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lims: requests/request_admin controller refactor
A new controller called requests_common now handles all common tasks like create/edit/delete requests & samples. The requests controller has only the grid definition and requests_admin controller has the request_type code and the sequencer data transfer code. Also fixed a form importer bug in forms.py
This commit is contained in:
Ramkrishna Chakrabarty
@@ -474,8 +474,7 @@ class Forms( BaseController ):
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return trans.response.send_redirect( web.url_for( controller='forms',
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action='new',
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status='error',
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message='Error in importing <b>%s</b> file' % csv_file,
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**kwd))
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message='Error in importing <b>%s</b> file' % csv_file.file))
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self.__imported_from_file = True
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return fields, list(layouts)
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def __validate_form(self, **kwd):
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@@ -84,7 +84,7 @@ class RequestsGrid( grids.Grid ):
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NameColumn( "Name",
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key="name",
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model_class=model.Request,
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link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ),
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link=( lambda item: iff( item.deleted, None, dict( operation="show", id=item.id ) ) ),
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attach_popup=True,
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filterable="advanced" ),
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DescriptionColumn( "Description",
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@@ -92,7 +92,7 @@ class RequestsGrid( grids.Grid ):
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model_class=model.Request,
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filterable="advanced" ),
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SamplesColumn( "Sample(s)",
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link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ),
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link=( lambda item: iff( item.deleted, None, dict( operation="show", id=item.id ) ) ), ),
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TypeColumn( "Type" ),
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grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
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grids.DeletedColumn( "Deleted",
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@@ -120,7 +120,8 @@ class RequestsGrid( grids.Grid ):
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]
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global_actions = [
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grids.GridAction( "Create new request", dict( controller='requests',
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grids.GridAction( "Create new request", dict( controller='requests_common',
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cntrller='requests',
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action='new',
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select_request_type='True' ) )
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]
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@@ -149,18 +150,36 @@ class Requests( BaseController ):
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action='list',
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status='error',
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message="Invalid request ID") )
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if operation == "show_request":
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return self.__show_request( trans, **kwd )
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if operation == "show":
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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cntrller='requests',
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action='show',
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**kwd ) )
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elif operation == "submit":
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return self.__submit_request( trans, **kwd )
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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cntrller='requests',
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action='submit',
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**kwd ) )
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elif operation == "delete":
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return self.__delete_request( trans, **kwd )
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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cntrller='requests',
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action='delete',
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**kwd ) )
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elif operation == "undelete":
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return self.__undelete_request( trans, **kwd )
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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cntrller='requests',
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action='undelete',
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**kwd ) )
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elif operation == "edit":
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return self.__edit_request( trans, **kwd )
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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cntrller='requests',
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action='edit',
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show=True, **kwd ) )
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elif operation == "events":
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return self.__request_events( trans, **kwd )
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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cntrller='requests',
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action='events',
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**kwd ) )
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# if there are one or more requests that has been rejected by the admin
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# recently, then show a message as a reminder to the user
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rlist = trans.sa_session.query( trans.app.model.Request ) \
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@@ -176,915 +195,4 @@ class Requests( BaseController ):
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% rejected
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# Render the list view
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return self.request_grid( trans, **kwd )
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def __request_events(self, trans, **kwd):
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try:
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request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
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except:
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message = "Invalid request ID"
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log.warn( message )
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return trans.response.send_redirect( web.url_for( controller='requests',
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action='list',
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status='error',
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message=message,
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**kwd) )
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events_list = []
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all_events = request.events
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for event in all_events:
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events_list.append((event.state, time_ago(event.update_time), event.comment))
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return trans.fill_template( '/requests/events.mako',
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events_list=events_list, request=request)
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def request_details(self, trans, id):
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'''
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Shows the request details
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'''
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request = trans.sa_session.query( trans.app.model.Request ).get( id )
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# list of widgets to be rendered on the request form
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request_details = []
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# main details
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request_details.append(dict(label='Description',
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value=request.desc,
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helptext=''))
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request_details.append(dict(label='Type',
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value=request.type.name,
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helptext=''))
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request_details.append(dict(label='State',
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value=request.state(),
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helptext=''))
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request_details.append(dict(label='Date created',
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value=request.create_time,
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helptext=''))
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# form fields
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for index, field in enumerate(request.type.request_form.fields):
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if field['required']:
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req = 'Required'
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else:
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req = 'Optional'
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if field['type'] == 'AddressField':
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if request.values.content[index]:
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request_details.append(dict(label=field['label'],
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value=trans.sa_session.query( trans.app.model.UserAddress ).get( int( request.values.content[index] ) ).get_html(),
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helptext=field['helptext']+' ('+req+')'))
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else:
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request_details.append(dict(label=field['label'],
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value=None,
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helptext=field['helptext']+' ('+req+')'))
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else:
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request_details.append(dict(label=field['label'],
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value=request.values.content[index],
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helptext=field['helptext']+' ('+req+')'))
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if request.notify:
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notify = 'Yes'
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else:
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notify = 'No'
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request_details.append(dict(label='Send email notification once the sequencing request is complete',
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value=notify,
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helptext=''))
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return request_details
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def __show_request(self, trans, **kwd):
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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add_sample = params.get('add_sample', False)
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try:
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request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
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except:
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return trans.response.send_redirect( web.url_for( controller='requests',
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action='list',
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status='error',
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message="Invalid request ID") )
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# get all data libraries accessible to this user
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libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
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current_samples = []
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for i, s in enumerate(request.samples):
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lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
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current_samples.append(dict(name=s.name,
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barcode=s.bar_code,
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library=s.library,
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folder=s.folder,
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dataset_files=s.dataset_files,
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field_values=s.values.content,
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lib_widget=lib_widget,
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folder_widget=folder_widget))
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if add_sample:
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lib_widget, folder_widget = self.__library_widgets(trans, request.user,
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len(current_samples)+1,
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libraries, None, **kwd)
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current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
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barcode='',
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library=None,
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folder=None,
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dataset_files=[],
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field_values=['' for field in request.type.sample_form.fields],
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lib_widget=lib_widget,
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folder_widget=folder_widget))
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return trans.fill_template( '/requests/show_request.mako',
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request=request,
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request_details=self.request_details(trans, request.id),
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current_samples=current_samples,
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sample_copy=self.__copy_sample(current_samples),
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details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False' ) ),
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message=message, status=status )
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def __library_widgets(self, trans, user, sample_index, libraries, sample=None, lib_id=None, folder_id=None, **kwd):
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'''
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This method creates the data library & folder selectbox for creating &
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editing samples. First we get a list of all the libraries accessible to
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the current user and display it in a selectbox. If the user has selected an
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existing library then display all the accessible sub folders of the selected
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data library.
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'''
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params = util.Params( kwd )
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# data library selectbox
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if not lib_id:
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lib_id = params.get( "sample_%i_library_id" % sample_index, 'none' )
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selected_lib = None
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if sample and lib_id == 'none':
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if sample.library:
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lib_id = str(sample.library.id)
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selected_lib = sample.library
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# create data library selectbox with refresh on change enabled
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lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
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lib_widget = SelectField( "sample_%i_library_id" % sample_index,
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refresh_on_change=True,
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refresh_on_change_values=lib_id_list )
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# fill up the options in the Library selectbox
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# first option 'none' is the value for "Select one" option
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if lib_id == 'none':
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lib_widget.add_option('Select one', 'none', selected=True)
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else:
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lib_widget.add_option('Select one', 'none')
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# all the libraries available to the selected user
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for lib, hidden_folder_ids in libraries.items():
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if str(lib.id) == str(lib_id):
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lib_widget.add_option(lib.name, lib.id, selected=True)
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selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
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else:
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lib_widget.add_option(lib.name, lib.id)
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lib_widget.refresh_on_change_values.append(lib.id)
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# create the folder selectbox
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folder_widget = SelectField( "sample_%i_folder_id" % sample_index )
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# when editing a request, either the user has already selected a subfolder or not
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if sample:
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if sample.folder:
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current_fid = sample.folder.id
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else:
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# when a folder not yet associated with the request then the
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# the current folder is set to the root_folder of the
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# parent data library if present.
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if sample.library:
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current_fid = sample.library.root_folder.id
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else:
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current_fid = params.get( "sample_%i_folder_id" % sample_index, 'none' )
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else:
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if folder_id:
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current_fid = folder_id
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else:
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current_fid = 'none'
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# first option
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if lib_id == 'none':
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folder_widget.add_option('Select one', 'none', selected=True)
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else:
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folder_widget.add_option('Select one', 'none')
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if selected_lib:
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# get all show-able folders for the selected library
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showable_folders = trans.app.security_agent.get_showable_folders( user, user.all_roles(),
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selected_lib,
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[ trans.app.security_agent.permitted_actions.LIBRARY_ADD ],
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selected_hidden_folder_ids )
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for f in showable_folders:
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if str(f.id) == str(current_fid):
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folder_widget.add_option(f.name, f.id, selected=True)
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else:
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folder_widget.add_option(f.name, f.id)
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return lib_widget, folder_widget
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def __update_samples(self, trans, request, **kwd):
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'''
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This method retrieves all the user entered sample information and
