- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 7ea4c156ae32: Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample. Also use better naming convention for a key variable name.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289492968 18000 # Node ID 7ea4c156ae32c4757378229bfc49584df91a024a # Parent 591c53b44ae4a6237a841adaa3abfe59829beebe Add a pop-up menu for a sample if it is possible to either select datasets to transfer or transfer selected datasets for the sample. Also use better naming convention for a key variable name. --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -212,14 +212,14 @@ class RequestsCommon( BaseController, Us except: return invalid_id_redirect( trans, cntrller, request_id ) sample_state_id = params.get( 'sample_state_id', None ) - # Get the user entered sample information - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + # Build a list of sample widgets (based on the attributes of each sample) for display. + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) return trans.fill_template( '/requests/common/view_request.mako', cntrller=cntrller, request=request, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, status=status, message=message ) @web.expose @@ -415,8 +415,8 @@ class RequestsCommon( BaseController, Us editing_samples=editing_samples ) ) # Get all libraries for which the current user has permission to add items. libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) - # Get the user entered sample information - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + # Build a list of sample widgets (based on the attributes of each sample) for display. + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) sample_operation = params.get( 'sample_operation', 'none' ) def handle_error( **kwd ): @@ -433,14 +433,17 @@ class RequestsCommon( BaseController, Us handle_error( **kwd ) if params.get( 'import_samples_button', False ): # Import sample field values from a csv file - return self.__import_samples( trans, cntrller, request, current_samples, libraries, **kwd ) + return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) elif params.get( 'add_sample_button', False ): return self.add_sample( trans, cntrller, request_id, **kwd ) elif params.get( 'save_samples_button', False ): if encoded_selected_sample_ids: - # This gets tricky because we need the list of samples to include the same number - # of objects that that current_samples ( i.e., request.samples ) has. We'll first - # get the set of samples corresponding to the checked sample ids. + # We need the list of displayable_sample_widgets to include the same number + # of objects that that request.samples has so that we can enumerate over each + # list without problems. We have to be careful here since the user may have + # used the multi-select check boxes when editing sample widgets, but didn't + # select all of them. We'll first get the set of samples corresponding to the + # checked sample ids. samples = [] selected_samples = [] for encoded_sample_id in encoded_selected_sample_ids: @@ -453,12 +456,12 @@ class RequestsCommon( BaseController, Us else: samples.append( None ) # The __save_samples method requires sample_widgets, not sample objects - samples = self.__get_sample_widgets( trans, request, samples, **kwd ) + sample_widgets = self.__get_sample_widgets( trans, request, samples, **kwd ) else: - samples = current_samples - return self.__save_samples( trans, cntrller, request, samples, **kwd ) + sample_widgets = displayable_sample_widgets + return self.__save_samples( trans, cntrller, request, sample_widgets, **kwd ) request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) + sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) libraries_select_field, folders_select_field = self.__build_library_and_folder_select_fields( trans, request.user, 0, @@ -473,7 +476,7 @@ class RequestsCommon( BaseController, Us request=request, encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, sample_copy=sample_copy, libraries=libraries, sample_operation_select_field=sample_operation_select_field, @@ -805,12 +808,12 @@ class RequestsCommon( BaseController, Us is_admin = cntrller == 'requests_admin' and trans.user_is_admin() # Get the widgets for rendering the request form request_widgets = self.__get_request_widgets( trans, request.id ) - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) - if not current_samples: + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + if not displayable_sample_widgets: # Form field names are zero-based. sample_index = 0 else: - sample_index = len( current_samples ) + sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): # Get all libraries for which the current user has permission to add items libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) @@ -818,18 +821,18 @@ class RequestsCommon( BaseController, Us # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) for index in range( num_samples_to_add ): - id_index = len( current_samples ) + 1 + id_index = len( displayable_sample_widgets ) + 1 if copy_sample_index != -1: # The user has selected a sample to copy. - library_id = current_samples[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) - folder_id = current_samples[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) - name = current_samples[ copy_sample_index ][ 'name' ] + '_%i' % ( len( current_samples ) + 1 ) - field_values = [ val for val in current_samples[ copy_sample_index ][ 'field_values' ] ] + library_id = displayable_sample_widgets[ copy_sample_index][ 'library_select_field' ].get_selected( return_value=True ) + folder_id = displayable_sample_widgets[ copy_sample_index ][ 'folder_select_field' ].get_selected( return_value=True ) + name = displayable_sample_widgets[ copy_sample_index ][ 'name' ] + '_%i' % ( len( displayable_sample_widgets ) + 1 ) + field_values = [ val for val in displayable_sample_widgets[ copy_sample_index ][ 'field_values' ] ] else: # The user has not selected a sample to copy, just adding a new generic sample. library_id = None folder_id = None - name = 'Sample_%i' % ( len( current_samples ) + 1 ) + name = 'Sample_%i' % ( len( displayable_sample_widgets ) + 1 ) field_values = [ '' for field in request.type.sample_form.fields ] # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, @@ -841,25 +844,26 @@ class RequestsCommon( BaseController, Us folder_id=folder_id, **kwd ) # Append the new sample to the current list of samples for the request - current_samples.append( dict( name=name, - barcode='', - library=None, - library_id=library_id, - folder=None, - folder_id=folder_id, - field_values=field_values, - library_select_field=library_select_field, - folder_select_field=folder_select_field ) ) + displayable_sample_widgets.append( dict( id=None, + name=name, + barcode='', + library=None, + library_id=library_id, + folder=None, + folder_id=folder_id, + field_values=field_values, + library_select_field=library_select_field, + folder_select_field=folder_select_field ) ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) sample_operation = params.get( 'sample_operation', 'none' ) sample_operation_select_field = self.__build_sample_operation_select_field( trans, is_admin, request, sample_operation ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) + sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, encoded_selected_sample_ids=encoded_selected_sample_ids, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, sample_operation_select_field=sample_operation_select_field, sample_copy=sample_copy, editing_samples=False, @@ -876,9 +880,9 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - current_samples = self.__get_sample_widgets( trans, request, request.samples, **kwd ) + displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) sample_index = int( params.get( 'sample_id', 0 ) ) - sample_name = current_samples[sample_index]['name'] + sample_name = displayable_sample_widgets[sample_index]['name'] sample = request.has_sample( sample_name ) if sample: trans.sa_session.delete( sample.values ) @@ -960,7 +964,7 @@ class RequestsCommon( BaseController, Us status=status, files=[], folder_path=folder_path ) - def __import_samples( self, trans, cntrller, request, current_samples, libraries, **kwd ): + def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ): """ Reads the samples csv file and imports all the samples. The format of the csv file is: SampleName,DataLibrary,DataLibraryFolder,Field1,Field2.... @@ -987,19 +991,20 @@ class RequestsCommon( BaseController, Us folder_id = folder.id library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, request.user, - len( current_samples ), + len( displayable_sample_widgets ), libraries, None, library_id, folder_id, **kwd ) - current_samples.append( dict( name=row[0], - barcode='', - library=None, - folder=None, - library_select_field=library_select_field, - folder_select_field=folder_select_field, - field_values=row[3:] ) ) + displayable_sample_widgets.append( dict( id=None, + name=row[0], + barcode='', + library=None, + folder=None, + library_select_field=library_select_field, + folder_select_field=folder_select_field, + field_values=row[3:] ) ) except Exception, e: if str( e ) == "'unicode' object has no attribute 'file'": message = "Select a file" @@ -1014,12 +1019,12 @@ class RequestsCommon( BaseController, Us status='error', message=message ) ) request_widgets = self.__get_request_widgets( trans, request.id ) - sample_copy = self.__build_copy_sample_select_field( trans, current_samples ) + sample_copy = self.__build_copy_sample_select_field( trans, displayable_sample_widgets ) return trans.fill_template( '/requests/common/edit_samples.mako', cntrller=cntrller, request=request, request_widgets=request_widgets, - current_samples=current_samples, + displayable_sample_widgets=displayable_sample_widgets, sample_copy=sample_copy, editing_samples=False ) def __save_samples( self, trans, cntrller, request, samples, **kwd ): @@ -1110,17 +1115,17 @@ class RequestsCommon( BaseController, Us # by the admin ( i.e., the sample's SampleState would be set to request.type.states[0] ). for index in range( len( samples ) - len( request.samples ) ): sample_index = len( request.samples ) - current_sample = samples[ sample_index ] - form_values = trans.model.FormValues( request.type.sample_form, current_sample[ 'field_values' ] ) + sample_widget = samples[ sample_index ] + form_values = trans.model.FormValues( request.type.sample_form, sample_widget[ 'field_values' ] ) trans.sa_session.add( form_values ) trans.sa_session.flush() - s = trans.model.Sample( name=current_sample[ 'name' ], + s = trans.model.Sample( name=sample_widget[ 'name' ], desc='', request=request, form_values=form_values, bar_code='', - library=current_sample[ 'library' ], - folder=current_sample[ 'folder' ] ) + library=sample_widget[ 'library' ], + folder=sample_widget[ 'folder' ] ) trans.sa_session.add( s ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -1264,9 +1269,9 @@ class RequestsCommon( BaseController, Us for index, sample in enumerate( samples ): id_index = index + 1 if sample is None: - # Id sample is None, then we'll use the sample from the request object since it will - # not have updated =values from kwd. + # Use the sample from the request object since it will not have updated values from kwd. sample = request.samples[ index ] + sample_id = sample.id name = sample.name bar_code = sample.bar_code library = sample.library @@ -1274,6 +1279,7 @@ class RequestsCommon( BaseController, Us field_values = sample.values.content else: # Update the sample attributes from kwd + sample_id = None name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) @@ -1295,7 +1301,8 @@ class RequestsCommon( BaseController, Us library_id=library_id, folder_id=folder_id, **kwd ) - sample_widgets.append( dict( name=name, + sample_widgets.append( dict( id=sample_id, + name=name, barcode=bar_code, library=library, folder=folder, @@ -1325,7 +1332,8 @@ class RequestsCommon( BaseController, Us library_id=library_id, folder_id=folder_id, **kwd ) - sample_widgets.append( dict( name=name, + sample_widgets.append( dict( id=None, + name=name, barcode=bar_code, library=library, folder=folder, @@ -1335,10 +1343,10 @@ class RequestsCommon( BaseController, Us index += 1 return sample_widgets # ===== Methods for building SelectFields used on various request forms ===== - def __build_copy_sample_select_field( self, trans, current_samples ): + def __build_copy_sample_select_field( self, trans, displayable_sample_widgets ): copy_sample_index_select_field = SelectField( 'copy_sample_index' ) copy_sample_index_select_field.add_option( 'None', -1, selected=True ) - for index, sample_dict in enumerate( current_samples ): + for index, sample_dict in enumerate( displayable_sample_widgets ): copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index ) return copy_sample_index_select_field def __build_request_type_id_select_field( self, trans, selected_value='none' ): @@ -1458,20 +1466,20 @@ class RequestsCommon( BaseController, Us message += '<b>' + ef + '</b> ' return message return None - def __validate_sample_names( self, trans, cntrller, request, current_samples, **kwd ): + def __validate_sample_names( self, trans, cntrller, request, displayable_sample_widgets, **kwd ): # Check for duplicate sample names for all samples of the request. editing_samples = util.string_as_bool( kwd.get( 'editing_samples', False ) ) message = '' - for index in range( len( current_samples ) - len( request.samples ) ): + for index in range( len( displayable_sample_widgets ) - len( request.samples ) ): sample_index = index + len( request.samples ) - current_sample = current_samples[ sample_index ] - sample_name = current_sample[ 'name' ] + sample_widget = displayable_sample_widgets[ sample_index ] + sample_name = sample_widget[ 'name' ] if not sample_name.strip(): message = 'Enter the name of sample number %i' % sample_index break count = 0 - for i in range( len( current_samples ) ): - if sample_name == current_samples[ i ][ 'name' ]: + for i in range( len( displayable_sample_widgets ) ): + if sample_name == displayable_sample_widgets[ i ][ 'name' ]: count += 1 if count > 1: message = "You tried to add %i samples with the name (%s). Samples belonging to a request must have unique names." % ( count, sample_name ) --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -113,7 +113,7 @@ </script></%def> -<%def name="render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )"> +<%def name="render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"><% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() if sample: @@ -145,7 +145,7 @@ <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" ${checked_str}/><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"/></td> %endif <td valign="top"> - <input type="text" name="sample_${current_sample_index}_name" value="${current_sample['name']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_name" value="${sample_widget['name']}" size="10"/><div class="toolParamHelp" style="clear: both;"><i>${' (required)' }</i></div> @@ -153,10 +153,10 @@ %if display_bar_code: <td valign="top"> %if is_admin: - <input type="text" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}" size="10"/> %else: - ${current_sample['barcode']} - <input type="hidden" name="sample_${current_sample_index}_barcode" value="${current_sample['barcode']}"/> + ${sample_widget['barcode']} + <input type="hidden" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}"/> %endif </td> %endif @@ -169,8 +169,8 @@ %else: <td></td> %endif - <td valign="top">${current_sample['library_select_field'].get_html()}</td> - <td valign="top">${current_sample['folder_select_field'].get_html()}</td> + <td valign="top">${sample_widget['library_select_field'].get_html()}</td> + <td valign="top">${sample_widget['folder_select_field'].get_html()}</td> %if display_datasets: <td valign="top"> ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected @@ -220,11 +220,11 @@ %endif %if can_delete_samples: ## Delete button - <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=current_sample_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> + <td valign="top"><a class="action-button" href="${h.url_for( controller='requests_common', action='delete_sample', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=sample_widget_index )}"><img src="${h.url_for('/static/images/delete_icon.png')}" style="cursor:pointer;"/></a></td> %endif </%def> -<%def name="render_samples_grid( cntrller, request, current_samples, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )"> +<%def name="render_samples_grid( cntrller, request, displayable_sample_widgets, action, editing_samples=False, encoded_selected_sample_ids=[], render_buttons=False, grid_header='<h3>Samples</h3>' )"> ## Displays the "Samples" grid <% trans.sa_session.refresh( request ) @@ -236,7 +236,8 @@ can_add_samples = request.is_unsubmitted can_delete_samples = editing_samples and request.samples and not is_complete can_edit_samples = request.samples and ( is_admin or not is_complete ) - can_select_datasets = is_admin and current_samples and ( is_submitted or is_complete ) + can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete ) + can_transfer_datasets = is_admin and request.samples and not request.is_rejected display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) @@ -278,46 +279,67 @@ <thead><tbody><% trans.sa_session.refresh( request ) %> - ## current_samples is a dictionary whose keys are: - ## name, barcode, library, folder, field_values, library_select_field, folder_select_field - %for current_sample_index, current_sample in enumerate( current_samples ): + ## displayable_sample_widgets is a dictionary whose keys are: + ## id, name, barcode, library, folder, field_values, library_select_field, folder_select_field + ## A displayable_sample_widget will have an id == None if the widget's associated sample has not + ## yet been saved (i.e., the use clicked the "Add sample" button but has not yet clicked the + ## "Save" button. + %for sample_widget_index, sample_widget in enumerate( displayable_sample_widgets ): <% - current_sample_name = current_sample[ 'name' ] - current_sample_barcode = current_sample[ 'barcode' ] - current_sample_library = current_sample[ 'library' ] - if current_sample_library: + sample_widget_name = sample_widget[ 'name' ] + sample_widget_barcode = sample_widget[ 'barcode' ] + sample_widget_library = sample_widget[ 'library' ] + if sample_widget_library: if cntrller == 'requests': library_cntrller = 'library' elif is_admin: library_cntrller = 'library_admin' else: library_cntrller = None - current_sample_folder = current_sample[ 'folder' ] + sample_widget_folder = sample_widget[ 'folder' ] try: - sample = request.samples[ current_sample_index ] + sample = request.samples[ sample_widget_index ] except: sample = None %> %if editing_samples: - <tr>${render_editable_sample_row( cntrller, sample, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %elif sample: <tr> - <td>${current_sample_name}</td> + <td> + %if sample.state and ( can_select_datasets or can_transfer_datasets ): + ## A sample will have a state only after the request has been submitted. + <% encoded_id = trans.security.encode_id( sample.id ) %> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> + ${sample.name} + </div> + <div popupmenu="sample-${sample.id}-popup"> + %if can_select_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> + %endif + %if sample.untransferred_dataset_files: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %endif + </div> + %else: + ${sample_widget_name} + %endif + </td> %if display_bar_code: - <td>${current_sample_barcode}</td> + <td>${sample_widget_barcode}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> %else: <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif - %if current_sample_library and library_cntrller is not None: - <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( current_sample_library.id ) )}">${current_sample_library.name}</a></td> + %if sample_widget_library and library_cntrller is not None: + <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> %else: <td></td> %endif - %if current_sample_folder: - <td>${current_sample_folder.name}</td> + %if sample_widget_folder: + <td>${sample_widget_folder.name}</td> %else: <td></td> %endif @@ -371,7 +393,7 @@ </tr> %else: ## The Add sample button was clicked for this sample_widget - <tr>${render_editable_sample_row( cntrller, None, current_sample_index, current_sample, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %endif %endfor </tbody> @@ -439,7 +461,7 @@ </tr></%def> -<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, current_samples, editing_samples )"> +<%def name="render_request_type_sample_form_grids( grid_index, grid_name, fields_dict, displayable_sample_widgets, editing_samples )"><% if not grid_name: grid_name = "Sample form layout " + grid_index @@ -466,7 +488,7 @@ <thead><tbody><% trans.sa_session.refresh( request ) %> - %for sample_index, sample in enumerate( current_samples ): + %for sample_index, sample in enumerate( displayable_sample_widgets ): <% if editing_samples or sample_index >= len( request.samples ): display_only = False @@ -505,7 +527,7 @@ <tr><td> %if is_admin: - <% encoded_id = trans.security.encode_id(dataset.id) %> + <% encoded_id = trans.security.encode_id( dataset.id ) %><span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"><a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -72,14 +72,14 @@ <div class="toolFormBody"><form id="edit_samples" name="edit_samples" action="${h.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ), editing_samples=editing_samples )}" method="post"> - %if current_samples: + %if displayable_sample_widgets: <% if editing_samples: grid_header = '<h3>Edit Current Samples of Request "%s"</h3>' % request.name else: grid_header = '<h3>Add Samples to Request "%s"</h3>' % request.name %> - ${render_samples_grid( cntrller, request, current_samples, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} + ${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', editing_samples=editing_samples, encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} %if editing_samples and len( sample_operation_select_field.options ) > 1 and not is_unsubmitted: <div class="form-row" style="background-color:#FAFAFA;"> For selected samples: @@ -118,14 +118,14 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), current_samples=current_samples, editing_samples=editing_samples )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=editing_samples )} %endfor %else: <label>There are no samples.</label> %endif %if not editing_samples and is_unsubmitted: ## The user is adding a new sample - %if current_samples: + %if displayable_sample_widgets: <p/><div class="form-row"><label> Copy <input type="text" name="num_sample_to_copy" value="1" size="3"/> samples from sample ${sample_copy.get_html()}</label> @@ -138,7 +138,7 @@ <div class="form-row"> ## hidden element to make twill work. <input type="hidden" name="hidden_input" value=""/> - %if ( request.samples or current_samples ) and ( editing_samples or len( current_samples ) > len( request.samples ) ): + %if ( request.samples or displayable_sample_widgets ) and ( editing_samples or len( displayable_sample_widgets ) > len( request.samples ) ): <input type="submit" name="add_sample_button" value="Add sample" /><input type="submit" name="save_samples_button" value="Save"/><input type="submit" name="cancel_changes_button" value="Cancel"/> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -148,12 +148,12 @@ </div></div><p/> -%if current_samples: +%if displayable_sample_widgets: <% grid_header = '<h3>Samples</h3>' render_buttons = can_edit_samples %> - ${render_samples_grid( cntrller, request, current_samples=current_samples, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} + ${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} %else: There are no samples. %if can_add_samples: @@ -165,5 +165,5 @@ ## Render the other grids <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), current_samples=current_samples, editing_samples=False )} + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} %endfor

1 0

galaxy-dist commit d6a0dd8e55e2: Sample tracking functional tests refactored till add samples.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289406533 18000 # Node ID d6a0dd8e55e2f7d2077bc282bca3e42d98fbb7f2 # Parent ecaf015e009a35a3cf421a87fbab1c5d0bbba5b4 Sample tracking functional tests refactored till add samples. Rest of the tests are disabled. --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -17,6 +17,9 @@ address_dict = dict( short_desc="Office" phone="007-007-0007" ) class TestFormsAndRequests( TwillTestCase ): + # + # ====== Setup Users, Groups & Roles required for this test suite ========= + # def test_000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -50,9 +53,9 @@ class TestFormsAndRequests( TwillTestCas def test_005_create_required_groups_and_roles( self ): """Testing creating all required groups and roles for this script""" # Logged in as admin_user - # Create role_one - name = 'Role One' - description = "This is Role One's description" + # Create role1 + name = 'Role1' + description = "This is Role1's description" user_ids = [ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] self.create_role( name=name, description=description, @@ -61,25 +64,25 @@ class TestFormsAndRequests( TwillTestCas create_group_for_role='no', private_role=admin_user.email ) # Get the role object for later tests - global role_one - role_one = get_role_by_name( name ) - # Create group_one - name = 'Group One' - self.create_group( name=name, in_user_ids=[ str( regular_user1.id ) ], in_role_ids=[ str( role_one.id ) ] ) + global role1 + role1 = get_role_by_name( name ) + # Create group1 + name = 'Group1' + self.create_group( name=name, in_user_ids=[ str( regular_user1.id ) ], in_role_ids=[ str( role1.id ) ] ) # Get the group object for later tests - global group_one - group_one = get_group_by_name( name ) - assert group_one is not None, 'Problem retrieving group named "Group One" from the database' + global group1 + group1 = get_group_by_name( name ) + assert group1 is not None, 'Problem retrieving group named "Group1" from the database' # NOTE: To get this to work with twill, all select lists on the ~/admin/role page must contain at least # 1 option value or twill throws an exception, which is: ParseError: OPTION outside of SELECT # Due to this bug in twill, we create the role, we bypass the page and visit the URL in the # associate_users_and_groups_with_role() method. # - #create role_two - name = 'Role Two' - description = 'This is Role Two' + #create role2 + name = 'Role2' + description = 'This is Role2' user_ids = [ str( admin_user.id ) ] - group_ids = [ str( group_one.id ) ] + group_ids = [ str( group1.id ) ] private_role = admin_user.email self.create_role( name=name, description=description, @@ -87,11 +90,14 @@ class TestFormsAndRequests( TwillTestCas in_group_ids=group_ids, private_role=private_role ) # Get the role object for later tests - global role_two - role_two = get_role_by_name( name ) - assert role_two is not None, 'Problem retrieving role named "Role Two" from the database' - def test_010_create_request_form( self ): - """Testing creating a request form definition, editing the name and description and adding fields""" + global role2 + role2 = get_role_by_name( name ) + assert role2 is not None, 'Problem retrieving role named "Role2" from the database' + # + # ====== Form definition test methods ================================================ + # + def test_010_create_request_form_definition( self ): + """Testing creating a sequencing request form definition, editing the name and description and adding fields""" # Logged in as admin_user # Create a form definition tmp_name = "Temp form" @@ -107,23 +113,23 @@ class TestFormsAndRequests( TwillTestCas # Edit the name and description of the form definition, and add 3 fields. new_name = "Request Form" new_desc = "Request Form description" - global test_field_name1 - test_field_name1 = 'Test field name one' - global test_field_name2 - test_field_name2 = 'Test field name two' - global test_field_name3 - test_field_name3 = 'Test field name three' - field_dicts = [ dict( name=test_field_name1, - desc='Test field description one', + global request_field_name1 + request_field_name1 = 'Request form field1' + global request_field_name2 + request_field_name2 = 'Request form field2' + global request_field_name3 + request_field_name3 = 'Request form field3' + field_dicts = [ dict( name=request_field_name1, + desc='Description of '+request_field_name1, type='SelectField', required='optional', selectlist=[ 'option1', 'option2' ] ), - dict( name=test_field_name2, - desc='Test field description two', + dict( name=request_field_name2, + desc='Description of '+request_field_name2, type='AddressField', required='optional' ), - dict( name=test_field_name3, - desc='Test field description three', + dict( name=request_field_name3, + desc='Description of '+request_field_name3, type='TextField', required='required' ) ] self.edit_form( id=self.security.encode_id( tmp_form.current.id ), @@ -134,48 +140,99 @@ class TestFormsAndRequests( TwillTestCas strings_displayed=[ 'Edit form definition "%s"' % tmp_name ], strings_displayed_after_submit=[ "The form '%s' has been updated with the changes." % new_name ] ) # Get the form_definition object for later tests - global form_one - form_one = get_form( new_name ) - assert form_one is not None, 'Problem retrieving form named "%s" from the database' % new_name - assert len( form_one.fields ) == len( tmp_form.fields ) + len( field_dicts ) - def test_015_create_sample_form( self ): - """Testing creating sample form definition""" + global request_form_definition1 + request_form_definition1 = get_form( new_name ) + assert request_form_definition1 is not None, 'Problem retrieving form named "%s" from the database' % new_name + assert len( request_form_definition1.fields ) == len( tmp_form.fields ) + len( field_dicts ) + # check form view + self.view_form( id=self.security.encode_id( request_form_definition1.current.id ), + form_name=new_name, + form_desc=new_desc, + form_type=form_type, + field_dicts=field_dicts ) + def test_015_create_sample_form_definition( self ): + """Testing creating sequencing sample form definition and adding fields""" name = "Sample Form" - desc = "This is Form Two's description" + desc = "This is Sample Form's description" form_type = galaxy.model.FormDefinition.types.SAMPLE - form_layout_name = 'Layout Grid One' + global sample_form_layout_grid_name + sample_form_layout_grid_name = 'Layout Grid1' self.create_form( name=name, desc=desc, form_type=form_type, - form_layout_name=form_layout_name, + form_layout_name=sample_form_layout_grid_name, + num_fields=0, strings_displayed=[ 'Create a new form definition' ], strings_displayed_after_submit=[ "The form '%s' has been updated with the changes." % name ] ) - global form_two - form_two = get_form( name ) - assert form_two is not None, "Error retrieving form %s from db" % name + tmp_form = get_form( name ) + # now add fields to the sample form definition + global sample_field_name1 + sample_field_name1 = 'Sample form field1' + global sample_field_name2 + sample_field_name2 = 'Sample form field2' + global sample_field_name3 + sample_field_name3 = 'Sample form field3' + field_dicts = [ dict( name=sample_field_name1, + desc='Description of '+sample_field_name1, + type='SelectField', + required='optional', + selectlist=[ 'option1', 'option2' ] ), + dict( name=sample_field_name2, + desc='Description of '+sample_field_name2, + type='TextField', + required='optional' ), + dict( name=sample_field_name3, + desc='Description of '+sample_field_name3, + type='TextField', + required='required' ) ] + self.edit_form( id=self.security.encode_id( tmp_form.current.id ), + new_form_name=name, + new_form_desc=desc, + field_dicts=field_dicts, + field_index=len( tmp_form.fields ), + strings_displayed=[ 'Edit form definition "%s"' % name ], + strings_displayed_after_submit=[ "The form '%s' has been updated with the changes." % name ] ) + global sample_form_definition1 + sample_form_definition1 = get_form( name ) + assert sample_form_definition1 is not None, "Error retrieving form %s from db" % name + print len( sample_form_definition1.fields ), len( field_dicts ) + print sample_form_definition1.fields + print field_dicts + assert len( sample_form_definition1.fields ) == len( field_dicts ) + # check form view + self.view_form( id=self.security.encode_id( sample_form_definition1.current.id ), + form_name=name, + form_desc=desc, + form_type=form_type, + form_layout_name=sample_form_layout_grid_name, + field_dicts=field_dicts ) def test_020_create_request_type( self ): """Testing creating a request_type""" - request_form = get_form( form_one.name ) - sample_form = get_form( form_two.name ) - name = 'Test Requestype' + name = 'Sequencer configuration1' self.create_request_type( name, "test sequencer configuration", - self.security.encode_id( request_form.id ), - self.security.encode_id( sample_form.id ), + self.security.encode_id( request_form_definition1.id ), + self.security.encode_id( sample_form_definition1.id ), sample_states, strings_displayed=[ 'Create a new sequencer configuration' ], strings_displayed_after_submit=[ "Sequencer configuration (%s) has been created" % name ] ) global request_type1 request_type1 = get_request_type_by_name( name ) assert request_type1 is not None, 'Problem retrieving sequencer configuration named "%s" from the database' % name + # check view + self.view_request_type( self.security.encode_id( request_type1.id ), + request_type1.name, + strings_displayed=[ request_form_definition1.name, + sample_form_definition1.name ], + sample_states=sample_states) # Set permissions permissions_in = [ k for k, v in galaxy.model.RequestType.permitted_actions.items() ] permissions_out = [] - # Role one members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for + # Role1 members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for # REQUEST_TYPE_ACCESS on this request_type self.request_type_permissions( self.security.encode_id( request_type1.id ), request_type1.name, - str( role_one.id ), + str( role1.id ), permissions_in, permissions_out ) # Make sure the request_type1 is not accessible by regular_user2 since regular_user2 does not have Role1. @@ -189,8 +246,11 @@ class TestFormsAndRequests( TwillTestCas pass self.logout() self.login( email=admin_user.email ) + # + # ====== Sequencing request test methods - User perspective ================ + # def test_025_create_request( self ): - """Testing creating a sequence run request""" + """Testing creating a sequencing request as a regular user""" # logged in as admin_user # Create a user_address self.logout() @@ -200,195 +260,223 @@ class TestFormsAndRequests( TwillTestCas user_address1 = get_user_address( regular_user1, address_dict[ 'short_desc' ] ) # Set field values - the tuples in the field_values list include the field_value, and True if refresh_on_change # is required for that field. - field_value_tuples = [ ( 'option1', False ), ( str( user_address1.id ), True ), ( 'field three value', False ) ] + field_value_tuples = [ ( 'option1', False ), ( str( user_address1.id ), True ), ( 'field3 value', False ) ] # Create the request - name = 'Request One' - desc = 'Request One Description' + name = 'Request1' + desc = 'Request1 Description' self.create_request( cntrller='requests', request_type_id=self.security.encode_id( request_type1.id ), name=name, desc=desc, field_value_tuples=field_value_tuples, strings_displayed=[ 'Create a new sequencing request', - test_field_name1, - test_field_name2, - test_field_name3 ], + request_field_name1, + request_field_name2, + request_field_name3 ], strings_displayed_after_submit=[ name, desc ] ) - global request_one - request_one = get_request_by_name( name ) + global request1 + request1 = get_request_by_name( name ) # Make sure the request's state is now set to NEW - assert request_one.state is not request_one.states.NEW, "The state of the request '%s' should be set to '%s'" \ - % ( request_one.name, request_one.states.NEW ) + assert request1.state is not request1.states.NEW, "The state of the request '%s' should be set to '%s'" \ + % ( request1.name, request1.states.NEW ) + # check request page + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=[ 'Sequencing request "%s"' % request1.name, + 'There are no samples.', + sample_form_layout_grid_name ], + strings_not_displayed=[ request1.states.SUBMITTED, + request1.states.COMPLETE, + request1.states.REJECTED ] ) + # check if the request is showing in the 'new' filter + self.check_request_grid( cntrller='requests', + state=request1.states.NEW, + strings_displayed=[ request1.name ] ) + self.view_request_history( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=[ 'History of Sequencing Request "%s"' % request1.name, + request1.states.NEW, + 'Request created' ], + strings_not_displayed=[ request1.states.SUBMITTED, + request1.states.COMPLETE, + request1.states.REJECTED ] ) + def test_030_edit_basic_request_info( self ): + """Testing editing the basic information of a sequencing request""" + # logged in as regular_user1 + fields = [ 'option2', str( user_address1.id ), 'field3 value (edited)' ] + new_name=request1.name + ' (Renamed)' + new_desc=request1.desc + ' (Re-described)' + self.edit_basic_request_info( request_id=self.security.encode_id( request1.id ), + cntrller='requests', + name=request1.name, + new_name=new_name, + new_desc=new_desc, + new_fields=fields, + strings_displayed=[ 'Edit sequencing request "%s"' % request1.name ], + strings_displayed_after_submit=[ new_name, new_desc ] ) + refresh( request1 ) + def test_035_add_samples_to_request( self ): + """Testing adding samples to request""" + # logged in as regular_user1 # Sample fields - the tuple represents a sample name and a list of sample form field values - sample_value_tuples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), - ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] + sample_value_tuples = [ ( 'Sample1', [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), + ( 'Sample2', [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ), + ( 'Sample3', [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ] strings_displayed_after_submit = [ 'Unsubmitted' ] for sample_name, field_values in sample_value_tuples: strings_displayed_after_submit.append( sample_name ) # Add samples to the request self.add_samples( cntrller='requests', - request_id=self.security.encode_id( request_one.id ), - request_name=request_one.name, + request_id=self.security.encode_id( request1.id ), + request_name=request1.name, sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'There are no samples.' ], + strings_displayed=[ 'Add Samples to Request "%s"' % request1.name, + '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) - def test_030_edit_basic_request_info( self ): - """Testing editing the basic information of a sequence run request""" - # logged in as regular_user1 - fields = [ 'option2', str( user_address1.id ), 'field three value (edited)' ] - new_name=request_one.name + ' (Renamed)' - new_desc=request_one.desc + ' (Re-described)' - self.edit_basic_request_info( request_id=self.security.encode_id( request_one.id ), - cntrller='requests', - name=request_one.name, - new_name=new_name, - new_desc=new_desc, - new_fields=fields, - strings_displayed=[ 'Edit sequencing request "%s"' % request_one.name ], - strings_displayed_after_submit=[ new_name, new_desc ] ) - refresh( request_one ) - # check if the request is showing in the 'new' filter - self.check_request_grid( cntrller='requests', - state=request_one.states.NEW, - strings_displayed=[ request_one.name ] ) - def test_035_submit_request( self ): - """Testing editing a sequence run request""" - # logged in as regular_user1 - self.submit_request( cntrller='requests', - request_id=self.security.encode_id( request_one.id ), - request_name=request_one.name, - strings_displayed_after_submit=[ 'The request has been submitted.' ] ) - refresh( request_one ) - # Make sure the request is showing in the 'submitted' filter - self.check_request_grid( cntrller='requests', - state=request_one.states.SUBMITTED, - strings_displayed=[ request_one.name ] ) - # Make sure the request's state is now set to 'submitted' - assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ - % ( request_one.name, request_one.states.SUBMITTED ) - def test_040_request_lifecycle( self ): - """Testing request life-cycle as it goes through all the states""" - # logged in as regular_user1 - self.logout() - self.login( email=admin_user.email ) - self.check_request_grid( cntrller='requests_admin', - state=request_one.states.SUBMITTED, - strings_displayed=[ request_one.name ] ) - self.visit_url( "%s/requests_common/view_request?cntrller=requests&id=%s" % ( self.url, self.security.encode_id( request_one.id ) ) ) - # TODO: add some string for checking on the page above... - # Set bar codes for the samples - bar_codes = [ '1234567890', '0987654321' ] - strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] - for bar_code in bar_codes: - strings_displayed_after_submit.append( bar_code ) - self.add_bar_codes( request_id=self.security.encode_id( request_one.id ), - request_name=request_one.name, - bar_codes=bar_codes, - samples=request_one.samples, - strings_displayed_after_submit=strings_displayed_after_submit ) - # Change the states of all the samples of this request to ultimately be COMPLETE - self.change_sample_state( request_id=self.security.encode_id( request_one.id ), - request_name=request_one.name, - sample_names=[ sample.name for sample in request_one.samples ], - sample_ids=[ sample.id for sample in request_one.samples ], - new_sample_state_id=request_type1.states[1].id, - new_state_name=request_type1.states[1].name ) - self.change_sample_state( request_id=self.security.encode_id( request_one.id ), - request_name=request_one.name, - sample_names=[ sample.name for sample in request_one.samples ], - sample_ids=[ sample.id for sample in request_one.samples ], - new_sample_state_id=request_type1.states[2].id, - new_state_name=request_type1.states[2].name ) - refresh( request_one ) - self.logout() - self.login( email=regular_user1.email ) - # check if the request's state is now set to 'complete' - self.check_request_grid( cntrller='requests', - state='Complete', - strings_displayed=[ request_one.name ] ) - assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ - % ( request_one.name, request_one.states.COMPLETE ) - - def test_045_admin_create_request_on_behalf_of_regular_user( self ): - """Testing creating and submitting a request as an admin on behalf of a regular user""" - # Logged in as regular_user1 - self.logout() - self.login( email=admin_user.email ) - # Create the request - name = "RequestTwo" - desc = 'Request Two Description' - # Set field values - the tuples in the field_values list include the field_value, and True if refresh_on_change - # is required for that field. - field_value_tuples = [ ( 'option2', False ), ( str( user_address1.id ), True ), ( 'field_2_value', False ) ] - self.create_request( cntrller='requests_admin', - request_type_id=self.security.encode_id( request_type1.id ), - other_users_id=self.security.encode_id( regular_user1.id ), - name=name, - desc=desc, - field_value_tuples=field_value_tuples, - strings_displayed=[ 'Create a new sequencing request', - test_field_name1, - test_field_name2, - test_field_name3 ], - strings_displayed_after_submit=[ "The request has been created." ] ) - global request_two - request_two = get_request_by_name( name ) - # Make sure the request is showing in the 'new' filter - self.check_request_grid( cntrller='requests_admin', - state=request_two.states.NEW, - strings_displayed=[ request_two.name ] ) - # Make sure the request's state is now set to 'new' - assert request_two.state is not request_two.states.NEW, "The state of the request '%s' should be set to '%s'" \ - % ( request_two.name, request_two.states.NEW ) - # Sample fields - the tuple represents a sample name and a list of sample form field values - sample_value_tuples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), - ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] - strings_displayed_after_submit = [ 'Unsubmitted' ] - for sample_name, field_values in sample_value_tuples: - strings_displayed_after_submit.append( sample_name ) - # Add samples to the request - self.add_samples( cntrller='requests_admin', - request_id=self.security.encode_id( request_two.id ), - request_name=request_two.name, - sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'There are no samples.' ], - strings_displayed_after_submit=strings_displayed_after_submit ) - # Submit the request - self.submit_request( cntrller='requests_admin', - request_id=self.security.encode_id( request_two.id ), - request_name=request_two.name, - strings_displayed_after_submit=[ 'The request has been submitted.' ] ) - refresh( request_two ) - # Make sure the request is showing in the 'submitted' filter - self.check_request_grid( cntrller='requests_admin', - state=request_two.states.SUBMITTED, - strings_displayed=[ request_two.name ] ) - # Make sure the request's state is now set to 'submitted' - assert request_two.state is not request_two.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ - % ( request_two.name, request_two.states.SUBMITTED ) - # Make sure both requests are showing in the 'All' filter - self.check_request_grid( cntrller='requests_admin', - state='All', - strings_displayed=[ request_one.name, request_two.name ] ) - def test_050_reject_request( self ): - """Testing rejecting a request""" - # Logged in as admin_user - self.reject_request( request_id=self.security.encode_id( request_two.id ), - request_name=request_two.name, - comment="Rejection test comment", - strings_displayed=[ 'Reject Sequencing Request "%s"' % request_two.name ], - strings_displayed_after_submit=[ 'Request (%s) has been rejected.' % request_two.name ] ) - refresh( request_two ) - # Make sure the request is showing in the 'rejected' filter - self.check_request_grid( cntrller='requests_admin', - state=request_two.states.REJECTED, - strings_displayed=[ request_two.name ] ) - # Make sure the request's state is now set to REJECTED - assert request_two.state is not request_two.states.REJECTED, "The state of the request '%s' should be set to '%s'" \ - % ( request_two.name, request_two.states.REJECTED ) +# def test_040_edit_samples_of_new_request( self ): +# """Testing editing the sample information of new request1""" +# # logged in as regular_user1 +# pass +# def test_035_submit_request( self ): +# """Testing editing a sequence run request""" +# # logged in as regular_user1 +# self.submit_request( cntrller='requests', +# request_id=self.security.encode_id( request1.id ), +# request_name=request1.name, +# strings_displayed_after_submit=[ 'The request has been submitted.' ] ) +# refresh( request1 ) +# # Make sure the request is showing in the 'submitted' filter +# self.check_request_grid( cntrller='requests', +# state=request1.states.SUBMITTED, +# strings_displayed=[ request1.name ] ) +# # Make sure the request's state is now set to 'submitted' +# assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ +# % ( request1.name, request1.states.SUBMITTED ) +# def test_040_request_lifecycle( self ): +# """Testing request life-cycle as it goes through all the states""" +# # logged in as regular_user1 +# self.logout() +# self.login( email=admin_user.email ) +# self.check_request_grid( cntrller='requests_admin', +# state=request1.states.SUBMITTED, +# strings_displayed=[ request1.name ] ) +# self.visit_url( "%s/requests_common/view_request?cntrller=requests&id=%s" % ( self.url, self.security.encode_id( request1.id ) ) ) +# # TODO: add some string for checking on the page above... +# # Set bar codes for the samples +# bar_codes = [ '1234567890', '0987654321' ] +# strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] +# for bar_code in bar_codes: +# strings_displayed_after_submit.append( bar_code ) +# self.add_bar_codes( request_id=self.security.encode_id( request1.id ), +# request_name=request1.name, +# bar_codes=bar_codes, +# samples=request1.samples, +# strings_displayed_after_submit=strings_displayed_after_submit ) +# # Change the states of all the samples of this request to ultimately be COMPLETE +# self.change_sample_state( request_id=self.security.encode_id( request1.id ), +# request_name=request1.name, +# sample_names=[ sample.name for sample in request1.samples ], +# sample_ids=[ sample.id for sample in request1.samples ], +# new_sample_state_id=request_type1.states[1].id, +# new_state_name=request_type1.states[1].name ) +# self.change_sample_state( request_id=self.security.encode_id( request1.id ), +# request_name=request1.name, +# sample_names=[ sample.name for sample in request1.samples ], +# sample_ids=[ sample.id for sample in request1.samples ], +# new_sample_state_id=request_type1.states[2].id, +# new_state_name=request_type1.states[2].name ) +# refresh( request1 ) +# self.logout() +# self.login( email=regular_user1.email ) +# # check if the request's state is now set to 'complete' +# self.check_request_grid( cntrller='requests', +# state='Complete', +# strings_displayed=[ request1.name ] ) +# assert request1.state is not request1.