Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-10 Thread Andreas Tille
Hi Sebastien,

On Tue, Oct 09, 2012 at 11:04:40AM +0200, Sebastien Jodogne wrote:
 
 (1) Should I create a Subversion tag for the upload by myself, or is
 this the responsibility of the uploader of the package?

I think we do not have any written rule for this.  I personally ask the
sponsee to add the tag once the package is *accepted* in unstable.  For
the case it doese not pass ftpmaster I do not see any reason for tagging
because the package has never hit the official mirrors.
 
 (2) I am not sure to understand how I should cope with the unit tests:
 a. Are they to be automatically run as a part of the build process
 (if the CMAKE_CROSSCOMPILING flag is OFF)?
 b. Are they to be distributed along with the Orthanc binaries (e.g.
 under the name /usr/share/orthanc/UnitTests)?
 c. Are they to be simply ignored (as it is the case for now)?

The tests should be run in the packaging process using identical files
that will be inside the package.  If  dh_auto_test  might not trigger
running the test suite you should probably enforce this using

  override_dh_auto_test

 (3) I would like to put my code on Subversion for backporting
 Orthanc to squeeze:
 a. Can I do it now, or should I wait for the sid package to be ready?

We do not have much examples for maintaining backports in SVN (probably
because most (if not all) of our packages build nicely on backports.  If
you need to change something I would consider it a good idea if it is
accessible via SVN.  For this I do see two options:

  1. Either really do the tagging of the upload before the package is
 in unstable while beeing prepared to deal with some rejection from
 ftpmaster - finally it is no real harm if we might remove a tag and
 add a proper one in case of some changes needed at ftpmaster request
  2. or you jast maintain backports in a branch which is fine as well

Feel free to decide which way might fit your workflow best.

 b. If I can work on this right now, how should I call this package
 (orthanc-0.2.2-6~bpo60+1 apparently [1]), and in which directory
 should I put the code in Subversion?

In the case of the second way use

   trunk/packages/orthanc/branches

otherwise you might like to keep working in trunk in case you only need
to change the d/changelog file for this and use proper tagging.

BTW, I personally prefer a versioning 0.2.2-1 for the first upload of a
package (independently what might have previousely existed on
mentors.d.o) but if Matthieu was fine with sponsering, yes the suggested
naming for the bpo package seems to be reasonable.
 
 We are working hard at the CHU of Liège on Orthanc, as it will
 greatly ease our data management for clinical processes.

Good luck with this.

Kind regards

 Andreas.

-- 
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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-10 Thread Mathieu Malaterre
[Filling in the blancs from Andreas email]

On Tue, Oct 9, 2012 at 11:04 AM, Sebastien Jodogne
s.jodo...@chu.ulg.ac.be wrote:
 By doing so, I have noticed that I forgot to submit a local copy of the
 mongoose-3.1.tar.gz third-party dependency yesterday. This means that the
 build of the package of yesterday will fail on the build machines, since a
 HTTP download will try and download mongoose. This has been fixed now, but
 the package should be re-sent. I am sorry for this inconvenience.

I contacted ftpmaster and asked for a removal of the package then. Thanks.

 Please also note that a new version of the upstream package (0.2.3) should
 be ready in less than two weeks. It will incorporate all the patches, will
 include more transparent support of Debian hardening and will be able to use
 the libgtest0-dev system package to build unit tests (as pointed out by
 Mathieu [2]). I think that working on improved hardening and unit testing in
 the current 0.2.2 version would thus be some waste of time.

ok, that's great !

 (1) Should I create a Subversion tag for the upload by myself, or is this
 the responsibility of the uploader of the package?

See Andreas answer.

 (2) I am not sure to understand how I should cope with the unit tests:
 a. Are they to be automatically run as a part of the build process (if the
 CMAKE_CROSSCOMPILING flag is OFF)?

Yes. If you have a Arch: any package. The test will be run as part of
the rebuild on the specific arch. This is a fantastic tool to test
cross-platform exectution.

 b. Are they to be distributed along with the Orthanc binaries (e.g. under
 the name /usr/share/orthanc/UnitTests)?

No. tests are build  run, but not installed.

 c. Are they to be simply ignored (as it is the case for now)?

You could potentially ignore a test on -say- ppc, until the bug is
fixed upstream...

 (3) I would like to put my code on Subversion for backporting Orthanc to
 squeeze:
 a. Can I do it now, or should I wait for the sid package to be ready?
 b. If I can work on this right now, how should I call this package
 (orthanc-0.2.2-6~bpo60+1 apparently [1]), and in which directory should I
 put the code in Subversion?