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returns an list of all the samples and their field values
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'''
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params = util.Params( kwd )
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details = params.get( 'details', 'hide' )
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edit_mode = params.get( 'edit_mode', 'False' )
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# get all data libraries accessible to this user
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libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
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current_samples = []
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for i, s in enumerate(request.samples):
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lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
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current_samples.append(dict(name=s.name,
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barcode=s.bar_code,
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library=s.library,
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folder=s.folder,
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field_values=s.values.content,
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lib_widget=lib_widget,
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folder_widget=folder_widget))
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if edit_mode == 'False':
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sample_index = len(request.samples)
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else:
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sample_index = 0
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while True:
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lib_id = None
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folder_id = None
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if params.get( 'sample_%i_name' % sample_index, '' ):
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# data library
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try:
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library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'sample_%i_library_id' % sample_index, None ) ) )
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lib_id = library.id
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except:
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library = None
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# folder
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try:
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folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'sample_%i_folder_id' % sample_index, None ) ) )
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folder_id = folder.id
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except:
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if library:
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folder = library.root_folder
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else:
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folder = None
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sample_info = dict( name=util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ),
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barcode=util.restore_text( params.get( 'sample_%i_barcode' % sample_index, '' ) ),
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library=library,
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folder=folder)
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sample_info['field_values'] = []
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for field_index in range(len(request.type.sample_form.fields)):
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sample_info['field_values'].append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) ))
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if edit_mode == 'False':
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sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans,
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request.user,
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sample_index,
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libraries,
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None, lib_id, folder_id, **kwd)
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current_samples.append(sample_info)
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else:
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sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans,
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request.user,
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sample_index,
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libraries,
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request.samples[sample_index],
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**kwd)
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current_samples[sample_index] = sample_info
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sample_index = sample_index + 1
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else:
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break
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return current_samples, details, edit_mode, libraries
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def __copy_sample(self, current_samples):
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copy_list = SelectField('copy_sample')
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copy_list.add_option('None', -1, selected=True)
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for i, s in enumerate(current_samples):
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copy_list.add_option(s['name'], i)
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return copy_list
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def __import_samples(self, trans, request, current_samples, details, libraries, **kwd):
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'''
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This method reads the samples csv file and imports all the samples
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The format of the csv file is:
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SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
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'''
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try:
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params = util.Params( kwd )
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edit_mode = params.get( 'edit_mode', 'False' )
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file_obj = params.get('file_data', '')
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reader = csv.reader(file_obj.file)
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for row in reader:
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lib_id = None
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folder_id = None
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lib = trans.sa_session.query( trans.app.model.Library ) \
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.filter( and_( trans.app.model.Library.table.c.name==row[1], \
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trans.app.model.Library.table.c.deleted==False ) )\
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.first()
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if lib:
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folder = trans.sa_session.query( trans.app.model.LibraryFolder ) \
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.filter( and_( trans.app.model.LibraryFolder.table.c.name==row[2], \
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trans.app.model.LibraryFolder.table.c.deleted==False ) )\
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.first()
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if folder:
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lib_id = lib.id
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folder_id = folder.id
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lib_widget, folder_widget = self.__library_widgets(trans, request.user, len(current_samples),
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libraries, None, lib_id, folder_id, **kwd)
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current_samples.append(dict(name=row[0],
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barcode='',
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library=None,
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folder=None,
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lib_widget=lib_widget,
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folder_widget=folder_widget,
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field_values=row[3:]))
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return trans.fill_template( '/admin/requests/show_request.mako',
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request=request,
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request_details=self.request_details(trans, request.id),
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current_samples=current_samples,
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sample_copy=self.__copy_sample(current_samples),
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details=details,
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edit_mode=edit_mode)
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except:
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return trans.response.send_redirect( web.url_for( controller='requests',
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action='list',
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operation='show_request',
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id=trans.security.encode_id(request.id),
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status='error',
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message='Error in importing samples file' ))
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@web.expose
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@web.require_login( "create/submit sequencing requests" )
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def show_request(self, trans, **kwd):
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params = util.Params( kwd )
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message = util.restore_text( params.get( 'message', '' ) )
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status = params.get( 'status', 'done' )
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try:
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request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
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except:
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return trans.response.send_redirect( web.url_for( controller='requests',
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action='list',
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status='error',
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message="Invalid request ID",
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**kwd) )
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# get the user entered sample details
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current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
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if params.get('import_samples_button', False) == 'Import samples':
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return self.__import_samples(trans, request, current_samples, details, libraries, **kwd)
|
||||
elif params.get('add_sample_button', False) == 'Add New':
|
||||
# add an empty or filled sample
|
||||
# if the user has selected a sample no. to copy then copy the contents
|
||||
# of the src sample to the new sample else an empty sample
|
||||
src_sample_index = int(params.get( 'copy_sample', -1 ))
|
||||
# get the number of new copies of the src sample
|
||||
num_sample_to_copy = int(params.get( 'num_sample_to_copy', 1 ))
|
||||
if src_sample_index == -1:
|
||||
for ns in range(num_sample_to_copy):
|
||||
# empty sample
|
||||
lib_widget, folder_widget = self.__library_widgets(trans, request.user,
|
||||
len(current_samples),
|
||||
libraries, None, **kwd)
|
||||
current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
|
||||
barcode='',
|
||||
library=None,
|
||||
folder=None,
|
||||
field_values=['' for field in request.type.sample_form.fields],
|
||||
lib_widget=lib_widget,
|
||||
folder_widget=folder_widget))
|
||||
else:
|
||||
src_library_id = current_samples[src_sample_index]['lib_widget'].get_selected()[1]
|
||||
src_folder_id = current_samples[src_sample_index]['folder_widget'].get_selected()[1]
|
||||
for ns in range(num_sample_to_copy):
|
||||
lib_widget, folder_widget = self.__library_widgets(trans, request.user,
|
||||
len(current_samples),
|
||||
libraries, sample=None,
|
||||
lib_id=src_library_id,
|
||||
folder_id=src_folder_id,
|
||||
**kwd)
|
||||
current_samples.append(dict(name=current_samples[src_sample_index]['name']+'_%i' % (len(current_samples)+1),
|
||||
barcode='',
|
||||
library_id='none',
|
||||
folder_id='none',
|
||||
field_values=[val for val in current_samples[src_sample_index]['field_values']],
|
||||
lib_widget=lib_widget,
|
||||
folder_widget=folder_widget))
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
elif params.get('save_samples_button', False) == 'Save':
|
||||
# check for duplicate sample names
|
||||
message = ''
|
||||
for index in range(len(current_samples)-len(request.samples)):
|
||||
sample_index = index + len(request.samples)
|
||||
sample_name = current_samples[sample_index]['name']
|
||||
if not sample_name.strip():
|
||||
message = 'Please 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']:
|
||||
count = count + 1
|
||||
if count > 1:
|
||||
message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
|
||||
break
|
||||
if message:
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details, edit_mode=edit_mode,
|
||||
status='error', message=message)
|
||||
# save all the new/unsaved samples entered by the user
|
||||
if edit_mode == 'False':
|
||||
for index in range(len(current_samples)-len(request.samples)):
|
||||
sample_index = len(request.samples)
|
||||
form_values = trans.app.model.FormValues(request.type.sample_form,
|
||||
current_samples[sample_index]['field_values'])
|
||||
trans.sa_session.add( form_values )
|
||||
trans.sa_session.flush()
|
||||
s = trans.app.model.Sample(current_samples[sample_index]['name'], '',
|
||||
request, form_values,
|
||||
current_samples[sample_index]['barcode'],
|
||||
current_samples[sample_index]['library'],
|
||||
current_samples[sample_index]['folder'],
|
||||
dataset_files=[])
|
||||
trans.sa_session.add( s )
|
||||
trans.sa_session.flush()
|
||||
else:
|
||||
status = 'done'
|
||||
message = 'Changes made to the sample(s) are saved. '
|
||||
for sample_index in range(len(current_samples)):
|
||||
sample = request.samples[sample_index]
|
||||
sample.name = current_samples[sample_index]['name']
|
||||
sample.library = current_samples[sample_index]['library']
|
||||
sample.folder = current_samples[sample_index]['folder']
|
||||
if request.submitted():
|
||||
bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode'])
|
||||
if bc_message:
|
||||
status = 'error'
|
||||
message += bc_message
|
||||
else:
|
||||
sample.bar_code = current_samples[sample_index]['barcode']
|
||||
trans.sa_session.add( sample )
|
||||
trans.sa_session.flush()
|
||||
form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
|
||||
form_values.content = current_samples[sample_index]['field_values']
|
||||
trans.sa_session.add( form_values )
|
||||
trans.sa_session.flush()
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id),
|
||||
status=status,
|
||||
message=message ))
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
edit_mode = 'True'
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details, libraries=libraries,
|
||||
edit_mode=edit_mode)
|
||||
elif params.get('cancel_changes_button', False) == 'Cancel':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
id=trans.security.encode_id(request.id)) )
|
||||
else:
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples=current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details, libraries=libraries,
|
||||
edit_mode=edit_mode, status=status, message=message)
|
||||
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def delete_sample(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
|
||||
current_samples, details, edit_mode = self.__update_samples( request, **kwd )
|
||||
sample_index = int(params.get('sample_id', 0))
|
||||
sample_name = current_samples[sample_index]['name']
|
||||
s = request.has_sample(sample_name)
|
||||
if s:
|
||||
trans.sa_session.delete( s.values )
|
||||
trans.sa_session.delete( s )
|
||||
trans.sa_session.flush()
|
||||
del current_samples[sample_index]
|
||||
return trans.fill_template( '/requests/show_request.mako',
|
||||
request=request,
|
||||
request_details=self.request_details(trans, request.id),
|
||||
current_samples = current_samples,
|
||||
sample_copy=self.__copy_sample(current_samples),
|
||||
details=details,
|
||||
edit_mode=edit_mode)
|
||||
def __select_request_type(self, trans, rtid):
|
||||
requesttype_list = trans.user.accessible_request_types(trans)
|
||||
rt_ids = ['none']
|
||||
for rt in requesttype_list:
|
||||
if not rt.deleted:
|
||||
rt_ids.append(str(rt.id))
|
||||
select_reqtype = SelectField('select_request_type',
|
||||
refresh_on_change=True,
|
||||
refresh_on_change_values=rt_ids[1:])
|
||||
if rtid == 'none':
|
||||
select_reqtype.add_option('Select one', 'none', selected=True)
|
||||
else:
|
||||
select_reqtype.add_option('Select one', 'none')
|
||||
for rt in requesttype_list:
|
||||
if not rt.deleted:
|
||||
if rtid == rt.id:
|
||||
select_reqtype.add_option(rt.name, rt.id, selected=True)
|
||||
else:
|
||||
select_reqtype.add_option(rt.name, rt.id)
|
||||
return select_reqtype
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def new(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
if params.get('select_request_type', False) == 'True':
|
||||
return trans.fill_template( '/requests/new_request.mako',
|
||||
select_request_type=self.__select_request_type(trans, 'none'),
|
||||
widgets=[],
|
||||
message=message,
|
||||
status=status)
|
||||
elif params.get('create', False) == 'True':
|
||||
if params.get('create_request_button', False) == 'Save' \
|
||||
or params.get('create_request_samples_button', False) == 'Add samples':
|
||||
request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
|
||||
if not util.restore_text(params.get('name', '')):
|
||||
message = 'Please enter the <b>Name</b> of the request'
|
||||
kwd['create'] = 'True'
|
||||
kwd['status'] = 'error'
|
||||
kwd['message'] = message
|
||||
kwd['create_request_button'] = None
|
||||
kwd['create_request_samples_button'] = None
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='new',
|
||||
**kwd) )
|
||||
request = self.__save_request(trans, None, **kwd)
|
||||
message = 'The new request named <b>%s</b> has been created' % request.name
|
||||
if params.get('create_request_button', False) == 'Save':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
message=message ,
|
||||
status='done') )
|
||||
elif params.get('create_request_samples_button', False) == 'Add samples':
|
||||
new_kwd = {}
|
||||
new_kwd['id'] = trans.security.encode_id(request.id)
|
||||
new_kwd['operation'] = 'show_request'
|
||||
new_kwd['add_sample'] = True
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
message=message ,
|
||||
status='done',
|
||||
**new_kwd) )
|
||||
else:
|
||||
return self.__show_request_form(trans, **kwd)
|
||||
elif params.get('refresh', False) == 'true':
|
||||
return self.__show_request_form(trans, **kwd)
|
||||
def __show_request_form(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
try:
|
||||
request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
|
||||
except:
|
||||
return trans.fill_template( '/requests/new_request.mako',
|
||||
select_request_type=self.__select_request_type(trans, 'none'),
|
||||
widgets=[],
|
||||
message=message,
|
||||
status=status)
|
||||
form_values = None
|
||||
select_request_type = self.__select_request_type(trans, request_type.id)
|
||||
# list of widgets to be rendered on the request form
|
||||
widgets = []
|
||||
widgets.append(dict(label='Name of the Experiment',
|
||||
widget=TextField('name', 40,
|
||||
util.restore_text( params.get( 'name', '' ) )),
|
||||
helptext='(Required)'))
|
||||
widgets.append(dict(label='Description',
|
||||
widget=TextField('desc', 40,
|
||||
util.restore_text( params.get( 'desc', '' ) )),
|
||||
helptext='(Optional)'))
|
||||
widgets = widgets + request_type.request_form.get_widgets( trans.user, **kwd )
|
||||
widgets.append(dict(label='Send email notification once the sequencing request is complete',
|
||||
widget=CheckboxField('email_notify', False),
|
||||
helptext=''))
|
||||
return trans.fill_template( '/requests/new_request.mako',
|
||||
select_request_type=select_request_type,
|
||||
request_type=request_type,
|
||||
widgets=widgets,
|
||||
message=message,
|
||||
status=status)
|
||||
def __validate(self, trans, request):
|
||||
'''
|
||||
Validates the request entered by the user
|
||||
'''
|
||||
empty_fields = []
|
||||
# check rest of the fields of the form
|
||||
for index, field in enumerate(request.type.request_form.fields):
|
||||
if field['required'] == 'required' and request.values.content[index] in ['', None]:
|
||||
empty_fields.append(field['label'])
|
||||
if empty_fields:
|
||||
message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
|
||||
for ef in empty_fields:
|
||||
message = message + '<b>' +ef + '</b><br/>'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
operation='edit',
|
||||
status = 'error',
|
||||
message=message,
|
||||
id=trans.security.encode_id(request.id) ))
|
||||
# now check the required fields of all the samples of this request
|
||||
for s in request.samples:
|
||||
for index, field in enumerate(request.type.sample_form.fields):
|
||||
if field['required'] == 'required' and s.values.content[index] in ['', None]:
|
||||
empty_fields.append((s.name, field['label']))
|
||||
if empty_fields:
|
||||
message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name
|
||||
for sname, ef in empty_fields:
|
||||
message = message + '<b>%s</b> field of sample <b>%s</b><br/>' % (ef, sname)
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
operation='show_request',
|
||||
status = 'error',
|
||||
message=message,
|
||||
id=trans.security.encode_id(request.id) ))
|
||||
def __save_request(self, trans, request=None, **kwd):
|
||||
'''
|
||||
This method saves a new request if request_id is None.
