mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
lims:
- added a new table 'sample_dataset' to store sample datasets & their info when they are transfered from the sequencer - the datasets transfer page now uses a grid to facilitate bulk renaming - bulk renaming possible to fix the problem with the way SOLiD generates datasets - the remote file browser is now independent of a specific sample, the user may select any sample when transferring datasets from the sequencer
This commit is contained in:
Ramkrishna Chakrabarty
@@ -1584,7 +1584,7 @@ class Sample( object ):
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COMPLETE = 'Complete',
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ERROR = 'Error')
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def __init__(self, name=None, desc=None, request=None, form_values=None,
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bar_code=None, library=None, folder=None, dataset_files=None):
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bar_code=None, library=None, folder=None):
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self.name = name
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self.desc = desc
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self.request = request
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@@ -1592,27 +1592,26 @@ class Sample( object ):
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self.bar_code = bar_code
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self.library = library
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self.folder = folder
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self.dataset_files = dataset_files
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def current_state(self):
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if self.events:
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return self.events[0].state
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return None
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def untransferred_dataset_files(self):
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count = 0
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for df in self.dataset_files:
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if df['status'] == self.transfer_status.NOT_STARTED:
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for df in self.datasets:
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if df.status == self.transfer_status.NOT_STARTED:
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count = count + 1
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return count
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def inprogress_dataset_files(self):
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count = 0
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for df in self.dataset_files:
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if df['status'] not in [self.transfer_status.NOT_STARTED, self.transfer_status.COMPLETE]:
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for df in self.datasets:
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if df.status not in [self.transfer_status.NOT_STARTED, self.transfer_status.COMPLETE]:
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count = count + 1
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return count
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def transferred_dataset_files(self):
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count = 0
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for df in self.dataset_files:
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if df['status'] == self.transfer_status.COMPLETE:
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for df in self.datasets:
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if df.status == self.transfer_status.COMPLETE:
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count = count + 1
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return count
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def dataset_size(self, filepath):
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@@ -1639,6 +1638,16 @@ class SampleEvent( object ):
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self.state = sample_state
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self.comment = comment
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class SampleDataset( object ):
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def __init__(self, sample=None, name=None, file_path=None,
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status=None, error_msg=None, size=None):
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self.sample = sample
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self.name = name
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self.file_path = file_path
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self.status = status
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self.error_msg = error_msg
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self.size = size
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class UserAddress( object ):
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def __init__(self, user=None, desc=None, name=None, institution=None,
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address=None, city=None, state=None, postal_code=None,
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@@ -574,7 +574,6 @@ Sample.table = Table('sample', metadata,
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Column( "bar_code", TrimmedString( 255 ), index=True ),
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Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
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Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
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Column( "dataset_files", JSONType() ),
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Column( "deleted", Boolean, index=True, default=False ) )
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SampleState.table = Table('sample_state', metadata,
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@@ -593,6 +592,17 @@ SampleEvent.table = Table('sample_event', metadata,
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Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ),
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Column( "comment", TEXT ) )
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SampleDataset.table = Table('sample_dataset', metadata,
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Column( "id", Integer, primary_key=True ),
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Column( "create_time", DateTime, default=now ),
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Column( "update_time", DateTime, default=now, onupdate=now ),
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Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ),
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Column( "name", TrimmedString( 255 ), nullable=False ),
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Column( "file_path", TrimmedString( 255 ), nullable=False ),
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Column( "status", TrimmedString( 255 ), nullable=False ),
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Column( "error_msg", TEXT ),
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Column( "size", TrimmedString( 255 ) ) )
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Page.table = Table( "page", metadata,
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Column( "id", Integer, primary_key=True ),
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Column( "create_time", DateTime, default=now ),
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@@ -792,6 +802,8 @@ assign_mapper( context, Sample, Sample.table,
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properties=dict(
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events=relation( SampleEvent, backref="sample",
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order_by=desc(SampleEvent.table.c.update_time) ),
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datasets=relation( SampleDataset, backref="sample",
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order_by=desc(SampleDataset.table.c.update_time) ),
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values=relation( FormValues,
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primaryjoin=( Sample.table.c.form_values_id == FormValues.table.c.id ) ),
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request=relation( Request,
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@@ -865,6 +877,9 @@ assign_mapper( context, SampleEvent, SampleEvent.table,
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assign_mapper( context, SampleState, SampleState.table,
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properties=None )
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assign_mapper( context, SampleDataset, SampleDataset.table,
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properties=None )
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assign_mapper( context, UserAddress, UserAddress.table,
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properties=dict(
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user=relation( User,
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@@ -146,7 +146,7 @@ class RequestsGrid( grids.Grid ):
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#
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# ---- Request Type Gridr ------------------------------------------------------
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# ---- Request Type Grid ------------------------------------------------------
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#
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class RequestTypeGrid( grids.Grid ):
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# Custom column types
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@@ -207,6 +207,57 @@ class RequestTypeGrid( grids.Grid ):
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action='create_request_type' ) )
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]
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# ---- Data Transfer Grid ------------------------------------------------------
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#
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class DataTransferGrid( grids.Grid ):
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# Custom column types
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class NameColumn( grids.TextColumn ):
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def get_value(self, trans, grid, sample_dataset):
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return sample_dataset.name
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class SizeColumn( grids.TextColumn ):
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def get_value(self, trans, grid, sample_dataset):
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return sample_dataset.size
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class StatusColumn( grids.TextColumn ):
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def get_value(self, trans, grid, sample_dataset):
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return sample_dataset.status
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# Grid definition
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title = "Sample Datasets"
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template = "admin/requests/datasets_grid.mako"
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model_class = model.SampleDataset
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default_sort_key = "-create_time"
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num_rows_per_page = 50
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preserve_state = True
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use_paging = True
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#default_filter = dict( deleted="False" )
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columns = [
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NameColumn( "Name",
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#key="name",
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model_class=model.SampleDataset,
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link=( lambda item: dict( operation="view", id=item.id ) ),
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attach_popup=True,
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filterable="advanced" ),
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SizeColumn( "Size",
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#key='size',
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model_class=model.SampleDataset,
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filterable="advanced" ),
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StatusColumn( "Status",
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#key='status',
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model_class=model.SampleDataset,
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filterable="advanced" ),