Can anyone backport something to oldstable from sid ? I do not believe
this is possible. I guess you need to talk to release team about this:
http://www.debian.org/doc/manuals/developers-reference/pkgs.html#upload-stable

 To the best of my knowledge, there is nothing in DICOM standard that is
 stated about such a JSON binding, nor even about a RESTful interface to
 DICOM stores. The closest match seems to be the WADO specification. In the
 absence of such a specification, Orthanc implements a custom HTTP API to
 close the gap.

 Please also note that besides simple access to DICOM objects (WADO is only
 for read access over HTTP), Orthanc will ultimately be able to transfer
 DICOM objects to other modalities (C-Store SCU), to download ZIP files
 containing series, to modify them (e.g. anonymization),... All this by using
 a simple RESTful interface that is usable from most programming languages
 (e.g. Python scripts).

 We are working hard at the CHU of Liège on Orthanc, as it will greatly ease
 our data management for clinical processes.

I do not understand the difference in between XML and JSON, but if
this make your process easier then it is fine with me. What I am
worried about is that DICOM is all about interoperability, while I do
not recall you ever posted your intentions on comp.protocols.dicom.

I have not looked at the implementation details, but how did you avoid
the whole BulkData handling of PS 3.19 with XML representation, simply
by using JSON instead. Does JSON supports arbitrary binary blobs ?

Thanks,
-- 
Mathieu


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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-09 Thread Mathieu Malaterre
Sébastien

On Mon, Oct 8, 2012 at 6:19 PM, Sebastien Jodogne
s.jodo...@chu.ulg.ac.be wrote:
 Well, I wasn't really happy about the following (but I uploaded anyway):

 $ cat d/rules
 ...
 override_dh_auto_install:
 cp $(CURDIR)/Build/Orthanc
 $(CURDIR)/debian/orthanc/usr/bin/orthanc
 gzip -c -9 $(CURDIR)/NEWS 
 $(CURDIR)/debian/orthanc/usr/share/doc/orthanc/changelog.gz

 What were you trying to do ?


 The cp command is used to convert the name of the binary to lowercase. The
 camel case naming in the upstream package is a convention I use for Windows
 builds.

debian only enforce lower case for package name. This is unneeded
IMHO. Some users might even be confused that suddenly debian package
uses orthanc, while Orthanc is used on *NIX boxes...

 The gzip command is used to install the upstream changelog.

 There are certainly better ways of doing so, unfortunately this is my first
 Debian packaging attempt :)

See Andreas comment.


 Also I'll remove -DDEBIAN_HARDENING=ON on the next upload, I just do
 not understand why it was used in the case of an explicit debian
 packaging...


 Indeed, this flag is not required on Debian sid. I have implemented this
 flag to allow backporting to squeeze, whose debhelper version is apparently
 not able to natively cope with hardening.

Technically there is nothing wrong, some duplicate work that is all.
What I fear is rather for advanced user:
http://www.debian.org/doc/debian-policy/ch-source.html#s-debianrules-options
Technically you should be able to control such compilation flags
outside of the cmake build system, eg if the user wants something
different from the default hardening.

 Not running the test suite is not a good idea.


 I have been obliged to do so, since it seems that the libgtest-dev package
 does not come with the required shared library. I could however easily
 modify the CMake files to statically link against gtest (only for the test
 suite of course).


When all else fails, read the instructions:
$ cat /usr/share/doc/libgtest-dev/README.Debian


 Finally, I would not use -DCMAKE_BUILD_TYPE=Debug, maybe something
 like MinSizeRel would be slightly better (-O2)


 I have indeed forgotten to replace Debug with Release.

Release is fine too.

 I will submit the last three modifications tomorrow morning. I will warn you
 when I will have done so.

 I will also try and close the ITP and the RFS bugs tomorrow.

 ...And thank for uploading the package!

Thanks for your contribution to the DICOM community !

As a side note, where is the implementation coming from, is this JSON
binding describe anywhere in the DICOM standard ?

Thanks.
-- 
Mathieu


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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-09 Thread Sebastien Jodogne

Dear Andreas and Mathieu,

I have just committed some modifications we have discussed yesterday.

By doing so, I have noticed that I forgot to submit a local copy of the 
mongoose-3.1.tar.gz third-party dependency yesterday. This means that 
the build of the package of yesterday will fail on the build machines, 
since a HTTP download will try and download mongoose. This has been 
fixed now, but the package should be re-sent. I am sorry for this 
inconvenience.


