Hello Birgit,

This issue has been resolved in changeset 7272:b761471d7590, which is currently 
available from our Galaxy central repository.  Both the Galaxy test and Galaxy 
main tool sheds are running this latest changeset revision.

Thanks very much for reporting this problem!

Greg Von Kuster


On Jun 14, 2012, at 12:45 PM, Birgit Crain wrote:

> Hi Greg
> I was using the Galaxy test toolshed to upload the files into a repository. 
> On my Mac where I develop the tools I have a local instance that I loaded 
> from zipped file (downloaded April galaxy-galaxy-dist-40f1816d6857.zip) 
> running python 2.7. 
> When I download the repository to a local instance on our server the tools 
> and .loc file install fine (except that I don't have my datatypes defined 
> right, working on that).
> 
> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete 
> Genomics, Inc.
> (650) 428-6023 office | (408) 605-3938 mobile
> bcr...@completegenomics.com
> 
> 
> From: Greg Von Kuster <g...@bx.psu.edu>
> Date: Wednesday, June 13, 2012 6:05 PM
> To: Birgit Crain <bcr...@completegenomics.com>
> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample
> 
> Hi Birgit,
> 
> What version of Galaxy are you running?  You can determine this by typing "hg 
> heads" in your Galaxy installation directory.  Also, what version of Python 
> are you running, and what database are you using?  Can you also provide the 
> complete paster log from you tool shed?
> 
> Thanks,
> 
> Greg Von Kuster
> 
> On Jun 13, 2012, at 6:13 PM, Birgit Crain wrote:
> 
>> Hi Greg
>> 
>> Thanks for the tip. The .file items appear when I tar the directory on my 
>> Mac, so I work around that issue and tar the directory on a UNIX server. 
>> Thus said I happily did the same with another directory that contains tools 
>> that are all dependent on the tool_data_table_conf.xml.sample and the 
>> tool-data/cg_crr_files.loc.sample file.
>> 
>> This directory has the following files:
>> 
>> cgatools/README.txt
>> cgatools/tool_data_table_conf.xml.sample
>> cgatools/datatypes_conf.xml
>> cgatools/lib/galaxy/datatypes/completegenomics.py
>> cgatools/tool-data/cg_crr_files.loc.sample
>> cgatools/tools/cg_cgatools/listvariants.xml
>> cgatools/tools/cg_cgatools/junctiondiff.xml
>> cgatools/tools/cg_cgatools/snpdiff.xml
>> cgatools/tools/cg_cgatools/calldiff.xml
>> cgatools/tools/cg_cgatools/testvariants.xml
>> cgatools/tools/cg_cgatools/varfilter.xml
>> cgatools/tools/cg_cgatools/listtestvariants.xml
>> cgatools/tools/cg_cgatools/join.xml
>> cgatools/tools/cg_cgatools/varfilter_wrapper.pl
>> 
>> When I upload this tar ball to the repository, one tool, calldiff, which is 
>> alphabetically the first one in the list, loads properly and for the others 
>> I get the following error message:
>> 
>> Metadata was defined for some items in revision 'e183f52194a5'. Correct the 
>> following problems if necessary and reset metadata.
>> join.xml - This file refers to a missing file cg_crr_files.loc. Upload a 
>> file named cg_crr_files.loc.sample to the repository to correct this error.
>> junctiondiff.xml - This file refers to a missing file cg_crr_files.loc. 
>> Upload a file named cg_crr_files.loc.sample to the repository to correct 
>> this error.
>> listtestvariants.xml - This file refers to a missing file cg_crr_files.loc. 
>> Upload a file named cg_crr_files.loc.sample to the repository to correct 
>> this error.
>> listvariants.xml - This file refers to a missing file cg_crr_files.loc. 
>> Upload a file named cg_crr_files.loc.sample to the repository to correct 
>> this error.
>> snpdiff.xml - This file refers to a missing file cg_crr_files.loc. Upload a 
>> file named cg_crr_files.loc.sample to the repository to correct this error.
>> testvariants.xml - This file refers to a missing file cg_crr_files.loc. 
>> Upload a file named cg_crr_files.loc.sample to the repository to correct 
>> this error.
>> varfilter.xml - This file refers to a missing file cg_crr_files.loc. Upload 
