galaxy-commits November 2010

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galaxy-dist commit b7f712cecaa9: Prevent Rename Dataset Action from allowing a blank input.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1289590343 18000 # Node ID b7f712cecaa9f527f1161f923ebe798eba526cb6 # Parent fc1f67023d86a69ea7229501b093d61748630f4c Prevent Rename Dataset Action from allowing a blank input. --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -60,14 +60,12 @@ class DefaultJobAction(object): class EmailAction(DefaultJobAction): name = "EmailAction" verbose_name = "Email Notification" - @classmethod def execute(cls, app, sa_session, action, job): smtp_server = app.config.smtp_server - if action.action_arguments: - if action.action_arguments.has_key('host'): - host = action.action_arguments['host'] + if action.action_arguments and action.action_arguments.has_key('host'): + host = action.action_arguments['host'] else: host = 'usegalaxy.org' if smtp_server is None: @@ -107,9 +105,8 @@ class EmailAction(DefaultJobAction): @classmethod def get_short_str(cls, pja): - if pja.action_arguments: - if pja.action_arguments.has_key('host'): - return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] + if pja.action_arguments and pja.action_arguments.has_key('host'): + return "Email the current user from server %s when this job is complete." % pja.action_arguments['host'] else: return "Email the current user when this job is complete." @@ -153,9 +150,11 @@ class RenameDatasetAction(DefaultJobActi @classmethod def execute(cls, app, sa_session, action, job): - for dataset_assoc in job.output_datasets: - if action.output_name == '' or dataset_assoc.name == action.output_name: - dataset_assoc.dataset.name = action.action_arguments['newname'] + # Prevent renaming a dataset to the empty string. + if action.action_arguments and action.action_arguments.has_key('newname') and action.action_arguments['newname'] != '': + for dataset_assoc in job.output_datasets: + if action.output_name == '' or dataset_assoc.name == action.output_name: + dataset_assoc.dataset.name = action.action_arguments['newname'] @classmethod def get_config_form(cls, trans): @@ -173,7 +172,11 @@ class RenameDatasetAction(DefaultJobActi @classmethod def get_short_str(cls, pja): - return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) + # Prevent renaming a dataset to the empty string. + if pja.action_arguments and pja.action_arguments.has_key('newname') and pja.action_arguments['newname'] != '': + return "Rename output '%s' to '%s'." % (pja.output_name, pja.action_arguments['newname']) + else: + return "Rename action used without a new name specified. Output name will be unchanged." class HideDatasetAction(DefaultJobAction):

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galaxy-dist commit cadf13f67c65: More changes to sample tracking functional tests
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289597856 18000 # Node ID cadf13f67c6593d99f8134ba10baa211a026439b # Parent ecc1cefbccba6135f824f9573f06c130fd6d08b4 More changes to sample tracking functional tests - assign target data library, editing samples, assign sample barcode --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -4,7 +4,9 @@ from base.twilltestcase import * from base.test_db_util import * sample_states = [ ( 'New', 'Sample entered into the system' ), - ( 'Received', 'Sample tube received' ), + ( 'Received', 'Sample tube received' ), + ( 'Library Started', 'Sample library preparation' ), + ( 'Run Started', 'Sequence run in progress' ), ( 'Done', 'Sequence run complete' ) ] address_dict = dict( short_desc="Office", name="James Bond", @@ -93,6 +95,49 @@ class TestFormsAndRequests( TwillTestCas global role2 role2 = get_role_by_name( name ) assert role2 is not None, 'Problem retrieving role named "Role2" from the database' + def test_006_create_library_and_folder( self ): + """Testing creating the target data library and folder""" + # Logged in as admin_user + for index in range( 0, 2 ): + name = 'library%s' % str( index + 1 ) + description = '%s description' % name + synopsis = '%s synopsis' % name + self.create_library( name=name, description=description, synopsis=synopsis ) + # Get the libraries for later use + global library1 + library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' ) + assert library1 is not None, 'Problem retrieving library (library1) from the database' + global library2 + library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' ) + assert library2 is not None, 'Problem retrieving library (library2) from the database' + # setup add_library_item permission to regular_user1 + # Set permissions on the library, sort for later testing. + permissions_in = [ 'LIBRARY_ACCESS' ] + permissions_out = [] + # Role1 members are: admin_user, regular_user1, regular_user3. + # Each of these users will be permitted for LIBRARY_ACCESS, LIBRARY_ADD on + # library1 and library2. + for library in [ library1, library2 ]: + self.library_permissions( self.security.encode_id( library.id ), + library.name, + str( role1.id ), + permissions_in, + permissions_out ) + # adding a folder + for library in [ library1, library2 ]: + name = "%s_folder1" % library.name + description = "%s description" % name + self.add_folder( 'library_admin', + self.security.encode_id( library.id ), + self.security.encode_id( library.root_folder.id ), + name=name, + description=description ) + global library1_folder1 + library1_folder1 = get_folder( library1.root_folder.id, 'library1_folder1', 'library1_folder1 description' ) + assert library1_folder1 is not None, 'Problem retrieving library folder named "library1_folder1" from the database' + global library2_folder1 + library2_folder1 = get_folder( library2.root_folder.id, 'library2_folder1', 'library2_folder1 description' ) + assert library2_folder1 is not None, 'Problem retrieving library folder named "library2_folder1" from the database' # # ====== Form definition test methods ================================================ # @@ -283,25 +328,25 @@ class TestFormsAndRequests( TwillTestCas self.view_request( cntrller='requests', request_id=self.security.encode_id( request1.id ), strings_displayed=[ 'Sequencing request "%s"' % request1.name, - 'There are no samples.', - sample_form_layout_grid_name ], + 'There are no samples.' ], strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, - request1.states.REJECTED ] ) + request1.states.REJECTED, + 'Submit request' ] ) # this button should NOT show up as there are no samples yet # check if the request is showing in the 'new' filter self.check_request_grid( cntrller='requests', state=request1.states.NEW, strings_displayed=[ request1.name ] ) self.view_request_history( cntrller='requests', request_id=self.security.encode_id( request1.id ), - strings_displayed=[ 'History of Sequencing Request "%s"' % request1.name, + strings_displayed=[ 'History of sequencing request "%s"' % request1.name, request1.states.NEW, 'Request created' ], strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, request1.states.REJECTED ] ) def test_030_edit_basic_request_info( self ): - """Testing editing the basic information of a sequencing request""" + """Testing editing the basic information and email settings of a sequencing request""" # logged in as regular_user1 fields = [ 'option2', str( user_address1.id ), 'field3 value (edited)' ] new_name=request1.name + ' (Renamed)' @@ -315,43 +360,186 @@ class TestFormsAndRequests( TwillTestCas strings_displayed=[ 'Edit sequencing request "%s"' % request1.name ], strings_displayed_after_submit=[ new_name, new_desc ] ) refresh( request1 ) + # now check email notification settings + check_sample_states = [ ( request1.type.states[0].name, request1.type.states[0].id, True ), + ( request1.type.states[2].name, request1.type.states[2].id, True ), + ( request1.type.states[4].name, request1.type.states[4].id, True ) ]#[ ( state.id, True ) for state in request1.type.states ] + strings_displayed = [ 'Edit sequencing request "%s"' % request1.name, + 'Email notification settings' ] + additional_emails = [ 'test@.bx.psu.edu', 'test2@.bx.psu.edu' ] + strings_displayed_after_submit = [ "The changes made to the email notification settings have been saved", + '\r\n'.join( additional_emails ) ] + self.edit_request_email_settings( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + check_request_owner=True, + additional_emails='\r\n'.join( additional_emails ), + check_sample_states=check_sample_states, + strings_displayed=strings_displayed, + strings_displayed_after_submit=strings_displayed_after_submit ) + # lastly check the details in the request page + strings_displayed = [ 'Sequencing request "%s"' % new_name, + new_desc ] + for field in fields: + strings_displayed.append( field ) + for state_name, id, is_checked in check_sample_states: + strings_displayed.append( state_name ) + for email in additional_emails: + strings_displayed.append( email ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_not_displayed=[] ) def test_035_add_samples_to_request( self ): """Testing adding samples to request""" # logged in as regular_user1 # Sample fields - the tuple represents a sample name and a list of sample form field values - sample_value_tuples = [ ( 'Sample1', [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), - ( 'Sample2', [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ), - ( 'Sample3', [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ] + target_library_info = dict(library=self.security.encode_id(library2.id), + folder=self.security.encode_id(library2_folder1.id) ) + sample_value_tuples = \ + [ ( 'Sample1', target_library_info, [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), + ( 'Sample2', target_library_info, [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ), + ( 'Sample3', target_library_info, [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ] strings_displayed_after_submit = [ 'Unsubmitted' ] - for sample_name, field_values in sample_value_tuples: + for sample_name, lib_info, field_values in sample_value_tuples: strings_displayed_after_submit.append( sample_name ) + # add the sample values too + for values in field_values: + strings_displayed_after_submit.append( values ) # Add samples to the request self.add_samples( cntrller='requests', request_id=self.security.encode_id( request1.id ), - request_name=request1.name, sample_value_tuples=sample_value_tuples, strings_displayed=[ 'Add Samples to Request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) -# def test_040_edit_samples_of_new_request( self ): -# """Testing editing the sample information of new request1""" -# # logged in as regular_user1 -# pass -# def test_035_submit_request( self ): -# """Testing editing a sequence run request""" -# # logged in as regular_user1 -# self.submit_request( cntrller='requests', -# request_id=self.security.encode_id( request1.id ), -# request_name=request1.name, -# strings_displayed_after_submit=[ 'The request has been submitted.' ] ) -# refresh( request1 ) -# # Make sure the request is showing in the 'submitted' filter -# self.check_request_grid( cntrller='requests', -# state=request1.states.SUBMITTED, -# strings_displayed=[ request1.name ] ) -# # Make sure the request's state is now set to 'submitted' -# assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ -# % ( request1.name, request1.states.SUBMITTED ) + # check the new sample field values on the request page + strings_displayed = [ 'Sequencing request "%s"' % request1.name, + 'Submit request' ] # this button should appear now + strings_displayed.extend( strings_displayed_after_submit ) + strings_displayed_count = [] + strings_displayed_count.append( ( library2.name, len( sample_value_tuples ) ) ) + strings_displayed_count.append( ( library2_folder1.name, len( sample_value_tuples ) ) ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_displayed_count=strings_displayed_count ) + def test_040_edit_samples_of_new_request( self ): + """Testing editing the sample information of new request1""" + # logged in as regular_user1 + # target data library - change it to library1 + target_library_info = dict(library=self.security.encode_id(library1.id), + folder=self.security.encode_id(library1_folder1.id) ) + new_sample_value_tuples = \ + [ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ), + ( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ), + ( 'Sample3_renamed', target_library_info, [ 'option2', 'sample3 field2 value edited', 'sample3 field3 value edited' ] ) ] + strings_displayed_after_submit = [ 'Unsubmitted' ] + for sample_name, lib_info, field_values in new_sample_value_tuples: + strings_displayed_after_submit.append( sample_name ) + # add the sample values too + for values in field_values: + strings_displayed_after_submit.append( values ) + # Add samples to the request + self.edit_samples( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + sample_value_tuples=new_sample_value_tuples, + strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name, + '<input type="text" name="sample_0_name" value="Sample1" size="10"/>' ], # sample name input field + strings_displayed_after_submit=strings_displayed_after_submit ) + # check the changed sample field values on the request page + strings_displayed = [ 'Sequencing request "%s"' % request1.name ] + strings_displayed.extend( strings_displayed_after_submit ) + strings_displayed_count = [] + strings_displayed_count.append( ( library1.name, len( new_sample_value_tuples ) ) ) + strings_displayed_count.append( ( library1_folder1.name, len( new_sample_value_tuples ) ) ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_displayed_count=strings_displayed_count ) + def test_045_submit_request( self ): + """Testing submitting a sequencing request""" + # logged in as regular_user1 + self.submit_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + request_name=request1.name, + strings_displayed_after_submit=[ 'The request has been submitted.' ] ) + refresh( request1 ) + # Make sure the request is showing in the 'submitted' filter + self.check_request_grid( cntrller='requests', + state=request1.states.SUBMITTED, + strings_displayed=[ request1.name ] ) + # Make sure the request's state is now set to 'submitted' + assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ + % ( request1.name, request1.states.SUBMITTED ) + # the sample state should appear once for each sample + strings_displayed_count = [ ( request1.type.states[0].name, len( request1.samples ) ) ] + # after submission, these buttons should not appear + strings_not_displayed = [ 'Add sample', 'Submit request' ] + # check the request page + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=[ request1.states.SUBMITTED ], + strings_displayed_count=strings_displayed_count, + strings_not_displayed=strings_not_displayed ) + strings_displayed=[ 'History of sequencing request "%s"' % request1.name, + 'Request submitted by %s' % regular_user1.email, + 'Request created' ] + strings_displayed_count = [ ( request1.states.SUBMITTED, 1 ) ] + self.view_request_history( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=strings_displayed, + strings_displayed_count=strings_displayed_count, + strings_not_displayed=[ request1.states.COMPLETE, + request1.states.REJECTED ] ) + # + # ====== Sequencing request test methods - Admin perspective ================ + # + def test_050_receive_request_as_admin( self ): + """Testing receiving a sequencing request and assigning it barcodes""" + self.logout() + self.login( email=admin_user.email ) + self.check_request_grid( cntrller='requests_admin', + state=request1.states.SUBMITTED, + strings_displayed=[ request1.name ] ) + strings_displayed = [ request1.states.SUBMITTED, + 'Reject this request' ] + strings_not_displayed = [ 'Add sample' ] + self.view_request( cntrller='requests_admin', + request_id=self.security.encode_id( request1.id ), + strings_not_displayed=strings_not_displayed ) + # Set bar codes for the samples + bar_codes = [ '10001', '10002', '10003' ] + strings_displayed_after_submit = [ 'Changes made to the samples have been saved.' ] + strings_displayed_after_submit.extend( bar_codes ) + self.add_bar_codes( cntrller='requests_admin', + request_id=self.security.encode_id( request1.id ), + bar_codes=bar_codes, + strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ], + strings_displayed_after_submit=strings_displayed_after_submit ) + # the second sample state should appear once for each sample + strings_displayed_count = [ ( request1.type.states[1].name, len( request1.samples ) ), + ( request1.type.states[0].name, 0 ) ] + # check the request page + self.view_request( cntrller='requests_admin', + request_id=self.security.encode_id( request1.id ), + strings_displayed=bar_codes, + strings_displayed_count=strings_displayed_count ) + # the sample state descriptions of the future states should not appear + # here the state names are not checked as all of them appear at the top of + # the page like: state1 > state2 > state3 + strings_not_displayed=[ request1.type.states[2].desc, + request1.type.states[3].desc, + request1.type.states[4].desc ] + # check history of each sample + for sample in request1.samples: + strings_displayed = [ 'Events for Sample "%s"' % sample.name, + 'Request submitted and sample state