Please also note that a new version of the upstream package (0.2.3) 
should be ready in less than two weeks. It will incorporate all the 
patches, will include more transparent support of Debian hardening and 
will be able to use the libgtest0-dev system package to build unit 
tests (as pointed out by Mathieu [2]). I think that working on improved 
hardening and unit testing in the current 0.2.2 version would thus be 
some waste of time.


I have some additional questions:

(1) Should I create a Subversion tag for the upload by myself, or is 
this the responsibility of the uploader of the package?


(2) I am not sure to understand how I should cope with the unit tests:
a. Are they to be automatically run as a part of the build process (if 
the CMAKE_CROSSCOMPILING flag is OFF)?
b. Are they to be distributed along with the Orthanc binaries (e.g. 
under the name /usr/share/orthanc/UnitTests)?

c. Are they to be simply ignored (as it is the case for now)?

(3) I would like to put my code on Subversion for backporting Orthanc to 
squeeze:

a. Can I do it now, or should I wait for the sid package to be ready?
b. If I can work on this right now, how should I call this package 
(orthanc-0.2.2-6~bpo60+1 apparently [1]), and in which directory should 
I put the code in Subversion?




As a side note, where is the implementation coming from, is this JSON
binding describe anywhere in the DICOM standard ?


To the best of my knowledge, there is nothing in DICOM standard that is 
stated about such a JSON binding, nor even about a RESTful interface to 
DICOM stores. The closest match seems to be the WADO specification. In 
the absence of such a specification, Orthanc implements a custom HTTP 
API to close the gap.


Please also note that besides simple access to DICOM objects (WADO is 
only for read access over HTTP), Orthanc will ultimately be able to 
transfer DICOM objects to other modalities (C-Store SCU), to download 
ZIP files containing series, to modify them (e.g. anonymization),... All 
this by using a simple RESTful interface that is usable from most 
programming languages (e.g. Python scripts).


We are working hard at the CHU of Liège on Orthanc, as it will greatly 
ease our data management for clinical processes.


Cheers,
Sébastien-


[1] http://wiki.debian.org/BuildingFormalBackports#Modifying_the_package
[2] # cat /usr/share/doc/libgtest-dev/README.Debian


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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-08 Thread Sebastien Jodogne

Hi Andreas,


   Have you thought of maintaining your package within the debian-med
umbrella org ?

http://www.debian.org/devel/debian-med/


Just back from vacation I read your conversation about orthanc
packaging.  Besides the obvious helpful technical hints I would like to
come back to the initial hint from Mathieu to join the Debian Med team.
[...]

To learn about the workflow in Debian Med team you might like to read
our policy document[1].  Feel free to ask if you have some remaining
questions.


Thank for your suggestion! I have successfully applied for membership to 
the Debian-Med project.


It seems that I will not have write access to the Subversion repository 
before tomorrow [1]. As soon as I am able to sync against Subversion, I 
will try and upload the source code of the Orthanc package to Debian-Med.


Regards,
Sébastien-

[1] 
http://wiki.debian.org/Alioth/SSH#A..._and_I.27ve_only_recently_been_added_to_a_project



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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-08 Thread Sebastien Jodogne

Dear all,


   Have you thought of maintaining your package within the debian-med
umbrella org ?

http://www.debian.org/devel/debian-med/


Just back from vacation I read your conversation about orthanc
packaging.  Besides the obvious helpful technical hints I would like to
come back to the initial hint from Mathieu to join the Debian Med team.


I have just uploaded the source code for the Debian packaging of Orthanc 
[1] to the Subversion repository of the Debian Med project [2].


I have not been able to append Orthanc to the imaging task of the 
debian-med Blends repository [3], presumably because of user 
restrictions. Here is a tentative description for Orthanc in Debian Med 
tasks:



Depends: orthanc
Homepage: https://code.google.com/p/orthanc/
WNPP: 689029
Responsible: Sebastien Jodogne s.jodo...@gmail.com
License: GPL
Pkg-Description: RESTful DICOM server for healthcare and medical research
 Orthanc aims at providing a simple, yet powerful standalone DICOM
 server. Orthanc can turn any computer running Windows or Linux into a
 DICOM store (in other words, a mini-PACS system). Its architecture is
 lightweight, meaning that no complex database administration is
 required, nor the installation of third-party dependencies.
 .
 What makes Orthanc unique is the fact that it provides a RESTful
 API. Thanks to this major feature, it is possible to drive Orthanc
 from any computer language. The DICOM tags of the stored medical
 images can be downloaded in the JSON file format. Furthermore,
 standard PNG images can be generated on-the-fly from the DICOM
 instances by Orthanc.
 .
 Orthanc lets its users focus on the content of the DICOM files,
 hiding the complexity of the DICOM format and of the DICOM protocol.


