# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1275671936 14400 # Node ID dd69c382eff1d3c0c160bc3ec392b06671317fd0 # Parent d01207f24908bc3f6d5323689f0aa46557f4d254 lims: added new feature where the datasets are be automatically renamed using a setting with the request_type. This makes solves the same dataset name problem on SOLiD

--- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -70,6 +70,15 @@ <input type="text" name="data_dir" value="" size="40"/></div><div class="form-row"> + <label>Add experiment name and the sample name to the dataset name?</label> + ${rename_dataset_selectbox.get_html()} + <div class="toolParamHelp" style="clear: both;"> + The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This + makes sure that dataset names remain unique in Galaxy even when they have the + same name in the sequencer. + </div> + </div> + <div class="form-row"><div style="float: left; width: 250px; margin-right: 10px;"><input type="hidden" name="new" value="submitted" size="40"/></div>

--- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1476,6 +1476,9 @@ class RequestEvent( object ): self.comment = comment

class RequestType( object ): + rename_dataset_options = Bunch( NO = 'Do not rename', + SAMPLE_NAME = 'Preprend sample name', + EXPERIMENT_AND_SAMPLE_NAME = 'Prepend experiment and sample name') permitted_actions = get_permitted_actions( filter='REQUEST_TYPE' ) def __init__(self, name=None, desc=None, request_form=None, sample_form=None, datatx_info=None):

--- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -62,6 +62,15 @@ <input type="text" name="data_dir" value="${request_type.datatx_info.get('data_dir', '')}" size="40"/></div><div class="form-row"> + <label>Add experiment name and the sample name to the dataset name?</label> + ${rename_dataset_selectbox.get_html()} + <div class="toolParamHelp" style="clear: both;"> + The datasets are renamed by prepending the experiment name and the sample name to the dataset name. <br/>This + makes sure that dataset names remain unique in Galaxy even when they have the + same name in the sequencer. + </div> + </div> + <div class="form-row"><input type="submit" name="save_changes" value="Save changes"/></div></form>

--- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -221,7 +221,6 @@ class RequestsAdmin( BaseController ):

@web.json def get_file_details( self, trans, id=None, file=None, folder_path=None ): - print >> sys.stderr, 'get_file_details', id, file def print_ticks(d): pass # Avoid caching @@ -1623,7 +1622,7 @@ class RequestsAdmin( BaseController ): else: sample.dataset_files.append(dict(filepath=filepath, status=sample.transfer_status.NOT_STARTED, - name=filepath.split('/')[-1], + name=self.__dataset_name(sample, filepath.split('/')[-1]), error_msg='', size=sample.dataset_size(filepath))) trans.sa_session.add( sample ) @@ -1638,7 +1637,16 @@ class RequestsAdmin( BaseController ): action='show_datatx_page', sample_id=trans.security.encode_id(sample.id), folder_path=folder_path)) - + + def __dataset_name(self, sample, filepath): + name = filepath.split('/')[-1] + opt = sample.request.type.datatx_info.get('rename_dataset', sample.request.type.rename_dataset_options.NO) + if opt == sample.request.type.rename_dataset_options.NO: + return name + elif opt == sample.request.type.rename_dataset_options.SAMPLE_NAME: + return sample.name+'_'+name + elif opt == sample.request.type.rename_dataset_options.EXPERIMENT_AND_SAMPLE_NAME: + return sample.request.name+'_'+sample.name+'_'+name def __setup_datatx_user(self, trans, library, folder): ''' This method sets up the datatx user: @@ -1830,7 +1838,8 @@ class RequestsAdmin( BaseController ): return trans.fill_template( '/admin/requests/view_request_type.mako', request_type=rt, forms=get_all_forms( trans ), - states_list=rt.states ) + states_list=rt.states, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans, rt) ) def __view_form(self, trans, **kwd): try: fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( trans.security.decode_id(kwd['id']) ) @@ -1855,7 +1864,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) elif params.get( 'remove_state_button', False ): rt_info, rt_states = self.__create_request_type_form(trans, **kwd) index = int(params.get( 'remove_state_button', '' ).split(" ")[2]) @@ -1864,7 +1874,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) elif params.get( 'save_request_type', False ): rt, message = self.__save_request_type(trans, **kwd) if not rt: @@ -1888,7 +1899,8 @@ class RequestsAdmin( BaseController ): rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=params.get( 'password', '' ), - data_dir=util.restore_text( params.get( 'data_dir', '' ) )) + data_dir=util.restore_text( params.get( 'data_dir', '' ) ), + rename_dataset=util.restore_text( params.get('rename_dataset', False) )) trans.sa_session.add( rt ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -1903,7 +1915,8 @@ class RequestsAdmin( BaseController ): rt_info_widgets=rt_info, rt_states_widgets=rt_states, message=message, - status=status) + status=status, + rename_dataset_selectbox=self.__rename_dataset_selectbox(trans)) def __create_request_type_form(self, trans, **kwd): request_forms=get_all_forms( trans, filter=dict(deleted=False), @@ -1949,6 +1962,19 @@ class RequestsAdmin( BaseController ): break return rt_info, rt_states

+ def __rename_dataset_selectbox(self, trans, rt=None): + if rt: + sel_opt = rt.datatx_info.get('rename_dataset', trans.app.model.RequestType.rename_dataset_options.NO) + else: + sel_opt = trans.app.model.RequestType.rename_dataset_options.NO + rename_dataset_selectbox = SelectField('rename_dataset') + for opt, opt_name in trans.app.model.RequestType.rename_dataset_options.items(): + if sel_opt == opt_name: + rename_dataset_selectbox.add_option(opt_name, opt_name, selected=True) + else: + rename_dataset_selectbox.add_option(opt_name, opt_name) + return rename_dataset_selectbox + def __save_request_type(self, trans, **kwd): params = util.Params( kwd ) rt = trans.app.model.RequestType() @@ -1960,7 +1986,8 @@ class RequestsAdmin( BaseController ): rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), password=params.get( 'password', '' ), - data_dir=util.restore_text( params.get( 'data_dir', '' ) )) + data_dir=util.restore_text( params.get( 'data_dir', '' ) ), + rename_dataset=util.restore_text( params.get('rename_dataset', '') )) trans.sa_session.add( rt ) trans.sa_session.flush() # set sample states

--- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -55,6 +55,8 @@

<h2>Data transfer from Sequencer</h2><h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3> +<br/> +<br/><ul class="manage-table-actions"> %if sample.request.submitted() and sample.inprogress_dataset_files(): @@ -131,7 +133,7 @@ <input type="submit" name="open_folder" value="Open folder"/><input type="submit" name="folder_up" value="Up"/></div> - <div class="form-row"> + <div class="form-row"><select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple> %for index, f in enumerate(files): <option value="${f}">${f}</option>