[galaxy-dev] Populating tool select menu with database data? code tag deprecated

2012-07-25 Thread Kohler Manuel 
Hi,
I have a question related to this Galaxy threads:
http://dev.list.galaxyproject.org/Populating-tool-select-menu-with-database
-data-tp4139069.html

I implemented the example with the deprecated code tag which is working
fine. But I do not invest time in a tag which might vanish soon. What is
the replacement for this tag or how is the way it should be done?

Here is what I want to do:
My ultimate goal is to load fastq.gz files from an external Data
Management System which I can connect via a JSON API. Here is the code
which generates the menu shwon in the attached screen shot:
Python code:

import jsonrpclib
server = 
jsonrpclib.Server('https://myserver/rmi-general-information-v1.json')

sessionToken = server.tryToAuthenticateForAllServices(user, password)
projects = server.listProjects(sessionToken)
experimentType = 'HT_SEQUENCING'



def getExperiments():  eList = []
  experiments = server.listExperiments(sessionToken, projects,
experimentType)
  for experiment in experiments:
eList.append([experiment['code'], experiment['code'], False])


  return eList
The corresponding XML file calls the getExperiments() function:

 inputs
  param name=experiment type=select label=Experiment:
  help=select Experiment
  dynamic_options=getExperiments()/


   outputs
  data format=fasta name=output label=more foo /


/outputs   code file=openbis_get_dataset.py /


Depending on the selection in the first drop down list (experiments) I
want to show/fill a second list which shows a list of items which are in
the selected experiment. Finally the fastq files should be listed. The
structure is like this:

*Experiment1
  - Sample1
+ fastq1.gz
+ fastq2.gz
+ fastq3.gz
  - Sample2
+ fastq1.gz
+ fastq2.gz
*Experiment2

  - Sample1
   + fastq1.gz








I am on Galaxy r7148.
If somebody could direct me in the right direction would be highly
appreciated.

Kind regards

Manuel


--
Manuel Kohler
Center for Information Sciences and Databases (C-ISD)
Department of Biosystems Science  Engineering (D-BSSE)
ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132






attachment: Screen shot 2012-07-25 at 3.10.18 PM.png___
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Re: [galaxy-dev] Populating tool select menu with database data?

2011-02-08 Thread Kempenaar, M (med) 
Hello Hans-Rudolf,

Do you know if the 'dynamic_options' attribute also works for control elements 
other then select menu's?
For example I want to present the user a set of checkboxes that correspond to 
column names from a file, could I use something like a loop that either 
iterates on data received from the 'dynamics_option' function or from a meta 
attribute?

To get a bit further off topic, I made a new tabular datatype that has a 
meta-attribute for storing column names, but I can't use them in my XML files.. 
Any ideas would be welcome!

Regards,

Marcel

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu on behalf of Hans-Rudolf Hotz
Sent: Tue 2/8/2011 10:04 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Populating tool select menu with database data?
 
Leandro

we use the dynamic_options attribute, eg:



  inputs
 param name=foo type=select label=what
   help=Use tickboxes to select 
   display=radio
   dynamic_options=ds_fooOptions()/
   /inputs
   outputs
 data format=fasta name=output label=more foo /

   /outputs
   code file=extra_code_for_foo_list.py /
help
/help

  /tool


and then we have a little python script (extra_code_for_foo_list.py) 
with the ds_fooOptions function, eg


def ds_fooOptions():
 List available foos as tuples of (displayName,value)
 foos = whatever python code is required to generate the tuples
 return foos



I hope this helps, Hans




On 02/08/2011 08:32 AM, Leandro Hermida wrote:
 Hi Dannon,

 Sorry that I didn't explain well  I have a local database with
 certain information and I would like to dynamically populate a Galaxy
 tool select menu with the results of a SQL statement.  Is this
 possible?

 best,
 Leandro


 On Mon, Feb 7, 2011 at 6:05 PM, Dannon Bakerdannonba...@me.com  wrote:
 Leandro,

 Could you elaborate on what you're trying to do, perhaps what database data 
 you're referring to?

 -Dannon


 On Feb 7, 2011, at 11:58 AM, Leandro Hermida wrote:

 Sorry to bug again,

 Does anyone know where I can find an example on how to dynamically
 populate a tool select menu with database data?

 regards,
 Leandro

 On Thu, Feb 3, 2011 at 3:32 PM, Leandro Hermida
 soft...@leandrohermida.com  wrote:
 Hi,

 Sorry I tried to search for this and couldn't find an example to this basic
 question where can I find an example on how to populate a tool select
 menu with database data?

 best,
 Leandro

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