public static void main(String[] args) throws IOException {
Formatter f = new Formatter();
String indexName = (args.length > 0) ? args[0] : "F:/nomads/NOMADS-cfsrr-timeseries.ncx";
RandomAccessFile raf = new RandomAccessFile(indexName, "r");
Grib1TimePartition gtc = Grib1TimePartitionBuilder.createFromIndex("test", null, raf);
gtc.showIndex(f);
System.out.printf("%s%n", f);
}
private boolean createPartitionedIndex(Formatter f) throws IOException {
long start = System.currentTimeMillis();
// create partitions based on TimePartitionCollections object
for (CollectionManager dcm : tpc.makePartitions()) {
tp.addPartition(dcm);
}
List<TimePartition.Partition> bad = new ArrayList<TimePartition.Partition>();
for (TimePartition.Partition dc : tp.getPartitions()) {
try {
dc.makeGribCollection(f); // ensure collection has been read successfully
if (trace) f.format(" Open partition %s%n", dc.getDcm().getCollectionName());
} catch (Throwable t) {
logger.error(" Failed to open partition " + dc.getName(), t);
f.format(" FAIL on partition %s (remove) %n", dc.getDcm().getCollectionName());
bad.add(dc); // LOOK may be a file leak ?
}
}
// remove ones that failed
for (TimePartition.Partition p : bad) tp.removePartition(p);
// choose the "canonical" partition, aka prototype
int n = tp.getPartitions().size();
if (n == 0) {
logger.error(" Nothing in this partition = " + tp.getName());
f.format(" FAIL Partition empty collection = %s%n", tp.getName());
return false;
}
int idx = tpc.getProtoIndex(n);
TimePartition.Partition canon = tp.getPartitions().get(idx);
f.format(" Using canonical partition %s%n", canon.getDcm().getCollectionName());
// check consistency across vert and ens coords
if (!checkPartitions(canon, f)) {
logger.error(
" Partition check failed, index not written on {} message = {}",
tp.getName(),
f.toString());
f.format(" FAIL Partition check collection = %s%n", tp.getName());
return false;
}
// make the time coordinates, place results into canon
createPartitionedTimeCoordinates(canon, f);
// ready to write the index file
writeIndex(canon, f);
// close open gc's
tp.cleanup();
long took = System.currentTimeMillis() - start;
f.format(" CreatePartitionedIndex took %d msecs%n", took);
return true;
}
@Override
protected boolean readPartitions(GribCollectionProto.GribCollectionIndex proto) {
for (int i = 0; i < proto.getPartitionsCount(); i++) {
GribCollectionProto.Partition pp = proto.getPartitions(i);
tp.addPartition(pp.getName(), pp.getFilename());
}
return proto.getPartitionsCount() > 0;
}
/*
MAGIC_START
version
sizeRecords
VariableRecords (sizeRecords bytes)
sizeIndex
GribCollectionIndex (sizeIndex bytes)
*/
private boolean writeIndex(TimePartition.Partition canon, Formatter f) throws IOException {
File file = tp.getIndexFile();
if (file.exists()) {
if (!file.delete()) logger.error("Cant delete " + file.getPath());
}
RandomAccessFile raf = new RandomAccessFile(file.getPath(), "rw");
raf.order(RandomAccessFile.BIG_ENDIAN);
try {
//// header message
raf.write(MAGIC_START.getBytes("UTF-8"));
raf.writeInt(version);
raf.writeLong(0); // no record section
GribCollectionProto.GribCollectionIndex.Builder indexBuilder =
GribCollectionProto.GribCollectionIndex.newBuilder();
indexBuilder.setName(tp.getName());
GribCollection canonGc = canon.makeGribCollection(f);
for (GribCollection.GroupHcs g : canonGc.getGroups())
indexBuilder.addGroups(writeGroupProto(g));
indexBuilder.setCenter(canonGc.getCenter());
indexBuilder.setSubcenter(canonGc.getSubcenter());
indexBuilder.setMaster(canonGc.getMaster());
indexBuilder.setLocal(canonGc.getLocal());
for (TimePartition.Partition p : tp.getPartitions()) {
indexBuilder.addPartitions(writePartitionProto(p.getName(), (TimePartition.Partition) p));
}
