Support nested compound dataset.

[hyoklee]

For the following HDF5 file, netCDF-C can handle it correctly but netCDF-Java can't.

netCDF-C CDL output:

netcdf comp_complex_more {
types:
  compound cmp1 {
    short i ;
    int j ;
  }; // cmp1
  compound cmp2 {
    cmp1 x ;
    double y(3) ;
  }; // cmp2
  compound cmp3 {
    cmp2 yy(3) ;
  }; // cmp3
dimensions:
    n = 4 ;
variables:
    cmp3 phony_compound_var(n) ;

netCDF-Java NcML output:

<?xml version="1.0" encoding="UTF-8"?>
<netcdf xmlns="http:https://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2" location="file:https://comp_complex_more.h5">
  <dimension name="n" length="4" />
  <variable name="phony_compound_var" shape="n" type="Structure">
    <variable name="yy" shape="3" type="Structure" />
  </variable>
</netcdf>

It doesn't show i,j,x,y.

[cwardgar]

I can confirm the problem and I have a unit test that demonstrates it. I think I have a fix too, but I don't have time to finish it just yet.

[cwardgar]

In TestNc4IospReading.issue273() I'm comparing the NetcdfFile produced via JNI calls to the C-library versus the NetcdfFile produced by H5iosp, which is pure Java.

Here's the JNI version, which is almost certainly the correct one:

netcdf /Users/cwardgar/Desktop/comp_complex_more\.h5\ (jni\) {
  dimensions:
    n = 4;
  variables:

    Structure {

      Structure {

        Structure {
          short i;
          int j;
        } x;

        double y(3);
      } yy(3);

    } phony_compound_var(n);


 data:
phony_compound_var =
  {
    yy =
      {
        x =            i =1
            j =100000

        y =
          {100000.285657, 100.1, 1.1415926}
      } cmp2(0)
      {
        x =            i =2
            j =200000

        y =
          {200000.151617, 200.2, 273.15}
      } cmp2(1)
      {
        x =            i =-1
            j =-100000

        y =
          {-100000.285657, -100.1, -1.1415926}
      } cmp2(2)
  } cmp3(0)
  {
    yy =
      {
        x =            i =3
            j =300000

        y =
          {300000.285657, 300.3, 3.1415926}
      } cmp2(0)
      {
        x =            i =4
            j =400000

        y =
          {400000.151617, 400.4, 473.15}
      } cmp2(1)
      {
        x =            i =-2
            j =-200000

        y =
          {-200000.285657, -200.2, -2.1415926}
      } cmp2(2)
  } cmp3(1)
  {
    yy =
      {
        x =            i =5
            j =500000

        y =
          {500000.285657, 500.5, 5.1415926}
      } cmp2(0)
      {
        x =            i =6
            j =600000

        y =
          {600000.151617, 600.6, 673.15}
      } cmp2(1)
      {
        x =            i =-3
            j =-300000

        y =
          {-300000.285657, -300.3, -3.1415926}
      } cmp2(2)
  } cmp3(2)
  {
    yy =
      {
        x =            i =7
            j =700000

        y =
          {700000.275657, 700.7, 7.1415926}
      } cmp2(0)
      {
        x =            i =8
            j =800000

        y =
          {800000.151617, 800.8, 873.15}
      } cmp2(1)
      {
        x =            i =-4
            j =-400000

        y =
          {-400000.285657, -400.4, -4.1415926}
      } cmp2(2)
  } cmp3(3)
}

Here's the H5iosp version:

netcdf /Users/cwardgar/Desktop/comp_complex_more\.h5 {
  dimensions:
    n = 4;
  variables:

    Structure {

      Structure {

        Structure {
          short i;
          int j;
        } x;

        double y(3);
      } yy(3);

    } phony_compound_var(n);


 data:
phony_compound_var =
  {
    yy =
      {
        x =            i =1
            j =100000

        y =
          {100000.285657, 100.1, 1.1415926}
      } yy(0)
      {
        x =            i =16370
            j =222298112

        y =
          {4.216208244882606E202, 7.897725394396646E-278, 4.95748257787734E-220}
      } yy(1)
      {
        x =            i =4710
            j =65535

        y =
          {-1.005413417931744E-221, 1.9035990250237878E185, -1.0209102935083844E-182}
      } yy(2)
  } phony_compound_var(0)
  {
    yy =
      {
        x =            i =3
            j =300000

        y =
          {300000.285657, 300.3, 3.1415926}
      } yy(0)
      {
        x =            i =16393
            j =444596224

        y =
          {4.067657446704244E202, 7.897725394396667E-278, -4.957482577877352E-220}
      } yy(1)
      {
        x =            i =-28058
            j =65534

        y =
          {6.282463199079756E43, 1.90359902534037E185, 1.9380845872298713E63}
      } yy(2)
  } phony_compound_var(1)
  {
    yy =
      {
        x =            i =5
            j =500000

        y =
          {500000.285657, 500.5, 5.1415926}
      } yy(0)
      {
        x =            i =16404
            j =666894336

        y =
          {9.217702764569826E74, -2.7200830941429086E23, 2.3817986479925644E-264}
      } yy(1)
      {
        x =            i =2355
            j =65533

        y =
          {8.48325333365319E-133, -9.255967814244581E61, 1.9380845874631876E63}
      } yy(2)
  } phony_compound_var(2)
  {
    yy =
      {
        x =            i =7
            j =700000

        y =
          {700000.275657, 700.7, 7.1415926}
      } yy(0)
      {
        x =            i =16412
            j =889192448

        y =
          {3.993382047615067E202, 7.897725394396687E-278, 4.281743078120584E44}
      } yy(1)
      {
        x =            i =18739
            j =65532

        y =
          {8.483253333496778E-133, 1.9035990256569527E185, -4.8071669131868766E-123}
      } yy(2)
  } phony_compound_var(3)
}

The metadata match (after I made a change to H5header.makeVariableMember()) but the actual data do not. Strangely, the phony_compound_var(i).yy(0) records match but the others do not. Why? Is it an offset issue? Perhaps endian-ness?

Anyway, I'm shelving this one for now. The HDF5-reading code is extremely complex and I have no idea how long it would take me to figure it out. Would probably need to debug the C and Java libraries side-by-side to find the difference. My work is on the "issue273" branch.