Good morning, I am trying to pass this info to by plugin mako that will display an output file in their history. With that info and the history data file location I can pass a URL for the file location to the tool in the mako doing the display.

Tools already have access to the user email etc. and the api key is encoded so I do not believe any more info is conveyed to the tool than is available already. For example we have a program that calls galaxy with an api key to bring up the correct history when they begin.

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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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 ___________________________________________________________

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:

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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 ___________________________________________________________

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:

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Hi, Bob

Can you be more clear about what you're trying to do in general?

Are you still working on a visualization plugin (I would assume so, since you mentioned a mako file)? If so, what are you attempting to do in the plugin?

Or are you working on a tool?

Thanks for the clarification, Carl

On Tue, Dec 29, 2015 at 6:21 PM, rbrown1422@comcast.net wrote:

Good morning team Maybe it would be better, and easier to pass the History ID to a mako file to access a file in the current History. 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.edu To: rbrown1422@comcast.net, galaxy-dev <galaxy-dev@lists.galaxyproject.org

...

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 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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---

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