[galaxy-dev] [hg] galaxy 3329: Sequencer data acquisition for LIMS

9 Feb 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/37b55fad152b
changeset: 3329:37b55fad152b
user:      rc
date:      Thu Feb 04 11:01:45 2010 -0500
description:
Sequencer data acquisition for LIMS
- Add a data transfer script which fetches datasets from the sequencer
- transfer_datasets.ini for setting up the separate user to login to Galaxy programmatically to add datasets to the data libraries.
- Added a dataset transfer page which includes remote file browser to select files for transfer

Removed library & folder foreign keys from the request table and added them to the sample table. Also the sample table now has a dataset_files column to store the datatsets and the their transfer status.
Add an egg for pexpect which is used in the remote file browser.
The request_type table has a new column datatx_info which stores all the login info for the sequencer machine

diffstat:

 eggs.ini                                                         |    2 +
 lib/galaxy/model/__init__.py                                     |   76 +-
 lib/galaxy/model/mapping.py                                      |   16 +-
 lib/galaxy/model/migrate/versions/0019_request_library_folder.py |    2 +-
 lib/galaxy/model/migrate/versions/0037_samples_library.py        |  124 +
 lib/galaxy/web/controllers/requests.py                           |  472 +++--
 lib/galaxy/web/controllers/requests_admin.py                     |  766 ++++++---
 lib/galaxy/web/framework/__init__.py                             |    4 +-
 scripts/galaxy_messaging/server/daemon.py                        |   34 +
 scripts/galaxy_messaging/server/data_transfer.py                 |  211 ++
 scripts/galaxy_messaging/server/galaxydb_interface.py            |   11 +
 templates/admin/forms/edit_form.mako                             |   42 +-
 templates/admin/forms/show_form_read_only.mako                   |    6 +-
 templates/admin/requests/create_request_type.mako                |   16 +
 templates/admin/requests/get_data.mako                           |  135 +
 templates/admin/requests/show_request.mako                       |  313 ++-
 templates/admin/requests/view_request_type.mako                  |   37 +-
 templates/requests/show_data.mako                                |   86 +
 templates/requests/show_request.mako                             |  299 ++-
 test/base/twilltestcase.py                                       |   25 +-
 test/functional/test_forms_and_requests.py                       |   18 +-
 21 files changed, 1981 insertions(+), 714 deletions(-)

diffs (truncated from 3628 to 3000 lines):

diff -r 44fff02fb036 -r 37b55fad152b eggs.ini

--- a/eggs.ini	Thu Feb 04 10:44:36 2010 -0500
+++ b/eggs.ini	Thu Feb 04 11:01:45 2010 -0500
@@ -40,6 +40,7 @@
 Paste = 1.6
 PasteDeploy = 1.3.3
 PasteScript = 1.7.3
+pexpect = 2.3
 Routes = 1.11
 simplejson = 1.5
 SQLAlchemy = 0.5.6
@@ -72,6 +73,7 @@
 DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz
 MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python-... http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz
 pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz
+pexpect = http://pexpect.sourceforge.net/pexpect-2.3.tar.gz
 psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2
 pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz
 pysam = http://bitbucket.org/kanwei/kanwei-pysam/get/e3c601a062fd.gz
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/lib/galaxy/model/__init__.py	Thu Feb 04 11:01:45 2010 -0500
@@ -53,6 +53,25 @@
                 if role not in roles:
                     roles.append( role )
         return roles
+    def accessible_libraries(self, trans, actions):
+        # get all permitted libraries for this user
+        all_libraries = trans.sa_session.query( trans.app.model.Library ) \
+                                        .filter( trans.app.model.Library.table.c.deleted == False ) \
+                                        .order_by( trans.app.model.Library.name )
+        roles = self.all_roles()
+        actions_to_check = actions
+        # The libraries dictionary looks like: { library : '1,2' }, library : '3' }
+        # Its keys are the libraries that should be displayed for the current user and whose values are a
+        # string of comma-separated folder ids, of the associated folders the should NOT be displayed.
+        # The folders that should not be displayed may not be a complete list, but it is ultimately passed
+        # to the calling method to keep from re-checking the same folders when the library / folder
+        # select lists are rendered.
+        libraries = {}
+        for library in all_libraries:
+            can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( self, roles, library, actions_to_check )
+            if can_show:
+                libraries[ library ] = hidden_folder_ids
+        return libraries
     
 class Job( object ):
     """
@@ -1206,21 +1225,15 @@
         self.form_definition_current = form_definition_current
         self.type = form_type
         self.layout = layout
-    def fields_of_grid(self, layout_grid_name):
-        fields_dict = {}
-        if not layout_grid_name:
-            for i, f in enumerate(self.fields):
-                fields_dict[i] = f
-        else:
-            layout_index = -1
-            for index, lg_name in enumerate(self.layout):
-                if lg_name == layout_grid_name:
-                    layout_index = index
-                    break
-            for i, f in enumerate(self.fields):
-                if f['layout'] == str(layout_index):
-                    fields_dict[i] = f
-        return fields_dict
+    def fields_of_grid(self, grid_index):
+        '''
+        This method returns the list of fields belonging to the given grid.
+        '''
+        gridfields = {}
+        for i, f in enumerate(self.fields):
+            if str(f['layout']) == str(grid_index):
+                gridfields[i] = f
+        return gridfields
     def get_widgets( self, user, contents=[], **kwd ):
         '''
         Return the list of widgets that comprise a form definition,
@@ -1254,6 +1267,9 @@
             if field[ 'type' ] == 'TextField':
                 field_widget.set_size( 40 )
                 field_widget.value = value
+            if field[ 'type' ] == 'NumberField':
+                field_widget.set_size( 40 )
+                field_widget.value = value
             elif field[ 'type' ] == 'TextArea':
                 field_widget.set_size( 3, 40 )
                 field_widget.value = value
@@ -1297,14 +1313,12 @@
                     REJECTED = 'Rejected',
                     COMPLETE = 'Complete')
     def __init__(self, name=None, desc=None, request_type=None, user=None, 
-                 form_values=None, library=None, folder=None):
+                 form_values=None):
         self.name = name
         self.desc = desc
         self.type = request_type
         self.values = form_values
         self.user = user
-        self.library = library
-        self.folder = folder
         self.samples_list = []
     def state(self):
         if self.events:
@@ -1340,23 +1354,45 @@
         self.comment = comment
         
 class RequestType( object ):
-    def __init__(self, name=None, desc=None, request_form=None, sample_form=None):
+    def __init__(self, name=None, desc=None, request_form=None, sample_form=None,
+                 datatx_info=None):
         self.name = name
         self.desc = desc
         self.request_form = request_form
         self.sample_form = sample_form
+        self.datatx_info = datatx_info
     
 class Sample( object ):
-    def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None):
+    transfer_status = Bunch( NOT_STARTED = 'Not started',
+                             IN_PROGRESS = 'In progress',
+                             COMPLETE = 'Complete',
+                             ERROR = 'Error')
+    def __init__(self, name=None, desc=None, request=None, form_values=None, 
+                 bar_code=None, library=None, folder=None, dataset_files=None):
         self.name = name
         self.desc = desc
         self.request = request
         self.values = form_values
         self.bar_code = bar_code
+        self.library = library
+        self.folder = folder
+        self.dataset_files = dataset_files
     def current_state(self):
         if self.events:
             return self.events[0].state
         return None
+    def untransfered_dataset_files(self):
+        count = 0
+        for df, status in self.dataset_files:
+            if status == self.transfer_status.NOT_STARTED:
+                count = count + 1
+        return count
+    def inprogress_dataset_files(self):
+        count = 0
+        for df, status in self.dataset_files:
+            if status == self.transfer_status.IN_PROGRESS:
+                count = count + 1
+        return count
 
 class SampleState( object ):
     def __init__(self, name=None, desc=None, request_type=None):
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/lib/galaxy/model/mapping.py	Thu Feb 04 11:01:45 2010 -0500
@@ -606,6 +606,7 @@
     Column( "desc", TEXT ),
     Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
     Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
+    Column( "datatx_info", JSONType() ),
     Column( "deleted", Boolean, index=True, default=False ) )
 
 FormValues.table = Table('form_values', metadata,
@@ -624,8 +625,6 @@
     Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
     Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ),
     Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
-    Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
-    Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
     Column( "deleted", Boolean, index=True, default=False ) )
 
 RequestEvent.table = Table('request_event', metadata,
@@ -645,6 +644,9 @@
     Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
     Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
     Column( "bar_code", TrimmedString( 255 ), index=True ),
+    Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
+    Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
+    Column( "dataset_files", JSONType() ),
     Column( "deleted", Boolean, index=True, default=False ) )
 
 SampleState.table = Table('sample_state', metadata,
@@ -838,6 +840,10 @@
                         primaryjoin=( Sample.table.c.form_values_id == FormValues.table.c.id ) ),
                     request=relation( Request,
                         primaryjoin=( Sample.table.c.request_id == Request.table.c.id ) ),
+                    folder=relation( LibraryFolder,
+                        primaryjoin=( Sample.table.c.folder_id == LibraryFolder.table.c.id ) ),                 
+                    library=relation( Library,
+                        primaryjoin=( Sample.table.c.library_id == Library.table.c.id ) ),
             ) )
 