set to %s' % request1.type.states[0].name, + request1.type.states[0].name, + request1.type.states[1].name ] + self.view_sample_history( cntrller='requests_admin', + sample_id=self.security.encode_id( sample.id ), + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) # def test_040_request_lifecycle( self ): # """Testing request life-cycle as it goes through all the states""" # # logged in as regular_user1 @@ -478,6 +666,17 @@ class TestFormsAndRequests( TwillTestCas self.logout() self.login( email=admin_user.email ) ################## + # Purge all libraries + ################## + for library in [ library1, library2 ]: + self.delete_library_item( 'library_admin', + self.security.encode_id( library.id ), + self.security.encode_id( library.id ), + library.name, + item_type='library' ) + self.purge_library( self.security.encode_id( library.id ), library.name ) + + ################## # Delete request_type permissions ################## for request_type in [ request_type1 ]: --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -861,16 +861,26 @@ class TwillTestCase( unittest.TestCase ) self.home() # Functions associated with browsers, cookies, HTML forms and page visits - + def check_page_for_string( self, patt ): """Looks for 'patt' in the current browser page""" page = self.last_page() - for subpatt in patt.split(): - if page.find( patt ) == -1: - fname = self.write_temp_file( page ) - errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) - raise AssertionError( errmsg ) - + if page.find( patt ) == -1: + fname = self.write_temp_file( page ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( patt, fname ) + raise AssertionError( errmsg ) + + def check_string_count_in_page( self, patt, min_count ): + """Checks the number of 'patt' occurrences in the current browser page""" + page = self.last_page() + patt_count = page.count( patt ) + # The number of occurrences of patt in the page should be at least min_count + # so show error if patt_count is less than min_count + if patt_count < min_count: + fname = self.write_temp_file( page ) + errmsg = "%i occurrences of '%s' found instead of %i.\npage content written to '%s' " % ( min_count, patt, patt_count, fname ) + raise AssertionError( errmsg ) + def check_string_not_in_page( self, patt ): """Checks to make sure 'patt' is NOT in the page.""" page = self.last_page() @@ -878,6 +888,16 @@ class TwillTestCase( unittest.TestCase ) fname = self.write_temp_file( page ) errmsg = "string (%s) incorrectly displayed in page.\npage content written to '%s'" % ( patt, fname ) raise AssertionError( errmsg ) + + def check_page(self, strings_displayed, strings_displayed_count, strings_not_displayed): + """Checks a page for strings displayed, not displayed and number of occurrences of a string""" + for check_str in strings_displayed: + self.check_page_for_string(check_str) + for check_str, count in strings_displayed_count: + self.check_string_count_in_page(check_str, count) + for check_str in strings_not_displayed: + self.check_string_not_in_page(check_str) + def write_temp_file( self, content, suffix='.html' ): fd, fname = tempfile.mkstemp( suffix=suffix, prefix='twilltestcase-' ) @@ -1435,7 +1455,7 @@ class TwillTestCase( unittest.TestCase ) self.check_page_for_string( check_str ) self.home() - # Requests stuff + # Sample tracking stuff def check_request_grid( self, cntrller, state, deleted=False, strings_displayed=[] ): self.visit_url( '%s/%s/browse_requests?sort=create_time&f-state=%s&f-deleted=%s' % \ ( self.url, cntrller, state.replace( ' ', '+' ), str( deleted ) ) ) @@ -1510,24 +1530,20 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() - def view_request( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): + def view_request( self, cntrller, request_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): self.visit_url( "%s/%s/browse_requests?operation=view_request&id=%s" % ( self.url, cntrller, request_id ) ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) - for check_str in strings_not_displayed: - self.check_string_not_in_page( check_str ) - def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): + self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) + def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): self.visit_url( "%s/requests_common/view_request_history?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) - for check_str in strings_displayed: - self.check_page_for_string( check_str ) - for check_str in strings_not_displayed: - self.check_string_not_in_page( check_str ) + self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) + def view_sample_history( self, cntrller, sample_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): + self.visit_url( "%s/requests_common/sample_events?cntrller=%s&sample_id=%s" % ( self.url, cntrller, sample_id ) ) + self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) def edit_basic_request_info( self, cntrller, request_id, name, new_name='', new_desc='', new_fields=[], strings_displayed=[], strings_displayed_after_submit=[] ): self.visit_url( "%s/requests_common/edit_basic_request_info?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - self.check_page_for_string( 'Edit sequencing request "%s"' % name ) if new_name: tc.fv( "1", "name", new_name ) if new_desc: @@ -1537,15 +1553,29 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "edit_basic_request_info_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - def add_samples( self, cntrller, request_id, request_name, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): + def edit_request_email_settings( self, cntrller, request_id, check_request_owner=True, additional_emails='', + check_sample_states=[], strings_displayed=[], strings_displayed_after_submit=[] ): + self.visit_url( "%s/requests_common/edit_basic_request_info?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + tc.fv( "2", "email_address", check_request_owner ) + tc.fv( "2", "additional_email_addresses", additional_emails ) + for state_name, state_id, is_checked in check_sample_states: + tc.fv( "2", "sample_state_%i" % state_id, is_checked ) + tc.submit( "edit_email_settings_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) + def add_samples( self, cntrller, request_id, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): url = "%s/requests_common/add_sample?cntrller=%s&request_id=%s&add_sample_button=Add+sample" % ( self.url, cntrller, request_id ) self.visit_url( url ) for check_str in strings_displayed: self.check_page_for_string( check_str ) - for sample_index, sample_info in enumerate( sample_value_tuples ): - sample_name = sample_info[0] - sample_field_values = sample_info[1] + for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + lib_widget_index = sample_index + 1 + tc.fv( "1", "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + tc.fv( "1", "sample_%i_folder_id" % lib_widget_index, target_library_info[ 'folder' ] ) for field_index, field_value in enumerate( sample_field_values ): tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) # Do not click on Add sample button when all the sample have been added @@ -1556,6 +1586,32 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def edit_samples( self, cntrller, request_id, sample_value_tuples, strings_displayed=[], strings_displayed_after_submit=[] ): + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id ) + self.visit_url( url ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): + tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) + lib_widget_index = sample_index + 1 + tc.fv( "1", "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % lib_widget_index, target_library_info[ 'library' ] ) + tc.fv( "1", "sample_%i_folder_id" % lib_widget_index, target_library_info[ 'folder' ] ) + for field_index, field_value in enumerate( sample_field_values ): + tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.submit( "save_samples_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) + def add_bar_codes( self, cntrller, request_id, bar_codes, strings_displayed=[], strings_displayed_after_submit=[] ): + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id ) + self.visit_url( url ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for sample_index, bar_code in enumerate( bar_codes ): + tc.fv( "1", "sample_%i_bar_code" % sample_index, bar_code ) + tc.submit( "save_samples_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) def submit_request( self, cntrller, request_id, request_name, strings_displayed_after_submit=[] ): self.visit_url( "%s/requests_common/submit_request?