[galaxy-commits] galaxy-dist commit 667fb4f9cd16: lims: added basic UI framework for operations on multiple samples

8 Sep 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User rc
# Date 1283200417 14400
# Node ID 667fb4f9cd16237bb74b15c13e7ff5f166a89177
# Parent  651228876e99e39af9c2f0cef70f8d60780f2b71
lims: added basic UI framework for operations on multiple samples
- first pass for state change mechanism for multiple samples
- UI enhancements: checkboxes to select samples & selectfield to select specific operation
- removed state change UI for individual samples in the sample_events page

next is selecting library for multiple samples

--- a/scripts/galaxy_messaging/server/galaxyweb_interface.py
+++ b/scripts/galaxy_messaging/server/galaxyweb_interface.py
@@ -106,11 +106,10 @@ class GalaxyWebInterface(object):
         # Encrypt
         return id_cipher.encrypt( s ).encode( 'hex' )
     
-    def update_request_state(self, request_id, sample_id):
+    def update_request_state(self, request_id):
         params = urllib.urlencode(dict( cntrller='requests_admin',
-                                        request_id=request_id,
-                                        sample_id=sample_id))
-        url = self.base_url + "/requests_admin/update_request_state"
+                                        request_id=request_id))
+        url = self.base_url + "/requests_common/update_request_state"
         f = self.opener.open(url, params)
         print url
         print params

--- a/scripts/galaxy_messaging/server/amqp_consumer.py
+++ b/scripts/galaxy_messaging/server/amqp_consumer.py
@@ -108,7 +108,7 @@ def recv_callback(msg):
                                        webconfig.get("data_transfer_user_login_info", "email"),
                                        webconfig.get("data_transfer_user_login_info", "password"),
                                        config.get("app:main", "id_secret"))
-        galaxyweb.update_request_state(galaxydb.get_request_id(sample_id), sample_id)
+        galaxyweb.update_request_state(galaxydb.get_request_id(sample_id))
         galaxyweb.logout()
 
 def main():

--- a/templates/requests/common/sample_events.mako
+++ b/templates/requests/common/sample_events.mako
@@ -45,28 +45,3 @@
         </tbody></table></div>
-%if cntrller == 'requests_admin' and trans.user_is_admin():
-    <div class="toolForm">
-        <div class="toolFormTitle">Change current state</div>
-        <div class="toolFormBody">
-            <form name="event" action="${h.url_for( controller='requests_admin', action='save_state', new=True, sample_id=sample.id)}" method="post" >
-                    %for w in widgets:
-                        <div class="form-row">
-                            <label>
-                                ${w[0]}
-                            </label>
-                            ${w[1].get_html()}
-                            %if w[0] == 'Comments':
-                                <div class="toolParamHelp" style="clear: both;">
-                                    Optional
-                                </div>
-                            %endif
-                        </div>
-                    %endfor
-                <div class="form-row">
-                    <input type="submit" name="add_event_button" value="Save"/>
-                </div>
-            </form>
-        </div>
-    </div>
-%endif

--- a/test/functional/test_forms_and_requests.py
+++ b/test/functional/test_forms_and_requests.py
@@ -301,8 +301,8 @@ class TestFormsAndRequests( TwillTestCas
         self.add_bar_codes( request_one.id, request_one.name, bar_codes, request_one.samples )
         # change the states of all the samples of this request
         for sample in request_one.samples:
-            self.change_sample_state( sample.name, sample.id, request_type.states[1].id, request_type.states[1].name )
-            self.change_sample_state( sample.name, sample.id, request_type.states[2].id, request_type.states[2].name )
+            self.change_sample_state( request_one.id, request_one.name, sample.name, sample.id, request_type.states[1].id, request_type.states[1].name )
+            self.change_sample_state( request_one.id, request_one.name, sample.name, sample.id, request_type.states[2].id, request_type.states[2].name )
         self.home()
         sa_session.refresh( request_one )
         self.logout()

