basedb-devel — BASE developers mailing list

[basedb-devel] BASE 3.0-alfa has been released

[Nicklas N. <ni...@th...>]

Hello all,

Today we are happy to announce the relase of BASE 3.0-alfa. If all goes 
well the final 3.0 release is expected in a couple of months. This 
release contains major changes which are mainly targeted at supporting 
sequencing experiments with expression like data.

Do not use this release on a production server. It is not certain that 
upgrading to the final 3.0 release will be possible. Upgrading existing 
servers will be possible from BASE 2.17 only. This alfa release can't be 
used to upgrade if PostgreSQL is used. This will be fixed before the 
final 3.0 release.

The 3.0 release is not binary-compatible with BASE 2. This means that 
existing plug-ins/extensions may not work until updated versions are 
available. There is more information about this in the upgrade instructions.

Note that since this is an alfa-version, there are features and 
functionality that are still missing and/or not working as expected. The 
documentation is not up to date in many places and information about 
many of the new features is missing. We will try to answer questions and 
help with problems on the mailing list.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.0-alfa/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [basedb-devel] Mage-Tab export plugin

[Pawel S. <Paw...@bc...>]

Great. Yes, I am planning to implement that as well.

Pawel

On 12/09/11 11:48, Gildas Le Corguillé wrote:
> Bonjour,
>
> This is good news if you can develope this plugin and I have enought 
> datas on Base2 to test it :P
>
> My contribution on the former plugin Tab2Mage was to add a feature to 
> manage pooling of samples (or extracts) and the possibility to have 
> several "Files[raw]" per RawBioAssay (ex : one cy3 and one cy5) 
> because we used nimblegen multi-color arrays.
> Are you plan to manage that feature ?
>
> Gildas
>
>
> Le 01/09/2011 14:43, Pawel Sztromwasser a écrit :
>> Hallo,
>>
>> I haven't been to the milestones page for a while, and I didn't know 
>> that work on BASE 3 was in such an advanced state. Great job guys! 
>> Support for sequencing data is excellent news for us.
>> Anyway, before it is released and before we are ready to migrate, we 
>> will certainly have experiments to export. We could keep using the 
>> Tab2Mage exporter this year, and the conversion script later, but I 
>> think I'd prefer to start working on the plugin now when we have 
>> time, develop against BASE 2 where we would have immediate use for 
>> it, and port to BASE 3 later after we migrate. It will not be a big 
>> change I hope.
>>
>> Gildas, I have actually started developing the plugin. If you're 
>> willing to contribute, I could send you the jar/code when it is 
>> more-or-less ready for testing, so we could debug it on our sites 
>> simultanously and make it bullet-proof;)
>>
>> Helen, IMO it is better with one format than two, so I think removing 
>> support for Tab2Mage (and providing conversion tools) is a move 
>> forward. One thing I was wondering, if there are any plans for an 
>> XML-based format for description of MA experiments? MAGE-ML is a bit 
>> too complex I guess, but an XML Schema equivalent to the current 
>> MageTab format would be favored by programmers and for programmatic 
>> access, in comparison with the tab-delimited files.
>>
>> Best wishes,
>> Pawel
>>
>> Nicklas Nordborg wrote:
>>> On 2011-09-01 09:15, Gildas Le Corguillé wrote:
>>>> Hello,
>>>>
>>>> Our group still interesting in this kind of exporter. It was the main
>>>> reason why we decided to use Base. We are in a public lab so we 
>>>> like to
>>>> share :P
>>>> Last year, I repaired the existing Tab2Mage-exporter module for Base.
>>>> So if you need help, I can spend some time on that. But I'm not
>>>> necessarily a good developer ^^'
>>>
>>> I think that a Mage-Tab exporter has to be developed by the BASE 
>>> community. We can provide space and user accounts on our 
>>> subversion+trac (baseplugins.thep.lu.se) if someone is interested to 
>>> start on this. Unfortunately we have no time to help with the actual 
>>> development. Of course, we'll try to answer questions and provide 
>>> the information that is necessary.
>>>
>>> As a starting point, we try to collect and document the major API 
>>> changes in http://base.thep.lu.se/ticket/1603
>>>
>>> My guess is that #1153 and #1597 are the major changes that cause 
>>> problems for the current Tab2Mage exporter.
>>>
>>> /Nicklas
>>>
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Special Offer -- Download ArcSight Logger for FREE!
>>> Finally, a world-class log management solution at an even better 
>>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>>> download Logger. Secure your free ArcSight Logger TODAY!
>>> http://p.sf.net/sfu/arcsisghtdev2dev
>>> _______________________________________________
>>> basedb-devel mailing list
>>> bas...@li...
>>> https://lists.sourceforge.net/lists/listinfo/basedb-devel
>>
>>
>>
>> ------------------------------------------------------------------------------
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>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
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>>
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>
>
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Re: [basedb-devel] Mage-Tab export plugin

[Gildas Le C. <lec...@sb...>]

Bonjour,

This is good news if you can develope this plugin and I have enought 
datas on Base2 to test it :P

My contribution on the former plugin Tab2Mage was to add a feature to 
manage pooling of samples (or extracts) and the possibility to have 
several "Files[raw]" per RawBioAssay (ex : one cy3 and one cy5) because 
we used nimblegen multi-color arrays.
Are you plan to manage that feature ?