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ +# % ( request1.name, request1.states.COMPLETE ) +# +# def test_045_admin_create_request_on_behalf_of_regular_user( self ): +# """Testing creating and submitting a request as an admin on behalf of a regular user""" +# # Logged in as regular_user1 +# self.logout() +# self.login( email=admin_user.email ) +# # Create the request +# name = "Request2" +# desc = 'Request2 Description' +# # Set field values - the tuples in the field_values list include the field_value, and True if refresh_on_change +# # is required for that field. +# field_value_tuples = [ ( 'option2', False ), ( str( user_address1.id ), True ), ( 'field_2_value', False ) ] +# self.create_request( cntrller='requests_admin', +# request_type_id=self.security.encode_id( request_type1.id ), +# other_users_id=self.security.encode_id( regular_user1.id ), +# name=name, +# desc=desc, +# field_value_tuples=field_value_tuples, +# strings_displayed=[ 'Create a new sequencing request', +# request_field_name1, +# request_field_name2, +# request_field_name3 ], +# strings_displayed_after_submit=[ "The request has been created." ] ) +# global request2 +# request2 = get_request_by_name( name ) +# # Make sure the request is showing in the 'new' filter +# self.check_request_grid( cntrller='requests_admin', +# state=request2.states.NEW, +# strings_displayed=[ request2.name ] ) +# # Make sure the request's state is now set to 'new' +# assert request2.state is not request2.states.NEW, "The state of the request '%s' should be set to '%s'" \ +# % ( request2.name, request2.states.NEW ) +# # Sample fields - the tuple represents a sample name and a list of sample form field values +# sample_value_tuples = [ ( 'Sample1', [ 'S1 Field 0 Value' ] ), +# ( 'Sample2', [ 'S2 Field 0 Value' ] ) ] +# strings_displayed_after_submit = [ 'Unsubmitted' ] +# for sample_name, field_values in sample_value_tuples: +# strings_displayed_after_submit.append( sample_name ) +# # Add samples to the request +# self.add_samples( cntrller='requests_admin', +# request_id=self.security.encode_id( request2.id ), +# request_name=request2.name, +# sample_value_tuples=sample_value_tuples, +# strings_displayed=[ 'There are no samples.' ], +# strings_displayed_after_submit=strings_displayed_after_submit ) +# # Submit the request +# self.submit_request( cntrller='requests_admin', +# request_id=self.security.encode_id( request2.id ), +# request_name=request2.name, +# strings_displayed_after_submit=[ 'The request has been submitted.' ] ) +# refresh( request2 ) +# # Make sure the request is showing in the 'submitted' filter +# self.check_request_grid( cntrller='requests_admin', +# state=request2.states.SUBMITTED, +# strings_displayed=[ request2.name ] ) +# # Make sure the request's state is now set to 'submitted' +# assert request2.state is not request2.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ +# % ( request2.name, request2.states.SUBMITTED ) +# # Make sure both requests are showing in the 'All' filter +# self.check_request_grid( cntrller='requests_admin', +# state='All', +# strings_displayed=[ request1.name, request2.name ] ) +# def test_050_reject_request( self ): +# """Testing rejecting a request""" +# # Logged in as admin_user +# self.reject_request( request_id=self.security.encode_id( request2.id ), +# request_name=request2.name, +# comment="Rejection test comment", +# strings_displayed=[ 'Reject Sequencing Request "%s"' % request2.name ], +# strings_displayed_after_submit=[ 'Request (%s) has been rejected.' % request2.name ] ) +# refresh( request2 ) +# # Make sure the request is showing in the 'rejected' filter +# self.check_request_grid( cntrller='requests_admin', +# state=request2.states.REJECTED, +# strings_displayed=[ request2.name ] ) +# # Make sure the request's state is now set to REJECTED +# assert request2.state is not request2.states.REJECTED, "The state of the request '%s' should be set to '%s'" \ +# % ( request2.name, request2.states.REJECTED ) def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" # Logged in as admin_user + self.logout() + self.login( email=admin_user.email ) ################## # Delete request_type permissions ################## @@ -402,12 +490,12 @@ class TestFormsAndRequests( TwillTestCas ################## # Mark all requests deleted ################## - for request in [ request_one, request_two ]: + for request in [ request1 ]: mark_obj_deleted( request ) ################## # Mark all forms deleted ################## - for form in [ form_one, form_two ]: + for form in [ request_form_definition1, sample_form_definition1 ]: self.mark_form_deleted( self.security.encode_id( form.current.id ) ) ################## # Mark all user_addresses deleted @@ -417,18 +505,18 @@ class TestFormsAndRequests( TwillTestCas ################## # Delete all non-private roles ################## - for role in [ role_one, role_two ]: + for role in [ role1, role2 ]: self.mark_role_deleted( self.security.encode_id( role.id ), role.name ) self.purge_role( self.security.encode_id( role.id ), role.name ) # Manually delete the role from the database refresh( role ) - delete( role ) + delete_obj( role ) ################## # Delete all groups ################## - for group in [ group_one ]: + for group in [ group1 ]: self.mark_group_deleted( self.security.encode_id( group.id ), group.name ) self.purge_group( self.security.encode_id( group.id ), group.name ) # Manually delete the group from the database refresh( group ) - delete( group ) + delete_obj( group ) --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -870,6 +870,14 @@ class TwillTestCase( unittest.TestCase ) fname = self.write_temp_file( page ) errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) + + def check_string_not_in_page( self, patt ): + """Checks to make sure 'patt' is NOT in the page.""" + page = self.last_page() + if page.find( patt ) != -1: + fname = self.write_temp_file( page ) + errmsg = "string (%s) incorrectly displayed in page.\npage content written to '%s'" % ( patt, fname ) + raise AssertionError( errmsg ) def write_temp_file( self, content, suffix='.html' ): fd, fname = tempfile.mkstemp( suffix=suffix, prefix='twilltestcase-' ) @@ -1330,6 +1338,9 @@ class TwillTestCase( unittest.TestCase ) if form_type == "Sequencing Sample Form": tc.submit( "add_layout_grid" ) tc.fv( "1", "grid_layout0", form_layout_name ) + # if not adding any fields at this time, remove the default empty field + if num_fields == 0: + tc.submit( "remove_button" ) # Add fields to the new form definition for index1 in range( num_fields ): field_name = 'field_name_%i' % index1 @@ -1357,9 +1368,8 @@ class TwillTestCase( unittest.TestCase ) else: tc.fv( "1", "field_type_0", field_type ) tc.fv( "1", field_default, field_default_contents ) + # All done... now save tc.submit( "save_changes_button" ) - if num_fields == 0: - self.visit_url( "%s/forms/manage" % self.url ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() @@ -1392,7 +1402,7 @@ class TwillTestCase( unittest.TestCase ) # SelectFields require a refresh_on_change self.refresh_form( field_type, field_type_value ) for option_index, option in enumerate( field_dict[ 'selectlist' ] ): - tc.submit( "addoption_0" ) + tc.submit( "addoption_%i" % index ) tc.fv( "1", "field_%i_option_%i" % ( index, option_index ), option ) else: tc.fv( "1", field_type, field_type_value ) @@ -1400,6 +1410,22 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() + def view_form( self, id, form_type='', form_name='', form_desc='', form_layout_name='', field_dicts=[] ): + '''View form details''' + self.home() + self.visit_url( "%s/forms/manage?operation=view&id=%s" % ( self.url, id ) ) + self.check_page_for_string( form_type ) + self.check_page_for_string( form_name ) + self.check_page_for_string( form_desc ) + self.check_page_for_string( form_layout_name ) + for i, field_dict in enumerate( field_dicts ): + self.check_page_for_string( field_dict[ 'name' ] ) + self.check_page_for_string( field_dict[ 'desc' ] ) + self.check_page_for_string( field_dict[ 'type' ] ) + if field_dict[ 'type' ].lower() == 'selectfield': + for option_index, option in enumerate( field_dict[ 'selectlist' ] ): + self.check_page_for_string( option ) + self.home() def mark_form_deleted( self, form_id ): """Mark a form_definition as deleted""" self.home() @@ -1445,6 +1471,17 @@ class TwillTestCase( unittest.TestCase ) check_str = "Permissions updated for sequencer configuration '%s'" % request_type_name self.check_page_for_string( check_str ) self.home() + def view_request_type( self, request_type_id, request_type_name, sample_states, strings_displayed=[] ): + '''View request_type details''' + self.home() + self.visit_url( "%s/requests_admin/browse_request_types?operation=view&id=%s" % ( self.url, request_type_id ) ) + self.check_page_for_string( 'Sequencer configuration information' ) + self.check_page_for_string( request_type_name ) + for name, desc in sample_states: + self.check_page_for_string( name ) + self.check_page_for_string( desc ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) def create_request( self, cntrller, request_type_id, name, desc, field_value_tuples, other_users_id='', strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( "%s/requests_common/create_request?cntrller=%s" % ( self.url, cntrller ) ) @@ -1473,6 +1510,18 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() + def view_request( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): + self.visit_url( "%s/%s/browse_requests?operation=view_request&id=%s" % ( self.url, cntrller, request_id ) ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for check_str in strings_not_displayed: + self.check_string_not_in_page( check_str ) + def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): + self.visit_url( "%s/requests_common/request_events?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for check_str in strings_not_displayed: + self.check_string_not_in_page( check_str ) def edit_basic_request_info( self, cntrller, request_id, name, new_name='', new_desc='', new_fields=[], strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( "%s/requests_common/edit_basic_request_info?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) @@ -1489,40 +1538,22 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) def add_samples( self, cntrller, request_id, request_name, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): - self.visit_url( "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=False" % ( self.url, cntrller, request_id ) ) + url = "%s/requests_common/add_sample?cntrller=%s&request_id=%s&add_sample_button=Add+sample" % ( self.url, cntrller, request_id ) + self.visit_url( url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - # Simulate clicking the add-sample_button on the form. (gvk: 9/21/10 - TODO : There must be a bug in the mako template - # because twill cannot find any forms on the page, but I cannot find it although I've spent time cleaning up the - # template code and looking for any problems. - url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=False" % ( self.url, cntrller, request_id ) - # This should work, but although twill does not thorw any exceptions, the button click never occurs - # There are multiple forms on this page, and we'll only be using the form named edit_samples. - # for sample_index, sample_value_tuple in enumerate( sample_value_tuples ): - # # Add the following form value to the already populated hidden field so that the edit_samples - # # form is the current form - # tc.fv( "1", "id", request_id ) - # tc.submit( 'add_sample_button' ) - for sample_index, sample_value_tuple in enumerate( sample_value_tuples ): - sample_name, field_values = sample_value_tuple - sample_name = sample_name.replace( ' ', '+' ) - field_name = "sample_%i_name" % sample_index - # The following form_value setting should work but since twill barfed on submitting the add_sample_button - # above, we have to simulate it by appending to the url. - # tc.fv( "1", field_name, sample_name ) - url += "&%s=%s" % ( field_name, sample_name ) - for field_index, field_value in enumerate( field_values ): - field_name = "sample_%i_field_%i" % ( sample_index, field_index ) - field_value = field_value.replace( ' ', '+' ) - # The following form_value setting should work but since twill barfed on submitting the add_sample_button - # above, we have to simulate it by appending to the url. - # tc.fv( "1", field_name, field_value ) - url += "&%s=%s" % ( field_name , field_value ) - # The following button submit should work but since twill barfed on submitting the add_sample_button - # above, we have to simulate it by appending to the url. - # tc.submit( "save_samples_button" ) - url += "&save_samples_button=Save" - self.visit_url( url ) + for sample_index, sample_info in enumerate( sample_value_tuples ): + sample_name = sample_info[0] + sample_field_values = sample_info[1] + tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + for field_index, field_value in enumerate( sample_field_values ): + tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + # Do not click on Add sample button when all the sample have been added + if sample_index < len( sample_value_tuples ) - 1: + tc.submit( "add_sample_button" ) + # select the correct form before submitting it + tc.fv( "1", "copy_sample_index", "-1" ) + tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) def submit_request( self, cntrller, request_id, request_name, strings_displayed_after_submit=[] ): --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -136,8 +136,10 @@ %endif <p/><div class="form-row"> + ## hidden element to make twill work. + <input type="hidden" name="hidden_input" value=""/> %if ( request.samples or current_samples ) and ( editing_samples or len( current_samples ) > len( request.samples ) ): - <input type="submit" name="add_sample_button" value="Add sample"/> + <input type="submit" name="add_sample_button" value="Add sample" /><input type="submit" name="save_samples_button" value="Save"/><input type="submit" name="cancel_changes_button" value="Cancel"/><div class="toolParamHelp" style="clear: both;">

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galaxy-dist commit ecaf015e009a: (recommit): porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1289402803 18000 # Node ID ecaf015e009a35a3cf421a87fbab1c5d0bbba5b4 # Parent 2c2a22396a2641a52dc5f200d26a3d947cf11cbd (recommit): porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility --- a/scripts/taxonomy/processTaxonomy.sh +++ b/scripts/taxonomy/processTaxonomy.sh @@ -10,5 +10,9 @@ cat gi_taxid_nucl.dmp gi_taxid_prot.dmp echo "Sorting gi2tax files..." sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp +echo "Removing parenthesis from names.dmp" +cat names.dmp | sed s/$/_/g | sed s/$/_/g > names.temporary +mv names.dmp names.dmp.orig +mv names.temporary names.dmp

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galaxy-dist commit 479b377ef455: fix the add sample bug in request page
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289333440 18000 # Node ID 479b377ef455f2d676fb84363b0b6d437d6af5f6 # Parent 7c60d74ba2df4488df90d08ed0ae9c7cc3871222 fix the add sample bug in request page --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -131,6 +131,8 @@ is_submitted = False is_unsubmitted = False display_checkboxes = False + display_bar_code = False + display_datasets = False %><% if display_checkboxes and trans.security.encode_id( sample.id ) in encoded_selected_sample_ids:

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galaxy-dist commit 9ee40043b826: rgHaploView tool version upgrade - now shows thumbnail of ld plots
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289322752 18000 # Node ID 9ee40043b826b3bc1e29f84996f9fe14dd119a45 # Parent a77b2888759e94861252ca65437e11ec298b3058 rgHaploView tool version upgrade - now shows thumbnail of ld plots --- a/tools/rgenetics/rgHaploView.xml +++ b/tools/rgenetics/rgHaploView.xml @@ -1,4 +1,4 @@ -<tool id="rgHaploView1" name="LD plots:" version="0.2"> +<tool id="rgHaploView1" name="LD plots:" version="0.3"><description>and comparisons with HapMap data</description> --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html @@ -9,9 +9,11 @@ </head><body><div class="document"> -<h4>rgenetics for Galaxy rgHaploView.py, wrapping HaploView</h4><br><div><hr><ul> +<h4>rgenetics for Galaxy rgHaploView.py, wrapping HaploView</h4><table><tr><td><a href="allnup.pdf"><img src="allnup.png" alt="Main combined LD image" hspace="10" align="middle"></td><td>Click the thumbnail at left to download the main combined LD image <a href=allnup.pdf>allnup.pdf</a></td></tr></table> +<br><div><hr><ul><li><a href="alljoin.pdf">alljoin.pdf - All pdf plots, each on a separate page</a></li><li><a href="allnup.pdf">allnup.pdf - All pdf plots on a single page</a></li> +<li><a href="allnup.png">allnup.png - allnup.png</a></li><li><a href="1_rgHaploViewtest1.pdf">1_rgHaploViewtest1.pdf - 1_rgHaploViewtest1.pdf</a></li><li><a href="1_rgHaploViewtest1.png">1_rgHaploViewtest1.png - 1_rgHaploViewtest1.png</a></li><li><a href="2_HapMap_YRI_22.pdf">2_HapMap_YRI_22.pdf - Hapmap data</a></li> @@ -33,7 +35,7 @@ Haploview 4.2 Java Version: 1.6.0_03 -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 @@ -41,9 +43,9 @@ Arguments: -n -pairwiseTagging -pedfile Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info Writing output to rgHaploViewtest1.ped.LD.PNG @@ -79,27 +81,37 @@ Downloading chromosome 22, analysis pane Writing output to Chromosome22YRI.LD.PNG -This is pdfjoin version 1.20 + ---- -Reading site configuration from /etc/pdfnup.conf + pdfjam: This is pdfjam version 2.06. - Temporary LaTeX file for this job is /var/tmp/22578.tex + pdfjam: Reading any site-wide or user-specific defaults... - Calling pdflatex... + (none found) - Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/alljoin.pdf + pdfjam: Effective call for this run of pdfjam: -This is pdfnup version 1.20 + /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf - -Reading site configuration from /etc/pdfnup.conf + pdfjam: Calling pdflatex... -Processing alljoin.pdf... + pdfjam: Finished. Output was to 'alljoin.pdf'. - Temporary LaTeX file for this job is /var/tmp/22621-1.tex + ---- - Calling pdflatex... + pdfjam: This is pdfjam version 2.06. - Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/allnup.pdf + pdfjam: Reading any site-wide or user-specific defaults... + + (none found) + + pdfjam: Effective call for this run of pdfjam: + + /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - + + pdfjam: Calling pdflatex... + + pdfjam: Finished. Output was to 'allnup.pdf'. PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin @@ -107,7 +119,7 @@ PATH=/usr/kerberos/bin:/usr/local/bin:/b -## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 @@ -123,7 +135,9 @@ PATH=/usr/kerberos/bin:/usr/local/bin:/b ## executing mogrify -format pdf -resize 800x400! *.png returned 0 -## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0 +## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 + +## executing convert -resize x300 allnup.pdf allnup.png returned 0 </pre><hr></div></body></html> Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS @@ -1,9 +1,9 @@ rs2283804 rs756632 -rs4820537 -rs3788347 -rs2283802 -rs4822363 rs4820539 rs16997606 +rs4822363 rs2267000 +rs3788347 +rs4820537 +rs2283802 Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed --- a/tools/rgenetics/rgHaploView.py +++ b/tools/rgenetics/rgHaploView.py @@ -47,7 +47,7 @@ class ldPlot: self.args=argv self.parseArgs(argv=self.args) self.setupRegions() - + def parseArgs(self,argv=[]): """ """ @@ -405,10 +405,10 @@ class ldPlot: p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) retval = p.wait() self.lf.write('## executing %s returned %d\n' % (vcl,retval)) - #vcl = ['convert', 'allnup.pdf', 'allnup.png'] # this fails - bad pdf? - #p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath) - #retval = p.wait() - #lf.write('## executing %s returned %d\n' % (vcl,retval)) + vcl = '%s -resize x300 allnup.pdf allnup.png' % (self.convert) + p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + self.lf.write('## executing %s returned %d\n' % (vcl,retval)) ste.close() # temp file used to catch haploview blather hblather = open(blog,'r').readlines() # to catch the blather os.unlink(blog) @@ -425,20 +425,16 @@ class ldPlot: outf.write(galhtmlprefix % progname) s = '<h4>rgenetics for Galaxy %s, wrapping HaploView</h4>' % (progname) outf.write(s) - """ - as at ashg 2009, convert fails on allnup.pdf - probably too complex... mainthumb = 'allnup.png' mainpdf = 'allnup.pdf' - if os.path.exists(mainpdf): - if not os.path.exists(mainthumb): + if os.path.exists(os.path.join(self.outfpath,mainpdf)): + if not os.path.exists(os.path.join(self.outfpath,mainthumb)): outf.write('<table><tr><td colspan="3"><a href="%s">Main combined LD plot</a></td></tr></table>\n' % (mainpdf)) else: - outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">') - outf.write('</td><td>Click this thumbnail to display the main combined LD image</td></tr></table>\n' % (mainpdf,mainthumb)) + outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">' % (mainpdf,mainthumb)) + outf.write('</td><td>Click the thumbnail at left to download the main combined LD image <a href=%s>%s</a></td></tr></table>\n' % (mainpdf,mainpdf)) else: outf.write('(No main image was generated - this usually means a Haploview error connecting to Hapmap site - please try later)<br/>\n') - outf.write('## Called as %s' % sys.argv) - """ outf.write('<br><div><hr><ul>\n') for i, data in enumerate( flist ): dn = os.path.split(data)[-1] @@ -515,3 +511,4 @@ if __name__ == "__main__": ld.doPlots() + --- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt +++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt @@ -3,12 +3,12 @@ Haploview 4.2 Java Version: 1.6.0_03 ***************************************************** -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using data file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using marker information file: /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info Writing output to rgHaploViewtest1.ped.LD.PNG Starting tagging. Writing output to rgHaploViewtest1.ped.TAGS @@ -26,21 +26,26 @@ Arguments: -n -chromosome 22 -panel YRI Max LD comparison distance = 200000kb Downloading chromosome 22, analysis panel YRI, 21784..21905 from HapMap release 21. Writing output to Chromosome22YRI.LD.PNG -This is pdfjoin version 1.20 -Reading site configuration from /etc/pdfnup.conf - Temporary LaTeX file for this job is /var/tmp/22578.tex - Calling pdflatex... - Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/alljoin.pdf -This is pdfnup version 1.20 -Reading site configuration from /etc/pdfnup.conf -Processing alljoin.pdf... - Temporary LaTeX file for this job is /var/tmp/22621-1.tex - Calling pdflatex... - Finished: output is /opt/galaxy/test-data/rgtestouts/rgHaploView/allnup.pdf + ---- + pdfjam: This is pdfjam version 2.06. + pdfjam: Reading any site-wide or user-specific defaults... + (none found) + pdfjam: Effective call for this run of pdfjam: + /usr/local/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --fitpaper 'true' --outfile alljoin.pdf -- 1_rgHaploViewtest1.pdf - 2_HapMap_YRI_22.pdf - + pdfjam: Calling pdflatex... + pdfjam: Finished. Output was to 'alljoin.pdf'. + ---- + pdfjam: This is pdfjam version 2.06. + pdfjam: Reading any site-wide or user-specific defaults... + (none found) + pdfjam: Effective call for this run of pdfjam: + /usr/local/bin/pdfjam --suffix nup --nup '2x1' --landscape --nup '1x2' --outfile allnup.pdf -- alljoin.pdf - + pdfjam: Calling pdflatex... + pdfjam: Finished. Output was to 'allnup.pdf'. PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /opt/galaxy/tool-data/shared/jars/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /tmp/foo/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0 @@ -48,5 +53,6 @@ PATH=/usr/kerberos/bin:/usr/local/bin:/b ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'HapMap YRI'" rgHaploViewtest1.tmp.png 2_HapMap_YRI_22.png returned 0 ### nimages=2 ## executing mogrify -format pdf -resize 800x400! *.png returned 0 -## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0 +## executing pdfjoin *.pdf --fitpaper true --outfile alljoin.pdf returned 0 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 +## executing convert -resize x300 allnup.pdf allnup.png returned 0 --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS @@ -14,12 +14,12 @@ rs2267006 rs2283804 1.0 rs4822363 rs4822363 1.0 Test Alleles Captured -rs2283804 rs2283804,rs2267006 +rs2283804 rs2267006,rs2283804 rs756632 rs756632 -rs4820537 rs4820537 -rs3788347 rs3788347 -rs2283802 rs2283802 -rs4822363 rs4822363 rs4820539 rs4820539 rs16997606 rs16997606 +rs4822363 rs4822363 rs2267000 rs2267000 +rs3788347 rs3788347 +rs4820537 rs4820537 +rs2283802 rs2283802 Binary file test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG has changed

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galaxy-dist commit 2c2a22396a26: Backed out changeset 081ce300b688 (some files accidentally committed).
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1289402767 18000 # Node ID 2c2a22396a2641a52dc5f200d26a3d947cf11cbd # Parent 081ce300b688968521edd30f25a020d96999cd64 Backed out changeset 081ce300b688 (some files accidentally committed). --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -388,7 +388,6 @@ class TestFormsAndRequests( TwillTestCas % ( request_two.name, request_two.states.REJECTED ) def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" - ''' # Logged in as admin_user ################## # Delete request_type permissions @@ -433,4 +432,3 @@ class TestFormsAndRequests( TwillTestCas # Manually delete the group from the database refresh( group ) delete( group ) - ''' --- a/static/welcome.html +++ b/static/welcome.html @@ -2,211 +2,20 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> -<link rel="stylesheet" href="style/base.css" type="text/css" /> -<style type="text/css"> - 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<div class="quickie"> - <img src="images/qk/quickie11_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie12_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_13_fastq_basic/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie13_small.png" border="0"> - </div> - </a> - </td> - - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_14_fastq_adv/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie14_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_15_lastz_frag/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie15_small.png" border="0"> - </div> - </a> - </td> - - - - </tr> - </table> -</div> - -<script type="text/javascript"> - // Scroll to last quickie in box - document.getElementById("previous").scrollLeft = 100000000; -</script> - -<br/> -<br/> -<br/> -<hr/> - -<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> - -This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, and <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>. -<p><small>Galaxy build: <b>$Rev 3885:1ab9d6b0ddfc$</b></small></p> -</div> -</div> + <div class="document"> + <div class="donemessagelarge"> + <strong>Hello world! It's running...</strong> + <hr> + To customize this page edit <code>static/welcome.html</code> + </div> + <br/> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <hr/> + This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. + </div></body></html> --- a/scripts/taxonomy/processTaxonomy.sh +++ b/scripts/taxonomy/processTaxonomy.sh @@ -10,9 +10,5 @@ cat gi_taxid_nucl.dmp gi_taxid_prot.dmp echo "Sorting gi2tax files..." sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp -echo "Removing parenthesis from names.dmp" -cat names.dmp | sed s/$/_/g | sed s/$/_/g > names.temporary -mv names.dmp names.dmp.orig -mv names.temporary names.dmp

1 0

galaxy-dist commit 081ce300b688: porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Anton Nekrutenko <anton(a)bx.psu.edu> # Date 1289402232 18000 # Node ID 081ce300b688968521edd30f25a020d96999cd64 # Parent 0e3fe3e7b21bfd78461869817c6b43db827d77f0 porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -388,6 +388,7 @@ class TestFormsAndRequests( TwillTestCas % ( request_two.name, request_two.states.REJECTED ) def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" + ''' # Logged in as admin_user ################## # Delete request_type permissions @@ -432,3 +433,4 @@ class TestFormsAndRequests( TwillTestCas # Manually delete the group from the database refresh( group ) delete( group ) + ''' --- a/static/welcome.html +++ b/static/welcome.html @@ -2,20 +2,211 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link rel="stylesheet" href="style/base.css" type="text/css" /> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> +<link rel="stylesheet" href="style/base.css" type="text/css" /> +<style type="text/css"> + + .quickie { + text-align: center; + background: black; + margin: 10px; + } + + .current-quickie { + width: 300px; + background: white; + margin: auto; + } + + .current-quickie img { + padding: 15px; + border: 1px solid #ccc; + margin: auto; + background-color: white; + -moz-border-radius:4px; + -webkit-border-radius:4px; + + } + + .previous { + width: 100%; + overflow: auto; + border: solid #ccc 1px; + -moz-border-radius:4px; + -webkit-border-radius:4px; + + } + .previous .quickie { + padding-top: 10px; + min-height: 90px; + min-width: 150px; + } + #screencasts { + max-width: 50em; + margin-left: auto; + margin-right: auto; + } + +</style> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> +<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> +<script type="text/javascript"> + +$(document).ready(function() { + $('.current-quickie').cycle({ + fx: 'fade', + pause: 1, + timeout: 1000, + speed: 1000 + }); +}); +</script></head><body> - <div class="document"> - <div class="donemessagelarge"> - <strong>Hello world! It's running...</strong> - <hr> - To customize this page edit <code>static/welcome.html</code> - </div> - <br/> - <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> - <hr/> - This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. - </div> +<div class="document"> +<h3 align="center">Here is what's happening...</h3> +<div align="center" class="current-quickie"> + <a target="_blank" href="http://usegalaxy.org/cloud"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"></a> + <a target="_blank" href="http://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_R…"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200"></a> + <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/ismb2010-demo"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /></a> + <a target="_blank" href="http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/Tutorial/Data…"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /></a> + <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a> +</div> + +<h3 align="center">Live Quickies</h3> + +<div class="previous" id="previous"> + <table border="0" cellpadding="0" cellspacing="0" width="100%"> + <tr> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie1_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie2_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie3_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie4_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie5_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie6_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie7_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie8_solid_single_end/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie8_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie9_solid_mate_pair/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie9_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie10_custom_genome/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie10_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_11_illumina_se/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie11_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie12_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_13_fastq_basic/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie13_small.png" border="0"> + </div> + </a> + </td> + + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_14_fastq_adv/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie14_small.png" border="0"> + </div> + </a> + </td> + <td> + <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_15_lastz_frag/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie15_small.png" border="0"> + </div> + </a> + </td> + + + + </tr> + </table> +</div> + +<script type="text/javascript"> + // Scroll to last quickie in box + document.getElementById("previous").scrollLeft = 100000000; +</script> + +<br/> +<br/> +<br/> +<hr/> + +<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> + +This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, and <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>. +<p><small>Galaxy build: <b>$Rev 3885:1ab9d6b0ddfc$</b></small></p> +</div> +</div></body></html> --- a/scripts/taxonomy/processTaxonomy.sh +++ b/scripts/taxonomy/processTaxonomy.sh @@ -10,5 +10,9 @@ cat gi_taxid_nucl.dmp gi_taxid_prot.dmp echo "Sorting gi2tax files..." sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp +echo "Removing parenthesis from names.dmp" +cat names.dmp | sed s/$/_/g | sed s/$/_/g > names.temporary +mv names.dmp names.dmp.orig +mv names.temporary names.dmp

1 0

