Hi Nate,

Thanks for fixing so fast... has this been committed to http://www.bx.psu.edu/hg/galaxy?

Best, Leandro

-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Thursday, May 21, 2009 18:46 To: Hermida, Leandro Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] bug with output files_path property dataset ID when Galaxy has shared histories

Leandro,

This is fixed in the latest commit.

Thanks, --nate

Hermida, Leandro wrote:

Hello,

I've developed a few tools for Galaxy and I think I ran into a bug

that

even exists in the latest version. As you know a Galaxy server maintains the same external dataset ID (i.e. viewable in the web URLs)

to the filesystem internal dataset ID (i.e. names in database/files/000/) if no user in the Galaxy server has yet shared

any

histories (and their datasets). But once sharing starts the external dataset IDs start differing from the internal dataset ID, and they are

always higher and Galaxy maintains this transparently. But this behavior seems to be broken with the output files_path property.

If you have a tool which uses the output files_path property like this

one I have:

<command interpreter="perl">search.pl $query_list $output1 $output1.files_path</command>

On my test server I've shared one history with a single dataset. So

my

external-internal offset is 1. The above tool then produces the following command:

perl /home/hermida/galaxy/galaxy_dist/tools/omics_data_miner/search.pl

/home/hermida/galaxy/galaxy_dist/database/files/000/dataset_28.dat /home/hermida/galaxy/galaxy_dist/database/files/000/dataset_31.dat /home/hermida/galaxy/galaxy_dist/database/tmp/dataset_32_files

Galaxy is not generating the correct files_path, it should end in dataset_31_files not 32. This bug causes the tool to completely break

when you are trying to view your output in the browser and I tried to circumvent the bug with symlinking magic but it can't fix the problem because symlinks start stepping on existing directories once you run

the

tool more than once.

Thanks for any help on how to fix the problem,

Leandro

------------------------------------------------------------------------

---

galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev

Hi again,

I checked on my search tool and the problem with files_path looks fixed. Thanks.

BTW what was the reasoning for moving files_path from tmp --> job_working_directory?

Cheers, Leandro

-----Original Message----- From: Hermida, Leandro Sent: Thursday, May 21, 2009 22:18 To: Nate Coraor Cc: galaxy-dev@bx.psu.edu Subject: RE: [galaxy-dev] bug with output files_path property dataset IDwhen Galaxy has shared histories

Sorry... I got it, forgot to pull first :)

leandro

-----Original Message----- From: galaxy-dev-bounces@bx.psu.edu [mailto:galaxy-dev-bounces@bx.psu.edu] On Behalf Of Hermida, Leandro Sent: Thursday, May 21, 2009 21:56 To: Nate Coraor Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] bug with output files_path property dataset IDwhen Galaxy has shared histories

Hi Nate,

Thanks for fixing so fast... has this been committed to http://www.bx.psu.edu/hg/galaxy?

Best, Leandro

-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Thursday, May 21, 2009 18:46 To: Hermida, Leandro Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] bug with output files_path property dataset ID when Galaxy has shared histories

Leandro,

This is fixed in the latest commit.

Thanks, --nate

Hermida, Leandro wrote:

Hello,

I've developed a few tools for Galaxy and I think I ran into a bug

that

even exists in the latest version. As you know a Galaxy server maintains the same external dataset ID (i.e. viewable in the web URLs)

to the filesystem internal dataset ID (i.e. names in database/files/000/) if no user in the Galaxy server has yet shared

any

histories (and their datasets). But once sharing starts the external dataset IDs start differing from the internal dataset ID, and they are

always higher and Galaxy maintains this transparently. But this behavior seems to be broken with the output files_path property.

If you have a tool which uses the output files_path property like this

one I have:

<command interpreter="perl">search.pl $query_list $output1 $output1.files_path</command>

On my test server I've shared one history with a single dataset. So

my

external-internal offset is 1. The above tool then produces the following command:

perl /home/hermida/galaxy/galaxy_dist/tools/omics_data_miner/search.pl

/home/hermida/galaxy/galaxy_dist/database/files/000/dataset_28.dat /home/hermida/galaxy/galaxy_dist/database/files/000/dataset_31.dat /home/hermida/galaxy/galaxy_dist/database/tmp/dataset_32_files

Galaxy is not generating the correct files_path, it should end in dataset_31_files not 32. This bug causes the tool to completely break

when you are trying to view your output in the browser and I tried to circumvent the bug with symlinking magic but it can't fix the problem because symlinks start stepping on existing directories once you run

the

tool more than once.

Thanks for any help on how to fix the problem,

Leandro

------------------------------------------------------------------------

---

galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev

_______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev