c2fb7 hiram Wed Feb 13 11:03:32 2019 -0800 minor formatting clean up before restructure refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 5c6c963..96ba815 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -1,1177 +1,1174 @@ /* hubApi - access mechanism to hub data resources. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "htmshell.h" #include "web.h" #include "cheapcgi.h" #include "cart.h" #include "hui.h" #include "udc.h" #include "knetUdc.h" #include "genbank.h" #include "trackHub.h" #include "hgConfig.h" #include "hCommon.h" #include "hPrint.h" #include "bigWig.h" #include "hubConnect.h" #include "obscure.h" #include "errCatch.h" #include "vcf.h" #include "bedTabix.h" #include "bamFile.h" #include "jsonParse.h" #include "jsonWrite.h" #include "chromInfo.h" #ifdef USE_HAL #include "halBlockViz.h" #endif /* +------------------+------------------+------+-----+---------+-------+ | 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 | | +------------------+------------------+------+-----+---------+-------+ */ struct hubPublic /* Table of public track data hub connections. */ { struct hubPublic *next; /* Next in singly linked list. */ char *hubUrl; /* URL to hub.ra file */ char *shortLabel; /* Hub short label. */ char *longLabel; /* Hub long label. */ char *registrationTime; /* Time first registered */ unsigned dbCount; /* Number of databases hub has data for. */ char *dbList; /* Comma separated list of databases. */ char *descriptionUrl; /* URL to description HTML */ }; /* Global Variables */ static struct cart *cart; /* CGI and other variables */ static struct hash *oldVars = NULL; static struct hash *trackCounter = NULL; static long totalTracks = 0; static boolean measureTiming = FALSE; /* set by CGI parameters */ static boolean allTrackSettings = FALSE; /* checkbox setting */ static char **shortLabels = NULL; /* public hub short labels in array */ // struct hubPublic *publicHubList = NULL; static int publicHubCount = 0; static 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 struct jsonWrite *jsonStartOutput() /* begin json output with standard header information for all requests */ { time_t timeNow = time(NULL); // struct tm tm; // gmtime_r(&timeNow, &tm); struct jsonWrite *jw = jsonWriteNew(); jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "apiVersion", "0.1"); jsonWriteString(jw, "source", "UCSantaCruz"); jsonWriteDateFromUnix(jw, "downloadTime", (long long) timeNow); jsonWriteNumber(jw, "downloadTimeStamp", (long long) timeNow); return jw; } static void jsonErrAbort(char *format, ...) /* Issue an error message in json format, and exit(0) */ { char errMsg[2048]; va_list args; va_start(args, format); vsnprintf(errMsg, sizeof(errMsg), format, args); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "error", errMsg); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); exit(0); } static void hubPublicJsonData(struct jsonWrite *jw, struct hubPublic *el) /* Print array data for one row from hubPublic table, order here * must be same as was stated in the columnName header element * TODO: need to figure out how to use the order of the columns as * they are in the 'desc' request */ { jsonWriteListStart(jw, NULL); jsonWriteString(jw, NULL, el->hubUrl); jsonWriteString(jw, NULL, el->shortLabel); jsonWriteString(jw, NULL, el->longLabel); jsonWriteString(jw, NULL, el->registrationTime); jsonWriteNumber(jw, NULL, (long long)el->dbCount); jsonWriteString(jw, NULL, el->dbList); jsonWriteString(jw, NULL, el->descriptionUrl); jsonWriteListEnd(jw); } int trackDbTrackCmp(const void *va, const void *vb) /* Compare to sort based on 'track' name; use shortLabel as secondary sort key. * Note: parallel code to hgTracks.c:tgCmpPriority */ { const struct trackDb *a = *((struct trackDb **)va); const struct trackDb *b = *((struct trackDb **)vb); int dif = strcmp(a->track, b->track); if (dif < 0) return -1; else if (dif == 0.0) return strcasecmp(a->shortLabel, b->shortLabel); else return 1; } 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]); // if (row[6]) ret->descriptionUrl = cloneString(row[6]); // else // ret->descriptionUrl = cloneString(""); return ret; } static struct hubPublic *hubPublicLoadAll() { char query[1024]; struct hubPublic *list = NULL; struct sqlConnection *conn = hConnectCentral(); 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() { long nowTime = clock1000(); timedOut = FALSE; if ((nowTime - enteredMainTime) > (1000 * timeOutSeconds)) timedOut= TRUE; return timedOut; } static void trackSettings(struct trackDb *tdb) /* process the settingsHash for a track */ { hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(tdb->settingsHash); while ((hel = hashNext(&hc)) != NULL) { 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); } 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() */ #ifdef NOT static void cloneTdb(struct trackDb *source, struct trackDb *destination) /* TBD: is there a cloneTdb() function somewhere else ? */ { destination->track = cloneString(source->track); destination->shortLabel = cloneString(source->shortLabel); destination->type = cloneString(source->type); destination->longLabel = cloneString(source->longLabel); destination->visibility = source->visibility; destination->priority = source->priority; destination->colorR = source->colorR; destination->colorG = source->colorG; destination->colorB = source->colorB; destination->altColorR = source->altColorR; destination->altColorG = source->altColorG; destination->altColorB = source->altColorB; destination->useScore = source->useScore; destination->private = source->private; destination->url = cloneString(source->url); destination->html = cloneString(source->html); destination->grp = cloneString(source->grp); destination->canPack = source->canPack; destination->settings = cloneString(source->settings); destination->settingsHash = source->settingsHash; } #endif static void hubTrackList(struct trackDb *tdb, struct trackHubGenome *genome) /* process the track list to show all tracks, return trackDb list */ { if (tdb) { struct hash *countTracks = hashNew(0); hPrintf(" <ul>\n"); struct trackDb *track = tdb; for ( ; track; track = track->next ) { -// char *bigDataUrl = hashFindVal(track->settingsHash, "bigDataUrl"); char *bigDataUrl = trackDbSetting(track, "bigDataUrl"); -// char *compositeTrack = hashFindVal(track->settingsHash, "compositeTrack"); char *compositeTrack = trackDbSetting(track, "compositeTrack"); -// char *superTrack = hashFindVal(track->settingsHash, "superTrack"); char *superTrack = trackDbSetting(track, "superTrack"); boolean depthSearch = cartUsualBoolean(cart, "depthSearch", FALSE); if (compositeTrack) hashIncInt(countTracks, "composite container"); else if (superTrack) hashIncInt(countTracks, "superTrack container"); else if (isEmpty(track->type)) hashIncInt(countTracks, "no type specified"); else hashIncInt(countTracks, track->type); if (depthSearch && bigDataUrl) { char *bigDataIndex = NULL; char *relIdxUrl = trackDbSetting(tdb, "bigDataIndex"); if (relIdxUrl != NULL) bigDataIndex = trackHubRelativeUrl(genome->trackDbFile, relIdxUrl); long chromCount = 0; long itemCount = 0; struct dyString *errors = newDyString(1024); int retVal = bbiBriefMeasure(track->type, bigDataUrl, bigDataIndex, &chromCount, &itemCount, errors); if (retVal) { hPrintf(" <li>%s : %s : <font color='red'>ERROR: %s</font></li>\n", track->track, track->type, errors->string); } else { if (startsWithWord("bigBed", track->type)) hPrintf(" <li>%s : %s : %ld chroms : %ld item count</li>\n", track->track, track->type, chromCount, itemCount); else if (startsWithWord("bigWig", track->type)) hPrintf(" <li>%s : %s : %ld chroms : %ld bases covered</li>\n", track->track, track->type, chromCount, itemCount); else hPrintf(" <li>%s : %s : %ld chroms : %ld count</li>\n", track->track, track->type, chromCount, itemCount); } } else { if (compositeTrack) hPrintf(" <li>%s : %s : composite track container</li>\n", track->track, track->type); else if (superTrack) hPrintf(" <li>%s : %s : superTrack container</li>\n", track->track, track->type); else if (! depthSearch) hPrintf(" <li>%s : %s : %s</li>\n", track->track, track->type, bigDataUrl); else hPrintf(" <li>%s : %s</li>\n", track->track, track->type); } if (allTrackSettings) trackSettings(track); /* show all settings */ if (timeOutReached()) break; } /* for ( ; track; track = track->next ) */ hPrintf(" <li>%d different track types</li>\n", countTracks->elCount); if (countTracks->elCount) { hPrintf(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(countTracks); while ((hel = hashNext(&hc)) != NULL) { int prevCount = ptToInt(hashFindVal(trackCounter, 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(" </ul>\n"); } hPrintf(" </ul>\n"); } } /* static struct trackDb *hubTrackList() */ static struct trackDb * assemblySettings(struct trackHubGenome *genome) /* display all the assembly 'settingsHash' */ { struct trackDb *retTbd = NULL; 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 */ { struct trackDb *tdb = trackHubTracksForGenome(genome->trackHub, genome); retTbd = tdb; hubTrackList(tdb, genome); } if (timeOutReached()) break; } hPrintf(" </ul>\n"); return retTbd; } static 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); } if (dbTrackList) *dbTrackList = assemblySettings(genome); else (void) assemblySettings(genome); 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(" <ul>\n"); struct hashEl *hel; struct hashCookie hc = hashFirst(trackCounter); while ((hel = hashNext(&hc)) != NULL) { hPrintf(" <li>%d - %s - total</li>\n", ptToInt(hel->val), hel->name); } hPrintf(" </ul>\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 void dbDbJsonData(struct jsonWrite *jw, struct dbDb *el) /* Print out dbDb table element in JSON format. * must be same as was stated in the columnName header element * TODO: need to figure out how to use the order of the columns as * they are in the 'desc' request */ { jsonWriteListStart(jw, NULL); jsonWriteString(jw, NULL, el->name); jsonWriteString(jw, NULL, el->description); jsonWriteString(jw, NULL, el->nibPath); jsonWriteString(jw, NULL, el->organism); jsonWriteString(jw, NULL, el->defaultPos); jsonWriteNumber(jw, NULL, (long long)el->active); jsonWriteNumber(jw, NULL, (long long)el->orderKey); jsonWriteString(jw, NULL, el->genome); jsonWriteString(jw, NULL, el->scientificName); jsonWriteString(jw, NULL, el->htmlPath); jsonWriteNumber(jw, NULL, (long long)el->hgNearOk); jsonWriteNumber(jw, NULL, (long long)el->hgPbOk); jsonWriteString(jw, NULL, el->sourceName); jsonWriteNumber(jw, NULL, (long long)el->taxId); jsonWriteListEnd(jw); } static boolean tableColumns(struct jsonWrite *jw, char *table) /* output the column names for the given table * return: TRUE on error, FALSE on success */ { jsonWriteListStart(jw, "columnNames"); char query[1024]; struct sqlConnection *conn = hConnectCentral(); sqlSafef(query, sizeof(query), "desc %s", table); struct sqlResult *sr = sqlGetResult(conn, query); char **row; row = sqlNextRow(sr); if (NULL == row) { jsonErrAbort("ERROR: can not 'desc' table '%s'", table); return TRUE; } while ((row = sqlNextRow(sr)) != NULL) jsonWriteString(jw, NULL, row[0]); sqlFreeResult(&sr); hDisconnectCentral(&conn); jsonWriteListEnd(jw); return FALSE; } static void jsonPublicHubs() /* output the hubPublic SQL table */ { struct sqlConnection *conn = hConnectCentral(); char *dataTime = sqlTableUpdate(conn, hubPublicTableName()); hDisconnectCentral(&conn); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); struct hubPublic *el = hubPublicLoadAll(); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteString(jw, "tableName", hubPublicTableName()); tableColumns(jw, hubPublicTableName()); jsonWriteListStart(jw, "publicHubData"); for ( ; el != NULL; el = el->next ) { hubPublicJsonData(jw, el); } jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } static int dbDbCmpName(const void *va, const void *vb) /* Compare two dbDb elements: name, ignore case. */ { const struct dbDb *a = *((struct dbDb **)va); const struct dbDb *b = *((struct dbDb **)vb); return strcasecmp(a->name, b->name); } static struct dbDb *ucscDbDb() /* return the dbDb table as an slList */ { char query[1024]; struct sqlConnection *conn = hConnectCentral(); sqlSafef(query, sizeof(query), "select * from dbDb"); struct dbDb *dbList = NULL, *el = NULL; struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { el = dbDbLoad(row); slAddHead(&dbList, el); } sqlFreeResult(&sr); hDisconnectCentral(&conn); slSort(&dbList, dbDbCmpName); return dbList; } static void jsonDbDb() /* output the dbDb SQL table */ { struct sqlConnection *conn = hConnectCentral(); char *dataTime = sqlTableUpdate(conn, "dbDb"); hDisconnectCentral(&conn); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); struct dbDb *dbList = ucscDbDb(); struct dbDb *el; struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteString(jw, "tableName", "dbDb"); tableColumns(jw, "dbDb"); jsonWriteListStart(jw, "ucscGenomes"); for ( el=dbList; el != NULL; el = el->next ) { dbDbJsonData(jw, el); } jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } static void chromInfoJsonOutput(FILE *f, char *db) /* for given db, if there is a track, list the chromosomes in that track, * for no track, simply list the chromosomes in the sequence */ { char *table = cgiOptionalString("track"); struct sqlConnection *conn = hAllocConn(db); /* in trackDb language: track == table */ if (table) { if (! sqlTableExists(conn, table)) jsonErrAbort("ERROR: endpoint: /list/chromosomes?db=%&table=%s ERROR table does not exist", db, table); if (sqlColumnExists(conn, table, "chrom")) { char *dataTime = sqlTableUpdate(conn, table); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "genome", db); jsonWriteString(jw, "track", table); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); struct slPair *list = NULL; char query[2048]; sqlSafef(query, sizeof(query), "select distinct chrom from %s", table); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { int size = hChromSize(db, row[0]); slAddHead(&list, slPairNew(row[0], intToPt(size))); } sqlFreeResult(&sr); slPairIntSort(&list); slReverse(&list); jsonWriteNumber(jw, "chromCount", (long long)slCount(list)); jsonWriteObjectStart(jw, "chromosomes"); struct slPair *el = list; for ( ; el != NULL; el = el->next ) jsonWriteNumber(jw, el->name, (long long)ptToInt(el->val)); jsonWriteObjectEnd(jw); /* chromosomes */ jsonWriteObjectEnd(jw); /* top level */ fputs(jw->dy->string,stdout); } else { jsonErrAbort("ERROR: table '%s' is not a position table, no chromosomes for genome: '%s'", table, db); } } else { char *dataTime = sqlTableUpdate(conn, "chromInfo"); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); struct chromInfo *ciList = createChromInfoList(NULL, db); struct chromInfo *el = ciList; struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "genome", db); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); jsonWriteNumber(jw, "chromCount", (long long)slCount(ciList)); jsonWriteObjectStart(jw, "chromosomes"); for ( ; el != NULL; el = el->next ) { jsonWriteNumber(jw, el->chrom, (long long)el->size); } jsonWriteObjectEnd(jw); /* chromosomes */ jsonWriteObjectEnd(jw); /* top level */ fputs(jw->dy->string,stdout); } hFreeConn(&conn); } static void recursiveTrackList(struct jsonWrite *jw, struct trackDb *tdb, char *type) { jsonWriteListStart(jw, type); struct trackDb *el; for (el = tdb; el != NULL; el = el->next ) { jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "track", el->track); jsonWriteString(jw, "shortLabel", el->shortLabel); jsonWriteString(jw, "type", el->type); jsonWriteString(jw, "longLabel", el->longLabel); if (tdbIsComposite(el)) { recursiveTrackList(jw, el->subtracks, "subtracks"); } if (tdb->parent && tdbIsSuperTrackChild(el)) jsonWriteString(jw, "superTrack", "TRUE"); jsonWriteObjectEnd(jw); } jsonWriteListEnd(jw); } static void trackDbJsonOutput(char *db, FILE *f) /* return track list from specified UCSC database name */ { struct sqlConnection *conn = hAllocConn(db); char *dataTime = sqlTableUpdate(conn, "trackDb"); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); hFreeConn(&conn); struct trackDb *tdbList = hTrackDb(db); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "db", db); jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); freeMem(dataTime); recursiveTrackList(jw, tdbList, "tracks"); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } /* static void trackDbJsonOutput(char *db, FILE *f) */ static void getTrackData() { } static void getSequenceData() /* given at least a db=name and chrom=chr, optionally start and end */ { char *db = cgiOptionalString("db"); char *chrom = cgiOptionalString("chrom"); char *start = cgiOptionalString("start"); char *end = cgiOptionalString("end"); if (isEmpty(db)) jsonErrAbort("missing URL db=<ucscDb> name for endpoint '/getData/sequence"); if (isEmpty(chrom)) jsonErrAbort("missing URL chrom=<name> for endpoint '/getData/sequence?db=%s", db); if (chromSeqFileExists(db, chrom)) { struct chromInfo *ci = hGetChromInfo(db, chrom); struct dnaSeq *seq = NULL; if (isEmpty(start) || isEmpty(end)) seq = hChromSeqMixed(db, chrom, 0, 0); else seq = hChromSeqMixed(db, chrom, sqlSigned(start), sqlSigned(end)); if (NULL == seq) jsonErrAbort("can not find sequence for chrom=%s for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "db", db); jsonWriteString(jw, "chrom", chrom); if (isEmpty(start) || isEmpty(end)) { jsonWriteNumber(jw, "start", (long long)0); jsonWriteNumber(jw, "end", (long long)ci->size); } else { jsonWriteNumber(jw, "start", (long long)sqlSigned(start)); jsonWriteNumber(jw, "end", (long long)sqlSigned(end)); } jsonWriteString(jw, "dna", seq->dna); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); freeDnaSeq(&seq); } else jsonErrAbort("can not