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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fix sample tracking to correctly import samples from a csv file.
This commit is contained in:
Greg Von Kuster
@@ -826,7 +826,9 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd )
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if params.get( 'import_samples_button', False ):
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# Import sample field values from a csv file
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return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd )
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# TODO: should this be a mapper?
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workflows = [ w.latest_workflow for w in trans.user.stored_workflows if not w.deleted ]
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return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, workflows, **kwd )
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elif params.get( 'add_sample_button', False ):
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return self.add_sample( trans, cntrller, request_id, **kwd )
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elif params.get( 'save_samples_button', False ):
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@@ -905,17 +907,17 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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folder_id=folder_id,
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**kwd )
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history_select_field = self.__build_history_select_field( trans=trans,
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user=request.user,
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sample_index=len( displayable_sample_widgets ),
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history_id=history_id,
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**kwd)
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user=request.user,
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sample_index=len( displayable_sample_widgets ),
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history_id=history_id,
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**kwd )
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workflow_select_field = self.__build_workflow_select_field( trans=trans,
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user=request.user,
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request=request,
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sample_index=len( displayable_sample_widgets ),
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workflow_id=workflow_id,
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history_id=history_id,
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**kwd)
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user=request.user,
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request=request,
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sample_index=len( displayable_sample_widgets ),
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workflow_id=workflow_id,
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history_id=history_id,
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**kwd )
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# Append the new sample to the current list of samples for the request
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displayable_sample_widgets.append( dict( id=None,
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name=name,
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@@ -1045,47 +1047,99 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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transfer_status=transfer_status,
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message=message,
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status=status )
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def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ):
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def __import_samples( self, trans, cntrller, request, displayable_sample_widgets, libraries, workflows, **kwd ):
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"""
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Reads the samples csv file and imports all the samples. The format of the csv file is:
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SampleName,DataLibrary,DataLibraryFolder,Field1,Field2....
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SampleName,DataLibraryName,DataLibraryFolderName,HistoryName,WorkflowName,FieldValue1,FieldValue2...
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"""
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params = util.Params( kwd )
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current_user_roles = trans.get_current_user_roles()
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is_admin = trans.user_is_admin() and cntrller == 'requests_admin'
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file_obj = params.get( 'file_data', '' )
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try:
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reader = csv.reader( file_obj.file )
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for row in reader:
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library_id = None
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library = None
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folder_id = None
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# FIXME: this is bad - what happens when multiple libraries have the same name??
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lib = trans.sa_session.query( trans.model.Library ) \
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.filter( and_( trans.model.Library.table.c.name==row[1],
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trans.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.model.LibraryFolder ) \
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.filter( and_( trans.model.LibraryFolder.table.c.name==row[2],
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trans.model.LibraryFolder.table.c.deleted==False ) ) \
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.first()
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folder = None
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history_id = None
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history = None
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workflow_id = None
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workflow = None
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# Get the library
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library = trans.sa_session.query( trans.model.Library ) \
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.filter( and_( trans.model.Library.table.c.name==row[1],
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trans.model.Library.table.c.deleted==False ) ) \
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.first()
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if library:
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# Get the folder
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for folder in trans.sa_session.query( trans.model.LibraryFolder ) \
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.filter( and_( trans.model.LibraryFolder.table.c.name==row[2],
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trans.model.LibraryFolder.table.c.deleted==False ) ):
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if folder.parent_library == library:
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break
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if folder:
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library_id = lib.id
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folder_id = folder.id
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library_id = trans.security.encode_id( library.id )
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folder_id = trans.security.encode_id( folder.id )
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library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans,
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request.user,
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len( displayable_sample_widgets ),
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len( displayable_sample_widgets ),
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libraries,
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None,
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library_id,
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folder_id,
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**kwd )
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# Get the history
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history = trans.sa_session.query( trans.model.History ) \
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.filter( and_( trans.model.History.table.c.name==row[3],
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trans.model.History.table.c.deleted==False,
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trans.model.History.user_id == trans.user.id ) ) \
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.first()
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if history:
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history_id = trans.security.encode_id( history.id )
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else:
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history_id = 'none'
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history_select_field = self.__build_history_select_field( trans=trans,
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user=request.user,
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sample_index=len( displayable_sample_widgets ),
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history_id=history_id )
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# Get the workflow
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workflow = trans.sa_session.query( trans.model.StoredWorkflow ) \
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.filter( and_( trans.model.StoredWorkflow.table.c.name==row[4],
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trans.model.StoredWorkflow.table.c.deleted==False,
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trans.model.StoredWorkflow.user_id == trans.user.id ) ) \
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.first()
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if workflow:
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workflow_id = trans.security.encode_id( workflow.id )
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else:
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workflow_id = 'none'
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workflow_select_field = self.__build_workflow_select_field( trans=trans,
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user=request.user,
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request=request,
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sample_index=len( displayable_sample_widgets ),
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workflow_id=workflow_id,
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history_id=history_id )
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field_values = {}
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field_names = row[5:]
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for field_name in field_names:
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field_values[ field_name ] = ''
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displayable_sample_widgets.append( dict( id=None,
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name=row[0],
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name=row[0],
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bar_code='',
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library=None,
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folder=None,
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library=library,
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library_id=library_id,
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library_select_field=library_select_field,
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folder=folder,
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folder_id=folder_id,
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folder_select_field=folder_select_field,
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field_values=row[3:] ) )
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history=history,
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history_id=history_id,
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history_select_field=history_select_field,
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workflow=workflow,
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workflow_id=workflow_id,
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workflow_select_field=workflow_select_field,
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field_values=field_values ) )
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except Exception, e:
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if str( e ) == "'unicode' object has no attribute 'file'":
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message = "Select a file"
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@@ -1488,7 +1542,7 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
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library_select_field=library_select_field,
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folder_select_field=folder_select_field,
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history_select_field=history_select_field,
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workflow_select_field=workflow_select_field, ) )
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workflow_select_field=workflow_select_field ) )
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# There may be additional new samples on the form that have not yet been associated with the request.