|
||||
'''
|
||||
params = util.Params( kwd )
|
||||
request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
|
||||
name = util.restore_text(params.get('name', ''))
|
||||
desc = util.restore_text(params.get('desc', ''))
|
||||
notify = CheckboxField.is_checked( params.get('email_notify', '') )
|
||||
# library
|
||||
try:
|
||||
library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'library_id', None ) ) )
|
||||
except:
|
||||
library = None
|
||||
try:
|
||||
folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'folder_id', None ) ) )
|
||||
except:
|
||||
if library:
|
||||
folder = library.root_folder
|
||||
else:
|
||||
folder = None
|
||||
# fields
|
||||
values = []
|
||||
for index, field in enumerate(request_type.request_form.fields):
|
||||
if field['type'] == 'AddressField':
|
||||
value = util.restore_text(params.get('field_%i' % index, ''))
|
||||
if value == 'new':
|
||||
# save this new address in the list of this user's addresses
|
||||
user_address = trans.app.model.UserAddress( user=trans.user )
|
||||
user_address.desc = util.restore_text(params.get('field_%i_short_desc' % index, ''))
|
||||
user_address.name = util.restore_text(params.get('field_%i_name' % index, ''))
|
||||
user_address.institution = util.restore_text(params.get('field_%i_institution' % index, ''))
|
||||
user_address.address = util.restore_text(params.get('field_%i_address1' % index, ''))+' '+util.restore_text(params.get('field_%i_address2' % index, ''))
|
||||
user_address.city = util.restore_text(params.get('field_%i_city' % index, ''))
|
||||
user_address.state = util.restore_text(params.get('field_%i_state' % index, ''))
|
||||
user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, ''))
|
||||
user_address.country = util.restore_text(params.get('field_%i_country' % index, ''))
|
||||
user_address.phone = util.restore_text(params.get('field_%i_phone' % index, ''))
|
||||
trans.sa_session.add( user_address )
|
||||
trans.sa_session.flush()
|
||||
trans.sa_session.refresh( trans.user )
|
||||
values.append(int(user_address.id))
|
||||
elif value == unicode('none'):
|
||||
values.append('')
|
||||
else:
|
||||
values.append(int(value))
|
||||
elif field['type'] == 'CheckboxField':
|
||||
values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') ))
|
||||
else:
|
||||
values.append(util.restore_text(params.get('field_%i' % index, '')))
|
||||
form_values = trans.app.model.FormValues(request_type.request_form, values)
|
||||
trans.sa_session.add( form_values )
|
||||
trans.sa_session.flush()
|
||||
if not request:
|
||||
request = trans.app.model.Request(name, desc, request_type,
|
||||
trans.user, form_values, notify)
|
||||
trans.sa_session.add( request )
|
||||
trans.sa_session.flush()
|
||||
trans.sa_session.refresh( request )
|
||||
# create an event with state 'New' for this new request
|
||||
comments = "Request created."
|
||||
event = trans.app.model.RequestEvent(request, request.states.NEW, comments)
|
||||
trans.sa_session.add( event )
|
||||
trans.sa_session.flush()
|
||||
else:
|
||||
request.name = name
|
||||
request.desc = desc
|
||||
request.type = request_type
|
||||
request.user = trans.user
|
||||
request.values = form_values
|
||||
request.notify = notify
|
||||
trans.sa_session.add( request )
|
||||
trans.sa_session.flush()
|
||||
return request
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def edit(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
try:
|
||||
request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid request ID",
|
||||
**kwd) )
|
||||
if params.get('show', False) == 'True':
|
||||
return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd)
|
||||
elif params.get('save_changes_request_button', False) == 'Save changes' \
|
||||
or params.get('edit_samples_button', False) == 'Edit samples':
|
||||
request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) )
|
||||
if not util.restore_text(params.get('name', '')):
|
||||
message = 'Please enter the <b>Name</b> of the request'
|
||||
kwd['status'] = 'error'
|
||||
kwd['message'] = message
|
||||
kwd['show'] = 'True'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='edit',
|
||||
**kwd) )
|
||||
request = self.__save_request(trans, request, **kwd)
|
||||
message = 'The changes made to the request named %s has been saved' % request.name
|
||||
if params.get('save_changes_request_button', False) == 'Save changes':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
message=message ,
|
||||
status='done') )
|
||||
elif params.get('edit_samples_button', False) == 'Edit samples':
|
||||
new_kwd = {}
|
||||
new_kwd['request_id'] = request.id
|
||||
new_kwd['edit_samples_button'] = 'Edit samples'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='show_request',
|
||||
message=message ,
|
||||
status='done',
|
||||
**new_kwd) )
|
||||
elif params.get('refresh', False) == 'true':
|
||||
return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd)
|
||||
|
||||
def __edit_request(self, trans, **kwd):
|
||||
try:
|
||||
request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
|
||||
except:
|
||||
message = "Invalid request ID"
|
||||
log.warn( message )
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message=message) )
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
select_request_type = self.__select_request_type(trans, request.type.id)
|
||||
# list of widgets to be rendered on the request form
|
||||
widgets = []
|
||||
if util.restore_text( params.get( 'name', '' ) ):
|
||||
name = util.restore_text( params.get( 'name', '' ) )
|
||||
else:
|
||||
name = request.name
|
||||
widgets.append(dict(label='Name',
|
||||
widget=TextField('name', 40, name),
|
||||
helptext='(Required)'))
|
||||
if util.restore_text( params.get( 'desc', '' ) ):
|
||||
desc = util.restore_text( params.get( 'desc', '' ) )
|
||||
else:
|
||||
desc = request.desc
|
||||
widgets.append(dict(label='Description',
|
||||
widget=TextField('desc', 40, desc),
|
||||
helptext='(Optional)'))
|
||||
widgets = widgets + request.type.request_form.get_widgets( trans.user, request.values.content, **kwd )
|
||||
widgets.append(dict(label='Send email notification once the sequencing request is complete',
|
||||
widget=CheckboxField('email_notify', request.notify),
|
||||
helptext=''))
|
||||
return trans.fill_template( '/requests/edit_request.mako',
|
||||
select_request_type=select_request_type,
|
||||
request_type=request.type,
|
||||
request=request,
|
||||
widgets=widgets,
|
||||
message=message,
|
||||
status=status)
|
||||
return self.__show_request_form(trans)
|
||||
def __delete_request(self, trans, **kwd):
|
||||
id_list = util.listify( kwd['id'] )
|
||||
delete_failed = []
|
||||
for id in id_list:
|
||||
try:
|
||||
request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
|
||||
except:
|
||||
message = "Invalid request ID"
|
||||
log.warn( message )
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message=message,
|
||||
**kwd) )
|
||||
# a request cannot be deleted once its submitted
|
||||
if not request.new():
|
||||
delete_failed.append(request.name)
|
||||
else:
|
||||
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()
|
||||
if not len(delete_failed):
|
||||
message = '%i request(s) has been deleted.' % len(id_list)
|
||||
status = 'done'
|
||||
else:
|
||||
message = '%i request(s) has been deleted. %i request %s could not be deleted as they have been submitted.' % (len(id_list)-len(delete_failed),
|
||||
len(delete_failed), str(delete_failed))
|
||||
status = 'warning'
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status=status,
|
||||
message=message) )
|
||||
def __undelete_request(self, trans, **kwd):
|
||||
id_list = util.listify( kwd['id'] )
|
||||
for id in id_list:
|
||||
try:
|
||||
request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) )
|
||||
except:
|
||||
message = "Invalid request ID"
|
||||
log.warn( message )
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message=message,
|
||||
**kwd) )
|
||||
request.deleted = False
|
||||
trans.sa_session.add( request )
|
||||
# undelete all the samples belonging to this request
|
||||
for s in request.samples:
|
||||
s.deleted = False
|
||||
trans.sa_session.add( s )
|
||||
trans.sa_session.flush()
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='done',
|
||||
message='%i request(s) has been undeleted.' % len(id_list) ) )
|
||||
def __submit_request(self, trans, **kwd):
|
||||
try:
|
||||
request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
|
||||
except:
|
||||
message = "Invalid request ID"
|
||||
log.warn( message )
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message=message,
|
||||
**kwd) )
|
||||
# check if all the required request and its sample fields have been filled
|
||||
self.__validate(trans, request)
|
||||
# change the request state to 'Submitted'
|
||||
comments = "Sequencing request is in progress."
|
||||
event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments)
|
||||
trans.sa_session.add( event )
|
||||
trans.sa_session.flush()
|
||||
# get the new state
|
||||
new_state = request.type.states[0]
|
||||
for s in request.samples:
|
||||
event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system')
|
||||
trans.sa_session.add( event )
|
||||
trans.sa_session.flush()
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
id=trans.security.encode_id(request.id),
|
||||
status='done',
|
||||
message='The request <b>%s</b> has been submitted.' % request.name
|
||||
) )
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def show_events(self, trans, **kwd):
|
||||
params = util.Params( kwd )
|
||||
try:
|
||||
sample_id = int(params.get('sample_id', False))
|
||||
sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
|
||||
except:
|
||||
message = "Invalid sample ID"
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message=message,
|
||||
**kwd) )
|
||||
events_list = []
|
||||
all_events = sample.events
|
||||
for event in all_events:
|
||||
events_list.append((event.state.name, event.state.desc, time_ago(event.update_time), event.comment))
|
||||
return trans.fill_template( '/sample/sample_events.mako',
|
||||
events_list=events_list,
|
||||
sample_name=sample.name,
|
||||
request=sample.request)
|
||||
#
|
||||
# Data transfer from sequencer
|
||||
#
|
||||
@web.expose
|
||||
@web.require_login( "create/submit sequencing requests" )
|
||||
def show_datatx_page( self, trans, **kwd ):
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
try:
|
||||
sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) )
|
||||
except:
|
||||
return trans.response.send_redirect( web.url_for( controller='requests',
|
||||
action='list',
|
||||
status='error',
|
||||
message="Invalid sample ID",
|
||||
**kwd) )
|
||||
return trans.fill_template( '/requests/show_data.mako',
|
||||
sample=sample, dataset_files=sample.dataset_files )
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -194,7 +194,7 @@ class DataTransfer(object):
|
||||
Update the data transfer status for this dataset in the database
|
||||
'''
|
||||
try:
|
||||
log.debug('Setting status "%s" for dataset "%s"' % ( status, str(dataset_index) ) )
|
||||
log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_index), str(self.sample_id) ) )
|
||||
df = from_json_string(self.galaxydb.get_sample_dataset_files(self.sample_id))
|
||||
if dataset_index == 'All':
|
||||
for dataset in self.dataset_files:
|
||||
|
||||
@@ -28,7 +28,7 @@ class GalaxyDbInterface(object):
|
||||
def __init__(self, dbstr):
|
||||
self.dbstr = dbstr
|
||||
self.db_engine = create_engine(self.dbstr)
|
||||
# self.db_engine.echo = True
|
||||
self.db_engine.echo = True
|
||||
self.metadata = MetaData(self.db_engine)
|
||||
self.session = sessionmaker(bind=self.db_engine)
|
||||
self.event_table = Table('sample_event', self.metadata, autoload=True )
|
||||
|
||||
@@ -1,26 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Create ${num_states} states for the '${request_type_name}' request type</div>
|
||||
<form name="new_form_fields" action="${h.url_for( controller='requests_admin', action='request_type', name=request_type_name, description=desc, num_states=num_states, request_form_id=request_form_id, sample_form_id=sample_form_id)}" method="post" >
|
||||
<div class="toolFormBody">
|
||||
%for element_count in range( num_states ):
|
||||
<div class="form-row">
|
||||
<label>${1+element_count}) State name:</label>
|
||||
<input type="text" name="state_name_${element_count}" value="" size="40"/>
|
||||
<label>State help text (optional):</label>
|
||||
<input type="text" name="state_desc_${element_count}" value="" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save_request_type" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
@@ -11,7 +11,7 @@
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', action='show_datatx_page', cntrller='requests_admin', sample_id=trans.security.encode_id(sample.id) )}">
|
||||
<span>Dataset transfer page</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
@@ -1,88 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$( function() {
|
||||
$( "select[refresh_on_change='true']").change( function() {
|
||||
var refresh = false;
|
||||
var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
|
||||
if ( refresh_on_change_values ) {
|
||||
refresh_on_change_values = refresh_on_change_values.value.split( ',' );
|
||||
var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
|
||||
for( i= 0; i < refresh_on_change_values.length; i++ ) {
|
||||
if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
|
||||
refresh = true;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
else {
|
||||
refresh = true;
|
||||
}
|
||||
if ( refresh ){
|
||||
$( "#edit_request" ).submit();
|
||||
}
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
<br/>
|
||||
<br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Edit request "${request.name}" from ${request.user.email}</div>
|
||||
%if len(select_request_type.options) == 1:
|
||||
There are no request types created for a new request.
