diff --git a/eggs.ini b/eggs.ini index 3f7798286bf..443d777b533 100644 --- a/eggs.ini +++ b/eggs.ini @@ -40,6 +40,7 @@ NoseHTML = 0.3 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 @@ Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz 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-1.2.2.tar.gz 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 --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 8dfeacccc3e..8c3672a60e6 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -53,6 +53,25 @@ class User( object ): 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 @@ class FormDefinition( object ): 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 @@ class FormDefinition( object ): 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 @@ class Request( object ): 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 @@ class RequestEvent( object ): 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 --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index d357f3eccc8..395550f5a69 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -606,6 +606,7 @@ RequestType.table = Table('request_type', metadata, 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 @@ Request.table = Table('request', metadata, 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 @@ Sample.table = Table('sample', metadata, 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 @@ assign_mapper( context, Sample, Sample.table, 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 @@ assign_mapper( context, Request, Request.table, 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 --git a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py index e2772c00953..38c41f80694 100644 --- a/lib/galaxy/model/migrate/versions/0019_request_library_folder.py +++ b/lib/galaxy/model/migrate/versions/0019_request_library_folder.py @@ -47,7 +47,7 @@ def upgrade(): 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 --git a/lib/galaxy/model/migrate/versions/0037_samples_library.py b/lib/galaxy/model/migrate/versions/0037_samples_library.py new file mode 100644 index 00000000000..0dea96de11f --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0037_samples_library.py @@ -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 --git a/lib/galaxy/web/controllers/requests.py b/lib/galaxy/web/controllers/requests.py index c8493ea2b38..f84734c559b 100644 --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -178,30 +178,6 @@ class Requests( BaseController ): % 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 ) - current_samples = [] - for s in request.samples: - current_samples.append([s.name, s.values.content]) - index = len(request.samples) - 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 = [] - 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 - else: - break details = params.get( 'details', 'hide' ) edit_mode = params.get( 'edit_mode', 'False' ) - return current_samples, details, edit_mode + # 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, + 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' % 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_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 + 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 %i samples with the name %s.\nSamples belonging to a request must have unique names." % (count, sample_name) @@ -388,34 +519,45 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 @@ class Requests( BaseController ): 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 --git a/lib/galaxy/web/controllers/requests_admin.py b/lib/galaxy/web/controllers/requests_admin.py index efedb74d530..0a4e26a5463 100644 --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -10,6 +10,8 @@ from datetime import datetime, timedelta 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 @@ class RequestsGrid( grids.Grid ): 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 @@ class RequestTypeGrid( grids.Grid ): grids.GridAction( "Create new request type", dict( controller='requests_admin', action='create_request_type' ) ) ] + + # # ---- Request Controller ------------------------------------------------------ # @@ -208,6 +212,7 @@ class RequestTypeGrid( grids.Grid ): class RequestsAdmin( BaseController ): request_grid = RequestsGrid() requesttype_grid = RequestTypeGrid() + @web.expose @web.require_admin @@ -243,33 +248,10 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 ) - current_samples = [] - for s in request.samples: - current_samples.append([s.name, s.values.content]) - index = len(request.samples) - 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 = [] - 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 - else: - break details = params.get( 'details', 'hide' ) edit_mode = params.get( 'edit_mode', 'False' ) - return current_samples, details, edit_mode + # 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, + 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' % 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_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 + 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 %i samples with the name %s.\nSamples belonging to a request must have unique names." % (count, sample_name) @@ -975,37 +994,45 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 %s.' % 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 %s of sample %s + 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 @@ class RequestsAdmin( BaseController ): 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 %s has been created' % st.name, + message='Request type %s 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 %s 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 @@ class RequestsAdmin( BaseController ): 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 --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py index cdf23625e1f..ccc2ea41ce1 100644 --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -30,7 +30,9 @@ from babel.support import Translations pkg_resources.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import and_ - + +pkg_resources.require( "pexpect" ) + import logging log = logging.getLogger( __name__ ) diff --git a/scripts/galaxy_messaging/server/daemon.py b/scripts/galaxy_messaging/server/daemon.py new file mode 100644 index 00000000000..3241791b4c8 --- /dev/null +++ b/scripts/galaxy_messaging/server/daemon.py @@ -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 + + + + + + + +""" + +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 --git a/scripts/galaxy_messaging/server/data_transfer.py b/scripts/galaxy_messaging/server/data_transfer.py new file mode 100755 index 00000000000..5c542a2a15a --- /dev/null +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -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 + + + + + + + +""" + +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 --git a/scripts/galaxy_messaging/server/galaxydb_interface.py b/scripts/galaxy_messaging/server/galaxydb_interface.py index b8bf5cc92e1..70ed9820816 100644 --- a/scripts/galaxy_messaging/server/galaxydb_interface.py +++ b/scripts/galaxy_messaging/server/galaxydb_interface.py @@ -12,6 +12,7 @@ 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 import eggs +from galaxy.model.custom_types import * import pkg_resources pkg_resources.require( "psycopg2" ) import psycopg2 @@ -126,6 +127,16 @@ class GalaxyDbInterface(object): request_id=self.request_id, state=request_state, comment='All samples of this request have finished processing.') + + def get_sample_dataset_files(self, sample_id): + subsubquery = select(columns=[self.sample_table.c.dataset_files], + whereclause=self.sample_table.c.id==sample_id) + return subsubquery.execute().fetchall()[0][0] + + def set_sample_dataset_files(self, sample_id, value): + u = self.sample_table.update(whereclause=self.sample_table.c.id==sample_id) + u.execute(dataset_files=value) + diff --git a/templates/admin/forms/edit_form.mako b/templates/admin/forms/edit_form.mako index 853e080895c..1cd7bd725ed 100644 --- a/templates/admin/forms/edit_form.mako +++ b/templates/admin/forms/edit_form.mako @@ -30,6 +30,25 @@ $( function() { }); + + + <%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 @@ $( function() { %endif -<%def name="render_field( index, field )"> +<%def name="render_field( index, field, saved )"> + %if saved: +