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]
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columns.append( grids.MulticolFilterColumn( "Search",
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cols_to_filter=[ columns[0] ],
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key="free-text-search",
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visible=False,
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filterable="standard" ) )
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operations = [
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grids.GridOperation( "Start Transfer", allow_multiple=True, condition=( lambda item: item.status in [model.Sample.transfer_status.NOT_STARTED] ) ),
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grids.GridOperation( "Rename", allow_multiple=True, allow_popup=False, condition=( lambda item: item.status in [model.Sample.transfer_status.NOT_STARTED] ) ),
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grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.status in [model.Sample.transfer_status.NOT_STARTED] ) ),
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]
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def apply_query_filter( self, trans, query, **kwd ):
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return query.filter_by( sample_id=kwd['sample_id'] )
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#
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# ---- Request Controller ------------------------------------------------------
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#
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@@ -214,6 +265,7 @@ class RequestTypeGrid( grids.Grid ):
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class RequestsAdmin( BaseController ):
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request_grid = RequestsGrid()
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requesttype_grid = RequestTypeGrid()
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datatx_grid = DataTransferGrid()
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@web.expose
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@@ -280,11 +332,11 @@ class RequestsAdmin( BaseController ):
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# Avoid caching
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trans.response.headers['Pragma'] = 'no-cache'
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trans.response.headers['Expires'] = '0'
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sample = trans.sa_session.query( self.app.model.Sample ).get( int(id) )
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datatx_info = sample.request.type.datatx_info
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request = trans.sa_session.query( self.app.model.Request ).get( int(id) )
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datatx_info = request.type.datatx_info
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cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( datatx_info['username'],
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datatx_info['host'],
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folder_path )
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datatx_info['host'],
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folder_path )
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output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n',
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pexpect.TIMEOUT:print_ticks},
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timeout=10)
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@@ -297,8 +349,8 @@ class RequestsAdmin( BaseController ):
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# Avoid caching
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trans.response.headers['Pragma'] = 'no-cache'
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trans.response.headers['Expires'] = '0'
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sample = trans.sa_session.query( self.app.model.Sample ).get( int(id) )
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return self.__get_files(trans, sample, folder_path)
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request = trans.sa_session.query( self.app.model.Request ).get( int(id) )
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return self.__get_files(trans, request.type, folder_path)
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def __reject_request(self, trans, **kwd):
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try:
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@@ -522,12 +574,120 @@ class RequestsAdmin( BaseController ):
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#
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# Data transfer from sequencer
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#
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@web.expose
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@web.require_admin
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def manage_datasets( self, trans, **kwd ):
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if 'operation' in kwd:
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operation = kwd['operation'].lower()
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if not kwd.get( 'id', None ):
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='list',
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status='error',
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message="Invalid sample dataset ID") )
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if operation == "view":
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sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(kwd['id']) )
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return trans.fill_template( '/admin/requests/dataset.mako',
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sample=sample_dataset.sample,
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sample_dataset=sample_dataset)
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def __get_files(self, trans, sample, folder_path):
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elif operation == "delete":
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id_list = util.listify( kwd['id'] )
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for id in id_list:
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sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) )
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sample_id = sample_dataset.sample_id
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trans.sa_session.delete( sample_dataset )
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trans.sa_session.flush()
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='manage_datasets',
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sample_id=sample_id,
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status='done',
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message="%i dataset(s) have been removed." % len(id_list)) )
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elif operation == "rename":
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id_list = util.listify( kwd['id'] )
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sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id_list[0]) )
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return trans.fill_template( '/admin/requests/rename_datasets.mako',
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sample=sample_dataset.sample,
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id_list=id_list )
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elif operation == "start transfer":
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id_list = util.listify( kwd['id'] )
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sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id_list[0]) )
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self.__start_datatx(trans, sample_dataset.sample, id_list)
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# Render the grid view
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try:
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sample = trans.sa_session.query( trans.app.model.Sample ).get( kwd['sample_id'] )
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except:
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='list',
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status='error',
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message="Invalid sample ID" ) )
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self.datatx_grid.title = 'Datasets of Sample "%s"' % sample.name
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self.datatx_grid.global_actions = [
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grids.GridAction( "Refresh",
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dict( controller='requests_admin',
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action='manage_datasets',
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sample_id=sample.id) ),
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grids.GridAction( "Select Datasets",
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dict(controller='requests_admin',
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action='get_data',
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request_id=sample.request.id,
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folder_path=sample.request.type.datatx_info['data_dir'],
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sample_id=sample.id,
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show_page=True)),
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grids.GridAction( 'Data Library "%s"' % sample.library.name,
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dict(controller='library_common',
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action='browse_library',
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cntrller='library_admin',
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id=trans.security.encode_id( sample.library.id))),
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grids.GridAction( "Browse this request",
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dict( controller='requests_admin',
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action='list',
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operation='show',
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id=trans.security.encode_id(sample.request.id)))]
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return self.datatx_grid( trans, **kwd )
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@web.expose
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@web.require_admin
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def rename_datasets( 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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sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id(kwd['sample_id']))
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except:
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='list',
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status='error',
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message="Invalid sample ID" ) )
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if params.get( 'save_button', False ):
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id_list = util.listify( kwd['id_list'] )
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for id in id_list:
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sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) )
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prepend = util.restore_text( params.get( 'prepend_%i' % sample_dataset.id, '' ) )
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name = util.restore_text( params.get( 'name_%i' % sample_dataset.id, sample_dataset.name ) )
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if prepend == 'None':
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sample_dataset.name = name
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else:
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sample_dataset.name = prepend+'_'+name
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trans.sa_session.add( sample_dataset )
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trans.sa_session.flush()
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return trans.fill_template( '/admin/requests/rename_datasets.mako',
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sample=sample, id_list=id_list,
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message='Changes saved successfully.',
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status='done' )
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='manage_datasets',
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sample_id=sample.id) )
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def __get_files(self, trans, request_type, folder_path):
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'''
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This method retrieves the filenames to be transfer from the remote host.