|
||||
%else:
|
||||
<div class="toolFormBody">
|
||||
<form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_admin', action='edit', request_id=request.id)}" method="post" >
|
||||
<div class="form-row">
|
||||
<label>
|
||||
Select Request Type:
|
||||
</label>
|
||||
${select_request_type.get_html()}
|
||||
</div>
|
||||
|
||||
%if select_request_type.get_selected() != ('Select one', 'none'):
|
||||
%for i, field in enumerate(widgets):
|
||||
<div class="form-row">
|
||||
<label>${field['label']}</label>
|
||||
${field['widget'].get_html()}
|
||||
%if field['label'] == 'Library' and new_library:
|
||||
${new_library.get_html()}
|
||||
%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${field['helptext']}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="hidden" name="refresh" value="true" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save_changes_request_button" value="Save changes"/>
|
||||
##<input type="submit" name="edit_samples_button" value="Edit samples"/>
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
@@ -1,36 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
<h2>History of Sequencing Request "${request.name}"</h2>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
<h3>User: ${request.user.email}</h3>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>State</th>
|
||||
<th>Last Update</th>
|
||||
<th>Comments</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
%for state, updated, comments in events_list:
|
||||
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
|
||||
<td><b><a>${state}</a></b></td>
|
||||
<td><a>${updated}</a></td>
|
||||
<td><a>${comments}</a></td>
|
||||
</tr>
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
@@ -1,227 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$(document).ready(function(){
|
||||
//hide the all of the element with class msg_body
|
||||
$(".msg_body").hide();
|
||||
//toggle the componenet with class msg_body
|
||||
$(".msg_head").click(function(){
|
||||
$(this).next(".msg_body").slideToggle(450);
|
||||
});
|
||||
});
|
||||
|
||||
|
||||
|
||||
|
||||
</script>
|
||||
|
||||
<script type="text/javascript">
|
||||
function display_file_details(sample_id, folder_path)
|
||||
{
|
||||
var w = document.get_data.files_list.selectedIndex;
|
||||
var selected_value = document.get_data.files_list.options[w].value;
|
||||
var cell = $("#file_details");
|
||||
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: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
|
||||
success : function ( data ) {
|
||||
cell.html( '<label>'+data+'</label>' )
|
||||
}
|
||||
});
|
||||
}
|
||||
else
|
||||
{
|
||||
cell.html( '' )
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
</script>
|
||||
|
||||
<script type="text/javascript">
|
||||
function open_folder1(sample_id, folder_path)
|
||||
{
|
||||
var w = document.get_data.files_list.selectedIndex;
|
||||
var selected_value = document.get_data.files_list.options[w].value;
|
||||
var cell = $("#file_details");
|
||||
if(selected_value.charAt(selected_value.length-1) == '/')
|
||||
{
|
||||
document.get_data.folder_path.value = document.get_data.folder_path.value+selected_value
|
||||
// Make ajax call
|
||||
$.ajax( {
|
||||
type: "POST",
|
||||
url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
|
||||
dataType: "json",
|
||||
data: { id: sample_id, folder_path: document.get_data.folder_path.value },
|
||||
success : function ( data ) {
|
||||
document.get_data.files_list.options.length = 0
|
||||
for(i=0; i<data.length; i++)
|
||||
{
|
||||
var newOpt = new Option(data[i], data[i]);
|
||||
document.get_data.files_list.options[i] = newOpt;
|
||||
}
|
||||
//cell.html( '<label>'+data+'</label>' )
|
||||
|
||||
}
|
||||
});
|
||||
}
|
||||
else
|
||||
{
|
||||
cell.html( '' )
|
||||
}
|
||||
}
|
||||
</script>
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
.msg_head {
|
||||
padding: 0px 0px;
|
||||
cursor: pointer;
|
||||
}
|
||||
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<h2>Data transfer from Sequencer</h2>
|
||||
<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
|
||||
<br/>
|
||||
<br/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
%if sample.request.submitted() and sample.inprogress_dataset_files():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
|
||||
<span>Refresh this page</span></a>
|
||||
</li>
|
||||
%endif
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(sample.request.type.id) )}">
|
||||
<span>Sequencer information</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( sample.library.id ) )}">
|
||||
<span>${sample.library.name} Data Library</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
%if len(dataset_files):
|
||||
## <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
|
||||
<div class="form-row">
|
||||
<h4>Sample Dataset(s)</h4>
|
||||
%if sample.untransferred_dataset_files():
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', start_transfer_button=True, sample_id=sample.id )}">
|
||||
<span>Start transfer</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
%endif
|
||||
<div class="form-row">
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Dataset File</th>
|
||||
<th>Transfer Status</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
%for dataset_index, dataset_file in enumerate(dataset_files):
|
||||
${sample_dataset_files( dataset_index, dataset_file['name'], dataset_file['status'] )}
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
## </form>
|
||||
##</div>
|
||||
|
||||
|
||||
<br/>
|
||||
<br/>
|
||||
%endif
|
||||
|
||||
##<div class="toolForm">
|
||||
<form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
|
||||
<div class="form-row">
|
||||
##<div class="toolFormTitle">Select files for transfer</div>
|
||||
<h4>Select files for transfer</h4>
|
||||
<div style="width: 60%;">
|
||||
<div class="form-row">
|
||||
<label>Folder path on the sequencer:</label>
|
||||
<input type="text" name="folder_path" value="${folder_path}" size="100"/>
|
||||
<input type="submit" name="browse_button" value="List contents"/>
|
||||
##<input type="submit" name="open_folder" value="Open folder"/>
|
||||
<input type="submit" name="folder_up" value="Up"/>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" ondblclick="open_folder1(${sample.id}, '${folder_path}')" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple>
|
||||
%for index, f in enumerate(files):
|
||||
<option value="${f}">${f}</option>
|
||||
%endfor
|
||||
</select>
|
||||
<br/>
|
||||
<div id="file_details" class="toolParamHelp" style="clear: both;">
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
After selecting dataset(s), be sure to click on the <b>Start transfer</b> button.
|
||||
Once the transfer is complete the dataset(s) will show up on this page.
|
||||
</div>
|
||||
<input type="submit" name="select_files_button" value="Select"/>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
|
||||
<%def name="sample_dataset_files( dataset_index, dataset_name, status )">
|
||||
<tr>
|
||||
<td>
|
||||
<label class="msg_head"><a href="${h.url_for( controller='requests_admin', action='dataset_details', sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}">${dataset_name}</a></label>
|
||||
## <div class="msg_head"><u>${dataset_file.split('/')[-1]}</u></div>
|
||||
## <div class="msg_body">
|
||||
## ${dataset_file}
|
||||
## </div>
|
||||
</td>
|
||||
<td>
|
||||
%if status not in [sample.transfer_status.NOT_STARTED, sample.transfer_status.COMPLETE]:
|
||||
<i>${status}</i>
|
||||
%else:
|
||||
${status}
|
||||
%endif
|
||||
</td>
|
||||
##<td></td>
|
||||
%if status == sample.transfer_status.NOT_STARTED:
|
||||
<td>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id, remove_dataset_button=True, dataset_index=dataset_index )}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
</td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
</tr>
|
||||
</%def>
|
||||
@@ -1,46 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
|
||||
<h2>Bar codes for Samples of Request "${request.name}"</h2>
|
||||
<h3>User: ${user.email}</h3>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
<form name="bar_codes" action="${h.url_for( controller='requests_admin', action='save_bar_codes', request_id=request.id)}" method="post" >
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Description</th>
|
||||
<th>Bar code</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
%for index, sample in enumerate(samples_list):
|
||||
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
|
||||
<td><b><a>${sample.name}</a></b></td>
|
||||
<td><a>${sample.desc}</a></td>
|
||||
<td>
|
||||
${widgets[index].get_html()}
|
||||
</td>
|
||||
</tr>
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save_bar_codes" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
@@ -1,63 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
<%def name="title()">Events for Sample ${sample.name}</%def>
|
||||
|
||||
<h2>Events for Sample "${sample.name}"</h2>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
<h3>User: ${sample.request.user.email}</h3>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>State</th>
|
||||
<th>Description</th>
|
||||
<th>Last Update</th>
|
||||
<th>Comments</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
%for state, desc, updated, comments in events_list:
|
||||
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
|
||||
<td><b><a>${state}</a></b></td>
|
||||
<td><a>${desc}</a></td>
|
||||
<td><a>${updated}</a></td>
|
||||
<td><a>${comments}</a></td>
|
||||
</tr>
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Change current state</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id=sample.id)}" method="post" >
|
||||
%for w in widgets:
|
||||
<div class="form-row">
|
||||
<label>
|
||||
${w[0]}
|
||||
</label>
|
||||
${w[1].get_html()}
|
||||
%if w[0] == 'Comments':
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Optional
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="add_event_button" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
@@ -34,7 +34,7 @@ $( function() {
|
||||
<br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list')}">
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, cntrller=cntrller, action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
@@ -45,7 +45,7 @@ $( function() {
|
||||
There are no request types created for a new request.
|
||||
%else:
|
||||
<div class="toolFormBody">
|
||||
<form name="edit_request" id="edit_request" action="${h.url_for( controller='requests', action='edit', request_id=request.id)}" method="post" >
|
||||
<form name="edit_request" id="edit_request" action="${h.url_for( controller='requests_common', cntrller=cntrller, action='edit', id=trans.security.encode_id(request.id))}" method="post" >
|
||||
<div class="form-row">
|
||||
<label>
|
||||
Select Request Type:
|
||||
@@ -4,11 +4,11 @@
|
||||
<h2>History of Sequencing Request "${request.name}"</h2>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list')}">
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list')}">
|
||||
<span>Browse all requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
@@ -0,0 +1,239 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$(document).ready(function(){
|
||||
//hide the all of the element with class msg_body
|
||||
$(".msg_body").hide();
|
||||
//toggle the componenet with class msg_body
|
||||
$(".msg_head").click(function(){
|
||||
$(this).next(".msg_body").slideToggle(450);
|
||||
});
|
||||
});
|
||||
|
||||
|
||||
|
||||
|
||||
</script>
|
||||
|
||||
<script type="text/javascript">
|
||||
function display_file_details(sample_id, folder_path)
|
||||
{
|
||||
var w = document.get_data.files_list.selectedIndex;
|
||||
var selected_value = document.get_data.files_list.options[w].value;
|
||||
var cell = $("#file_details");
|
||||
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: sample_id, folder_path: document.get_data.folder_path.value+selected_value },
|
||||
success : function ( data ) {
|
||||
cell.html( '<label>'+data+'</label>' )
|
||||
}
|
||||
});
|
||||
}
|
||||
else
|
||||
{
|
||||
cell.html( '' )
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
</script>
|
||||
|
||||
<script type="text/javascript">
|
||||
function open_folder1(sample_id, folder_path)
|
||||
{
|
||||
var w = document.get_data.files_list.selectedIndex;
|
||||
var selected_value = document.get_data.files_list.options[w].value;
|
||||
var cell = $("#file_details");
|
||||
if(selected_value.charAt(selected_value.length-1) == '/')
|
||||
{
|
||||
document.get_data.folder_path.value = document.get_data.folder_path.value+selected_value
|
||||
// Make ajax call
|
||||
$.ajax( {
|
||||
type: "POST",
|
||||
url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
|
||||
dataType: "json",
|
||||
data: { id: sample_id, folder_path: document.get_data.folder_path.value },
|
||||
success : function ( data ) {
|
||||
document.get_data.files_list.options.length = 0
|
||||
for(i=0; i<data.length; i++)
|
||||
{
|
||||
var newOpt = new Option(data[i], data[i]);
|
||||
document.get_data.files_list.options[i] = newOpt;
|
||||
}
|
||||
//cell.html( '<label>'+data+'</label>' )
|
||||
|
||||
}
|
||||
});
|
||||
}
|
||||
else
|
||||
{
|
||||
cell.html( '' )
|
||||
}
|
||||
}
|
||||
</script>
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
.msg_head {
|
||||
padding: 0px 0px;
|
||||
cursor: pointer;
|
||||
}
|
||||
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<h2>Data transfer from Sequencer</h2>
|
||||
<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
|
||||
<br/>
|
||||
<br/>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
%if sample.request.submitted() and sample.inprogress_dataset_files():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
|
||||
<span>Refresh this page</span></a>
|
||||
</li>
|
||||
%endif
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(sample.request.type.id) )}">
|
||||
<span>Sequencer information</span></a>
|
||||
</li>
|
||||
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( sample.library.id ) )}">
|
||||
<span>${sample.library.name} Data Library</span></a>
|
||||
</li>
|
||||
%else:
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
|
||||
<span>${sample.library.name} Data Library</span></a>
|
||||
</li>
|
||||
%endif
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(sample.request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
%if len(dataset_files):
|
||||
<div class="form-row">
|
||||
<h4>Sample Dataset(s)</h4>
|
||||
%if sample.untransferred_dataset_files() and cntrller == 'requests_admin':
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', start_transfer_button=True, sample_id=sample.id )}">
|
||||
<span>Start transfer</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
%endif
|
||||
<div class="form-row">
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Dataset File</th>
|
||||
<th>Transfer Status</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
%for dataset_index, dataset_file in enumerate(dataset_files):
|
||||
${sample_dataset_files( dataset_index, dataset_file['name'], dataset_file['status'] )}
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
%else:
|
||||
<div class="form-row">
|
||||
There are no dataset files associated with this sample.
