Test version v2r17b2

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Test version v2r17b2

Mariette
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
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virtual desktops. With this all-in-one solution, easily deploy virtual
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costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
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Re: Test version v2r17b2

Joshua Orvis
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users


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infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
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Re: Test version v2r17b2

Mariette

Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users



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infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox


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Re: Test version v2r17b2

Arze, Cesar
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
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infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox


_______________________________________________
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Re: Test version v2r17b2

Mariette

Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox


_______________________________________________
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ergatis.ini.txt (14K) Download Attachment
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Re: Test version v2r17b2

Arze, Cesar
Hi Jerome (sorry for calling you Mariette, was on cruise control this morning),

Your config looks good but you are missing one new variable that is needed for the new login system:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the 
;; same folder that houses the global ID repository
session_db_dir = /opt/ergatis/global_id_repository
The error you're encountering is a bug. I am testing a quick fix right now and can provide you with a fix that should take care of the issue.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 9:52 AM, Mariette wrote:


Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox


_______________________________________________
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------------------------------------------------------------------------------
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new or port existing apps to sell to consumers worldwide. Explore the
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<ergatis.ini.txt>------------------------------------------------------------------------------
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Re: Test version v2r17b2

Mariette

Hi,
the value in the config file I sent you is present:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the
;; same folder that houses the global ID repository
session_db_dir = /usr/local/bioinfo/src/ergatisng6/v2r17b2/global_id_repository

Thanks for your time,
looking forward the quick fix,
Jerome







Le 03/01/2012 19:13, Arze, Cesar a écrit :
Hi Jerome (sorry for calling you Mariette, was on cruise control this morning),

Your config looks good but you are missing one new variable that is needed for the new login system:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the 
;; same folder that houses the global ID repository
session_db_dir = /opt/ergatis/global_id_repository
The error you're encountering is a bug. I am testing a quick fix right now and can provide you with a fix that should take care of the issue.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 9:52 AM, Mariette wrote:


Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox


_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

------------------------------------------------------------------------------
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Get the SDK and tools to simplify cross-platform app development. Create
new or port existing apps to sell to consumers worldwide. Explore the
Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join
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Re: Test version v2r17b2

Mariette

Hi,

just as information, the test of the package CGI/Session.pm is missing when performing the perl Maekefile.pl command
in the version 17b2, which is required by the user interface.

Jerome




Le 04/01/2012 11:14, Mariette a écrit :

Hi,
the value in the config file I sent you is present:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the
;; same folder that houses the global ID repository
session_db_dir = /usr/local/bioinfo/src/ergatisng6/v2r17b2/global_id_repository

Thanks for your time,
looking forward the quick fix,
Jerome







Le 03/01/2012 19:13, Arze, Cesar a écrit :
Hi Jerome (sorry for calling you Mariette, was on cruise control this morning),

Your config looks good but you are missing one new variable that is needed for the new login system:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the 
;; same folder that houses the global ID repository
session_db_dir = /opt/ergatis/global_id_repository
The error you're encountering is a bug. I am testing a quick fix right now and can provide you with a fix that should take care of the issue.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 9:52 AM, Mariette wrote:


Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
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costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
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Re: Test version v2r17b2

Mariette

Hi again,

When running some pipeline, I have the following error, but can't understand what it means.

Software error:

failed to extract a repository_root from /ng6/share/tmp/ergatis/ng6/pyrocleaner/400_pyrocleaner/GJPX9IN06.pyrocleaner.stderr.  expected a workflow/runtime subdirectory somewhere. at /var/www/html/ergatisv17/cgi/view_formatted_log_source.cgi line 32.

Am I missing something ?
thanks

Jerome




Le 05/01/2012 13:56, Mariette a écrit :

Hi,

just as information, the test of the package CGI/Session.pm is missing when performing the perl Maekefile.pl command
in the version 17b2, which is required by the user interface.

