Export history now seems to be working fine. My best guess is that the problem with exporting a history to file was caused by a more general problem after an update that I fixed separately. Apologies that I jumped the gun on asking for help.

Todd

On 5/20/2012 3:01 PM, Todd Oakley wrote:
Hi Jeremy,
I am no longer getting the same Error when exporting a history. However, I've now encountered a new problem. Namely, I am never able to actually download the file that Galaxy tells me it produced. I never can get past the web page that says:

Exporting History 'name of history here'. Use this link to download the archive or import it to another Galaxy server: <link to history here>

I thought at first perhaps this was just taking time, but after a few hours, I still got the same. Also, I tested a very simple history with 1 tiny file, and got the same result.

I'm using Firefox, and our Galaxy instance uses only Galaxy as the web server, no Apache or nginx

Thanks again for any advice!

Todd



On 4/26/2012 10:35 AM, Jeremy Goecks wrote:
I reproduced myself, diagnosed the issue, and committed a fix to -central. Once you update your Galaxy (or you update to the next distribution when it becomes available), the export should work.

Best,
J.

On Apr 26, 2012, at 12:49 PM, Todd Oakley wrote:

Sorry, I don't use the main Galaxy instance, I imagine I won't be able to reproduce the bug there anyway. Most of the tools I use are in-house for phylogenetics (we'll put them up on the tool shed in the next few weeks). I can ask a postdoc in my lab to try to export some histories, as he uses the main instance.

We can try to debug here. Can you point to a place to start looking (I haven't looked at the Galaxy code at all beyond universe.ini and tools)?

Thanks,

Todd

On 4/26/2012 5:41 AM, Jeremy Goecks wrote:
Hi Todd,

History export is a beta feature and hasn't been fully tested yet. We'll look into this, but it's difficult to diagnose a bug on a local instance. Can you reproduce on either our main or test server?

Thanks,
J.

On Apr 25, 2012, at 8:08 PM, Todd Oakley wrote:

Hello,
I'd am trying to export histories to upload to another galaxy instance.

For some histories, it works fine. However, for others, I get an error. When I turn on debug, I get the error pasted below. Any thoughts on what is the cause of "object has no attribute 'hid'"?

Thanks!
Todd



  Server Error

Module paste.exceptions.errormiddleware:*143* in |__call__|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>app_iter *=* self*.*application*(*environ*,* start_response*)*|
Module paste.debug.prints:*98* in |__call__|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>environ*,* self*.*app*)*|
Module paste.wsgilib:*539* in |intercept_output|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>app_iter *=* application*(*environ*,* replacement_start_response*)*|
Module paste.recursive:*80* in |__call__|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*632* in |__call__|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*145* in |__call__|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>body *=* method*(* trans*,* ****kwargs *)*|
Module galaxy.web.controllers.history:*591* in |export_archive|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>history_exp_tool*.*execute*(* trans*,* incoming *=* params*,* set_output_hid *=* True *)*|
Module galaxy.tools:*1276* in |execute|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* self*.*tool_action*.*execute*(* self*,* trans*,* incoming*=*incoming*,* set_output_hid*=*set_output_hid*,* history*=*history*,* ****kwargs *)*|
Module galaxy.tools.actions.history_imp_exp:*103* in |execute|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>include_deleted*=*incoming*[* 'include_deleted' *]* *)*|
Module galaxy.tools.imp_exp:*419* in |setup_job|
|>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>input_datasets *=* *[* assoc*.*dataset*.*hid *for* assoc *in* job*.*input_datasets *]*|
*AttributeError: 'NoneType' object has no attribute 'hid'*
--

***************************************
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***************************************

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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

   http://lists.bx.psu.edu/

--

***************************************
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***************************************

Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/>
Twitter: @UCSB_OakleyLab

*Recent Papers: *

  * Cnidocyte discharge regulated by opsin and light
    BMC Biology Paper <http://tinyurl.com/7dajl2q> | Scientific
    American Write-up
    
<http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/>

  * Sponge Larvae Could be Guided by Cryptochrome
    J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> |
    Nature News
    <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>



--

***************************************
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***************************************

Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/>
Twitter: @UCSB_OakleyLab

*Recent Papers: *

  * Cnidocyte discharge regulated by opsin and light
    BMC Biology Paper <http://tinyurl.com/7dajl2q> | Scientific
    American Write-up
    
<http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/>

  * Sponge Larvae Could be Guided by Cryptochrome
    J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> |
    Nature News
    <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

   http://lists.bx.psu.edu/

--

***************************************
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***************************************

Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/>
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper <http://tinyurl.com/7dajl2q> | Scientific American
   Write-up
   
<http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/>

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> |
   Nature News
   <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

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