Okay - I just checked out a clean Galaxy without modifications and I
don't see any problems with uploads. So this is likely something to do
with your setup - if I had to guess I would guess that your
job_conf.xml configuration is somehow incorrect - the job is getting
creating but nothing is running it. Can you verify this by looking in
the logs? I would imagine you do see lines like:

galaxy.tools.actions.upload_common INFO 2014-08-15 12:04:04,306 tool
upload1 created job id 2

for the uploads but nothing like:

galaxy.jobs.runners DEBUG 2014-08-15 12:04:05,119 (2) command is:
python /home/john/workspace/galaxy-central-fresh/tools/data_source/upload.py
....

You could also verify this is the problem by doing something other
than uploading - maybe a data source tool? I have attached a tool that
doesn't require any existing files or external data sources that I use
for testing stuff like this - maybe see if it runs?

If no jobs run - can you attach your job_conf.xml and we can try to
debug the problem from there.

If other tools run than it is likely not a job related problem - in
that case can you answer some questions - Are you using a proxy - if
so which one? Can you attach the configuration? Is the upload.xml tool
in your tool_conf.xml? Have you made modifications to it?

-John

On Fri, Aug 15, 2014 at 10:47 AM, Iry Witham <iry.wit...@jax.org> wrote:
> I have checked and everything appears correct.  I did notice that in the
> /database/tmp/upload_store/ there are files that when I cat them they are
> the files I am/have attempted to upload.  However, they do not get moved to
> the /ftp directory.  I am wondering if this is due to a misconfiguration in
> the universe.wsgi.ini or if it could be related to proftpd or postgres.
> Unfortunately I am under a very tight deadline and need to figure this out.
> Any assistance will be appreciated.
>
> Thanks,
> Iry
>
> From: Michael Mason <mma...@benaroyaresearch.org>
> Date: Thursday, August 14, 2014 12:48 PM
> To: Iry Witham <iry.wit...@jax.org>, "galaxy-dev@lists.bx.psu.edu"
> <galaxy-dev@lists.bx.psu.edu>
> Subject: Re: [galaxy-dev] Upload file not working with new install
>
> No sure if this will help but you may want to check this. We just fixed a
> problem from uploading small files via the ftp directory. Our nfs mount was
> set to cache file meta data about every 30 sec. This proved problematic when
> uploading a small fasta file that previously uploaded.  Every time we tried
> uploading, it finished with no errors but was empty. Turning the nfs caching
> off fixed this.
>
> From: Iry Witham <iry.wit...@jax.org>
> Date: Thursday, August 14, 2014 9:34 AM
> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
> Subject: [galaxy-dev] Upload file not working with new install
>
> Hi Team,
>
> I have installed a fresh version of Galaxy and am having an issue with the
> 'Upload File' tool.  When I attempt to use it it just sits and spins.  No
> data gets uploaded.  I have looked through the universe.wsgi.ini file and
> cannot find anything there that stands out.  Can you point me to a possible
> solution?
>
> Thanks,
> Iry
>
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<tool id="exit_code" name="Exit Code" version="1.0.0">
  <command>echo "$exit_code" > $output; exit $exit_code</command>
  <inputs>
    <param name="exit_code" type="integer" value="0" />
  </inputs>
  <outputs>
    <data format="txt" name="output">
    </data>
  </outputs>
  <stdio>
    <exit_code range="1:"   level="fatal"   description="Failing exit code." />
  </stdio>
  <tests>
  </tests>
</tool>
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