Mercurial > repos > pieterlukasse > prims_metabolomics
annotate primsfilters.py @ 23:85fd05d0d16c
New tool to Query multiple public repositories for elemental compositions
from accurate mass values detected by high-resolution mass spectrometers
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 03 Apr 2014 16:44:11 +0200 |
| parents | cd4f13119afa |
| children |
| rev | line source |
|---|---|
| 19 | 1 import logging |
| 2 log = logging.getLogger( __name__ ) | |
| 3 | |
| 4 | |
| 5 def restrict_prims_metabolomics( context, tool ): | |
| 6 """ | |
| 7 This tool filter will hide prims_metabolomics tools for non-metabolomics users. | |
| 8 This can be enabled by adding the following to the | |
| 9 ``app:main`` section of ``universe_wsgi.ini``:: | |
| 10 | |
| 11 tool_filters = primsfilters:restrict_prims_metabolomics | |
| 12 | |
| 13 and by adding this file to the folder: | |
| 14 | |
| 15 <galaxy-dist>/lib/galaxy/tools/filters | |
| 16 | |
| 17 This is optional and can be used in case some control is desired on whom | |
| 18 gets to see the prims_metabolomics tools. When not using this file and the | |
| 19 settings mentioned above, all prims_metabolomics tools will be visible to | |
| 20 all users. | |
| 21 """ | |
| 22 # for debugging: import pydevd;pydevd.settrace("L0136815.wurnet.nl") | |
| 23 user = context.trans.user | |
|
22
cd4f13119afa
Small fix in filters part and improvement in query_metexp time logging
pieter.lukasse@wur.nl
parents:
19
diff
changeset
|
24 metabolomics_tools = [ "msclust2", "combine_output", "create_poly_model", "lookup_library", |
|
cd4f13119afa
Small fix in filters part and improvement in query_metexp time logging
pieter.lukasse@wur.nl
parents:
19
diff
changeset
|
25 "NDIStext2tabular", "rankfilterGCMS_tabular", "filter_on_rank", |
|
cd4f13119afa
Small fix in filters part and improvement in query_metexp time logging
pieter.lukasse@wur.nl
parents:
19
diff
changeset
|
26 "export_to_metexp_tabular", "query_metexp" ] |
| 19 | 27 found_match = False |
| 28 # iterate over the tool (partial)ids and look for a match (this is compatible with tool shed given ids): | |
| 29 for partial_id in metabolomics_tools: | |
| 30 if tool.id.find("/"+ partial_id + "/") >= 0: | |
| 31 found_match = True | |
| 32 break | |
| 33 # the second part of this if is compatible with the ids when NOT using tool shed: | |
| 34 if found_match or tool.id in metabolomics_tools: | |
| 35 # logging.warn( 'FILTER MATCHED: %s' %(tool.name)) | |
| 36 | |
| 37 for user_role in user.roles: | |
| 38 if user_role.role.name == "PRIMS_METABOLOMICS": | |
| 39 return True | |
| 40 # not found to have the role, return false: | |
| 41 return False | |
| 42 else: | |
| 43 # return true for any other tool | |
| 44 return True |