Re: [galaxy-dev] no capsule export from a local tool shed

2014-09-11 Thread Christophe Antoniewski 
Dave,

Thank you very much, it worked indeed.
The gz export does not work yet, but this is apparently now due to a
problem with mercurial (An error occurred while processing your request: -
Archive type not allowed: gz).
Anyway, this is not a main issue and we are going to be able to focus on
the tools, without apache.

Thank thank thank

Chris



Christophe Antoniewski



Drosophila Genetics and Epigenetics
Laboratoire de Biologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
christophe.antoniew...@upmc.fr
http://bio-dev.snv.jussieu.fr/

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/

2014-09-11 15:18 GMT+02:00 Dave Bouvier :

> Christophe,
>
> Unfortunately, exporting a capsule without a proxy in front of the tool
> shed will fail to find dependencies if the dependencies were defined with
> the proxy in place. One solution would be to re-upload the dependency
> definitions without using the proxy, leaving the changeset_revision and
> toolshed attributes undefined. This will make the tool shed recalculate
> tool shed URLs and changeset revisions for the dependency relationships,
> and the capsule export should then find them.
>
>--Dave B.
>
> On 09/10/2014 12:11 PM, Christophe Antoniewski wrote:
>
>>
>> I am replying to myself to report limited progresses... :
>>
>> if we run the tool shed server without apache, the "export capsule" job
>> works, except that the repository dependencies are not seen (no "Export
>> repository dependencies?" checkbox to check). Without this new layer of
>> complication, we would leave apache which is not really required for
>> tool development in our local toolshed. But "Export repository
>> dependencies" matters...
>>
>> Sure we are missing something around Apache and tool_shed_wsgi.ini
>> configuration, but still lost..
>>
>> Chris
>>
>>
>> Christophe Antoniewski
>>
>>
>> Drosophila Genetics and Epigenetics
>> Laboratoire de Biologie du Développement
>> 9, Quai St Bernard, Boîte courrier 24
>> 75252 Paris Cedex 05
>> christophe.antoniew...@upmc.fr 
>> http://bio-dev.snv.jussieu.fr/
>>
>> Tel +33 1 44 27 34 39
>> Fax+33 1 44 27 34 45
>> Mobile+33 6 68 60 51 50
>>
>> http://drosophile.org
>>
>> http://www.sciencesenmarche.org/
>>
>>
>> 2014-09-08 19:24 GMT+02:00 Christophe Antoniewski
>> > >:
>>
>> Hi,
>>
>> Here is a question maybe to Greg:
>>
>> Since the GCC2014 we started a local toolshed following the
>> instructions in
>> http://gregvonkuster.org/galaxy-tool-shed-framework-
>> building-galaxy-tools/
>>
>> It works nicely, except that today I tried to export repository
>> capsules ("export this revision") from the local toolshed and it
>> returns the following error (see below). I cannot remember whether I
>> had ever tested this particular action since the local tool shed set
>> up. Thus I even cannot say whether the bug is due to an original
>> misconfiguration or it happened later on.
>>
>> I can add that the local toolshed is served by apache with rewriting
>> rules (I am saying this because in addition it is not possible to
>> download repositories as gz archives etc... and suspect that there
>> is maybe a problem, in addition, with the apache config).
>>
>> Any help appreciated !
>>
>> Regards
>>
>> Christophe
>>
>> ---
>>
>> URL:
>> http://lbcd41.snv.jussieu.fr/toolshed/repository/export?
>> repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f
>> Module galaxy.web.framework.middleware.error:*149* in |__call__|
>> |>>
>> > repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
>> *=* self*.*application*(*environ*,* sr_checker*)*|
>> Module paste.debug.prints:*106* in |__call__|
>> |>>
>> > repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>
>> environ*,*
>> self*.*app*)*|
>> Module paste.wsgilib:*543* in |intercept_output|
>> |>>
>> > repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
>> *=* application*(*environ*,* replacement_start_response*)*|
>> Module paste.recursive:*84* in |__call__|
>> |>>
>> > repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
>> self*.*application*(*environ*,* start_response*)*|
>> Module paste.httpexceptions:*633* in |__call__|
>> |>>
>> > repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
>> self*.*application*(*environ*,* start_response*)*|
>>

Re: [galaxy-dev] no capsule export from a local tool shed

2014-09-11 Thread Dave Bouvier 

Christophe,

Unfortunately, exporting a capsule without a proxy in front of the tool 
shed will fail to find dependencies if the dependencies were defined 
with the proxy in place. One solution would be to re-upload the 
dependency definitions without using the proxy, leaving the 
changeset_revision and toolshed attributes undefined. This will make the 
tool shed recalculate tool shed URLs and changeset revisions for the 
dependency relationships, and the capsule export should then find them.