GribCollectionProto.GribCollectionIndex index = indexBuilder.build();
byte[] b = index.toByteArray();
NcStream.writeVInt(raf, b.length); // message size
raf.write(b); // message - all in one gulp
f.format("GribCollectionTimePartitionedIndex= %d bytes%n", b.length);
} finally {
f.format("file size = %d bytes%n", raf.length());
raf.close();
}
return true;
}
@Override
protected GribCollection.VariableIndex readVariable(
GribCollectionProto.Variable pv, GribCollection.GroupHcs group) {
int discipline = pv.getDiscipline();
int category = pv.getCategory();
int param = pv.getParameter();
int levelType = pv.getLevelType();
int intvType = pv.getIntervalType();
String intvName = pv.getIntvName();
boolean isLayer = pv.getIsLayer();
int ensDerivedType = pv.getEnsDerivedType();
int probType = pv.getProbabilityType();
String probabilityName = pv.getProbabilityName();
int cdmHash = pv.getCdmHash();
long recordsPos = pv.getRecordsPos();
int recordsLen = pv.getRecordsLen();
int timeIdx = pv.getTimeIdx();
int vertIdx = pv.getVertIdx();
int ensIdx = pv.getEnsIdx();
int tableVersion = pv.getTableVersion();
List<Integer> groupnoList = pv.getGroupnoList();
List<Integer> varnoList = pv.getVarnoList();
List<Integer> flagList = pv.getFlagList();
return tp.makeVariableIndex(
group,
tableVersion,
discipline,
category,
param,
levelType,
isLayer,
intvType,
intvName,
ensDerivedType,
probType,
probabilityName,
-1,
cdmHash,
timeIdx,
vertIdx,
ensIdx,
recordsPos,
recordsLen,
groupnoList,
varnoList,
flagList);
}
private boolean createPartitionedTimeCoordinates(TimePartition.Partition canon, Formatter f)
throws IOException {
List<TimePartition.Partition> partitions = tp.getPartitions();
boolean ok = true;
// for each group in canonical Partition
for (GribCollection.GroupHcs firstGroup : canon.makeGribCollection(f).getGroups()) {
String gname = firstGroup.getId();
if (trace) f.format(" Check Group %s%n", gname);
// get list of corresponding groups from all the time partition, so we dont have to keep
// looking it up
List<PartGroup> pgList = new ArrayList<PartGroup>(partitions.size());
for (TimePartition.Partition dc : partitions) {
GribCollection.GroupHcs gg = dc.makeGribCollection(f).findGroupById(gname);
if (gg == null) logger.error(" Cant find group {} in partition {}", gname, dc.getName());
else pgList.add(new PartGroup(gg, dc));
}
// unique time coordinate unions
List<TimeCoordUnion> unionList = new ArrayList<TimeCoordUnion>();
// for each variable in canonical Partition
for (GribCollection.VariableIndex viCanon : firstGroup.varIndex) {
if (trace) f.format(" Check variable %s%n", viCanon);
TimeCoord tcCanon = viCanon.getTimeCoord();
List<TimeCoord> tcPartitions = new ArrayList<TimeCoord>(pgList.size());
// for each partition, get the time index
for (PartGroup pg : pgList) {
// get corresponding variable
GribCollection.VariableIndex vi2 = pg.group.findVariableByHash(viCanon.cdmHash);
if (vi2 == null) { // apparently not in the file
f.format(
" WARN Cant find variable %s in partition %s / %s%n",
viCanon, pg.tpp.getName(), pg.group.getId());
tcPartitions.add(null);
} else {
if (vi2.timeIdx < 0 || vi2.timeIdx >= pg.group.timeCoords.size()) {
logger.error(" timeIdx out of range var= {} on partition {}", vi2, pg.tpp.getName());
tcPartitions.add(null);
} else {
TimeCoord tc2 = vi2.getTimeCoord();
if (tc2.isInterval() != tcCanon.isInterval()) {
logger.error(
" timeIdx wrong interval type var= {} on partition {}", vi2, pg.tpp.getName());
tcPartitions.add(null);
} else {
tcPartitions.add(tc2);
}
}
}
}
// union of time coordinates
TimeCoordUnion union = new TimeCoordUnion(tcCanon.getCode(), tcPartitions, tcCanon);
// store result in the first group
viCanon.partTimeCoordIdx =
TimeCoordUnion.findUnique(unionList, union); // this merges identical TimeCoordUnion
}
