3bbad1670f2e44ca41d06c657b8f8636abfce4fb hiram Wed Mar 27 14:47:11 2019 -0700 provide list chrom function for hubs refs #18869 diff --git src/hg/hubApi/list.c src/hg/hubApi/list.c index 8b0358d..24b75db 100644 --- src/hg/hubApi/list.c +++ src/hg/hubApi/list.c @@ -125,41 +125,178 @@ { } // jsonWriteListStart(jw, "ucscGenomes"); jsonWriteObjectStart(jw, "ucscGenomes"); for ( el=dbList; el != NULL; el = el->next ) { dbDbJsonData(jw, el, columnCount, columnNames); } // jsonWriteListEnd(jw); jsonWriteObjectEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); hDisconnectCentral(&conn); } +static void hubChromInfoJsonOutput(FILE *f, char *hubUrl, char *genome) +/* for given hubUrl list the chromosomes in the sequence for specified genome + */ +{ +struct trackHub *hub = errCatchTrackHubOpen(hubUrl); +struct trackHubGenome *ge = NULL; +char *track = cgiOptionalString("track"); + +if (isEmpty(genome)) + apiErrAbort("must specify a 'genome=name' with hubUrl for endpoint: /list/chromosomes?hubUrl=%s&genome=<empty>", hubUrl); + +struct trackHubGenome *foundGenome = NULL; + +for (ge = hub->genomeList; ge; ge = ge->next) + { + if (sameOk(genome, ge->name)) + { + foundGenome = ge; + continue; /* found genome */ + } + } +if (NULL == foundGenome) + apiErrAbort("can not find specified 'genome=%s' for endpoint: /list/chromosomes?hubUrl=%s&genome=%s", genome, hubUrl, genome); + +struct jsonWrite *jw = apiStartOutput(); +jsonWriteString(jw, "hubUrl", hubUrl); +jsonWriteString(jw, "genome", genome); +if (isNotEmpty(track)) + { + jsonWriteString(jw, "track", track); + struct trackDb *tdb = obtainTdb(foundGenome, NULL); + if (NULL == tdb) + apiErrAbort("failed to find a track hub definition in genome=%s for endpoint '/list/chromosomes' give hubUrl=%s'", genome, hubUrl); + + struct trackDb *thisTrack = findTrackDb(track, tdb); + if (NULL == thisTrack) + apiErrAbort("failed to find specified track=%s in genome=%s for endpoint '/getdata/track' given hubUrl='%s'", track, genome, hubUrl); + + char *bigDataUrl = trackDbSetting(thisTrack, "bigDataUrl"); + struct bbiFile *bbi = bigFileOpen(thisTrack->type, bigDataUrl); + struct bbiChromInfo *chrList = bbiChromList(bbi); + slSort(chrList, chromInfoCmp); + struct bbiChromInfo *el = chrList; + jsonWriteNumber(jw, "chromCount", (long long)slCount(chrList)); + jsonWriteObjectStart(jw, "chromosomes"); + for ( ; el; el = el->next ) + { + jsonWriteNumber(jw, el->name, (long long)el->size); + } + jsonWriteObjectEnd(jw); /* chromosomes */ + } +else + { + struct chromInfo *ci = trackHubAllChromInfo(foundGenome->name); + slSort(ci, chromInfoCmp); + jsonWriteNumber(jw, "chromCount", (long long)slCount(ci)); + jsonWriteObjectStart(jw, "chromosomes"); + struct chromInfo *el = ci; + 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); + +#ifdef NOT +char *table = cgiOptionalString("track"); +struct sqlConnection *conn = hAllocConn(db); +/* in trackDb language: track == table */ +if (table) + { + if (! sqlTableExists(conn, table)) + apiErrAbort("can not find specified 'track=%s' for endpoint: /list/chromosomes?db=%s&track=%s", table, db, table); + if (sqlColumnExists(conn, table, "chrom")) + { + char *dataTime = sqlTableUpdate(conn, table); + time_t dataTimeStamp = sqlDateToUnixTime(dataTime); + replaceChar(dataTime, ' ', 'T'); /* ISO 8601 */ + struct jsonWrite *jw = apiStartOutput(); + 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 + apiErrAbort("track '%s' is not a position track, request