Discussion:
[BlueObelisk-discuss] Current status of JCAMP parsers
Peter Murray-Rust
2012-01-08 11:05:53 UTC
Permalink
Does anyone know what the current state of the Open Source JCAMP parsing
library at http://sourceforge.net/projects/jcamp-dx is?

We are running a workshop next week in which we are creating semantic
spectral resources and some of the current JDX files fail against the
library. Is anyone coordinating bugfixes?


--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Egon Willighagen
2012-01-08 11:12:04 UTC
Permalink
On Sun, Jan 8, 2012 at 12:05 PM, Peter Murray-Rust <***@cam.ac.uk> wrote:
> Does anyone know what the current state of the Open Source JCAMP parsing
> library at http://sourceforge.net/projects/jcamp-dx is?

Peter, since you are one of the three project leaders of that project,
I guess the most likely answer is that there is nothing happening
(given your Q)... Or, are you wondering if people have forked the
library?

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
Peter Murray-Rust
2012-01-08 11:26:07 UTC
Permalink
On Sun, Jan 8, 2012 at 11:12 AM, Egon Willighagen <
***@gmail.com> wrote:

> On Sun, Jan 8, 2012 at 12:05 PM, Peter Murray-Rust <***@cam.ac.uk>
> wrote:
> > Does anyone know what the current state of the Open Source JCAMP parsing
> > library at http://sourceforge.net/projects/jcamp-dx is?
>
> Peter, since you are one of the three project leaders of that project,
> I guess the most likely answer is that there is nothing happening
> (given your Q)... Or, are you wondering if people have forked the
> library?
>

I fear you are right. I also assume there is no other activity elsewhere on
this library. My recollection is:
* original library from CREON donated to F/OSS but no longer maintained by
them
* additions from our group for uploading spectra
* ANTLR parser added by ?Thomas Weber?

Since spectroscopy is not my current thing I haven't looked at things for
some years.

P.


>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>



--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Antony Williams
2012-01-08 16:21:48 UTC
Permalink
My recollection is that CreonLabcontrol was purchased by Waters so it would be Waters that would need to provide any update probably. Confirmed by Wikipedia: http://limswiki.org/index.php/Creon_Lab_Control_AG (which I didn't expect!)

Waters have definitely continued to work on spectral display since the acquisition. Cheers

Antony Williams PhD, FRSC
VP Strategic Development
ChemSpider, Royal Society of Chemistry
Learn About.Me<http://about.me/ChemConnector>
Phone: +1 (919) 201-1516
Email: ***@rsc.org<mailto:***@rsc.org>
Twitter: http://twitter.com/ChemConnector
________________________________
From: Peter Murray-Rust [***@cam.ac.uk]
Sent: Sunday, January 08, 2012 6:26 AM
To: Egon Willighagen
Cc: BlueObelisk-Discuss; semantic-physical-***@googlegroups.com
Subject: Re: [BlueObelisk-discuss] Current status of JCAMP parsers



On Sun, Jan 8, 2012 at 11:12 AM, Egon Willighagen <***@gmail.com<mailto:***@gmail.com>> wrote:
On Sun, Jan 8, 2012 at 12:05 PM, Peter Murray-Rust <***@cam.ac.uk<mailto:***@cam.ac.uk>> wrote:
> Does anyone know what the current state of the Open Source JCAMP parsing
> library at http://sourceforge.net/projects/jcamp-dx is?

Peter, since you are one of the three project leaders of that project,
I guess the most likely answer is that there is nothing happening
(given your Q)... Or, are you wondering if people have forked the
library?

I fear you are right. I also assume there is no other activity elsewhere on this library. My recollection is:
* original library from CREON donated to F/OSS but no longer maintained by them
* additions from our group for uploading spectra
* ANTLR parser added by ?Thomas Weber?

Since spectroscopy is not my current thing I haven't looked at things for some years.

P.


Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers



--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

DISCLAIMER:

This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening. The Royal Society of Chemistry is a charity, registered in England and Wales, number 207890 - Registered office: Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF
Peter Murray-Rust
2012-01-08 17:19:08 UTC
Permalink
Thanks Tony,
My recollection (about 2005) was that Creon donated the JCAMP library
software as Open Source but indicated that they wouldn't be supporting it.
I have now written code to ingest, if not understand, Bruker JCAMP.

On Sun, Jan 8, 2012 at 4:21 PM, Antony Williams <***@rsc.org> wrote:

> My recollection is that CreonLabcontrol was purchased by Waters so it
> would be Waters that would need to provide any update probably. Confirmed
> by Wikipedia: http://limswiki.org/index.php/Creon_Lab_Control_AG (which I
> didn't expect!)
>
> Waters have definitely continued to work on spectral display since the
> acquisition. Cheers
>
> Antony Williams PhD, FRSC
> VP Strategic Development
> ChemSpider, Royal Society of Chemistry
> Learn About.Me<http://about.me/ChemConnector>
> Phone: +1 (919) 201-1516
> Email: ***@rsc.org<mailto:***@rsc.org>
> Twitter: http://twitter.com/ChemConnector
> ________________________________
>


--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Antony Williams
2012-01-09 03:42:54 UTC
Permalink
Not sure whether this is of any value but Bob Lancashire's JSPecView applet has JCAMP reading built in and is Open Source. Might be of value to look into that code?

Antony Williams PhD, FRSC
VP Strategic Development
ChemSpider, Royal Society of Chemistry
Learn About.Me<http://about.me/ChemConnector>
Phone: +1 (919) 201-1516
Email: ***@rsc.org<mailto:***@rsc.org>
Twitter: http://twitter.com/ChemConnector
________________________________
From: ***@googlemail.com [***@googlemail.com] On Behalf Of Peter Murray-Rust [***@cam.ac.uk]
Sent: Sunday, January 08, 2012 12:19 PM
To: Antony Williams
Cc: Egon Willighagen; BlueObelisk-Discuss; semantic-physical-***@googlegroups.com
Subject: Re: [BlueObelisk-discuss] Current status of JCAMP parsers

Thanks Tony,
My recollection (about 2005) was that Creon donated the JCAMP library software as Open Source but indicated that they wouldn't be supporting it. I have now written code to ingest, if not understand, Bruker JCAMP.

On Sun, Jan 8, 2012 at 4:21 PM, Antony Williams <***@rsc.org<mailto:***@rsc.org>> wrote:
My recollection is that CreonLabcontrol was purchased by Waters so it would be Waters that would need to provide any update probably. Confirmed by Wikipedia: http://limswiki.org/index.php/Creon_Lab_Control_AG (which I didn't expect!)

Waters have definitely continued to work on spectral display since the acquisition. Cheers

Antony Williams PhD, FRSC
VP Strategic Development
ChemSpider, Royal Society of Chemistry
Learn About.Me<http://about.me/ChemConnector>
Phone: +1 (919) 201-1516<tel:%2B1%20%28919%29%20201-1516>
Email: ***@rsc.org<mailto:***@rsc.org><mailto:***@rsc.org<mailto:***@rsc.org>>
Twitter: http://twitter.com/ChemConnector
________________________________


--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069

DISCLAIMER:

This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening. The Royal Society of Chemistry is a charity, registered in England and Wales, number 207890 - Registered office: Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF
Peter Murray-Rust
2012-01-09 08:21:06 UTC
Permalink
On Mon, Jan 9, 2012 at 3:42 AM, Antony Williams <***@rsc.org> wrote:

> Not sure whether this is of any value but Bob Lancashire's JSPecView
> applet has JCAMP reading built in and is Open Source. Might be of value to
> look into that code?
>

Thanks,
Indeed and JSpecview has its own CML convention.