galaxy-dist commit a77b2888759e: Streamline the sample tracking UI in selecting and transferring sample datasets.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289275808 18000 # Node ID a77b2888759e94861252ca65437e11ec298b3058 # Parent 2875445df9906828bc804e9b0923160f902b3fac Streamline the sample tracking UI in selecting and transferring sample datasets. --- a/templates/requests/common/sample_datasets.mako +++ b/templates/requests/common/sample_datasets.mako @@ -1,5 +1,5 @@ <%def name="render_sample_datasets( sample )"> - ${len( sample.transferred_dataset_files )} / ${len( sample.datasets )} + ${len( sample.datasets )} / ${len( sample.transferred_dataset_files )} </%def> ${render_sample_datasets( sample )} --- /dev/null +++ b/templates/admin/requests/view_sample_dataset.mako @@ -0,0 +1,72 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<br/><br/> + +<% + sample = sample_dataset.sample + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + can_manage_datasets = is_admin and sample.untransferred_dataset_files +%> + +<ul class="manage-table-actions"> + %if can_manage_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Manage sample datasets</a></li> + %endif + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> +</ul> + +<div class="toolForm"> + <div class="toolFormTitle">"${sample.name}" Dataset</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.name} + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>File path:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.file_path} + </div> + <div class="toolParamHelp" style="clear: both;"> + This file is contained in a sub-directory of the data directory configured for the sequencer. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Size:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.size} + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Date this dataset was selected for this sample:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.create_time} + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Transfer status:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${sample_dataset.status} + </div> + <div style="clear: both"></div> + </div> + %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.ERROR: + <div class="form-row"> + <label>Transfer error:</label> + ${sample_dataset.error_msg} + </div> + <div style="clear: both"></div> + %endif + </div> +</div> --- a/templates/admin/requests/get_data.mako +++ /dev/null @@ -1,114 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -${h.js( "ui.core", "jquery.cookie" )} -<link href='/static/june_2007_style/blue/dynatree_skin/ui.dynatree.css' rel='stylesheet' type='text/css'> -${h.js( "jquery.dynatree" )} - -<script type="text/javascript"> - $(function(){ - $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) { - _log("debug", "ajaxComplete: %o", this); // dom element listening - }); - // --- Initialize sample trees - $("#tree").dynatree({ - title: "${request.type.datatx_info['data_dir']}", - rootVisible: true, - minExpandLevel: 0, // 1: root node is not collapsible - persist: false, - checkbox: true, - selectMode: 3, - onPostInit: function(isReloading, isError) { -// alert("reloading: "+isReloading+", error:"+isError); - logMsg("onPostInit(%o, %o) - %o", isReloading, isError, this); - // Re-fire onActivate, so the text is updated - this.reactivate(); - }, - fx: { height: "toggle", duration: 200 }, - // initAjax is hard to fake, so we pass the children as object array: - initAjax: {url: "${h.url_for( controller='requests_admin', action='open_folder' )}", - dataType: "json", - data: { id: "${request.id}", key: "${request.type.datatx_info['data_dir']}" }, - }, - onLazyRead: function(dtnode){ - dtnode.appendAjax({ - url: "${h.url_for( controller='requests_admin', action='open_folder' )}", - dataType: "json", - data: { id: "${request.id}", key: dtnode.data.key }, - }); - }, - onSelect: function(select, dtnode) { - // Display list of selected nodes - var selNodes = dtnode.tree.getSelectedNodes(); - // convert to title/key array - var selKeys = $.map(selNodes, function(node){ - return node.data.key; - }); - document.get_data.selected_files.value = selKeys.join(",") - }, - onActivate: function(dtnode) { - var cell = $("#file_details"); - var selected_value = dtnode.data.key - if(selected_value.charAt(selected_value.length-1) != '/') { - // Make ajax call - $.ajax( { - type: "POST", - url: "${h.url_for( controller='requests_admin', action='get_file_details' )}", - dataType: "json", - data: { id: "${request.id}", folder_path: dtnode.data.key }, - success : function ( data ) { - cell.html( '<label>'+data+'</label>' ) - } - }); - } else { - cell.html( '' ) - } - }, - }); - }); - -</script> - -<br/> -<br/> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration "${request.type.name}"</a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - </li> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Select files for transfer</div> - <form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', cntrller=cntrller, request_id=trans.security.encode_id( request.id ))}" method="post" > - <div class="form-row"> - <label>Sample:</label> - ${sample_id_select_field.get_html()} - <div class="toolParamHelp" style="clear: both;"> - Select the sample with which you want to associate the datasets - </div> - </div> - <div class="form-row" > - <label>Select dataset files in the sequencer:</label> - <div id="tree" > - Loading... - </div> - <input id="selected_files" name="selected_files" type="hidden" size=40"/> - <div class="toolParamHelp" style="clear: both;"> - To select a folder, select all the individual files in that folder. - </div> - </div> - <div class="form-row"> - <div id="file_details" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - <div class="form-row"> - <input type="submit" name="select_show_datasets_button" value="Select & show datasets"/> - <input type="submit" name="select_more_button" value="Select more"/> - </div> - </form> -</div> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -58,7 +58,7 @@ class RequestsGrid( grids.Grid ): columns = [ NameColumn( "Name", key="name", - link=( lambda item: iff( item.deleted, None, dict( operation="view_request", id=item.id ) ) ), + link=( lambda item: dict( operation="view_request", id=item.id ) ), attach_popup=True, filterable="advanced" ), DescriptionColumn( "Description", @@ -318,11 +318,10 @@ class RequestsCommon( BaseController, Us trans.sa_session.flush() trans.sa_session.refresh( request ) # Create an event with state 'New' for this new request + comment = "Request created by %s" % trans.user.email if request.user != trans.user: - sample_event_comment = "Request created by user %s for user %s." % ( trans.user.email, request.user.email ) - else: - sample_event_comment = "Request created." - event = trans.model.RequestEvent( request, request.states.NEW, sample_event_comment ) + comment += " on behalf of %s." % request.user.email + event = trans.model.RequestEvent( request, request.states.NEW, comment ) trans.sa_session.add( event ) trans.sa_session.flush() else: @@ -361,11 +360,10 @@ class RequestsCommon( BaseController, Us status='error', message=message ) ) # Change the request state to 'Submitted' - if request.user.email is not trans.user: - sample_event_comment = "Request submitted by %s on behalf of %s." % ( trans.user.email, request.user.email ) - else: - sample_event_comment = "" - event = trans.model.RequestEvent( request, request.states.SUBMITTED, sample_event_comment ) + comment = "Request submitted by %s" % trans.user.email + if request.user != trans.user: + comment += " on behalf of %s." % request.user.email + event = trans.model.RequestEvent( request, request.states.SUBMITTED, comment ) trans.sa_session.add( event ) # Change the state of each of the samples of this request # request.type.states is the list of SampleState objects configured @@ -511,23 +509,39 @@ class RequestsCommon( BaseController, Us id_list = util.listify( kwd.get( 'id', '' ) ) message = util.restore_text( params.get( 'message', '' ) ) status = util.restore_text( params.get( 'status', 'done' ) ) + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() num_deleted = 0 + not_deleted = [] for id in id_list: ok_for_now = True try: + # This block will handle bots that do not send valid request ids. request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( id ) ) except: ok_for_now = False if ok_for_now: - request.deleted = True - trans.sa_session.add( request ) - # Delete all the samples belonging to this request - for s in request.samples: - s.deleted = True - trans.sa_session.add( s ) - trans.sa_session.flush() - num_deleted += 1 + # We will only allow the request to be deleted by a non-admin user if not request.submitted + if is_admin or not request.is_submitted: + request.deleted = True + trans.sa_session.add( request ) + # Delete all the samples belonging to this request + for s in request.samples: + s.deleted = True + trans.sa_session.add( s ) + comment = "Request marked deleted by %s." % trans.user.email + # There is no DELETED state for a request, so keep the current request state + event = trans.model.RequestEvent( request, request.state, comment ) + trans.sa_session.add( event ) + trans.sa_session.flush() + num_deleted += 1 + else: + not_deleted.append( request ) message += '%i requests have been deleted.' % num_deleted + if not_deleted: + message += ' Contact the administrator to delete the following submitted requests: ' + for request in not_deleted: + message += '%s, ' % request.name + message = message.rstrip( ', ' ) return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_requests', status=status, @@ -543,6 +557,7 @@ class RequestsCommon( BaseController, Us for id in id_list: ok_for_now = True try: + # This block will handle bots that do not send valid request ids. request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( id ) ) except: ok_for_now = False @@ -553,6 +568,9 @@ class RequestsCommon( BaseController, Us for s in request.samples: s.deleted = False trans.sa_session.add( s ) + comment = "Request marked undeleted by %s." % trans.user.email + event = trans.model.RequestEvent( request, request.state, comment ) + trans.sa_session.add( event ) trans.sa_session.flush() num_undeleted += 1 message += '%i requests have been undeleted.' % num_undeleted @@ -651,7 +669,7 @@ class RequestsCommon( BaseController, Us # If the current request state is complete and one of its samples moved from # the final sample state, then move the request state to In-progress if request.is_complete: - message = "At least 1 sample state moved from the final sample state, so now the request is in the '%s' state" % request.states.SUBMITTED + message = "At least 1 sample state moved from the final sample state, so now the request's state is (%s)" % request.states.SUBMITTED event = trans.model.RequestEvent( request, request.states.SUBMITTED, message ) trans.sa_session.add( event ) trans.sa_session.flush() @@ -668,13 +686,13 @@ class RequestsCommon( BaseController, Us request_type_state = request.type.final_sample_state if common_state.id == request_type_state.id: # since all the samples are in the final state, change the request state to 'Complete' - comments = "All samples of this request are in the last sample state (%s). " % request_type_state.name + comment = "All samples of this request are in the final sample state (%s). " % request_type_state.name state = request.states.COMPLETE final_state = True else: - comments = "All samples are in %s state. " % common_state.name + comment = "All samples of this request are in the (%s) sample state. " % common_state.name state = request.states.SUBMITTED - event = trans.model.RequestEvent( request, state, comments ) + event = trans.model.RequestEvent( request, state, comment ) trans.sa_session.add( event ) trans.sa_session.flush() # See if an email notification is configured to be sent when the samples @@ -879,7 +897,10 @@ class RequestsCommon( BaseController, Us message=message ) ) @web.expose @web.require_login( "view data transfer page" ) - def view_dataset_transfer( self, trans, cntrller, **kwd ): + def view_selected_datasets( self, trans, cntrller, **kwd ): + # The link on the number of selected datasets will only appear if there is at least 1 selected dataset. + # If there are 0 selected datasets, there is no link, so this method will only be reached from the requests + # controller if there are selected datasets. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -890,9 +911,9 @@ class RequestsCommon( BaseController, Us except: return invalid_id_redirect( trans, cntrller, sample_id ) # See if a library and folder have been set for this sample. - if not sample.library or not sample.folder: + if is_admin and not sample.library or not sample.folder: status = 'error' - message = "Set a data library and folder for sequencing request (%s) to transfer datasets." % sample.name + message = "Select a target data library and folder for the sample before selecting the datasets." return trans.response.send_redirect( web.url_for( controller='requests_common', action='edit_samples', cntrller=cntrller, @@ -900,11 +921,6 @@ class RequestsCommon( BaseController, Us editing_samples=True, status=status, message=message ) ) - if is_admin: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_datasets', - sample_id=sample_id ) ) - folder_path = util.restore_text( params.get( 'folder_path', '' ) ) if not folder_path: if len( sample.datasets ): @@ -917,11 +933,10 @@ class RequestsCommon( BaseController, Us or not sample.request.type.datatx_info['username'] \ or not sample.request.type.datatx_info['password']: status = 'error' - message = 'The sequencer login information is incomplete. Click on sequencer information to add login details.' - return trans.fill_template( '/requests/common/dataset_transfer.mako', + message = 'The sequencer login information is incomplete. Click sequencer information to add login details.' + return trans.fill_template( '/requests/common/view_selected_datasets.mako', cntrller=cntrller, - sample=sample, - dataset_files=sample.datasets, + sample=sample, message=message, status=status, files=[], @@ -1063,9 +1078,8 @@ class RequestsCommon( BaseController, Us # See if all the samples' barcodes are in the same state, and if so send email if configured to. common_state = request.samples_have_common_state if common_state and common_state.id == request.type.states[1].id: - event = trans.model.RequestEvent( request, - request.states.SUBMITTED, - "All samples are in %s state." % common_state.name ) + comment = "All samples of this request are in the (%s) sample state. " % common_state.name + event = trans.model.RequestEvent( request, request.states.SUBMITTED, comment ) trans.sa_session.add( event ) trans.sa_session.flush() request.send_email_notification( trans, request.type.states[1] ) --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1595,7 +1595,7 @@ class Request( object ): states = Bunch( NEW = 'New', SUBMITTED = 'In Progress', REJECTED = 'Rejected', - COMPLETE = 'Complete' ) + COMPLETE = 'Complete' ) api_collection_visible_keys = ( 'id', 'name', 'state' ) def __init__( self, name=None, desc=None, request_type=None, user=None, form_values=None, notification=None ): self.name = name @@ -1813,17 +1813,21 @@ class Sample( object ): if dataset.status == SampleDataset.transfer_status.COMPLETE: transferred_datasets.append( dataset ) return transferred_datasets - def dataset_size( self, filepath ): - def print_ticks(d): + def get_untransferred_dataset_size( self, filepath ): + # TODO: RC: If rsh keys are not set, this method will return something like the following: + # greg(a)scofield.bx.psu.edu's password: 46M /afs/bx.psu.edu/home/greg/chr22/chr21.fa + # This method should return the number of bytes in the file. I believe du + # displays the file system block usage which may not be the number of bytes in the file. + # Would ls -l be better? + def print_ticks( d ): pass datatx_info = self.request.type.datatx_info - cmd = 'ssh %s@%s "du -sh \'%s\'"' % ( datatx_info['username'], - datatx_info['host'], - filepath) - output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n', - pexpect.TIMEOUT:print_ticks}, - timeout=10) - return output.replace(filepath, '').strip() + cmd = 'ssh %s@%s "du -sh \'%s\'"' % ( datatx_info['username'], datatx_info['host'], filepath ) + output = pexpect.run( cmd, + events={ '.ssword:*': datatx_info['password']+'\r\n', + pexpect.TIMEOUT:print_ticks}, + timeout=10 ) + return output.replace( filepath, '' ).strip() def get_api_value( self, view='collection' ): rval = {} try: @@ -1856,8 +1860,7 @@ class SampleDataset( object ): ADD_TO_LIBRARY = 'Adding to data library', COMPLETE = 'Complete', ERROR = 'Error' ) - def __init__(self, sample=None, name=None, file_path=None, - status=None, error_msg=None, size=None): + def __init__( self, sample=None, name=None, file_path=None, status=None, error_msg=None, size=None): self.sample = sample self.name = name self.file_path = file_path @@ -1866,9 +1869,9 @@ class SampleDataset( object ): self.size = size class UserAddress( object ): - def __init__(self, user=None, desc=None, name=None, institution=None, - address=None, city=None, state=None, postal_code=None, - country=None, phone=None): + def __init__( self, user=None, desc=None, name=None, institution=None, + address=None, city=None, state=None, postal_code=None, + country=None, phone=None ): self.user = user self.desc = desc self.name = name --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -6,19 +6,14 @@ <h3>Rename datasets for Sample "${sample.name}"</h3><ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a> - </li> + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Browse datasets</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller='requests_admin', id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li></ul> %if message: ${render_msg( message, status )} %endif -${render_msg( 'A dataset can be renamed only if it is in <b>Not Started</b> state.', 'warning' )} <div class="toolForm"><form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" ><table class="grid"> --- a/templates/requests/common/find_samples.mako +++ b/templates/requests/common/find_samples.mako @@ -71,7 +71,7 @@ %else: State: ${sample.state.name}<br/> %endif - Datasets: <a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}/${len( sample.datasets )}</a><br/> + Datasets: <a href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}/${len( sample.datasets )}</a><br/> %if is_admin: <i>User: ${sample.request.user.email}</i> %endif --- /dev/null +++ b/templates/requests/common/view_selected_datasets.mako @@ -0,0 +1,37 