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1629,6 +1629,7 @@ All samples in state:     %(sample_state
             event = trans.app.model.RequestEvent(self, self.state(), comments)
             trans.sa_session.add(event)
             trans.sa_session.flush()
+        return comments
     
 class RequestEvent( object ):
     def __init__(self, request=None, request_state=None, comment=''):
@@ -1651,6 +1652,28 @@ class RequestType( object ):
         self.datatx_info = datatx_info
     def last_state(self):
         return self.states[-1]
+    
+    def change_state_widgets(self, trans, sample=None):
+        if sample:
+            curr_state = sample.current_state()
+        else:
+            curr_state = self.states[0]
+        states_input = SelectField('select_state')
+        for state in self.states:
+            if curr_state.name == state.name:
+                states_input.add_option(state.name, state.id, selected=True)
+            else:
+                states_input.add_option(state.name, state.id)
+        widgets = []
+        if sample:
+            widgets.append(('Select the new state of the sample from the list of possible state(s)',
+                          states_input))
+        else:
+            widgets.append(('Select the new state of the selected sample(s) from the list of possible state(s)',
+                          states_input))
+        widgets.append(('Comments', TextArea('comment')))
+        title = 'Change current state'
+        return widgets, title
         
 class RequestTypePermissions( object ):
     def __init__( self, action, request_type, role ):
@@ -1659,6 +1682,8 @@ class RequestTypePermissions( object ):
         self.role = role
     
 class Sample( object ):
+    bulk_operations = Bunch(CHANGE_STATE = 'Change state', 
+                            SELECT_LIBRARY = 'Select data library and folder')
     transfer_status = Bunch( NOT_STARTED = 'Not started',
                              IN_QUEUE = 'In queue',
                              TRANSFERRING = 'Transferring dataset',

--- a/lib/galaxy/web/controllers/requests_common.py
+++ b/lib/galaxy/web/controllers/requests_common.py
@@ -515,7 +515,7 @@ class RequestsCommon( BaseController, Us
     @web.require_login( "create/submit sequencing requests" )
     def events(self, trans, **kwd):
         params = util.Params( kwd )
-        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        cntrller = params.get( 'cntrller', 'requests'  )
         try:
             request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
         except:
@@ -533,21 +533,63 @@ class RequestsCommon( BaseController, Us
                                     cntrller=cntrller,
                                     events_list=events_list, request=request)
     @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def settings(self, trans, **kwd):
+    @web.require_admin
+    def update_request_state( self, trans, **kwd ):
         params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
         cntrller = params.get( 'cntrller', 'requests'  )
         try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
         except:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID",
+                                                              **kwd) )
+        # check if all the samples of the current request are in the sample state
+        common_state = request.common_state()
+        if not common_state:
+            # if the current request state is complete and one of its samples moved from
+            # the final sample state, then move the request state to In-progress
+            if request.complete():
+                status='done'
+                message = "One or more samples' state moved from the final sample state. Now request in '%s' state" % request.states.SUBMITTED
+                event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, message)
+                trans.sa_session.add( event )
+                trans.sa_session.flush()
+            else:
+                message = ''
+                status = 'ok'
             return trans.response.send_redirect( web.url_for( controller=cntrller,
                                                               action='list',
-                                                              status='error',
-                                                              message="Invalid request ID") )
-        return trans.fill_template( '/requests/common/settings.mako', 
-                                    cntrller=cntrller, request=request)
-        
+                                                              operation='show',
+                                                              id=trans.security.encode_id(request.id),
+                                                              status=status,
+                                                              message=message ) )
+        final_state = False
+        if common_state.id == request.type.last_state().id:
+            # since all the samples are in the final state, change the request state to 'Complete'
+            comments = "All samples of this request are in the last sample state (%s). " % request.type.last_state().name
+            state = request.states.COMPLETE
+            final_state = True
+        else:
+            comments = "All samples are in %s state. " % common_state.name
+            state = request.states.SUBMITTED
+        event = trans.app.model.RequestEvent(request, state, comments)
+        trans.sa_session.add( event )
+        trans.sa_session.flush()
+        # check if an email notification is configured to be sent when the samples 
+        # are in this state
+        retval = request.send_email_notification(trans, common_state, final_state)
+        if retval:
+            message = comments + retval
+        else:
+            message = comments
+        return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                          action='list',
+                                                          operation='show',
+                                                          id=trans.security.encode_id(request.id),
+                                                          status='done',
+                                                          message=message ) )
     @web.expose
     @web.require_login( "create/submit sequencing requests" )
     def show(self, trans, **kwd):
@@ -588,9 +630,10 @@ class RequestsCommon( BaseController, Us
                                         folder_widget=folder_widget))
         return trans.fill_template( '/requests/common/show_request.mako',
                                     cntrller=cntrller,
-                                    request=request,
+                                    request=request, selected_samples=[],
                                     request_details=self.request_details(trans, request.id),
                                     current_samples=current_samples,
+                                    sample_ops=self.__sample_operation_selectbox(trans, request, **kwd),
                                     sample_copy=self.__copy_sample(current_samples), 
                                     details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False'  ) ),
                                     message=message, status=status )
@@ -663,7 +706,7 @@ class RequestsCommon( BaseController, Us
             else:
                 break
         return current_samples, details, edit_mode, libraries
-
+    
     def __library_widgets(self, trans, user, sample_index, libraries, sample=None, lib_id=None, folder_id=None, **kwd):
         '''
         This method creates the data library & folder selectbox for creating &
@@ -736,7 +779,6 @@ class RequestsCommon( BaseController, Us
                 else:
                     folder_widget.add_option(f.name, f.id)
         return lib_widget, folder_widget
-
     def __copy_sample(self, current_samples):
         copy_list = SelectField('copy_sample')
         copy_list.add_option('None', -1, selected=True)  
@@ -744,6 +786,44 @@ class RequestsCommon( BaseController, Us
             copy_list.add_option(s['name'], i)
         return copy_list  
     