 assign_mapper( context, FormValues, FormValues.table,
@@ -856,11 +862,7 @@
                                                backref="requests" ),
                                 samples=relation( Sample,
                                                   primaryjoin=( Request.table.c.id == Sample.table.c.request_id ),
-                                                  order_by=asc(Sample.table.c.update_time) ),
-                                folder=relation( LibraryFolder,
-                                                 primaryjoin=( Request.table.c.folder_id == LibraryFolder.table.c.id ) ),                 
-                                library=relation( Library,
-                                                  primaryjoin=( Request.table.c.library_id == Library.table.c.id ) ),
+                                                  order_by=asc(Sample.table.c.id) ),
                                 events=relation( RequestEvent, backref="request",
                                                  order_by=desc(RequestEvent.table.c.update_time) )
                               ) )
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/model/migrate/versions/0019_request_library_folder.py
--- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py	Thu Feb 04 11:01:45 2010 -0500
@@ -47,7 +47,7 @@
         try:
             LibraryFolder_table = Table( "library_folder", metadata, autoload=True )
         except NoSuchTableError:
-            Request_table = None
+            LibraryFolder_table = None
             log.debug( "Failed loading table library_folder" )
         # Add 1 foreign key constraint to the library_folder table
         if Request_table and LibraryFolder_table:
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/model/migrate/versions/0037_samples_library.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/model/migrate/versions/0037_samples_library.py	Thu Feb 04 11:01:45 2010 -0500
@@ -0,0 +1,124 @@
+"""
+This migration script removes the library_id & folder_id fields in the 'request' table and 
+adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table 
+to store the sequencer login information. Finally, this adds a 'dataset_files' column to
+the sample table. 
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+import sys, logging
+from galaxy.model.custom_types import *
+from sqlalchemy.exc import *
+
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+
+
+def upgrade():
+    print __doc__
+    # Load existing tables
+    metadata.reflect()
+    # retuest_type table
+    try:
+        RequestType_table = Table( "request_type", metadata, autoload=True )
+    except NoSuchTableError:
+        RequestType_table = None
+        log.debug( "Failed loading table request_type" )
+    if RequestType_table:
+        # Add the datatx_info column in 'request_type' table
+        try:
+            col = Column( "datatx_info", JSONType() )
+            col.create( RequestType_table )
+            assert col is RequestType_table.c.datatx_info
+        except Exception, e:
+            log.debug( "Adding column 'datatx_info' to request_type table failed: %s" % ( str( e ) ) )   
+    # request table
+    try:
+        Request_table = Table( "request", metadata, autoload=True )
+    except NoSuchTableError:
+        Request_table = None
+        log.debug( "Failed loading table request" )
+    if Request_table:
+        # Delete the library_id column in 'request' table
+        try:
+            Request_table.c.library_id.drop()
+        except Exception, e:
+            log.debug( "Deleting column 'library_id' to request table failed: %s" % ( str( e ) ) )   
+        # Delete the folder_id column in 'request' table
+        try:
+            Request_table.c.folder_id.drop()
+        except Exception, e:
+            log.debug( "Deleting column 'folder_id' to request table failed: %s" % ( str( e ) ) )   
+    # sample table
+    try:
+        Sample_table = Table( "sample", metadata, autoload=True )
+    except NoSuchTableError:
+        Sample_table = None
+        log.debug( "Failed loading table sample" )
+    if Sample_table:
+        # Add the dataset_files column in 'sample' table
+        try:
+            col = Column( "dataset_files", JSONType() )
+            col.create( Sample_table )
+            assert col is Sample_table.c.dataset_files
+        except Exception, e:
+            log.debug( "Adding column 'dataset_files' to sample table failed: %s" % ( str( e ) ) )
+        # library table
+        try:
+            Library_table = Table( "library", metadata, autoload=True )
+        except NoSuchTableError:
+            Library_table = None
+            log.debug( "Failed loading table library" )
+        if Library_table:
+            # Add the library_id column in 'sample' table
+            try:
+                col = Column( "library_id", Integer, index=True )
+                col.create( Sample_table )
+                assert col is Sample_table.c.library_id
+            except Exception, e:
+                log.debug( "Adding column 'library_id' to sample table failed: %s" % ( str( e ) ) )
+            # add the foreign key constraint
+            try:
+                cons = ForeignKeyConstraint( [Sample_table.c.library_id],
+                                             [Library_table.c.id],
+                                             name='sample_library_id_fk' )
+                # Create the constraint
+                cons.create()
+            except Exception, e:
+                log.debug( "Adding foreign key constraint 'sample_library_id_fk' to table 'library' failed: %s" % ( str( e ) ) )
+        # library_folder table
+        try:
+            LibraryFolder_table = Table( "library_folder", metadata, autoload=True )
+        except NoSuchTableError:
+            LibraryFolder_table = None
+            log.debug( "Failed loading table library_folder" )
+        if LibraryFolder_table:
+            # Add the library_id column in 'sample' table
+            try:
+                col = Column( "folder_id", Integer, index=True )
+                col.create( Sample_table )
+                assert col is Sample_table.c.folder_id
+            except Exception, e:
+                log.debug( "Adding column 'folder_id' to sample table failed: %s" % ( str( e ) ) )
+            # add the foreign key constraint
+            try:
+                cons = ForeignKeyConstraint( [Sample_table.c.folder_id],
+                                             [LibraryFolder_table.c.id],
+                                             name='sample_folder_id_fk' )
+                # Create the constraint
+                cons.create()
+            except Exception, e:
+                log.debug( "Adding foreign key constraint 'sample_folder_id_fk' to table 'library_folder' failed: %s" % ( str( e ) ) )
+
+
+def downgrade():
+    pass
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/web/controllers/requests.py
--- a/lib/galaxy/web/controllers/requests.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/lib/galaxy/web/controllers/requests.py	Thu Feb 04 11:01:45 2010 -0500
@@ -178,30 +178,6 @@
                              % rejected 
         # Render the list view
         return self.request_grid( trans, **kwd )
-    def __show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        add_sample = params.get('add_sample', False)
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID" ) )
-        current_samples = []
-        for s in request.samples:
-            current_samples.append([s.name, s.values.content])
-        if add_sample:
-            current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
-        return trans.fill_template( '/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details='hide', edit_mode='False',
-                                    msg=msg, messagetype=messagetype )
     def __request_events(self, trans, **kwd):
         try:
             request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
@@ -239,22 +215,6 @@
         request_details.append(dict(label='Date created', 
                                     value=request.create_time, 
                                     helptext=''))
-        # library associated        
-        if request.library:
-            value = request.library.name
-        else:
-            value = None
-        request_details.append( dict( label='Data library', 
-                                      value=value, 
-                                      helptext='Data library where the resultant dataset will be stored' ) )
-        # folder associated
-        if request.folder:
-            value = request.folder.name
-        else:
-            value = None
-        request_details.append( dict( label='Data library folder', 
-                                      value=value, 
-                                      helptext='Data library folder where the resultant dataset will be stored' ) )
         # form fields
         for index, field in enumerate(request.type.request_form.fields):
             if field['required']:
@@ -276,36 +236,190 @@
                                             value=request.values.content[index],
                                             helptext=field['helptext']+' ('+req+')'))
         return request_details   
-    def __update_samples(self, request, **kwd):
+    def __show_request(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        add_sample = params.get('add_sample', False)
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID") )
+        # get all data libraries accessible to this user
+        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
+        current_samples = []
+        for i, s in enumerate(request.samples):
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
+            current_samples.append(dict(name=s.name,
+                                        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))
+        if add_sample:
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                               len(current_samples)+1, 
+                                                               libraries, None, **kwd)
+            current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
+                                        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))
+        return trans.fill_template( '/requests/show_request.mako',
+                                    request=request,
+                                    request_details=self.request_details(trans, request.id),
+                                    current_samples=current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False'  ) ),
+                                    msg=msg, messagetype=messagetype )
+    def __library_widgets(self, trans, user, sample_index, libraries, sample=None, **kwd):
+        '''
+        This method creates the data library & folder selectbox for creating &
+        editing samples. First we get a list of all the libraries accessible to
+        the current user and display it in a selectbox. If the user has selected an
+        existing library then display all the accessible sub folders of the selected 
+        data library. 
+        '''
+        params = util.Params( kwd )
+        # data library selectbox
+        lib_id = params.get( "sample_%i_library_id" % sample_index, 'none'  )
+        selected_lib = None
+        if sample and lib_id == 'none':
+            if sample.library:
+                lib_id = str(sample.library.id)
+                selected_lib = sample.library
+        # create data library selectbox with refresh on change enabled
+        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
+        lib_widget = SelectField( "sample_%i_library_id" % sample_index, 
+                                refresh_on_change=True, 
+                                refresh_on_change_values=lib_id_list )
+        # fill up the options in the Library selectbox
+        # first option 'none' is the value for "Select one" option
+        if lib_id == 'none':
+            lib_widget.add_option('Select one', 'none', selected=True)
+        else:
+            lib_widget.add_option('Select one', 'none')
+        # all the libraries available to the selected user
+        for lib, hidden_folder_ids in libraries.items():
+            if str(lib.id) == lib_id:
+                lib_widget.add_option(lib.name, lib.id, selected=True)
+                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
+            else:
+                lib_widget.add_option(lib.name, lib.id)
+            lib_widget.refresh_on_change_values.append(lib.id)
+        # create the folder selectbox
+        folder_widget = SelectField( "sample_%i_folder_id" % sample_index )
+        # when editing a request, either the user has already selected a subfolder or not
+        if sample:
+            if sample.folder:
+                current_fid = sample.folder.id
+            else: 
+                # when a folder not yet associated with the request then the 
+                # the current folder is set to the root_folder of the 
+                # parent data library if present. 
+                if sample.library:
+                    current_fid = sample.library.root_folder.id
+                else:
+                    current_fid = params.get( "sample_%i_folder_id" % sample_index, 'none'  )
+        else:
+            current_fid = 'none'
+        # first option
+        if lib_id == 'none':
+            folder_widget.add_option('Select one', 'none', selected=True)
+        else:
+            folder_widget.add_option('Select one', 'none')
+        if selected_lib:
+            # get all show-able folders for the selected library
+            showable_folders = trans.app.security_agent.get_showable_folders( user, user.all_roles(), 
+                                                                              selected_lib, 
+                                                                              [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], 
+                                                                              selected_hidden_folder_ids )
+            for f in showable_folders:
+                if str(f.id) == str(current_fid):
+                    folder_widget.add_option(f.name, f.id, selected=True)
+                else:
+                    folder_widget.add_option(f.name, f.id)
+        return lib_widget, folder_widget
+    def __update_samples(self, trans, request, **kwd):
         '''
         This method retrieves all the user entered sample information and
         returns an list of all the samples and their field values
         '''
         params = util.Params( kwd )
+        details = params.get( 'details', 'hide' )
+        edit_mode = params.get( 'edit_mode', 'False' )
+        # get all data libraries accessible to this user
+        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
+        
         current_samples = []
-        for s in request.samples:
-            current_samples.append([s.name, s.values.content])
-        index = len(request.samples) 
+        for i, s in enumerate(request.samples):
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
+            current_samples.append(dict(name=s.name,
+                                        barcode=s.bar_code,
+                                        library=s.library,
+                                        folder=s.folder,
+                                        field_values=s.values.content,
+                                        lib_widget=lib_widget,
+                                        folder_widget=folder_widget))
+        if edit_mode == 'False':
+            sample_index = len(request.samples) 
+        else:
+            sample_index = 0
         while True:
-            if params.get( 'sample_%i_name' % index, ''  ):
-                sample_index = index
-                sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                sample_values = []
+            if params.get( 'sample_%i_name' % sample_index, ''  ):
+                # data library
+                try:
+                    library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'sample_%i_library_id' % sample_index, None ) ) )
+                except:
+                    library = None
+                # folder
+                try:
+                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'sample_%i_folder_id' % sample_index, None ) ) )
+                except:
+                    if library:
+                        folder = library.root_folder
+                    else:
+                        folder = None
+                sample_info = dict( name=util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) ),
+                                    barcode=util.restore_text( params.get( 'sample_%i_barcode' % sample_index, ''  ) ),
+                                    library=library,
+                                    folder=folder)
+                sample_info['field_values'] = []
                 for field_index in range(len(request.type.sample_form.fields)):
-                    sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                current_samples.append([sample_name, sample_values])
-                index = index + 1
+                    sample_info['field_values'].append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
+                if edit_mode == 'False':
+                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
+                                                                                                     request.user, 
+                                                                                                     sample_index, 
+                                                                                                     libraries, 
+                                                                                                     None, **kwd)
+                    current_samples.append(sample_info)
+                else:
+                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
+                                                                                                     request.user, 
+                                                                                                     sample_index, 
+                                                                                                     libraries, 
+                                                                                                     request.samples[sample_index], 
+                                                                                                     **kwd)
+                    current_samples[sample_index] =  sample_info
+                sample_index = sample_index + 1
             else:
                 break
-        details = params.get( 'details', 'hide' )
-        edit_mode = params.get( 'edit_mode', 'False' )
-        return current_samples, details, edit_mode
+        return current_samples, details, edit_mode, libraries
     def __copy_sample(self, current_samples):
         copy_list = SelectField('copy_sample')
         copy_list.add_option('None', -1, selected=True)  
         for i, s in enumerate(current_samples):
-            copy_list.add_option(s[0], i)
-        return copy_list   
+            copy_list.add_option(s['name'], i)
+        return copy_list    
     @web.expose
     @web.require_login( "create/submit sequencing requests" )
     def show_request(self, trans, **kwd):
@@ -321,7 +435,7 @@
                                                               message="Invalid request ID",
                                                               **kwd) )
         # get the user entered sample details
-        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
+        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
         if params.get('import_samples_button', False) == 'Import samples':
             try:
                 file_obj = params.get('file_data', '')
@@ -349,10 +463,27 @@
             src_sample_index = int(params.get( 'copy_sample', -1  ))
             if src_sample_index == -1:
                 # empty sample
-                current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
+                lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                                   len(current_samples), 
+                                                                   libraries, None, **kwd)
+                current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
+                                            barcode='',
+                                            library=None,
+                                            folder=None,
+                                            field_values=['' for field in request.type.sample_form.fields],
+                                            lib_widget=lib_widget,
+                                            folder_widget=folder_widget))
             else:
-                current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1),
-                                                                  [val for val in current_samples[src_sample_index][1]]])
+                lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                                   len(current_samples), 
+                                                                   libraries, None, **kwd)
+                current_samples.append(dict(name=current_samples[src_sample_index]['name']+'_%i' % (len(current_samples)+1),
+                                            barcode='',
+                                            library_id='none',
+                                            folder_id='none',
+                                            field_values=[val for val in current_samples[src_sample_index]['field_values']],
+                                            lib_widget=lib_widget,
+                                            folder_widget=folder_widget))
             return trans.fill_template( '/requests/show_request.mako',
                                         request=request,
                                         request_details=self.request_details(trans, request.id),
@@ -365,13 +496,13 @@
             msg = ''
             for index in range(len(current_samples)-len(request.samples)):
                 sample_index = index + len(request.samples)
-                sample_name = current_samples[sample_index][0]
+                sample_name = current_samples[sample_index]['name']
                 if not sample_name.strip():
                     msg = 'Please enter the name of sample number %i' % sample_index
                     break
                 count = 0
                 for i in range(len(current_samples)):
-                    if sample_name == current_samples[i][0]:
+                    if sample_name == current_samples[i]['name']:
                         count = count + 1
                 if count > 1: 
                     msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
@@ -388,34 +519,45 @@
             if edit_mode == 'False':
                 for index in range(len(current_samples)-len(request.samples)):
                     sample_index = len(request.samples)
-                    sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                    sample_values = []
-                    for field_index in range(len(request.type.sample_form.fields)):
-                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                    form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
+                    form_values = trans.app.model.FormValues(request.type.sample_form, 
+                                                             current_samples[sample_index]['field_values'])
                     trans.sa_session.add( form_values )
                     trans.sa_session.flush()                    
-                    s = trans.app.model.Sample(sample_name, '', request, form_values)
+                    s = trans.app.model.Sample(current_samples[sample_index]['name'], '', 
+                                               request, form_values, 
+                                               current_samples[sample_index]['barcode'],
+                                               current_samples[sample_index]['library'],
+                                               current_samples[sample_index]['folder'], 
+                                               dataset_files=[])
                     trans.sa_session.add( s )
                     trans.sa_session.flush()
             else:
+                messagetype = 'done'
+                msg = 'Changes made to the sample(s) are saved. '
                 for sample_index in range(len(current_samples)):
-                    sample_name = current_samples[sample_index][0]
-                    new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                    sample_values = []
-                    for field_index in range(len(request.type.sample_form.fields)):
-                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                    sample = request.has_sample(sample_name)
-                    if sample:
-                        form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
-                        form_values.content = sample_values
-                        sample.name = new_sample_name
-                        trans.sa_session.add( sample )
-                        trans.sa_session.flush()
+                    sample = request.samples[sample_index]
+                    sample.name = current_samples[sample_index]['name'] 
+                    sample.library = current_samples[sample_index]['library']
+                    sample.folder = current_samples[sample_index]['folder']
+                    if request.submitted():
+                        bc_msg = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode'])
+                        if bc_msg:
+                            messagetype = 'error'
+                            msg += bc_msg
+                        else:
+                            sample.bar_code = current_samples[sample_index]['barcode']
+                    trans.sa_session.add( sample )
+                    trans.sa_session.flush()
+                    form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
+                    form_values.content = current_samples[sample_index]['field_values']
+                    trans.sa_session.add( form_values )
+                    trans.sa_session.flush()
             return trans.response.send_redirect( web.url_for( controller='requests',
-                                                              action='list',
-                                                              operation='show_request',
-                                                              id=trans.security.encode_id(request.id)) )
+                                                          action='list',
+                                                          operation='show_request',
+                                                          id=trans.security.encode_id(request.id),
+                                                          messagetype=messagetype,
+                                                          msg=msg ))
         elif params.get('edit_samples_button', False) == 'Edit samples':
             edit_mode = 'True'
             return trans.fill_template( '/requests/show_request.mako',
@@ -423,13 +565,21 @@
                                         request_details=self.request_details(trans, request.id),
                                         current_samples=current_samples,
                                         sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
+                                        details=details, libraries=libraries,
                                         edit_mode=edit_mode)
         elif params.get('cancel_changes_button', False) == 'Cancel':
             return trans.response.send_redirect( web.url_for( controller='requests',
                                                           action='list',
                                                           operation='show_request',
                                                           id=trans.security.encode_id(request.id)) )
+        else:
+            return trans.fill_template( '/requests/show_request.mako',
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details, libraries=libraries,
+                                        edit_mode=edit_mode, messagetype=messagetype, msg=msg)
 
