Ejemplo n.º 1
0
 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);
 }
Ejemplo n.º 2
0
  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;
  }
Ejemplo n.º 3
0
 @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;
 }
Ejemplo n.º 4
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;
  }
Ejemplo n.º 5
0
  @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);
  }
Ejemplo n.º 6
0
  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;
  }
Ejemplo n.º 7
0
  // 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;
  }