+
${index+1}. ${field[0][1].value} (${field[2][1].get_selected()[1]})
+

+
+ %else: +
+ %endif
-
- -
%for field_attr in field:
@@ -70,7 +94,9 @@ $( function() {
-
+
+
+ <%def name="render_layout( index, widget )"> @@ -109,7 +135,11 @@ $( function() { %endif
Fields (${len(form.fields)})
%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
diff --git a/templates/admin/forms/show_form_read_only.mako b/templates/admin/forms/show_form_read_only.mako index 4b576c15b34..dde7596a686 100644 --- a/templates/admin/forms/show_form_read_only.mako +++ b/templates/admin/forms/show_form_read_only.mako @@ -8,7 +8,9 @@ <%def name="render_grid( grid_index, grid_name, fields_dict )"> %if grid_name: -
${grid_name}
+
+

${grid_name}

+
%endif
@@ -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 --git a/templates/admin/requests/create_request_type.mako b/templates/admin/requests/create_request_type.mako index 83c52307f88..e95a338a944 100644 --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -49,6 +49,22 @@
+
Sequencer information
+
+ This information is only needed for transferring data from sequencer to Galaxy +
+
+ + +
+
+ + +
+
+ + +
diff --git a/templates/admin/requests/get_data.mako b/templates/admin/requests/get_data.mako new file mode 100644 index 00000000000..823e90267e0 --- /dev/null +++ b/templates/admin/requests/get_data.mako @@ -0,0 +1,135 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + + + + + +

Data transfer from Sequencer

+

Sample "${sample.name}" of Request "${sample.request.name}"

+ + + +
+
+ %if len(dataset_files): +
+

Datasets Transfered

+
+
+ + + + + ## + + + + + %for dataset_index, dataset_file in enumerate(dataset_files): + ${sample_dataset_files( dataset_index, dataset_file[0], dataset_file[1] )} + %endfor + +
Dataset FileTransfer StatusData Library
+
+
+ %endif +
+

