Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Michael Dondrup
Hi Lincoln and all,

I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
experimental and the code is just an ugly hack atm.

Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
these are non-disruptive for other applications, I simply don't understand gbrowse well enough.

The code is in this gbrowse-fork:

https://github.com/mdondrup/GBrowse

There is some perldoc in conf/plugins/SAMLAutheticator

I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
do it more smoothly. In particular, I have the following questions:

- how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
- What does a private session mean?

 - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
stays logged in. I am looking for a solution (the other way around works).
One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.
   
I hope you find my attempt useful and I am looking forward to your criticism.

Best
Michael



Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:

> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>
>  TestAuthenticator.pm
>  LDAPAuthenticate.pm
>  PamAuthenticate.pm
>
> Lincoln
>
>
> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
> Hi,
>
> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
> federated authentication. That worked quite nicely, such that I now am looking
> for a similar solution for Gbrowse that would allow for single sign on to both
> Tripal and Gbrowse.
>
> Has anybody done or attempted this before and is
> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
> but maybe there is a more more integrated solution already.
>
> Thank you
> Michael
>
>
>
>
> [1] http://simplesamlphp.org/
> [2] http://zxid.org/
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>


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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Lincoln Stein
Hi Michael,

Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?

Lincoln


On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
Hi Lincoln and all,

I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
experimental and the code is just an ugly hack atm.

Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
these are non-disruptive for other applications, I simply don't understand gbrowse well enough.

The code is in this gbrowse-fork:

https://github.com/mdondrup/GBrowse

There is some perldoc in conf/plugins/SAMLAutheticator

I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
do it more smoothly. In particular, I have the following questions:

- how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
- What does a private session mean?

 - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
stays logged in. I am looking for a solution (the other way around works).
One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.

I hope you find my attempt useful and I am looking forward to your criticism.

Best
Michael



Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:

> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>
>  TestAuthenticator.pm
>  LDAPAuthenticate.pm
>  PamAuthenticate.pm
>
> Lincoln
>
>
> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
> Hi,
>
> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
> federated authentication. That worked quite nicely, such that I now am looking
> for a similar solution for Gbrowse that would allow for single sign on to both
> Tripal and Gbrowse.
>
> Has anybody done or attempted this before and is
> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
> but maybe there is a more more integrated solution already.
>
> Thank you
> Michael
>
>
>
>
> [1] http://simplesamlphp.org/
> [2] http://zxid.org/
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> <a href="tel:416%20673-8514" value="+14166738514">416 673-8514
> Assistant: Renata Musa <[hidden email]>




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
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Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Michael Dondrup
Hi,
I can recommend simpleSAMLphp as idp. This is about everything you need in addition to net::saml and gbrowse and php to run the IdP. I can make a little guide and attach my config files, for setting up the IDP if you want.
Michael



On 6. feb. 2013, at 17:55, Lincoln Stein <[hidden email]> wrote:

Hi Michael,

Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?

Lincoln


On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
Hi Lincoln and all,

I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
experimental and the code is just an ugly hack atm.

Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
these are non-disruptive for other applications, I simply don't understand gbrowse well enough.

The code is in this gbrowse-fork:

https://github.com/mdondrup/GBrowse

There is some perldoc in conf/plugins/SAMLAutheticator

I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
do it more smoothly. In particular, I have the following questions:

- how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
- What does a private session mean?

 - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
stays logged in. I am looking for a solution (the other way around works).
One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.

I hope you find my attempt useful and I am looking forward to your criticism.

Best
Michael



Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:

> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>
>  TestAuthenticator.pm
>  LDAPAuthenticate.pm
>  PamAuthenticate.pm
>
> Lincoln
>
>
> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
> Hi,
>
> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
> federated authentication. That worked quite nicely, such that I now am looking
> for a similar solution for Gbrowse that would allow for single sign on to both
> Tripal and Gbrowse.
>
> Has anybody done or attempted this before and is
> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
> but maybe there is a more more integrated solution already.
>
> Thank you
> Michael
>
>
>
>
> [1] http://simplesamlphp.org/
> [2] http://zxid.org/
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> <a href="tel:416%20673-8514" value="+14166738514">416 673-8514
> Assistant: Renata Musa <[hidden email]>




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Lincoln Stein
Thanks, that would be great.