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<br/>
|
||||
<br/>
|
||||
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
<form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', cntrller=cntrller, action='get_data', sample_id=sample.id)}" method="post" >
|
||||
<div class="form-row">
|
||||
##<div class="toolFormTitle">Select files for transfer</div>
|
||||
<h4>Select files for transfer</h4>
|
||||
<div style="width: 60%;">
|
||||
<div class="form-row">
|
||||
<label>Folder path on the sequencer:</label>
|
||||
<input type="text" name="folder_path" value="${folder_path}" size="100"/>
|
||||
<input type="submit" name="browse_button" value="List contents"/>
|
||||
##<input type="submit" name="open_folder" value="Open folder"/>
|
||||
<input type="submit" name="folder_up" value="Up"/>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" ondblclick="open_folder1(${sample.id}, '${folder_path}')" onChange="display_file_details(${sample.id}, '${folder_path}')" multiple>
|
||||
%for index, f in enumerate(files):
|
||||
<option value="${f}">${f}</option>
|
||||
%endfor
|
||||
</select>
|
||||
<br/>
|
||||
<div id="file_details" class="toolParamHelp" style="clear: both;">
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
After selecting dataset(s), be sure to click on the <b>Start transfer</b> button.
|
||||
Once the transfer is complete the dataset(s) will show up on this page.
|
||||
</div>
|
||||
<input type="submit" name="select_files_button" value="Select"/>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
%endif
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
<%def name="sample_dataset_files( dataset_index, dataset_name, status )">
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
<label class="msg_head"><a href="${h.url_for( controller='requests_admin', action='dataset_details', sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}">${dataset_name}</a></label>
|
||||
%else:
|
||||
${dataset_name}
|
||||
%endif
|
||||
</td>
|
||||
<td>
|
||||
%if status not in [sample.transfer_status.NOT_STARTED, sample.transfer_status.COMPLETE]:
|
||||
<i>${status}</i>
|
||||
%else:
|
||||
${status}
|
||||
%endif
|
||||
</td>
|
||||
##<td></td>
|
||||
%if status == sample.transfer_status.NOT_STARTED and cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
<td>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id, remove_dataset_button=True, dataset_index=dataset_index )}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
</td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
</tr>
|
||||
</%def>
|
||||
@@ -5,12 +5,12 @@
|
||||
self.has_left_panel=False
|
||||
self.has_right_panel=False
|
||||
self.active_view="requests"
|
||||
|
||||
self.message_box_visible=False
|
||||
%>
|
||||
</%def>
|
||||
|
||||
<%def name="center_panel()">
|
||||
|
||||
<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="sample", action="list", request_id=request_id )}"> </iframe>
|
||||
<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="requests", action="list" )}"> </iframe>
|
||||
|
||||
</%def>
|
||||
</%def>
|
||||
+9
-12
@@ -44,7 +44,7 @@ $( function() {
|
||||
<br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list')}">
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, cntrller=cntrller, action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
@@ -55,10 +55,10 @@ $( function() {
|
||||
There are no request types created for a new request.
|
||||
%else:
|
||||
<div class="toolFormBody">
|
||||
<form name="new_request" id="new_request" action="${h.url_for( controller='requests_admin', action='new', create=True )}" method="post" >
|
||||
<form name="new_request" id="new_request" action="${h.url_for( controller='requests_common', action='new', cntrller=cntrller)}" method="post" >
|
||||
<div class="form-row">
|
||||
<label>
|
||||
Select Request Type
|
||||
Select request type
|
||||
</label>
|
||||
${select_request_type.get_html()}
|
||||
</div>
|
||||
@@ -68,26 +68,23 @@ $( function() {
|
||||
<div class="form-row">
|
||||
<label>${field['label']}</label>
|
||||
${field['widget'].get_html()}
|
||||
%if field['label'] == 'Library' and new_library:
|
||||
${new_library.get_html()}
|
||||
%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${field['helptext']}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="hidden" name="refresh" value="true" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="create_request_button" value="Save"/>
|
||||
<input type="submit" name="create_request_samples_button" value="Add samples"/>
|
||||
</div>
|
||||
%endif
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="hidden" name="refresh" value="true" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
@@ -0,0 +1,7 @@
|
||||
<%def name="render_sample_datasets( cntrller, sample )">
|
||||
<a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
|
||||
</%def>
|
||||
|
||||
|
||||
|
||||
${render_sample_datasets( cntrller, sample )}
|
||||
@@ -0,0 +1,65 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
<%def name="title()">Events for Sample ${sample.name}</%def>
|
||||
|
||||
<h2>Events for Sample "${sample.name}"</h2>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(sample.request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
<h3>User: ${sample.request.user.email}</h3>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>State</th>
|
||||
<th>Description</th>
|
||||
<th>Last Update</th>
|
||||
<th>Comments</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
%for state, desc, updated, comments in events_list:
|
||||
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
|
||||
<td><b><a>${state}</a></b></td>
|
||||
<td><a>${desc}</a></td>
|
||||
<td><a>${updated}</a></td>
|
||||
<td><a>${comments}</a></td>
|
||||
</tr>
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Change current state</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id=sample.id)}" method="post" >
|
||||
%for w in widgets:
|
||||
<div class="form-row">
|
||||
<label>
|
||||
${w[0]}
|
||||
</label>
|
||||
${w[1].get_html()}
|
||||
%if w[0] == 'Comments':
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Optional
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<input type="submit" name="add_event_button" value="Save"/>
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
@@ -0,0 +1,5 @@
|
||||
<%def name="render_sample_state( cntrller, sample )">
|
||||
<a href="${h.url_for( controller='requests_common', cntrller=cntrller, action='sample_events', sample_id=sample.id)}">${sample.current_state().name}</a>
|
||||
</%def>
|
||||
|
||||
${render_sample_state( cntrller, sample )}
|
||||
+284
-265
@@ -1,11 +1,9 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
<%namespace file="/requests/sample_state.mako" import="render_sample_state" />
|
||||
<%namespace file="/requests/sample_datasets.mako" import="render_sample_datasets" />
|
||||
<%namespace file="/requests/common/sample_state.mako" import="render_sample_state" />
|
||||
<%namespace file="/requests/common/sample_datasets.mako" import="render_sample_datasets" />
|
||||
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$( function() {
|
||||
@@ -70,11 +68,11 @@ $(document).ready(function(){
|
||||
// Make ajax call
|
||||
$.ajax( {
|
||||
type: "POST",
|
||||
url: "${h.url_for( controller='requests_admin', action='sample_state_updates' )}",
|
||||
url: "${h.url_for( controller='requests_common', action='sample_state_updates' )}",
|
||||
dataType: "json",
|
||||
data: { ids: ids.join( "," ), states: states.join( "," ) },
|
||||
success : function ( data ) {
|
||||
$.each( data, function( id, val ) {
|
||||
$.each( data, function( id, val, cntrller ) {
|
||||
// Replace HTML
|
||||
var cell1 = $("#sampleState-" + id);
|
||||
cell1.html( val.html_state );
|
||||
@@ -127,217 +125,36 @@ $(document).ready(function(){
|
||||
|
||||
%if request.unsubmitted() and request.samples:
|
||||
<li>
|
||||
<a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
|
||||
<a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller=cntrller, action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Submit request</span></a>
|
||||
</li>
|
||||
%endif
|
||||
%if request.submitted():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Reject', id=trans.security.encode_id(request.id))}">
|
||||
<span>Reject request</span></a>
|
||||
</li>
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
%if request.submitted():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='reject', id=trans.security.encode_id(request.id))}">
|
||||
<span>Reject request</span></a>
|
||||
</li>
|
||||
%endif
|
||||
%endif
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='events', id=trans.security.encode_id(request.id) )}">
|
||||
<span>History</span></a>
|
||||
</li>
|
||||
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
|
||||
</ul>
|
||||
|
||||
<%def name="show_basic_info_form( sample_index, sample, info )">
|
||||
<td>
|
||||
<input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${' (required)' }</i>
|
||||
</div>
|
||||
</td>
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<td></td>
|
||||
%else:
|
||||
<td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<td>Unsubmitted</td>
|
||||
%else:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
<td>${info['lib_widget'].get_html()}</td>
|
||||
<td>${info['folder_widget'].get_html()}</td>
|
||||
%if request.submitted() or request.complete():
|
||||
%if sample:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td>
|
||||
%else:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
|
||||
%endif
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
## This function displays the "Basic Information" grid
|
||||
<%def name="render_basic_info_grid()">
|
||||
<h4>Sample Information</h4>
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Barcode</th>
|
||||
<th>State</th>
|
||||
<th>Data Library</th>
|
||||
<th>Folder</th>
|
||||
%if request.submitted() or request.complete():
|
||||
<th>Dataset(s) Transferred</th>
|
||||
%endif
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
%>
|
||||
%for sample_index, info in enumerate(current_samples):
|
||||
<%
|
||||
if sample_index in range(len(request.samples)):
|
||||
sample = request.samples[sample_index]
|
||||
else:
|
||||
sample = None
|
||||
%>
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
${show_basic_info_form( sample_index, sample, info )}
|
||||
</tr>
|
||||
%else:
|
||||
<tr>
|
||||
%if sample_index in range(len(request.samples)):
|
||||
<td>${info['name']}</td>
|
||||
<td>${info['barcode']}</td>
|
||||
%if sample.request.unsubmitted():
|
||||
<td>Unsubmitted</td>
|
||||
%else:
|
||||
<td id="sampleState-${sample.id}">${render_sample_state( sample )}</td>
|
||||
%endif
|
||||
|
||||
## <td>
|
||||
## %if sample:
|
||||
## %if sample.request.unsubmitted():
|
||||
## Unsubmitted
|
||||
## %else:
|
||||
## <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
|
||||
## %endif
|
||||
## %endif
|
||||
## </td>
|
||||
%if info['library']:
|
||||
<td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if info['folder']:
|
||||
<td>${info['folder'].name}</td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if request.submitted() or request.complete():
|
||||
<td id="sampleDatasets-${sample.id}">
|
||||
${render_sample_datasets( sample )}
|
||||
## <a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
|
||||
</td>
|
||||
%endif
|
||||
|
||||
|
||||
%else:
|
||||
${show_basic_info_form( sample_index, sample, info )}
|
||||
%endif
|
||||
%if request.unsubmitted() or request.rejected():
|
||||
<td>
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
%endif
|
||||
%endif
|
||||
</td>
|
||||
%endif
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</%def>
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
|
||||
<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
|
||||
<td>
|
||||
${sample_name}
|
||||
</td>
|
||||
%for field_index, field in fields_dict.items():
|
||||
<td>
|
||||
%if field['type'] == 'TextField':
|
||||
<input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
|
||||
%elif field['type'] == 'SelectField':
|
||||
<select name="sample_${index}_field_${field_index}" last_selected_value="2">
|
||||
%for option_index, option in enumerate(field['selectlist']):
|
||||
%if option == sample_values[field_index]:
|
||||
<option value="${option}" selected>${option}</option>
|
||||
%else:
|
||||
<option value="${option}">${option}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
%elif field['type'] == 'WorkflowField':
|
||||
<select name="sample_${index}_field_${field_index}">
|
||||
%if str(sample_values[field_index]) == 'none':
|
||||
<option value="none" selected>Select one</option>
|
||||
%else:
|
||||
<option value="none">Select one</option>
|
||||
%endif
|
||||
%for option_index, option in enumerate(request.user.stored_workflows):
|
||||
%if not option.deleted:
|
||||
%if str(option.id) == str(sample_values[field_index]):
|
||||
<option value="${option.id}" selected>${option.name}</option>
|
||||
%else:
|
||||
<option value="${option.id}">${option.name}</option>
|
||||
%endif
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
%elif field['type'] == 'CheckboxField':
|
||||
<input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
|
||||
%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${'('+field['required']+')' }</i>
|
||||
</div>
|
||||
</td>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
|
||||
<td>
|
||||
${sample_name}
|
||||
</td>
|
||||
%for field_index, field in fields_dict.items():
|
||||
<td>
|
||||
%if sample_values[field_index]:
|
||||
%if field['type'] == 'WorkflowField':
|
||||
%if str(sample_values[field_index]) != 'none':
|
||||
<% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
|
||||
<a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a>
|
||||
%endif
|
||||
%else:
|
||||
${sample_values[field_index]}
|
||||
%endif
|
||||
%else:
|
||||
<i>None</i>
