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 jireland@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%20...
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_...', '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 dan@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_... HTTP/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 nate@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 dan@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:
-- 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)