Gildas


Le 01/09/2011 14:43, Pawel Sztromwasser a écrit :
> Hallo,
>
> I haven't been to the milestones page for a while, and I didn't know 
> that work on BASE 3 was in such an advanced state. Great job guys! 
> Support for sequencing data is excellent news for us.
> Anyway, before it is released and before we are ready to migrate, we 
> will certainly have experiments to export. We could keep using the 
> Tab2Mage exporter this year, and the conversion script later, but I 
> think I'd prefer to start working on the plugin now when we have time, 
> develop against BASE 2 where we would have immediate use for it, and 
> port to BASE 3 later after we migrate. It will not be a big change I 
> hope.
>
> Gildas, I have actually started developing the plugin. If you're 
> willing to contribute, I could send you the jar/code when it is 
> more-or-less ready for testing, so we could debug it on our sites 
> simultanously and make it bullet-proof;)
>
> Helen, IMO it is better with one format than two, so I think removing 
> support for Tab2Mage (and providing conversion tools) is a move 
> forward. One thing I was wondering, if there are any plans for an 
> XML-based format for description of MA experiments? MAGE-ML is a bit 
> too complex I guess, but an XML Schema equivalent to the current 
> MageTab format would be favored by programmers and for programmatic 
> access, in comparison with the tab-delimited files.
>
> Best wishes,
> Pawel
>
> Nicklas Nordborg wrote:
>> On 2011-09-01 09:15, Gildas Le Corguillé wrote:
>>> Hello,
>>>
>>> Our group still interesting in this kind of exporter. It was the main
>>> reason why we decided to use Base. We are in a public lab so we like to
>>> share :P
>>> Last year, I repaired the existing Tab2Mage-exporter module for Base.
>>> So if you need help, I can spend some time on that. But I'm not
>>> necessarily a good developer ^^'
>>
>> I think that a Mage-Tab exporter has to be developed by the BASE 
>> community. We can provide space and user accounts on our 
>> subversion+trac (baseplugins.thep.lu.se) if someone is interested to 
>> start on this. Unfortunately we have no time to help with the actual 
>> development. Of course, we'll try to answer questions and provide the 
>> information that is necessary.
>>
>> As a starting point, we try to collect and document the major API 
>> changes in http://base.thep.lu.se/ticket/1603
>>
>> My guess is that #1153 and #1597 are the major changes that cause 
>> problems for the current Tab2Mage exporter.
>>
>> /Nicklas
>>
>>
>> ------------------------------------------------------------------------------ 
>>
>> Special Offer -- Download ArcSight Logger for FREE!
>> Finally, a world-class log management solution at an even better 
>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
>> _______________________________________________
>> basedb-devel mailing list
>> bas...@li...
>> https://lists.sourceforge.net/lists/listinfo/basedb-devel
>
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
>
>
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel

Re: [basedb-devel] Mage-Tab export plugin

[Pawel S. <paw...@ii...>]

Hallo,

I haven't been to the milestones page for a while, and I didn't know 
that work on BASE 3 was in such an advanced state. Great job guys! 
Support for sequencing data is excellent news for us.
Anyway, before it is released and before we are ready to migrate, we 
will certainly have experiments to export. We could keep using the 
Tab2Mage exporter this year, and the conversion script later, but I 
think I'd prefer to start working on the plugin now when we have time, 
develop against BASE 2 where we would have immediate use for it, and 
port to BASE 3 later after we migrate. It will not be a big change I hope.
 
Gildas, I have actually started developing the plugin. If you're willing 
to contribute, I could send you the jar/code when it is more-or-less 
ready for testing, so we could debug it on our sites simultanously and 
make it bullet-proof;)

Helen, IMO it is better with one format than two, so I think removing 
support for Tab2Mage (and providing conversion tools) is a move forward. 
One thing I was wondering, if there are any plans for an XML-based 
format for description of MA experiments? MAGE-ML is a bit too complex I 
guess, but an XML Schema equivalent to the current MageTab format would 
be favored by programmers and for programmatic access, in comparison 
with the tab-delimited files.

Best wishes,
Pawel

Nicklas Nordborg wrote:
> On 2011-09-01 09:15, Gildas Le Corguillé wrote:
>   
>> Hello,
>>
>> Our group still interesting in this kind of exporter. It was the main
>> reason why we decided to use Base. We are in a public lab so we like to
>> share :P
>> Last year, I repaired the existing Tab2Mage-exporter module for Base.
>> So if you need help, I can spend some time on that. But I'm not
>> necessarily a good developer ^^'
>>     
>
> I think that a Mage-Tab exporter has to be developed by the BASE 
> community. We can provide space and user accounts on our subversion+trac 
> (baseplugins.thep.lu.se) if someone is interested to start on this. 
> Unfortunately we have no time to help with the actual development. Of 
> course, we'll try to answer questions and provide the information that 
> is necessary.
>
> As a starting point, we try to collect and document the major API 
> changes in http://base.thep.lu.se/ticket/1603
>
> My guess is that #1153 and #1597 are the major changes that cause 
> problems for the current Tab2Mage exporter.
>
> /Nicklas
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better 
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel
>   