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'''
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datatx_info = sample.request.type.datatx_info
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datatx_info = request_type.datatx_info
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if not datatx_info['host'] or not datatx_info['username'] or not datatx_info['password']:
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message = "Error in sequencer login information."
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return trans.response.send_redirect( web.url_for( controller='requests_common',
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@@ -555,123 +715,152 @@ class RequestsAdmin( BaseController ):
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return output.splitlines()
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def __get_files_in_dir(self, trans, sample, folder_path):
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tmpfiles = self.__get_files(trans, sample, folder_path)
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for tf in tmpfiles:
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if tf[-1] == os.sep:
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self.__get_files_in_dir(trans, sample, os.path.join(folder_path, tf))
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# def __get_files_in_dir(self, trans, sample, folder_path):
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# tmpfiles = self.__get_files(trans, sample, folder_path)
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# for tf in tmpfiles:
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# if tf[-1] == os.sep:
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# self.__get_files_in_dir(trans, sample, os.path.join(folder_path, tf))
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# else:
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# sample.dataset_files.append([os.path.join(folder_path, tf),
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# sample.transfer_status.NOT_STARTED])
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# trans.sa_session.add( sample )
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# trans.sa_session.flush()
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# return
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def __samples_selectbox(self, trans, request, sample_id=None):
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samples_selectbox = SelectField('sample_id')
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for i, s in enumerate(request.samples):
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if str(s.id) == sample_id:
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samples_selectbox.add_option(s.name, s.id, selected=True)
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else:
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sample.dataset_files.append([os.path.join(folder_path, tf),
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sample.transfer_status.NOT_STARTED])
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trans.sa_session.add( sample )
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trans.sa_session.flush()
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return
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samples_selectbox.add_option(s.name, s.id)
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return samples_selectbox
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@web.expose
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@web.require_admin
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def get_data(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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sample = trans.sa_session.query( trans.app.model.Sample ).get( kwd['sample_id'] )
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request = trans.sa_session.query( trans.app.model.Request ).get( kwd['request_id'] )
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except:
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return trans.response.send_redirect( web.url_for( controller='requests_admin',
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action='list',
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status='error',
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message="Invalid sample ID" ) )
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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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folder_path = util.restore_text( params.get( 'folder_path',
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sample.request.type.datatx_info['data_dir'] ) )
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message="Invalid request ID" ) )
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files_list = util.listify( params.get( 'files_list', '' ) )
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if params.get( 'start_transfer_button', False ) == 'True':
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return self.__start_datatx(trans, sample)
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folder_path = util.restore_text( params.get( 'folder_path',
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request.type.datatx_info['data_dir'] ) )
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sbox = self.__samples_selectbox(trans, request, kwd.get('sample_id', None))
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if not folder_path:
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return trans.fill_template( '/requests/common/get_data.mako',
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cntrller='requests_admin',
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sample=sample, files=[],
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dataset_files=sample.dataset_files,
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return trans.fill_template( '/admin/requests/get_data.mako',
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cntrller='requests_admin', request=request,
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samples_selectbox=sbox, files=[],
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folder_path=folder_path )
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if folder_path[-1] != os.sep:
|
||||
folder_path = folder_path+os.sep
|
||||
if params.get( 'browse_button', False ):
|
||||
if params.get( 'show_page', False ):
|
||||
if kwd.get('sample_id', None):
|
||||
sample = trans.sa_session.query( trans.app.model.Sample ).get( kwd['sample_id'] )
|
||||
if sample.datasets:
|
||||
folder_path = os.path.dirname(sample.datasets[-1].file_path)
|
||||
return trans.fill_template( '/admin/requests/get_data.mako',
|
||||
cntrller='requests_admin', request=request,
