55b54d043a87a29773ca196c360a0af1346947ec hiram Mon Feb 18 07:05:59 2019 -0800 the trackDb from hubs appears to be flattened ? refs #18869 diff --git src/hg/hubApi/getData.c src/hg/hubApi/getData.c index 835e65f..6f40d0a 100644 --- src/hg/hubApi/getData.c +++ src/hg/hubApi/getData.c @@ -33,61 +33,59 @@ /* 'track' name in trackDb refers to a SQL 'table' */ if (isEmpty(db)) apiErrAbort("missing URL db= name for endpoint '/getData/track"); if (isEmpty(table)) apiErrAbort("missing URL track= name for endpoint '/getData/track"); struct sqlConnection *conn = hAllocConn(db); if (! sqlTableExists(conn, table)) apiErrAbort("can not find specified 'track=%s' for endpoint: /getData/track?db=%s&track=%s", table, db, table); struct jsonWrite *jw = apiStartOutput(); jsonWriteString(jw, "db", db); jsonWriteString(jw, "track", table); char *dataTime = sqlTableUpdate(conn, table); time_t dataTimeStamp = sqlDateToUnixTime(dataTime); -replaceChar(dataTime, ' ', 'T'); +replaceChar(dataTime, ' ', 'T'); /* ISO 8601 */ jsonWriteString(jw, "dataTime", dataTime); jsonWriteNumber(jw, "dataTimeStamp", (long long)dataTimeStamp); +char query[4096]; /* no chrom specified, return entire table */ if (isEmpty(chrom)) { - char query[4096]; sqlSafef(query, sizeof(query), "select * from %s", table); tableDataOutput(conn, jw, query, table); } else if (isEmpty(start) || isEmpty(end)) { if (! sqlColumnExists(conn, table, "chrom")) - apiErrAbort("track '%s' is not a position track, request table without chrom specification, genome: '%s'", table, db); + apiErrAbort("track '%s' is not a position track, request track without chrom specification, genome: '%s'", table, db); jsonWriteString(jw, "chrom", chrom); struct chromInfo *ci = hGetChromInfo(db, chrom); jsonWriteNumber(jw, "start", (long long)0); jsonWriteNumber(jw, "end", (long long)ci->size); - char query[4096]; sqlSafef(query, sizeof(query), "select * from %s where chrom='%s'", table, chrom); tableDataOutput(conn, jw, query, table); } else { if (! sqlColumnExists(conn, table, "chrom")) - apiErrAbort("track '%s' is not a position track, request table without chrom specification, genome: '%s'", table, db); + apiErrAbort("track '%s' is not a position track, request track without chrom specification, genome: '%s'", table, db); jsonWriteString(jw, "chrom", chrom); jsonWriteNumber(jw, "start", (long long)sqlSigned(start)); jsonWriteNumber(jw, "end", (long long)sqlSigned(end)); - char query[4096]; sqlSafef(query, sizeof(query), "select * from %s where chrom='%s' AND chromEnd > %d AND chromStart < %d", table, chrom, sqlSigned(start), sqlSigned(end)); tableDataOutput(conn, jw, query, table); } jsonWriteObjectEnd(jw); fputs(jw->dy->string,stdout); hFreeConn(&conn); } static void getSequenceData() /* return DNA sequence, 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");