|
||||
%endif
|
||||
</td>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="form-row">
|
||||
@@ -351,7 +168,7 @@ $(document).ready(function(){
|
||||
<i>None</i>
|
||||
%else:
|
||||
%if rd['label'] == 'State':
|
||||
<a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
|
||||
<a href="${h.url_for( controller=cntrller, action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
|
||||
%else:
|
||||
${rd['value']}
|
||||
%endif
|
||||
@@ -374,63 +191,8 @@ $(document).ready(function(){
|
||||
|
||||
<br/>
|
||||
|
||||
|
||||
<%def name="render_grid( grid_index, grid_name, fields_dict )">
|
||||
<br/>
|
||||
<div class="msg_list">
|
||||
%if grid_name:
|
||||
<h4 class="msg_head"><u>${grid_name}</u></h4>
|
||||
%else:
|
||||
<h4>Grid ${grid_index}</h4>
|
||||
%endif
|
||||
%if edit_mode == 'False' or len(current_samples) <= len(request.samples):
|
||||
<div class="msg_body">
|
||||
%else:
|
||||
<div class="msg_body2">
|
||||
%endif
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
%for index, field in fields_dict.items():
|
||||
<th>
|
||||
${field['label']}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${field['helptext']}</i>
|
||||
</div>
|
||||
</th>
|
||||
%endfor
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
%>
|
||||
%for sample_index, sample in enumerate(current_samples):
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
|
||||
</tr>
|
||||
%else:
|
||||
<tr>
|
||||
%if sample_index in range(len(request.samples)):
|
||||
${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
|
||||
%else:
|
||||
${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
|
||||
%endif
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
<div class="toolForm">
|
||||
##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests_common', cntrller=cntrller, action='request_page', edit_mode=edit_mode )}" method="post" >
|
||||
<div class="form-row">
|
||||
%if current_samples:
|
||||
## first render the basic info grid
|
||||
@@ -498,7 +260,7 @@ $(document).ready(function(){
|
||||
%endif
|
||||
|
||||
%endif
|
||||
<input type="hidden" name="request_id" value="${request.id}" />
|
||||
<input type="hidden" name="id" value="${trans.security.encode_id(request.id)}" />
|
||||
</form>
|
||||
</div>
|
||||
|
||||
@@ -506,7 +268,7 @@ $(document).ready(function(){
|
||||
|
||||
%if request.unsubmitted():
|
||||
<div class="toolForm">
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
|
||||
<form id="import" name="import" action="${h.url_for( controller='requests_common', action='request_page', edit_mode=edit_mode, request_id=trans.security.encode_id(request.id) )}" enctype="multipart/form-data" method="post" >
|
||||
<div class="form-row">
|
||||
<div class="msg_list">
|
||||
<h4 class="msg_head"><u>Import samples from csv file</u></h4>
|
||||
@@ -521,8 +283,265 @@ $(document).ready(function(){
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<input type="hidden" name="request_id" value="${request.id}" />
|
||||
## <input type="hidden" name="request_id" value="${request.id}" />
|
||||
</form>
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<%def name="render_grid( grid_index, grid_name, fields_dict )">
|
||||
<br/>
|
||||
<div class="msg_list">
|
||||
%if grid_name:
|
||||
<h4 class="msg_head"><u>${grid_name}</u></h4>
|
||||
%else:
|
||||
<h4>Grid ${grid_index}</h4>
|
||||
%endif
|
||||
%if edit_mode == 'False' or len(current_samples) <= len(request.samples):
|
||||
<div class="msg_body">
|
||||
%else:
|
||||
<div class="msg_body2">
|
||||
%endif
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
%for index, field in fields_dict.items():
|
||||
<th>
|
||||
${field['label']}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${field['helptext']}</i>
|
||||
</div>
|
||||
</th>
|
||||
%endfor
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
%>
|
||||
%for sample_index, sample in enumerate(current_samples):
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
|
||||
</tr>
|
||||
%else:
|
||||
<tr>
|
||||
%if sample_index in range(len(request.samples)):
|
||||
${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
|
||||
%else:
|
||||
${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
|
||||
%endif
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
## This function displays the "Basic Information" grid
|
||||
<%def name="render_basic_info_grid()">
|
||||
<h4>Sample Information</h4>
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Barcode</th>
|
||||
<th>State</th>
|
||||
<th>Data Library</th>
|
||||
<th>Folder</th>
|
||||
%if request.submitted() or request.complete():
|
||||
<th>Dataset(s) Transferred</th>
|
||||
%endif
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
%>
|
||||
%for sample_index, info in enumerate(current_samples):
|
||||
<%
|
||||
if sample_index in range(len(request.samples)):
|
||||
sample = request.samples[sample_index]
|
||||
else:
|
||||
sample = None
|
||||
%>
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
${show_basic_info_form( sample_index, sample, info )}
|
||||
</tr>
|
||||
%else:
|
||||
<tr>
|
||||
%if sample_index in range(len(request.samples)):
|
||||
<td>${info['name']}</td>
|
||||
<td>${info['barcode']}</td>
|
||||
%if sample.request.unsubmitted():
|
||||
<td>Unsubmitted</td>
|
||||
%else:
|
||||
<td id="sampleState-${sample.id}">${render_sample_state( cntrller, sample )}</td>
|
||||
%endif
|
||||
%if info['library']:
|
||||
<td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if info['folder']:
|
||||
<td>${info['folder'].name}</td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if request.submitted() or request.complete():
|
||||
<td id="sampleDatasets-${sample.id}">
|
||||
${render_sample_datasets( cntrller, sample )}
|
||||
</td>
|
||||
%endif
|
||||
|
||||
|
||||
%else:
|
||||
${show_basic_info_form( sample_index, sample, info )}
|
||||
%endif
|
||||
%if request.unsubmitted() or request.rejected():
|
||||
<td>
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', cntrller=cntrller, action='delete_sample', request_id=request.id, sample_id=sample_index )}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
%endif
|
||||
%endif
|
||||
</td>
|
||||
%endif
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</%def>
|
||||
|
||||
<%def name="show_basic_info_form( sample_index, sample, info )">
|
||||
<td>
|
||||
<input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${' (required)' }</i>
|
||||
</div>
|
||||
</td>
|
||||
%if cntrller == 'requests':
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<td></td>
|
||||
%else:
|
||||
<td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%elif cntrller == 'requests_admin':
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<td></td>
|
||||
%else:
|
||||
<td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%endif
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<td>Unsubmitted</td>
|
||||
%else:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='sample_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
<td>${info['lib_widget'].get_html()}</td>
|
||||
<td>${info['folder_widget'].get_html()}</td>
|
||||
%if request.submitted() or request.complete():
|
||||
%if sample:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td>
|
||||
%else:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
|
||||
%endif
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
|
||||
<td>
|
||||
${sample_name}
|
||||
</td>
|
||||
%for field_index, field in fields_dict.items():
|
||||
<td>
|
||||
%if sample_values[field_index]:
|
||||
%if field['type'] == 'WorkflowField':
|
||||
%if str(sample_values[field_index]) != 'none':
|
||||
<% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
|
||||
<a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a>
|
||||
%endif
|
||||
%else:
|
||||
${sample_values[field_index]}
|
||||
%endif
|
||||
%else:
|
||||
<i>None</i>
|
||||
%endif
|
||||
</td>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
|
||||
<td>
|
||||
${sample_name}
|
||||
</td>
|
||||
%for field_index, field in fields_dict.items():
|
||||
<td>
|
||||
%if field['type'] == 'TextField':
|
||||
<input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
|
||||
%elif field['type'] == 'SelectField':
|
||||
<select name="sample_${index}_field_${field_index}" last_selected_value="2">
|
||||
%for option_index, option in enumerate(field['selectlist']):
|
||||
%if option == sample_values[field_index]:
|
||||
<option value="${option}" selected>${option}</option>
|
||||
%else:
|
||||
<option value="${option}">${option}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
%elif field['type'] == 'WorkflowField':
|
||||
<select name="sample_${index}_field_${field_index}">
|
||||
%if str(sample_values[field_index]) == 'none':
|
||||
<option value="none" selected>Select one</option>
|
||||
%else:
|
||||
<option value="none">Select one</option>
|
||||
%endif
|
||||
%for option_index, option in enumerate(request.user.stored_workflows):
|
||||
%if not option.deleted:
|
||||
%if str(option.id) == str(sample_values[field_index]):
|
||||
<option value="${option.id}" selected>${option.name}</option>
|
||||
%else:
|
||||
<option value="${option.id}">${option.name}</option>
|
||||
%endif
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
%elif field['type'] == 'CheckboxField':
|
||||
<input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
|
||||
%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${'('+field['required']+')' }</i>
|
||||
</div>
|
||||
</td>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -1,94 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$( function() {
|
||||
$( "select[refresh_on_change='true']").change( function() {
|
||||
var refresh = false;
|
||||
var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
|
||||
if ( refresh_on_change_values ) {
|
||||
refresh_on_change_values = refresh_on_change_values.value.split( ',' );
|
||||
var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
|
||||
for( i= 0; i < refresh_on_change_values.length; i++ ) {
|
||||
if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
|
||||
refresh = true;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
else {
|
||||
refresh = true;
|
||||
}
|
||||
if ( refresh ){
|
||||
$( "#new_request" ).submit();
|
||||
}
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
<%def name="javascripts()">
|
||||
${parent.javascripts()}
|
||||
${h.js("jquery.autocomplete", "autocomplete_tagging" )}
|
||||
</%def>
|
||||
|
||||
<%def name="stylesheets()">
|
||||
${parent.stylesheets()}
|
||||
${h.css( "autocomplete_tagging" )}
|
||||
</%def>
|
||||
|
||||
<br/>
|
||||
<br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Add a new request</div>
|
||||
%if len(select_request_type.options) == 1:
|
||||
There are no request types created for a new request.
|
||||
%else:
|
||||
<div class="toolFormBody">
|
||||
<form name="new_request" id="new_request" action="${h.url_for( controller='requests', action='new', create=True )}" method="post" >
|
||||
<div class="form-row">
|
||||
<label>
|
||||
Select Request Type:
|
||||
</label>
|
||||
${select_request_type.get_html()}
|
||||
</div>
|
||||
|
||||
%if select_request_type.get_selected() != ('Select one', 'none'):
|
||||
%for i, field in enumerate(widgets):
|
||||
<div class="form-row">
|
||||
<label>${field['label']}</label>
|
||||
${field['widget'].get_html()}
|
||||
##%if field['label'] == 'Data library' and new_library:
|
||||
## ${new_library.get_html()}
|
||||
##%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${field['helptext']}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="hidden" name="refresh" value="true" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="create_request_button" value="Save"/>
|
||||
<input type="submit" name="create_request_samples_button" value="Add samples"/>
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
@@ -1,7 +0,0 @@
|
||||
<%def name="render_sample_datasets( sample )">
|
||||
<a href="${h.url_for(controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id))}">${sample.transferred_dataset_files()}/${len(sample.dataset_files)}</a>
|
||||
</%def>
|
||||
|
||||
|
||||
|
||||
${render_sample_datasets( sample )}
|
||||
@@ -1,5 +0,0 @@
|
||||
<%def name="render_sample_state( sample )">
|
||||
<a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
|
||||
</%def>
|
||||
|
||||
${render_sample_state( sample )}
|
||||
@@ -1,86 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$(document).ready(function(){
|
||||
//hide the all of the element with class msg_body
|
||||
$(".msg_body").hide();
|
||||
//toggle the componenet with class msg_body
|
||||
$(".msg_head").click(function(){
|
||||
$(this).next(".msg_body").slideToggle(450);
|
||||
});
|
||||
});
|
||||
</script>
|
||||
<style type="text/css">
|
||||
.msg_head {
|
||||
padding: 0px 0px;
|
||||
cursor: pointer;
|
||||
}
|
||||
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<h2>Data transfer from Sequencer</h2>
|
||||
<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
%if sample.request.submitted() and sample.inprogress_dataset_files():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
|
||||
<span>Refresh this page</span></a>
|
||||
</li>
|
||||
%endif
|
||||
%if sample.library:
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
|
||||
<span>${sample.library.name} Data Library</span></a>
|
||||
</li>
|
||||
%endif
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
<form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
|
||||
<div class="form-row">
|
||||
%if len(dataset_files):
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Dataset File</th>
|
||||
<th>Transfer Status</th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
%for dataset_index, dataset_file in enumerate(dataset_files):
|
||||
${sample_dataset_files( dataset_index, dataset_file[0], dataset_file[1] )}
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
%else:
|
||||
There are no dataset files.
