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 marten@bx.psu.eduTo: rbrown1422@comcast.netCc: galaxy-dev galaxy-dev@lists.galaxyproject.orgSent: 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-w...
Thank you. M.
On Mon, Dec 28, 2015 at 8:32 AM rbrown1422@comcast.net 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 marten@bx.psu.eduTo: rbrown1422@comcast.net, galaxy-dev galaxy-dev@lists.galaxyproject.orgSent: 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 rbrown1422@comcast.net 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 ___________________________________________________________
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