Could someone explain how I could further improve the package? I thank 
you much in advance!


Cheers,
Sébastien-


[1] https://code.google.com/p/orthanc/
[2] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/orthanc/
[3] http://debian-med.alioth.debian.org/tasks/imaging


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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-08 Thread Sebastien Jodogne

Well, I wasn't really happy about the following (but I uploaded anyway):

$ cat d/rules
...
override_dh_auto_install:
cp $(CURDIR)/Build/Orthanc $(CURDIR)/debian/orthanc/usr/bin/orthanc
gzip -c -9 $(CURDIR)/NEWS 
$(CURDIR)/debian/orthanc/usr/share/doc/orthanc/changelog.gz

What were you trying to do ?


The cp command is used to convert the name of the binary to lowercase. 
The camel case naming in the upstream package is a convention I use for 
Windows builds.


The gzip command is used to install the upstream changelog.

There are certainly better ways of doing so, unfortunately this is my 
first Debian packaging attempt :)



Also I'll remove -DDEBIAN_HARDENING=ON on the next upload, I just do
not understand why it was used in the case of an explicit debian
packaging...


Indeed, this flag is not required on Debian sid. I have implemented this 
flag to allow backporting to squeeze, whose debhelper version is 
apparently not able to natively cope with hardening.



Not running the test suite is not a good idea.


I have been obliged to do so, since it seems that the libgtest-dev 
package does not come with the required shared library. I could however 
easily modify the CMake files to statically link against gtest (only for 
the test suite of course).



Finally, I would not use -DCMAKE_BUILD_TYPE=Debug, maybe something
like MinSizeRel would be slightly better (-O2)


I have indeed forgotten to replace Debug with Release.

I will submit the last three modifications tomorrow morning. I will warn 
you when I will have done so.


I will also try and close the ITP and the RFS bugs tomorrow.

...And thank for uploading the package!

Sébastien-


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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-08 Thread Mathieu Malaterre
On Mon, Oct 8, 2012 at 6:19 PM, Sebastien Jodogne
s.jodo...@chu.ulg.ac.be wrote:
 I will also try and close the ITP and the RFS bugs tomorrow.

Please do not touch the ITP. This is part of the upload process, once
the package is uploaded the ITP is automagically closed.

Thanks
-- 
Mathieu


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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-08 Thread Andreas Tille
Hi Sebastien,

On Mon, Oct 08, 2012 at 05:22:31PM +0200, Sebastien Jodogne wrote:
 
 I have just uploaded the source code for the Debian packaging of
 Orthanc [1] to the Subversion repository of the Debian Med project
 [2].

From a (very quick!) view this looks good.  (I hope imaging experts will
keep on helping you - if not please ping me again at end of this week.)
 
 I have not been able to append Orthanc to the imaging task of the
 debian-med Blends repository [3], presumably because of user
 restrictions.

The Debian Med tasks are defined in the Blends project of Alioth where
you need to subscribe as well (or need to become a Debian Developer
;-).)  Because I do not think it makes real sense to subscribe just to
inject this single package I added it for you.

 Here is a tentative description for Orthanc in Debian
 Med tasks:
 
 
 Depends: orthanc
 Homepage: https://code.google.com/p/orthanc/
 WNPP: 689029
 Responsible: Sebastien Jodogne s.jodo...@gmail.com
 License: GPL
 Pkg-Description: RESTful DICOM server for healthcare and medical research
  Orthanc aims at providing a simple, yet powerful standalone DICOM
  server. Orthanc can turn any computer running Windows or Linux into a
  DICOM store (in other words, a mini-PACS system). Its architecture is
  lightweight, meaning that no complex database administration is
  required, nor the installation of third-party dependencies.
  .
  What makes Orthanc unique is the fact that it provides a RESTful
  API. Thanks to this major feature, it is possible to drive Orthanc
  from any computer language. The DICOM tags of the stored medical
  images can be downloaded in the JSON file format. Furthermore,
  standard PNG images can be generated on-the-fly from the DICOM
  instances by Orthanc.
  .
  Orthanc lets its users focus on the content of the DICOM files,
  hiding the complexity of the DICOM format and of the DICOM protocol.
 

Thanks for this nice preparation!  The good news is that everything
except the first line (Depends) is obtained automagically if a package
is in VCS ... modulo some delay where some cron job needs to fetch the
information.  So if everything will went fine tomorrow evening the
package should be updated.  Feel free to check this and ping me if
this is not the case.
 
 Could someone explain how I could further improve the package? I
 thank you much in advance!