I have now got a system that reads Bruker JCAMP files - I think the problem
was a new features that confused the parser. That will also work for the
"Topspin" format (except for the binary (real, imag) components of the
spectrum. I think the format of these is known/tractable


>
> Antony Williams PhD, FRSC
> VP Strategic Development
> ChemSpider, Royal Society of Chemistry
> Learn About.Me<http://about.me/ChemConnector>
> Phone: +1 (919) 201-1516
> Email: ***@rsc.org<mailto:***@rsc.org>
> Twitter: http://twitter.com/ChemConnector
> ________________________________
> From: ***@googlemail.com [***@googlemail.com]
> On Behalf Of Peter Murray-Rust [***@cam.ac.uk]
> Sent: Sunday, January 08, 2012 12:19 PM
> To: Antony Williams
> Cc: Egon Willighagen; BlueObelisk-Discuss;
> semantic-physical-***@googlegroups.com
> Subject: Re: [BlueObelisk-discuss] Current status of JCAMP parsers
>
> Thanks Tony,
> My recollection (about 2005) was that Creon donated the JCAMP library
> software as Open Source but indicated that they wouldn't be supporting it.
> I have now written code to ingest, if not understand, Bruker JCAMP.
>
> On Sun, Jan 8, 2012 at 4:21 PM, Antony Williams <***@rsc.org<mailto:
> ***@rsc.org>> wrote:
> My recollection is that CreonLabcontrol was purchased by Waters so it
> would be Waters that would need to provide any update probably. Confirmed
> by Wikipedia: http://limswiki.org/index.php/Creon_Lab_Control_AG (which I
> didn't expect!)
>
> Waters have definitely continued to work on spectral display since the
> acquisition. Cheers
>
> Antony Williams PhD, FRSC
> VP Strategic Development
> ChemSpider, Royal Society of Chemistry
> Learn About.Me<http://about.me/ChemConnector>
> Phone: +1 (919) 201-1516<tel:%2B1%20%28919%29%20201-1516>
> Email: ***@rsc.org<mailto:***@rsc.org><mailto:
> ***@rsc.org<mailto:***@rsc.org>>
> Twitter: http://twitter.com/ChemConnector
> ________________________________
>
>
> --
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069
>
> DISCLAIMER:
>
> This communication (including any attachments) is intended for the use of
> the addressee only and may contain confidential, privileged or copyright
> material. It may not be relied upon or disclosed to any other person
> without the consent of the RSC. If you have received it in error, please
> contact us immediately. Any advice given by the RSC has been carefully
> formulated but is necessarily based on the information available, and the
> RSC cannot be held responsible for accuracy or completeness. In this
> respect, the RSC owes no duty of care and shall not be liable for any
> resulting damage or loss. The RSC acknowledges that a disclaimer cannot
> restrict liability at law for personal injury or death arising through a
> finding of negligence. The RSC does not warrant that its emails or
> attachments are Virus-free: Please rely on your own screening. The Royal
> Society of Chemistry is a charity, registered in England and Wales, number
> 207890 - Registered office: Thomas Graham House, Science Park, Milton Road,
> Cambridge CB4 0WF
>



--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Stefan Kuhn
2012-02-15 23:49:05 UTC
Permalink
Hi Peter,
I might be able to shed some light on this. The parser was donated since we
(Steinbeck group) explicitly asked for it. It was considered to be complete
then and over time, steady maintenance had been done I think mainly by me (as
you can see from cvs history). I think it was one of the most succesfull
projects in term of effort/return ratio. There were even patches provided by
the general public, which is pretty good for academic open source, I think.
Then some people believed they can do better and forced themselves onto the
project. The succes is that a patch a submitted a couple of month ago is
still unapplied, obviously because nobody even bothers. And judging from your
question even the status is unclear. Ah, what a great community...
A technical comment: You said something about handling bruker files. Not sure
if this is a standard thing or an extension, but note the library was once
the jcamp-dx reference implementation. I am not sure about the official
status now, but I think it's worth keeping that. In order to do this, I
introduced a strict and relaxed mode, which might be good for the bruker
parts as well.
Have fun
Stefan