|
||||
samples_selectbox=sbox, files=[],
|
||||
folder_path=folder_path,
|
||||
status=status, message=message )
|
||||
elif params.get( 'browse_button', False ):
|
||||
# get the filenames from the remote host
|
||||
files = self.__get_files(trans, sample, folder_path)
|
||||
files = self.__get_files(trans, request.type, folder_path)
|
||||
if folder_path[-1] != os.sep:
|
||||
folder_path += os.sep
|
||||
return trans.fill_template( '/requests/common/get_data.mako',
|
||||
cntrller='requests_admin',
|
||||
sample=sample, files=files,
|
||||
dataset_files=sample.dataset_files,
|
||||
folder_path=folder_path )
|
||||
return trans.fill_template( '/admin/requests/get_data.mako',
|
||||
cntrller='requests_admin', request=request,
|
||||
samples_selectbox=sbox, files=files,
|
||||
folder_path=folder_path,
|
||||
status=status, message=message )
|
||||
elif params.get( 'folder_up', False ):
|
||||
if folder_path[-1] == os.sep:
|
||||
folder_path = os.path.dirname(folder_path[:-1])
|
||||
# get the filenames from the remote host
|
||||
files = self.__get_files(trans, sample, folder_path)
|
||||
files = self.__get_files(trans, request.type, folder_path)
|
||||
if folder_path[-1] != os.sep:
|
||||
folder_path += os.sep
|
||||
return trans.fill_template( '/requests/common/get_data.mako',
|
||||
cntrller='requests_admin',
|
||||
sample=sample, files=files,
|
||||
dataset_files=sample.dataset_files,
|
||||
folder_path=folder_path )
|
||||
return trans.fill_template( '/admin/requests/get_data.mako',
|
||||
cntrller='requests_admin',request=request,
|
||||
samples_selectbox=sbox, files=files,
|
||||
folder_path=folder_path,
|
||||
status=status, message=message )
|
||||
elif params.get( 'open_folder', False ):
|
||||
if len(files_list) == 1:
|
||||
folder_path = os.path.join(folder_path, files_list[0])
|
||||
# get the filenames from the remote host
|
||||
files = self.__get_files(trans, sample, folder_path)
|
||||
files = self.__get_files(trans, request.type, folder_path)
|
||||
if folder_path[-1] != os.sep:
|
||||
folder_path += os.sep
|
||||
return trans.fill_template( '/requests/common/get_data.mako',
|
||||
cntrller='requests_admin',
|
||||
sample=sample, files=files,
|
||||
dataset_files=sample.dataset_files,
|
||||
folder_path=folder_path )
|
||||
elif params.get( 'remove_dataset_button', False ):
|
||||
# get the filenames from the remote host
|
||||
files = self.__get_files(trans, sample, folder_path)
|
||||
dataset_index = int(params.get( 'dataset_index', 0 ))
|
||||
del sample.dataset_files[dataset_index]
|
||||
trans.sa_session.add( sample )
|
||||
trans.sa_session.flush()
|
||||
return trans.fill_template( '/requests/common/get_data.mako',
|
||||
cntrller='requests_admin',
|
||||
sample=sample, files=files,
|
||||
dataset_files=sample.dataset_files,
|
||||
folder_path=folder_path)
|
||||
elif params.get( 'select_files_button', False ):
|
||||
folder_files = []
|
||||
if len(files_list):
|
||||
for f in files_list:
|
||||
filepath = os.path.join(folder_path, f)
|
||||
if f[-1] == os.sep:
|
||||
# the selected item is a folder so transfer all the
|
||||
# folder contents
|
||||
# FIXME
|
||||
#self.__get_files_in_dir(trans, sample, filepath)
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='get_data',
|
||||
sample_id=sample.id,
|
||||
folder_path=folder_path,
|
||||
open_folder=True))
|
||||
else:
|
||||
sample.dataset_files.append(dict(filepath=filepath,
|
||||
status=sample.transfer_status.NOT_STARTED,
|
||||
name=self.__dataset_name(sample, filepath.split('/')[-1]),
|
||||
error_msg='',
|
||||
size=sample.dataset_size(filepath)))
|
||||
trans.sa_session.add( sample )
|
||||
trans.sa_session.flush()
|
||||
return trans.fill_template( '/admin/requests/get_data.mako',
|
||||
cntrller='requests_admin', request=request,
|
||||
samples_selectbox=sbox, files=files,
|
||||
folder_path=folder_path,
|
||||
status=status, message=message )
|
||||
elif params.get( 'select_show_datasets_button', False ):
|
||||
sample = trans.sa_session.query( trans.app.model.Sample ).get( kwd['sample_id'] )
|
||||
retval = self.__save_sample_datasets(trans, sample, files_list, folder_path)
|
||||
if retval: message='The dataset(s) %s have been selected for sample <b>%s</b>' %(str(retval)[1:-1].replace("'", ""), sample.name)
|
||||
else: message = None
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='manage_datasets',
|
||||
sample_id=sample.id,
|
||||
status='done',
|
||||
message=message) )
|
||||
elif params.get( 'select_more_button', False ):
|
||||
sample = trans.sa_session.query( trans.app.model.Sample ).get( kwd['sample_id'] )
|
||||
retval = self.__save_sample_datasets(trans, sample, files_list, folder_path)
|
||||
if retval: message='The dataset(s) %s have been selected for sample <b>%s</b>' %(str(retval)[1:-1].replace("'", ""), sample.name)
|
||||
else: message = None
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='get_data',
|
||||
sample_id=sample.id,
|
||||
request_id=sample.request.id,
|
||||
folder_path=folder_path,
|
||||
open_folder=True))
|
||||
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_common',
|
||||
cntrller='requests_admin' ,
|
||||
action='show_datatx_page',
|
||||
sample_id=trans.security.encode_id(sample.id),
|
||||
folder_path=folder_path))
|
||||
sample_id=sample.id,
|
||||
open_folder=True,
|
||||
status='done',
|
||||
message=message))
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='get_data',
|
||||
request_id=sample.request.id,
|
||||
folder_path=folder_path,
|
||||
show_page=True))
|
||||
|
||||
def __save_sample_datasets(self, trans, sample, files_list, folder_path):
|
||||
files = []
|
||||
if len(files_list):
|
||||
for f in files_list:
|
||||
filepath = os.path.join(folder_path, f)
|
||||
if f[-1] == os.sep:
|
||||
# the selected item is a folder so transfer all the
|
||||
# folder contents
|
||||
# FIXME
|
||||
#self.__get_files_in_dir(trans, sample, filepath)
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='get_data',
|
||||
request=sample.request,
|
||||
folder_path=folder_path,
|
||||
open_folder=True))
|
||||
else:
|
||||
sample_dataset = trans.app.model.SampleDataset( sample=sample,
|
||||
file_path=filepath,
|
||||
status=sample.transfer_status.NOT_STARTED,
|
||||
name=self.__dataset_name(sample, filepath.split('/')[-1]),
|
||||
error_msg='',
|
||||
size=sample.dataset_size(filepath))
|
||||
trans.sa_session.add( sample_dataset )
|
||||
trans.sa_session.flush()
|
||||
files.append(str(sample_dataset.name))
|
||||
return files
|
||||
|
||||
|
||||
def __dataset_name(self, sample, filepath):
|
||||
name = filepath.split('/')[-1]
|
||||
@@ -735,7 +924,7 @@ class RequestsAdmin( BaseController ):
|
||||
trans.sa_session.flush()
|
||||
return datatx_user
|
||||
|
||||
def __send_message(self, trans, datatx_info, sample):
|
||||