Jerome




Le 04/01/2012 11:14, Mariette a écrit :

Hi,
the value in the config file I sent you is present:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the
;; same folder that houses the global ID repository
session_db_dir = /usr/local/bioinfo/src/ergatisng6/v2r17b2/global_id_repository

Thanks for your time,
looking forward the quick fix,
Jerome







Le 03/01/2012 19:13, Arze, Cesar a écrit :
Hi Jerome (sorry for calling you Mariette, was on cruise control this morning),

Your config looks good but you are missing one new variable that is needed for the new login system:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the 
;; same folder that houses the global ID repository
session_db_dir = /opt/ergatis/global_id_repository
The error you're encountering is a bug. I am testing a quick fix right now and can provide you with a fix that should take care of the issue.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 9:52 AM, Mariette wrote:


Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
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infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox


_______________________________________________
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new or port existing apps to sell to consumers worldwide. Explore the
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<ergatis.ini.txt>------------------------------------------------------------------------------
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Get the SDK and tools to simplify cross-platform app development. Create
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Re: Test version v2r17b2

Arze, Cesar
Jerome,

You are running into an issue based off some (naive) assumptions I made when updating some of the interface codebase to restrict access to viewing pipelines/pipelines resources to the person who created the pipeline when the proper switch is flipped in the config file. For the time being you can apply the patch I am attaching and it should clear up the issue. 

'patch -u /path/to/view_formatted_log_source.cgi view_formatted_log_source.patch'  should do the trick

I am going to fix this issue and likely push out a new release with this and the fix to address the other bug you found. Thanks for being so patient through all of this.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu


On Jan 5, 2012, at 9:14 AM, Mariette wrote:


Hi again,

When running some pipeline, I have the following error, but can't understand what it means.

Software error:

failed to extract a repository_root from /ng6/share/tmp/ergatis/ng6/pyrocleaner/400_pyrocleaner/GJPX9IN06.pyrocleaner.stderr.  expected a workflow/runtime subdirectory somewhere. at /var/www/html/ergatisv17/cgi/view_formatted_log_source.cgi line 32.

Am I missing something ?
thanks

Jerome




Le 05/01/2012 13:56, Mariette a écrit :

Hi,

just as information, the test of the package CGI/Session.pm is missing when performing the perl Maekefile.pl command
in the version 17b2, which is required by the user interface.

Jerome




Le 04/01/2012 11:14, Mariette a écrit :

Hi,
the value in the config file I sent you is present:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the
;; same folder that houses the global ID repository
session_db_dir = /usr/local/bioinfo/src/ergatisng6/v2r17b2/global_id_repository

Thanks for your time,
looking forward the quick fix,
Jerome







Le 03/01/2012 19:13, Arze, Cesar a écrit :
Hi Jerome (sorry for calling you Mariette, was on cruise control this morning),

Your config looks good but you are missing one new variable that is needed for the new login system:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the 
;; same folder that houses the global ID repository
session_db_dir = /opt/ergatis/global_id_repository
The error you're encountering is a bug. I am testing a quick fix right now and can provide you with a fix that should take care of the issue.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 9:52 AM, Mariette wrote:


Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

------------------------------------------------------------------------------
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infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual
desktops for less than the cost of PCs and save 60% on VDI infrastructure
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
_______________________________________________
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------------------------------------------------------------------------------
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_______________________________________________
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<ergatis.ini.txt>------------------------------------------------------------------------------
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Get the SDK and tools to simplify cross-platform app development. Create
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Re: Test version v2r17b2

Arze, Cesar
Jerome,

Here is the patch to fix the issue you encountered when attempting to look at the ergatis configuration from the admin tab. Can be executed with 'patch -u /path/to/view_formatted_ini_source.cgi view_formatted_ini_source.patch

Cesar


On Jan 5, 2012, at 9:37 AM, Arze, Cesar wrote:

Jerome,

You are running into an issue based off some (naive) assumptions I made when updating some of the interface codebase to restrict access to viewing pipelines/pipelines resources to the person who created the pipeline when the proper switch is flipped in the config file. For the time being you can apply the patch I am attaching and it should clear up the issue. 

'patch -u /path/to/view_formatted_log_source.cgi view_formatted_log_source.patch'  should do the trick

I am going to fix this issue and likely push out a new release with this and the fix to address the other bug you found. Thanks for being so patient through all of this.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu


On Jan 5, 2012, at 9:14 AM, Mariette wrote:


Hi again,

When running some pipeline, I have the following error, but can't understand what it means.

