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 pieter.lukasse@wur.nl 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

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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:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Lukasse, Pieter Sent: donderdag 19 maart 2015 17:39 To: 'Martin Čech'; galaxy-dev@lists.galaxyproject.org 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 [mailto:marten@bx.psu.edu] Sent: donderdag 19 maart 2015 15:02 To: Lukasse, Pieter; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org 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 <pieter.lukasse@wur.nlmailto:pieter.lukasse@wur.nl> 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.nlhttp://www.pri.wur.nl/

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