[galaxy-dev] synchronous data depositing
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/
Re: [galaxy-dev] synchronous data depositing
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/ ___ 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/
Re: [galaxy-dev] synchronous data depositing
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=textname=Homo%20sapiens%20genes%20(GRCh37.p5)URL= http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1resultsButton=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) ?xml version=1.0? !-- If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in the initial response. If value of 'URL_method' is 'post', any additional params coming back in the initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile everything including and beyond the first '' is truncated from URL. They said they'll let us know when this is fixed at their end. -- tool name=BioMart id=test_me tool_type=data_source version=1.0.1 descriptionCentral server/description command interpreter=pythondata_source.py $output $__app__.config.output_size_limit/command inputs action=http://www.biomart.org/biomart/martview; check_values=false method=get target=_top displaygo to BioMart Central $GALAXY_URL/display param name=GALAXY_URL type=baseurl value=/tool_runner/test_me / /inputs request_param_translation request_param galaxy_name=URL remote_name=URL missing= append_param separator=amp; first_separator=? join== value name=_export missing=1 / value name=GALAXY_URL missing=0 / /append_param /request_param request_param galaxy_name=data_type remote_name=exportView_outputformat missing=tabular value_translation value galaxy_value=tabular remote_value=TSV / /value_translation /request_param request_param galaxy_name=URL_method remote_name=URL_method missing=get / request_param galaxy_name=dbkey remote_name=dbkey missing=? / request_param galaxy_name=organism remote_name=organism missing= / request_param galaxy_name=table remote_name=table missing= / request_param galaxy_name=description remote_name=description missing= / request_param galaxy_name=name remote_name=name missing=Biomart query / request_param galaxy_name=info
Re: [galaxy-dev] synchronous data depositing
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=textname=Homo%20sapiens%20genes%20(GRCh37.p5)URL=http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1resultsButton=1 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 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 ___ 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/
Re: [galaxy-dev] synchronous data depositing
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.comwrote:
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=textname=Homo%20sapiens%20genes%20%28GRCh37.p5%29URL=http://www.biomart.org/biomart/martview/1a5fc0bddc9f81dba837a1b1a5063691?do_export=1resultsButton=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',
'defaulthsapiens_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',
'defaulthsapiens_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=textname=Homo%20sapiens%20genes%20(GRCh37.p5)URL=
http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1resultsButton=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.eduwrote:
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
Re: [galaxy-dev] synchronous data depositing
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=textname=Homo%20sapiens%20genes%20%28GRCh37.p5%29URL=http://www.biomart.org/biomart/martview/1a5fc0bddc9f81dba837a1b1a5063691?do_export=1resultsButton=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',
'defaulthsapiens_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',
'defaulthsapiens_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=textname=Homo%20sapiens%20genes%20(GRCh37.p5)URL=http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1resultsButton=1
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 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
Re: [galaxy-dev] synchronous data depositing
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.comwrote:
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.comwrote:
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=textname=Homo%20sapiens%20genes%20%28GRCh37.p5%29URL=http://www.biomart.org/biomart/martview/1a5fc0bddc9f81dba837a1b1a5063691?do_export=1resultsButton=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',
'defaulthsapiens_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',
'defaulthsapiens_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.eduwrote:
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=textname=Homo%20sapiens%20genes%20(GRCh37.p5)URL=
http://www.biomart.org/biomart/martview/534024a0e03f1befd52ca87ba741b6c9?do_export=1resultsButton=1HTTP/1.1;
302 -