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed_after_submit: @@ -1568,20 +1624,6 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "reject_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) - def add_bar_codes( self, request_id, request_name, bar_codes, samples, strings_displayed_after_submit=[] ): - # We have to simulate the form submission here since twill barfs on the page - # gvk - 9/22/10 - TODO: make sure the mako template produces valid html - url = "%s/requests_common/edit_samples?cntrller=requests_admin&id=%s&editing_samples=True" % ( self.url, request_id ) - for index, field_value in enumerate( bar_codes ): - sample_field_name = "sample_%i_name" % index - sample_field_value = samples[ index ].name.replace( ' ', '+' ) - field_name = "sample_%i_bar_code" % index - url += "&%s=%s" % ( field_name, field_value ) - url += "&%s=%s" % ( sample_field_name, sample_field_value ) - url += "&save_samples_button=Save" - self.visit_url( url ) - for check_str in strings_displayed_after_submit: - self.check_page_for_string( check_str ) def change_sample_state( self, request_id, request_name, sample_names, sample_ids, new_sample_state_id, new_state_name, comment='', strings_displayed=[], strings_displayed_after_submit=[] ): # We have to simulate the form submission here since twill barfs on the page --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -155,6 +155,8 @@ %elif editing_samples: <p/><div class="form-row"> + ## hidden element to make twill work. + <input type="hidden" name="hidden_input" value=""/><input type="submit" name="save_samples_button" value="Save"/><input type="submit" name="cancel_changes_button" value="Cancel"/><div class="toolParamHelp" style="clear: both;">

1 0

galaxy-dist commit b124f54952de: Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1289591135 18000 # Node ID b124f54952dee106f4ca87ea89a7f828c41562c3 # Parent b7f712cecaa9f527f1161f923ebe798eba526cb6 Small fixes and refactor to workflows: remove unused ensure_popup_helper(), and fix extra comma that was returning error in IE. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -13,7 +13,6 @@ ensure_dd_helper(); make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); - ensure_popup_helper(); ## handle_minwidth_hint = rp.handle_minwidth_hint; </script></%def> @@ -82,8 +81,7 @@ "${initial_text}": function() { // Show/hide menu and update vars, user preferences. var menu = $('#tool-search'); - if (menu.is(":visible")) - { + if (menu.is(":visible")) { // Hide menu. pref_value = "False"; menu_option_text = "Search Tools"; @@ -91,9 +89,7 @@ // Reset search. reset_tool_search(true); - } - else - { + } else { // Show menu. pref_value = "True"; menu_option_text = "Hide Search"; @@ -158,18 +154,17 @@ var next = this_label.next(); var no_visible_tools = true; // Look through tools following label and, if none are visible, hide label. - while (next.length != 0 && next.hasClass("toolTitle")) - { - if (next.is(":visible")) - { + while (next.length !== 0 && next.hasClass("toolTitle")) { + if (next.is(":visible")) { no_visible_tools = false; break; + } else { + next = next.next(); } - else - next = next.next(); } - if (no_visible_tools) + if (no_visible_tools) { this_label.hide(); + } }); } else { $("#search-no-results").show(); @@ -211,9 +206,9 @@ scroll_to_nodes(); canvas_manager.draw_overview(); // Determine if any parameters were 'upgraded' and provide message - upgrade_message = "" - $.each( data['upgrade_messages'], function( k, v ) { - upgrade_message += ( "<li>Step " + ( parseInt(k) + 1 ) + ": " + workflow.nodes[k].name + "<ul>"); + upgrade_message = ""; + $.each( data.upgrade_messages, function( k, v ) { + upgrade_message += ( "<li>Step " + ( parseInt(k, 10) + 1 ) + ": " + workflow.nodes[k].name + "<ul>"); $.each( v, function( i, vv ) { upgrade_message += "<li>" + vv +"</li>"; }); @@ -256,7 +251,7 @@ "Layout": layout_editor, "Save" : save_current_workflow, ##"Load a Workflow" : load_workflow, - "Close": close_editor, + "Close": close_editor }); function edit_workflow_outputs(){ @@ -297,21 +292,21 @@ workflow.has_changes = true; }); $('#workflow-output-area').show(); - }; + } function layout_editor() { workflow.layout(); workflow.fit_canvas_to_nodes(); scroll_to_nodes(); canvas_manager.draw_overview(); - }; + } function edit_workflow_attributes() { workflow.clear_active_node(); $('.right-content').hide(); $('#edit-attributes').show(); - }; + } $.jStore.engineReady(function() { // On load, set the size to the pref stored in local storage if it exists @@ -354,7 +349,11 @@ // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly $("#close-viewport").click( function() { - $("#overview-border").css("right") == "0px" ? hide_overview() : show_overview(); + if ( $("#overview-border").css("right") === "0px" ) { + hide_overview(); + } else { + show_overview(); + } }); // Unload handler @@ -405,7 +404,7 @@ function scroll_to_nodes() { var cv = $("#canvas-viewport"); - var cc = $("#canvas-container") + var cc = $("#canvas-container"); var top, left; if ( cc.width() < cv.width() ) { left = ( cv.width() - cc.width() ) / 2; @@ -436,14 +435,14 @@ node.init_field_data( data ); }, error: function( x, e ) { - var m = "error loading field data" - if ( x.status == 0 ) { - m += ", server unavailable" + var m = "error loading field data"; + if ( x.status === 0 ) { + m += ", server unavailable"; } node.error( m ); } }); - }; + } function add_node_for_module( type, title ) { node = prebuild_node( type, title ); @@ -466,7 +465,7 @@ node.error( m ); } }); - }; + } <% from galaxy.jobs.actions.post import ActionBox @@ -500,12 +499,12 @@ } function new_pja(action_type, target, node){ - if (node.post_job_actions == undefined){ + if (node.post_job_actions === undefined){ //New tool node, set up dict. node.post_job_actions = {}; } - if (node.post_job_actions[action_type+target] == undefined){ - var new_pja = new Object(); + if (node.post_job_actions[action_type+target] === undefined){ + var new_pja = {}; new_pja.action_type = action_type; new_pja.output_name = target; node.post_job_actions[action_type+target] = null; @@ -513,7 +512,7 @@ display_pja(new_pja, node); workflow.active_form_has_changes = true; return true; - }else{ + } else { return false; } } @@ -576,7 +575,7 @@ var value = $(this).attr( 'value' ); options[ $(this).text() ] = function() { $(form).append( "<input type='hidden' name='"+name+"' value='"+value+"' />" ).submit(); - } + }; }); b.insertAfter( this ); $(this).remove(); @@ -613,9 +612,9 @@ "Don't Save": do_close } ); } else { - window.document.location = "${next_url}" + window.document.location = "${next_url}"; } - } + }; var save_current_workflow = function ( eventObj, success_callback ) { show_modal( "Saving workflow", "progress" ); @@ -634,14 +633,14 @@ type: "POST", data: { id: "${trans.security.encode_id( stored.id )}", - workflow_data: function() { return JSON.stringify( workflow.to_simple() ) }, + workflow_data: function() { return JSON.stringify( workflow.to_simple() ); }, "_": "true" }, dataType: 'json', success: function( data ) { var body = $("<div></div>").text( data.message ); if ( data.errors ) { - body.addClass( "warningmark" ) + body.addClass( "warningmark" ); var errlist = $( "<ul/>" ); $.each( data.errors, function( i, v ) { $("<li></li>").text( v ).appendTo( errlist ); @@ -663,7 +662,7 @@ } } }); - } + }; // We bind to ajaxStop because of auto-saving, since the form submission ajax // call needs to be completed so that the new data is saved @@ -677,7 +676,7 @@ } else { savefn(success_callback); } - } + }; </script></%def>

1 0