def __send_message(self, trans, datatx_info, sample, id_list):
|
||||
'''
|
||||
This method creates the xml message and sends it to the rabbitmq server
|
||||
'''
|
||||
@@ -752,20 +941,20 @@ class RequestsAdmin( BaseController ):
|
||||
</data_transfer>'''
|
||||
dataset_xml = \
|
||||
'''<dataset>
|
||||
<index>%(INDEX)s</index>
|
||||
<dataset_id>%(ID)s</dataset_id>
|
||||
<name>%(NAME)s</name>
|
||||
<file>%(FILE)s</file>
|
||||
</dataset>'''
|
||||
datasets = ''
|
||||
for index, dataset in enumerate(sample.dataset_files):
|
||||
if dataset['status'] == sample.transfer_status.NOT_STARTED:
|
||||
datasets = datasets + dataset_xml % dict(INDEX=str(index),
|
||||
NAME=dataset['name'],
|
||||
FILE=dataset['filepath'])
|
||||
sample.dataset_files[index]['status'] = sample.transfer_status.IN_QUEUE
|
||||
|
||||
trans.sa_session.add( sample )
|
||||
trans.sa_session.flush()
|
||||
for id in id_list:
|
||||
sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) )
|
||||
if sample_dataset.status == sample.transfer_status.NOT_STARTED:
|
||||
datasets = datasets + dataset_xml % dict(ID=str(sample_dataset.id),
|
||||
NAME=sample_dataset.name,
|
||||
FILE=sample_dataset.file_path)
|
||||
sample_dataset.status = sample.transfer_status.IN_QUEUE
|
||||
trans.sa_session.add( sample_dataset )
|
||||
trans.sa_session.flush()
|
||||
data = xml % dict(DATA_HOST=datatx_info['host'],
|
||||
DATA_USER=datatx_info['username'],
|
||||
DATA_PASSWORD=datatx_info['password'],
|
||||
@@ -790,7 +979,7 @@ class RequestsAdmin( BaseController ):
|
||||
chan.close()
|
||||
conn.close()
|
||||
|
||||
def __start_datatx(self, trans, sample):
|
||||
def __start_datatx(self, trans, sample, id_list):
|
||||
# data transfer user
|
||||
datatx_user = self.__setup_datatx_user(trans, sample.library, sample.folder)
|
||||
# validate sequecer information
|
||||
@@ -799,46 +988,19 @@ class RequestsAdmin( BaseController ):
|
||||
not datatx_info['username'] or \
|
||||
not datatx_info['password']:
|
||||
message = "Error in sequencer login information."
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_common',
|
||||
cntrller='requests_admin' ,
|
||||
action='show_datatx_page',
|
||||
sample_id=trans.security.encode_id(sample.id),
|
||||
status='error',
|
||||
message=message))
|
||||
self.__send_message(trans, datatx_info, sample)
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_common',
|
||||
cntrller='requests_admin' ,
|
||||
action='show_datatx_page',
|
||||
sample_id=trans.security.encode_id(sample.id),
|
||||
folder_path=datatx_info['data_dir']))
|
||||
@web.expose
|
||||
@web.require_admin
|
||||
def dataset_details( self, trans, **kwd ):
|
||||
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_admin',
|
||||
action='list',
|
||||
action='manage_datasets',
|
||||
sample_id=sample.id,
|
||||
status='error',
|
||||
message="Invalid sample ID" ) )
|
||||
params = util.Params( kwd )
|
||||
message = util.restore_text( params.get( 'message', '' ) )
|
||||
status = params.get( 'status', 'done' )
|
||||
dataset_index = int( params.get( 'dataset_index', '' ) )
|
||||
if params.get('save', '') == 'Save':
|
||||
sample.dataset_files[dataset_index]['name'] = util.restore_text( params.get( 'name',
|
||||
sample.dataset_files[dataset_index]['name'] ) )
|
||||
trans.sa_session.add( sample )
|
||||
trans.sa_session.flush()
|
||||
status = 'done'
|
||||
message = 'Saved the changes made to the dataset.'
|
||||
return trans.fill_template( '/admin/requests/dataset.mako',
|
||||
sample=sample,
|
||||
dataset_index=dataset_index,
|
||||
message=message,
|
||||
status=status)
|
||||
message=message) )
|
||||
self.__send_message(trans, datatx_info, sample, id_list)
|
||||
message="%i dataset(s) have been queued for transfer from the sequencer. Click on <b>Refresh</b> button above to get the latest transfer status." % len(id_list)
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='manage_datasets',
|
||||
sample_id=sample.id,
|
||||
status='done',
|
||||
message=message) )
|
||||
|
||||
#
|
||||
##
|
||||
#### Request Type Stuff ###################################################
|
||||
##
|
||||
|
||||
@@ -34,7 +34,7 @@ class RequestsCommon( BaseController ):
|
||||
if sample.current_state().name != state:
|
||||
rval[id] = {
|
||||
"state": sample.current_state().name,
|
||||
"datasets": len(sample.dataset_files),
|
||||
"datasets": len(sample.datasets),
|
||||
"html_state": unicode( trans.fill_template( "requests/common/sample_state.mako", sample=sample, cntrller=cntrller ), 'utf-8' ),
|
||||
"html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako", trans=trans, sample=sample, cntrller=cntrller ), 'utf-8' )
|
||||
}
|
||||
@@ -518,7 +518,6 @@ class RequestsCommon( BaseController ):
|
||||
barcode=s.bar_code,
|
||||
library=s.library,
|
||||
folder=s.folder,
|
||||
dataset_files=s.dataset_files,
|
||||
field_values=s.values.content,
|
||||
lib_widget=lib_widget,
|
||||
folder_widget=folder_widget))
|
||||
@@ -530,7 +529,6 @@ class RequestsCommon( BaseController ):
|
||||
barcode='',
|
||||
library=None,
|
||||
folder=None,
|
||||
dataset_files=[],
|
||||
field_values=['' for field in request.type.sample_form.fields],
|
||||
lib_widget=lib_widget,
|
||||
folder_widget=folder_widget))
|
||||
@@ -792,8 +790,7 @@ class RequestsCommon( BaseController ):
|
||||
request, form_values,
|
||||
current_samples[sample_index]['barcode'],
|
||||
current_samples[sample_index]['library'],
|
||||
current_samples[sample_index]['folder'],
|
||||
dataset_files=[])
|
||||
current_samples[sample_index]['folder'])
|
||||
trans.sa_session.add( s )
|
||||
trans.sa_session.flush()
|
||||
|
||||
@@ -1078,12 +1075,17 @@ class RequestsCommon( BaseController ):
|
||||
operation='show',
|
||||
status='error',
|
||||
message="Set a data library and folder for <b>%s</b> to transfer dataset(s)." % sample.name,
|
||||
id=trans.security.encode_id(sample.request.id) ) )
|
||||
id=trans.security.encode_id(sample.request.id) ) )
|
||||
if cntrller == 'requests_admin':
|
||||
return trans.response.send_redirect( web.url_for( controller='requests_admin',
|
||||
action='manage_datasets',
|
||||
sample_id=sample.id) )
|
||||
|
||||
if params.get( 'folder_path', '' ):
|
||||
folder_path = util.restore_text( params.get( 'folder_path', '' ) )
|
||||
else:
|
||||
if len(sample.dataset_files):
|
||||
folder_path = os.path.dirname(sample.dataset_files[-1]['filepath'][:-1])
|
||||
if len(sample.datasets):
|
||||
folder_path = os.path.dirname(sample.datasets[-1]['filepath'][:-1])
|
||||
else:
|
||||
folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') )
|
||||
if folder_path and folder_path[-1] != os.sep:
|
||||
@@ -1094,6 +1096,6 @@ class RequestsCommon( BaseController ):
|
||||
message = 'The sequencer login information is incomplete. Click on the <b>Sequencer information</b> to add login details.'
