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Added a new updater for number of sample datasets. The number of sample datasets now updates automatically.

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The sample states now gets updated only when barcodes are associated with them.
Fixed rename dataset bug for AB Solid external service.
This commit is contained in:
Ramkrishna Chakrabarty
2011-01-14 15:09:43 -05:00
parent a3ed7733a6
commit ba0e5491ae
10 changed files with 114 additions and 22 deletions
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external_service_types/applied_biosystems_solid.xml
+1 -2
View File
@@ -3,8 +3,7 @@
<version>3</version>
<data_transfer_settings>
<data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password'
data_location='data_location' rename_dataset='rename_dataset' />
<data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location' rename_dataset='rename_dataset' />
</data_transfer_settings>
<run_details>
external_service_types/simple_unknown_sequencer.xml
+1 -2
View File
@@ -7,8 +7,7 @@ This is only for backward compatibility
<description></description>
<version></version>
<data_transfer_settings>
<data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password'
data_location='data_location' rename_dataset='rename_dataset' />
<data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location'/>
</data_transfer_settings>
<form type="external_service" name="Simple unknown sequencer form" description="">
<fields>
lib/galaxy/model/__init__.py
+16 -7
View File
@@ -1717,6 +1717,14 @@ class Request( object, APIItem ):
if not sample.library:
samples.append( sample )
return samples
@property
def samples_with_bar_code( self ):
# Return all samples that have associated bar code
samples = []
for sample in self.samples:
if sample.bar_code:
samples.append( sample )
return samples
def send_email_notification( self, trans, common_state, final_state=False ):
# Check if an email notification is configured to be sent when the samples
# are in this state
@@ -1804,18 +1812,19 @@ class ExternalService( object ):
def get_external_service_type( self, trans ):
return trans.app.external_service_types.all_external_service_types[ self.external_service_type_id ]
def load_data_transfer_settings( self, trans ):
trans.app.external_service_types.reload( self.external_service_type_id )
self.data_transfer = {}
external_service_type = self.get_external_service_type( trans )
for data_transfer_type, data_transfer in external_service_type.data_transfer.items():
for data_transfer_type, data_transfer_obj in external_service_type.data_transfer.items():
if data_transfer_type == self.data_transfer_types.SCP:
scp_configs = {}
automatic_transfer = self.form_values.content.get( data_transfer.config.get( 'automatic_transfer', 'false' ), 'false' )
automatic_transfer = self.form_values.content.get( data_transfer_obj.config.get( 'automatic_transfer', 'false' ), 'false' )
scp_configs[ 'automatic_transfer' ] = util.string_as_bool( automatic_transfer )
scp_configs[ 'host' ] = self.form_values.content.get( data_transfer.config.get( 'host', '' ), '' )
scp_configs[ 'user_name' ] = self.form_values.content.get( data_transfer.config.get( 'user_name', '' ), '' )
scp_configs[ 'password' ] = self.form_values.content.get( data_transfer.config.get( 'password', '' ), '' )
scp_configs[ 'data_location' ] = self.form_values.content.get( data_transfer.config.get( 'data_location', '' ), '' )
scp_configs[ 'rename_dataset' ] = self.form_values.content.get( data_transfer.config.get( 'rename_dataset', '' ), '' )
scp_configs[ 'host' ] = self.form_values.content.get( data_transfer_obj.config.get( 'host', '' ), '' )
scp_configs[ 'user_name' ] = self.form_values.content.get( data_transfer_obj.config.get( 'user_name', '' ), '' )
scp_configs[ 'password' ] = self.form_values.content.get( data_transfer_obj.config.get( 'password', '' ), '' )
scp_configs[ 'data_location' ] = self.form_values.content.get( data_transfer_obj.config.get( 'data_location', '' ), '' )
scp_configs[ 'rename_dataset' ] = self.form_values.content.get( data_transfer_obj.config.get( 'rename_dataset', '' ), '' )
self.data_transfer[ self.data_transfer_types.SCP ] = scp_configs
def populate_actions( self, trans, item, param_dict=None ):
return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict )
lib/galaxy/sample_tracking/data_transfer.py
+11 -6
View File
@@ -2,7 +2,6 @@ import logging, sys
class DataTransferFactory( object ):
type = None
config = {}
def parse( self ):
pass
@@ -11,14 +10,20 @@ class ScpDataTransferFactory( DataTransferFactory ):
def __init__( self ):
pass
def parse( self, config_file, elem ):
