no capsule export from a local tool shed

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no capsule export from a local tool shed

Christophe Antoniewski-2
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
[hidden email]
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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Re: no capsule export from a local tool shed

Christophe Antoniewski-2

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
[hidden email]
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 <[hidden email]>:
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
[hidden email]
http://bio-dev.snv.jussieu.fr/

Tel <a href="tel:%2B33%201%2044%2027%2034%2039" value="+33144273439" target="_blank">+33 1 44 27 34 39
Fax <a href="tel:%2B33%201%2044%2027%2034%2045" value="+33144273445" target="_blank">+33 1 44 27 34 45
Mobile <a href="tel:%2B33%206%2068%2060%2051%2050" value="+33668605150" target="_blank">+33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: no capsule export from a local tool shed

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
> [hidden email] <mailto:[hidden email]>
> 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
> <[hidden email]
> <mailto:[hidden email]>>:
>
>     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__|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
>     *=* self*.*application*(*environ*,* sr_checker*)*|
>     Module paste.debug.prints:*106* in |__call__|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>environ*,*
>     self*.*app*)*|
>     Module paste.wsgilib:*543* in |intercept_output|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
>     *=* application*(*environ*,* replacement_start_response*)*|
>     Module paste.recursive:*84* in |__call__|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
>     self*.*application*(*environ*,* start_response*)*|
>     Module paste.httpexceptions:*633* in |__call__|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
>     self*.*application*(*environ*,* start_response*)*|
>     Module galaxy.web.framework.base:*132* in |__call__|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
>     self*.*handle_request*(* environ*,* start_response *)*|
>     Module galaxy.web.framework.base:*190* in |handle_request|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>body
>     *=* method*(* trans*,* ****kwargs *)*|
>     Module galaxy.webapps.tool_shed.controllers.repository:*1249* in
>     |export|
>     |>>
>     <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>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
>     [hidden email] <mailto:[hidden email]>
>     http://bio-dev.snv.jussieu.fr/
>
>     Tel +33 1 44 27 34 39 <tel:%2B33%201%2044%2027%2034%2039>
>     Fax+33 1 44 27 34 45 <tel:%2B33%201%2044%2027%2034%2045>
>     Mobile+33 6 68 60 51 50 <tel:%2B33%206%2068%2060%2051%2050>
>
>     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/
>
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in your mail client.  To manage your subscriptions to this
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Re: no capsule export from a local tool shed

Christophe Antoniewski-2
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
[hidden email]
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 <[hidden email]>:
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
[hidden email] <mailto:[hidden email]>
http://bio-dev.snv.jussieu.fr/

Tel <a href="tel:%2B33%201%2044%2027%2034%2039" value="+33144273439" target="_blank">+33 1 44 27 34 39
Fax<a href="tel:%2B33%201%2044%2027%2034%2045" value="+33144273445" target="_blank">+33 1 44 27 34 45
Mobile<a href="tel:%2B33%206%2068%2060%2051%2050" value="+33668605150" target="_blank">+33 6 68 60 51 50

http://drosophile.org

http://www.sciencesenmarche.org/


2014-09-08 19:24 GMT+02:00 Christophe Antoniewski
<[hidden email]
<mailto:[hidden email]>>:

    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__|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
    *=* self*.*application*(*environ*,* sr_checker*)*|
    Module paste.debug.prints:*106* in |__call__|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>environ*,*
    self*.*app*)*|
    Module paste.wsgilib:*543* in |intercept_output|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>app_iter
    *=* application*(*environ*,* replacement_start_response*)*|
    Module paste.recursive:*84* in |__call__|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
    self*.*application*(*environ*,* start_response*)*|
    Module paste.httpexceptions:*633* in |__call__|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
    self*.*application*(*environ*,* start_response*)*|
    Module galaxy.web.framework.base:*132* in |__call__|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>*return*
    self*.*handle_request*(* environ*,* start_response *)*|
    Module galaxy.web.framework.base:*190* in |handle_request|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>body
    *=* method*(* trans*,* ****kwargs *)*|
    Module galaxy.webapps.tool_shed.controllers.repository:*1249* in
    |export|
    |>>
    <http://lbcd41.snv.jussieu.fr/toolshed/repository/export?repository_id=8b0bee1f52868c9e&changeset_revision=73f6de7efb1f#>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
    [hidden email] <mailto:[hidden email]>
    http://bio-dev.snv.jussieu.fr/

    Tel <a href="tel:%2B33%201%2044%2027%2034%2039" value="+33144273439" target="_blank">+33 1 44 27 34 39 <tel:%2B33%201%2044%2027%2034%2039>
    Fax<a href="tel:%2B33%201%2044%2027%2034%2045" value="+33144273445" target="_blank">+33 1 44 27 34 45 <tel:%2B33%201%2044%2027%2034%2045>
    Mobile<a href="tel:%2B33%206%2068%2060%2051%2050" value="+33668605150" target="_blank">+33 6 68 60 51 50 <tel:%2B33%206%2068%2060%2051%2050>

    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:
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___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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