Re: [basedb-devel] Mage-Tab export plugin

[Nicklas N. <ni...@th...>]

On 2011-09-01 09:15, Gildas Le Corguillé wrote:
> Hello,
>
> Our group still interesting in this kind of exporter. It was the main
> reason why we decided to use Base. We are in a public lab so we like to
> share :P
> Last year, I repaired the existing Tab2Mage-exporter module for Base.
> So if you need help, I can spend some time on that. But I'm not
> necessarily a good developer ^^'

I think that a Mage-Tab exporter has to be developed by the BASE 
community. We can provide space and user accounts on our subversion+trac 
(baseplugins.thep.lu.se) if someone is interested to start on this. 
Unfortunately we have no time to help with the actual development. Of 
course, we'll try to answer questions and provide the information that 
is necessary.

As a starting point, we try to collect and document the major API 
changes in http://base.thep.lu.se/ticket/1603

My guess is that #1153 and #1597 are the major changes that cause 
problems for the current Tab2Mage exporter.

/Nicklas

Re: [basedb-devel] Mage-Tab export plugin

[Gildas Le C. <lec...@sb...>]

Hello,

Our group still interesting in this kind of exporter. It was the main 
reason why we decided to use Base. We are in a public lab so we like to 
share :P
Last year, I repaired the existing Tab2Mage-exporter module for Base.
So if you need help, I can spend some time on that. But I'm not 
necessarily a good developer ^^'

Cheers

Gildas




Le 31/08/2011 20:11, Nicklas Nordborg a écrit :
> On 2011-08-31 09:43, Pawel Sztromwasser wrote:
>> Hello BASE developers,
>>
>> By the end of the year ArrayExpress is going to remove a possibility of
>> importing experiments using the Tab2Mage format. The only supported
>> format will be Mage-Tab. We have been extensively using Tab2Mage and the
>> BASE plugin that exports experiments in this format. I was wondering if
>> anyone else is developing or planning to develop a plugin that would
>> support Mage-Tab?
> It would certainly be nice to see something happening in this area. One
> good reason to start on something new is that the Tab2Mage plug-in (and
> probably a lot of other plug-ins) will not work with the upcoming BASE 3
> release. The roadmap on the BASE site says September 15 but it will be
> postponed a month or two. I still think that if someone is interested to
> do this it would be possible to start developing against the BASE trunk
> code. The API is still a moving target but my hope is that most major
> changes (including database schema changes) have been settled within a
> few weeks.
>
> /Nicklas
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel

Re: [basedb-devel] Mage-Tab export plugin

[Nicklas N. <ni...@th...>]

On 2011-08-31 09:43, Pawel Sztromwasser wrote:
> Hello BASE developers,
>
> By the end of the year ArrayExpress is going to remove a possibility of
> importing experiments using the Tab2Mage format. The only supported
> format will be Mage-Tab. We have been extensively using Tab2Mage and the
> BASE plugin that exports experiments in this format. I was wondering if
> anyone else is developing or planning to develop a plugin that would
> support Mage-Tab?

It would certainly be nice to see something happening in this area. One 
good reason to start on something new is that the Tab2Mage plug-in (and 
probably a lot of other plug-ins) will not work with the upcoming BASE 3 
release. The roadmap on the BASE site says September 15 but it will be 
postponed a month or two. I still think that if someone is interested to 
do this it would be possible to start developing against the BASE trunk 
code. The API is still a moving target but my hope is that most major 
changes (including database schema changes) have been settled within a 
few weeks.

/Nicklas

Re: [basedb-devel] Mage-Tab export plugin

[Helen P. <par...@eb...>]

Dear Base developers,

we have perl code that converts Tab2Mage into MAGE-TAB, which we use 
internally which we can make available. If the removal of Tab2mage is a 
serious problem for this community please let me know, we may run the 
conversion code as a service in that case,

best regards

Helen Parkinson

On 31/08/2011 08:43, Pawel Sztromwasser wrote:
> Hello BASE developers,
>
> By the end of the year ArrayExpress is going to remove a possibility 
> of importing experiments using the Tab2Mage format. The only supported 
> format will be Mage-Tab. We have been extensively using Tab2Mage and 
> the BASE plugin that exports experiments in this format. I was 
> wondering if anyone else is developing or planning to develop a plugin 
> that would support Mage-Tab?
>
> Regards,
> Pawel Sztromwasser
>
>
> ------------------------------------------------------------------------------
> Special Offer -- Download ArcSight Logger for FREE!
> Finally, a world-class log management solution at an even better
> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
> download Logger. Secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsisghtdev2dev
>
>
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel

-- 
Helen Parkinson, PhD
Team Leader
Functional Genomics Group
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi
www.ebi.ac.uk/fgpt/

[basedb-devel] Mage-Tab export plugin

[Pawel S. <paw...@ii...>]

Hello BASE developers,

By the end of the year ArrayExpress is going to remove a possibility of 
importing experiments using the Tab2Mage format. The only supported 
format will be Mage-Tab. We have been extensively using Tab2Mage and the 
BASE plugin that exports experiments in this format. I was wondering if 
anyone else is developing or planning to develop a plugin that would 
support Mage-Tab?