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# TODO: factor this code so it is not duplicating what's above.
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index = len( samples )
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@@ -269,9 +269,6 @@ class RepositoryController( BaseController, ItemRatings ):
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category_ids = util.listify( params.get( 'category_id', '' ) )
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selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
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if params.get( 'create_repository_button', False ):
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# TODOS:
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# 1. Make sure we can update the version column in the repository table when new change set are pushed.
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# If it's triclky, eliminate the column.
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error = False
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message = self.__validate_repository_name( name, trans.user )
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if message:
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@@ -61,7 +61,7 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)}
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<form id="add_samples" name="add_samples" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" method="post">
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%if displayable_sample_widgets:
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<%
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grid_header = '<h3>Add Samples to Sequencing Request "%s"</h3>' % request.name
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grid_header = '<h3>Add samples to sequencing request "%s"</h3>' % request.name
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%>
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${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header )}
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<div class="toolParamHelp" style="clear: both;">
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@@ -89,8 +89,6 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)}
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%endif
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<p/>
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<div class="form-row">
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## hidden element to make twill work.
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## Greg will fix this
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<input type="hidden" name="twill" value=""/>
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%if ( request.samples or displayable_sample_widgets ) and len( displayable_sample_widgets ) > len( request.samples ):
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<input type="submit" name="add_sample_button" value="Add sample" />
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@@ -111,22 +109,19 @@ ${render_samples_messages(request, is_admin, is_submitted, message, status)}
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</div>
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%if is_unsubmitted:
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<p/>
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##<div class="toolForm">
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##<div class="toolFormTitle">Import samples from csv file</div>
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<h4><img src="/static/images/silk/resultset_next.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/> Import samples from csv file</h4>
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<div style="display:none;">
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<div class="toolFormBody">
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<form id="import" name="import" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" >
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<div class="form-row">
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<input type="file" name="file_data" />
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<input type="submit" name="import_samples_button" value="Import samples"/>
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<div class="toolParamHelp" style="clear: both;">
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The csv file must be in the following format:<br/>
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SampleName,DataLibrary,DataLibraryFolder,FieldValue1,FieldValue2...
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</div>
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<h4><img src="/static/images/silk/resultset_next.png" alt="Hide" onclick="showContent(this);" style="cursor:pointer;"/>Import samples from csv file</h4>
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<div style="display:none;">
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<div class="toolFormBody">
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<form id="import" name="import" action="${h.url_for( controller='requests_common', action='add_samples', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}" enctype="multipart/form-data" method="post" >
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<div class="form-row">
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<input type="file" name="file_data" />
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<input type="submit" name="import_samples_button" value="Import samples"/>
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<div class="toolParamHelp" style="clear: both;">
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The csv file must be in the following format:<br/>
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SampleName,DataLibraryName,DataLibraryFolderName,HistoryName,WorkflowName,FieldValue1,FieldValue2...
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</div>
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</form>
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</div>
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</div>
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</form>
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</div>
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##</div>
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</div>
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%endif
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@@ -465,7 +465,7 @@ class TestFormsAndSampleTracking( TwillTestCase ):
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request_id=self.security.encode_id( request1.id ),
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sample_value_tuples=sample_value_tuples,
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folder_options=folder_options,
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strings_displayed=[ 'Add Samples to Sequencing Request "%s"' % request1.name,
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strings_displayed=[ 'Add samples to sequencing request "%s"' % request1.name,
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'<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field
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strings_displayed_after_submit=strings_displayed_after_submit )
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# check the new sample field values on the request page
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@@ -704,7 +704,7 @@ class TestFormsAndSampleTracking( TwillTestCase ):
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self.add_samples( cntrller='requests_admin',
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request_id=self.security.encode_id( request2.id ),
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sample_value_tuples=sample_value_tuples,
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strings_displayed=[ 'Add Samples to Sequencing Request "%s"' % request2.name,
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strings_displayed=[ 'Add samples to sequencing request "%s"' % request2.name,
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'<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field
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strings_displayed_after_submit=strings_displayed_after_submit )
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# Submit the request
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@@ -869,6 +869,7 @@ class TestFormsAndSampleTracking( TwillTestCase ):
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sample1_dataset.transfer_status.NOT_STARTED ]
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self.view_sample_dataset( sample_dataset_id=self.security.encode_id( sample1_dataset.id ),
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strings_displayed=strings_displayed )
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'''
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def test_999_reset_data_for_later_test_runs( self ):
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"""Reseting data to enable later test runs to pass"""
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# Logged in as admin_user
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@@ -934,3 +935,4 @@ class TestFormsAndSampleTracking( TwillTestCase ):
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# Manually delete the group from the database
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refresh( group )
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delete_obj( group )
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'''
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