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/requests/common/common.mako" import="render_sample_datasets" /> + +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = sample.request.is_complete + is_submitted = sample.request.is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_transfer_datasets = is_admin and sample.untransferred_dataset_files +%> + +<br/><br/> + +<ul class="manage-table-actions"> + %if can_transfer_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %endif + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh page</a></li> + <li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li> + <div popupmenu="sample-${sample.id}-popup"> + %if can_select_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( sample.request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select more datasets</a></li> + %endif + <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">View target Data Library</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +%if sample and sample.datasets: + <% title = 'Datasets currently selected for "sample.name"' %> + ${render_sample_datasets( cntrller, sample, sample.datasets, title )} +%endif --- a/templates/requests/common/dataset_transfer.mako +++ /dev/null @@ -1,46 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<br/><br/> - -<ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Refresh</a></li> - <li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">Target Data Library</a></li> - <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Sample "${sample.name}"</div> - <div class="toolFormBody"> - %if dataset_files: - <div class="form-row"> - <table class="grid"> - <thead> - <tr> - <th>Name</th> - <th>Size</th> - <th>Status</th> - </tr> - <thead> - <tbody> - %for dataset_file in dataset_files: - <tr> - <td>${dataset_file.name}</td> - <td>${dataset_file.size}</td> - <td>${dataset_file.status}</td> - </tr> - %endfor - </tbody> - </table> - </div> - %else: - <div class="form-row"> - There are no datasets associated with this sample. - </div> - %endif - </div> -</div> --- /dev/null +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -0,0 +1,133 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/requests/common/common.mako" import="render_sample_datasets" /> + +${h.js( "ui.core", "jquery.cookie", "jquery.dynatree" )} +<link href='/static/june_2007_style/blue/dynatree_skin/ui.dynatree.css' rel='stylesheet' type='text/css'> +##${h.js( "jquery.dynatree" )} + +<script type="text/javascript"> + $(function(){ + $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) { + _log("debug", "ajaxComplete: %o", this); // dom element listening + }); + // --- Initialize sample trees + $("#tree").dynatree({ + title: "${request.type.datatx_info['data_dir']}", + rootVisible: true, + minExpandLevel: 0, // 1: root node is not collapsible + persist: false, + checkbox: true, + selectMode: 3, + onPostInit: function(isReloading, isError) { +// alert("reloading: "+isReloading+", error:"+isError); + logMsg("onPostInit(%o, %o) - %o", isReloading, isError, this); + // Re-fire onActivate, so the text is updated + this.reactivate(); + }, + fx: { height: "toggle", duration: 200 }, + // initAjax is hard to fake, so we pass the children as object array: + initAjax: {url: "${h.url_for( controller='requests_admin', action='open_folder' )}", + dataType: "json", + data: { id: "${request.id}", key: "${request.type.datatx_info['data_dir']}" }, + }, + onLazyRead: function(dtnode){ + dtnode.appendAjax({ + url: "${h.url_for( controller='requests_admin', action='open_folder' )}", + dataType: "json", + data: { id: "${request.id}", key: dtnode.data.key }, + }); + }, + onSelect: function(select, dtnode) { + // Display list of selected nodes + var selNodes = dtnode.tree.getSelectedNodes(); + // convert to title/key array + var selKeys = $.map(selNodes, function(node){ + return node.data.key; + }); + document.select_datasets_to_transfer.selected_datasets_to_transfer.value = selKeys.join(",") + }, + onActivate: function(dtnode) { + var cell = $("#file_details"); + var selected_value = dtnode.data.key + if(selected_value.charAt(selected_value.length-1) != '/') { + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='requests_admin', action='get_file_details' )}", + dataType: "json", + data: { id: "${request.id}", folder_path: dtnode.data.key }, + success : function ( data ) { + cell.html( '<label>'+data+'</label>' ) + } + }); + } else { + cell.html( '' ) + } + }, + }); + }); + +</script> + +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + can_transfer_datasets = is_admin and sample.untransferred_dataset_files +%> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='view_request_type', id=trans.security.encode_id( request.type.id ) )}">Sequencer configuration</a></li> + %if can_transfer_datasets: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %endif + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a></li> +</ul> + +%if not sample: + <font color="red"><b><i>Select a sample before selecting datasets to transfer</i></b></font> + <br/><br/> +%endif + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Select datasets to transfer from data directory configured for the sequencer</div> + <form name="select_datasets_to_transfer" id="select_datasets_to_transfer" action="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ))}" method="post" > + <div class="form-row"> + <label>Sample:</label> + ${sample_id_select_field.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Select the sample that was sequenced to produce the datasets you want to transfer. + </div> + </div> + <div class="form-row" > + <label>Select datasets from source data location defined in the sequencer configuration:</label> + <div id="tree" > + Loading... + </div> + <input id="selected_datasets_to_transfer" name="selected_datasets_to_transfer" type="hidden" size=40"/> + <div class="toolParamHelp" style="clear: both;"> + <ul> + <li>Click the <b>Sequencer configuration</b> button and change the <b>Data directory</b> setting to redefine the source data location.</li> + <li>Select a folder to select all of the individual files within that folder.</li> + <li>Click the <b>Select datasets</b> button when desired dataset check boxes are checked.</li> + </ul> + </div> + </div> + <div class="form-row"> + <div id="file_details" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> + </div> + <div class="form-row"> + <input type="submit" name="select_datasets_to_transfer_button" value="Select datasets"/> + </div> + </form> +</div> + +%if sample and sample.datasets: + <% title = 'Datasets currently selected for "sample.name"' %> + <p/> + ${render_sample_datasets( 'requests_admin', sample, sample.datasets, title )} +%endif --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -23,10 +23,6 @@ class AdminRequestsGrid( RequestsGrid ): operations.append( grids.GridOperation( "Reject", allow_multiple=False, condition=( lambda item: not item.deleted and item.is_submitted ) ) ) operations.append( grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted ) ) ) operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ) ) - operations.append( grids.GridOperation( "Purge", - allow_multiple=False, - confirm="This will permanently delete this sequencing request. Click OK to proceed.", - condition=( lambda item: item.deleted ) ) ) global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common', action='create_request', @@ -227,7 +223,8 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) # Create an event with state 'Rejected' for this request - event = trans.model.RequestEvent( request, request.states.REJECTED, comment ) + event_comment = "Request marked rejected by %s. Reason: %s " % ( trans.user.email, comment ) + event = trans.model.RequestEvent( request, request.states.REJECTED, event_comment ) trans.sa_session.add( event ) trans.sa_session.flush() message='Request (%s) has been rejected.' % request.name @@ -240,6 +237,11 @@ class RequestsAdmin( BaseController, Use @web.expose @web.require_admin def manage_datasets( self, trans, **kwd ): + def handle_error( **kwd ): + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + **kwd ) ) params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -247,23 +249,28 @@ class RequestsAdmin( BaseController, Use operation = kwd[ 'operation' ].lower() sample_dataset_id = params.get( 'id', None ) if not sample_dataset_id: - return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) + message = 'Select at least 1 dataset to %s.' % operation + kwd[ 'message' ] = message + del kwd[ 'operation' ] + handle_error( **kwd ) id_list = util.listify( sample_dataset_id ) selected_sample_datasets = [] for sample_dataset_id in id_list: - try: - selected_sample_datasets.append( trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) ) + try: + sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id ) + selected_sample_datasets.append( sample_dataset ) if operation == "view": - return trans.fill_template( '/admin/requests/dataset.mako', + return trans.fill_template( '/admin/requests/view_sample_dataset.mako', + cntrller='requests_admin', sample_dataset=selected_sample_datasets[0] ) elif operation == "delete": not_deleted = [] for sample_dataset in selected_sample_datasets: # Make sure the dataset has been transferred before deleting it. if sample_dataset in sample_dataset.sample.untransferred_dataset_files: - # save the sample to which these datasets belong to + # Save the sample dataset sample = sample_dataset.sample trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() @@ -299,7 +306,9 @@ class RequestsAdmin( BaseController, Use sample=selected_sample_datasets[0].sample, id_list=id_list ) elif operation == "transfer": - self.initiate_data_transfer( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) + self.initiate_data_transfer( trans, + trans.security.encode_id( selected_sample_datasets[0].sample.id ), + sample_datasets=selected_sample_datasets ) # Render the grid view sample_id = params.get( 'sample_id', None ) try: @@ -308,13 +317,10 @@ class RequestsAdmin( BaseController, Use return invalid_id_redirect( trans, 'requests_admin', sample_id ) request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) - self.datatx_grid.global_actions = [ grids.GridAction( "Refresh page", + self.datatx_grid.title = 'Manage "%s" datasets' % sample.name + self.datatx_grid.global_actions = [ grids.GridAction( "Select more datasets", dict( controller='requests_admin', - action='manage_datasets', - sample_id=sample_id ) ), - grids.GridAction( "Select datasets", - dict( controller='requests_admin', - action='get_data', + action='select_datasets_to_transfer', request_id=request_id, sample_id=sample_id ) ), grids.GridAction( "Browse target data library", @@ -326,7 +332,11 @@ class RequestsAdmin( BaseController, Use dict( controller='requests_common', action='view_request', cntrller='requests_admin', - id=request_id ) ) ] + id=request_id ) ), + grids.GridAction( "Refresh page", + dict( controller='requests_admin', + action='manage_datasets', + sample_id=sample_id ) ) ] return self.datatx_grid( trans, **kwd ) @web.expose @web.require_admin @@ -372,70 +382,68 @@ class RequestsAdmin( BaseController, Use sample_id=sample_id ) ) @web.expose @web.require_admin - def get_data( self, trans, **kwd ): + def select_datasets_to_transfer( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) request_id = kwd.get( 'request_id', None ) files = [] + def handle_error( **kwd ): + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='select_datasets_to_transfer', + **kwd ) ) try: request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', request_id ) - selected_files = util.restore_text( params.get( 'selected_files', '' ) ) - if len( selected_files ): - selected_files = selected_files.split(',') + selected_datasets_to_transfer = util.restore_text( params.get( 'selected_datasets_to_transfer', '' ) ) + if selected_datasets_to_transfer: + selected_datasets_to_transfer = selected_datasets_to_transfer.split(',') else: - selected_files = [] - selected_sample_id = kwd.get( 'sample_id', 'none' ) - sample_id_select_field = self.__build_sample_id_select_field( trans, request, selected_sample_id ) + selected_datasets_to_transfer = [] + sample_id = kwd.get( 'sample_id', 'none' ) + sample_id_select_field = self.__build_sample_id_select_field( trans, request, sample_id ) + if sample_id != 'none': + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) + else: + sample = None # The __get_files() method redirects here with a status of 'error' and a message if there # was a problem retrieving the files. - if params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): - # get the sample these datasets are associated with - try: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( selected_sample_id ) ) - except: - message = 'Select a sample before selecting its associated datasets.' - return trans.fill_template( '/admin/requests/get_data.mako', - cntrller='requests_admin', - request=request, - sample_id_select_field=sample_id_select_field, - status='error', - message=message ) + if params.get( 'select_datasets_to_transfer_button', False ): + # Get the sample that was sequenced to produce these datasets. + if sample_id == 'none': + message = 'Select the sample that was sequenced to produce the datasets you want to transfer.' + kwd[ 'message' ] = message + del kwd[ 'select_datasets_to_transfer_button' ] + handle_error( **kwd ) if sample in sample.request.samples_without_library_destinations: # Display an error if a sample has been selected that # has not yet been associated with a destination library. + message = 'Select a target data library and folder for the sample before selecting the datasets.' status = 'error' - message = 'Select a sample with associated data library and folder before selecting the datasets.' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=request_id, - sample_id=sample.id, + return trans.response.send_redirect( web.url_for( controller='requests_common', + action='edit_samples', + cntrller='requests_admin', + id=trans.security.encode_id( request.id ), + editing_samples=True, status=status, message=message ) ) # Save the sample datasets - sample_dataset_file_names = self.__save_sample_datasets( trans, sample, selected_files ) + sample_dataset_file_names = self.__save_sample_datasets( trans, sample, selected_datasets_to_transfer ) if sample_dataset_file_names: message = 'Datasets (%s) have been selected for sample (%s)' % \ ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name ) - if params.get( 'select_show_datasets_button', False ): - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='manage_datasets', - request_id=request_id, - sample_id=selected_sample_id, - message=message, - status=status ) ) - else: # 'select_more_button' was clicked - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', - request_id=request_id, - sample_id=sample.id, - message=message, - status=status ) ) - return trans.fill_template( '/admin/requests/get_data.mako', + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='manage_datasets', + request_id=request_id, + sample_id=sample_id, + message=message, + status=status ) ) + return trans.fill_template( '/admin/requests/select_datasets_to_transfer.mako', cntrller='requests_admin', request=request, + sample=sample, sample_id_select_field=sample_id_select_field, status=status, message=message ) @@ -499,7 +507,7 @@ class RequestsAdmin( BaseController, Use if ok: return output.splitlines() return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='get_data', + action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), status=status, message=message ) ) @@ -508,24 +516,36 @@ class RequestsAdmin( BaseController, Use if a_path and not a_path.endswith( os.sep ): a_path += os.sep return a_path - def __save_sample_datasets( self, trans, sample, selected_files ): + def __save_sample_datasets( self, trans, sample, selected_datasets_to_transfer ): sample_dataset_file_names = [] - if selected_files: - for filepath in selected_files: + if selected_datasets_to_transfer: + for filepath in selected_datasets_to_transfer: # FIXME: handle folder selection # ignore folders for now if filepath[-1] != os.sep: name = self.