Regards,
Pawel Sztromwasser

Re: [basedb-devel] Truncated files

[Pawel S. <paw...@ii...>]

Sorry, wrong mailing list:)

Pawel Sztromwasser wrote:
> In BASE it was a Tomcat problem. Hope it helps:
> http://www.mail-archive.com/bas...@li.../msg01838.html 
>
>
> Pawel

[basedb-devel] Truncated files

[Pawel S. <paw...@ii...>]

In BASE it was a Tomcat problem. Hope it helps:
http://www.mail-archive.com/bas...@li.../msg01838.html

Pawel

Re: [basedb-devel] Programmatic login using a token

[Pawel S. <paw...@ii...>]

See my short replies inline.

Nicklas Nordborg wrote:
> On 2011-08-01 10:51, Pawel Sztromwasser wrote:
>   
>> Hi Nicklas,
>>
>>     
>>> Thanks for the suggestions. Maybe I am missing something but wouldn't
>>> it be possible to send the username and password to the STS as part of
>>> the BASE login? Or, use an empty password string?
>>>       
>> I should have explained the use case better. It does not relate to the
>> manual login to BASE using the web interface where one types in a
>> username and password. For this we have already implemented and set up
>> an authentication plugin that sends the username and password typed in
>> by a user to the STS service for verification (just like you suggest).
>> Now I am planning to enable programmatic access to BASE (via Web
>> services) from another system that shares identity management (STS) with
>> BASE. The idea is that the user that is logged in to any of these, has
>> obtained a token and is able to access his/her resources in the other
>> system without any further authentication, using only the token (single
>> sign-on). In this federated authentication system one application will
>> be able to automatically integrate resources available to a user in
>> several distinct systems.
>>
>> Since the common authentication mechanism will be based on tokens, I
>> don't expect an application to provide a username/password pair anytime
>> when it needs to access resources hosted in a different system.
>> Currently all the login methods in BASE are username/password oriented,
>> but with the minor change I suggest, it could be easily extended to
>> cover token-like objects as well. At least in programmatic access
>> scenarios, but I can't see a need for any other.
>>     
>
> Ok, I understand that this is a bit different than the usual login 
> procedure. But I think there is also already another possible way to 
> solve this. It could be done in a similar way that we are doing with the 
> job agents. They use a "master" user account with a known 
> username+password that is used to login to BASE. The account should have 
> the "Act as another user" permissions assigned to a role (eg. just as 
> the "Job agent" role that is pre-installed in BASE).
>
> Then the SessionControl.impersonateLogin() can be used to login as any 
> user without having to provide a password. You'll have to find the 
> internal id of the user but that is more or less the same thing that is 
> done in the diff for SessionControl that you posted in the original post.
>   
Ahhh, clever. And no change to BASE required. It looks promising, I will give it a try.

>   
>>> In any case, I am not sure that supplying a TokenAuthenticator object
>>> as a parameter to the login method is a good idea, since it would be
>>> very easy to to provide an implementation that just accept anything.
>>>       
>> I was thinking similarly, but how does it differ from supplying a login
>> method in an authenticator plugin? That method could accept anything as
>> well. Access to SessionControl.login(Token, TokenAuthenticator)
>> operation in only from the code deployed together with BASE server (in
>> my case in implementation of Web services deployed within BASE), so an
>> environment that a BASE administrator should have full control over. The
>> same as external authentication plugins.
>>     
>
> The difference is that the administrator sets up the authenticator to 
> use in the configuration files and it is not possible for the calling 
> code to change this. Ok, some "mean" code could probably get around 
> this, so it is good to have control over the server environment. Despite 
> this, I think the public BASE api shouldn't provide this kind of 
> flexibility. I would prefer a solution where the administrator can setup 
> exactly how the authentication should happen.
>   
Fair enough.
> /Nicklas
>
> ------------------------------------------------------------------------------
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>   

Re: [basedb-devel] Programmatic login using a token

[Nicklas N. <ni...@th...>]

On 2011-08-01 10:51, Pawel Sztromwasser wrote:
> Hi Nicklas,
>
>> Thanks for the suggestions. Maybe I am missing something but wouldn't
>> it be possible to send the username and password to the STS as part of
>> the BASE login? Or, use an empty password string?
>
> I should have explained the use case better. It does not relate to the
> manual login to BASE using the web interface where one types in a
> username and password. For this we have already implemented and set up
> an authentication plugin that sends the username and password typed in
> by a user to the STS service for verification (just like you suggest).
> Now I am planning to enable programmatic access to BASE (via Web
> services) from another system that shares identity management (STS) with
> BASE. The idea is that the user that is logged in to any of these, has
> obtained a token and is able to access his/her resources in the other
> system without any further authentication, using only the token (single
> sign-on). In this federated authentication system one application will
> be able to automatically integrate resources available to a user in
> several distinct systems.
>
> Since the common authentication mechanism will be based on tokens, I
> don't expect an application to provide a username/password pair anytime
> when it needs to access resources hosted in a different system.
> Currently all the login methods in BASE are username/password oriented,
> but with the minor change I suggest, it could be easily extended to
> cover token-like objects as well. At least in programmatic access
> scenarios, but I can't see a need for any other.