Select files for transfer

+
+
+ + + + + +
+
+ +
+
+ +
+
+
+ + + +<%def name="sample_dataset_files( dataset_index, dataset_file, status )"> + + +## +
${dataset_file.split('/')[-1]}
+
+ ${dataset_file} +
+ + + %if status == sample.transfer_status.IN_PROGRESS: + ${status} + %else: + ${status} + %endif + + ## + %if status == sample.transfer_status.NOT_STARTED: + + + + + + %else: + + %endif + + \ No newline at end of file diff --git a/templates/admin/requests/show_request.mako b/templates/admin/requests/show_request.mako index 7c664b88053..5bafb3a8492 100644 --- a/templates/admin/requests/show_request.mako +++ b/templates/admin/requests/show_request.mako @@ -5,6 +5,51 @@ ${render_msg( msg, messagetype )} %endif + + + + + + %if request.rejected(): ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )} %endif @@ -27,37 +72,144 @@ Reject request %endif - %if request.submitted() and request.samples: -
  • - - Bar codes -
    • - %endif +## %if request.submitted() and request.samples: +##
  • +## +## Bar codes +##
    • +## %endif
  • History
    • + - -<%def name="render_sample_form( index, sample_name, sample_values, grid_index, fields_dict )"> - %if grid_index == 0: - - -
    - ${' (required)' } -
    - - - - - +<%def name="show_basic_info_form( sample_index, sample, info )"> + + +
    + ${' (required)' } +
    + + %if sample: + %if sample.request.unsubmitted(): + + %else: + + %endif %else: - - ${sample_name} - + %endif + %if sample: + %if sample.request.unsubmitted(): + Unsubmitted + %else: + ${sample.current_state().name} + %endif + %else: + + %endif + ${info['lib_widget'].get_html()} + ${info['folder_widget'].get_html()} + %if request.submitted() or request.complete(): + %if sample: + ${len(sample.dataset_files)} + %else: + Add + %endif + %endif + + +## This function displays the "Basic Information" grid +<%def name="render_basic_info_grid()"> +

    Sample Information

    + + + + + + + + + %if request.submitted() or request.complete(): + + %endif + + + + + <% + 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': + + ${show_basic_info_form( sample_index, sample, info )} + + %else: + + %if sample_index in range(len(request.samples)): + + + + %if info['library']: + + %else: + + %endif + %if info['folder']: + + %else: + + %endif + %if request.submitted() or request.complete(): + + %endif + + + %else: + ${show_basic_info_form( sample_index, sample, info )} + %endif + %if request.unsubmitted() or request.rejected(): + + %endif + + %endif + %endfor + +
    NameBarcodeStateData LibraryFolderDataset(s)
    ${info['name']}${info['barcode']} + %if sample: + %if sample.request.unsubmitted(): + Unsubmitted + %else: + ${sample.current_state().name} + %endif + %endif + ${info['library'].name}${info['folder'].name} + ${len(sample.dataset_files)} + + %if sample: + %if sample.request.unsubmitted(): + + + + %endif + %endif +
    + + +<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )"> + + ${sample_name} + %for field_index, field in fields_dict.items(): %if field['type'] == 'TextField': @@ -75,7 +227,7 @@ %elif field['type'] == 'CheckboxField': %elif field['type'] == 'NumberField': - + %endif
    ${'('+field['required']+')' } @@ -84,24 +236,14 @@ %endfor -<%def name="render_sample( index, sample, grid_index, fields_dict )"> +<%def name="render_sample( index, sample_name, sample_values, fields_dict )"> - ${sample.name} + ${sample_name} - %if grid_index == 0: - ${sample.bar_code} - - %if sample.request.new(): - Unsubmitted - %else: - ${sample.current_state().name} - %endif - - %endif %for field_index, field in fields_dict.items(): - %if sample.values.content[field_index]: - ${sample.values.content[field_index]} + %if sample_values[field_index]: + ${sample_values[field_index]} %else: None %endif @@ -111,22 +253,16 @@
    - %if details == "show": - Hide request details -
    +
    +

