Unable to load attribute info from object header

[gregmacfarlane]

I am using the R API to load a .omx file I exported from Cube with the cube2omx.exe tool. I can see the resulting tables from my matrix files in AMPKHWY16.omx using HDFView for Ubuntu, so I think that step worked, which is why I'm filing this issue here.

But I cannot read these tables into R, using Ubuntu or OSX. For example,

library(rhdf5)
source("omx.r")
listOMX("AMPK16HWY.omx")
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
  #000: H5A.c line 550 in H5Aopen(): unable to load attribute info from object header
    major: Attribute
    minor: Unable to initialize object
  #001: H5Oattribute.c line 530 in H5O_attr_open_by_name(): can't locate attribute
    major: Attribute
    minor: Object not found
HDF5: unable to open attribute
Error: Error in h5checktype(). Argument not of class H5IdComponent.

I filed this here because I can look into the tables with HDFView. On the other hand, I can run through the examples in text_omx.r with no difficulty, so the problem might be in cube2omx.exe or my use of it.

[e-lo]

@gregmacfarlane , can you post your omx file somewhere so that we can fiddle?

[gregmacfarlane]

Here's a link to the omx file. I can also provide the cube matrix if that will be helpful. https://www.dropbox.com/s/o0sud05zqqcd6zo/AMPK16HWY.omx?dl=0

[bstabler]

Hi Greg,

The problem is the assumption that the NA and Description attributes are required…

for( i in 1:length(Names) ) { H5Data <- H5Dopen( H5Group, Names[i] ) H5Attr <- H5Aopen( H5Data, "NA" ) Attr$navalue <- H5Aread( H5Attr ) H5Attr <- H5Aopen( H5Data, "Description" ) Attr$description <- H5Aread( H5Attr ) }

But the specification says these are optional…

https://sites.google.com/site/openmodeldata/draft-omx-spec

I’ll correct the R code now.

Ben Stabler, GISP Senior Supervising Planner, Systems Analysis Parsons Brinckerhoff 400 SW Sixth Avenue, Suite 802 Portland, OR 97204 503-478-2859 (office) 503-360-5798 (cell) stabler@pbworld.commailto:stabler@pbworld.com www.pbworld.comhttp://www.pbworld.com/

From: Greg Macfarlane [mailto:notifications@github.com] Sent: Tuesday, August 26, 2014 5:43 AM To: osPlanning/omx Subject: Re: [omx] Unable to load attribute info from object header (#12)

Here's a link to the omx file. I can also provide the cube matrix if that will be helpful. https://www.dropbox.com/s/o0sud05zqqcd6zo/AMPK16HWY.omx?dl=0

— Reply to this email directly or view it on GitHubhttps://github.com/osPlanning/omx/issues/12#issuecomment-53414266.

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[gregmacfarlane]

Awesome; confirmed that the new commit works.

[billyc]

You guys are amazing.