Ok, I understand that this is a bit different than the usual login 
procedure. But I think there is also already another possible way to 
solve this. It could be done in a similar way that we are doing with the 
job agents. They use a "master" user account with a known 
username+password that is used to login to BASE. The account should have 
the "Act as another user" permissions assigned to a role (eg. just as 
the "Job agent" role that is pre-installed in BASE).

Then the SessionControl.impersonateLogin() can be used to login as any 
user without having to provide a password. You'll have to find the 
internal id of the user but that is more or less the same thing that is 
done in the diff for SessionControl that you posted in the original post.


>> In any case, I am not sure that supplying a TokenAuthenticator object
>> as a parameter to the login method is a good idea, since it would be
>> very easy to to provide an implementation that just accept anything.
>
>
> I was thinking similarly, but how does it differ from supplying a login
> method in an authenticator plugin? That method could accept anything as
> well. Access to SessionControl.login(Token, TokenAuthenticator)
> operation in only from the code deployed together with BASE server (in
> my case in implementation of Web services deployed within BASE), so an
> environment that a BASE administrator should have full control over. The
> same as external authentication plugins.

The difference is that the administrator sets up the authenticator to 
use in the configuration files and it is not possible for the calling 
code to change this. Ok, some "mean" code could probably get around 
this, so it is good to have control over the server environment. Despite 
this, I think the public BASE api shouldn't provide this kind of 
flexibility. I would prefer a solution where the administrator can setup 
exactly how the authentication should happen.

/Nicklas

Re: [basedb-devel] Programmatic login using a token

[Pawel S. <paw...@ii...>]

Hi Nicklas,

> Thanks for the suggestions. Maybe I am missing something but wouldn't it 
> be possible to send the username and password to the STS as part of the 
> BASE login? Or, use an empty password string?

I should have explained the use case better. It does not relate to the 
manual login to BASE using the web interface where one types in a 
username and password. For this we have already implemented and set up 
an authentication plugin that sends the username and password typed in 
by a user to the STS service for verification (just like you suggest). 
Now I am planning to enable programmatic access to BASE (via Web 
services) from another system that shares identity management (STS) with 
BASE. The idea is that the user that is logged in to any of these, has 
obtained a token and is able to access his/her resources in the other 
system without any further authentication, using only the token (single 
sign-on). In this federated authentication system one application will 
be able to automatically integrate resources available to a user in 
several distinct systems.

Since the common authentication mechanism will be based on tokens, I 
don't expect an application to provide a username/password pair anytime 
when it needs to access resources hosted in a different system. 
Currently all the login methods in BASE are username/password oriented, 
but with the minor change I suggest, it could be easily extended to 
cover token-like objects as well. At least in programmatic access 
scenarios, but I can't see a need for any other.

I am not sure if I got your suggestion with empty password right, so 
correct me if I am wrong. The token is not a simple string (it is 
actually a little XML document), and passing it as a username (with 
empty password) to the authenticator plugin would not be a nice solution.

> In any case, I am not sure that supplying a TokenAuthenticator object as 
> a parameter to the login method is a good idea, since it would be very 
> easy to to provide an implementation that just accept anything.


I was thinking similarly, but how does it differ from supplying a login 
method in an authenticator plugin? That method could accept anything as 
well. Access to SessionControl.login(Token, TokenAuthenticator) 
operation in only from the code deployed together with BASE server (in 
my case in implementation of Web services deployed within BASE), so an 
environment that a BASE administrator should have full control over. The 
same as external authentication plugins.

Pawel

Nicklas Nordborg wrote:
> On 2011-07-26 22:47, Pawel Sztromwasser wrote:
>   
>> Hello BASE team!
>>
>> Extending a little on our recent developments regarding external
>> authentication in BASE [1], I am working now on a Web service interface
>> to BASE that will authenticate users based on secure tokens issued by a
>> trusted STS. The STS authenticates users with username and password, and
>> issues a crypted token confirming their credentials. The token is valid
>> for a limited time and can be used for authentication in applications
>> and services that trust the STS.
>>
>> The STS token does not contain a password, only a user id, so with
>> current implementation of SessionControl I was unable to log in. I added
>> one method to the SessionControl class (see attached diff), included a
>> TokenAuthenticator interface (attached), and everything worked nice. The
>> extra operation allows to log in using a single token object and a
>> validator that can verify the token. The operation contains substantial
>> parts of SessionControl.verifyUserExternal(), which can be extracted to
>> a separate method. The TokenAuthenticator interface and original
>> Authenticator interface are also quite similar, so they could maybe
>> share a common ancestor.
>>
>> I know that the change is in the heart of BASE, but it is little and
>> would provide additional way of programmatic interaction with BASE. If
>> they pass the tests, could you consider including the changes to the
>> BASE codebase?
>>
>>     
>
> Thanks for the suggestions. Maybe I am missing something but wouldn't it 
> be possible to send the username and password to the STS as part of the 
> BASE login? Or, use an empty password string?
>
> In any case, I am not sure that supplying a TokenAuthenticator object as 
> a parameter to the login method is a good idea, since it would be very 
> easy to to provide an implementation that just accept anything.
>
> There are also some plans to change the authentication as part of BASE 3 
> development (http://base.thep.lu.se/ticket/1599). There is not much 
> information since we haven't been thinking very much about this and at 
> the moment I am not sure if we will have time to do it before releasing 
> BASE 3. It depends a bit on when some of the other BASE 3 features are 
> needed in production. I'll keep a link to this thread so that we don't 
> forget it.
>
> /Nicklas
>
> ------------------------------------------------------------------------------
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Re: [basedb-devel] Programmatic login using a token