galaxy-dist commit fc1f67023d86: Fixes for building target library and folder SelectFields for transferring sample datasets. All folders are now present in the target folder SelectField. Move security-related methods from the model's User class to the security agent where they belong.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289574787 18000 # Node ID fc1f67023d86a69ea7229501b093d61748630f4c # Parent dc4af741ffc455c4737aff67c7d7de48c8628392 Fixes for building target library and folder SelectFields for transferring sample datasets. All folders are now present in the target folder SelectField. Move security-related methods from the model's User class to the security agent where they belong. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -52,40 +52,6 @@ class User( object ): if role not in roles: roles.append( role ) return roles - def accessible_libraries( self, trans, actions ): - # TODO: eliminate this method - instead use - # trans.app.security_agent.get_accessible_libraries(). - # 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 - def accessible_request_types( self, trans ): - active_request_types = trans.sa_session.query( trans.app.model.RequestType ) \ - .filter( trans.app.model.RequestType.table.c.deleted == False ) \ - .order_by( trans.app.model.RequestType.name ) - # Filter active_request_types to those that can be accessed by this user - role_ids = [ r.id for r in self.all_roles() ] - accessible_request_types = set() - for request_type in active_request_types: - for permission in request_type.actions: - if permission.role.id in role_ids: - accessible_request_types.add( request_type ) - accessible_request_types = [ request_type for request_type in accessible_request_types ] - return accessible_request_types class Job( object ): """ --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -77,7 +77,8 @@ class Requests( BaseController ): kwd[ 'message' ] = message # Allow the user to create a new request only if they have permission to access a # (sequencer configuration) request type. - if len( trans.user.accessible_request_types( trans ) ): + accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user ) + if accessible_request_types: self.request_grid.global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common', action='create_request', cntrller='requests' ) ) ] --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -414,7 +414,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, id=request_id, editing_samples=editing_samples ) ) - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build a list of sample widgets (based on the attributes of each sample) for display. displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) @@ -815,7 +815,7 @@ class RequestsCommon( BaseController, Us else: sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) @@ -1214,20 +1214,14 @@ class RequestsCommon( BaseController, Us else: folder = None return library, folder + def __get_active_folders( self, library ): + """Return all of the active folders for the received library""" + root_folder = library.root_folder + active_folders = [ root_folder ] + for folder in root_folder.active_folders: + active_folders.append( folder ) + return active_folders # ===== Methods for handling form definition widgets ===== - def __get_accessible_libraries( self, trans, user ): - # Return a dictionary whose keys are libraries that user can - # access and whose values are empty string ''. This is because - # methods expect the dictionary instead of a simple list because - # this method replaces the deprecated model.User.accessible_libraries() - # method. TODO: fix methods that call this method to expect the list - # returne dby trans.app.securoty_agent.get_accessible_libraries() and - # then eliminate this method. - accessible_libraries = trans.app.security_agent.get_accessible_libraries( trans, user ) - accessible_libraries_dict = odict() - for library in accessible_libraries: - accessible_libraries_dict[ library ] = '' - return accessible_libraries_dict def __get_request_widgets( self, trans, id ): """Get the widgets for the request""" request = trans.sa_session.query( trans.model.Request ).get( id ) @@ -1275,7 +1269,7 @@ class RequestsCommon( BaseController, Us # Build the list of widgets which will be used to render each sample row on the request page if not request: return sample_widgets - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build the list if sample widgets, populating the values from kwd. for index, sample in enumerate( samples ): id_index = index + 1 @@ -1361,7 +1355,7 @@ class RequestsCommon( BaseController, Us copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index ) return copy_sample_index_select_field def __build_request_type_id_select_field( self, trans, selected_value='none' ): - accessible_request_types = trans.user.accessible_request_types( trans ) + accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user ) return build_select_field( trans, accessible_request_types, 'name', 'request_type_id', selected_value=selected_value, refresh_on_change=True ) def __build_user_id_select_field( self, trans, selected_value='none' ): active_users = trans.sa_session.query( trans.model.User ) \ @@ -1388,11 +1382,9 @@ class RequestsCommon( BaseController, Us def __build_library_and_folder_select_fields( self, trans, user, sample_index, libraries, sample=None, library_id=None, folder_id=None, **kwd ): # Create the library_id SelectField for a specific sample. The received libraries param is a list of all the libraries # accessible to the current user, and we add them as options to the library_select_field. If the user has selected an - # existing library then display all the accessible folders of the selected library in the folder_select_field. - # - # The libraries dictionary looks like: { library : '1,2' }, library : '3' }. Its keys are the libraries that - # should be displayed for the current user and its values are strings of comma-separated folder ids that should - # NOT be displayed. + # existing library then display all the folders of the selected library in the folder_select_field. Library folders do + # not have ACCESS permissions associated with them (only LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE), so all folders will + # be present in the folder_select_field for each library selected. params = util.Params( kwd ) library_select_field_name= "sample_%i_library_id" % sample_index folder_select_field_name = "sample_%i_folder_id" % sample_index @@ -1401,15 +1393,11 @@ class RequestsCommon( BaseController, Us if not folder_id: folder_id = params.get( folder_select_field_name, None ) selected_library = None - selected_hidden_folder_ids = [] - showable_folders = [] if library_id not in [ None, 'none' ]: - # If we have a selected library, get the list of it's folders that are not accessible to the current user - for library, hidden_folder_ids in libraries.items(): + for library in libraries: encoded_id = trans.security.encode_id( library.id ) if encoded_id == str( library_id ): selected_library = library - selected_hidden_folder_ids = hidden_folder_ids.split( ',' ) break elif sample and sample.library and library_id == 'none': # The user previously selected a library but is now resetting the selection to 'none' @@ -1417,21 +1405,17 @@ class RequestsCommon( BaseController, Us elif sample and sample.library: library_id = trans.security.encode_id( sample.library.id ) selected_library = sample.library - # sample_%i_library_id SelectField with refresh on change enabled + # Build the sample_%i_library_id SelectField with refresh on change enabled library_select_field = build_select_field( trans, - libraries.keys(), + libraries, 'name', library_select_field_name, initial_value='none', selected_value=str( library_id ).lower(), refresh_on_change=True ) - # Get all accessible folders for the selected library, if one is indeed selected + # Get all folders for the selected library, if one is indeed selected if selected_library: - showable_folders = trans.app.security_agent.get_showable_folders( user, - user.all_roles(), - selected_library, - [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], - selected_hidden_folder_ids ) + folders = self.__get_active_folders( selected_library ) if folder_id: selected_folder_id = folder_id elif sample and sample.folder: @@ -1440,11 +1424,12 @@ class RequestsCommon( BaseController, Us selected_folder_id = trans.security.encode_id( selected_library.root_folder.id ) else: selected_folder_id = 'none' + folders = [] # TODO: Change the name of the library root folder to "Library root" to clarify to the # user that it is the root folder. We probably should just change this in the Library code, # and update the data in the db. folder_select_field = build_select_field( trans, - showable_folders, + folders, 'name', folder_select_field_name, initial_value='none', --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -84,7 +84,7 @@ [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types( trans ) ) ) ) + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) %> ## Visualization menu. --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -60,6 +60,8 @@ class RBACAgent: raise "Unimplemented Method" def get_private_user_role( self, user ): raise "Unimplemented Method" + def get_accessible_request_types( self, trans, user ): + raise "Unimplemented Method" def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): raise "Unimplemented Method" def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): @@ -76,6 +78,8 @@ class RBACAgent: raise "Unimplemented Method" def get_accessible_libraries( self, trans, user ): raise "Unimplemented Method" + def get_permitted_libraries( self, trans, user, actions ): + raise "Unimplemented Method" def folder_is_public( self, library ): raise "Unimplemented Method" def make_folder_public( self, folder, count=0 ): @@ -247,7 +251,7 @@ class GalaxyRBACAgent( RBACAgent ): def can_access_library( self, roles, library ): return self.library_is_public( library ) or self.allow_action( roles, self.permitted_actions.LIBRARY_ACCESS, library ) def get_accessible_libraries( self, trans, user ): - """Return all data libraries that user can access""" + """Return all data libraries that the received user can access""" accessible_libraries = [] current_user_role_ids = [ role.id for role in user.all_roles() ] library_access_action = self.permitted_actions.LIBRARY_ACCESS.action @@ -499,6 +503,20 @@ class GalaxyRBACAgent( RBACAgent ): else: permissions[ action ] = [ item_permission.role ] return permissions + def get_accessible_request_types( self, trans, user ): + """Return all ReqquestTypes that the received user has permission to access.""" + active_request_types = trans.sa_session.query( trans.app.model.RequestType ) \ + .filter( trans.app.model.RequestType.table.c.deleted == False ) \ + .order_by( trans.app.model.RequestType.name ) + # Filter active_request_types to those that can be accessed by the received user + role_ids = [ r.id for r in user.all_roles() ] + accessible_request_types = set() + for request_type in active_request_types: + for permission in request_type.actions: + if permission.role.id in role_ids: + accessible_request_types.add( request_type ) + accessible_request_types = [ request_type for request_type in accessible_request_types ] + return accessible_request_types def copy_dataset_permissions( self, src, dst ): if not isinstance( src, self.model.Dataset ): src = src.dataset @@ -731,6 +749,34 @@ class GalaxyRBACAgent( RBACAgent ): else: raise 'Invalid class (%s) specified for target_library_item (%s)' % \ ( target_library_item.__class__, target_library_item.__class__.__name__ ) + def get_permitted_libraries( self, trans, user, actions ): + """ + This method is historical (it is not currently used), but may be useful again at some + point. It returns a dictionary whose keys are library objects and whose values are a + comma-separated string of folder ids. This method works with the show_library_item() + method below, and it returns libraries for which the received user has permission to + perform the received actions. Here is an example call to this method to return all + libraries for which the received user has LIBRARY_ADD permission: + libraries = trans.app.security_agent.get_permitted_libraries( trans, user, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + """ + 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 = 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 = self.show_library_item( self, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids + return libraries def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): """ This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a

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galaxy-dist commit dc4af741ffc4: Fixed missing substitution of get_id_tag for a galaxy_job_id in drmaa runner.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1289573664 18000 # Node ID dc4af741ffc455c4737aff67c7d7de48c8628392 # Parent dbe6ab1eaa7ca7f9754c22bb2f6edd3fc26e3432 Fixed missing substitution of get_id_tag for a galaxy_job_id in drmaa runner. --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -175,7 +175,7 @@ class DRMAAJobRunner( BaseJobRunner ): log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) # runJob will raise if there's a submit problem job_id = self.ds.runJob(jt) - log.info("(%s) queued as %s" % ( galaxy_job_id, job_id ) ) + log.info("(%s) queued as %s" % ( galaxy_id_tag, job_id ) ) # store runner information for tracking if Galaxy restarts job_wrapper.set_runner( runner_url, job_id )

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galaxy-dist commit ba34d996fff5: Merge.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1289568520 18000 # Node ID ba34d996fff5669eca98ff98c6035a68ac93bd34 # Parent 2389c323a1e6a50de6d48d5431d16d830ccef021 # Parent a6cd0223a53b4f9498a0dde69dcef53387188e5f Merge. --- a/templates/requests/common/events.mako +++ /dev/null @@ -1,53 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<% - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_reject_request = is_admin and request.is_submitted - can_add_samples = request.is_unsubmitted -%> - -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> - <div popupmenu="request-${request.id}-popup"> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> - %endif - %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> - %endif - %if can_reject_request: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> - %endif - </div> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>History of Sequencing Request "${request.name}"</h2> - -<div class="toolForm"> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div> --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA file using tabular output, e.g. from BLAST. - -Takes five command line options, tabular BLAST filename, ID column number -(using one based counting), input FASTA filename, and two output FASTA -filenames (for records with and without any BLAST hits). - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. -""" -import sys -from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - -#Parse Command Line -blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] -blast_col = int(blast_col)-1 -assert blast_col >= 0 - -#Read tabular BLAST file and record all queries with hit(s) -ids = set() -blast_handle = open(blast_file, "rU") -for line in blast_handle: - ids.add(line.split("\t")[blast_col]) -blast_handle.close() - -#Write filtered FASTA file based on IDs from BLAST file -reader = fastaReader(open(in_file, "rU")) -positive_writer = fastaWriter(open(out_positive_file, "w")) -negative_writer = fastaWriter(open(out_negative_file, "w")) -for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifer. - if record.identifier and record.identifier.split()[0][1:] in ids: - positive_writer.write(record) - else: - negative_writer.write(record) -positive_writer.close() -negative_writer.close() -reader.close() --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ /dev/null @@ -1,37 +0,0 @@ -<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"> - <description>Divide a FASTA file based on BLAST hits</description> - <command interpreter="python"> - blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file - </command> - <inputs> - <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/> - <param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="select" label="Column containing FASTA identifiers"> - <option value="1">Column 1 - BLAST query ID</option> - <option value="2">Column 2 - BLAST match ID</option> - </param> - </inputs> - <outputs> - <data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> - <data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" /> - </outputs> - <requirements> - </requirements> - <tests> - </tests> - <help> - -**What it does** - -Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divide the FASTA file in two: those sequence with a -BLAST hit, and those without. - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. - -This allows you to filter the FASTA file for the subjects in the BLAST search, -rather than filtering the FASTA file for the queries in the BLAST search. - - </help> -</tool>

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galaxy-dist commit dbe6ab1eaa7c: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289568820 18000 # Node ID dbe6ab1eaa7ca7f9754c22bb2f6edd3fc26e3432 # Parent b5b6b92a71e960691bb514af32ba2e21a731bd4e # Parent ba34d996fff5669eca98ff98c6035a68ac93bd34 merge

1 0