On Sunday 08 January 2012 11:05:53 Peter Murray-Rust wrote:
> Does anyone know what the current state of the Open Source JCAMP parsing
> library at http://sourceforge.net/projects/jcamp-dx is?
>
> We are running a workshop next week in which we are creating semantic
> spectral resources and some of the current JDX files fail against the
> library. Is anyone coordinating bugfixes?
Peter Murray-Rust
2012-02-15 23:09:25 UTC
Permalink
On Wed, Feb 15, 2012 at 11:49 PM, Stefan Kuhn <***@web.de> wrote:

> Hi Peter,
> I might be able to shed some light on this. The parser was donated since we
> (Steinbeck group) explicitly asked for it. It was considered to be complete
> then and over time, steady maintenance had been done I think mainly by me
> (as
> you can see from cvs history). I think it was one of the most succesfull
> projects in term of effort/return ratio. There were even patches provided
> by
> the general public, which is pretty good for academic open source, I think.
>

Where is the site, please?


> Then some people believed they can do better and forced themselves onto the
> project. The succes is that a patch a submitted a couple of month ago is
> still unapplied, obviously because nobody even bothers. And judging from
> your
> question even the status is unclear. Ah, what a great community...
> A technical comment: You said something about handling bruker files. Not
> sure
> if this is a standard thing or an extension, but note the library was once
> the jcamp-dx reference implementation. I am not sure about the official
> status now, but I think it's worth keeping that. In order to do this, I
> introduced a strict and relaxed mode, which might be good for the bruker
> parts as well.
>

Bruker have a JCAMP file with their vocabularly extensions and packaging
their non-JCAMP files.


> Have fun
> Stefan
>

--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
Stefan Kuhn
2012-02-16 19:32:02 UTC
Permalink
> Where is the site, please?
Not exactly sure what you mean, but the project site is at
http://sourceforge.net/projects/jcamp-dx/, including CVS and patch tracker.
Stefan
Norm Reitzel
2012-02-15 23:01:43 UTC
Permalink
On Wed, 15 Feb 2012 23:49:05 +0000
Stefan Kuhn <***@web.de> wrote:

> Hi Peter,
> I might be able to shed some light on this. The parser was donated since we
> (Steinbeck group) explicitly asked for it. It was considered to be complete
> then and over time, steady maintenance had been done I think mainly by me (as
> you can see from cvs history). I think it was one of the most succesfull
> projects in term of effort/return ratio. There were even patches provided by
> the general public, which is pretty good for academic open source, I think.
> Then some people believed they can do better and forced themselves onto the
> project. The succes is that a patch a submitted a couple of month ago is
> still unapplied, obviously because nobody even bothers. And judging from your
> question even the status is unclear. Ah, what a great community...
> A technical comment: You said something about handling bruker files. Not sure
> if this is a standard thing or an extension, but note the library was once
> the jcamp-dx reference implementation. I am not sure about the official
> status now, but I think it's worth keeping that. In order to do this, I
> introduced a strict and relaxed mode, which might be good for the bruker
> parts as well.

Fwiw, the Bruker files have never been the problem, Vartian cum Agilent files are the problem.

-- Norm Reitzel (Univ Texas)

> Have fun
> Stefan
>
> On Sunday 08 January 2012 11:05:53 Peter Murray-Rust wrote:
> > Does anyone know what the current state of the Open Source JCAMP parsing
> > library at http://sourceforge.net/projects/jcamp-dx is?
> >
> > We are running a workshop next week in which we are creating semantic
> > spectral resources and some of the current JDX files fail against the
> > library. Is anyone coordinating bugfixes?
>
>
>
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