+    def __sample_operation_selectbox(self, trans, request, **kwd):
+        params = util.Params( kwd )
+        cntrller = util.restore_text( params.get( 'cntrller', 'requests'  ) )
+        if cntrller == 'requests_admin' and trans.user_is_admin():
+            if request.complete():
+                bulk_operations = [trans.app.model.Sample.bulk_operations.CHANGE_STATE]
+            if request.rejected():
+                bulk_operations = [trans.app.model.Sample.bulk_operations.SELECT_LIBRARY]
+            else:
+                bulk_operations = [s for i, s in trans.app.model.Sample.bulk_operations.items()]
+        else:
+            if request.complete():
+                bulk_operations = []
+            else:
+                bulk_operations = [trans.app.model.Sample.bulk_operations.SELECT_LIBRARY]
+        op_list = SelectField('select_sample_operation', 
+                              refresh_on_change=True, 
+                              refresh_on_change_values=bulk_operations)
+        sel_op = kwd.get('select_sample_operation', 'none')
+        if sel_op == 'none':
+            op_list.add_option('Select operation', 'none', True)
+        else:
+            op_list.add_option('Select operation', 'none')
+        for s in bulk_operations:
+            if s == sel_op:
+                op_list.add_option(s, s, True)
+            else:
+                op_list.add_option(s, s)
+        return op_list
+    
+    def __selected_samples(self, trans, request, **kwd):
+        params = util.Params( kwd )
+        selected_samples = []
+        for s in request.samples:
+            if CheckboxField.is_checked(params.get('select_sample_%i' % s.id, '')):
+                selected_samples.append(s.id)
+        return selected_samples
+
     @web.expose
     @web.require_login( "create/submit sequencing requests" )
     def request_page(self, trans, **kwd):
@@ -760,6 +840,15 @@ class RequestsCommon( BaseController, Us
                                                               message="Invalid request ID") )
         # get the user entered sample details
         current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
+        selected_samples = self.__selected_samples(trans, request, **kwd)
+        sample_ops = self.__sample_operation_selectbox(trans, request,**kwd)
+        if params.get('select_sample_operation', 'none') != 'none' and not len(selected_samples):
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              id=trans.security.encode_id(request.id),
+                                                              status='error',
+                                                              message='Select at least one sample before selecting an operation.' ))
         if params.get('import_samples_button', False) == 'Import samples':
             return self.__import_samples(trans, cntrller, request, current_samples, details, libraries, **kwd)
         elif params.get('add_sample_button', False) == 'Add New':
@@ -805,7 +894,8 @@ class RequestsCommon( BaseController, Us
                                         request_details=self.request_details(trans, request.id),
                                         current_samples=current_samples,
                                         sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
+                                        details=details, selected_samples=selected_samples,
+                                        sample_ops=sample_ops,
                                         edit_mode=edit_mode)
         elif params.get('save_samples_button', False) == 'Save':
             # check for duplicate sample names
@@ -826,11 +916,12 @@ class RequestsCommon( BaseController, Us
             if message:
                 return trans.fill_template( '/requests/common/show_request.mako',
                                             cntrller=cntrller,
-                                            request=request,
+                                            request=request, selected_samples=selected_samples,
                                             request_details=self.request_details(trans, request.id),
                                             current_samples = current_samples,
                                             sample_copy=self.__copy_sample(current_samples), 
                                             details=details, edit_mode=edit_mode,
+                                            sample_ops=sample_ops,
                                             status='error', message=message)
             # save all the new/unsaved samples entered by the user
             if edit_mode == 'False':
@@ -899,10 +990,11 @@ class RequestsCommon( BaseController, Us
             edit_mode = 'True'
             return trans.fill_template( '/requests/common/show_request.mako',
                                         cntrller=cntrller,
-                                        request=request,
+                                        request=request, selected_samples=selected_samples,
                                         request_details=self.request_details(trans, request.id),
                                         current_samples=current_samples,
                                         sample_copy=self.__copy_sample(current_samples), 
+                                        sample_ops=sample_ops,
                                         details=details, libraries=libraries,
                                         edit_mode=edit_mode)
         elif params.get('cancel_changes_button', False) == 'Cancel':
@@ -910,14 +1002,33 @@ class RequestsCommon( BaseController, Us
                                                               action='list',
                                                               operation='show',
                                                               id=trans.security.encode_id(request.id)) )
+        elif params.get('change_state_button', False) == 'Save':
+            comments = util.restore_text( params.comment )
+            selected_state = int( params.select_state )
+            new_state = trans.sa_session.query( trans.app.model.SampleState ).get( selected_state )
+            for sample_id in selected_samples:
+                sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
+                event = trans.app.model.SampleEvent(sample, new_state, comments)
+                trans.sa_session.add( event )
+                trans.sa_session.flush()
+            return trans.response.send_redirect( web.url_for( controller='requests_common',
+                                                              cntrller=cntrller, 
+                                                              action='update_request_state',
+                                                              request_id=request.id ))
+        elif params.get('change_state_button', False) == 'Cancel':
+            return trans.response.send_redirect( web.url_for( controller=cntrller,
+                                                              action='list',
+                                                              operation='show',
+                                                              id=trans.security.encode_id(request.id)) )
         else:
             return trans.fill_template( '/requests/common/show_request.mako',
-                                        cntrller=cntrller,
-                                        request=request,
+                                        cntrller=cntrller, 
+                                        request=request, selected_samples=selected_samples,
                                         request_details=self.request_details(trans, request.id),
                                         current_samples=current_samples,
                                         sample_copy=self.__copy_sample(current_samples), 
                                         details=details, libraries=libraries,
+                                        sample_ops=sample_ops, 
                                         edit_mode=edit_mode, status=status, message=message)
             