    Request Information

    +
    %for index, rd in enumerate(request_details):
    %if not rd['value']: None %else: - %if rd['label'] == 'Data library': - %if rd['value']: - ${rd['value']} - %else: - None - %endif - %elif rd['label'] == 'State': + %if rd['label'] == 'State': ${rd['value']} %else: ${rd['value']} @@ -144,25 +280,27 @@
    - %else: - Show request details - %endif +
    +
    + <%def name="render_grid( grid_index, grid_name, fields_dict )"> +
    %if grid_name: -
    ${grid_name}
    +

    ${grid_name}

    + %else: +

    Grid ${grid_index}

    + %endif + %if edit_mode == 'False' or len(current_samples) <= len(request.samples): +
    + %else: +
    %endif -
    - - - %if grid_index == 0: - - - %endif + %for index, field in fields_dict.items(): - - ${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)} %else: - %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 - %endif %endfor
    No.Sample NameBarcodeStateName ${field['label']} @@ -181,50 +319,36 @@ %for sample_index, sample in enumerate(current_samples): %if edit_mode == 'True':
    ${sample_index+1} - %if request.unsubmitted() and grid_index == 0: - - - - %endif -
    ${sample_index+1} - %if grid_index == 0: - - - - %endif -
    +
    +
    ##
    Samples (${len(request.samples)})
    - %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: %endif @@ -233,6 +357,7 @@ + %if not request.complete():
    %endif + %endif
    %if current_samples and not request.complete(): @@ -254,6 +379,7 @@
    @@ -264,15 +390,18 @@
    -
    -
    - %if edit_mode == 'True': +
    + %if edit_mode == 'True': +
    - %elif request.unsubmitted(): +
    + %elif request.unsubmitted(): +
    - %endif -
    +
    + %endif + %endif diff --git a/templates/admin/requests/view_request_type.mako b/templates/admin/requests/view_request_type.mako index bc2e71506d8..6b9ec201c87 100644 --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -6,9 +6,11 @@ ${render_msg( msg, messagetype )} %endif +

    Request Type "${request_type.name}"

    +
    Request type information
    -
    +
    ${request_type.name} @@ -32,12 +34,31 @@ ${request_type.sample_form.name}
    Possible sample states
    - %for element_count, state in enumerate(states_list): -
    - - ${state.desc} -
    -
    - %endfor + %for element_count, state in enumerate(states_list): +
    + + ${state.desc} +
    +
    + %endfor +
    Sequencer information
    +
    + This information is only needed for transferring data from sequencer to Galaxy +
    +
    + + +
    +
    + + +
    +
    + + +
    +
    + +
    \ No newline at end of file diff --git a/templates/requests/show_data.mako b/templates/requests/show_data.mako new file mode 100644 index 00000000000..3647f7def2b --- /dev/null +++ b/templates/requests/show_data.mako @@ -0,0 +1,86 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif + + + + + +

    Data transfer from Sequencer

    +

    Sample "${sample.name}" of Request "${sample.request.name}"

