wrong validation message in toolshed

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wrong validation message in toolshed

Lukasse, Pieter

Hi ,

 

I’m getting this error message, which is not correct since the file IS available in the repository.

 

Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata.
create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.

 

I installed the package anyway and it works, which proves there is no real problem.

 

See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2  

 

Regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Department of Bioinformatics (Bioscience)

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


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Re: wrong validation message in toolshed

Martin Čech
Hi Pieter,

there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this line: <code file="match_library.py" />)

After you correct these links you might want to 'Reset repository metadata'.

Martin

On Thu, Mar 19, 2015 at 8:18 AM Lukasse, Pieter <[hidden email]> wrote:

Hi ,

 

I’m getting this error message, which is not correct since the file IS available in the repository.

 

Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata.
create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.

 

I installed the package anyway and it works, which proves there is no real problem.

 

See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2  

 

Regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Department of Bioinformatics (Bioscience)

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur

http://www.pri.wur.nl

 

___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: wrong validation message in toolshed

Lukasse, Pieter

Hi Martin,

 

Thanks. I fixed the problems in the .xml files, now referring to “../match_library.py” .

 

Now the error I get when I try to reset the repository metadata is 502:

 

502 Bad Gateway


nginx/1.2.1

 

 

Regards,

 

Pieter

 

From: Martin Čech [mailto:[hidden email]]
Sent: donderdag 19 maart 2015 15:02
To: Lukasse, Pieter; [hidden email]
Subject: Re: [galaxy-dev] wrong validation message in toolshed

 

Hi Pieter,

there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this line: <code file="match_library.py" />)

 

After you correct these links you might want to 'Reset repository metadata'.

 

Martin

 

On Thu, Mar 19, 2015 at 8:18 AM Lukasse, Pieter <[hidden email]> wrote:

Hi ,

 

I’m getting this error message, which is not correct since the file IS available in the repository.

 

Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata.
create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.

 

I installed the package anyway and it works, which proves there is no real problem.

 

See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2  

 

Regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Department of Bioinformatics (Bioscience)

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur

http://www.pri.wur.nl

 

___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: wrong validation message in toolshed

Lukasse, Pieter

I now noticed that another repository I own also only works after I choose “reset all metadata” at Tool Shed. See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/primo_multiomics

This repository does not seem to have any problems... Could there be something wrong with Tool Shed and our version of Galaxy (incompatibility issues)? And why would “reset all metadata” on tool shed solve the issue? Now for every commit I make, I seem to have to do this...strange.

 

Thanks,

 

Pieter

 

From: galaxy-dev [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 19 maart 2015 17:39
To: 'Martin Čech'; [hidden email]
Subject: Re: [galaxy-dev] wrong validation message in toolshed

 

Hi Martin,

 

Thanks. I fixed the problems in the .xml files, now referring to “../match_library.py” .

 

Now the error I get when I try to reset the repository metadata is 502:

 

502 Bad Gateway


nginx/1.2.1

 

 

Regards,

 

Pieter

 

From: Martin Čech [[hidden email]]
Sent: donderdag 19 maart 2015 15:02
To: Lukasse, Pieter; [hidden email]
Subject: Re: [galaxy-dev] wrong validation message in toolshed

 

Hi Pieter,

there seems to be either multiple incorrect links to the file or the wrappers expect multiple files that are missing from the repo. E.g. your wrapper library_lookup.xml refers to a file /GCMS/match_library.py which does not exist. (on this line: <code file="match_library.py" />)

 

After you correct these links you might want to 'Reset repository metadata'.

 

Martin

 

On Thu, Mar 19, 2015 at 8:18 AM Lukasse, Pieter <[hidden email]> wrote:

Hi ,

 

I’m getting this error message, which is not correct since the file IS available in the repository.

 

Metadata may have been defined for some items in revision 'f70b775dcaa5'. Correct the following problems if necessary and reset metadata.
create_model.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
library_lookup.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_metexp.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
query_mass_repos.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
rankfilterGCMS_tabular.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.
metams_lcms_annotate.xml - This file refers to a missing file match_library.py. Upload a file named match_library.py to the repository to correct this error.

 

I installed the package anyway and it works, which proves there is no real problem.

 

See https://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_metabolomics2  

 

Regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Department of Bioinformatics (Bioscience)

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

T: +31-317481122;
M: +31-628189540;
skype: pieter.lukasse.wur

http://www.pri.wur.nl

 

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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


___________________________________________________________
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:
  https://lists.galaxyproject.org/

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