   --Dave B.

On 09/10/2014 12:11 PM, Christophe Antoniewski wrote:


I am replying to myself to report limited progresses... :

if we run the tool shed server without apache, the "export capsule" job
works, except that the repository dependencies are not seen (no "Export
repository dependencies?" checkbox to check). Without this new layer of
complication, we would leave apache which is not really required for
tool development in our local toolshed. But "Export repository
dependencies" matters...

Sure we are missing something around Apache and tool_shed_wsgi.ini
configuration, but still lost..

Chris


Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
christophe.antoniew...@upmc.fr 
http://bio-dev.snv.jussieu.fr/

Tel +33 1 44 27 34 39
Fax+33 1 44 27 34 45
Mobile+33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/


2014-09-08 19:24 GMT+02:00 Christophe Antoniewski
mailto:christophe.antoniew...@snv.jussieu.fr>>:

Hi,

Here is a question maybe to Greg:

Since the GCC2014 we started a local toolshed following the
instructions in
http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/

It works nicely, except that today I tried to export repository
capsules ("export this revision") from the local toolshed and it
returns the following error (see below). I cannot remember whether I
had ever tested this particular action since the local tool shed set
up. Thus I even cannot say whether the bug is due to an original
misconfiguration or it happened later on.

I can add that the local toolshed is served by apache with rewriting
rules (I am saying this because in addition it is not possible to
download repositories as gz archives etc... and suspect that there
is maybe a problem, in addition, with the apache config).

Any help appreciated !

Regards

Christophe

---

URL:

http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f
Module galaxy.web.framework.middleware.error:*149* in |__call__|
|>>

app_iter
*=* self*.*application*(*environ*,* sr_checker*)*|
Module paste.debug.prints:*106* in |__call__|
|>>

environ*,*
self*.*app*)*|
Module paste.wsgilib:*543* in |intercept_output|
|>>

app_iter
*=* application*(*environ*,* replacement_start_response*)*|
Module paste.recursive:*84* in |__call__|
|>>

*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*633* in |__call__|
|>>

*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*132* in |__call__|
|>>

*return*
self*.*handle_request*(* environ*,* start_response *)*|
Module galaxy.web.framework.base:*190* in |handle_request|
|>>

body
*=* method*(* trans*,* kwargs *)*|
Module galaxy.webapps.tool_shed.controllers.repository:*1249* in
|export|
|>>

repositories_archive_filename
*=* os*.*path*.*basename*(* repositories_archive*.*name *)*|
*AttributeError: 'NoneType' object has no attribute 'name'*


Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Re: [galaxy-dev] no capsule export from a local tool shed

2014-09-10 Thread Christophe Antoniewski 
I am replying to myself to report limited progresses... :

if we run the tool shed server without apache, the "export capsule" job
works, except that the repository dependencies are not seen (no "Export
repository dependencies?" checkbox to check). Without this new layer of
complication, we would leave apache which is not really required for tool
development in our local toolshed. But "Export repository dependencies"
matters...

Sure we are missing something around Apache and tool_shed_wsgi.ini
configuration, but still lost..