table without chrom specification, genome: '%s'", table, db); + } +else + { + char *dataTime = sqlTableUpdate(conn, "chromInfo"); + time_t dataTimeStamp = sqlDateToUnixTime(dataTime); + replaceChar(dataTime, ' ', 'T'); /* ISO 8601 */ + struct chromInfo *ciList = createChromInfoList(NULL, db); + slSort(ciList, chromInfoCmp); + struct chromInfo *el = ciList; + struct jsonWrite *jw = apiStartOutput(); + 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); +#endif +} + 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) { - /* XXX TBD - expand this to a hub to get chromosomes from hub big* file */ if (! sqlTableExists(conn, table)) apiErrAbort("can not find specified 'track=%s' for endpoint: /list/chromosomes?db=%s&track=%s", table, db, table); if (sqlColumnExists(conn, table, "chrom")) { char *dataTime = sqlTableUpdate(conn, table); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); /* ISO 8601 */ struct jsonWrite *jw = apiStartOutput(); 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]; @@ -176,35 +313,35 @@ 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 apiErrAbort("track '%s' is not a position track, request table without chrom specification, genome: '%s'", table, db); } else { - /* XXX TBD - expand this to a hub to get chromosomes from hub 2bit file */ char *dataTime = sqlTableUpdate(conn, "chromInfo"); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); replaceChar(dataTime, ' ', 'T'); /* ISO 8601 */ struct chromInfo *ciList = createChromInfoList(NULL, db); + slSort(ciList, chromInfoCmp); struct chromInfo *el = ciList; struct jsonWrite *jw = apiStartOutput(); 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); @@ -215,31 +352,30 @@ static void recursiveTrackList(struct jsonWrite *jw, struct trackDb *tdb) /* output trackDb tags only for real tracks, not containers, * recursive when subtracks exist */ { if (! ( tdbIsComposite(tdb) || tdbIsCompositeView(tdb) ) ) { jsonWriteObjectStart(jw, tdb->track); jsonWriteString(jw, "shortLabel", tdb->shortLabel); jsonWriteString(jw, "type", tdb->type); jsonWriteString(jw, "longLabel", tdb->longLabel); if (tdb->parent) jsonWriteString(jw, "parent", tdb->parent->track); if (tdb->settingsHash) { - jsonWriteString(jw, "hasSettingsHash", "TRUE"); 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)) jsonWriteString(jw, hel->name, "empty"); else jsonWriteString(jw, hel->name, (char *)hel->val); } } jsonWriteObjectEnd(jw); } @@ -357,29 +493,34 @@ jsonWriteString(jw, "hubUrl", hubUrl); jsonWriteObjectStart(jw, genome); struct trackDb *el = NULL; for (el = tdbList; el != NULL; el = el->next ) { recursiveTrackList(jw, el); } jsonWriteObjectEnd(jw); jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); } } else if (sameWord("chromosomes", words[1])) { char *hubUrl = cgiOptionalString("hubUrl"); -// char *genome = cgiOptionalString("genome"); + char *genome = cgiOptionalString("genome"); char *db = cgiOptionalString("db"); if (isEmpty(hubUrl) && isEmpty(db)) - apiErrAbort("ERROR: must supply hubUrl or db name to return chromosome list"); + apiErrAbort("ERROR: must '%s' '%s' supply hubUrl or db name to return chromosome list", hubUrl, db); if (isEmpty(hubUrl)) // missing hubUrl implies UCSC database { chromInfoJsonOutput(stdout, db); return; } + else + { + hubChromInfoJsonOutput(stdout, hubUrl, genome); + return; + } } else apiErrAbort("do not recognize endpoint function: '/%s/%s'", words[0], words[1]); } /* void apiList(char *words[MAX_PATH_INFO]) */