>> a file named cg_crr_files.loc.sample to the repository to correct this error.
>> 
>> For the invalid tools is show this explanation:
>> 
>> [Errno 2] No such file or directory: 
>> '/var/opt/galaxy/g2cmnty/tmp/work_tmp/cg_crr_files.loc'
>> 
>> 
>> But I know the file is there …. Any suggestions? - I attached the tar ball 
>> for a closer look.
>> Thanks
>> 
>> 
>> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete 
>> Genomics, Inc.
>> (650) 428-6023 office | (408) 605-3938 mobile
>> bcr...@completegenomics.com
>> 
>> 
>> From: Greg Von Kuster <g...@bx.psu.edu>
>> Date: Wednesday, June 13, 2012 6:09 AM
>> To: Birgit Crain <bcr...@completegenomics.com>
>> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample
>> 
>> Hello Birgit,
>> 
>> Your archive included several "._" scripts for some reason.  None of these 
>> were valid xml files, but since they have a .xml extension, the tool shed 
>> attempts to parse them which results in the error message you got:
>> 
>> not well-formed (invalid token): line 1, column 0
>> 
>> Here is the contents of your achive:
>> 
>> -rw-r--r--   1 gvk  wheel   6148 Jun  6 16:09 .DS_Store
>> -rw-r--r--   1 gvk  wheel    171 May 25 13:44 
>> ._Calculate_TestVariants_Variant_Frequencies.xml
>> -rwxr-xr-x   1 gvk  wheel    171 May  3 19:19 
>> ._Calculate_TestVariants_Variant_Frequencies_0_1_0.pl
>> -rw-r--r--   1 gvk  wheel    171 May 31 13:39 ._List_Unique_Variants.xml
>> -rwxr-xr-x   1 gvk  wheel    171 May  3 12:50 ._List_Unique_Variants_2_1_0.pl
>> -rw-r--r--   1 gvk  wheel   1950 May 25 13:44 
>> Calculate_TestVariants_Variant_Frequencies.xml
>> -rwxr-xr-x   1 gvk  wheel   9242 May  3 19:19 
>> Calculate_TestVariants_Variant_Frequencies_0_1_0.pl
>> -rw-r--r--   1 gvk  wheel  13625 May 31 13:39 List_Unique_Variants.xml
>> -rwxr-xr-x   1 gvk  wheel  22321 May  3 12:50 List_Unique_Variants_2_1_0.pl
>> 
>> I eliminated all of the "._" files and created a new archive which uploaded 
>> successfully.  I've attached the archive.
>> 
>> 
>> Greg Von Kuster
>> 
>>  
>> On Jun 12, 2012, at 4:38 PM, Birgit Crain wrote:
>> 
>>> Thanks, Greg
>>> 
>>> I tried uploading the same tar ball without the 
>>> tool_data_table_config.xml.sample file and the tools load fine (to 
>>> troubleshoot I added only tools that actually do not depend on the file). 
>>> As soon as I add the .sample file to the tar ball I get the error message.
>>> 
>>> Thanks, Birgit
>>> 
>>> From: Greg Von Kuster <g...@bx.psu.edu>
>>> Date: Tuesday, June 12, 2012 1:18 PM
>>> To: Birgit Crain <bcr...@completegenomics.com>
>>> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample
>>> 
>>> Hi Birgit,
>>> 
>>> I don't see any problem with your xml definition below.  Are you sure the 
>>> problem is not with another file in the tarball?  If you can send me the 
>>> tarball, I'll take a look.
>>> 
>>> Greg Von Kuster
>>> 
>>> 
>>> On Jun 12, 2012, at 4:09 PM, Birgit Crain wrote:
>>> 
>>>> Hi 
>>>> 
>>>> I'm developing tools that use an entry in the tool_data_table_config.xml 
>>>> file. For upload into a repository I created a 
>>>> tool_data_table_config.xml.sample file with the corresponding table entry. 
>>>> The structure for the file I copied from the  tool_data_table_config.xml. 
>>>> in the galaxy download.
>>>> 
>>>> <tables>
>>>> <!-- Start location of cgatools crr files -->
>>>> <table name="cg_crr_files" comment_char="#">
>>>> <columns>value, dbkey, name, path</columns>
>>>> <file path="tool-data/cg_crr_files.loc" />
>>>> </table>
>>>> <!-- End Location of cgatools crr files -->
>>>> </tables>
>>>> 
>>>> When I upload the tar ball into the repository the tools won't load 
>>>> properly and I get the following message:
>>>> 
>>>> not well-formed (invalid token): line 1, column 0
>>>> 
>>>> Any suggestions what I'm missing or how to fix this error?
>>>> 
>>>> Thanks, Birgit
>>>> 
>>>>  
>>>>  
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>>  
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