|
||||
return trans.fill_template( '/requests/common/get_data.mako',
|
||||
cntrller=cntrller, sample=sample,
|
||||
dataset_files=sample.dataset_files,
|
||||
dataset_files=sample.datasets,
|
||||
message=message, status=status, files=[],
|
||||
folder_path=folder_path )
|
||||
|
||||
@@ -70,12 +70,12 @@ class DataTransfer(object):
|
||||
self.config_id_secret = config_id_secret
|
||||
count=0
|
||||
while True:
|
||||
index = self.get_value_index(self.dom, 'index', count)
|
||||
dataset_id = self.get_value_index(self.dom, 'dataset_id', count)
|
||||
file = self.get_value_index(self.dom, 'file', count)
|
||||
name = self.get_value_index(self.dom, 'name', count)
|
||||
if file:
|
||||
self.dataset_files.append(dict(name=name,
|
||||
index=int(index),
|
||||
dataset_id=int(dataset_id),
|
||||
file=file))
|
||||
else:
|
||||
break
|
||||
@@ -149,7 +149,7 @@ class DataTransfer(object):
|
||||
def print_ticks(d):
|
||||
pass
|
||||
for i, df in enumerate(self.dataset_files):
|
||||
self.update_status(Sample.transfer_status.TRANSFERRING, df['index'])
|
||||
self.update_status(Sample.transfer_status.TRANSFERRING, df['dataset_id'])
|
||||
try:
|
||||
cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.username,
|
||||
self.host,
|
||||
@@ -168,7 +168,7 @@ class DataTransfer(object):
|
||||
raise Exception(msg)
|
||||
except Exception, e:
|
||||
msg = traceback.format_exc()
|
||||
self.update_status('Error', df['index'], msg)
|
||||
self.update_status('Error', df['dataset_id'], msg)
|
||||
|
||||
|
||||
def add_to_library(self):
|
||||
@@ -189,29 +189,17 @@ class DataTransfer(object):
|
||||
log.debug(e)
|
||||
self.error_and_exit(str(e))
|
||||
|
||||
def update_status(self, status, dataset_index='All', msg=''):
|
||||
def update_status(self, status, dataset_id='All', msg=''):
|
||||
'''
|
||||
Update the data transfer status for this dataset in the database
|
||||
'''
|
||||
try:
|
||||
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':
|
||||
log.debug('Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str(dataset_id), str(self.sample_id) ) )
|
||||
if dataset_id == 'All':
|
||||
for dataset in self.dataset_files:
|
||||
df[dataset['index']]['status'] = status
|
||||
if status == 'Error':
|
||||
df[dataset['index']]['error_msg'] = msg
|
||||
else:
|
||||
df[dataset['index']]['error_msg'] = ''
|
||||
|
||||
self.galaxydb.set_sample_dataset_status(dataset['dataset_id'], status, msg)
|
||||
else:
|
||||
df[dataset_index]['status'] = status
|
||||
if status == 'Error':
|
||||
df[dataset_index]['error_msg'] = msg
|
||||
else:
|
||||
df[dataset_index]['error_msg'] = ''
|
||||
|
||||
self.galaxydb.set_sample_dataset_files(self.sample_id, to_json_string(df))
|
||||
self.galaxydb.set_sample_dataset_status(dataset_id, status, msg)
|
||||
log.debug('done.')
|
||||
except:
|
||||
log.error(traceback.format_exc())
|
||||
@@ -229,12 +217,12 @@ class DataTransfer(object):
|
||||
rc = rc + node.data
|
||||
return rc
|
||||
|
||||
def get_value_index(self, dom, tag_name, index):
|
||||
def get_value_index(self, dom, tag_name, dataset_id):
|
||||
'''
|
||||
This method extracts the tag value from the xml message
|
||||
'''
|
||||
try:
|
||||
nodelist = dom.getElementsByTagName(tag_name)[index].childNodes
|
||||
nodelist = dom.getElementsByTagName(tag_name)[dataset_id].childNodes
|
||||
except:
|
||||
return None
|
||||
rc = ""
|
||||
|
||||
@@ -28,11 +28,12 @@ class GalaxyDbInterface(object):
|
||||
def __init__(self, dbstr):
|
||||
self.dbstr = dbstr
|
||||
self.db_engine = create_engine(self.dbstr)
|
||||
self.db_engine.echo = False
|
||||
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 )
|
||||
self.sample_table = Table('sample', self.metadata, autoload=True )
|
||||
self.sample_dataset_table = Table('sample_dataset', self.metadata, autoload=True )
|
||||
self.request_table = Table('request', self.metadata, autoload=True )
|
||||
self.request_event_table = Table('request_event', self.metadata, autoload=True )
|
||||
self.state_table = Table('sample_state', self.metadata, autoload=True )
|
||||
@@ -105,7 +106,7 @@ class GalaxyDbInterface(object):
|
||||
create_time=datetime.utcnow(),
|
||||
sample_id=sample_id,
|
||||
sample_state_id=int(new_state_id),
|
||||
comment='bar code scanner')
|
||||
comment='Update by barcode scan')
|
||||
# if all the samples for this request are in the final state
|
||||
# then change the request state to 'Complete'
|
||||
result = select(columns=[self.sample_table.c.id],
|
||||
@@ -126,23 +127,22 @@ class GalaxyDbInterface(object):
|
||||
request_id=self.request_id,
|
||||
state=request_state,
|
||||
comment='All samples of this request have finished processing.')