             
     @web.expose
@@ -441,7 +591,7 @@
         request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
         current_samples, details, edit_mode = self.__update_samples( request, **kwd )
         sample_index = int(params.get('sample_id', 0))
-        sample_name = current_samples[sample_index][0]
+        sample_name = current_samples[sample_index]['name']
         s = request.has_sample(sample_name)
         if s:
             trans.sa_session.delete( s )
@@ -454,23 +604,6 @@
                                     sample_copy=self.__copy_sample(current_samples), 
                                     details=details,
                                     edit_mode=edit_mode)
-        
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def toggle_request_details(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        # TODO: Fix the following - can we get a Request.id == 0???
-        request = trans.sa_session.query( trans.app.model.Request ).get(int(params.get('request_id', 0)))
-        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
-        return trans.fill_template( '/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details=details,
-                                    edit_mode=edit_mode)
     def __select_request_type(self, trans, rtid):
         requesttype_list = trans.sa_session.query( trans.app.model.RequestType )\
                                            .order_by( trans.app.model.RequestType.name.asc() )
@@ -563,10 +696,6 @@
                             widget=TextField('desc', 40,
                                              util.restore_text( params.get( 'desc', ''  ) )), 
                             helptext='(Optional)'))
-       
-        # libraries selectbox
-        libui = self.__library_ui(trans, request=None, **kwd)
-        widgets = widgets + libui
         widgets = widgets + request_type.request_form.get_widgets( trans.user, **kwd )
         return trans.fill_template( '/requests/new_request.mako',
                                     select_request_type=select_request_type,
@@ -574,110 +703,6 @@
                                     widgets=widgets,
                                     msg=msg,
                                     messagetype=messagetype)
-    def __library_ui(self, trans, request=None, **kwd):
-        '''
-        This method creates the data library & folder selectbox for new &
-        editing requests. First we get a list of all the libraries accessible to
-        the current user and display it in a selectbox. If the user has select an
-        existing library then display all the accessible sub folders of the selected 
-        data library. 
-        '''
-        params = util.Params( kwd )
-        lib_id = params.get( 'library_id', 'none'  )
-        selected_lib = None
-        # if editing a request and the user has already associated a library to
-        # this request, then set the selected_lib to the request.library
-        if request and lib_id == 'none':
-            if request.library:
-                lib_id = str(request.library.id)
-                selected_lib = request.library
-        # get all permitted libraries for this user
-        all_libraries = trans.sa_session.query( trans.app.model.Library ) \
-                                        .filter( trans.app.model.Library.table.c.deleted == False ) \
-                                        .order_by( trans.app.model.Library.name )
-        current_user_roles = trans.get_current_user_roles()
-        actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ]
-        libraries = odict()
-        for library in all_libraries:
-            can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( trans.user, current_user_roles, library, actions_to_check )
-            if can_show:
-                libraries[ library ] = hidden_folder_ids
-        # create data library selectbox with refresh on change enabled
-        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
-        lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list )
-        # fill up the options in the Library selectbox
-        # first option 'none' is the value for "Select one" option
-        if lib_id == 'none':
-            lib_list.add_option('Select one', 'none', selected=True)
-        else:
-            lib_list.add_option('Select one', 'none')
-        # add all the libraries available to the user to the library selectbox
-        for lib, hidden_folder_ids in libraries.items():
-            if str(lib.id) == lib_id:
-                lib_list.add_option(lib.name, lib.id, selected=True)
-                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
-            else:
-                lib_list.add_option(lib.name, lib.id)
-            lib_list.refresh_on_change_values.append(lib.id)
-        # new library option
-        if lib_id == 'new':
-            lib_list.add_option('Create a new data library', 'new', selected=True)
-        else:
-            lib_list.add_option('Create a new data library', 'new')
-        # data library widget
-        lib_widget = dict(label='Data library', 
-                          widget=lib_list, 
-                          helptext='Data library where the resultant dataset will be stored.')
-        # show the folder widget only if the user has selected a valid library above
-        if selected_lib:
-            # when editing a request, either the user has already selected a subfolder or not
-            if request:
-                if request.folder:
-                    current_fid = request.folder.id
-                else: 
-                    # when a folder not yet associated with the request then the 
-                    # the current folder is set to the root_folder of the 
-                    # parent data library if present. 
-                    if request.library:
-                        current_fid = request.library.root_folder.id
-                    else:
-                        current_fid = params.get( 'folder_id', 'none'  )
-            else:
-                current_fid = params.get( 'folder_id', 'none'  )
-            # create the folder selectbox
-            folder_list = SelectField( 'folder_id')
-            # first option
-            if lib_id == 'none':
-                folder_list.add_option('Select one', 'none', selected=True)
-            else:
-                folder_list.add_option('Select one', 'none')
-            # get all show-able folders for the selected library
-            showable_folders = trans.app.security_agent.get_showable_folders( trans.user,
-                                                                              current_user_roles, 
-                                                                              selected_lib, 
-                                                                              actions_to_check, 
-                                                                              selected_hidden_folder_ids )
-            # add all the folders to the folder selectbox
-            for f in showable_folders:
-                if str(f.id) == str(current_fid):
-                    folder_list.add_option(f.name, f.id, selected=True)
-                else:
-                    folder_list.add_option(f.name, f.id)
-            # folder widget
-            folder_widget = dict(label='Folder', 
-                                 widget=folder_list, 
-                                 helptext='Folder of the selected data library where the resultant dataset will be stored.')
-        if lib_id == 'new':
-            new_lib = dict(label='Create a new data library', 
-                           widget=TextField('new_library_name', 40,
-                                     util.restore_text( params.get( 'new_library_name', ''  ) )), 
-                           helptext='Enter a name here to request a new data library')
-            return [lib_widget, new_lib]
-        else:
-            if selected_lib:
-                return [lib_widget, folder_widget]
-            else:
-                return [lib_widget]
     def __validate(self, trans, request):
         '''
         Validates the request entered by the user 
@@ -747,8 +772,7 @@
         trans.sa_session.flush()
         if not request:
             request = trans.app.model.Request(name, desc, request_type, 
-                                              trans.user, form_values,
-                                              library=library, folder=folder)
+                                              trans.user, form_values)
             trans.sa_session.add( request )
             trans.sa_session.flush()
             trans.sa_session.refresh( request )
@@ -763,8 +787,6 @@
             request.type = request_type
             request.user = trans.user
             request.values = form_values
-            request.library = library
-            request.folder = folder
             trans.sa_session.add( request )
             trans.sa_session.flush()
         return request
@@ -844,9 +866,6 @@
         widgets.append(dict(label='Description', 
                             widget=TextField('desc', 40, desc), 
                             helptext='(Optional)'))
-        # libraries selectbox
-        libui = self.__library_ui(trans, request, **kwd)
-        widgets = widgets + libui
         widgets = widgets + request.type.request_form.get_widgets( trans.user, request.values.content, **kwd )
         return trans.fill_template( '/requests/edit_request.mako',
                                     select_request_type=select_request_type,
@@ -966,3 +985,22 @@
                                     events_list=events_list,
                                     sample_name=sample.name,
                                     request=sample.request)
+    #
+    # Data transfer from sequencer
+    #
+    @web.expose
+    @web.require_login( "create/submit sequencing requests" )
+    def show_datatx_page( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' ) 
+        try:
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid sample ID",
+                                                              **kwd) )
+        return trans.fill_template( '/requests/show_data.mako', 
+                                    sample=sample, dataset_files=sample.dataset_files )
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/lib/galaxy/web/controllers/requests_admin.py	Thu Feb 04 11:01:45 2010 -0500
@@ -10,6 +10,8 @@
 from galaxy.web.controllers.forms import get_all_forms
 from sqlalchemy.sql.expression import func, and_
 from sqlalchemy.sql import select
+import pexpect
+import ConfigParser
 
 log = logging.getLogger( __name__ )
 
@@ -110,9 +112,9 @@
                        visible=False, 
                        filterable="advanced" ),
         StateColumn( "State", 
+                     key='state',
                      model_class=model.Request,
                      event_class=model.RequestEvent,
-                     key='state',
                      filterable="advanced",
                      link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ),
                      ),
@@ -201,6 +203,8 @@
         grids.GridAction( "Create new request type", dict( controller='requests_admin', 
                                                            action='create_request_type' ) )
     ]
+    
+
 #
 # ---- Request Controller ------------------------------------------------------ 
 #
@@ -208,6 +212,7 @@
 class RequestsAdmin( BaseController ):
     request_grid = RequestsGrid()
     requesttype_grid = RequestTypeGrid()
+
     
