h5gen or any h5dump-generated-XML to HDF5

Astor · February 2, 2012, 10:07pm

Hello, I was trying to download the h5gen software, a tool to
transform XML into HDF5 that is referenced everywhere in the web as
being in http://hdf.ncsa.uiuc.edu/java-hdf5-html/

The browser can't access to the page, I just wanted to know if it still
exists.

If not, does someone knows if there's any way to go back from the xml
output of h5dump to the hdf5 file used to generate it?

Any help would be very appreciated, thank you very much.

Astor

Peter_Cao · February 6, 2012, 7:44pm

Astor,

h5gen was removed a few years ago. It is not available anymore.

We are working on a new version of HDF5 XML schema and
planning to develop tools to handle HDF5 XML (HDF5 to XML
or XML to HDF5).

The first draft of the schema has been sent out to the forum
a few months ago. Other work is still in early stage of planning.

···

On 2/2/2012 4:07 PM, fname lname wrote:

Hello, I was trying to download the h5gen software, a tool to
transform XML into HDF5 that is referenced everywhere in the web as
being in http://hdf.ncsa.uiuc.edu/java-hdf5-html/

The browser can't access to the page, I just wanted to know if it still exists.

If not, does someone knows if there's any way to go back from the xml output of h5dump to the hdf5 file used to generate it?

Any help would be very appreciated, thank you very much.

Astor

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Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

--
Thank you!
--pc

mdehsadn · April 11, 2013, 3:07pm

Could I ask if there has been progress on HDF5/XML?

I am part of a initiative developing data format standards for biochemical
data. We already have an established XML based standard, where data arrays
are stored as Base-64 encoded binary. These files are averaging about 2Gb or
more each now. We want to establish a sister binary format, quite possibly
based on HDF5. It seems that with HDF5/XML, we could simply create an XSLT
transform and that would be it. Otherwise, we would have to describe the
mapping and implement convertors in C or Java.

Kind regards,
Andy

···

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Peter_Cao · April 11, 2013, 4:59pm

Hi Andy,

Our HDF5/XML development is in halt because there is little demand for it.

Could you give us more details on what exact you need for HDF5/XML?

Assume what you have now:
1) XML files based on your XML standard or schema
2) Raw data in binary

Assume below is what you need
1) convert XML structure to HDF5 file structure
2) import the data to HDF5 datasets

Here is what you need:
1) an XSLT to transform your XML file to HDF5 XML files
2) generate HDF5 files from your HDF5 XML files.
#1) should be straightforward.
#2) can be hard. we currently do not have a tool to convert XML to HDF5.

FYI: we are moving to support HDF5/JSON. The work is still in R&D
stage. When HDF5/JSON is available, you can write an XSLT to convert
your XML files to HDF5 JSON.

Thanks
--pc

···

On 4/11/2013 10:07 AM, mdehsadn wrote:

Could I ask if there has been progress on HDF5/XML?

I am part of a initiative developing data format standards for biochemical
data. We already have an established XML based standard, where data arrays
are stored as Base-64 encoded binary. These files are averaging about 2Gb or
more each now. We want to establish a sister binary format, quite possibly
based on HDF5. It seems that with HDF5/XML, we could simply create an XSLT
transform and that would be it. Otherwise, we would have to describe the
mapping and implement convertors in C or Java.

Kind regards,
Andy

--
View this message in context: http://hdf-forum.184993.n3.nabble.com/h5gen-or-any-h5dump-generated-XML-to-HDF5-tp3719793p4026080.html
Sent from the hdf-forum mailing list archive at Nabble.com.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
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hyoklee · April 12, 2013, 4:16am

Here's one hack you guys can try without asking a new tool.

Create NcML file (a variant of XML) and use NetCDF-Java to generate an
NetCDF-3 file [1].
Then convert the NetCDF-3 to NetCDF-4 using NCO [2].

The converted NetCDF-4 file is HDF5 file.
You got the HDF5 from XML (NcML).
Q.E.D.

[1] http://www.unidata.ucar.edu/software/netcdf/ncml/
[2] Usage of NCO to Access HDF Files

···

--
HDF: Software that Powers Science

On Thu, Apr 11, 2013 at 11:59 AM, Peter Cao <xcao@hdfgroup.org> wrote:

Hi Andy,

Our HDF5/XML development is in halt because there is little demand for it.

Could you give us more details on what exact you need for HDF5/XML?

Assume what you have now:
1) XML files based on your XML standard or schema
2) Raw data in binary

Assume below is what you need
1) convert XML structure to HDF5 file structure
2) import the data to HDF5 datasets

Here is what you need:
1) an XSLT to transform your XML file to HDF5 XML files
2) generate HDF5 files from your HDF5 XML files.
#1) should be straightforward.
#2) can be hard. we currently do not have a tool to convert XML to HDF5.

FYI: we are moving to support HDF5/JSON. The work is still in R&D
stage. When HDF5/JSON is available, you can write an XSLT to convert
your XML files to HDF5 JSON.

Thanks
--pc

On 4/11/2013 10:07 AM, mdehsadn wrote:

Could I ask if there has been progress on HDF5/XML?

I am part of a initiative developing data format standards for biochemical
data. We already have an established XML based standard, where data arrays
are stored as Base-64 encoded binary. These files are averaging about 2Gb
or
more each now. We want to establish a sister binary format, quite possibly
based on HDF5. It seems that with HDF5/XML, we could simply create an XSLT
transform and that would be it. Otherwise, we would have to describe the
mapping and implement convertors in C or Java.

Kind regards,
Andy

--
View this message in context:
http://hdf-forum.184993.n3.nabble.com/h5gen-or-any-h5dump-generated-XML-to-HDF5-tp3719793p4026080.html
Sent from the hdf-forum mailing list archive at Nabble.com.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

Astor · February 7, 2012, 10:34am

Thanks for the answer Peter.

Too bad that it's not available, even though I think it's great that the
tools for XML2HDF5 are being developed...

I would really need to use at least the old version, isn't it possible to
have acess to the old executable or sources, just for a proof of concept?

Isn't anyone there who has the executable maybe in an old backup?

Thank you again.

Astor

···

------------------------------

Message: 2
Date: Mon, 06 Feb 2012 13:44:54 -0600
From: Peter Cao <xcao@hdfgroup.org>
To: HDF Users Discussion List <hdf-forum@hdfgroup.org>
Subject: Re: [Hdf-forum] h5gen or any h5dump-generated-XML to HDF5
Message-ID: <4F302DB6.5070602@hdfgroup.org

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