Good afternoon Martin,
I believe I have a better approach, by passing the history_id and dataset_id to
my config visualization plugin mako file. As you can see in the attachment,
both of them appear in the call, but the mako doesn't execute and I get the
following error. If I do hard code the path in the mako and not pass the
history_id I can get the mako to display a canned file.
Your thoughts?
Thanks
bob
1. mako.xml data_sources
<data_sources> <data_source>
<model_class>HistoryDatasetAssociation</model_class> <test
test_attr="extension">MDA_zip</test> <to_param
param_attr="id">history_id</to_param> <to_param
param_attr="id">dataset_id</to_param> </data_source> </data_sources>
<params> <param type="dataset" var_name_in_template="data"
required="true">dataset_id</param> <param type="history"
var_name_in_template="history" required="true">history_id</param> </params>
2. and mako codes to retrieve parameters.
var chmDatasetID = '${trans.security.encode_id( dataset.id
)}';
var chmHistoryId = '${trans.security.encode_id( history.id
)}';
and also tried looking in galaxy docs var chmHistoryId =
'${trans.security.encode_id( trans.history.id )}';
3. but still get the errors below
10.nnn.nnn.4 - - [28/Dec/2015:10:53:54 -0400] "GET
/visualization/show/MDAheatmap?history_id=ebfb8f50c6abde6d&dataset_id=3cc0effd29705aa3
HTTP/1.1" 200 - "http://10.nn.nnn.4:8082/"; "Mozilla/5.0 (Macintosh; Intel Mac
OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.106
Safari/537.36"galaxy.webapps.galaxy.controllers.visualization ERROR 2015-12-28
10:53:55,583 error rendering visualization (MDAheatmap): 'required param
history_id not found in URL'Traceback (most recent call last): File
"/home/rbrown/HM_galaxy/lib/galaxy/webapps/galaxy/controllers/visualization.py",
line 749, in render return plugin.render( trans=trans, embedded=embedded,
**kwargs ) File
"/home/rbrown/HM_galaxy/lib/galaxy/visualization/plugins/plugin.py", line 137,
in render render_vars = self._build_render_vars( config, trans=trans,
**kwargs ) File
"/home/rbrown/HM_galaxy/lib/galaxy/visualization/plugins/plugin.py", line 185,
in _build_render_vars resources = self._config_to_resources( trans, config )
File "/home/rbrown/HM_galaxy/lib/galaxy/visualization/plugins/plugin.py", line
224, in _config_to_resources resources =
self.resource_parser.parse_parameter_dictionary( trans, expected_params,
config, param_modifiers ) File
"/home/rbrown/HM_galaxy/lib/galaxy/visualization/plugins/resource_parser.py",
line 88, in parse_parameter_dictionary raise KeyError( 'required param %s
not found in URL' % ( param_name ) )KeyError: 'required param history_id not
found in URL'
=================
----- Original Message -----From: Martin Čech <[email protected]>To:
[email protected]: galaxy-dev <[email protected]>Sent:
Mon, 28 Dec 2015 17:12:18 -0000 (UTC)Subject: Re: [galaxy-dev] how to access
current user's apikey or History Id
Hello Bob,
please see the links that John posted before. They are relevant, especially
this one:
http://dev.list.galaxyproject.org/find-UUID-of-current-history-in-tool-XML-wrapper-td4667113.html
Thank you.
M.
On Mon, Dec 28, 2015 at 8:32 AM <[email protected]> wrote:
Good morning Martin,
Then maybe it would be better, and easier?, to pass the History ID to a mako
file. Is there a galaxy predefined item for the History ID similar to the
Dataset_id that can be passed?
Thanks
bob
----- Original Message -----From: Martin Čech <[email protected]>To:
[email protected], galaxy-dev <[email protected]>Sent:
Sat, 26 Dec 2015 14:49:31 -0000 (UTC)Subject: Re: [galaxy-dev] how to access
current user's apikey
Good morning,
I hope there is not, because tool should not have access to user's credentials.
If you explain a bit what are you trying to do we can probably be of more help.
Thank you for using Galaxy.
Martin
On Sat, Dec 26, 2015 at 9:27 AM <[email protected]> wrote:
Good morning team,
Is there a way to access the current user's API Key similar to seeing their
email address via a tool's xml parameter "$__user_email__" ?
Thanks,
Bob
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
