Sorry - this truly is the last question.  Besides my question above on the
expected response type from my page, how do I get Galaxy to skip the
intermediate "Execute" button before the resubmission?

Sorry for all the questions and thanks for your help.
-James


On Thu, Dec 1, 2011 at 10:11 AM, James Ireland <jirel...@5amsolutions.com>wrote:

> Excellent!  Thanks, Dan.
>
> I'm now getting the post resubmits from Galaxy.  Works great!  Last
> question - can you provide any info on the expected http response type from
> my page back to Galaxy after the resubmit?  Returning a standard html
> response or text/csv doesn't seem to be cutting it.
>
>
>
> On Thu, Dec 1, 2011 at 9:13 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
>
>> Hi James,
>>
>> tools/data_source/yeastmine.xml is a good example of a relatively simple
>> configuration. Ideally, the <request_param_translation/> tagset would not
>> be required, if a more specific data_type parameter value was being
>> provided by the external site.
>>
>>
>> Thanks for using Galaxy,
>>
>> Dan
>>
>>
>> On Dec 1, 2011, at 12:05 PM, James Ireland wrote:
>>
>> Hi Dan,
>>
>> BTW - is there a particular tool/tool.xml I should focus on for a
>> demonstration of current best practices?
>>
>> Thanks,
>>  -James
>>
>>
>> On Thu, Dec 1, 2011 at 8:40 AM, James Ireland 
>> <jirel...@5amsolutions.com>wrote:
>>
>>> Hi Dan,
>>>
>>> Ahhh... ok.  I had seen two forms of the url ad was wondering what was
>>> up.
>>>
>>> So, simply removing the param creates a poorly formed url:
>>>
>>>
>>> http://127.0.0.1:8080/tool_runner?tool_id=test_me?type=text&name=Homo%20sapiens%20genes%20%28GRCh37.p5%29&URL=http://www.biomart.org/biomart/martview/1a5fc0bddc9f81dba837a1b1a5063691?do_export=1&resultsButton=1
>>>
>>> Which causes much wailing and nashing of teeth...
>>>
>>> Tool 'test_me?type=text' does not exist,
>>> kwd={'hsapiens_gene_ensembl__feature_page__attribute.ensembl_gene_id':
>>> u'on', 'hsapiens_gene_ensembl__filter.go_parent_name': u'',
>>> 'hsapiens_gene_ensembl__filter.encode_region': u'5:131256415:132256414',
>>> 'hsapiens_gene_ensembl__filtergroup.gene__visibility': u'show',
>>> 'hsapiens_gene_ensembl__filter.start': u'1',
>>> 'hsapiens_gene_ensembl__filter.marker_end': u'',
>>> 'hsapiens_gene_ensembl__filter.id_list_limit_filters': u'ensembl_gene_id',
>>> 'hsapiens_gene_ensembl__filter.type': u'manual_picks', 'export_subset':
>>> u'10', 'hsapiens_gene_ensembl__filter.somatic_variation_source': u'COSMIC',
>>> 'default____hsapiens_gene_ensembl__homologs__attributelist':
>>> [u'hsapiens_gene_ensembl__homologs__attribute.ensembl_gene_id',
>>> u'hsapiens_gene_ensembl__homologs__attribute.ensembl_transcript_id'],
>>> 'hsapiens_gene_ensembl__transcript_event__attribute.ensembl_gene_id':
>>> u'on', 'hsapiens_gene_ensembl__snp__attribute.ensembl_gene_id': u'on',
>>> 'hsapiens_gene_ensembl__filtergroup.protein__visibility': u'hide',
>>> 'exportView_outputformat': u'TSV', 'export_saveto': u'text',
>>> 'export_dataset': u'0', 'URL': u'
>>> http://www.biomart.org/biomart/martview/1a5fc0bddc9f81dba837a1b1a5063691?do_export=1',
>>> 'default____hsapiens_gene_ensembl__transcript_event__attributelist':
>>> [u'hsapiens_gene_ensembl__transcript_event__attribute.ensembl_gene_id',
>>> u'hsapiens_gene_ensembl__transcript_event__attribute.ensembl_transcript_id'],
>>> 'hsapiens_gene_ensembl__filter.transcript_status': u'KNOWN',
>>> 'hsapiens_gene_ensembl__filter.with_transmembrane_domain': u'only',
>>> 'menuNumber': u'0', 'hsapiens_gene_ensembl__filter.protein_fam_id_b...
>>> etc, etc
>>>
>>> If I correct the URL by hand (change the second ? to &) and resubmit,
>>> that seems to work!  I'll try using this url form on my own page now.
>>>
>>> I'm surprised that the legacy url works until I change the tool name!
>>> If you hear no more from me, you can assume it worked.
>>>
>>> Thanks!
>>>  -James
>>>
>>> On Thu, Dec 1, 2011 at 8:25 AM, Daniel Blankenberg <d...@bx.psu.edu>wrote:
>>>
>>>> Hi James,
>>>>