Lincoln


On Wed, Feb 6, 2013 at 10:30 AM, Michael Dondrup <[hidden email]> wrote:
Hi,
I can recommend simpleSAMLphp as idp. This is about everything you need in addition to net::saml and gbrowse and php to run the IdP. I can make a little guide and attach my config files, for setting up the IDP if you want.
Michael



On 6. feb. 2013, at 17:55, Lincoln Stein <[hidden email]> wrote:

Hi Michael,

Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?

Lincoln


On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
Hi Lincoln and all,

I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
experimental and the code is just an ugly hack atm.

Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
these are non-disruptive for other applications, I simply don't understand gbrowse well enough.

The code is in this gbrowse-fork:

https://github.com/mdondrup/GBrowse

There is some perldoc in conf/plugins/SAMLAutheticator

I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
do it more smoothly. In particular, I have the following questions:

- how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
- What does a private session mean?

 - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
stays logged in. I am looking for a solution (the other way around works).
One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.

I hope you find my attempt useful and I am looking forward to your criticism.

Best
Michael



Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:

> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>
>  TestAuthenticator.pm
>  LDAPAuthenticate.pm
>  PamAuthenticate.pm
>
> Lincoln
>
>
> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
> Hi,
>
> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
> federated authentication. That worked quite nicely, such that I now am looking
> for a similar solution for Gbrowse that would allow for single sign on to both
> Tripal and Gbrowse.
>
> Has anybody done or attempted this before and is
> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
> but maybe there is a more more integrated solution already.
>
> Thank you
> Michael
>
>
>
>
> [1] http://simplesamlphp.org/
> [2] http://zxid.org/
> ------------------------------------------------------------------------------
> Monitor your physical, virtual and cloud infrastructure from a single
> web console. Get in-depth insight into apps, servers, databases, vmware,
> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
> Pricing starts from $795 for 25 servers or applications!
> http://p.sf.net/sfu/zoho_dev2dev_nov
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> <a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
> Assistant: Renata Musa <[hidden email]>




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Free Next-Gen Firewall Hardware Offer
Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Michael Dondrup
Hi,
I made a wiki page with some documentation. (Noticed that it is a quite lengthy process).

https://github.com/mdondrup/GBrowse/wiki/Single-Sign-On-for-GBrowse-and-Tripal

Please contact me if anything is unclear.

Best
Michael

On Feb 6, 2013, at 7:39 PM, Lincoln Stein wrote:

> Thanks, that would be great.
>
> Lincoln
>
>
> On Wed, Feb 6, 2013 at 10:30 AM, Michael Dondrup <[hidden email]> wrote:
> Hi,
> I can recommend simpleSAMLphp as idp. This is about everything you need in addition to net::saml and gbrowse and php to run the IdP. I can make a little guide and attach my config files, for setting up the IDP if you want.
> Michael
>
>
>
> On 6. feb. 2013, at 17:55, Lincoln Stein <[hidden email]> wrote:
>
>> Hi Michael,
>>
>> Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?
>>
>> Lincoln
>>
>>
>> On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
>> Hi Lincoln and all,
>>
>> I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
>> This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
>> using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
>> experimental and the code is just an ugly hack atm.
>>
>> Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
>> plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
>> these are non-disruptive for other applications, I simply don't understand gbrowse well enough.
>>
>> The code is in this gbrowse-fork:
>>
>> https://github.com/mdondrup/GBrowse
>>
>> There is some perldoc in conf/plugins/SAMLAutheticator
>>
>> I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
>> do it more smoothly. In particular, I have the following questions:
>>
>> - how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
>> - What does a private session mean?
>>
>>  - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
>> stays logged in. I am looking for a solution (the other way around works).
>> One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
>> insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.
>>
>> I hope you find my attempt useful and I am looking forward to your criticism.
>>
>> Best
>> Michael
>>
>>
>>
>> Michael Dondrup
>> Postdoctoral fellow
>> Sea Lice Research Centre/Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>> On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:
>>
>> > That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>> >
>> >  TestAuthenticator.pm
>> >  LDAPAuthenticate.pm
>> >  PamAuthenticate.pm
>> >
>> > Lincoln
>> >
>> >
>> > On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
>> > Hi,
>> >
>> > I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
>> > federated authentication. That worked quite nicely, such that I now am looking
>> > for a similar solution for Gbrowse that would allow for single sign on to both
>> > Tripal and Gbrowse.
>> >
>> > Has anybody done or attempted this before and is
>> > willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
>> > but maybe there is a more more integrated solution already.
>> >
>> > Thank you
>> > Michael
>> >
>> >
>> >
>> >
>> > [1] http://simplesamlphp.org/
>> > [2] http://zxid.org/
>> > ------------------------------------------------------------------------------
>> > Monitor your physical, virtual and cloud infrastructure from a single
>> > web console. Get in-depth insight into apps, servers, databases, vmware,
>> > SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>> > Pricing starts from $795 for 25 servers or applications!
>> > http://p.sf.net/sfu/zoho_dev2dev_nov
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> >
>> >
>> > --
>> > Lincoln D. Stein
>> > Director, Informatics and Biocomputing Platform
>> > Ontario Institute for Cancer Research
>> > 101 College St., Suite 800
>> > Toronto, ON, Canada M5G0A3
>> > 416 673-8514
>> > Assistant: Renata Musa <[hidden email]>
>>
>>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>


------------------------------------------------------------------------------
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Buy your Sophos next-gen firewall before the end March 2013
and get the hardware for free! Learn more.
http://p.sf.net/sfu/sophos-d2d-feb
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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Stephen Ficklin-2
HI Michael,

This is great.  I'd like to make a link to your documentation on the
Tripal site under our own Documentation section
(http://tripal.info/documentation) if you don't mind.  Although I don't
see the steps required for integrating Simple SAML with Drupal in your
writeup.  I assume it's just a module you install with some
configuration?   I think this is also useful for folks who have more
than one Tripal site who would like single sign-on across all of them.

Thanks!
Stephen

On 2/8/2013 6:30 AM, Michael Dondrup wrote:

> Hi,
> I made a wiki page with some documentation. (Noticed that it is a quite lengthy process).
>
> https://github.com/mdondrup/GBrowse/wiki/Single-Sign-On-for-GBrowse-and-Tripal
>
> Please contact me if anything is unclear.
>
> Best
> Michael
>
> On Feb 6, 2013, at 7:39 PM, Lincoln Stein wrote:
>
>> Thanks, that would be great.
>>
>> Lincoln
>>
>>
>> On Wed, Feb 6, 2013 at 10:30 AM, Michael Dondrup <[hidden email]> wrote:
>> Hi,
>> I can recommend simpleSAMLphp as idp. This is about everything you need in addition to net::saml and gbrowse and php to run the IdP. I can make a little guide and attach my config files, for setting up the IDP if you want.
>> Michael
>>
>>
>>
>> On 6. feb. 2013, at 17:55, Lincoln Stein <[hidden email]> wrote:
>>
>>> Hi Michael,
>>>
>>> Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?
>>>
>>> Lincoln
>>>
>>>
>>> On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
>>> Hi Lincoln and all,
>>>
>>> I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
>>> This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
>>> using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
>>> experimental and the code is just an ugly hack atm.
>>>
>>> Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
>>> plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
>>> these are non-disruptive for other applications, I simply don't understand gbrowse well enough.
>>>
>>> The code is in this gbrowse-fork:
>>>
>>> https://github.com/mdondrup/GBrowse
>>>
>>> There is some perldoc in conf/plugins/SAMLAutheticator
>>>
>>> I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
>>> do it more smoothly. In particular, I have the following questions:
>>>
>>> - how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
>>> - What does a private session mean?
>>>
>>>   - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
>>> stays logged in. I am looking for a solution (the other way around works).
>>> One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
>>> insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.
>>>
>>> I hope you find my attempt useful and I am looking forward to your criticism.
>>>
>>> Best
>>> Michael
>>>
>>>
>>>
>>> Michael Dondrup
>>> Postdoctoral fellow
>>> Sea Lice Research Centre/Department of Informatics
>>> University of Bergen
>>> Thormøhlensgate 55, N-5008 Bergen,
>>> Norway
>>>
>>> On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:
>>>
>>>> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>>>>
>>>>   TestAuthenticator.pm
>>>>   LDAPAuthenticate.pm
>>>>   PamAuthenticate.pm
>>>>
>>>> Lincoln
>>>>
>>>>
>>>> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
>>>> Hi,
>>>>
>>>> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
>>>> federated authentication. That worked quite nicely, such that I now am looking
>>>> for a similar solution for Gbrowse that would allow for single sign on to both
>>>> Tripal and Gbrowse.
>>>>
>>>> Has anybody done or attempted this before and is
>>>> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
>>>> but maybe there is a more more integrated solution already.
>>>>
>>>> Thank you
>>>> Michael
>>>>
>>>>
>>>>
>>>>
>>>> [1] http://simplesamlphp.org/
>>>> [2] http://zxid.org/
>>>> ------------------------------------------------------------------------------
>>>> Monitor your physical, virtual and cloud infrastructure from a single
>>>> web console. Get in-depth insight into apps, servers, databases, vmware,
>>>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>>>> Pricing starts from $795 for 25 servers or applications!
>>>> http://p.sf.net/sfu/zoho_dev2dev_nov
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]>
>>>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]>
>>
>>
>> --
>> Lincoln D. Stein
>> Director, Informatics and Biocomputing Platform
>> Ontario Institute for Cancer Research
>> 101 College St., Suite 800
>> Toronto, ON, Canada M5G0A3
>> 416 673-8514
>> Assistant: Renata Musa <[hidden email]>
>
> ------------------------------------------------------------------------------
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> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
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> Gmod-tripal-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Michael Dondrup
Hi Stephen,

please go ahead. I was planning to write the Drupal integration up next week. I am using the module http://drupal.org/project/simplesamlphp_auth
which integrates simpleSAMLphp nicely and makes Drupal an SP.  One can have a mix of SAML accounts and local accounts (always recommended for the
administrator). Just a word of warning, the guide is not suitable for production use (yet), because I have omitted  everything, that makes this setup secure.

Best
Michael


On Feb 8, 2013, at 2:40 PM, Stephen Ficklin wrote:

> HI Michael,
>
> This is great.  I'd like to make a link to your documentation on the Tripal site under our own Documentation section (http://tripal.info/documentation) if you don't mind.  Although I don't see the steps required for integrating Simple SAML with Drupal in your writeup.  I assume it's just a module you install with some configuration?   I think this is also useful for folks who have more than one Tripal site who would like single sign-on across all of them.
>
> Thanks!
> Stephen
>
> On 2/8/2013 6:30 AM, Michael Dondrup wrote:
>> Hi,
>> I made a wiki page with some documentation. (Noticed that it is a quite lengthy process).
>>
>> https://github.com/mdondrup/GBrowse/wiki/Single-Sign-On-for-GBrowse-and-Tripal
>>
>> Please contact me if anything is unclear.
>>
>> Best
>> Michael
>>
>> On Feb 6, 2013, at 7:39 PM, Lincoln Stein wrote:
>>
>>> Thanks, that would be great.
>>>
>>> Lincoln
>>>
>>>
>>> On Wed, Feb 6, 2013 at 10:30 AM, Michael Dondrup <[hidden email]> wrote:
>>> Hi,
>>> I can recommend simpleSAMLphp as idp. This is about everything you need in addition to net::saml and gbrowse and php to run the IdP. I can make a little guide and attach my config files, for setting up the IDP if you want.
>>> Michael
>>>
>>>
>>>
>>> On 6. feb. 2013, at 17:55, Lincoln Stein <[hidden email]> wrote:
>>>
>>>> Hi Michael,
>>>>
>>>> Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?
>>>>
>>>> Lincoln
>>>>
>>>>
>>>> On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
>>>> Hi Lincoln and all,
>>>>
>>>> I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
>>>> This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
>>>> using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
>>>> experimental and the code is just an ugly hack atm.
>>>>
>>>> Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
>>>> plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
>>>> these are non-disruptive for other applications, I simply don't understand gbrowse well enough.
>>>>
>>>> The code is in this gbrowse-fork:
>>>>
>>>> https://github.com/mdondrup/GBrowse
>>>>
>>>> There is some perldoc in conf/plugins/SAMLAutheticator
>>>>
>>>> I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
>>>> do it more smoothly. In particular, I have the following questions:
>>>>
>>>> - how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
>>>> - What does a private session mean?
>>>>
>>>>  - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
>>>> stays logged in. I am looking for a solution (the other way around works).
>>>> One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
>>>> insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.
>>>>
>>>> I hope you find my attempt useful and I am looking forward to your criticism.
>>>>
>>>> Best
>>>> Michael
>>>>
>>>>
>>>>
>>>> Michael Dondrup
>>>> Postdoctoral fellow
>>>> Sea Lice Research Centre/Department of Informatics
>>>> University of Bergen
>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>> Norway
>>>>
>>>> On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:
>>>>
>>>>> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>>>>>
>>>>>  TestAuthenticator.pm
>>>>>  LDAPAuthenticate.pm
>>>>>  PamAuthenticate.pm
>>>>>
>>>>> Lincoln
>>>>>
>>>>>
>>>>> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
>>>>> Hi,
>>>>>
>>>>> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
>>>>> federated authentication. That worked quite nicely, such that I now am looking
>>>>> for a similar solution for Gbrowse that would allow for single sign on to both
>>>>> Tripal and Gbrowse.
>>>>>
>>>>> Has anybody done or attempted this before and is
>>>>> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
>>>>> but maybe there is a more more integrated solution already.
>>>>>
>>>>> Thank you
>>>>> Michael
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> [1] http://simplesamlphp.org/
>>>>> [2] http://zxid.org/
>>>>> ------------------------------------------------------------------------------
>>>>> Monitor your physical, virtual and cloud infrastructure from a single
>>>>> web console. Get in-depth insight into apps, servers, databases, vmware,
>>>>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>>>>> Pricing starts from $795 for 25 servers or applications!
>>>>> http://p.sf.net/sfu/zoho_dev2dev_nov
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Lincoln D. Stein
>>>>> Director, Informatics and Biocomputing Platform
>>>>> Ontario Institute for Cancer Research
>>>>> 101 College St., Suite 800
>>>>> Toronto, ON, Canada M5G0A3
>>>>> 416 673-8514
>>>>> Assistant: Renata Musa <[hidden email]>
>>>>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]>
>>
>> ------------------------------------------------------------------------------
>> Free Next-Gen Firewall Hardware Offer
>> Buy your Sophos next-gen firewall before the end March 2013
>> and get the hardware for free! Learn more.
>> http://p.sf.net/sfu/sophos-d2d-feb
>> _______________________________________________
>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>


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Re: [Gmod-tripal-devel] [Gmod-gbrowse] Gbrowse SAML integration

Michael Dondrup-3
Hi,
I have now added additional documentation on creating federated login in Drupal/Tripal:

http://tripal.info/documentation/tripal_saml_integration

The page with details on the experimental GBrowse setup is now linked here:
 
http://tripal.info/documentation/single_signon

Please have a look. I appreciate your feedback.