     @web.expose
     @web.require_admin
@@ -243,33 +248,10 @@
                 return self.__request_events( 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 )
-    def __show_request(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        add_sample = params.get('add_sample', False)
-        try:
-            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
-        except:
-            return trans.response.send_redirect( web.url_for( controller='requests_admin',
-                                                              action='list',
-                                                              status='error',
-                                                              message="Invalid request ID") )
-        current_samples = []
-        for s in request.samples:
-            current_samples.append([s.name, s.values.content])
-        if add_sample:
-            current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details='hide', edit_mode='False',
-                                    msg=msg, messagetype=messagetype )
     @web.expose
     @web.require_admin
     def edit(self, trans, **kwd):
@@ -346,9 +328,6 @@
         widgets.append(dict(label='Description', 
                             widget=TextField('desc', 40, desc), 
                             helptext='(Optional)'))
-        # libraries selectbox
-        libui = self.__library_ui(trans, request.user, request, **kwd)
-        widgets = widgets + libui
         widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd )
         return trans.fill_template( '/admin/requests/edit_request.mako',
                                     select_request_type=select_request_type,
@@ -504,6 +483,9 @@
             events_list.append((event.state, time_ago(event.update_time), event.comment))
         return trans.fill_template( '/admin/requests/events.mako', 
                                     events_list=events_list, request=request)
+        
+    def __upload_datasets(self, trans, **kwd):
+        return trans.fill_template( '/admin/requests/upload_datasets.mako' )
 #
 #---- Request Creation ----------------------------------------------------------
 #    
@@ -609,9 +591,6 @@
                             widget=TextField('desc', 40,
                                              util.restore_text( params.get( 'desc', ''  ) )), 
                             helptext='(Optional)'))
-        # libraries selectbox
-        libui = self.__library_ui(trans, user, **kwd)
-        widgets = widgets + libui
         widgets = widgets + request_type.request_form.get_widgets( user, **kwd )
         return trans.fill_template( '/admin/requests/new_request.mako',
                                     select_request_type=select_request_type,
@@ -640,119 +619,6 @@
                 else:
                     select_user.add_option(user.email, user.id)
         return select_user
-    def __library_ui(self, trans, user, request=None, **kwd):
-        '''
-        This method creates the data library & folder selectbox for new &
-        editing requests. First we get a list of all the libraries accessible to
-        the current user and display it in a selectbox. If the user has select an
-        existing library then display all the accessible sub folders of the selected 
-        data library. 
-        '''
-        params = util.Params( kwd )
-        lib_id = params.get( 'library_id', 'none'  )
-        # if editing a request and the user has already associated a library to
-        # this request, then set the selected_lib to the request.library
-        selected_lib = None
-        if request and lib_id == 'none':
-            if request.library:
-                lib_id = str(request.library.id)
-                selected_lib = request.library
-        # if new request no user is selected initially, none of the libraries are 
-        # listed in the selectfield
-        if not user:
-            libraries = {}
-        else:
-            # get all permitted libraries for this user
-            all_libraries = trans.sa_session.query( trans.app.model.Library ) \
-                                            .filter( trans.app.model.Library.table.c.deleted == False ) \
-                                            .order_by( trans.app.model.Library.name )
-            roles = user.all_roles()
-            actions_to_check = [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ]
-            # The libraries dictionary looks like: { library : '1,2' }, library : '3' }
-            # Its keys are the libraries that should be displayed for the current user and whose values are a
-            # string of comma-separated folder ids, of the associated folders the should NOT be displayed.
-            # The folders that should not be displayed may not be a complete list, but it is ultimately passed
-            # to the calling method to keep from re-checking the same folders when the library / folder
-            # select lists are rendered.
-            libraries = {}
-            for library in all_libraries:
-                can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( user, roles, library, actions_to_check )
-                if can_show:
-                    libraries[ library ] = hidden_folder_ids
-        # create data library selectbox with refresh on change enabled
-        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
-        lib_list = SelectField( 'library_id', refresh_on_change=True, refresh_on_change_values=lib_id_list )
-        # fill up the options in the Library selectbox
-        # first option 'none' is the value for "Select one" option
-        if lib_id == 'none':
-            lib_list.add_option('Select one', 'none', selected=True)
-        else:
-            lib_list.add_option('Select one', 'none')
-        # all the libraries available to the selected user
-        for lib, hidden_folder_ids in libraries.items():
-            if str(lib.id) == lib_id:
-                lib_list.add_option(lib.name, lib.id, selected=True)
-                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
-            else:
-                lib_list.add_option(lib.name, lib.id)
-            lib_list.refresh_on_change_values.append(lib.id)
-        # new data library option
-        if lib_id == 'new':
-            lib_list.add_option('Create a new data library', 'new', selected=True)
-        else:
-            lib_list.add_option('Create a new data library', 'new')
-        # widget
-        lib_widget = dict(label='Data library', 
-                          widget=lib_list, 
-                          helptext='Data library where the resultant dataset will be stored.')
-        # show the folder widget only if the user has selected a valid library above
-        if selected_lib:
-            # when editing a request, either the user has already selected a subfolder or not
-            if request:
-                if request.folder:
-                    current_fid = request.folder.id
-                else: 
-                    # when a folder not yet associated with the request then the 
-                    # the current folder is set to the root_folder of the 
-                    # parent data library if present. 
-                    if request.library:
-                        current_fid = request.library.root_folder.id
-                    else:
-                        current_fid = params.get( 'folder_id', 'none'  )
-            else:
-                current_fid = params.get( 'folder_id', 'none'  )
-            # create the folder selectbox
-            folder_list = SelectField( 'folder_id')
-            # first option
-            if lib_id == 'none':
-                folder_list.add_option('Select one', 'none', selected=True)
-            else:
-                folder_list.add_option('Select one', 'none')
-            # get all show-able folders for the selected library
-            showable_folders = trans.app.security_agent.get_showable_folders( user, roles, 
-                                                                              selected_lib, 
-                                                                              actions_to_check, 
-                                                                              selected_hidden_folder_ids )
-            for f in showable_folders:
-                if str(f.id) == str(current_fid):
-                    folder_list.add_option(f.name, f.id, selected=True)
-                else:
-                    folder_list.add_option(f.name, f.id)
-            # folder widget
-            folder_widget = dict(label='Folder', 
-                                 widget=folder_list, 
-                                 helptext='Folder of the selected data library where the resultant dataset will be stored.')
-        if lib_id == 'new':
-            new_lib = dict(label='Create a new data library', 
-                           widget=TextField('new_library_name', 40,
-                                     util.restore_text( params.get( 'new_library_name', ''  ) )), 
-                           helptext='Enter a name here to request a new data library')
-            return [lib_widget, new_lib]
-        else:
-            if selected_lib:
-                return [lib_widget, folder_widget]
-            else:
-                return [lib_widget]
     def __validate(self, trans, request):
         '''
         Validates the request entered by the user 
@@ -787,18 +653,6 @@
             user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'select_user', '' ) ) )
         name = util.restore_text(params.get('name', ''))
         desc = util.restore_text(params.get('desc', ''))
-        # library
-        try:
-            library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'library_id', None ) ) )
-        except:
-            library = None
-        try:
-            folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'folder_id', None ) ) )
-        except:
-            if library:
-                folder = library.root_folder
-            else:
-                folder = None
         # fields
         values = []
         for index, field in enumerate(request_type.request_form.fields):
@@ -833,8 +687,7 @@
         trans.sa_session.flush()
         if not request:
             request = trans.app.model.Request(name, desc, request_type, 
-                                              user, form_values,
-                                              library=library, folder=folder)
+                                              user, form_values)
             trans.sa_session.add( request )
             trans.sa_session.flush()
             trans.sa_session.refresh( request )
@@ -852,46 +705,195 @@
             request.type = request_type
             request.user = user
             request.values = form_values
-            request.library = library
-            request.folder = folder
             trans.sa_session.add( request )
             trans.sa_session.flush()
-        
         return request
-
-
 #
 #---- Request Page ----------------------------------------------------------
 #    
-    def __update_samples(self, request, **kwd):
+    def __show_request(self, trans, **kwd):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' )
+        add_sample = params.get('add_sample', False)
+        try:
+            request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid request ID") )
+        # get all data libraries accessible to this user
+        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
+        current_samples = []
+        for i, s in enumerate(request.samples):
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
+            current_samples.append(dict(name=s.name,
+                                        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))
+        if add_sample:
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                               len(current_samples)+1, 
+                                                               libraries, None, **kwd)
+            current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
+                                        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))
+        return trans.fill_template( '/admin/requests/show_request.mako',
+                                    request=request,
+                                    request_details=self.request_details(trans, request.id),
+                                    current_samples=current_samples,
+                                    sample_copy=self.__copy_sample(current_samples), 
+                                    details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False'  ) ),
+                                    msg=msg, messagetype=messagetype )
+    def __library_widgets(self, trans, user, sample_index, libraries, sample=None, **kwd):
+        '''
+        This method creates the data library & folder selectbox for creating &
+        editing samples. First we get a list of all the libraries accessible to
+        the current user and display it in a selectbox. If the user has selected an
+        existing library then display all the accessible sub folders of the selected 
+        data library. 
+        '''
+        params = util.Params( kwd )
+        # data library selectbox
+        lib_id = params.get( "sample_%i_library_id" % sample_index, 'none'  )
+        selected_lib = None
+        if sample and lib_id == 'none':
+            if sample.library:
+                lib_id = str(sample.library.id)
+                selected_lib = sample.library
+        # create data library selectbox with refresh on change enabled
+        lib_id_list = ['new'] + [str(lib.id) for lib in libraries.keys()]
+        lib_widget = SelectField( "sample_%i_library_id" % sample_index, 
+                                refresh_on_change=True, 
+                                refresh_on_change_values=lib_id_list )
+        # fill up the options in the Library selectbox
+        # first option 'none' is the value for "Select one" option
+        if lib_id == 'none':
+            lib_widget.add_option('Select one', 'none', selected=True)
+        else:
+            lib_widget.add_option('Select one', 'none')
+        # all the libraries available to the selected user
+        for lib, hidden_folder_ids in libraries.items():
+            if str(lib.id) == lib_id:
+                lib_widget.add_option(lib.name, lib.id, selected=True)
+                selected_lib, selected_hidden_folder_ids = lib, hidden_folder_ids.split(',')
+            else:
+                lib_widget.add_option(lib.name, lib.id)
+            lib_widget.refresh_on_change_values.append(lib.id)
+        # create the folder selectbox
+        folder_widget = SelectField( "sample_%i_folder_id" % sample_index )
+        # when editing a request, either the user has already selected a subfolder or not
+        if sample:
+            if sample.folder:
+                current_fid = sample.folder.id
+            else: 
+                # when a folder not yet associated with the request then the 
+                # the current folder is set to the root_folder of the 
+                # parent data library if present. 
+                if sample.library:
+                    current_fid = sample.library.root_folder.id
+                else:
+                    current_fid = params.get( "sample_%i_folder_id" % sample_index, 'none'  )
+        else:
+            current_fid = 'none'
+        # first option
+        if lib_id == 'none':
+            folder_widget.add_option('Select one', 'none', selected=True)
+        else:
+            folder_widget.add_option('Select one', 'none')
+        if selected_lib:
+            # get all show-able folders for the selected library
+            showable_folders = trans.app.security_agent.get_showable_folders( user, user.all_roles(), 
+                                                                              selected_lib, 
+                                                                              [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], 
+                                                                              selected_hidden_folder_ids )
+            for f in showable_folders:
+                if str(f.id) == str(current_fid):
+                    folder_widget.add_option(f.name, f.id, selected=True)
+                else:
+                    folder_widget.add_option(f.name, f.id)
+        return lib_widget, folder_widget
+    def __update_samples(self, trans, request, **kwd):
         '''
         This method retrieves all the user entered sample information and
         returns an list of all the samples and their field values
         '''
         params = util.Params( kwd )
+        details = params.get( 'details', 'hide' )
+        edit_mode = params.get( 'edit_mode', 'False' )
+        # get all data libraries accessible to this user
+        libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
+        
         current_samples = []
-        for s in request.samples:
-            current_samples.append([s.name, s.values.content])
-        index = len(request.samples) 
+        for i, s in enumerate(request.samples):
+            lib_widget, folder_widget = self.__library_widgets(trans, request.user, i, libraries, s, **kwd)
+            current_samples.append(dict(name=s.name,
+                                        barcode=s.bar_code,
+                                        library=s.library,
+                                        folder=s.folder,
+                                        field_values=s.values.content,
+                                        lib_widget=lib_widget,
+                                        folder_widget=folder_widget))
+        if edit_mode == 'False':
+            sample_index = len(request.samples) 
+        else:
+            sample_index = 0
         while True:
-            if params.get( 'sample_%i_name' % index, ''  ):
-                sample_index = index
-                sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                sample_values = []
+            if params.get( 'sample_%i_name' % sample_index, ''  ):
+                # data library
+                try:
+                    library = trans.sa_session.query( trans.app.model.Library ).get( int( params.get( 'sample_%i_library_id' % sample_index, None ) ) )
+                except:
+                    library = None
+                # folder
+                try:
+                    folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( params.get( 'sample_%i_folder_id' % sample_index, None ) ) )
+                except:
+                    if library:
+                        folder = library.root_folder
+                    else:
+                        folder = None
+                sample_info = dict( name=util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) ),
+                                    barcode=util.restore_text( params.get( 'sample_%i_barcode' % sample_index, ''  ) ),
+                                    library=library,
+                                    folder=folder)
+                sample_info['field_values'] = []
                 for field_index in range(len(request.type.sample_form.fields)):
-                    sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                current_samples.append([sample_name, sample_values])
-                index = index + 1
+                    sample_info['field_values'].append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
+                if edit_mode == 'False':
+                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
+                                                                                                     request.user, 
+                                                                                                     sample_index, 
+                                                                                                     libraries, 
+                                                                                                     None, **kwd)
+                    current_samples.append(sample_info)
+                else:
+                    sample_info['lib_widget'], sample_info['folder_widget'] = self.__library_widgets(trans, 
+                                                                                                     request.user, 
+                                                                                                     sample_index, 
+                                                                                                     libraries, 
+                                                                                                     request.samples[sample_index], 
+                                                                                                     **kwd)
+                    current_samples[sample_index] =  sample_info
+                sample_index = sample_index + 1
             else:
                 break
-        details = params.get( 'details', 'hide' )
-        edit_mode = params.get( 'edit_mode', 'False' )
-        return current_samples, details, edit_mode
+        return current_samples, details, edit_mode, libraries
     def __copy_sample(self, current_samples):
         copy_list = SelectField('copy_sample')
         copy_list.add_option('None', -1, selected=True)  
         for i, s in enumerate(current_samples):
-            copy_list.add_option(s[0], i)
+            copy_list.add_option(s['name'], i)
         return copy_list   
     @web.expose
     @web.require_login( "create/submit sequencing requests" )
@@ -908,7 +910,7 @@
                                                               message="Invalid request ID",
                                                               **kwd) )
         # get the user entered sample details
-        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
+        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
         if params.get('import_samples_button', False) == 'Import samples':
             try:
                 file_obj = params.get('file_data', '')
@@ -936,10 +938,27 @@
             src_sample_index = int(params.get( 'copy_sample', -1  ))
             if src_sample_index == -1:
                 # empty sample
-                current_samples.append(['Sample_%i' % (len(current_samples)+1),['' for field in request.type.sample_form.fields]])
+                lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                                   len(current_samples), 
+                                                                   libraries, None, **kwd)
+                current_samples.append(dict(name='Sample_%i' % (len(current_samples)+1),
+                                            barcode='',
+                                            library=None,
+                                            folder=None,
+                                            field_values=['' for field in request.type.sample_form.fields],
+                                            lib_widget=lib_widget,
+                                            folder_widget=folder_widget))
             else:
-                current_samples.append([current_samples[src_sample_index][0]+'_%i' % (len(current_samples)+1),
-                                                                  [val for val in current_samples[src_sample_index][1]]])
+                lib_widget, folder_widget = self.__library_widgets(trans, request.user, 
+                                                                   len(current_samples), 
+                                                                   libraries, None, **kwd)
+                current_samples.append(dict(name=current_samples[src_sample_index]['name']+'_%i' % (len(current_samples)+1),
+                                            barcode='',
+                                            library_id='none',
+                                            folder_id='none',
+                                            field_values=[val for val in current_samples[src_sample_index]['field_values']],
+                                            lib_widget=lib_widget,
+                                            folder_widget=folder_widget))
             return trans.fill_template( '/admin/requests/show_request.mako',
                                         request=request,
                                         request_details=self.request_details(trans, request.id),
@@ -952,13 +971,13 @@
             msg = ''
             for index in range(len(current_samples)-len(request.samples)):
                 sample_index = index + len(request.samples)
-                sample_name = current_samples[sample_index][0]
+                sample_name = current_samples[sample_index]['name']
                 if not sample_name.strip():
                     msg = 'Please enter the name of sample number %i' % sample_index
                     break
                 count = 0
                 for i in range(len(current_samples)):
-                    if sample_name == current_samples[i][0]:
+                    if sample_name == current_samples[i]['name']:
                         count = count + 1
                 if count > 1: 
                     msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name)
@@ -975,37 +994,45 @@
             if edit_mode == 'False':
                 for index in range(len(current_samples)-len(request.samples)):
                     sample_index = len(request.samples)
-                    sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                    sample_values = []
-                    for field_index in range(len(request.type.sample_form.fields)):
-                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                    form_values = trans.app.model.FormValues(request.type.sample_form, sample_values)
+                    form_values = trans.app.model.FormValues(request.type.sample_form, 
+                                                             current_samples[sample_index]['field_values'])
                     trans.sa_session.add( form_values )
                     trans.sa_session.flush()                    
-                    s = trans.app.model.Sample(sample_name, '', request, form_values)
+                    s = trans.app.model.Sample(current_samples[sample_index]['name'], '', 
+                                               request, form_values, 
+                                               current_samples[sample_index]['barcode'],
+                                               current_samples[sample_index]['library'],
+                                               current_samples[sample_index]['folder'], 
+                                               dataset_files=[])
                     trans.sa_session.add( s )
                     trans.sa_session.flush()
             else:
-                for index in range(len(current_samples)):
-                    sample_index = index
-                    sample_name = current_samples[sample_index][0]
-                    new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, ''  ) )
-                    sample_values = []
-                    for field_index in range(len(request.type.sample_form.fields)):
-                        sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), ''  ) ))
-                    sample = request.has_sample(sample_name)
-                    if sample:
-                        form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
-                        form_values.content = sample_values
-                        trans.sa_session.add( form_values )
-                        trans.sa_session.flush()
-                        sample.name = new_sample_name
-                        trans.sa_session.add( sample )
-                        trans.sa_session.flush()
+                messagetype = 'done'
+                msg = 'Changes made to the sample(s) are saved. '
+                for sample_index in range(len(current_samples)):
+                    sample = request.samples[sample_index]
+                    sample.name = current_samples[sample_index]['name'] 
+                    sample.library = current_samples[sample_index]['library']
+                    sample.folder = current_samples[sample_index]['folder']
+                    if request.submitted():
+                        bc_msg = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode'])
+                        if bc_msg:
+                            messagetype = 'error'
+                            msg += bc_msg
+                        else:
+                            sample.bar_code = current_samples[sample_index]['barcode']
+                    trans.sa_session.add( sample )
+                    trans.sa_session.flush()
+                    form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id )
+                    form_values.content = current_samples[sample_index]['field_values']
+                    trans.sa_session.add( form_values )
+                    trans.sa_session.flush()
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                           action='list',
                                                           operation='show_request',
-                                                          id=trans.security.encode_id(request.id)) )
+                                                          id=trans.security.encode_id(request.id),
+                                                          messagetype=messagetype,
+                                                          msg=msg ))
         elif params.get('edit_samples_button', False) == 'Edit samples':
             edit_mode = 'True'
             return trans.fill_template( '/admin/requests/show_request.mako',
@@ -1013,13 +1040,21 @@
                                         request_details=self.request_details(trans, request.id),
                                         current_samples=current_samples,
                                         sample_copy=self.__copy_sample(current_samples), 
-                                        details=details,
+                                        details=details, libraries=libraries,
                                         edit_mode=edit_mode)
         elif params.get('cancel_changes_button', False) == 'Cancel':
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                           action='list',
                                                           operation='show_request',
                                                           id=trans.security.encode_id(request.id)) )
+        else:
+            return trans.fill_template( '/admin/requests/show_request.mako',
+                                        request=request,
+                                        request_details=self.request_details(trans, request.id),
+                                        current_samples=current_samples,
+                                        sample_copy=self.__copy_sample(current_samples), 
+                                        details=details, libraries=libraries,
+                                        edit_mode=edit_mode, messagetype=messagetype, msg=msg)
 