Chris


Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
christophe.antoniew...@upmc.fr
http://bio-dev.snv.jussieu.fr/

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/

2014-09-08 19:24 GMT+02:00 Christophe Antoniewski <
christophe.antoniew...@snv.jussieu.fr>:

> Hi,
>
> Here is a question maybe to Greg:
>
> Since the GCC2014 we started a local toolshed following the instructions
> in
> http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/
>
> It works nicely, except that today I tried to export repository capsules
> ("export this revision") from the local toolshed and it returns the
> following error (see below). I cannot remember whether I had ever tested
> this particular action since the local tool shed set up. Thus I even cannot
> say whether the bug is due to an original misconfiguration or it happened
> later on.
>
> I can add that the local toolshed is served by apache with rewriting rules
> (I am saying this because in addition it is not possible to download
> repositories as gz archives etc... and suspect that there is maybe a
> problem, in addition, with the apache config).
>
> Any help appreciated !
>
> Regards
>
> Christophe
>
> ---
>
> URL:
> http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f
> Module galaxy.web.framework.middleware.error:*149* in __call__
> >>
> 
> app_iter *=* self*.*application*(*environ*,* sr_checker*)*
> Module paste.debug.prints:*106* in __call__
> >>
> 
> environ*,* self*.*app*)*
> Module paste.wsgilib:*543* in intercept_output
> >>
> 
> app_iter *=* application*(*environ*,* replacement_start_response*)*
> Module paste.recursive:*84* in __call__
> >>
> 
> *return* self*.*application*(*environ*,* start_response*)*
> Module paste.httpexceptions:*633* in __call__
> >>
> 
> *return* self*.*application*(*environ*,* start_response*)*
> Module galaxy.web.framework.base:*132* in __call__
> >>
> 
> *return* self*.*handle_request*(* environ*,* start_response *)*
> Module galaxy.web.framework.base:*190* in handle_request
> >>
> 
> body *=* method*(* trans*,* kwargs *)*
> Module galaxy.webapps.tool_shed.controllers.repository:*1249* in export
> >>
> 
> repositories_archive_filename *=* os*.*path*.*basename*(*
> repositories_archive*.*name *)*
> *AttributeError: 'NoneType' object has no attribute 'name'*
>
>
> Christophe Antoniewski
>
>
> Drosophila Genetics and Epigenetics
> Laboratoire de Biologie du Développement
> 9, Quai St Bernard, Boîte courrier 24
> 75252 Paris Cedex 05
> christophe.antoniew...@upmc.fr
> http://bio-dev.snv.jussieu.fr/
>
> Tel +33 1 44 27 34 39
> Fax +33 1 44 27 34 45
> Mobile +33 6 68 60 51 50
>
> http://drosophile.org
>
> http://www.sciencesenmarche.org/
>
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[galaxy-dev] no capsule export from a local tool shed

2014-09-08 Thread Christophe Antoniewski 
Hi,

Here is a question maybe to Greg:

Since the GCC2014 we started a local toolshed following the instructions in
http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/

It works nicely, except that today I tried to export repository capsules
("export this revision") from the local toolshed and it returns the
following error (see below). I cannot remember whether I had ever tested
this particular action since the local tool shed set up. Thus I even cannot
say whether the bug is due to an original misconfiguration or it happened
later on.

I can add that the local toolshed is served by apache with rewriting rules
(I am saying this because in addition it is not possible to download
repositories as gz archives etc... and suspect that there is maybe a
problem, in addition, with the apache config).

Any help appreciated !

Regards

Christophe

---

URL:
http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f
Module galaxy.web.framework.middleware.error:*149* in __call__
>>

app_iter *=* self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call__
>>

environ*,* self*.*app*)*
Module paste.wsgilib:*543* in intercept_output
>>

app_iter *=* application*(*environ*,* replacement_start_response*)*
Module paste.recursive:*84* in __call__
>>

*return* self*.*application*(*environ*,* start_response*)*
Module paste.httpexceptions:*633* in __call__
>>

*return* self*.*application*(*environ*,* start_response*)*
Module galaxy.web.framework.base:*132* in __call__
>>

*return* self*.*handle_request*(* environ*,* start_response *)*
Module galaxy.web.framework.base:*190* in handle_request
>>

body *=* method*(* trans*,* kwargs *)*
Module galaxy.webapps.tool_shed.controllers.repository:*1249* in export
>>

repositories_archive_filename *=* os*.*path*.*basename*(*
repositories_archive*.*name *)*
*AttributeError: 'NoneType' object has no attribute 'name'*


Christophe Antoniewski


Drosophila Genetics and Epigenetics
Laboratoire de Biologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05
christophe.antoniew...@upmc.fr
http://bio-dev.snv.jussieu.fr/

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/