Best
Michael

On Feb 8, 2013, at 3:03 PM, Michael Dondrup wrote:

> Hi Stephen,
>
> please go ahead. I was planning to write the Drupal integration up next week. I am using the module http://drupal.org/project/simplesamlphp_auth
> which integrates simpleSAMLphp nicely and makes Drupal an SP.  One can have a mix of SAML accounts and local accounts (always recommended for the
> administrator). Just a word of warning, the guide is not suitable for production use (yet), because I have omitted  everything, that makes this setup secure.
>
> Best
> Michael
>
>
> On Feb 8, 2013, at 2:40 PM, Stephen Ficklin wrote:
>
>> HI Michael,
>>
>> This is great.  I'd like to make a link to your documentation on the Tripal site under our own Documentation section (http://tripal.info/documentation) if you don't mind.  Although I don't see the steps required for integrating Simple SAML with Drupal in your writeup.  I assume it's just a module you install with some configuration?   I think this is also useful for folks who have more than one Tripal site who would like single sign-on across all of them.
>>
>> Thanks!
>> Stephen
>>
>> On 2/8/2013 6:30 AM, Michael Dondrup wrote:
>>> Hi,
>>> I made a wiki page with some documentation. (Noticed that it is a quite lengthy process).
>>>
>>> https://github.com/mdondrup/GBrowse/wiki/Single-Sign-On-for-GBrowse-and-Tripal
>>>
>>> Please contact me if anything is unclear.
>>>
>>> Best
>>> Michael
>>>
>>> On Feb 6, 2013, at 7:39 PM, Lincoln Stein wrote:
>>>
>>>> Thanks, that would be great.
>>>>
>>>> Lincoln
>>>>
>>>>
>>>> On Wed, Feb 6, 2013 at 10:30 AM, Michael Dondrup <[hidden email]> wrote:
>>>> Hi,
>>>> I can recommend simpleSAMLphp as idp. This is about everything you need in addition to net::saml and gbrowse and php to run the IdP. I can make a little guide and attach my config files, for setting up the IDP if you want.
>>>> Michael
>>>>
>>>>
>>>>
>>>> On 6. feb. 2013, at 17:55, Lincoln Stein <[hidden email]> wrote:
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> Thank you very much for doing this. I will walk through your code and try to tease out the generic bits into the main source code. Since I have never used SAML before, can you recommend a testing environment that I can set up on a local or virtual machine?
>>>>>
>>>>> Lincoln
>>>>>
>>>>>
>>>>> On Wed, Feb 6, 2013 at 8:17 AM, Michael Dondrup <[hidden email]> wrote:
>>>>> Hi Lincoln and all,
>>>>>
>>>>> I have finally managed to make a SAML 2 PlugIn for GBrowse based on Net::SAML, that does more or less what I want.
>>>>> This module could be used to implement single-sign-on (and single sign out) between e.g. Tripal and GBrowse,
>>>>> using the SimpleSAMLphp extension in Drupal, and this PlugIn in GBrowse. However, it is pretty much
>>>>> experimental and the code is just an ugly hack atm.
>>>>>
>>>>> Due to the interaction pattern of  SAML, which requires a http-redirect to and from the identity provider
>>>>> plus tokens added to the URL, I thought I had to make a few slight changes to the core modules. I hope,
>>>>> these are non-disruptive for other applications, I simply don't understand gbrowse well enough.
>>>>>
>>>>> The code is in this gbrowse-fork:
>>>>>
>>>>> https://github.com/mdondrup/GBrowse
>>>>>
>>>>> There is some perldoc in conf/plugins/SAMLAutheticator
>>>>>
>>>>> I am not sure if I can ask to anyone to review my code, but I hope somebody could look at this, and give me suggestions, how to
>>>>> do it more smoothly. In particular, I have the following questions:
>>>>>
>>>>> - how do I terminate a GBrowse session correctly from perl? I'm sort of getting rid of the GBrowse session but I am not sure, if that is sufficient.
>>>>> - What does a private session mean?
>>>>>