     def __import_samples(self, trans, cntrller, request, current_samples, details, libraries, **kwd):
@@ -1014,21 +1125,12 @@ class RequestsCommon( BaseController, Us
             trans.sa_session.delete( s.values )
             trans.sa_session.delete( s )
             trans.sa_session.flush()
-        del current_samples[sample_index]  
         return trans.response.send_redirect( web.url_for( controller=cntrller,
                                                           action='list',
                                                           operation='show',
                                                           id=trans.security.encode_id(request.id),
                                                           status='done',
                                                           message='Sample <b>%s</b> has been deleted.' % sample_name ))
-        return trans.fill_template( '/requests/common/show_request.mako',
-                                    controller=cntrller,
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details=details,
-                                    edit_mode=edit_mode)
     def request_details(self, trans, id):
         '''
         Shows the request details
@@ -1087,11 +1189,10 @@ class RequestsCommon( BaseController, Us
             events_list.append((event.state.name, event.state.desc, 
                                 time_ago(event.update_time), 
                                 event.comment))
-        widgets, title = self.__change_state_widgets(trans, sample)
         return trans.fill_template( '/requests/common/sample_events.mako', 
                                     cntrller=cntrller,
                                     events_list=events_list,
-                                    sample=sample, widgets=widgets, title=title)
+                                    sample=sample)
     def __change_state_widgets(self, trans, sample):
         possible_states = sample.request.type.states 
         curr_state = sample.current_state() 