galaxy-dist commit ecc1cefbccba: Enhance GFFReader to read and return complete features (genes/transcripts), which are composed of multiple intervals/blocks. This required hacking around a couple limitations of bx-python, but these can be easily fixed when bx-python is updated. Use enhanced functionality to correctly create converted datasets for visualizing GFF files.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289591537 18000 # Node ID ecc1cefbccba6135f824f9573f06c130fd6d08b4 # Parent b124f54952dee106f4ca87ea89a7f828c41562c3 Enhance GFFReader to read and return complete features (genes/transcripts), which are composed of multiple intervals/blocks. This required hacking around a couple limitations of bx-python, but these can be easily fixed when bx-python is updated. Use enhanced functionality to correctly create converted datasets for visualizing GFF files. Also updated GOPS tools to use a simpler GFF reader wrapper to read in intervals and convert to BED coordinates. --- a/tools/new_operations/gops_subtract.py +++ b/tools/new_operations/gops_subtract.py @@ -44,11 +44,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper --- a/tools/new_operations/gops_intersect.py +++ b/tools/new_operations/gops_intersect.py @@ -44,11 +44,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper @@ -66,10 +66,10 @@ def main(): fix_strand=True ) out_file = open( out_fname, "w" ) - + try: for line in intersect( [g1,g2], pieces=pieces, mincols=mincols ): - if type( line ) == GenomicInterval: + if isinstance( line, GenomicInterval ): if in1_gff_format: line = convert_bed_coords_to_gff( line ) out_file.write( "%s\n" % "\t".join( line.fields ) ) --- /dev/null +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py @@ -0,0 +1,55 @@ +#!/usr/bin/env python + +""" +Convert from GFF file to interval index file. + +usage: + python gff_to_interval_index_converter.py [input] [output] +""" + +from __future__ import division + +import sys, fileinput +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from galaxy.tools.util.gff_util import * +from bx.interval_index_file import Indexes + +def main(): + # Arguments + input_fname, out_fname = sys.argv[1:] + + # Do conversion. + chr_col, start_col, end_col, strand_col = ( 0, 3, 4, 6 ) + index = Indexes() + offset = 0 + reader_wrapper = GFFReaderWrapper( fileinput.FileInput( input_fname ), + chrom_col=chr_col, + start_col=start_col, + end_col=end_col, + strand_col=strand_col, + fix_strand=True ) + for feature in list( reader_wrapper ): + # TODO: need to address comments: + # if comment: + # increment_offset. + + # Add feature; index expects BED coordinates. + convert_gff_coords_to_bed( feature ) + index.add( feature.chrom, feature.start, feature.end, offset ) + + # Increment offset by feature length; feature length is all + # intervals/lines that comprise feature. + feature_len = 0 + for interval in feature.intervals: + # HACK: +1 for EOL char. Need bx-python to provide raw_line itself + # b/c TableReader strips EOL characters, thus changing the line + # length. + feature_len += len( interval.raw_line ) + 1 + offset += feature_len + + index.write( open(out_fname, "w") ) + +if __name__ == "__main__": + main() + --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py @@ -14,7 +14,7 @@ import pkg_resources; pkg_resources.requ from galaxy.visualization.tracks.summary import * from bx.intervals.io import * from bx.cookbook import doc_optparse -from galaxy.tools.util.gff_util import GFFReaderWrapper +from galaxy.tools.util.gff_util import * def main(): # Read options, args. @@ -40,9 +40,12 @@ def main(): strand_col=strand_col, fix_strand=True ) st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) - for line in list( reader_wrapper ): - if type( line ) is GenomicInterval: - st.insert_range( line.chrom, long( line.start ), long( line.end ) ) + for feature in list( reader_wrapper ): + if isinstance( feature, GenomicInterval ): + # Tree expects BED coordinates. + if type( feature ) is GFFFeature: + convert_gff_coords_to_bed( feature ) + st.insert_range( feature.chrom, long( feature.start ), long( feature.end ) ) st.write(out_fname) --- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml +++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml @@ -1,6 +1,6 @@ -<tool id="CONVERTER_gff_to_interval_index_0" name="Convert BED to Interval Index" version="1.0.0" hidden="true"> +<tool id="CONVERTER_gff_to_interval_index_0" name="Convert GFF to Interval Index" version="1.0.0" hidden="true"> - <command interpreter="python">interval_to_interval_index_converter.py $input1 $output1 --gff</command> + <command interpreter="python">gff_to_interval_index_converter.py $input1 $output1</command><inputs><page><param format="gff" name="input1" type="data" label="Choose GFF file"/> --- a/tools/new_operations/flanking_features.py +++ b/tools/new_operations/flanking_features.py @@ -153,11 +153,11 @@ def main(): # Set readers to handle either GFF or default format. if in1_gff_format: - in1_reader_wrapper = GFFReaderWrapper + in1_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in1_reader_wrapper = NiceReaderWrapper if in2_gff_format: - in2_reader_wrapper = GFFReaderWrapper + in2_reader_wrapper = GFFIntervalToBEDReaderWrapper else: in2_reader_wrapper = NiceReaderWrapper --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -2,25 +2,173 @@ Provides utilities for working with GFF files. """ -from bx.intervals.io import NiceReaderWrapper, GenomicInterval +from bx.intervals.io import * + +class GFFInterval( GenomicInterval ): + """ + A GFF interval, including attributes. If file is strictly a GFF file, + only attribute is 'group.' + """ + def __init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, default_strand, \ + fix_strand=False, raw_line='' ): + GenomicInterval.__init__( self, reader, fields, chrom_col, start_col, end_col, strand_col, \ + default_strand, fix_strand=fix_strand ) + self.raw_line = raw_line + self.attributes = parse_gff_attributes( fields[8] ) + +class GFFFeature( GenomicInterval ): + """ + A GFF feature, which can include multiple intervals. + """ + def __init__( self, reader, chrom_col, start_col, end_col, strand_col, default_strand, \ + fix_strand=False, intervals=[] ): + GenomicInterval.__init__( self, reader, intervals[0].fields, chrom_col, start_col, end_col, \ + strand_col, default_strand, fix_strand=fix_strand ) + self.intervals = intervals + # Use intervals to set feature attributes. + for interval in self.intervals: + # Error checking. + if interval.chrom != self.chrom: + raise ValueError( "interval chrom does not match self chrom: %i != %i" % \ + ( interval.chrom, self.chrom ) ) + if interval.strand != self.strand: + raise ValueError( "interval strand does not match self strand: %s != %s" % \ + ( interval.strand, self.strand ) ) + # Set start, end of interval. + if interval.start < self.start: + self.start = interval.start + if interval.end > self.end: + self.end = interval.end + +class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ): + """ + Reader wrapper that reads GFF intervals/lines and automatically converts + them to BED format. + """ + + def parse_row( self, line ): + # HACK: this should return a GFF interval, but bx-python operations + # require GenomicInterval objects and subclasses will not work. + interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ + self.end_col, self.strand_col, self.default_strand, \ + fix_strand=self.fix_strand ) + interval = convert_gff_coords_to_bed( interval ) + return interval class GFFReaderWrapper( NiceReaderWrapper ): """ - Reader wrapper converts GFF format--starting and ending coordinates are 1-based, closed--to the - 'traditional'/BED interval format--0 based, half-open. This is useful when using GFF files as inputs - to tools that expect traditional interval format. + Reader wrapper for GFF files. + + Wrapper has two major functions: + (1) group entries for GFF file (via group column), GFF3 (via id attribute ), + or GTF (via gene_id/transcript id); + (2) convert coordinates from GFF format--starting and ending coordinates + are 1-based, closed--to the 'traditional'/BED interval format--0 based, + half-open. This is useful when using GFF files as inputs to tools that + expect traditional interval format. """ + + def __init__( self, reader, **kwargs ): + """ + Create wrapper. Defaults are group_entries=False and + convert_coords_to_bed=True to support backward compatibility. + """ + NiceReaderWrapper.