self.config = {}
# TODO: The 'automatic_transfer' setting is for future use. If set to True, we will need to
# ensure the sample has an associated destination data library before it moves to a certain state
# ( e.g., Run started ).
self.config[ 'automatic_transfer' ] = elem.get( 'automatic_transfer' )
self.config[ 'host' ] = elem.get( 'host' )
self.config[ 'user_name' ] = elem.get( 'user_name' )
self.config[ 'password' ] = elem.get( 'password' )
self.config[ 'data_location' ] = elem.get( 'data_location' )
self.config['automatic_transfer'] = elem.get( 'automatic_transfer' )
self.config['host'] = elem.get( 'host' )
self.config['user_name'] = elem.get( 'user_name' )
self.config['password'] = elem.get( 'password' )
self.config['data_location'] = elem.get( 'data_location' )
# 'rename_dataset' is optional and it may not be defined in all external types
# It is only used is AB SOLiD external service type for now
rename_dataset = elem.get( 'rename_dataset', None )
if rename_dataset:
self.config['rename_dataset'] = rename_dataset
# Validate
for name, value in self.config.items():
assert value, "'%s' attribute missing in 'data_transfer' element of type 'scp' in external_service_type xml config file: '%s'." % ( name, config_file )
lib/galaxy/sample_tracking/external_service_types.py
+1
View File
@@ -60,6 +60,7 @@ class ExternalServiceType( object ):
self.config_file = external_service_type_xml_config
self.parse( root )
self.visible = visible
root.clear()
def parse( self, root ):
# Get the name
self.name = root.get( "name" )
lib/galaxy/web/controllers/requests_admin.py
+2 -1
View File
@@ -387,7 +387,7 @@ class RequestsAdmin( BaseController, UsesFormDefinitions ):
kwd[ 'message' ] = message
del kwd[ 'select_datasets_to_transfer_button' ]
handle_error( **kwd )
if sample in sample.request.samples_without_library_destinations:
if not sample.library:
# Display an error if a sample has been selected that
# has not yet been associated with a destination library.
message = 'Select a target data library and folder for the sample before selecting the datasets.'
@@ -487,6 +487,7 @@ class RequestsAdmin( BaseController, UsesFormDefinitions ):
status=status,
message=message ) )
def __save_sample_datasets( self, trans, sample, selected_datasets_to_transfer, external_service ):
external_service.load_data_transfer_settings( trans )
scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_types.SCP ]
sample_dataset_file_names = []
if selected_datasets_to_transfer:
lib/galaxy/web/controllers/requests_common.py
+18 -1
View File
@@ -107,12 +107,29 @@ class RequestsCommon( BaseController, UsesFormDefinitions ):
sample = trans.sa_session.query( self.app.model.Sample ).get( id )
if sample.state.name != state:
rval[ id ] = { "state": sample.state.name,
"datasets": len( sample.datasets ),
"html_state": unicode( trans.fill_template( "requests/common/sample_state.mako",
sample=sample),
'utf-8' ) }
return rval
@web.json
def sample_datasets_updates( self, trans, ids=None, datasets=None ):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
# Create new HTML for any that have changed
rval = {}
if ids is not None and datasets is not None:
ids = map( int, ids.split( "," ) )
number_of_datasets_list = map(int, datasets.split( "," ) )
for id, number_of_datasets in zip( ids, number_of_datasets_list ):
sample = trans.sa_session.query( self.app.model.Sample ).get( id )
if len(sample.datasets) != number_of_datasets:
rval[ id ] = { "datasets": len( sample.datasets ),
"html_datasets": unicode( trans.fill_template( "requests/common/sample_datasets.mako",
sample=sample),
'utf-8' ) }
return rval
@web.json
def dataset_transfer_status_updates( self, trans, ids=None, transfer_status_list=None ):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
templates/requests/common/common.mako
+50 -2
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@@ -98,7 +98,7 @@
data: { ids: ids.join( "," ), states: states.join( "," ) },
success : function ( data ) {
$.each( data, function( id, val ) {
// Replace HTML
// Replace sample state HTML
var cell1 = $("#sampleState-" + id);
cell1.html( val.html_state );
sample_states[ parseInt( id ) ] = val.state;
@@ -113,6 +113,54 @@
};
// Sample Datasets Updater
//
// Looks for changes in the number sample datasets using an async request. Keeps
// calling itself (via setTimeout) until all samples are in a terminal
// state.
