Hi all,

I solved my server problems and I'm up and running, but sadly the same problem persists. I can not use the data_manager tools to fetch a reference genome from file. If I launch the script from the command line I get:

No handlers could be found for logger "galaxy.util.json"

Traceback (most recent call last):
File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py", line 350, in <module>
if __name__ == "__main__": main()
File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py", line 335, in main
target_directory = params[ 'output_data' ][0]['extra_files_path']
KeyError: 'output_data'

So on one hand I get the "no logger" message (same as in the interface) and on the other hand, looking at the file that is generated by the data_manager I get a JSON dict without the params_dict or the output_data keys.

dataset_XXXXX.dat consistently gets this kind of content:

{"data_tables": {"all_fasta": [{"path": "sm52.fa", "dbkey": "sm52", "name": "Schistosoma mansoni v5.2", "value": "sm52"}]}}

Are these two different problems? Could you point me to a solution?

Cheers!

Cristian

From: tuto345@hotmail.com
To: dannon.baker@gmail.com
Date: Thu, 4 Dec 2014 16:01:53 +0000
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] No handlers could be found for logger "galaxy.util.json"

Hi Dannon,

I got it running! The problem was the main handler had crashed and (had not seen that the main.pid was missing).

I restarted the server and everything is running now.

Sorry for the waste of time!

Cristian

From: tuto345@hotmail.com
To: dannon.baker@gmail.com
Date: Thu, 4 Dec 2014 15:47:00 +0000
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] No handlers could be found for logger "galaxy.util.json"

Hi Dannon,

I started the installation of the server about a month or so back. I did a hg update -U recently...

$ hg tip

changeset: 14854:26aab19109ce

branch: stable

tag: tip

user: Nate Coraor <nate@bx.psu.edu>

date: Thu Nov 27 09:00:14 2014 -0500

summary: Update tag latest_2014.10.06 for changeset acb2548443ae

Any ideas?

Cristian

Date: Thu, 4 Dec 2014 10:22:22 -0500
Subject: Re: [galaxy-dev] No handlers could be found for logger "galaxy.util.json"
From: dannon.baker@gmail.com
To: tuto345@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Hi Cristian,

What revision of Galaxy are you running? I believe this was fixed a while back.

-Dannon

On Thu, Dec 4, 2014 at 10:14 AM, C. Ch. <tuto345@hotmail.com> wrote:

Hi All,

While trying to use the data_manager_fetch_genome_all_fasta to create a reference genome I get the following error:
No handlers could be found for logger "galaxy.util.json"

I'm on the latest version of galaxy.

Any idea what is wrong?

Thanks!
Cristian

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