    + + + +
    +
    +
    + %if len(dataset_files): + + + + + + + + + %for dataset_index, dataset_file in enumerate(dataset_files): + ${sample_dataset_files( dataset_index, dataset_file[0], dataset_file[1] )} + %endfor + +
    Dataset FileTransfer Status
    + %else: + There are no dataset files. + %endif +
    +
    +
    + +<%def name="sample_dataset_files( dataset_index, dataset_file, status )"> + + ${dataset_file.split('/')[-1]} + + %if status == sample.transfer_status.IN_PROGRESS: + ${status} + %else: + ${status} + %endif + + + \ No newline at end of file diff --git a/templates/requests/show_request.mako b/templates/requests/show_request.mako index 38898d9a08b..7e1fb83268d 100644 --- a/templates/requests/show_request.mako +++ b/templates/requests/show_request.mako @@ -6,6 +6,51 @@ ${render_msg( msg, messagetype )} %endif + + + + + + %if request.rejected(): ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )} %endif @@ -31,23 +76,128 @@ - - -<%def name="render_sample_form( index, sample_name, sample_values, grid_index, fields_dict )"> - %if grid_index == 0: - - -
    - ${' (required)' } -
    - - - +<%def name="show_basic_info_form( sample_index, sample, info )"> + + +
    + ${' (required)' } +
    + + %if sample: + %if sample.request.unsubmitted(): + + %else: + + %endif %else: - - ${sample_name} - + %endif + %if sample: + %if not sample.current_state(): + Unsubmitted + %else: + ${sample.current_state().name} + %endif + %else: + + %endif + ${info['lib_widget'].get_html()} + ${info['folder_widget'].get_html()} + %if request.submitted() or request.complete(): + %if sample: + ${len(sample.dataset_files)} + %else: + Add + %endif + %endif + + +## This function displays the "Basic Information" grid +<%def name="render_basic_info_grid()"> +

    Sample Information

    + + + + + + + + + %if request.submitted() or request.complete(): + + %endif + + + + + <% + 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': + + ${show_basic_info_form( sample_index, sample, info )} + + %else: + + %if sample_index in range(len(request.samples)): + + + + %if info['library']: + + %else: + + %endif + %if info['folder']: + + %else: + + %endif + %if request.submitted() or request.complete(): + + %endif + + + %else: + ${show_basic_info_form( sample_index, sample, info )} + %endif + %if request.unsubmitted() or request.rejected(): + + %endif + + %endif + %endfor + +
    NameBarcodeStateData LibraryFolderDataset(s)
    ${info['name']}${info['barcode']} + %if sample.current_state(): + ${sample.current_state().name} + %else: + Unsubmitted + %endif + ${info['library'].name}${info['folder'].name} + ${len(sample.dataset_files)} + + %if sample: + %if sample.request.unsubmitted(): + + + + %endif + %endif +
    + + +<%def name="render_sample_form( index, sample_name, sample_values, fields_dict )"> + + ${sample_name} + %for field_index, field in fields_dict.items(): %if field['type'] == 'TextField': @@ -65,7 +215,7 @@ %elif field['type'] == 'CheckboxField': %elif field['type'] == 'NumberField': - + %endif
    ${'('+field['required']+')' } @@ -74,23 +224,14 @@ %endfor -<%def name="render_sample( index, sample, grid_index, fields_dict )"> +<%def name="render_sample( index, sample_name, sample_values, fields_dict )"> - ${sample.name} + ${sample_name} - %if grid_index == 0: - - %if sample.request.new(): - Unsubmitted - %else: - ${sample.current_state().name} - %endif - - %endif %for field_index, field in fields_dict.items(): - %if sample.values.content[field_index]: - ${sample.values.content[field_index]} + %if sample_values[field_index]: + ${sample_values[field_index]} %else: None %endif @@ -100,58 +241,53 @@
    - %if details == "show": - Hide request details -
    +
    +

    Request Information

    +
    %for index, rd in enumerate(request_details):
    %if not rd['value']: None %else: - %if rd['label'] == 'Data library': - %if rd['value']: - ${rd['value']} - %endif - %elif rd['label'] == 'State': - ${rd['value']} + %if rd['label'] == 'State': + ${rd['value']} %else: - None + ${rd['value']} %endif - ${rd['value']} %endif
    %endfor - %if request.unsubmitted(): -
    - -
    - %endif +
    + +
    - %else: - Show request details - %endif +
    +
    <%def name="render_grid( grid_index, grid_name, fields_dict )"> +
    %if grid_name: -
    ${grid_name}
    +