|
||||
%endif
|
||||
</div>
|
||||
</form>
|
||||
</div>
|
||||
|
||||
<%def name="sample_dataset_files( dataset_index, dataset_file, status )">
|
||||
<tr>
|
||||
<td>${dataset_file.split('/')[-1]}</td>
|
||||
<td>
|
||||
%if status == sample.transfer_status.IN_PROGRESS:
|
||||
<i>${status}</i>
|
||||
%else:
|
||||
${status}
|
||||
%endif
|
||||
</td>
|
||||
</tr>
|
||||
</%def>
|
||||
@@ -1,430 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<script type="text/javascript">
|
||||
$( function() {
|
||||
$( "select[refresh_on_change='true']").change( function() {
|
||||
var refresh = false;
|
||||
var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
|
||||
if ( refresh_on_change_values ) {
|
||||
refresh_on_change_values = refresh_on_change_values.value.split( ',' );
|
||||
var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
|
||||
for( i= 0; i < refresh_on_change_values.length; i++ ) {
|
||||
if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
|
||||
refresh = true;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
else {
|
||||
refresh = true;
|
||||
}
|
||||
if ( refresh ){
|
||||
$( "#show_request" ).submit();
|
||||
}
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
<script type="text/javascript">
|
||||
$(document).ready(function(){
|
||||
//hide the all of the element with class msg_body
|
||||
$(".msg_body").hide();
|
||||
//toggle the componenet with class msg_body
|
||||
$(".msg_head").click(function(){
|
||||
$(this).next(".msg_body").slideToggle(450);
|
||||
});
|
||||
});
|
||||
</script>
|
||||
<style type="text/css">
|
||||
.msg_head {
|
||||
padding: 0px 0px;
|
||||
cursor: pointer;
|
||||
}
|
||||
|
||||
}
|
||||
</style>
|
||||
|
||||
%if request.rejected():
|
||||
${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
|
||||
%endif
|
||||
|
||||
<div class="grid-header">
|
||||
<h2>Sequencing Request "${request.name}"</h2>
|
||||
</div>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
%if request.unsubmitted() and request.samples:
|
||||
<li>
|
||||
<a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Submit request</span></a>
|
||||
</li>
|
||||
%endif
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
|
||||
<span>History</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<%def name="show_basic_info_form( sample_index, sample, info )">
|
||||
<td>
|
||||
<input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${' (required)' }</i>
|
||||
</div>
|
||||
</td>
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<td></td>
|
||||
%else:
|
||||
<td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if sample:
|
||||
%if not sample.current_state():
|
||||
<td>Unsubmitted</td>
|
||||
%else:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
<td>${info['lib_widget'].get_html()}</td>
|
||||
<td>${info['folder_widget'].get_html()}</td>
|
||||
%if request.submitted() or request.complete():
|
||||
%if sample:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td>
|
||||
%else:
|
||||
<td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
|
||||
%endif
|
||||
%endif
|
||||
</%def>
|
||||
|
||||
## This function displays the "Basic Information" grid
|
||||
<%def name="render_basic_info_grid()">
|
||||
<h4>Sample Information</h4>
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
<th>Barcode</th>
|
||||
<th>State</th>
|
||||
<th>Data Library</th>
|
||||
<th>Folder</th>
|
||||
%if request.submitted() or request.complete():
|
||||
<th>Dataset(s) Transferred</th>
|
||||
%endif
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
%>
|
||||
%for sample_index, info in enumerate(current_samples):
|
||||
<%
|
||||
if sample_index in range(len(request.samples)):
|
||||
sample = request.samples[sample_index]
|
||||
else:
|
||||
sample = None
|
||||
%>
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
${show_basic_info_form( sample_index, sample, info )}
|
||||
</tr>
|
||||
%else:
|
||||
<tr>
|
||||
%if sample_index in range(len(request.samples)):
|
||||
<td>${info['name']}</td>
|
||||
<td>${info['barcode']}</td>
|
||||
<td>
|
||||
%if sample.current_state():
|
||||
<a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
|
||||
%else:
|
||||
Unsubmitted
|
||||
%endif
|
||||
</td>
|
||||
%if info['library']:
|
||||
<td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if info['folder']:
|
||||
<td>${info['folder'].name}</td>
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
%if request.submitted() or request.complete():
|
||||
<td>
|
||||
<a href="${h.url_for( controller='requests', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
|
||||
</td>
|
||||
%endif
|
||||
|
||||
|
||||
%else:
|
||||
${show_basic_info_form( sample_index, sample, info )}
|
||||
%endif
|
||||
%if request.unsubmitted() or request.rejected():
|
||||
<td>
|
||||
%if sample:
|
||||
%if sample.request.unsubmitted():
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
|
||||
<img src="${h.url_for('/static/images/delete_icon.png')}" />
|
||||
<span></span></a>
|
||||
%endif
|
||||
%endif
|
||||
</td>
|
||||
%endif
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</%def>
|
||||
|
||||
<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
|
||||
<td>
|
||||
${sample_name}
|
||||
</td>
|
||||
%for field_index, field in fields_dict.items():
|
||||
<td>
|
||||
%if field['type'] == 'TextField':
|
||||
<input type="text" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
|
||||
%elif field['type'] == 'SelectField':
|
||||
<select name="sample_${index}_field_${field_index}" last_selected_value="2">
|
||||
%for option_index, option in enumerate(field['selectlist']):
|
||||
%if option == sample_values[field_index]:
|
||||
<option value="${option}" selected>${option}</option>
|
||||
%else:
|
||||
<option value="${option}">${option}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
%elif field['type'] == 'WorkflowField':
|
||||
<select name="sample_${index}_field_${field_index}">
|
||||
%if str(sample_values[field_index]) == 'none':
|
||||
<option value="none" selected>Select one</option>
|
||||
%else:
|
||||
<option value="none">Select one</option>
|
||||
%endif
|
||||
%for option_index, option in enumerate(request.user.stored_workflows):
|
||||
%if not option.deleted:
|
||||
%if str(option.id) == str(sample_values[field_index]):
|
||||
<option value="${option.id}" selected>${option.name}</option>
|
||||
%else:
|
||||
<option value="${option.id}">${option.name}</option>
|
||||
%endif
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
%elif field['type'] == 'CheckboxField':
|
||||
<input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
|
||||
%endif
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${'('+field['required']+')' }</i>
|
||||
</div>
|
||||
</td>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
|
||||
<td>
|
||||
${sample_name}
|
||||
</td>
|
||||
%for field_index, field in fields_dict.items():
|
||||
<td>
|
||||
%if sample_values[field_index]:
|
||||
%if field['type'] == 'WorkflowField':
|
||||
%if str(sample_values[field_index]) != 'none':
|
||||
<% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %>
|
||||
<a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a>
|
||||
%endif
|
||||
%else:
|
||||
${sample_values[field_index]}
|
||||
%endif
|
||||
%else:
|
||||
<i>None</i>
|
||||
%endif
|
||||
|
||||
</td>
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="render_grid( grid_index, grid_name, fields_dict )">
|
||||
<br/>
|
||||
<div class="msg_list">
|
||||
%if grid_name:
|
||||
<h4 class="msg_head"><u>${grid_name}</u></h4>
|
||||
%else:
|
||||
<h4>Grid ${grid_index}</h4>
|
||||
%endif
|
||||
%if edit_mode == 'False' or len(current_samples) <= len(request.samples):
|
||||
<div class="msg_body">
|
||||
%else:
|
||||
<div class="msg_body2">
|
||||
%endif
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Name</th>
|
||||
%for index, field in fields_dict.items():
|
||||
<th>
|
||||
${field['label']}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<i>${field['helptext']}</i>
|
||||
</div>
|
||||
</th>
|
||||
%endfor
|
||||
<th></th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
<%
|
||||
trans.sa_session.refresh( request )
|
||||
%>
|
||||
%for sample_index, sample in enumerate(current_samples):
|
||||
%if edit_mode == 'True':
|
||||
<tr>
|
||||
${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
|
||||
</tr>
|
||||
%else:
|
||||
<tr>
|
||||
%if sample_index in range(len(request.samples)):
|
||||
${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
|
||||
%else:
|
||||
${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
|
||||
%endif
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
<div class="toolForm">
|
||||
<form id="request_details" name="request_details" >
|
||||
<div class="form-row">
|
||||
<div class="msg_list">
|
||||
<h4 class="msg_head"><u>Request Information</u></h4>
|
||||
<div class="msg_body">
|
||||
%for index, rd in enumerate(request_details):
|
||||
<div class="form-row">
|
||||
<label>${rd['label']}</label>
|
||||
%if not rd['value']:
|
||||
<i>None</i>
|
||||
%else:
|
||||
%if rd['label'] == 'State':
|
||||
<a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
|
||||
%else:
|
||||
${rd['value']}
|
||||
%endif
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
%endfor
|
||||
<div class="form-row">
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
|
||||
<span>Edit request details</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
|
||||
<div class="form-row">
|
||||
%if current_samples:
|
||||
## first render the basic info grid
|
||||
${render_basic_info_grid()}
|
||||
## then render the other grid(s)
|
||||
<% trans.sa_session.refresh( request.type.sample_form ) %>
|
||||
%for grid_index, grid_name in enumerate(request.type.sample_form.layout):
|
||||
${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
|
||||
<br/>
|
||||
%endfor
|
||||
%else:
|
||||
<label>There are no samples.</label>
|
||||
%endif
|
||||
</div>
|
||||
%if request.unsubmitted() and edit_mode == 'False':
|
||||
<table class="grid">
|
||||
<tbody>
|
||||
<tr>
|
||||
<div class="form-row">
|
||||
<td>
|
||||
%if current_samples:
|
||||
<label>Copy </label>
|
||||
<input type="integer" name="num_sample_to_copy" value="1" size="3"/>
|
||||
<label>sample(s) from sample</label>
|
||||
${sample_copy.get_html()}
|
||||
%endif
|
||||
<input type="submit" name="add_sample_button" value="Add New"/>
|
||||
</td>
|
||||
<td>
|
||||
%if len(current_samples) and len(current_samples) <= len(request.samples):
|
||||
<input type="submit" name="edit_samples_button" value="Edit samples"/>
|
||||
%endif
|
||||
</td>
|
||||
</div>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
%endif
|
||||
%if request.unsubmitted() and (request.samples or current_samples):
|
||||
<div class="form-row">
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
<input type="hidden" name="refresh" value="true" size="40"/>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save_samples_button" value="Save"/>
|
||||
%if edit_mode == 'True':
|
||||
<input type="submit" name="cancel_changes_button" value="Cancel"/>
|
||||
%endif
|
||||
</div>
|
||||
%endif
|
||||
<input type="hidden" name="request_id" value="${request.id}" />
|
||||
</form>
|
||||
</div>
|
||||
|
||||
|
||||
<br/>
|
||||
%if request.unsubmitted():
|
||||
<div class="toolForm">
|
||||
<form id="show_request" name="show_request" action="${h.url_for( controller='requests', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
|
||||
<div class="form-row">
|
||||
<div class="msg_list">
|
||||
<h4 class="msg_head"><u>Import samples from csv file</u></h4>
|
||||
<div class="msg_body">
|
||||
<input type="file" name="file_data" />
|
||||
<input type="submit" name="import_samples_button" value="Import samples"/>
|
||||
<br/>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
The csv file must be in the following format:<br/>
|
||||
SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<input type="hidden" name="request_id" value="${request.id}" />