[Nicklas N. <ni...@th...>]

On 2011-07-26 22:47, Pawel Sztromwasser wrote:
> Hello BASE team!
>
> Extending a little on our recent developments regarding external
> authentication in BASE [1], I am working now on a Web service interface
> to BASE that will authenticate users based on secure tokens issued by a
> trusted STS. The STS authenticates users with username and password, and
> issues a crypted token confirming their credentials. The token is valid
> for a limited time and can be used for authentication in applications
> and services that trust the STS.
>
> The STS token does not contain a password, only a user id, so with
> current implementation of SessionControl I was unable to log in. I added
> one method to the SessionControl class (see attached diff), included a
> TokenAuthenticator interface (attached), and everything worked nice. The
> extra operation allows to log in using a single token object and a
> validator that can verify the token. The operation contains substantial
> parts of SessionControl.verifyUserExternal(), which can be extracted to
> a separate method. The TokenAuthenticator interface and original
> Authenticator interface are also quite similar, so they could maybe
> share a common ancestor.
>
> I know that the change is in the heart of BASE, but it is little and
> would provide additional way of programmatic interaction with BASE. If
> they pass the tests, could you consider including the changes to the
> BASE codebase?
>

Thanks for the suggestions. Maybe I am missing something but wouldn't it 
be possible to send the username and password to the STS as part of the 
BASE login? Or, use an empty password string?

In any case, I am not sure that supplying a TokenAuthenticator object as 
a parameter to the login method is a good idea, since it would be very 
easy to to provide an implementation that just accept anything.

There are also some plans to change the authentication as part of BASE 3 
development (http://base.thep.lu.se/ticket/1599). There is not much 
information since we haven't been thinking very much about this and at 
the moment I am not sure if we will have time to do it before releasing 
BASE 3. It depends a bit on when some of the other BASE 3 features are 
needed in production. I'll keep a link to this thread so that we don't 
forget it.

/Nicklas

[basedb-devel] Programmatic login using a token

[Pawel S. <Paw...@bc...>]

Hello BASE team!

Extending a little on our recent developments regarding external 
authentication in BASE [1], I am working now on a Web service interface 
to BASE that will authenticate users based on secure tokens issued by a 
trusted STS. The STS authenticates users with username and password, and 
issues a crypted token confirming their credentials. The token is valid 
for a limited time and can be used for authentication in applications 
and services that trust the STS.

The STS token does not contain a password, only a user id, so with 
current implementation of SessionControl I was unable to log in. I added 
one method to the SessionControl class (see attached diff), included a 
TokenAuthenticator interface (attached), and everything worked nice. The 
extra operation allows to log in using a single token object and a 
validator that can verify the token. The operation contains substantial 
parts of SessionControl.verifyUserExternal(), which can be extracted to 
a separate method. The TokenAuthenticator interface and original 
Authenticator interface are also quite similar, so they could maybe 
share a common ancestor.

I know that the change is in the heart of BASE, but it is little and 
would provide additional way of programmatic interaction with BASE. If 
they pass the tests, could you consider including the changes to the 
BASE codebase?

Best wishes,
Pawel Sztromwasser

[1] 
http://www.mail-archive.com/bas...@li.../msg00433.html)

[basedb-devel] BASE 2.17.2 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We are happy to announce the release of BASE 2.17.2. This is a bugfix
release that fixes a few minor bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.17.2&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

[basedb-devel] BASE 2.17.1 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We are happy to announce the release of BASE 2.17.1. This is a bugfix
release that fixes a few minor bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.17.1&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [basedb-devel] External authentication

[Nicklas N. <ni...@th...>]

On 2011-03-01 12:58, Pawel Sztromwasser wrote:
> Hi Nicklas,
>
> I changed the Application.getAuthenticator() to use a separate
> classloader for external login plugin (attached a diff to the ticket
> #1575) and I was able to verify user's credentials using an STS service.

Thanks for the patch. It seems simple enough. I think the exception 
handling might need to be improved since it was assumed that the 
external system always knew if it was a bad login or a bad password.

> I got a bit unexpected behavior of BASE that tried to create a new
> account for the user after it failed finding it by an externalId. Of
> course, I had not set the externalId in advance. The logins of the
> external STS service and BASE account happened to be the same, so the
> whole process failed violating the unique-key constraint on login
> column. This is sth I will need to consider when integrating two sets of
> users from different applications.

The external authentication assumes that no "local" accounts except the 
root user account exists on the BASE server. The root account is handled 
as a special case so that it is possible to access BASE even if the 
external authentication system is down.