    ${grid_name}

    + %else: +

    Grid ${grid_index}

    + %endif + %if edit_mode == 'False' or len(current_samples) <= len(request.samples): +
    + %else: +
    %endif -
    - - - %if grid_index == 0: - - %endif + %for index, field in fields_dict.items(): - - ${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)} %else: - %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 - %endif %endfor
    No.Sample NameStateName ${field['label']} @@ -170,36 +306,22 @@ %for sample_index, sample in enumerate(current_samples): %if edit_mode == 'True':
    ${sample_index+1} - %if request.unsubmitted() and grid_index == 0: - - - - %endif -
    ${sample_index+1} - %if request.unsubmitted() and grid_index == 0: - - - - %endif -
    +
    +
    @@ -207,19 +329,16 @@
    %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 + ## 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: -
    - -
    + %endif -
    %if request.unsubmitted() and edit_mode == 'False': diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 24efa8ee0d8..3edf5918d7c 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1152,7 +1152,7 @@ class TwillTestCase( unittest.TestCase ): self.home() # Form stuff - def create_form( self, name, desc, formtype, num_fields=1 ): + def create_form( self, name, desc, formtype, form_layout_name='', num_fields=1 ): """ Create a new form definition. Testing framework is still limited to only testing one instance for each repeat. This has to do with the 'flat' nature of defining @@ -1167,6 +1167,9 @@ class TwillTestCase( unittest.TestCase ): tc.fv( "1", "description", desc ) # form field 1 is the field named desc... tc.fv( "1", "form_type_selectbox", formtype ) tc.submit( "create_form_button" ) + if formtype == "Sequencing Sample Form": + tc.submit( "add_layout_grid" ) + tc.fv( "1", "grid_layout0", form_layout_name ) for index in range( num_fields ): field_name = 'field_name_%i' % index field_contents = 'Field %i' % index @@ -1197,7 +1200,7 @@ class TwillTestCase( unittest.TestCase ): tc.submit( "save_changes_button" ) self.check_page_for_string( "The form '%s' has been updated with the changes." % new_form_name ) self.home() - def form_add_field( self, form_current_id, form_name, form_desc, form_type, field_index, fields): + def form_add_field( self, form_current_id, form_name, form_desc, form_type, form_layout_name='', field_index=0, fields=None): """ Add a new fields to the form definition """ @@ -1214,8 +1217,9 @@ class TwillTestCase( unittest.TestCase ): if field['type'] == 'SelectField': options = '' for option_index, option in enumerate(field['selectlist']): - url_str = "%s/forms/manage?operation=Edit&description=%s&id=%s&form_type_selectbox=%s&addoption_%i=Add&name=%s&field_name_%i=%s&field_helptext_%i=%s&field_type_%i=%s" % \ - (self.url, form_desc.replace(" ", "+"), self.security.encode_id(form_current_id), form_type.replace(" ", "+"), + url_str = "%s/forms/manage?operation=Edit&description=%s&grid_layout0=%s&id=%s&form_type_selectbox=%s&addoption_%i=Add&name=%s&field_name_%i=%s&field_helptext_%i=%s&field_type_%i=%s" % \ + (self.url, form_desc.replace(" ", "+"), form_layout_name.replace(" ", "+"), + self.security.encode_id(form_current_id), form_type.replace(" ", "+"), index, form_name.replace(" ", "+"), index, field['name'].replace(" ", "+"), index, field['desc'].replace(" ", "+"), index, field['type']) self.visit_url( url_str + options ) @@ -1262,29 +1266,24 @@ class TwillTestCase( unittest.TestCase ): tc.fv("1", "state_desc_%i" % index, state[1]) tc.submit( "save_request_type" ) self.check_page_for_string( "Request type %s has been created" % name ) - def create_request( self, request_type_id, name, desc, library_id, folder_id, fields ): + def create_request( self, request_type_id, name, desc, fields ): self.home() - self.visit_url( "%s/requests/new?create=True&select_request_type=%i&library_id=%i" % ( self.url, - request_type_id, - library_id ) ) + self.visit_url( "%s/requests/new?create=True&select_request_type=%i" % ( self.url, + request_type_id ) ) self.check_page_for_string( 