|
||||
</form>
|
||||
</div>
|
||||
%endif
|
||||
@@ -1,45 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
<%def name="title()">Events for Sample ${sample_name}</%def>
|
||||
|
||||
|
||||
<h2>Events for Sample "${sample_name}"</h2>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests', action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
|
||||
<div class="toolForm">
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>State</th>
|
||||
<th>Description</th>
|
||||
<th>Updated</th>
|
||||
<th>Comments</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
%for state, desc, updated, comments in events_list:
|
||||
<tr class="libraryRow libraryOrFolderRow" id="libraryRow">
|
||||
<td><b><a>${state}</a></b></td>
|
||||
<td><a>${desc}</a></td>
|
||||
<td><a>${updated}</a></td>
|
||||
<td><a>${comments}</a></td>
|
||||
</tr>
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
+21
-18
@@ -1485,14 +1485,13 @@ class TwillTestCase( unittest.TestCase ):
|
||||
url ="%s&%s=%s" % ( url, key, role_ids_str )
|
||||
self.home()
|
||||
self.visit_url( "%s/%s" % ( self.url, url ) )
|
||||
print url
|
||||
check_str = "Permissions updated for request type '%s'" % request_type_name
|
||||
self.check_page_for_string( check_str )
|
||||
self.home()
|
||||
def create_request( self, request_type_id, name, desc, fields ):
|
||||
self.home()
|
||||
self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % ( self.url,
|
||||
request_type_id ) )
|
||||
self.visit_url( "%s/requests_common/new?select_request_type=%i&refresh=true&cntrller=requests" % ( self.url,
|
||||
request_type_id ) )
|
||||
self.check_page_for_string( 'Add a new request' )
|
||||
tc.fv( "1", "name", name )
|
||||
tc.fv( "1", "desc", desc )
|
||||
@@ -1514,21 +1513,20 @@ class TwillTestCase( unittest.TestCase ):
|
||||
self.check_page_for_string( new_desc )
|
||||
def add_samples( self, request_id, request_name, samples ):
|
||||
self.home()
|
||||
url = "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )
|
||||
url = "%s/requests/list?operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) )
|
||||
self.visit_url( url )
|
||||
self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
|
||||
self.check_page_for_string( 'There are no samples.' )
|
||||
# this redundant stmt below is add so that the second form in
|
||||
# the page gets selected
|
||||
tc.fv( "3", "request_id", request_id )
|
||||
url = ["%s/requests_common/request_page?cntrller=requests&edit_mode=False&id=%s" % ( self.url, self.security.encode_id( request_id ) )]
|
||||
for sample_index, sample in enumerate(samples):
|
||||
tc.submit( "add_sample_button" )
|
||||
self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
|
||||
sample_name, fields = sample
|
||||
tc.fv( "3", "sample_%i_name" % sample_index, sample_name )
|
||||
url.append("sample_%i_name=%s" % (sample_index, sample_name.replace(' ', '+')))
|
||||
for field_index, field_value in enumerate(fields):
|
||||
tc.fv( "3", "sample_%i_field_%i" % ( sample_index, field_index ), field_value )
|
||||
tc.submit( "save_samples_button" )
|
||||
url.append("sample_%i_field_%i=%s" % ( sample_index, field_index , field_value.replace(' ', '+') ))
|
||||
url.append("save_samples_button=Save")
|
||||
self.visit_url('&'.join(url))
|
||||
for sample_name, fields in samples:
|
||||
self.check_page_for_string( sample_name )
|
||||
self.check_page_for_string( 'Unsubmitted' )
|
||||
@@ -1549,19 +1547,24 @@ class TwillTestCase( unittest.TestCase ):
|
||||
tc.fv( "1", "comment", comment )
|
||||
tc.submit( "reject_button" )
|
||||
self.check_page_for_string( 'Request <b>%s</b> has been rejected.' % request_name )
|
||||
self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) ))
|
||||
self.visit_url( "%s/requests/list?&operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) ))
|
||||
self.check_page_for_string( comment )
|
||||
def add_bar_codes( self, request_id, request_name, bar_codes ):
|
||||
def add_bar_codes( self, request_id, request_name, bar_codes, samples ):
|
||||
self.home()
|
||||
self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) )
|
||||
self.check_page_for_string( 'Bar codes for Samples of Request "%s"' % request_name )
|
||||
url = "%s/requests/list?operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) )
|
||||
self.visit_url( url )
|
||||
self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
|
||||
url = ["%s/requests_common/request_page?save_samples_button=Save&cntrller=requests&edit_mode=True&id=%s" % ( self.url, self.security.encode_id( request_id ) )]
|
||||
for index, bar_code in enumerate(bar_codes):
|
||||
tc.fv( "1", "sample_%i_bar_code" % index, bar_code )
|
||||
tc.submit( "save_bar_codes" )
|
||||
self.check_page_for_string( 'Bar codes have been saved for this request' )
|
||||
url.append("sample_%i_barcode=%s" % (index, bar_code ))
|
||||
url.append("sample_%i_name=%s" % (index, samples[index].name.replace(' ', '+') ))
|
||||
self.visit_url('&'.join(url))
|
||||
self.check_page_for_string( 'Changes made to the sample(s) are saved.' )
|
||||
for index, bar_code in enumerate(bar_codes):
|
||||
self.check_page_for_string( bar_code )
|
||||
def change_sample_state( self, sample_name, sample_id, new_state_id, new_state_name, comment='' ):
|
||||
self.home()
|
||||
self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) )
|
||||
self.visit_url( "%s/requests_common/sample_events?cntrller=requests_admin&sample_id=%i" % (self.url, sample_id) )
|
||||
self.check_page_for_string( 'Events for Sample "%s"' % sample_name )
|
||||
tc.fv( "1", "select_state", str(new_state_id) )
|
||||
tc.fv( "1", "comment", comment )
|
||||
|
||||
@@ -189,7 +189,7 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
# Make sure the request_type is not accessible by regular_user2 since regular_user2 does not have Role1.
|
||||
self.logout()
|
||||
self.login( email=regular_user2.email )
|
||||
self.visit_url( '%s/requests/new?create=True&select_request_type=%i' % (self.url, request_type.id) )
|
||||
self.visit_url( '%s/requests_common/new?cntrller=requests&select_request_type=True' % self.url )
|
||||
try:
|
||||
self.check_page_for_string( 'There are no request types created for a new request.' )
|
||||
raise AssertionError, 'The request_type %s is accessible by %s when it should be restricted' % ( request_type.name, regular_user2.email )
|
||||
@@ -304,12 +304,12 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
self.logout()
|
||||
self.login( email='test@bx.psu.edu' )
|
||||
self.check_request_admin_grid(state=request_one.states.SUBMITTED, request_name=request_one.name)
|
||||
self.visit_url( "%s/requests_admin/list?sort=-create_time&operation=show_request&id=%s" \
|
||||
self.visit_url( "%s/requests_admin/list?operation=show&id=%s" \
|
||||
% ( self.url, self.security.encode_id( request_one.id ) ))
|
||||
self.check_page_for_string( 'Sequencing Request "%s"' % request_one.name )
|
||||
# set bar codes for the samples
|
||||
bar_codes = [ '1234567890', '0987654321' ]
|
||||
self.add_bar_codes( request_one.id, request_one.name, bar_codes )
|
||||
self.add_bar_codes( request_one.id, request_one.name, bar_codes, request_one.samples )
|
||||
# change the states of all the samples of this request
|
||||
for sample in request_one.samples:
|
||||
self.change_sample_state( sample.name, sample.id, request_type.states[1].id, request_type.states[1].name )
|
||||
@@ -328,11 +328,12 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
self.login( email='test@bx.psu.edu' )
|
||||
request_name = "RequestTwo"
|
||||
# simulate request creation
|
||||
url_str = '%s/requests_admin/new?create=True&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&library_id=%i&folder_id=%i&refresh=True&field_2=%s&field_0=%s&field_1=%i' \
|
||||
% ( self.url, request_type.id, regular_user.id, request_name, library_one.id, library_one.root_folder.id, "field_2_value", 'option1', user_address.id )
|
||||
url_str = '%s/requests_common/new?cntrller=requests_admin&create_request_button=Save&select_request_type=%i&select_user=%i&name=%s&refresh=True&field_2=%s&field_0=%s&field_1=%i' \
|
||||
% ( self.url, request_type.id, regular_user.id, request_name, "field_2_value", 'option1', user_address.id )
|
||||
print url_str
|
||||
self.home()
|
||||
self.visit_url( url_str )
|
||||
self.check_page_for_string( "The new request named %s has been created" % request_name )
|
||||
self.check_page_for_string( "The new request named <b>%s</b> has been created" % request_name )
|
||||
global request_two
|
||||
request_two = sa_session.query( galaxy.model.Request ) \
|
||||
.filter( and_( galaxy.model.Request.table.c.name==request_name,
|
||||
@@ -370,44 +371,44 @@ class TestFormsAndRequests( TwillTestCase ):
|
||||
# check if the request's state is now set to 'submitted'
|
||||
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_055_reset_data_for_later_test_runs( self ):
|
||||
"""Reseting data to enable later test runs to pass"""
|
||||
# Logged in as admin_user
|
||||
# remove the request_type permissions
|
||||
rt_actions = sa_session.query( galaxy.model.RequestTypePermissions ) \
|
||||
.filter(and_(galaxy.model.RequestTypePermissions.table.c.request_type_id==request_type.id) ) \
|
||||
.order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) ) \
|
||||
.all()
|
||||
for a in rt_actions:
|
||||
sa_session.delete( a )
|
||||
sa_session.flush()
|
||||
##################
|
||||
# Purge all libraries
|
||||
##################
|
||||
for library in [ library_one ]:
|
||||
self.delete_library_item( 'library_admin',
|
||||
self.security.encode_id( library.id ),
|
||||
self.security.encode_id( library.id ),
|
||||
library.name,
|
||||
item_type='library' )
|
||||
self.purge_library( self.security.encode_id( library.id ), library.name )
|
||||
##################
|
||||
# Eliminate all non-private roles
|
||||
##################
|
||||
for role in [ role_one, role_two ]:
|
||||
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
|
||||
sa_session.refresh( role )
|
||||
sa_session.delete( role )
|
||||
sa_session.flush()
|
||||
##################
|
||||
# Eliminate all groups
|
||||
##################
|
||||
for group in [ group_one ]:
|
||||
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 )
|
||||
sa_session.delete( group )
|
||||
sa_session.flush()
|
||||
# def test_055_reset_data_for_later_test_runs( self ):
|
||||
# """Reseting data to enable later test runs to pass"""
|
||||
# # Logged in as admin_user
|
||||
# # remove the request_type permissions
|
||||
# rt_actions = sa_session.query( galaxy.model.RequestTypePermissions ) \
|
||||
# .filter(and_(galaxy.model.RequestTypePermissions.table.c.request_type_id==request_type.id) ) \
|
||||
# .order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) ) \
|
||||
# .all()
|
||||
# for a in rt_actions:
|
||||
# sa_session.delete( a )
|
||||
# sa_session.flush()
|
||||
# ##################
|
||||
# # Purge all libraries
|
||||
# ##################
|
||||
# for library in [ library_one ]:
|
||||
# self.delete_library_item( 'library_admin',
|
||||
# self.security.encode_id( library.id ),
|
||||
# self.security.encode_id( library.id ),
|
||||
# library.name,
|
||||
# item_type='library' )
|
||||
# self.purge_library( self.security.encode_id( library.id ), library.name )
|
||||
# ##################
|
||||
# # Eliminate all non-private roles
|
||||
# ##################
|
||||
# for role in [ role_one, role_two ]:
|
||||
# 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
|
||||
# sa_session.refresh( role )
|
||||
# sa_session.delete( role )
|
||||
# sa_session.flush()
|
||||
# ##################
|
||||
# # Eliminate all groups
|
||||
# ##################
|
||||
# for group in [ group_one ]:
|
||||
# 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 )
|
||||
# sa_session.delete( group )
|
||||
# sa_session.flush()
|
||||
|
||||
Reference in New Issue
Block a user