> But there is another problem I was struggling with. And apparently not
> only me [1]. Tomcat/axis/java has a problem when two
> axis2-kernel-x.x.jar jars are in the classpath. Even if the versions are
> the same. I tried multiple combinations with axis2 1.4 and 1.5.1. I
> downgraded the plugin to use axis2-1.3 and rampart1.3. I stripped-down
> the set of jars that my plugin uses, trying to use as many libraries
> shipped with BASE as possible. In principle it should work as long as
> all the dependencies were satisfied (by parent classloader of webapp),
> but when axis2-kernel was not loaded by the same classloader as Apache
> Rampart jars, I couldn't get rampart to engage.
>
> It seems like it is impossible to have axis2 in more than one location
> in the classpath. The only way it works is when only one
> axis2-kernel.jar is loaded by tomcat. So I either need to include all
> dependencies of my plugin into the /WEB-INF/lib directory of BASE, and
> use axis2 shipped with BASE; or I remove the axis2-kernel-1.3.jar from
> WEB-INF/lib of BASE and load it together with my plugin and rest of its
> dependencies. The latter one will of course break BASE's Web Services. I
> haven't had problems with other jars, despite I use different version of
> (for example) axiom libraries. No conflicts with other axis2 libraries,
> only axis2-kernel.
>
> I am happy because it works now, although with BASE's axis2 1.3. But I
> can imagine that in some time I might need to use newer axis2, and then
> I will have to try to upgrade it in BASE as well. If it is backwards
> compatible, it should go smooth, and the BASE Web Services will work.
> But it would be still good to test. Is there a test suite available for
> BASE Web Services that I could try? Or maybe you were considering
> upgrade yourself?
>

Class loading can be problematic sometimes. I don't know of any specific 
problems with Axis, but it seems like you have investigated this more 
than me.

We have tried to upgrade to Axis 1.5 but unfortunately there is a bug 
when handling date values. http://base.thep.lu.se/ticket/1353#comment:8
It seems like it has been fixed but for some reason the fix hasn't been 
released yet.

/Nicklas

Re: [basedb-devel] External authentication

[Pawel S. <Paw...@bc...>]

Hi Nicklas,

I changed the Application.getAuthenticator() to use a separate 
classloader for external login plugin (attached a diff to the ticket 
#1575) and I was able to verify user's credentials using an STS service.

I got a bit unexpected behavior of BASE that tried to create a new 
account for the user after it failed finding it by an externalId. Of 
course, I had not set the externalId in advance. The logins of the 
external STS service and BASE account happened to be the same, so the 
whole process failed violating the unique-key constraint on login 
column. This is sth I will need to consider when integrating two sets of 
users from different applications.

But there is another problem I was struggling with. And apparently not 
only me [1]. Tomcat/axis/java has a problem when two 
axis2-kernel-x.x.jar jars are in the classpath. Even if the versions are 
the same. I tried multiple combinations with axis2 1.4 and 1.5.1. I 
downgraded the plugin to use axis2-1.3 and rampart1.3. I stripped-down 
the set of jars that my plugin uses, trying to use as many libraries 
shipped with BASE as possible. In principle it should work as long as 
all the dependencies were satisfied (by parent classloader of webapp), 
but when axis2-kernel was not loaded by the same classloader as Apache 
Rampart jars, I couldn't get rampart to engage.

It seems like it is impossible to have axis2 in more than one location 
in the classpath. The only way it works is when only one 
axis2-kernel.jar is loaded by tomcat. So I either need to include all 
dependencies of my plugin into the /WEB-INF/lib directory of BASE, and 
use axis2 shipped with BASE; or I remove the axis2-kernel-1.3.jar from 
WEB-INF/lib of BASE and load it together with my plugin and rest of its 
dependencies. The latter one will of course break BASE's Web Services. I 
haven't had problems with other jars, despite I use different version of 
(for example) axiom libraries. No conflicts with other axis2 libraries, 
only axis2-kernel.

I am happy because it works now, although with BASE's axis2 1.3. But I 
can imagine that in some time I might need to use newer axis2, and then 
I will have to try to upgrade it in BASE as well. If it is backwards 
compatible, it should go smooth, and the BASE Web Services will work. 
But it would be still good to test. Is there a test suite available for 
BASE Web Services that I could try? Or maybe you were considering 
upgrade yourself?

Pawel

[1] https://issues.apache.org/jira/browse/AXIS2-2972



Nicklas Nordborg wrote:
> I added a ticket:http://base.thep.lu.se/ticket/1575
>
> /Nicklas
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel
>    

[basedb-devel] BASE 2.17 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We are happy to announce the release of BASE 2.17. This is a major
release which include new functionality and enhancements as well as some 
bug fixes. Worth mentioning is the "bioplate events" feature which makes 
it possible to batch edit biomaterial on a bioplate.

For a complete list of changes, see:
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.17&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

[basedb-devel] BASE 2.16.2 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We are happy to announce the release of BASE 2.16.2. This is a bugfix
release that fixes a few non-critical bugs and is the last 2.16.x
release before BASE 2.17

For a complete list of changes, see:
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.16.2&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [basedb-devel] External authentication

[Nicklas N. <ni...@th...>]

On 2011-02-01 13:24, Pawel Sztromwasser wrote:
> Sorry, just noticed that you mentioned the
> ...basedb.util.JarClassLoader, not a regular Java class loader as I
> initially  thought.