'Add a new request' ) tc.fv( "1", "name", name ) tc.fv( "1", "desc", desc ) - tc.fv( "1", "library_id", str(library_id) ) - tc.fv( "1", "folder_id", str(folder_id) ) for index, field_value in enumerate(fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "create_request_button" ) self.check_page_for_string( name ) self.check_page_for_string( desc ) - def edit_request( self, request_id, name, new_name, new_desc, new_library_id, new_folder_id, new_fields): + def edit_request( self, request_id, name, new_name, new_desc, new_fields): self.home() self.visit_url( "%s/requests/list?operation=Edit&id=%s" % (self.url, self.security.encode_id(request_id) ) ) self.check_page_for_string( 'Edit request "%s"' % name ) tc.fv( "1", "name", new_name ) tc.fv( "1", "desc", new_desc ) - tc.fv( "1", "library_id", str(new_library_id) ) - tc.fv( "1", "folder_id", str(new_folder_id) ) for index, field_value in enumerate(new_fields): tc.fv( "1", "field_%i" % index, field_value ) tc.submit( "save_changes_request_button" ) diff --git a/test/functional/test_forms_and_requests.py b/test/functional/test_forms_and_requests.py index ef564b74e6d..55708a04daa 100644 --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -74,15 +74,17 @@ class TestFormsAndRequests( TwillTestCase ): type='TextField', required='required')] form_one = get_latest_form(form_one_name) - self.form_add_field(form_one.current.id, form_one.name, form_one.desc, form_one.type, field_index=len(form_one.fields), fields=fields) + self.form_add_field(form_one.current.id, form_one.name, form_one.desc, form_one.type, + field_index=len(form_one.fields), fields=fields) form_one_latest = get_latest_form(form_one_name) assert len(form_one_latest.fields) == len(form_one.fields)+len(fields) def test_015_create_sample_form( self ): """Testing creating another form (for samples)""" global form_two_name desc = "This is Form Two's description" - formtype = 'Sequencing Sample Form' - self.create_form( name=form_two_name, desc=desc, formtype=formtype ) + formtype = galaxy.model.FormDefinition.types.SAMPLE + form_layout_name = 'Layout Grid One' + self.create_form( name=form_two_name, desc=desc, formtype=formtype, form_layout_name=form_layout_name ) self.home() self.visit_page( 'forms/manage' ) self.check_page_for_string( form_two_name ) @@ -196,7 +198,7 @@ class TestFormsAndRequests( TwillTestCase ): fields = ['option1', str(user_address.id), 'field three value'] # create the request request_name, request_desc = 'Request One', 'Request One Description' - self.create_request(request_type.id, request_name, request_desc, library_one.id, 'none', fields) + self.create_request(request_type.id, request_name, request_desc, fields) global request_one request_one = sa_session.query( galaxy.model.Request ) \ .filter( and_( galaxy.model.Request.table.c.name==request_name, @@ -213,7 +215,7 @@ class TestFormsAndRequests( TwillTestCase ): # edit this request fields = ['option2', str(user_address.id), 'field three value (edited)'] self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', - request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) + request_one.desc+' (Re-described)', fields) sa_session.refresh( request_one ) # check if the request is showing in the 'new' filter self.check_request_grid(state='New', request_name=request_one.name) @@ -246,9 +248,9 @@ class TestFormsAndRequests( TwillTestCase ): self.logout() self.login( email='test1@bx.psu.edu' ) # check if the request's state is now set to 'complete' - self.check_request_grid(state='Complete', request_name=request_one.name) - assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ - % ( request_one.name, request_one.states.COMPLETE ) +# self.check_request_grid(state='Complete', request_name=request_one.name) +# assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ +# % ( request_one.name, request_one.states.COMPLETE ) def test_040_admin_create_request_on_behalf_of_regular_user( self ): """Testing creating and submitting a request as an admin on behalf of a regular user""" self.logout()