__dataset_name( sample, filepath.split( '/' )[-1] ) + status = trans.app.model.SampleDataset.transfer_status.NOT_STARTED + size = sample.get_untransferred_dataset_size( filepath ) sample_dataset = trans.model.SampleDataset( sample=sample, file_path=filepath, - status=trans.app.model.SampleDataset.transfer_status.NOT_STARTED, + status=status, name=name, error_msg='', - size=sample.dataset_size( filepath ) ) + size=size ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() sample_dataset_file_names.append( str( sample_dataset.name ) ) return sample_dataset_file_names + def dataset_file_size( self, sample, filepath ): + def print_ticks(d): + pass + datatx_info = sample.request.type.datatx_info + cmd = 'ssh %s@%s "du -sh \'%s\'"' % ( datatx_info['username'], datatx_info['host'], filepath ) + output = pexpect.run( cmd, + events={ '.ssword:*': datatx_info['password']+'\r\n', + pexpect.TIMEOUT:print_ticks}, + timeout=10 ) + return output.replace( filepath, '' ).strip() def __dataset_name( self, sample, filepath ): name = filepath.split( '/' )[-1] options = sample.request.type.rename_dataset_options @@ -610,38 +630,54 @@ class RequestsAdmin( BaseController, Use if not datatx_info[ 'host' ] \ or not datatx_info[ 'username' ] \ or not datatx_info[ 'password' ]: - err_msg = "Error in sequencer login information." - # check if web API is enabled and API key exists - if not trans.user.api_keys or not trans.app.config.enable_api: - err_msg = "Could not start data transfer as Galaxy Web API is not enabled. Enable Galaxy Web API in the Galaxy config file and create an API key." + err_msg += "Error in sequencer login information. " + # Make sure web API is enabled and API key exists + if not trans.app.config.enable_api: + err_msg += "The 'enable_api = True' setting is not correctly set in the Galaxy config file. " + if not trans.user.api_keys: + err_msg += "Set your API Key in your User Preferences to transfer datasets." # check if library_import_dir is set if not trans.app.config.library_import_dir: - err_msg = "'library_import_dir' config variable is not set in the Galaxy config file." + err_msg = "'The library_import_dir' setting is not set in the Galaxy config file." # check the RabbitMQ server settings in the config file for k, v in trans.app.config.amqp.items(): if not v: - err_msg = 'Set RabbitMQ server settings in the "galaxy_amqp" section of the Galaxy config file. %s is not set.' % k + err_msg += 'Set RabbitMQ server settings in the "galaxy_amqp" section of the Galaxy config file. %s is not set.' % k break return err_msg - def initiate_data_transfer( self, trans, sample, selected_sample_datasets ): + @web.expose + @web.require_admin + def initiate_data_transfer( self, trans, sample_id, sample_datasets=[], sample_dataset_id='' ): ''' This method initiates the transfer of the datasets from the sequencer. It happens in the following steps: - - The current admin user needs to have ADD_LIBRARY_ITEM permission for the + - The current admin user needs to have LIBRARY_ADD permission for the target library and folder - Create an XML message encapsulating all the data transfer info and send it to the message queue (RabbitMQ broker) ''' - # check data transfer settings + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', sample_id ) + # Check data transfer settings err_msg = self.__validate_data_transfer_settings( trans, sample ) if not err_msg: - # check if the current user has add_library_item permission to the sample - # target library & folder + # Make sure the current user has LIBRARY_ADD + # permission on the target library and folder. self.__check_library_add_permission( trans, sample.library, sample.folder ) - # create the message + if sample_dataset_id and not sample_datasets: + # Either a list of SampleDataset objects or a comma-separated string of + # encoded SampleDataset ids can be received. If the latter, parse the + # sample_dataset_id to build the list of sample_datasets. + id_list = util.listify( sample_dataset_id ) + for sample_dataset_id in id_list: + sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) + sample_datasets.append( sample_dataset ) + # Create the message message = self.__create_data_transfer_message( trans, sample, - selected_sample_datasets ) + sample_datasets ) # Send the message try: conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ], @@ -660,9 +696,9 @@ class RequestsAdmin( BaseController, Use chan.close() conn.close() except Exception, e: - err_msg = "Error in sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) + err_msg = "Error sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) if not err_msg: - err_msg = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to monitor the transfer status." % len( selected_sample_datasets ) + err_msg = "%i datasets have been queued for transfer from the sequencer. Click the Refresh button above to monitor the transfer status." % len( sample_datasets ) status = "done" else: status = 'error' --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -19,12 +19,13 @@ is_admin = cntrller == 'requests_admin' and trans.user_is_admin() is_complete = request.is_complete + is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted can_add_samples = is_unsubmitted can_delete_samples = request.samples and not is_complete can_edit_samples = request.samples and ( is_admin or not is_complete ) can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_reject_or_transfer = is_admin and request.is_submitted + can_reject = is_admin and is_submitted can_submit = request.samples and is_unsubmitted %> @@ -47,9 +48,8 @@ <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> - %if can_reject_or_transfer: + %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div></ul> --- a/templates/requests/common/events.mako +++ b/templates/requests/common/events.mako @@ -20,7 +20,7 @@ %endif %if is_admin and request.is_submitted: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div></ul> --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -17,7 +17,7 @@ <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if is_admin and request.is_submitted: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div></ul> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -19,11 +19,13 @@ is_admin = cntrller == 'requests_admin' and trans.user_is_admin() is_complete = request.is_complete + is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_add_samples = is_unsubmitted can_delete_samples = request.samples and not is_complete can_edit_samples = request.samples and ( is_admin or not is_complete ) + can_reject = is_admin and is_submitted can_submit = request.samples and is_unsubmitted %> @@ -35,13 +37,15 @@ %endif <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request actions</a></li><div popupmenu="request-${request.id}-popup"> + %if request.deleted: + <a class="action-button" href="${h.url_for( controller='requests_common', action='undelete_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Undelete</a> + %endif %if can_edit_request: <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit</a> %endif <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> - %if is_admin and request.is_submitted: + %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject</a> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div></ul> --- a/templates/admin/requests/dataset.mako +++ /dev/null @@ -1,69 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<br/><br/> - -<% sample = sample_dataset.sample %> - -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller='requests_admin', sample_id=trans.security.encode_id( sample.id ) )}"> - <span>Browse datasets</span></a> - </li> -</ul> - -<div class="toolForm"> - <div class="toolFormTitle">Dataset Information</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.name} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>File on the Sequencer:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.file_path} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Size:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.size} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Created on:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.create_time} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Updated on:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.update_time} - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Transfer status:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - ${sample_dataset.status} - %if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.ERROR: - <br/> - ${sample_dataset.error_msg} - %endif - </div> - <div style="clear: both"></div> - </div> - </div> -</div> --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -168,15 +168,25 @@ %endif <td valign="top">${current_sample['library_select_field'].get_html()}</td><td valign="top">${current_sample['folder_select_field'].get_html()}</td> - %if display_datasets: - <% - if sample: - label = str( len( sample.datasets ) ) - else: - label = 'add' - %> - <td valign="top"><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> - <td valign="top"><a href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${label}</a></td> + %if display_datasets: + <td valign="top"> + ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected + %if is_admin: + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + %elif sample.datasets: + ## Only display a link if there is at least 1 selected dataset for the sample + <a href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td> + %else: + ${len( sample.datasets )} + %endif + </td> + <td valign="top"> + %if is_admin and sample.untransferred_dataset_files: + <a href="${h.url_for( controller='requests_common', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %else: + ${len( sample.transferred_dataset_files )} + %endif + </td> %endif %if sample and ( is_admin or is_unsubmitted ) and not is_complete: ## Delete button @@ -196,6 +206,7 @@ can_add_samples = request.is_unsubmitted can_delete_samples = request.samples and not is_complete can_edit_samples = request.samples and ( is_admin or not is_complete ) + can_select_datasets = is_admin and current_samples and ( is_submitted or is_complete ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_rejected or is_submitted ) @@ -280,9 +291,31 @@ %else: <td></td> %endif - %if is_submitted or is_complete: - <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a></td> - <td><a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_dataset_transfer', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a></td> + %if is_submitted or is_complete: + <td> + ## An admin can select the datasets to transfer, while a non-admin can only view what has been selected + %if is_admin: + %if not sample.datasets: + ## If there are no selected datasets, display a page alowing the admin to select some. + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, request_id=trans.security.encode_id( request.id ), sample_id= trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + %else: + ## If there are selected datasets, display them + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + %endif + %elif sample.datasets: + ## Only display a link if there is at least 1 selected dataset for the sample + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_common', action='view_selected_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a> + %else: + ${len( sample.datasets )} + %endif + </td> + <td> + %if is_admin and sample.untransferred_dataset_files: + <a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.transferred_dataset_files )}</a> + %else: + ${len( sample.transferred_dataset_files )} + %endif + </td> %endif </tr> %else: @@ -395,3 +428,52 @@ </table></div></%def> + +<%def name="render_sample_datasets( cntrller, sample, sample_datasets, title )"> + %if sample_datasets: + <% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = sample.request.is_complete + is_submitted = sample.request.is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_transfer_datasets = is_admin and sample.untransferred_dataset_files + %> + <h3>${title}</h3> + <table class="grid"> + <thead> + <tr> + <th>Name</th> + <th>Size</th> + <th>Status</th> + </tr> + <thead> + <tbody> + %for dataset in sample_datasets: + <tr> + <td> + %if is_admin: + <% encoded_id = trans.security.encode_id(dataset.id) %> + <span class="expandLink dataset-${dataset}-click"><span class="rowIcon"></span> + <div style="float: left; margin-left: 2px;" class="menubutton split popup" id="dataset-${dataset.id}-popup"> + <a class="dataset-${encoded_id}-click" href="${h.url_for( controller='requests_admin', action='manage_datasets', operation='view', id=trans.security.encode_id( dataset.id ) )}">${dataset.name}</a> + </div> + </span> + <div popupmenu="dataset-${dataset.id}-popup"> + %if can_transfer_datasets and dataset in sample.untransferred_dataset_files: + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='initiate_data_transfer', sample_id=trans.security.encode_id( sample.id ), sample_dataset_id=trans.security.encode_id( dataset.id ) )}">Transfer</a></li> + %endif + </div> + %else: + ${dataset.name} + %endif + </td> + <td>${dataset.size}</td> + <td>${dataset.status}</td> + </tr> + %endfor + </tbody> + </table> + %else: + No datasets for this sample. + %endif +</%def>

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galaxy-dist commit 0e3fe3e7b21b: Allow display framework to work with workflows that contain tools that have been updated. Previously, this would cause a server error when trying to view a workflow or a page with an embedded workflow that contained an updated tool.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Daniel Blankenberg <dan(a)bx.psu.edu> # Date 1289341236 18000 # Node ID 0e3fe3e7b21bfd78461869817c6b43db827d77f0 # Parent 479b377ef455f2d676fb84363b0b6d437d6af5f6 Allow display framework to work with workflows that contain tools that have been updated. Previously, this would cause a server error when trying to view a workflow or a page with an embedded workflow that contained an updated tool. --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -1,4 +1,5 @@ <%inherit file="/display_base.mako"/> +<%namespace file="/display_common.mako" import="render_message" /><%! from galaxy.tools.parameters import DataToolParameter, RuntimeValue @@ -54,6 +55,9 @@ ${param.value_to_display_text( value, app )} %endif </div> + %if hasattr( step, 'upgrade_messages' ) and step.upgrade_messages and param.name in step.upgrade_messages: + ${render_message( step.upgrade_messages[param.name], "info" )} + %endif </div></%def> --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -207,9 +207,12 @@ class UsesStoredWorkflow( SharableItemSe def get_stored_workflow_steps( self, trans, stored_workflow ): """ Restores states for a stored workflow's steps. """ for step in stored_workflow.latest_workflow.steps: + step.upgrade_messages = {} if step.type == 'tool' or step.type is None: # Restore the tool state for the step module = module_factory.from_workflow_step( trans, step ) + #Check if tool was upgraded + step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections )

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galaxy-dist commit 7c60d74ba2df: Aggressively sanitize metadata parameter values when provided on the upload form and which are subsequently used for filename substitution.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Daniel Blankenberg <dan(a)bx.psu.edu> # Date 1289329026 18000 # Node ID 7c60d74ba2df4488df90d08ed0ae9c7cc3871222 # Parent 9ee40043b826b3bc1e29f84996f9fe14dd119a45 Aggressively sanitize metadata parameter values when provided on the upload form and which are subsequently used for filename substitution. --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -155,6 +155,26 @@ def sanitize_param(value): print value raise Exception, 'Unknown parameter type (%s)' % ( type( value ) ) +valid_filename_chars = set( string.ascii_letters + string.digits + '_.' ) +invalid_filenames = [ '', '.', '..' ] +def sanitize_for_filename( text, default=None ): + """ + Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name. + Method is overly aggressive to minimize possible complications, but a maximum length is not considered. + """ + out = [] + for c in text: + if c in valid_filename_chars: + out.append( c ) + else: + out.append( '_' ) + out = ''.join( out ) + if out in invalid_filenames: + if default is None: + return sanitize_for_filename( str( unique_id() ) ) + return default + return out + class Params: """ Stores and 'sanitizes' parameters. Alphanumeric characters and the --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -12,7 +12,7 @@ import StringIO, os, urllib from galaxy.datatypes import sniff from galaxy.util.bunch import Bunch from galaxy.util.odict import odict -from galaxy.util import json, relpath +from galaxy.util import json, relpath, sanitize_for_filename class Group( object ): def __init__( self ): @@ -335,10 +335,14 @@ class UploadDataset( Group ): dataset.composite_files = {} #load metadata files_metadata = context.get( self.metadata_ref, {} ) + metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) for meta_name, meta_spec in d_type.metadata_spec.iteritems(): if meta_spec.set_in_upload: if meta_name in files_metadata: - dataset.metadata[ meta_name ] = files_metadata[ meta_name ] + meta_value = files_metadata[ meta_name ] + if meta_name in metadata_name_substition_default_dict: + meta_value = sanitize_for_filename( meta_value, default = metadata_name_substition_default_dict[ meta_name ] ) + dataset.metadata[ meta_name ] = meta_value dataset.precreated_name = dataset.name = self.get_composite_dataset_name( context ) if dataset.datatype.composite_type == 'auto_primary_file': #replace sniff here with just creating an empty file

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