Check the code for DataFileType.getValidator(): 
http://base.thep.lu.se/browser/tags/2.16.1/src/core/net/sf/basedb/core/DataFileType.java#L629

It is more or less something like that that you need.

/Nicklas

Re: [basedb-devel] External authentication

[Pawel S. <Paw...@bc...>]

Sorry, just noticed that you mentioned the 
...basedb.util.JarClassLoader, not a regular Java class loader as I 
initially  thought.

On 01/02/11 13:17, Pawel Sztromwasser wrote:
> Thanks for a quick reply. I really wanted to avoid selecting jars and so
> on since BASE has over 50 of them, and maven downloads over 60 for my
> plugin. Lots of manual work that needs to be done every time BASE is
> upgraded.
>
> I will try to change the Application class as you suggested. I have
> already located the place which needs a fix, but was unsure of playing
> so close to the core of the application. What about using the
> net.sf.basedb.util.JarClassLoader, as regular plugins do?
>
> I will post a patch when ready and tested.
> Cheers,
> Pawel
>
> On 01/02/11 13:03, Nicklas Nordborg wrote:
>> On 2011-02-01 11:29, Pawel Sztromwasser wrote:s
>>> Hi,
>>>
>>> I am working on an external authentication plugin for BASE that will use
>>> an STS Web service to authenticate users. The plugin uses a bunch of
>>> external jars for WS communication, but with different versions then
>>> BASE. I was hoping for the same classloading mechanism as for regular
>>> plugins (separate classloaders), but it looks like external
>>> authentication plugins uses the default classloader of the webapp. Could
>>> this be changed? How else could I install my plugin, without messing
>>> with BASE's jars?
>> That part of BASE is not very "pluginified". I am not aware of any real
>> case that uses external authentication so it would be very interesting
>> to see if you succeed.
>>
>> It's quite common that there are dependencies to different versions of
>> 3rd-party JAR files, but it usually works if the latest one is used. But
>> of course, it may not work if the API has changed in an incompatible way.
>>
>> If you can't get it to work by clever selection of JAR files, then you
>> might have to modify the Application.getAuthenticator() method so that
>> it uses a different class loader. It shouldn't be too difficult. It
>> could for example pick up a JAR path from the base.config file and then
>> use the net.sf.basedb.util.JarClassLoader.getInstance(path) to create a
>> class loader. Dependencies need to be listed in the MANIFEST.MF in the
>> same way as for plug-ins. There is a short notice about this at
>> http://base.thep.lu.se/chrome/site/latest/html/developerdoc/plugin_developer/plugin_developer.organize.html
>> and
>> http://base.thep.lu.se/chrome/site/latest/api/net/sf/basedb/util/JarClassLoader.html
>>
>> As always, patches are welcome :)
>>
>> /Nicklas
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> basedb-devel mailing list
>> bas...@li...
>> https://lists.sourceforge.net/lists/listinfo/basedb-devel
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel

Re: [basedb-devel] External authentication

[Pawel S. <Paw...@bc...>]

Thanks for a quick reply. I really wanted to avoid selecting jars and so 
on since BASE has over 50 of them, and maven downloads over 60 for my 
plugin. Lots of manual work that needs to be done every time BASE is 
upgraded.

I will try to change the Application class as you suggested. I have 
already located the place which needs a fix, but was unsure of playing 
so close to the core of the application. What about using the 
net.sf.basedb.util.JarClassLoader, as regular plugins do?

I will post a patch when ready and tested.
Cheers,
Pawel

On 01/02/11 13:03, Nicklas Nordborg wrote:
> On 2011-02-01 11:29, Pawel Sztromwasser wrote:s
>> Hi,
>>
>> I am working on an external authentication plugin for BASE that will use
>> an STS Web service to authenticate users. The plugin uses a bunch of
>> external jars for WS communication, but with different versions then
>> BASE. I was hoping for the same classloading mechanism as for regular
>> plugins (separate classloaders), but it looks like external
>> authentication plugins uses the default classloader of the webapp. Could
>> this be changed? How else could I install my plugin, without messing
>> with BASE's jars?
> That part of BASE is not very "pluginified". I am not aware of any real
> case that uses external authentication so it would be very interesting
> to see if you succeed.
>
> It's quite common that there are dependencies to different versions of
> 3rd-party JAR files, but it usually works if the latest one is used. But
> of course, it may not work if the API has changed in an incompatible way.
>
> If you can't get it to work by clever selection of JAR files, then you
> might have to modify the Application.getAuthenticator() method so that
> it uses a different class loader. It shouldn't be too difficult. It
> could for example pick up a JAR path from the base.config file and then
> use the net.sf.basedb.util.JarClassLoader.getInstance(path) to create a
> class loader. Dependencies need to be listed in the MANIFEST.MF in the
> same way as for plug-ins. There is a short notice about this at
> http://base.thep.lu.se/chrome/site/latest/html/developerdoc/plugin_developer/plugin_developer.organize.html
> and
> http://base.thep.lu.se/chrome/site/latest/api/net/sf/basedb/util/JarClassLoader.html
>
> As always, patches are welcome :)
>
> /Nicklas
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> basedb-devel mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-devel