|
||||
|
||||
def get_sample_dataset_files(self, sample_id):
|
||||
subsubquery = select(columns=[self.sample_table.c.dataset_files],
|
||||
whereclause=self.sample_table.c.id==sample_id)
|
||||
return subsubquery.execute().fetchall()[0][0]
|
||||
|
||||
def set_sample_dataset_files(self, sample_id, value):
|
||||
u = self.sample_table.update(whereclause=self.sample_table.c.id==sample_id)
|
||||
u.execute(dataset_files=value)
|
||||
|
||||
|
||||
def set_sample_dataset_status(self, id, new_status, msg=None):
|
||||
u = self.sample_dataset_table.update(whereclause=self.sample_dataset_table.c.id==int(id))
|
||||
u.execute(status=new_status)
|
||||
if new_status == 'Error':
|
||||
u.execute(error_msg=msg)
|
||||
else:
|
||||
u.execute(error_msg='')
|
||||
return
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
print '''This file should not be run directly. To start the Galaxy AMQP Listener:
|
||||
%sh run_galaxy_listener.sh'''
|
||||
dbstr = 'postgres://postgres:postgres@localhost/galaxy_uft'
|
||||
dbstr = 'postgres://postgres:postgres@localhost/g2'
|
||||
|
||||
parser = optparse.OptionParser()
|
||||
parser.add_option('-n', '--name', help='name of the sample field', dest='name', \
|
||||
|
||||
@@ -12,60 +12,44 @@
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_common', action='show_datatx_page', cntrller='requests_admin', sample_id=trans.security.encode_id(sample.id) )}">
|
||||
<span>Dataset transfer page</span></a>
|
||||
<span>Browse datasets</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Dataset details</div>
|
||||
<div class="toolFormTitle">Dataset Information</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="dataset_details" action="${h.url_for( controller='requests_admin', action='dataset_details', save_changes=True, sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}" method="post" >
|
||||
<%
|
||||
dataset = sample.dataset_files[dataset_index]
|
||||
%>
|
||||
<div class="form-row">
|
||||
<label>Name:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
%if dataset['status'] in [sample.transfer_status.IN_QUEUE, sample.transfer_status.NOT_STARTED]:
|
||||
<input type="text" name="name" value="${dataset['name']}" size="60"/>
|
||||
%else:
|
||||
${dataset['name']}
|
||||
%endif
|
||||
|
||||
${sample_dataset.name}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>File on the Sequencer:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${dataset['filepath']}
|
||||
##<input type="text" name="filepath" value="${dataset['filepath']}" size="100" readonly/>
|
||||
${sample_dataset.file_path}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Size:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${dataset.get('size', 'Unknown')}
|
||||
${sample_dataset.size}
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Transfer status:</label>
|
||||
<div style="float: left; width: 250px; margin-right: 10px;">
|
||||
${dataset['status']}
|
||||
${sample_dataset.status}
|
||||
<br/>
|
||||
%if dataset['status'] == sample.transfer_status.ERROR:
|
||||
${dataset['error_msg']}
|
||||
%if sample_dataset.status == sample.transfer_status.ERROR:
|
||||
${sample_dataset.error_msg}
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%if dataset['status'] in [sample.transfer_status.IN_QUEUE, sample.transfer_status.NOT_STARTED]:
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save" value="Save"/>
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
@@ -0,0 +1,32 @@
|
||||
|
||||
|
||||
|
||||
<%def name="custom_javascripts()">
|
||||
<script type="text/javascript">
|
||||
$("#select-dataset-action-button").bind( "click", function(e) {
|
||||
alert('afdhblvi')
|
||||
$.ajax({
|
||||
url: "${h.url_for( controller='requests_admin', action='remote_file_browser' )}",
|
||||
data: {id: 6},
|
||||
error: function() { alert( "Couldn't create new browser" ) },
|
||||
success: function(form_html) {
|
||||
show_modal("Select file", form_html, {
|
||||
"Cancel": function() { window.location = "${h.url_for( controller='requests_admin', action='list' )}"; },
|
||||
"Continue": function() { $(document).trigger("convert_dbkeys"); continue_fn(); }
|
||||
});
|
||||
$("#new-title").focus();
|
||||
replace_big_select_inputs();
|
||||
}
|
||||
});
|
||||
}
|
||||
</script>
|
||||
</%def>
|
||||
|
||||
<%def name="javascripts()">
|
||||
${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )}
|
||||
${self.custom_javascripts()}
|
||||
${parent.javascripts()}
|
||||
</%def>
|
||||
|
||||
<%inherit file="/grid_base.mako"/>
|
||||
|
||||
@@ -0,0 +1,144 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
|
||||
<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(request_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: request_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(request_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: request_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>
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
<br/>
|
||||
<br/>
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(request.type.id) )}">
|
||||
<span>Sequencer information</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<form name="get_data" id="get_data" action="${h.url_for( controller='requests_admin', cntrller=cntrller, action='get_data', request_id=request.id)}" method="post" >
|
||||
<div class="toolFormTitle">Select files for transfer</div>
|
||||
<div class="toolForm">
|
||||
<div class="form-row">
|
||||
<label>Sample:</label>
|
||||
${samples_selectbox.get_html()}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Select the sample with which you want to associate the dataset(s)
|
||||
</div>
|
||||
<br/>
|
||||
<label>Folder path on the sequencer:</label>
|
||||