Software error:

failed to extract a repository_root from /ng6/share/tmp/ergatis/ng6/pyrocleaner/400_pyrocleaner/GJPX9IN06.pyrocleaner.stderr.  expected a workflow/runtime subdirectory somewhere. at /var/www/html/ergatisv17/cgi/view_formatted_log_source.cgi line 32.

Am I missing something ?
thanks

Jerome




Le 05/01/2012 13:56, Mariette a écrit :

Hi,

just as information, the test of the package CGI/Session.pm is missing when performing the perl Maekefile.pl command
in the version 17b2, which is required by the user interface.

Jerome




Le 04/01/2012 11:14, Mariette a écrit :

Hi,
the value in the config file I sent you is present:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the
;; same folder that houses the global ID repository
session_db_dir = /usr/local/bioinfo/src/ergatisng6/v2r17b2/global_id_repository

Thanks for your time,
looking forward the quick fix,
Jerome







Le 03/01/2012 19:13, Arze, Cesar a écrit :
Hi Jerome (sorry for calling you Mariette, was on cruise control this morning),

Your config looks good but you are missing one new variable that is needed for the new login system:

;; If authentication is enabled this folder must be defined (and writable) as user session
;; metadata is written here and required when ergatis authentication is enabled. Ideally this folder
;; should be in an area that would not undergo any sort of periodic cleanup. An ideal location is the 
;; same folder that houses the global ID repository
session_db_dir = /opt/ergatis/global_id_repository
The error you're encountering is a bug. I am testing a quick fix right now and can provide you with a fix that should take care of the issue.

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 9:52 AM, Mariette wrote:


Hi,
you can find it in attachement,
thanks for your time,
Jerome






Le 03/01/2012 14:33, Arze, Cesar a écrit :
Hi Mariette,

Do you mind posting the contents of your ergatis.ini for me?

Thanks!

Cesar Arze
Bioinformatics Software Engineer II
Institute for Genome Sciences - University of Maryland School of Medicine
BioPark II
801 W. Baltimore Street
Baltimore, MD 21201
Tel: 410-706-2302
http://www.igs.umaryland.edu

On Jan 3, 2012, at 5:48 AM, Mariette wrote:


Thanks Joshua,
I haven't took the previous config file but started from scratch. The 2 values your pointing are settled (to the global id repository for the first one and at 0 for the other one).
I figured out that in the admin when I click on the view ergatis settings I got the following error:

Software error:

failed to extract a repository root, project identifier or pipeline ID from ergatis.ini. Expected a workflow/runtime subdirectory somewhere. at /var/www/html/ng6/ergatisv2r17/cgi/view_formatted_ini_source.cgi line 38.


Doese someone have the same problem ??




Le 02/01/2012 21:47, Joshua Orvis a écrit :
Jerome -

Some new things have been added to the ergatis.ini file in the authentication section, such as session information for logged in users when authentication is on.  If you just copied over your previous configuration file some of these new settings might be missing and causing login issues.  If you still have your downloaded copy you can look there, else the latest one for comparison is here:

http://ergatis.svn.sourceforge.net/viewvc/ergatis/trunk/htdocs/cgi/ergatis.ini?revision=7539&view=markup

Specifically, look in the [authentication] section for new parameters like 'session_db_dir' and 'per_account_pipeline_security'

Joshua




On Mon, Jan 2, 2012 at 10:23 AM, Mariette <[hidden email]> wrote:
Hi everyone,

We are testing the new version of ergatis. Everything went pretty well.
However the login functionality is no longer working.
When clinking on login, the form appear; I enter the login/password and
it redirct to the index page. However, where with the
previous version there was "user [logout]" displayed, now it is still
displayed login. The user is not login as far as when I run a
pipeline, we have a permission denied error when trying to write on the
output directory.

The config used is exactly the same than with the old version.
Nothing appears in the apache logs.
What could be the problem ?

Thanks,
Jerome

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view_formatted_ini_source.patch (1K) Download Attachment