var sample_datasets_updater = function ( sample_datasets ) {
// Check if there are any items left to track
var empty = true;
for ( i in sample_datasets ) {
empty = false;
break;
}
if ( ! empty ) {
setTimeout( function() { sample_datasets_updater_callback( sample_datasets ) }, 1000 );
}
};
var sample_datasets_updater_callback = function ( sample_datasets ) {
// Build request data
var ids = []
var datasets = []
$.each( sample_datasets, function ( id, num_of_datasets ) {
ids.push( id );
datasets.push( num_of_datasets );
});
// Make ajax call
$.ajax( {
type: "POST",
url: "${h.url_for( controller='requests_common', action='sample_datasets_updates' )}",
dataType: "json",
data: { ids: ids.join( "," ), datasets: datasets.join( "," ) },
success : function ( data ) {
$.each( data, function( id, val ) {
// Replace sample datasets HTML
var cell2 = $("#sampleDatasets-" + id);
cell2.html( val.html_datasets );
sample_datasets[ parseInt( id ) ] = val.datasets;
});
sample_datasets_updater( sample_datasets );
},
error: function() {
// Just retry, like the old method, should try to be smarter
sample_datasets_updater( sample_datasets );
}
});
};
// Sample Dataset Transfer Status Updater
//
// It is used to update the transfer status on Manage Datasets page for a sample
@@ -392,7 +440,7 @@
## An admin can select the datasets to transfer, while a non-admin can only view what has been selected
%if is_admin:
## This link will direct the admin to a page allowing them to manage datasets.
<a href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
<a id="sampleDatasets-${sample.id}" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${len( sample.datasets )}</a>
%elif sample.datasets:
## Since this is a regular user, only display a link if there is at least 1
## selected dataset for the sample.
templates/requests/common/sample_datasets.mako
+5
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@@ -0,0 +1,5 @@
<%def name="render_sample_datasets( sample )">
${len( sample.datasets )}
</%def>
${render_sample_datasets( sample )}
templates/requests/common/view_request.mako
+9 -1
View File
@@ -144,12 +144,20 @@
${states}
<div style="clear: both"></div>
</div>
%if request.samples and request.is_submitted:
## Sample state updater
%if request.samples and request.is_submitted and request.samples_with_bar_code:
<script type="text/javascript">
// Updater
sample_state_updater( {${ ",".join( [ '"%s" : "%s"' % ( s.id, s.state.name ) for s in request.samples ] ) }});
</script>
%endif
## Number of sample state updater
%if request.samples and request.is_submitted:
<script type="text/javascript">
// Updater
sample_datasets_updater( {${ ",".join( [ '"%s" : "%s"' % ( s.id, len(s.datasets) ) for s in request.samples ] ) }});
</script>
%endif
</div>
</div>
</div>