             
     @web.expose
@@ -1029,9 +1064,9 @@
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
         request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
-        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
+        current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd )
         sample_index = int(params.get('sample_id', 0))
-        sample_name = current_samples[sample_index][0]
+        sample_name = current_samples[sample_index]['name']
         s = request.has_sample(sample_name)
         if s:
             trans.sa_session.delete( s )
@@ -1044,22 +1079,6 @@
                                     sample_copy=self.__copy_sample(current_samples), 
                                     details=details,
                                     edit_mode=edit_mode)
-        
-    @web.expose
-    @web.require_login( "create/submit sequencing requests" )
-    def toggle_request_details(self, trans, **kwd):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) )
-        current_samples, details, edit_mode = self.__update_samples( request, **kwd )
-        return trans.fill_template( '/admin/requests/show_request.mako',
-                                    request=request,
-                                    request_details=self.request_details(trans, request.id),
-                                    current_samples = current_samples,
-                                    sample_copy=self.__copy_sample(current_samples), 
-                                    details=details,
-                                    edit_mode=edit_mode)
     @web.expose
     @web.require_admin
     def request_details(self, trans, id):
@@ -1085,23 +1104,6 @@
         request_details.append(dict(label='Date created', 
                                     value=request.create_time, 
                                     helptext=''))
-        # library associated
-        if request.library:
-			value=request.library.name
-        else:
-			value = None
-        request_details.append(dict(label='Data library', 
-                                    value=value, 
-                                    helptext='Data library where the resultant dataset will be stored'))
-        # folder associated
-        if request.folder:
-            value = request.folder.name
-        else:
-            value = None
-        request_details.append( dict( label='Data library folder', 
-                                      value=value, 
-                                      helptext='Data library folder where the resultant dataset will be stored' ) )
-
         # form fields
         for index, field in enumerate(request.type.request_form.fields):
             if field['required']:
@@ -1122,6 +1124,33 @@
                                             value=request.values.content[index],
                                             helptext=field['helptext']+' ('+req+')'))
         return request_details
+    def __validate_barcode(self, trans, sample, barcode):
+        '''
+        This method makes sure that the given barcode about to be assigned to 
+        the given sample is gobally unique. That is, barcodes must be unique 
+        across requests in Galaxy LIMS 
+        '''
+        msg = ''
+        for index in range(len(sample.request.samples)):
+            # check for empty bar code
+            if not barcode.strip():
+                msg = 'Please fill the barcode for sample <b>%s</b>.' % samples[index].name
+                break
+            # check all the saved bar codes
+            all_samples = trans.sa_session.query( trans.app.model.Sample )
+            for s in all_samples:
+                if barcode == s.bar_code:
+                    if sample.id == s.id:
+                        continue
+                    else:
+                        msg = '''The bar code <b>%s</b> of sample <b>%s</b>  
+                                 belongs another sample. The sample bar codes must be 
+                                 unique throughout the system''' % \
+                                 (barcode, sample.name)
+                        break
+            if msg:
+                break
+        return msg
     @web.expose
     @web.require_admin
     def bar_codes(self, trans, **kwd):
@@ -1233,7 +1262,12 @@
         for s in request.samples:
             if s.current_state().id != request.type.states[-1].id:
                 complete = False
-        if complete:
+        if request.complete() and not complete:
+            comments = "Sample(s) " % request.type.states[-1].name
+            event = trans.app.model.RequestEvent(request, request.states.COMPLETE, comments)
+            trans.sa_session.add( event )
+            trans.sa_session.flush()
+        elif complete:
             # change the request state to 'Complete'
             comments = "All samples of this request are in the last sample state (%s)." % request.type.states[-1].name
             event = trans.app.model.RequestEvent(request, request.states.COMPLETE, comments)
@@ -1279,7 +1313,7 @@
         event = trans.app.model.SampleEvent(sample, new_state, comments)
         trans.sa_session.add( event )
         trans.sa_session.flush()
-        self.__set_request_state( trans, sample.request )
+        #self.__set_request_state( trans, sample.request )
         return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                           action='show_events',
                                                           sample_id=sample.id))
@@ -1306,7 +1340,217 @@
         return trans.fill_template( '/admin/samples/events.mako', 
                                     events_list=events_list,
                                     sample=sample, widgets=widgets, title=title)
+
+    #
+    # Data transfer from sequencer
+    #
+    @web.expose
+    @web.require_admin
+    def show_datatx_page( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' ) 
+        try:
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) )
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid sample ID",
+                                                              **kwd) )
+        return trans.fill_template( '/admin/requests/get_data.mako', 
+                                    sample=sample, dataset_files=sample.dataset_files,
+                                    msg=msg, messagetype=messagetype, files=[],
+                                    folder_path=util.restore_text( params.get( 'folder_path', ''  ) ))
+    def __get_files(self, trans, sample, folder_path):
+        '''
+        This method retrieves the filenames to be transfer from the remote host.
+        '''
+        datatx_info = sample.request.type.datatx_info
+        if not datatx_info['host'] or not datatx_info['username'] or not datatx_info['password']:
+            msg = "Error in sequencer login information." 
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='show_datatx_page', 
+                                                              sample_id=trans.security.encode_id(sample.id),
+                                                              messagetype='error',
+                                                              msg=msg))
+        def print_ticks(d):
+            pass
+        cmd  = 'ssh %s@%s "ls -F %s"' % ( datatx_info['username'],
+                                          datatx_info['host'],
+                                          folder_path)
+        output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n', 
+                                          pexpect.TIMEOUT:print_ticks}, 
+                                          timeout=10)
+        if 'No such file or directory' in output:
+            msg = "No such folder (%s) exists on the sequencer." % folder_path
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='show_datatx_page',
+                                                              sample_id=trans.security.encode_id(sample.id),
+                                                              msg=msg, messagetype='error',
+                                                              folder_path=folder_path )) 
+        files = output.split()[2:]
+        return files
+
+    @web.expose
+    @web.require_admin
+    def get_data(self, trans, **kwd):
+        try:
+            sample = trans.sa_session.query( trans.app.model.Sample ).get( kwd['sample_id']  )
+        except:
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='list',
+                                                              status='error',
+                                                              message="Invalid sample ID" ) )
+        params = util.Params( kwd )
+        msg = util.restore_text( params.get( 'msg', ''  ) )
+        messagetype = params.get( 'messagetype', 'done' ) 
+        folder_path = util.restore_text( params.get( 'folder_path', ''  ) )
+        files_list = util.listify( params.get( 'files_list', ''  ) ) 
+        if not folder_path:
+            return trans.fill_template( '/admin/requests/get_data.mako',
+                                        sample=sample, files=[], 
+                                        dataset_files=sample.dataset_files,
+                                        folder_path=folder_path )
+        if folder_path[-1] != os.sep:
+            folder_path = folder_path+os.sep
+        if params.get( 'browse_button', False ):
+            # get the filenames from the remote host
+            files = self.__get_files(trans, sample, folder_path)
+            return trans.fill_template( '/admin/requests/get_data.mako',
+                                        sample=sample, files=files, 
+                                        dataset_files=sample.dataset_files,
+                                        folder_path=folder_path )
+        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)
+            return trans.fill_template( '/admin/requests/get_data.mako',
+                                        sample=sample, files=files, 
+                                        dataset_files=sample.dataset_files,
+                                        folder_path=folder_path )
+        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)
+            return trans.fill_template( '/admin/requests/get_data.mako',
+                                        sample=sample, files=files, 
+                                        dataset_files=sample.dataset_files,
+                                        folder_path=folder_path )
+        elif params.get( 'remove_dataset_button', False ):
+            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( '/admin/requests/get_data.mako', 
+                                        sample=sample, 
+                                        dataset_files=sample.dataset_files)
+        elif params.get( 'start_transfer_button', False ):
+            for f in files_list:
+                sample.dataset_files.append([os.path.join(folder_path, f),
+                                             sample.transfer_status.NOT_STARTED])
+            trans.sa_session.add( sample )
+            trans.sa_session.flush()
+            return self.__start_datatx(trans, sample)
+            
+    def __setup_datatx_user(self, trans, library, folder):
+        '''
+        This method sets up the datatx user:
+        - Checks if the user exists already, if not creates the user
+        - Checks if the user had ADD_LIBRARY permission on the target library
+          and the target folder, if not sets up the permissions.
+        '''
+        # Retrieve the upload user login information from the config file
+        config = ConfigParser.ConfigParser()
+        config.read('transfer_datasets.ini')
+        email = config.get("data_transfer_user_login_info", "email")
+        password = config.get("data_transfer_user_login_info", "password")
+        # check if the user already exists
+        datatx_user = trans.sa_session.query( trans.app.model.User ) \
+                                      .filter( trans.app.model.User.table.c.email==email ) \
+                                      .first()
+        if not datatx_user:
+            # if not create the user
+            datatx_user = trans.app.model.User( email=email )
+            datatx_user.set_password_cleartext( password )
+            if trans.app.config.use_remote_user:
+                datatx_user.external = True
+            trans.sa_session.add( datatx_user )
+            trans.sa_session.flush()
+            trans.app.security_agent.create_private_user_role( datatx_user )
+            trans.app.security_agent.user_set_default_permissions( datatx_user, history=False, dataset=False )
+        for role in datatx_user.all_roles():
+            if role.name == datatx_user.email and role.description == 'Private Role for %s' % datatx_user.email:
+                datatx_user_private_role = role
+                break
+        def check_permission(item_actions, role):
+            for item_permission in item_actions:
+                if item_permission.action == trans.app.security_agent.permitted_actions.LIBRARY_ADD.action \
+                    and item_permission.role.id == role.id:
+                    return True
+            return False
+        # check if this user has 'add' permissions on the target library & folder
+        # if not, set 'ADD' permission
+        if not check_permission(library.actions, datatx_user_private_role):
+            lp = trans.app.model.LibraryPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action,
+                                                     library, 
+                                                     datatx_user_private_role )
+            trans.sa_session.add( lp )
+        if not check_permission(folder.actions, datatx_user_private_role):
+            dp = trans.app.model.LibraryFolderPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action,
+                                                           folder, 
+                                                           datatx_user_private_role )
+            trans.sa_session.add( dp )
+            trans.sa_session.flush()
+        return datatx_user
+
+    def __start_datatx(self, trans, sample):
+        # data transfer user
+        datatx_user = self.__setup_datatx_user(trans, sample.library, sample.folder)
+        # validate sequecer information
+        datatx_info = sample.request.type.datatx_info
+        if not datatx_info['host'] or \
+           not datatx_info['username'] or \
+           not datatx_info['password']:
+            msg = "Error in sequencer login information." 
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='show_datatx_page', 
+                                                              sample_id=trans.security.encode_id(sample.id),
+                                                              messagetype='error',
+                                                              msg=msg))
+        transfer_script = "scripts/galaxy_messaging/server/daemon.py"
+        for index, dataset in enumerate(sample.dataset_files):
+            dfile = dataset[0]
+            status = dataset[1]
+            if status == sample.transfer_status.NOT_STARTED:
+                cmd = "python %s %s %s %s %s %s %s %s %s" % ( transfer_script,
+                                                              datatx_info['host'],
+                                                              datatx_info['username'],
+                                                              datatx_info['password'],
+                                                              dfile,
+                                                              sample.id,
+                                                              index,
+                                                              trans.security.encode_id(sample.library.id), 
+                                                              trans.security.encode_id(sample.folder.id))   
+                # set the transfer status
+                sample.dataset_files[index][1] = sample.transfer_status.IN_PROGRESS
+                trans.sa_session.add( sample )
+                trans.sa_session.flush()
+                os.system(cmd)
+        # set the sample state to the last state
+        if sample.current_state().id != sample.request.type.states[-1].id:
+            event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1], 
+                                                'The dataset are ready & are being transfered to Galaxy')
+            trans.sa_session.add( event )
+            trans.sa_session.flush()
+        return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                          action='show_datatx_page', 
+                                                          sample_id=trans.security.encode_id(sample.id)))
+
     