find specified chrom=%s in sequence for endpoint '/getData/sequence?db=%s&chrom=%s", chrom, db, chrom); } #define MAX_PATH_INFO 32 static void apiGetData(char *words[MAX_PATH_INFO]) /* 'getData' function, words[1] is the subCommand */ { if (sameWord("track", words[1])) getTrackData(); else if (sameWord("sequence", words[1])) getSequenceData(); else jsonErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); } static void apiList(char *words[MAX_PATH_INFO]) /* 'list' function words[1] is the subCommand */ { if (sameWord("publicHubs", words[1])) jsonPublicHubs(); else if (sameWord("ucscGenomes", words[1])) jsonDbDb(); else if (sameWord("hubGenomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); if (isEmpty(hubUrl)) jsonErrAbort("must supply hubUrl='http:...' some URL to a hub for /list/hubGenomes"); struct trackHub *hub = NULL; struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { hub = trackHubOpen(hubUrl, ""); } errCatchEnd(errCatch); if (errCatch->gotError) { jsonErrAbort("error opening hubUrl: '%s', '%s'", hubUrl, errCatch->message->string); } errCatchFree(&errCatch); if (hub->genomeList) { struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "hubUrl", hubUrl); jsonWriteListStart(jw, "genomes"); struct slName *theList = genomeList(hub, NULL, NULL); slNameSort(&theList); struct slName *el = theList; for ( ; el ; el = el->next ) { jsonWriteString(jw, NULL, el->name); } jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } } else if (sameWord("tracks", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); char *genome = cgiOptionalString("genome"); char *db = cgiOptionalString("db"); if (isEmpty(hubUrl) && isEmpty(db)) jsonErrAbort("ERROR: must supply hubUrl or db name to return track list"); if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database { trackDbJsonOutput(db, stdout); // only need db for this function return; } if (isEmpty(genome) || isEmpty(hubUrl)) { if (isEmpty(genome)) warn("# must supply genome='someName' the name of a genome in a hub for /list/tracks\n"); if (isEmpty(hubUrl)) jsonErrAbort("ERROR: must supply hubUrl='http:...' some URL to a hub for /list/genomes"); } struct trackHub *hub = trackHubOpen(hubUrl, ""); if (hub->genomeList) { struct trackDb *dbTrackList = NULL; (void) genomeList(hub, &dbTrackList, genome); slSort(dbTrackList, trackDbTrackCmp); struct jsonWrite *jw = jsonStartOutput(); jsonWriteString(jw, "hubUrl", hubUrl); jsonWriteString(jw, "genome", genome); recursiveTrackList(jw, dbTrackList, "tracks"); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } } else if (sameWord("chromosomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); // char *genome = cgiOptionalString("genome"); char *db = cgiOptionalString("db"); if (isEmpty(hubUrl) && isEmpty(db)) jsonErrAbort("ERROR: must supply hubUrl or db name to return chromosome list"); if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database { chromInfoJsonOutput(stdout, db); return; } } else jsonErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); } 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) jsonErrAbort("unknown endpoint command: '/%s'", pathInfo); struct hashEl *hel = hashLookup(apiFunctionHash, words[0]); if (hel == NULL) jsonErrAbort("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 * ucscDb) { hPrintf("<p>Tracks in UCSC genome: '%s'<br>\n", ucscDb); struct trackDb *tdbList = hTrackDb(ucscDb); struct trackDb *track; hPrintf("<ul>\n"); for (track = tdbList; track != NULL; track = track->next ) { hPrintf("<li>%s</li>\n", track->track); if (allTrackSettings) trackSettings(track); /* show all settings */ } hPrintf("</ul>\n"); hPrintf("</p>\n"); } static void showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb) { hPrintf("<h2>Example URLs to return json data structures:</h2>\n"); hPrintf("<ul>\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&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, 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("</ul>\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; 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 = trackHubOpen(urlInput, ""); if (measureTiming) { long thisTime = clock1000(); hPrintf("<em>hub open time: %ld millis</em><br>\n", thisTime - lastTime); } hPrintf("<h3>ucscDb: '%s'</h2>\n", ucscDb); struct trackHubGenome *hubGenome = hub->genomeList; 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. */ 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; }