--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -321,8 +321,6 @@ class RequestsAdmin( BaseController, Use
                 return self.__reject_request( trans, **kwd )
             elif operation == "view_type":
                 return self.__view_request_type( trans, **kwd )
-            elif operation == "upload_datasets":
-                return self.__upload_datasets( trans, **kwd )
         # Render the grid view
         return self.request_grid( trans, **kwd )
 
@@ -399,191 +397,6 @@ class RequestsAdmin( BaseController, Use
                                                           action='list',
                                                           status='done',
                                                           message='Request <b>%s</b> has been rejected.' % request.name) )
-    
-    def __upload_datasets(self, trans, **kwd):
-        return trans.fill_template( '/admin/requests/upload_datasets.mako' )
-            
-
-    @web.expose
-    @web.require_admin
-    def bar_codes(self, trans, **kwd):
-        params = util.Params( kwd )
-        message = util.restore_text( params.get( 'message', ''  ) )
-        status = params.get( 'status', 'done' )
-        request_id = params.get( 'request_id', None )
-        if request_id:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( request_id ))
-        if not request:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        widgets = []
-        for index, sample in enumerate(request.samples):
-            if sample.bar_code:
-                bc = sample.bar_code
-            else:
-                bc = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
-            widgets.append(TextField('sample_%i_bar_code' % index, 
-                                     40, 
-                                     bc))
-        return trans.fill_template( '/admin/samples/bar_codes.mako', 
-                                    samples_list=[s for s in request.samples],
-                                    user=request.user, request=request, widgets=widgets, 
-                                    status=status,
-                                    message=message)
-    @web.expose
-    @web.require_admin
-    def save_bar_codes(self, trans, **kwd):
-        params = util.Params( kwd )
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        # validate 
-        # bar codes need to be globally unique
-        message = ''
-        for index in range(len(request.samples)):
-            bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
-            # check for empty bar code
-            if not bar_code.strip():
-                message = 'Please fill the barcode for sample <b>%s</b>.' % request.samples[index].name
-                break
-            # check all the unsaved bar codes
-            count = 0
-            for i in range(len(request.samples)):
-                if bar_code == util.restore_text(params.get('sample_%i_bar_code' % i, '')):
-                    count = count + 1
-            if count > 1:
-                message = '''The barcode <b>%s</b> of sample <b>%s</b> belongs
-                         another sample in this request. The sample barcodes must
-                         be unique throughout the system''' % \
-                         (bar_code, request.samples[index].name)
-                break
-            # check all the saved bar codes
-            all_samples = trans.sa_session.query( trans.app.model.Sample )
-            for sample in all_samples:
-                if bar_code == sample.bar_code:
-                    message = '''The bar code <b>%s</b> of sample <b>%s</b>  
-                             belongs another sample. The sample bar codes must be 
-                             unique throughout the system''' % \
-                             (bar_code, request.samples[index].name)
-                    break
-            if message:
-                break
-        if message:
-            widgets = []
-            for index, sample in enumerate(request.samples):
-                if sample.bar_code:
-                    bc = sample.bar_code
-                else:
-                    bc = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
-                widgets.append(TextField('sample_%i_bar_code' % index, 
-                                         40, 
-                                         util.restore_text(params.get('sample_%i_bar_code' % index, ''))))
-            return trans.fill_template( '/admin/samples/bar_codes.mako', 
-                                        samples_list=[s for s in request.samples],
-                                        user=request.user, request=request, widgets=widgets, status='error',
-                                        message=message)
-        # now save the bar codes
-        for index, sample in enumerate(request.samples):
-            bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, ''))
-            sample.bar_code = bar_code
-            trans.sa_session.add( sample )
-            trans.sa_session.flush()
-        # change the state of all the samples to the next state
-        # get the new state
-        new_state = request.type.states[1]
-        for s in request.samples:
-            event = trans.app.model.SampleEvent(s, new_state, 'Bar code added to this sample')
-            trans.sa_session.add( event )
-            trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          action='list',
-                                                          operation='show_request',
-                                                          id=trans.security.encode_id(request.id),
-                                                          message='Bar codes have been saved for this request',
-                                                          status='done'))
-    @web.expose
-    @web.require_admin
-    def update_request_state( self, trans, **kwd ):
-        params = util.Params( kwd )
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) )
-            sample_id = int(params.get('sample_id', False))
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID",
-                                                              **kwd) )
-        # check if all the samples of the current request are in the sample state
-        common_state = request.common_state()
-        if not common_state:
-            # if the current request state is complete and one of its samples moved from
-            # the final sample state, then move the request state to In-progress
-            if request.complete():
-                event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, "One or more samples' state moved from the final sample state.")
-                trans.sa_session.add( event )
-                trans.sa_session.flush()
-            return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                              cntrller='requests_admin', 
-                                                              action='sample_events',
-                                                              sample_id=sample_id))
-        final_state = False
-        if common_state.id == request.type.last_state().id:
-            # since all the samples are in the final state, change the request state to 'Complete'
-            comments = "All samples of this request are in the last sample state (%s)." % request.type.last_state().name
-            state = request.states.COMPLETE
-            final_state = True
-        else:
-            comments = "All samples are in %s state." % common_state.name
-            state = request.states.SUBMITTED
-        event = trans.app.model.RequestEvent(request, state, comments)
-        trans.sa_session.add( event )
-        trans.sa_session.flush()
-        # check if an email notification is configured to be sent when the samples 
-        # are in this state
-#        if common_state.id in request.notification['sample_states']:
-        request.send_email_notification(trans, common_state, final_state)
-        return trans.response.send_redirect( web.url_for( controller='requests_common',
-                                                          cntrller='requests_admin', 
-                                                          action='sample_events',
-                                                          sample_id=sample_id))
-
-    @web.expose
-    @web.require_admin
-    def save_state(self, trans, **kwd):
-        params = util.Params( kwd )
-        try:
-            sample_id = int(params.get('sample_id', False))
-            sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id )
-        except:
-            message = "Invalid sample ID"
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message=message,
-                                                              **kwd) )
-        comments = util.restore_text( params.comment )
-        selected_state = int( params.select_state )
-        new_state = trans.sa_session.query( trans.app.model.SampleState ) \
-                                    .filter( and_( trans.app.model.SampleState.table.c.request_type_id == sample.request.type.id,
-                                                   trans.app.model.SampleState.table.c.id == selected_state ) ) \
-                                    .first()
-        event = trans.app.model.SampleEvent(sample, new_state, comments)
-        trans.sa_session.add( event )
-        trans.sa_session.flush()
-        return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                          cntrller='requests_admin', 
-                                                          action='update_request_state',
-                                                          request_id=sample.request.id,
-                                                          sample_id=sample.id))
     #
     # Data transfer from sequencer
     #