I'm slowly working down some past vacation backlog.  As I said above
please ping me in case you might need further help.

Many thanks for your interest in Debian Med and the preparation of the
package 

Andreas.

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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-08 Thread Andreas Tille
On Mon, Oct 08, 2012 at 06:19:20PM +0200, Sebastien Jodogne wrote:
 override_dh_auto_install:
  cp $(CURDIR)/Build/Orthanc $(CURDIR)/debian/orthanc/usr/bin/orthanc
  gzip -c -9 $(CURDIR)/NEWS 
 $(CURDIR)/debian/orthanc/usr/share/doc/orthanc/changelog.gz
 
 What were you trying to do ?
 
 The cp command is used to convert the name of the binary to
 lowercase. The camel case naming in the upstream package is a
 convention I use for Windows builds.

OK.
 
 The gzip command is used to install the upstream changelog.

This should rather be done using

   override_dh_installchangelogs
 
 There are certainly better ways of doing so, unfortunately this is
 my first Debian packaging attempt :)

That's perfectly fine - its our pleasure to teach you to finally enhance
our team.
 
 Also I'll remove -DDEBIAN_HARDENING=ON on the next upload, I just do
 not understand why it was used in the case of an explicit debian
 packaging...
 
 Indeed, this flag is not required on Debian sid. I have implemented
 this flag to allow backporting to squeeze, whose debhelper version
 is apparently not able to natively cope with hardening.

That's OK in principle - if I'm not totally missleaded it does not harm
in sid and if it is helpful for backporting (I'm not really sure if this
is actually the case) it might remain.
 
 Not running the test suite is not a good idea.
 
 I have been obliged to do so, since it seems that the libgtest-dev
 package does not come with the required shared library.

Filing a bug report against libgtest-dev?

 I could
 however easily modify the CMake files to statically link against
 gtest (only for the test suite of course).

This might help to successfully run the test suite however, what you
would test in this case is not what finally will end up inside the
package so the point of running the test suite is not fullfilled.

 Finally, I would not use -DCMAKE_BUILD_TYPE=Debug, maybe something
 like MinSizeRel would be slightly better (-O2)
 
 I have indeed forgotten to replace Debug with Release.
 
 I will submit the last three modifications tomorrow morning. I will
 warn you when I will have done so.
 
 I will also try and close the ITP and the RFS bugs tomorrow.

As Matthieu said this is not needed.
 
Kind regards

   Andreas. 

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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-10-06 Thread Andreas Tille
Hi Sébastien,

On Sun, Sep 30, 2012 at 06:29:33PM +0200, Mathieu Malaterre wrote:
 Salut Sébastien,
 
   Have you thought of maintaining your package within the debian-med
 umbrella org ?
 
 http://www.debian.org/devel/debian-med/

Just back from vacation I read your conversation about orthanc
packaging.  Besides the obvious helpful technical hints I would like to
come back to the initial hint from Mathieu to join the Debian Med team.
You would profit from several advantages - for instance you could bypass
the uploads to mentors and commit your packaging to a VCS (either Git or
SVN at your choice) where potential sponsors of the team could drop
changes with helpful comments directly which might make the process
much more smooth.

To learn about the workflow in Debian Med team you might like to read
our policy document[1].  Feel free to ask if you have some remaining
questions.

Kind regards

  Andreas.

[1] debian-med.alioth.debian.org/docs/policy.html

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Re: Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research

2012-09-30 Thread Mathieu Malaterre
Salut Sébastien,

  Have you thought of maintaining your package within the debian-med
umbrella org ?

http://www.debian.org/devel/debian-med/

On Fri, Sep 28, 2012 at 5:54 PM, Sébastien Jodogne s.jodo...@gmail.com wrote:
 Package: sponsorship-requests
 Severity: wishlist


 Dear mentors,

 I am looking for a sponsor for my package orthanc:

  * Package name: orthanc
Version : 0.2.1-3
Upstream Author : Sebastien Jodogne s.jodo...@gmail.com
  * URL : https://code.google.com/p/orthanc/
  * License : GPL

 It builds those binary packages:

   orthanc - A lightweight, RESTful DICOM server for healthcare and
 medical research

 To access further information about this package, please visit the
 following URL:
 http://mentors.debian.net/package/orthanc

 Alternatively, one can download the package with dget using this command:
 dget -x 
 http://mentors.debian.net/debian/pool/main/o/orthanc/orthanc_0.2.1-3.dsc

 More information about orthanc can be obtained from:
 https://code.google.com/p/orthanc/.

 Regards,
 S. Jodogne-


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