<input type="text" name="folder_path" value="${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: 60%; width: 98%; height: 150px; font-size: 100%;" ondblclick="open_folder1(${request.id}, '${folder_path}')" onChange="display_file_details(${request.id}, '${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_show_datasets_button" value="Select & show datasets"/>
|
||||
<input type="submit" name="select_more_button" value="Select more"/>
|
||||
</div>
|
||||
</div>
|
||||
</form>
|
||||
@@ -0,0 +1,66 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
<h3>Rename datasets for Sample "${sample.name}"</h3>
|
||||
<br/>
|
||||
${render_msg('A dataset can be renamed only if its status is "Not Started"', 'ok')}
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=sample.id )}">
|
||||
<span>Browse datasets</span></a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show', id=trans.security.encode_id(sample.request.id) )}">
|
||||
<span>Browse this request</span></a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id(sample.id))}" method="post" >
|
||||
<table class="grid">
|
||||
<thead>
|
||||
<tr>
|
||||
<th>Prepend directory name</th>
|
||||
<th>Name</th>
|
||||
<th>Path on Sequencer</th>
|
||||
</tr>
|
||||
<thead>
|
||||
<tbody>
|
||||
%for id in id_list:
|
||||
<%
|
||||
sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id(id) )
|
||||
import os
|
||||
id = trans.security.decode_id(id)
|
||||
%>
|
||||
%if sample_dataset.status == trans.app.model.Sample.transfer_status.NOT_STARTED:
|
||||
<tr>
|
||||
<td>
|
||||
<select name="prepend_${sample_dataset.id}" last_selected_value="2">
|
||||
<option value="None" selected></option>
|
||||
%for option_index, option in enumerate(sample_dataset.file_path.split(os.sep)[:-1]):
|
||||
%if option.strip():
|
||||
<option value="${option}">${option}</option>
|
||||
%endif
|
||||
%endfor
|
||||
</select>
|
||||
</td>
|
||||
<td>
|
||||
<input type="text" name="name_${sample_dataset.id}" value="${sample_dataset.name}" size="100"/>
|
||||
</td>
|
||||
<td>
|
||||
${sample_dataset.file_path}
|
||||
</td>
|
||||
</tr>
|
||||
%endif
|
||||
%endfor
|
||||
</tbody>
|
||||
</table>
|
||||
<br/>
|
||||
<div class="form-row">
|
||||
<input type="submit" name="save_button" value="Save"/>
|
||||
<input type="submit" name="cancel_button" value="Close"/>
|
||||
</div>
|
||||
</form>
|
||||
@@ -79,6 +79,8 @@
|
||||
class_plural = "Libraries"
|
||||
elif a_class == model.HistoryDatasetAssociation:
|
||||
class_plural = "Datasets"
|
||||
elif a_class == model.SampleDataset:
|
||||
class_plural = "Sample Datasets"
|
||||
elif a_class == model.FormDefinitionCurrent:
|
||||
class_plural = "Forms"
|
||||
else:
|
||||
|
||||
@@ -94,8 +94,7 @@ $(document).ready(function(){
|
||||
</style>
|
||||
|
||||
|
||||
<h2>Data transfer from Sequencer</h2>
|
||||
<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
|
||||
<h2>Datasets of Sample "${sample.name}"</h2>
|
||||
<br/>
|
||||
<br/>
|
||||
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
<%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()}/${len(sample.dataset_files)}</a>
|
||||
<a href="${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.datasets)}</a>
|
||||
</%def>
|
||||
|
||||
|
||||
|
||||
@@ -147,30 +147,29 @@ $(document).ready(function(){
|
||||
</div>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
|
||||
%if request.unsubmitted() and request.samples:
|
||||
<li>
|
||||
<li><a class="action-button" id="seqreq-${request.id}-popup" class="menubutton">Sequencing Request Actions</a></li>
|
||||
<div popupmenu="seqreq-${request.id}-popup">
|
||||
%if request.unsubmitted() and request.samples:
|
||||
<a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller=cntrller, action='list', operation='Submit', id=trans.security.encode_id(request.id) )}">
|
||||
<span>Submit request</span></a>
|
||||
</li>
|
||||
%endif
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
%if request.submitted():
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='reject', id=trans.security.encode_id(request.id))}">
|
||||
<span>Reject request</span></a>
|
||||
</li>
|
||||
<span>Submit</span></a>
|
||||
%endif
|
||||
%endif
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='Edit', id=trans.security.encode_id(request.id))}">
|
||||
<span>Edit</span></a>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='events', id=trans.security.encode_id(request.id) )}">
|
||||
<span>History</span></a>
|
||||
</li>
|
||||
%if cntrller == 'requests_admin' and trans.user_is_admin():
|
||||
%if request.submitted():
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='reject', id=trans.security.encode_id(request.id))}">
|
||||
<span>Reject</span></a>
|
||||
<a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', show_page=True, request_id=request.id)}">
|
||||
<span>Select dataset(s) to transfer</span></a>
|
||||
%endif
|
||||
%endif
|
||||
</div>
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller=cntrller, action='list')}">
|
||||
<span>Browse requests</span></a>
|
||||
</li>
|
||||
|
||||
</ul>
|
||||
|
||||
|
||||
@@ -396,12 +395,21 @@ $(document).ready(function(){
|
||||
<td>${info['name']}</td>
|
||||
<td>${info['barcode']}</td>
|
||||
%if sample.request.unsubmitted():
|
||||
<td>Unsubmitted</td>
|
||||
##<td>Unsubmitted</td>
|
||||
<td>
|
||||
<div id="history-name-container">
|
||||
<div id="history-name" class="tooltip editable-text" title="Click to rename history">Unsubmitted</div>
|
||||
</div>
|
||||
</td>
|
||||
%else:
|
||||
<td id="sampleState-${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 ) )}">${info['library'].name}</a></td>
|
||||
%if cntrller == 'requests':
|
||||
<td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
|
||||
%elif cntrller == 'requests_admin':
|
||||
<td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
|
||||
%endif
|
||||
%else:
|
||||
<td></td>
|
||||
%endif
|
||||
|
||||
Reference in New Issue
Block a user