--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -1562,13 +1562,17 @@ class TwillTestCase( unittest.TestCase )
         self.check_page_for_string( 'Changes made to the sample(s) are saved.' )
         for index, bar_code in enumerate(bar_codes):
             self.check_page_for_string( bar_code )
-    def change_sample_state( self, sample_name, sample_id, new_state_id, new_state_name, comment='' ):
+    def change_sample_state( self, request_id, request_name, sample_name, sample_id, new_state_id, new_state_name, comment='' ):
         self.home()
+        url = "%s/requests/list?operation=show&id=%s" % ( self.url, self.security.encode_id( request_id ) )
+        self.visit_url( url )
+        self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
+        url = "%s/requests_common/request_page?cntrller=requests_admin&edit_mode=False&id=%s&comment=%s&change_state_button=Save&select_sample_operation=%s&refresh=true&select_sample_%i=true&select_sample_%i=true&select_state=%i" % \
+              (self.url, self.security.encode_id( request_id ), comment, "Change%20state", sample_id, sample_id, new_state_id )
+        self.visit_url( url )        
+        self.check_page_for_string( 'Sequencing Request "%s"' % request_name )
         self.visit_url( "%s/requests_common/sample_events?cntrller=requests_admin&sample_id=%i" % (self.url, sample_id) )
         self.check_page_for_string( 'Events for Sample "%s"' % sample_name )
-        tc.fv( "1", "select_state", str(new_state_id) )
-        tc.fv( "1", "comment", comment )
-        tc.submit( "add_event_button" )
         self.check_page_for_string( new_state_name )
     def add_user_address( self, user_id, address_dict ):
         self.home()

