[netCDF #NRW-974703]: invalid HDF5 variable size prevents reading range in Java

Hi Garret,

John Caron wrote:
> final Variable variable = 
> file.findVariable("/Chromosomes/Summary.StartIndex");
> 
> indicates a member variable "StartIndex" of the structure "Summary"
> 
> Garret Wilson wrote:
> > I'm not sure I'm following you. Are you saying that the Variable I am
> > reading is a member of a Structure? (yes/no)

Yes.

> > Are you saying that the API documentation "...this returns only the
> > variable's data in the first Structure, so that the Array shape is the
> > same as the Variable" applies to the Variable I am trying to read? (yes/no)

Yes.

 http://www.unidata.ucar.edu/software/netcdf-java/CDM/
  #+BEGIN_QUOTE
A Structure is a type of Variable that contains other Variables,
analogous to a struct in C, or a row in a relational database. In
general, the data in a Structure are physically stored close
together on disk, so that it is efficient to retrieve all of the
data in a Structure at the same time. A Variable contained in a
Structure is a member Variable, and can only be read in the
context of its containing Structure.

Opening your dataset in the netCDF-Java ToolsUI [1] "NcDump" tab, I get the 
following

netcdf 
20130212_CN021_P3_222k_B02_WD7195FBPAT10231Nat_Nat_Std_CHTNWD_OP3_14.mip222k.oschp
{
  ...
  group: Chromosomes {
    variables:

      Structure {
        byte Chromosome;
            :_Unsigned = "true";
        int Display_&size;
        char Display(4);
        int StartIndex;
            :_Unsigned = "true";
        int MarkerCount;
            :_Unsigned = "true";
        float MinSignal;
        float MaxSignal;
        float MedianCnState;
        float HomFrequency;
        float HetFrequency;
        float Mosaicism;
        float LOH;
        float MedianSignal;
      } Summary(24);
  }
  ...
}

netCDF has two data models:

1) The netCDF-3 data model ("classic") was made up of files, dimensions, 
attributes, and variables where the variables were simple multi-dimensional 
arrays.

2) 
Here is a snippet from the netCDF enhanced data model



Ticket Details
===================
Ticket ID: NRW-974703
Department: Support netCDF Java
Priority: High
Status: Closed