+        
 ##
 #### Request Type Stuff ###################################################
 ##
@@ -1379,16 +1623,36 @@
                                         msg=msg,
                                         messagetype=messagetype)
         elif params.get( 'save_request_type', False ):
-            st, msg = self.__save_request_type(trans, **kwd)
-            if not st:
+            rt, msg = self.__save_request_type(trans, **kwd)
+            if not rt:
                 return trans.fill_template( '/admin/requests/create_request_type.mako', 
                                             forms=get_all_forms( trans ),
                                             msg=msg,
                                             messagetype='error')
             return trans.response.send_redirect( web.url_for( controller='requests_admin',
                                                               action='manage_request_types',
-                                                              message='Request type <b>%s</b> has been created' % st.name,
+                                                              message='Request type <b>%s</b> has been created' % rt.name,
                                                               status='done') )
+        elif params.get( 'save_changes', False ):
+            try:
+                rt = trans.sa_session.query( trans.app.model.RequestType ).get( int(kwd['rt_id']) )
+            except:
+                return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                                  action='manage_request_types',
+                                                                  msg='Invalid request type ID',
+                                                                  messagetype='error') )
+            # data transfer info
+            rt.datatx_info = dict(host=util.restore_text( params.get( 'host', ''  ) ),
+                                  username=util.restore_text( params.get( 'username', ''  ) ),
+                                  password=util.restore_text( params.get( 'password', ''  ) )) 
+            trans.sa_session.add( rt )
+            trans.sa_session.flush()
+            return trans.response.send_redirect( web.url_for( controller='requests_admin',
+                                                              action='manage_request_types',
+                                                              operation='view',
+                                                              id=trans.security.encode_id(rt.id),
+                                                              msg='Changes made to request type <b>%s</b> has been saved' % rt.name,
+                                                              messagetype='done') )
         else:
             rt_info, rt_states = self.__create_request_type_form(trans, **kwd)
             return trans.fill_template( '/admin/requests/create_request_type.mako',
@@ -1448,6 +1712,10 @@
         rt.desc = util.restore_text( params.get( 'desc', '' ) )
         rt.request_form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.request_form_id ) )
         rt.sample_form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.sample_form_id ) )
+        # data transfer info
+        rt.datatx_info = dict(host=util.restore_text( params.get( 'host', ''  ) ),
+                              username=util.restore_text( params.get( 'username', ''  ) ),
+                              password=util.restore_text( params.get( 'password', ''  ) )) 
         trans.sa_session.add( rt )
         trans.sa_session.flush()
         # set sample states
diff -r 44fff02fb036 -r 37b55fad152b lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/lib/galaxy/web/framework/__init__.py	Thu Feb 04 11:01:45 2010 -0500
@@ -30,7 +30,9 @@
 
 pkg_resources.require( "SQLAlchemy >= 0.4" )
 from sqlalchemy import and_
-            
+
+pkg_resources.require( "pexpect" )
+
 import logging
 log = logging.getLogger( __name__ )
 
diff -r 44fff02fb036 -r 37b55fad152b scripts/galaxy_messaging/server/daemon.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/galaxy_messaging/server/daemon.py	Thu Feb 04 11:01:45 2010 -0500
@@ -0,0 +1,34 @@
+#!/usr/bin/python
+"""
+
+Data Transfer Script Daemon
+
+This script is called from Galaxy LIMS once the lab admin starts the data 
+transfer process using the user interface. This creates a child process and 
+this child process starts the data_transfer.py script as a new process
+
+This script passes all the arguments from Galaxy LIMS to the data_transfer.py script
+
+Usage:
+
+python daemon.py <sequencer_host> 
+                <username> 
+                <password> 
+                <source_file> 
+                <sample_id>
+                <dataset_index>
+                <library_id>
+                <folder_id>
+"""
+
+import sys, os
+# Perform first fork.
+try:
+    pid = os.fork( )
+    if pid > 0:
+        sys.exit(0) # Exit first parent.
+except OSError, e:
+    sys.stderr.write("fork #1 failed: (%d) %sn" % (e.errno, e.strerror))
+    sys.exit(1)
+os.execv(os.path.join( os.getcwd(), "scripts/galaxy_messaging/server/data_transfer.py"), sys.argv)
+
diff -r 44fff02fb036 -r 37b55fad152b scripts/galaxy_messaging/server/data_transfer.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/galaxy_messaging/server/data_transfer.py	Thu Feb 04 11:01:45 2010 -0500
@@ -0,0 +1,211 @@
+#!/usr/bin/python
+"""
+
+Data Transfer Script: Sequencer to Galaxy
+
+This script is called from Galaxy LIMS once the lab admin starts the data 
+transfer process using the user interface.
+
+Usage:
+
+python data_transfer.py <sequencer_host> 
+                        <username> 
+                        <password> 
+                        <source_file> 
+                        <sample_id>
+                        <dataset_index>
+                        <library_id>
+                        <folder_id>
+"""
+ 
+import ConfigParser
+import sys, os, time, traceback
+import optparse
+import urllib,urllib2, cookielib, shutil
+import logging
+from galaxydb_interface import GalaxyDbInterface
+
+assert sys.version_info[:2] >= ( 2, 4 )
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] ) # remove scripts/ from the path
+sys.path = new_path
+
+from galaxy.util.json import from_json_string, to_json_string
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "pexpect" )
+import pexpect
+
+pkg_resources.require( "simplejson" )
+import simplejson
+
+curr_dir = os.getcwd()
+logfile = os.path.join(curr_dir, 'data_transfer.log')
+logging.basicConfig(filename=logfile, level=logging.DEBUG, 
+        format="%(asctime)s [%(levelname)s] %(message)s")
+
+class DataTransfer(object):
+    
+    def __init__(self, host, username, password, remote_file, sample_id, 
+                 dataset_index, library_id, folder_id):
+        self.host = host
+        self.username = username
+        self.password = password
+        self.remote_file = remote_file
+        self.sample_id = sample_id
+        self.dataset_index = dataset_index
+        self.library_id = library_id
+        self.folder_id = folder_id
+        try:
+            # Retrieve the upload user login information from the config file
+            config = ConfigParser.ConfigParser()
+            config.read('universe_wsgi.ini')
+            self.server_host = config.get("server:main", "host")
+            self.server_port = config.get("server:main", "port")
+            self.database_connection = config.get("app:main", "database_connection")
+            self.import_dir = config.get("app:main", "library_import_dir")
+            # create the destination directory within the import directory
+            self.server_dir = os.path.join( self.import_dir, 'datatx_'+str(os.getpid()) )
+            os.mkdir(self.server_dir)
+            if not os.path.exists(self.server_dir):
+                raise Exception
+        except:
+            logging.error(traceback.format_exc())
+            logging.error('FATAL ERROR')
+            if self.database_connection:
+                self.update_status('Error')
+            sys.exit(1)
+     
+    def start(self):
+        '''
+        This method executes the file transfer from the sequencer, adds the dataset
+        to the data library & finally updates the data transfer status in the db
+        '''
+        # datatx
+        self.transfer_file()
+        # add the dataset to the given library 
+        self.add_to_library()
+        # update the data transfer status in the db
+        self.update_status('Complete')
+        # cleanup
+        self.cleanup()    
+        sys.exit(0)
+        
+    def cleanup(self):
+        '''
+        remove the directory created to store the dataset files temporarily
+        before adding the same to the data library
+        '''
+        try:
+            shutil.rmtree( self.server_dir )
+        except:
+            self.error_and_exit()
+
+            
+    def error_and_exit(self):
+        '''
+        This method is called any exception is raised. This prints the traceback 
+        and terminates this script
+        '''
+        logging.error(traceback.format_exc())
+        logging.error('FATAL ERROR')
+        self.update_status('Error')
+        sys.exit(1)
+        
+    def transfer_file(self):
+        '''
+        This method executes a scp process using pexpect library to transfer
+        the dataset file from the remote sequencer to the Galaxy server
+        '''
+        def print_ticks(d):
+            pass
+        try:
+            cmd = "scp %s@%s:%s %s" % ( self.username,
+                                        self.host,
+                                        self.remote_file,
+                                        self.server_dir)
+            logging.debug(cmd)
+            output = pexpect.run(cmd, events={'.ssword:*': self.password+'\r\n', 
+                                              pexpect.TIMEOUT:print_ticks}, 
+                                              timeout=10)
+            logging.debug(output)
+            if not os.path.exists(os.path.join(self.server_dir, os.path.basename(self.remote_file))):
+                raise Exception
+        except:
+            self.error_and_exit()
+
+        
+    def add_to_library(self):
+        '''
+        This method adds the dataset file to the target data library & folder
+        by opening the corresponding url in Galaxy server running.  
+        '''
+        try:
+            logging.debug('Adding %s to library...' % os.path.basename(self.remote_file))
+            # Retrieve the upload user login information from the config file
+            config = ConfigParser.ConfigParser()
+            config.read('transfer_datasets.ini')
+            email = config.get("data_transfer_user_login_info", "email")
+            password = config.get("data_transfer_user_login_info", "password")
+            # create url
+            base_url =  "http://%s:%s" % (self.server_host, self.server_port)
+            # login 
+            url = "%s/user/login?email=%s&password=%s" % (base_url, email, password)
+            cj = cookielib.CookieJar()
+            opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj))
+            f = opener.open(url)
+            if f.read().find("Now logged in as "+email) == -1:
+                # if the user doesnt exist, create the user
+                url = "%s/user/create?email=%s&username=%s&password=%s&confirm=%s&create_user_button=Submit" % ( base_url, email, email, password, password )
+                f = opener.open(url)
+                if f.read().find("Now logged in as "+email) == -1:
+                    raise Exception
+            # after login, add dataset to the library
+            params = urllib.urlencode(dict( cntrller='library_admin',
+                                            tool_id='upload1',
+                                            tool_state='None',
+                                            library_id=self.library_id,
+                                            folder_id=self.folder_id,
+                                            upload_option='upload_directory',
+                                            file_type='auto',
+                                            server_dir=os.path.basename(self.server_dir),
+                                            dbkey='',
+                                            runtool_btn='Upload to library'))
+            #url = "http://localhost:8080/library_common/upload_library_dataset?cntrller=library_admin&tool_id=upload1&tool_state=None&library_id=adb5f5c93f827949&folder_id=adb5f5c93f827949&upload_option=upload_directory&file_type=auto&server_dir=003&dbkey=%3F&message=&runtool_btn=Upload+to+library"
+            #url = base_url+"/library_common/upload_library_dataset?library_id=adb5f5c93f827949&tool_id=upload1&file_type=auto&server_dir=datatx_22858&dbkey=%3F&upload_option=upload_directory&folder_id=529fd61ab1c6cc36&cntrller=library_admin&tool_state=None&runtool_btn=Upload+to+library"
+            url = base_url+"/library_common/upload_library_dataset"
+            logging.debug(url)
+            logging.debug(params)
+            f = opener.open(url, params)
+            #print f.read()
+        except:
+            self.error_and_exit()
+
+    def update_status(self, status):
+        '''
+        
+        '''
+        try:
+            galaxy = GalaxyDbInterface(self.database_connection)
+            df = from_json_string(galaxy.get_sample_dataset_files(self.sample_id))
+            logging.debug(df)
+            df[self.dataset_index][1] = status
+        
+            galaxy.set_sample_dataset_files(self.sample_id, to_json_string(df))
+            logging.debug("######################\n"+str(from_json_string(galaxy.get_sample_dataset_files(self.sample_id))[self.dataset_index]))
+        except:
+            logging.error(traceback.format_exc())
+            logging.error('FATAL ERROR')
+            sys.exit(1)
+
+if __name__ == '__main__':
+    logging.info('STARTING %i %s' % (os.getpid(), str(sys.argv)))
+    logging.info('daemonized %i' % os.getpid())
+    #
+    # Start the daemon
+    #    
+    dt = DataTransfer(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4],
+                      int(sys.argv[5]), int(sys.argv[6]), sys.argv[7], sys.argv[8])
+    dt.start()
+
+
diff -r 44fff02fb036 -r 37b55fad152b scripts/galaxy_messaging/server/galaxydb_interface.py
--- a/scripts/galaxy_messaging/server/galaxydb_interface.py	Thu Feb 04 10:44:36 2010 -0500
+++ b/scripts/galaxy_messaging/server/galaxydb_interface.py	Thu Feb 04 11:01:45 2010 -0500
@@ -12,6 +12,7 @@
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 from galaxy import eggs
+from galaxy.model.custom_types import *
 import pkg_resources
 pkg_resources.require( "psycopg2" )
 import psycopg2
@@ -126,6 +127,16 @@
                       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)
+        
 