>>>>> - Single Logout does work only partially: If the SAML session is terminated outside of GBrowse, then the plugin doesn't recognize it and GBrowse
>>>>> stays logged in. I am looking for a solution (the other way around works).
>>>>> One idea was to check in every call to gbrowse, if the SAML session is still valid (including the redirects) and discard the session if not. When I tried to
>>>>> insert such check into the gbrowses cgi directly however, the imag rendering didn't work any more.
>>>>>
>>>>> I hope you find my attempt useful and I am looking forward to your criticism.
>>>>>
>>>>> Best
>>>>> Michael
>>>>>
>>>>>
>>>>>
>>>>> Michael Dondrup
>>>>> Postdoctoral fellow
>>>>> Sea Lice Research Centre/Department of Informatics
>>>>> University of Bergen
>>>>> Thormøhlensgate 55, N-5008 Bergen,
>>>>> Norway
>>>>>
>>>>> On Nov 19, 2012, at 4:30 PM, Lincoln Stein wrote:
>>>>>
>>>>>> That would be a great thing. I'm not aware of this being done, but the Net::SAML perl module is relatively straightforward, and I have tried to make the GBrowse authentication hooks easy as well. See the following modules in conf/plugins/ for example code:
>>>>>>
>>>>>> TestAuthenticator.pm
>>>>>> LDAPAuthenticate.pm
>>>>>> PamAuthenticate.pm
>>>>>>
>>>>>> Lincoln
>>>>>>
>>>>>>
>>>>>> On Mon, Nov 19, 2012 at 3:45 AM, Michael Dondrup <[hidden email]> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I have recently tried to integrate Drupal/Tripal with simpleSAMLphp[1] for
>>>>>> federated authentication. That worked quite nicely, such that I now am looking
>>>>>> for a similar solution for Gbrowse that would allow for single sign on to both
>>>>>> Tripal and Gbrowse.
>>>>>>
>>>>>> Has anybody done or attempted this before and is
>>>>>> willing to share their perl-code? I am aware of ZXID and Net::SAML[2] perl modules,
>>>>>> but maybe there is a more more integrated solution already.
>>>>>>
>>>>>> Thank you
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> [1] http://simplesamlphp.org/
>>>>>> [2] http://zxid.org/
>>>>>> ------------------------------------------------------------------------------
>>>>>> Monitor your physical, virtual and cloud infrastructure from a single
>>>>>> web console. Get in-depth insight into apps, servers, databases, vmware,
>>>>>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>>>>>> Pricing starts from $795 for 25 servers or applications!
>>>>>> http://p.sf.net/sfu/zoho_dev2dev_nov
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Lincoln D. Stein
>>>>>> Director, Informatics and Biocomputing Platform
>>>>>> Ontario Institute for Cancer Research
>>>>>> 101 College St., Suite 800
>>>>>> Toronto, ON, Canada M5G0A3
>>>>>> 416 673-8514
>>>>>> Assistant: Renata Musa <[hidden email]>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Lincoln D. Stein
>>>>> Director, Informatics and Biocomputing Platform
>>>>> Ontario Institute for Cancer Research
>>>>> 101 College St., Suite 800
>>>>> Toronto, ON, Canada M5G0A3
>>>>> 416 673-8514
>>>>> Assistant: Renata Musa <[hidden email]>
>>>>
>>>>
>>>> --
>>>> Lincoln D. Stein
>>>> Director, Informatics and Biocomputing Platform
>>>> Ontario Institute for Cancer Research
>>>> 101 College St., Suite 800
>>>> Toronto, ON, Canada M5G0A3
>>>> 416 673-8514
>>>> Assistant: Renata Musa <[hidden email]>
>>>
>>> ------------------------------------------------------------------------------
>>> Free Next-Gen Firewall Hardware Offer
>>> Buy your Sophos next-gen firewall before the end March 2013
>>> and get the hardware for free! Learn more.
>>> http://p.sf.net/sfu/sophos-d2d-feb
>>> _______________________________________________
>>> Gmod-tripal-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
>
>
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