--- a/templates/requests/common/show_request.mako
+++ b/templates/requests/common/show_request.mako
@@ -113,6 +113,36 @@ function showContent(vThis)
             }
         });
     };
+    
+	function checkAllFields()
+	{
+		var chkAll = document.getElementById('checkAll');
+		var checks = document.getElementsByTagName('input');
+		var boxLength = checks.length;
+		var allChecked = false;
+		var totalChecked = 0;
+        if ( chkAll.checked == true )
+        {
+            for ( i=0; i < boxLength; i++ )
+            {
+	            if ( checks[i].name.indexOf( 'select_sample_' ) != -1)
+	            {
+	               checks[i].checked = true;
+	            }
+	        }
+        }
+        else
+        {
+            for ( i=0; i < boxLength; i++ )
+            {
+                if ( checks[i].name.indexOf( 'select_sample_' ) != -1)
+                {
+                   checks[i].checked = false
+                }
+            }
+        }
+	}
+
 </script><style type="text/css">
@@ -261,6 +291,40 @@ function showContent(vThis)
             %if current_samples:
                 ## first render the basic info grid 
                 ${render_basic_info_grid()}
+		        %if not request.new() and edit_mode == 'False' and len(sample_ops.options) > 1:
+                    <div class="form-row" style="background-color:#FAFAFA;">
+	                    For selected sample(s): 
+                        ${sample_ops.get_html()}
+                    </div>
+                    %if 'none' not in sample_ops.get_selected() and len(selected_samples):
+                        <div class="form-row" style="background-color:#FAFAFA;">
+                            %if trans.app.model.Sample.bulk_operations.CHANGE_STATE in sample_ops.get_selected():
+                                <%
+                                    widgets, title = request.type.change_state_widgets(trans)
+                                %>
+			                    %for w in widgets:
+			                        <div class="form-row">
+			                            <label>
+			                                ${w[0]}:
+			                            </label>
+			                            ${w[1].get_html()}
+			                            %if w[0] == 'Comments':
+			                                <div class="toolParamHelp" style="clear: both;">
+			                                    Optional
+			                                </div>
+			                            %endif
+			                        </div>
+			                    %endfor
+		                        <div class="form-row">
+		                            <input type="submit" name="change_state_button" value="Save"/>
+		                            <input type="submit" name="change_state_button" value="Cancel"/>
+		                        </div>
+		                    %elif trans.app.model.Sample.bulk_operations.SELECT_LIBRARY in sample_ops.get_selected():
+		                        ${current_samples[0]}
+                            %endif
+                        </div>
+                    %endif
+		        %endif
                 ## then render the other grid(s)
                 <% trans.sa_session.refresh( request.type.sample_form ) %>
                 %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
@@ -407,6 +471,7 @@ function showContent(vThis)
     <table class="grid"><thead><tr>
+                <th><input type="checkbox" id="checkAll" name=select_all_samples value="true" onclick='checkAllFields(1);'><input type="hidden" name=select_all_samples value="true"></th><th>Name</th><th>Barcode</th><th>State</th>
@@ -436,6 +501,11 @@ function showContent(vThis)
                 %else:
                     <tr>
                         %if sample_index in range(len(request.samples)):
+                            %if sample.id in selected_samples:
+                                <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true" checked><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"></td>
+                            %else:
+                                <td><input type="checkbox" name=select_sample_${sample.id} id="sample_checkbox" value="true"><input type="hidden" name=select_sample_${sample.id} id="sample_checkbox" value="true"></td>
+                            %endif
                             <td>${info['name']}</td><td>${info['barcode']}</td>
                             %if sample.request.unsubmitted():
@@ -486,6 +556,7 @@ function showContent(vThis)
 </%def><%def name="show_basic_info_form( sample_index, sample, info )">
+    <td></td><td><input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/><div class="toolParamHelp" style="clear: both;">

    

[galaxy-commits] galaxy-dist commit 667fb4f9cd16: lims: added basic UI framework for operations on multiple samples

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