 
 
diff -r 44fff02fb036 -r 37b55fad152b templates/admin/forms/edit_form.mako
--- a/templates/admin/forms/edit_form.mako	Thu Feb 04 10:44:36 2010 -0500
+++ b/templates/admin/forms/edit_form.mako	Thu Feb 04 11:01:45 2010 -0500
@@ -30,6 +30,25 @@
 });
 </script>
 
+<script type="text/javascript">
+$(document).ready(function(){
+    //hide the all of the element with class msg_body
+    $(".msg_body").hide();
+    //toggle the componenet with class msg_body
+    $(".msg_head").click(function(){
+        $(this).next(".msg_body").slideToggle(450);
+    });
+});
+</script>
+<style type="text/css">
+.msg_head {
+    padding: 0px 0px;
+    cursor: pointer;
+}
+
+}
+</style>
+
 <%def name="render_selectbox_options( index, field_attr )">
     %if field_attr[0] == 'Type':
         %if field_attr[1].get_selected()[0] == 'SelectField':
@@ -55,11 +74,16 @@
     %endif
 </%def>
 
-<%def name="render_field( index, field )">
+<%def name="render_field( index, field, saved )">
+    %if saved:        
+        <h4 class="msg_head"> 
+            <div class="form-row">${index+1}. ${field[0][1].value} (${field[2][1].get_selected()[1]})</div>
+        </h4>
+        <div class="msg_body">
+    %else:
+        <div class="msg_body2">
+    %endif
     <div class="repeat-group-item">
-        <div class="form-row">
-            <label>Field ${1+index}</label>
-        </div>
         %for field_attr in field:
             <div class="form-row">
                 <label>${field_attr[0]}</label>
@@ -70,7 +94,9 @@
         <div class="form-row">
             <input type="submit" name="remove_button" value="Remove field ${index+1}"/>
         </div>
-   </div>
+    </div>
+    </div>
+    
 </%def>
 
 <%def name="render_layout( index, widget )">
@@ -109,7 +135,11 @@
         %endif
         <div class="toolFormTitle">Fields (${len(form.fields)})</div>
         %for ctr, field in enumerate(field_details):
-            ${render_field( ctr, field )}
+            %if ctr < len(form.fields):
+                ${render_field( ctr, field, True )}
+            %else:
+                ${render_field( ctr, field, False )}
+            %endif
         %endfor
         <div class="form-row">
             <input type="submit" name="add_field_button" value="Add field"/>
diff -r 44fff02fb036 -r 37b55fad152b templates/admin/forms/show_form_read_only.mako
--- a/templates/admin/forms/show_form_read_only.mako	Thu Feb 04 10:44:36 2010 -0500
+++ b/templates/admin/forms/show_form_read_only.mako	Thu Feb 04 11:01:45 2010 -0500
@@ -8,7 +8,9 @@
 
 <%def name="render_grid( grid_index, grid_name, fields_dict )">
     %if grid_name:
-        <div class="toolFormTitle">${grid_name}</div>
+        <div class="form-row">
+        <h4>${grid_name}</h4>
+        </div>
     %endif
     <div style="clear: both"></div>
     <table class="grid">
@@ -83,7 +85,7 @@
                 ${render_grid( 0, '', form.fields_of_grid( None ) )}
             %else:
                 %for grid_index, grid_name in enumerate(form.layout):
-                    ${render_grid( grid_index, grid_name, form.fields_of_grid( grid_name ) )}
+                    ${render_grid( grid_index, grid_name, form.fields_of_grid( grid_index ) )}
                 %endfor
             %endif
         %else:
diff -r 44fff02fb036 -r 37b55fad152b templates/admin/requests/create_request_type.mako
--- a/templates/admin/requests/create_request_type.mako	Thu Feb 04 10:44:36 2010 -0500
+++ b/templates/admin/requests/create_request_type.mako	Thu Feb 04 11:01:45 2010 -0500
@@ -49,6 +49,22 @@
             <div class="form-row">
                 <input type="submit" name="add_state_button" value="Add state"/>
             </div>
+            <div class="toolFormTitle">Sequencer information</div>
+            <div class="form-row">
+                This information is only needed for transferring data from sequencer to Galaxy
+            </div>
+            <div class="form-row">
+                <label>Hostname or IP Address:</label>
+                <input type="text" name="host" value="" size="40"/>
+            </div>
+            <div class="form-row">
+                <label>Username:</label>
+                <input type="text" name="username" value="" size="40"/>
+            </div>
+            <div class="form-row">
+                <label>Password:</label>
+                <input type="password" name="password" value="" size="40"/>
+            </div>
             <div class="form-row">
                 <div style="float: left; width: 250px; margin-right: 10px;">
                     <input type="hidden" name="new" value="submitted" size="40"/>
diff -r 44fff02fb036 -r 37b55fad152b templates/admin/requests/get_data.mako
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/admin/requests/get_data.mako	Thu Feb 04 11:01:45 2010 -0500
@@ -0,0 +1,135 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<script type="text/javascript">
+$(document).ready(function(){
+    //hide the all of the element with class msg_body
+    $(".msg_body").hide();
+    //toggle the componenet with class msg_body
+    $(".msg_head").click(function(){
+        $(this).next(".msg_body").slideToggle(450);
+    });
+});
+</script>
+<style type="text/css">
+.msg_head {
+    padding: 0px 0px;
+    cursor: pointer;
+}
+
+}
+</style>
+
+
+<h2>Data transfer from Sequencer</h2>
+<h3>Sample "${sample.name}" of Request "${sample.request.name}"</h3>
+
+<ul class="manage-table-actions">
+##    %if sample.request.submitted() and sample.untransfered_dataset_files():
+##    <li>
+##        <a class="action-button" href="${h.url_for( controller='requests_admin', action='start_datatx', id=trans.security.encode_id(sample.id) )}">
+##        <span>Start data transfer</span></a>
+##    </li>
+##    %endif
+    %if sample.request.submitted() and sample.inprogress_dataset_files():
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">
+        <span>Refresh this page</span></a>
+    </li>
+    %endif
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_request_types', operation='view', id=trans.security.encode_id(sample.request.type.id) )}">
+        <span>Sequencer information</span></a>
+    </li>
+    <li>
+        <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( sample.library.id ) )}">
+        <span>${sample.library.name} Data Library</span></a>
+    </li>
+    <li>
+        <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(sample.request.id) )}">
+        <span>Browse this request</span></a>
+    </li>
+</ul>
+
+<div class="toolForm">
+    <form name="get_data" action="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id)}" method="post" >
+        %if len(dataset_files):
+            <div class="form-row">
+            <h4>Datasets Transfered</h4>
+            <div class="form-row">
+                <table class="grid">
+                <thead>
+                    <tr>
+                        <th>Dataset File</th>
+                        <th>Transfer Status</th>
+                        ##<th>Data Library</th>
+                        <th></th>
+                    </tr>
+                <thead>
+                    <tbody>
+                        %for dataset_index, dataset_file in enumerate(dataset_files):
+                            ${sample_dataset_files( dataset_index, dataset_file[0], dataset_file[1] )}
+                        %endfor
+                    </tbody>
+                </table>
+            </div>
+            </div>
+        %endif
+        <div class="form-row">
+            <h4>Select files for transfer</h4>
+            <div style="width: 60%;">
+                <div class="form-row">
+                    <label>Folder path on the sequencer:</label>
+                    <input type="text" name="folder_path" value="${folder_path}" size="100"/>
+                    <input type="submit" name="browse_button" value="List contents"/>
+                    <input type="submit" name="open_folder" value="Open folder"/>
+                    <input type="submit" name="folder_up" value="Up"/>
+                </div>
+                <div class="form-row">
+                <select name="files_list" id="files_list" style="max-width: 98%; width: 98%; height: 150px; font-size: 100%;" multiple>
+                    %for index, f in enumerate(files):
+                        <option value="${f}">${f}</option>
+                    %endfor
+                </select> 
+                </div>
+                <div class="form-row">
+                    <input type="submit" name="start_transfer_button" value="Transfer"/>
+                </div>
+            </div>
+        </div>
+    </form>
+</div>
+
+<%def name="sample_dataset_files( dataset_index, dataset_file, status )">
+    <tr>
+        <td>
+##            <label class="msg_head"><a href="${h.url_for( controller='requests_admin', action='show_dataset_file', sample_id=trans.security.encode_id(sample.id), dataset_index=dataset_index )}">${dataset_file.split('/')[-1]}</a></label>
+            <div class="msg_head"><u>${dataset_file.split('/')[-1]}</u></div>
+            <div class="msg_body">
+                ${dataset_file}
+            </div>
+        </td>
+        <td>
+            %if status == sample.transfer_status.IN_PROGRESS: 
+                <i>${status}</i>
+            %else:
+                ${status}
+            %endif
+        </td>
+        ##<td></td>
+        %if status == sample.transfer_status.NOT_STARTED: 
+        <td>
+            <a class="action-button" href="${h.url_for( controller='requests_admin', action='get_data', sample_id=sample.id, remove_dataset_button=True, dataset_index=dataset_index )}">
+            <img src="${h.url_for('/static/images/delete_icon.png')}" />
+            <span></span></a>
+        </td>
+        %else:
+            <td></td>
+        %endif
+    </tr>
+</%def>
\ No newline at end of file
diff -r 44fff02fb036 -r 37b55fad152b templates/admin/requests/show_request.mako
--- a/templates/admin/requests/show_request.mako	Thu Feb 04 10:44:36 2010 -0500
+++ b/templates/admin/requests/show_request.mako	Thu Feb 04 11:01:45 2010 -0500
@@ -5,6 +5,51 @@
     ${render_msg( msg, messagetype )}
 %endif
 
+<script type="text/javascript">
+$( function() {
+    $( "select[refresh_on_change='true']").change( function() {
+        var refresh = false;
+        var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' )
+        if ( refresh_on_change_values ) {
+            refresh_on_change_values = refresh_on_change_values.value.split( ',' );
+            var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' );
+            for( i= 0; i < refresh_on_change_values.length; i++ ) {
+                if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){
+                    refresh = true;
+                    break;
+                }
+            }
+        }
+        else {
+            refresh = true;
+        }
+        if ( refresh ){
+            $( "#show_request" ).submit();
+        }
+    });
+});
+</script>
+
+
+<script type="text/javascript">
+$(document).ready(function(){
+    //hide the all of the element with class msg_body
+    $(".msg_body").hide();
+    //toggle the componenet with class msg_body
+    $(".msg_head").click(function(){
+        $(this).next(".msg_body").slideToggle(450);
+    });
+});
+</script>
+<style type="text/css">
+.msg_head {
+    padding: 15px 0px;
+    cursor: pointer;
+}
+
+}
+</style>
+
 %if request.rejected():
     ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}
 %endif
@@ -27,37 +72,144 @@
             <span>Reject request</span></a>
         </li>
     %endif
-    %if request.submitted() and request.samples:
-        <li>
-            <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}">
-            <span>Bar codes</span></a>
-        </li>
-    %endif
+##    %if request.submitted() and request.samples:
+##        <li>
+##            <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}">
+##            <span>Bar codes</span></a>
+##        </li>
+##    %endif
     <li>
         <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">
         <span>History</span></a>
     </li>
 