>>>> For legacy reasons, Biomart uses a special-cased GALAXY_URL parameter,
>>>> which is likely the source of the problem. If you remove the '<param
>>>> name="GALAXY_URL" ... />' input parameter, restart Galaxy and reload
>>>> the Galaxy interface, does it then work correctly?
>>>>
>>>>
>>>> Thanks for using Galaxy,
>>>>
>>>> Dan
>>>>
>>>> On Dec 1, 2011, at 11:18 AM, James Ireland wrote:
>>>>
>>>> Hi Dan,
>>>>
>>>> Thanks for the quick response!
>>>>
>>>> I have a feeling this is something silly that I'm missing.  As a
>>>> reality check I simply created a copy of the biomart.xml tool.xml file and
>>>> called it test_me.xml.  I  changed the tool_id and GALAXY_URL in the xml
>>>> file as you'll see and added a link in my tool_config.  Selecting this tool
>>>> from the Get Data folder brings me to Biomart as expected.  When I hit
>>>> "go", I have the same issue of just being redirected to the welcome page.
>>>> The server output is shown below.  The unchanged biomart tool continues to
>>>> work fine.
>>>>
>>>> Galaxy server output:
>>>>
>>>> 127.0.0.1 - - [01/Dec/2011:08:08:27 -0700] "POST
>>>> /tool_runner/test_me?type=text&name=Homo%20sapiens%20genes%20(GRCh37.p5)&URL=
>>>> http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1&resultsButton=1HTTP/1.1";
>>>>  302 - "
>>>> http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9";
>>>> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101
>>>> Firefox/8.0.1"
>>>>
>>>> Here's my Galaxy revision info:
>>>> changeset:   6056:338ead4737ba
>>>> tag:         tip
>>>> user:        Nate Coraor <n...@bx.psu.edu>
>>>> date:        Thu Sep 29 16:45:19 2011 -0400
>>>>
>>>> Thanks again,
>>>>  -James
>>>>
>>>> P.S.  It's my pleasure to use Galaxy!  ;)
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Dec 1, 2011 at 7:06 AM, Daniel Blankenberg <d...@bx.psu.edu>wrote:
>>>>
>>>>> Hi James,
>>>>>
>>>>> Can you let us know which revision of Galaxy that you are using (hg
>>>>> head) and any log output that appears when accessing or running the tool?
>>>>> Also the list of parameters and values that are being POSTed to Galaxy and
>>>>> a copy of your tool.xml file would be useful.
>>>>>
>>>>>
>>>>> Thanks for using Galaxy,
>>>>>
>>>>> Dan
>>>>>
>>>>>
>>>>>
>>>>> On Dec 1, 2011, at 5:08 AM, James Ireland wrote:
>>>>>
>>>>> Greetings,
>>>>>
>>>>> I've been attempting to return data to Galaxy via the synchronous data
>>>>> depositing protocol.  Using the Biomart, UCSC Table Browser, etc as
>>>>> examples in the data_source tools directory, I've been able to get the
>>>>> initial GET request to my site just fine.  However, when I POST back to
>>>>> galaxy I immediately get a redirect to the welcome page and Galaxy never
>>>>> resubmits back to my site.
>>>>>
>>>>> I was wondering if there is more to the protocol than is covered here:
>>>>> http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources or perhaps
>>>>> configuration I need to perform on my local Galaxy installation to
>>>>> correctly handle the POSTs back to tool_runner?  Also, are there any code
>>>>> examples I should be looking at?
>>>>>
>>>>> Thanks for your help!
>>>>> -James
>>>>>
>>>>>
>>>>> --
>>>>> J Ireland
>>>>> www.5amsolutions.com | Software for Life(TM)
>>>>> m: 415 484-DATA (3282)
>>>>> ___________________________________________________________
>>>>> 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/
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> J Ireland
>>>> www.5amsolutions.com | Software for Life(TM)
>>>> m: 415 484-DATA (3282)
>>>> <test_me.xml>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> J Ireland
>>> www.5amsolutions.com | Software for Life(TM)
>>> m: 415 484-DATA (3282)
>>>
>>
>>
>>
>> --
>> J Ireland
>> www.5amsolutions.com | Software for Life(TM)
>> m: 415 484-DATA (3282)
>>
>>
>>
>
>
> --
> J Ireland
> www.5amsolutions.com | Software for Life(TM)
> m: 415 484-DATA (3282)
>



-- 
J Ireland
www.5amsolutions.com | Software for Life(TM)
m: 415 484-DATA (3282)
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