/* turn TimeIndex into TimeCoord
for (int tidx = 0; tidx <unionList.size(); tidx++) {
TimeCoordUnion union = unionList.get(tidx);
f.format(" %s %d: timeIndexList=", firstGroup.hcs.getName(), tidx);
for (int idx : union.) f.format("%d,",idx);
f.format("%n");
} */
// store results in first group
firstGroup.timeCoordPartitions = unionList;
}
return ok;
}
// consistency check on variables : compare each variable to corresponding one in proto
// also set the groupno and partno for each partition
private boolean checkPartitions(TimePartition.Partition canon, Formatter f) throws IOException {
List<TimePartition.Partition> partitions = tp.getPartitions();
int npart = partitions.size();
boolean ok = true;
// for each group in canonical Partition
GribCollection canonGc = canon.makeGribCollection(f);
for (GribCollection.GroupHcs firstGroup : canonGc.getGroups()) {
String gname = firstGroup.getId();
if (trace) f.format(" Check Group %s%n", gname);
// hash proto variables for quick lookup
Map<Integer, GribCollection.VariableIndex> check =
new HashMap<Integer, GribCollection.VariableIndex>(firstGroup.varIndex.size());
List<GribCollection.VariableIndex> varIndexP =
new ArrayList<GribCollection.VariableIndex>(firstGroup.varIndex.size());
for (GribCollection.VariableIndex vi : firstGroup.varIndex) {
TimePartition.VariableIndexPartitioned vip = tp.makeVariableIndexPartitioned(vi, npart);
varIndexP.add(vip);
check.put(vi.cdmHash, vip); // replace with its evil twin
}
firstGroup.varIndex = varIndexP; // replace with its evil twin
// for each partition
for (int partno = 0; partno < npart; partno++) {
TimePartition.Partition tpp = partitions.get(partno);
if (trace) f.format(" Check Partition %s%n", tpp.getName());
// get corresponding group
GribCollection gc = tpp.makeGribCollection(f);
int groupIdx = gc.findGroupIdxById(firstGroup.getId());
if (groupIdx < 0) {
f.format(" Cant find group %s in partition %s%n", gname, tpp.getName());
ok = false;
continue;
}
GribCollection.GroupHcs group = gc.getGroup(groupIdx);
// for each variable in partition group
for (int varIdx = 0; varIdx < group.varIndex.size(); varIdx++) {
GribCollection.VariableIndex vi2 = group.varIndex.get(varIdx);
if (trace) f.format(" Check variable %s%n", vi2);
int flag = 0;
GribCollection.VariableIndex vi1 = check.get(vi2.cdmHash); // compare with proto variable
if (vi1 == null) {
f.format(
" WARN Cant find variable %s from %s in proto - ignoring that variable%n",
vi2, tpp.getName());
continue; // we can tolerate this
}
// compare vert coordinates
VertCoord vc1 = vi1.getVertCoord();
VertCoord vc2 = vi2.getVertCoord();
if ((vc1 == null) != (vc2 == null)) {
f.format(
" ERR Vert coordinates existence on variable %s in %s doesnt match%n",
vi2, tpp.getName());
ok = false;
} else if ((vc1 != null) && !vc1.equalsData(vc2)) {
f.format(
" WARN Vert coordinates values on variable %s in %s dont match%n",
vi2, tpp.getName());
f.format(" canon vc = %s%n", vc1);
f.format(" this vc = %s%n", vc2);
flag |= TimePartition.VERT_COORDS_DIFFER;
}
// compare ens coordinates
EnsCoord ec1 = vi1.getEnsCoord();
EnsCoord ec2 = vi2.getEnsCoord();
if ((ec1 == null) != (ec2 == null)) {
f.format(
" ERR Ensemble coordinates existence on variable %s in %s doesnt match%n",
vi2, tpp.getName());
ok = false;
} else if ((ec1 != null) && !ec1.equalsData(ec2)) {
f.format(
" WARN Ensemble coordinates values on variable %s in %s dont match%n",
vi2, tpp.getName());
f.format(" canon ec = %s%n", ec1);
f.format(" this ec = %s%n", ec2);
flag |= TimePartition.ENS_COORDS_DIFFER;
}
((TimePartition.VariableIndexPartitioned) vi1)
.setPartitionIndex(partno, groupIdx, varIdx, flag);
} // loop over variable
} // loop over partition
} // loop over group
if (ok) f.format(" Partition check: vert, ens coords OK%n");
return ok;
}