+
 </ul>
 
+<%def name="show_basic_info_form( sample_index, sample, info )">
+    <td>
+        <input type="text" name=sample_${sample_index}_name value="${info['name']}" size="10"/>
+        <div class="toolParamHelp" style="clear: both;">
+            <i>${' (required)' }</i>
+        </div>
+    </td>
+    %if sample:
+        %if sample.request.unsubmitted():
+            <td></td>
+        %else:
+            <td><input type="text" name=sample_${sample_index}_barcode value="${info['barcode']}" size="10"/></td>
+        %endif
+    %else:
+        <td></td>
+    %endif
+    %if sample:
+        %if sample.request.unsubmitted():
+            <td>Unsubmitted</td>
+        %else:
+            <td><a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a></td>
+        %endif    
+    %else:
+        <td></td>
+    %endif
+    <td>${info['lib_widget'].get_html()}</td>
+    <td>${info['folder_widget'].get_html()}</td>
+    %if request.submitted() or request.complete(): 
+        %if sample:
+            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a></td> 
+        %else:
+            <td><a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">Add</a></td>
+        %endif 
+    %endif 
+</%def>
 
-<%def name="render_sample_form( index, sample_name, sample_values, grid_index, fields_dict )">
-    %if grid_index == 0:
-        <td>
-            <input type="text" name=sample_${index}_name value="${sample_name}" size="10"/>
-            <div class="toolParamHelp" style="clear: both;">
-                <i>${' (required)' }</i>
-            </div>
-        </td>
-        <td>
-        </td>
-        <td>
-        </td>
-    %else:
-        <td>
-            ${sample_name}
-        </td>
-    %endif
+## This function displays the "Basic Information" grid
+<%def name="render_basic_info_grid()">
+    <h4>Sample Information</h4>
+    <table class="grid">
+        <thead>
+            <tr>
+                <th>Name</th>
+                <th>Barcode</th>
+                <th>State</th>
+                <th>Data Library</th>
+                <th>Folder</th>
+                %if request.submitted() or request.complete(): 
+                    <th>Dataset(s)</th>
+                %endif
+                <th></th>
+            </tr>
+        <thead>
+        <tbody>
+            <%
+            trans.sa_session.refresh( request )
+            %>
+            %for sample_index, info in enumerate(current_samples):
+                <% 
+                    if sample_index in range(len(request.samples)):
+                        sample = request.samples[sample_index]
+                    else:
+                        sample = None 
+                %>
+                %if edit_mode == 'True':
+                    <tr>
+                        ${show_basic_info_form( sample_index, sample, info )}
+                    </tr>      
+                %else:
+                    <tr>
+                        %if sample_index in range(len(request.samples)):
+                            <td>${info['name']}</td>
+                            <td>${info['barcode']}</td>
+                            <td>
+                                %if sample:
+                                    %if sample.request.unsubmitted():
+                                        Unsubmitted
+                                    %else:
+                                        <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
+                                    %endif
+                                %endif
+                            </td>
+                            %if info['library']:
+                                <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller='library', id=trans.security.encode_id( info['library'].id ) )}">${info['library'].name}</a></td>
+                            %else:
+                                <td></td>
+                            %endif
+                            %if info['folder']:
+                                <td>${info['folder'].name}</td>
+                            %else:
+                                <td></td>
+                            %endif
+                            %if request.submitted() or request.complete(): 
+                                <td>
+                                    <a href="${h.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id) )}">${len(sample.dataset_files)}</a>
+                                </td>
+                            %endif
+                            
+                            
+                        %else:                                                            
+                            ${show_basic_info_form( sample_index, sample, info )}
+                        %endif
+                        %if request.unsubmitted() or request.rejected(): 
+                            <td>
+                                %if sample:
+                                    %if sample.request.unsubmitted():
+                                        <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index )}">
+                                        <img src="${h.url_for('/static/images/delete_icon.png')}" />
+                                        <span></span></a>
+                                    %endif
+                                %endif
+                            </td>
+                        %endif
+                    </tr>  
+                %endif
+            %endfor
+        </tbody>
+    </table>
+</%def>
+
+<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )">
+    <td>
+        ${sample_name}
+    </td>
     %for field_index, field in fields_dict.items():
         <td>
             %if field['type'] == 'TextField':
@@ -75,7 +227,7 @@
             %elif field['type'] == 'CheckboxField':
                 <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/>
             %elif field['type'] == 'NumberField':
-                <input type=int name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
+                <input type="int" name="sample_${index}_field_${field_index}" value="${sample_values[field_index]}" size="7"/>
             %endif
             <div class="toolParamHelp" style="clear: both;">
                 <i>${'('+field['required']+')' }</i>
@@ -84,24 +236,14 @@
     %endfor   
 </%def>
 
-<%def name="render_sample( index, sample, grid_index, fields_dict )">
+<%def name="render_sample( index, sample_name, sample_values, fields_dict )">
     <td>
-        ${sample.name}
+        ${sample_name}
     </td>
-    %if grid_index == 0:
-        <td>${sample.bar_code}</td>
-        <td>
-            %if sample.request.new():
-                Unsubmitted
-            %else:
-                <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a>
-            %endif    
-        </td>
-    %endif
     %for field_index, field in fields_dict.items():
         <td>
-            %if sample.values.content[field_index]:
-                ${sample.values.content[field_index]}
+            %if sample_values[field_index]:
+                ${sample_values[field_index]}
             %else:
                 <i>None</i>
             %endif
@@ -111,22 +253,16 @@
 
 <div class="toolForm">
     <div class="form-row">
-        %if details == "show":
-            <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="hide"  )}">Hide request details</a>
-            </div>
+        <div class="msg_list">
+            <h4 class="msg_head">Request Information</h4>
+            <div class="msg_body">
                 %for index, rd in enumerate(request_details):
                     <div class="form-row">
                         <label>${rd['label']}</label>
                         %if not rd['value']:
                             <i>None</i>
                         %else:                      
-                            %if rd['label'] == 'Data library':
-                                %if rd['value']:
-                                    <a href="${h.url_for( controller='library_common', action='browse_library', cntrller='requests_admin', id=trans.security.encode_id( request.library.id ) )}">${rd['value']}</a>
-                                %else:
-                                    <i>None</i>
-                                %endif
-                            %elif rd['label'] == 'State':
+                            %if rd['label'] == 'State':
                                 <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a>
                             %else:
                                 ${rd['value']}     
@@ -144,25 +280,27 @@
                 </ul>
                 </div>
             </div>
-        %else:
-            <a href="${h.url_for( controller='requests_admin', action='toggle_request_details', request_id=request.id, details="show"  )}">Show request details</a>        
-        %endif
+        </div>
+    </div>
 </div>
 
+
 <%def name="render_grid( grid_index, grid_name, fields_dict )">
+    <div class="msg_list">
     %if grid_name:
-        <div class="toolFormTitle">${grid_name}</div>
+        <h4 class="msg_head">${grid_name}</h4>
+    %else:
+        <h4>Grid ${grid_index}</h4>
     %endif
-    <div style="clear: both"></div>
+    %if edit_mode == 'False' or len(current_samples) <= len(request.samples):
+        <div class="msg_body">
+    %else:
+        <div class="msg_body2">
+    %endif
     <table class="grid">
         <thead>
             <tr>
-                <th>No.</th>
-                <th>Sample Name</th>
-                %if grid_index == 0:
-                    <th>Barcode</th>
-                    <th>State</th>
-                %endif
+                <th>Name</th>
                 %for index, field in fields_dict.items():
                     <th>
                         ${field['label']}
@@ -181,50 +319,36 @@
             %for sample_index, sample in enumerate(current_samples):
                 %if edit_mode == 'True':
                     <tr>
-                        <td>${sample_index+1}</td>
-                        ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)}
-                        <td>
-                            %if request.unsubmitted() and grid_index == 0:
-                                <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
-                                <img src="${h.url_for('/static/images/delete_icon.png')}" />
-                                <span></span></a>
-                            %endif
-                        </td>
+                        ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
                     </tr>      
                 %else:
                     <tr>
-                        <td>${sample_index+1}</td>
                         %if sample_index in range(len(request.samples)):
-                            ${render_sample( sample_index, request.samples[sample_index], grid_index, fields_dict )}
+                            ${render_sample( sample_index, sample['name'], sample['field_values'], fields_dict )}
                         %else:                                                            
-                            ${render_sample_form( sample_index, sample[0], sample[1], grid_index, fields_dict)}
+                            ${render_sample_form( sample_index, sample['name'], sample['field_values'], fields_dict)}
                         %endif
-                        <td>
-                            %if grid_index == 0:
-                                <a class="action-button" href="${h.url_for( controller='requests_admin', action='delete_sample', request_id=request.id, sample_id=sample_index)}">
-                                <img src="${h.url_for('/static/images/delete_icon.png')}" />
-                                <span></span></a>
-                            %endif
-                        </td>
                     </tr>  
                 %endif
             %endfor
         </tbody>
     </table>
+    </div>
+    </div>
 </%def>
 
 <div class="toolForm">
     ##<div class="toolFormTitle">Samples (${len(request.samples)})</div>
     <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" >
         <div class="form-row">
-            %if current_samples: 
-                %if not request.type.sample_form.layout:
-                    ${render_grid( 0, "", request.type.sample_form.fields_of_grid( None ) )}
-                %else:
-                    %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
-                        ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_name ) )}
-                    %endfor
-                %endif
+            %if current_samples:
+                ## first render the basic info grid 
+                ${render_basic_info_grid()}
+                ## then render the other grid(s)
+                <% trans.sa_session.refresh( request.type.sample_form ) %>
+                %for grid_index, grid_name in enumerate(request.type.sample_form.layout):
+                    ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )}
+                %endfor
             %else:
                 <label>There are no samples.</label>
             %endif
@@ -233,6 +357,7 @@
             <table class="grid">
                 <tbody>
                     <tr>
+                        %if not request.complete():
                         <div class="form-row">
                             <td>
                                 %if current_samples and not request.complete():                        
@@ -254,6 +379,7 @@
                             </td>
                             %endif
                         </div>
+                        %endif
                     </tr> 
                 </tbody>
             </table>
@@ -264,15 +390,18 @@
                     <input type="hidden" name="refresh" value="true" size="40"/>
                 </div>
               <div style="clear: both"></div>
-            </div>
-            <div class="form-row">
-                %if edit_mode == 'True':   
+            </div>            
+            %if edit_mode == 'True':   
+                <div class="form-row">
                     <input type="submit" name="save_samples_button" value="Save"/>
                     <input type="submit" name="cancel_changes_button" value="Cancel"/>
-                %elif request.unsubmitted():
+                </div>
+            %elif request.unsubmitted():
+                <div class="form-row">
                     <input type="submit" name="save_samples_button" value="Save"/>
-                %endif
-            </div>
+                </div>
+            %endif
+            
         %endif
         <input type="hidden" name="request_id" value="${request.id}" />
     </form>
diff -r 44fff02fb036 -r 37b55fad152b templates/admin/requests/view_request_type.mako
--- a/templates/admin/requests/view_request_type.mako	Thu Feb 04 10:44:36 2010 -0500
+++ b/templates/admin/requests/view_request_type.mako	Thu Feb 04 11:01:45 2010 -0500
@@ -6,9 +6,11 @@
     ${render_msg( msg, messagetype )}
 %endif
 
+<h2>Request Type "${request_type.name}"</h2>
+
 <div class="toolForm">
     <div class="toolFormTitle">Request type information</div>
-    <form name="library">
+    <form name="view_request_type" action="${h.url_for( controller='requests_admin', action='create_request_type', rt_id=request_type.id)}" method="post" >
         <div class="form-row">
             <label>Name</label>
             ${request_type.name}
@@ -32,12 +34,31 @@
             ${request_type.sample_form.name}
         </div>    
         <div class="toolFormTitle">Possible sample states</div>
-            %for element_count, state in enumerate(states_list):
-                <div class="form-row">
-                    <label>${1+element_count}. ${state.name}</label>
-                    ${state.desc}
-                </div>
-                <div style="clear: both"></div>
-            %endfor
+        %for element_count, state in enumerate(states_list):
+            <div class="form-row">
+                <label>${1+element_count}. ${state.name}</label>
+                ${state.desc}
+            </div>
+            <div style="clear: both"></div>
+        %endfor
+        <div class="toolFormTitle">Sequencer information</div>
+        <div class="form-row">
+            This information is only needed for transferring data from sequencer to Galaxy
+        </div>
+        <div class="form-row">
+            <label>Hostname or IP Address:</label>
+            <input type="text" name="host" value="${request_type.datatx_info['host']}" size="40"/>
+        </div>

    

[galaxy-dev] [hg] galaxy 3329: Sequencer data acquisition for LIMS

Greg Von Kuster