__init__( self, reader, **kwargs ) + self.group_entries = kwargs.get( 'group_entries', False ) + self.convert_coords_to_bed = kwargs.get( 'convert_coords_to_bed', True ) + self.last_line = None + self.cur_offset = 0 + self.seed_interval = None + def parse_row( self, line ): - interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, self.end_col, \ - self.strand_col, self.default_strand, fix_strand=self.fix_strand ) - interval = convert_gff_coords_to_bed( interval ) + interval = GFFInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, \ + self.end_col, self.strand_col, self.default_strand, \ + fix_strand=self.fix_strand, raw_line=line ) + if self.convert_coords_to_bed: + interval = convert_gff_coords_to_bed( interval ) return interval + def next( self ): + """ Returns next GFFFeature. """ + + # + # Helper function. + # + + def handle_parse_error( parse_error ): + """ Actions to take when ParseError found. """ + if self.outstream: + if self.print_delegate and hasattr(self.print_delegate,"__call__"): + self.print_delegate( self.outstream, e, self ) + self.skipped += 1 + # no reason to stuff an entire bad file into memmory + if self.skipped < 10: + self.skipped_lines.append( ( self.linenum, self.current_line, str( e ) ) ) + + # + # Get next GFFFeature + # + + # If there is no seed interval, set one. Also, if there are no more + # intervals to read, this is where iterator dies. + if not self.seed_interval: + while not self.seed_interval: + try: + self.seed_interval = GenomicIntervalReader.next( self ) + except ParseError, e: + handle_parse_error( e ) + + # Initialize feature name from seed. + feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF + feature_id = self.seed_interval.attributes.get( 'id', None ) # For GFF3 + feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) # For GTF + feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None ) # For GTF + + # Read all intervals associated with seed. + feature_intervals = [] + feature_intervals.append( self.seed_interval ) + while True: + try: + interval = GenomicIntervalReader.next( self ) + except StopIteration, e: + # No more intervals to read, but last feature needs to be + # returned. + interval = None + break + except ParseError, e: + handle_parse_error( e ) + + # If interval not associated with feature, break. + group = interval.attributes.get( 'group', None ) + if group and feature_group != group: + break + id = interval.attributes.get( 'id', None ) + if id and feature_id != id: + break + gene_id = interval.attributes.get( 'gene_id', None ) + transcript_id = interval.attributes.get( 'transcript_id', None ) + if transcript_id and transcript_id != feature_transcript_id and gene_id and \ + gene_id != feature_gene_id: + break + + # Interval associated with feature. + feature_intervals.append( interval ) + + # Last interval read is the seed for the next interval. + self.seed_interval = interval + + # Return GFF feature with all intervals. + return GFFFeature( self, self.chrom_col, self.start_col, self.end_col, self.strand_col, \ + self.default_strand, fix_strand=self.fix_strand, \ + intervals=feature_intervals ) + + def convert_bed_coords_to_gff( interval ): """ - Converts an interval object's coordinates from BED format to GFF format. Accepted object types include - GenomicInterval and list (where the first element in the list is the interval's start, and the second - element is the interval's end). + Converts an interval object's coordinates from BED format to GFF format. + Accepted object types include GenomicInterval and list (where the first + element in the list is the interval's start, and the second element is + the interval's end). """ if type( interval ) is GenomicInterval: interval.start += 1 @@ -30,9 +178,10 @@ def convert_bed_coords_to_gff( interval def convert_gff_coords_to_bed( interval ): """ - Converts an interval object's coordinates from GFF format to BED format. Accepted object types include - GenomicInterval and list (where the first element in the list is the interval's start, and the second - element is the interval's end). + Converts an interval object's coordinates from GFF format to BED format. + Accepted object types include GenomicInterval and list (where the first + element in the list is the interval's start, and the second element is + the interval's end). """ if type( interval ) is GenomicInterval: interval.start -= 1 @@ -42,10 +191,15 @@ def convert_gff_coords_to_bed( interval def parse_gff_attributes( attr_str ): """ - Parses a GFF/GTF attribute string and returns a dictionary of name-value pairs. - The general format for a GFF3 attributes string is name1=value1;name2=value2 - The general format for a GTF attribute string is name1 "value1" ; name2 "value2" - """ + Parses a GFF/GTF attribute string and returns a dictionary of name-value + pairs. The general format for a GFF3 attributes string is + name1=value1;name2=value2 + The general format for a GTF attribute string is + name1 "value1" ; name2 "value2" + The general format for a GFF attribute string is a single string that + denotes the interval's group; in this case, method returns a dictionary + with a single key-value pair, and key name is 'group' + """ attributes_list = attr_str.split(";") attributes = {} for name_value_pair in attributes_list: @@ -53,6 +207,9 @@ def parse_gff_attributes( attr_str ): pair = name_value_pair.strip().split(" ") if len( pair ) == 1: pair = name_value_pair.strip().split("=") + if len( pair ) == 1: + # Could not split for some reason -- raise exception? + continue if pair == '': continue name = pair[0].strip() @@ -61,4 +218,9 @@ def parse_gff_attributes( attr_str ): # Need to strip double quote from values value = pair[1].strip(" \"") attributes[ name ] = value + + if len( attributes ) == 0: + # Could not split attributes string, so entire string must be + # 'group' attribute. This is the case for strictly GFF files. + attributes['group'] = attr_str return attributes

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galaxy-dist commit 10d0ffe5b7e2: Include BLAST-XML to tabular in tool_conf.xml.sample
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286962559 -3600 # Node ID 10d0ffe5b7e22b2d122945ab5b7fa951a18c6e4a # Parent caed55b53f5a811226e0bfa1c177e7b3e57a909a Include BLAST-XML to tabular in tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -268,6 +268,7 @@ <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /><tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools">

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galaxy-dist commit dfc848840870: Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289503442 18000 # Node ID dfc848840870fa9936a69e62322446fcb940fb40 # Parent ca23ea683d26df004e666ede82950c712e3ac637 Various sample tracking bug fixes: samples no longer require bar codes, change all references to 'barcode' to be 'bar_code' since that is what the model uses, and mixing the 2 is not maintainable, enhance sample popup menu options, fix broken logic that handles bulk sample library and folderr changes. --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -725,7 +725,7 @@ class RequestsCommon( BaseController, Us search_type = params.get( 'search_type', '' ) request_states = util.listify( params.get( 'request_states', '' ) ) samples = [] - if search_type == 'barcode': + if search_type == 'bar_code': samples = trans.sa_session.query( trans.model.Sample ) \ .filter( and_( trans.model.Sample.table.c.deleted==False, func.lower( trans.model.Sample.table.c.bar_code ).like( "%" + search_string.lower() + "%" ) ) ) \ @@ -763,7 +763,7 @@ class RequestsCommon( BaseController, Us display='checkboxes' ) # Build the search_type SelectField selected_value = kwd.get( 'search_type', 'sample name' ) - types = [ 'sample name', 'barcode', 'dataset' ] + types = [ 'sample name', 'bar_code', 'dataset' ] search_type = build_select_field( trans, types, 'self', 'search_type', selected_value=selected_value, refresh_on_change=False ) # Build the search_box TextField search_box = TextField( 'search_box', 50, kwd.get('search_box', '' ) ) @@ -846,7 +846,7 @@ class RequestsCommon( BaseController, Us # Append the new sample to the current list of samples for the request displayable_sample_widgets.append( dict( id=None, name=name, - barcode='', + bar_code='', library=None, library_id=library_id, folder=None, @@ -999,7 +999,7 @@ class RequestsCommon( BaseController, Us **kwd ) displayable_sample_widgets.append( dict( id=None, name=row[0], - barcode='', + bar_code='', library=None, folder=None, library_select_field=library_select_field, @@ -1029,7 +1029,10 @@ class RequestsCommon( BaseController, Us editing_samples=False ) def __save_samples( self, trans, cntrller, request, samples, **kwd ): # Here we handle saving all new samples added by the user as well as saving - # changes to any subset of the request's samples. + # changes to any subset of the request's samples. A sample will not have an + # associated SampleState until the request is submitted, at which time the + # sample is automatically associated with the first SampleState configured by + # the admin for the request's RequestType. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1065,7 +1068,7 @@ class RequestsCommon( BaseController, Us # Send the encoded sample_ids to update_sample_state. # TODO: make changes necessary to just send the samples... encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) - # Make sure all samples have a unique barcode if the state is changing + # Make sure all samples have a unique bar_code if the state is changing for sample_index in range( len( samples ) ): current_sample = samples[ sample_index ] if current_sample is None: @@ -1073,13 +1076,15 @@ class RequestsCommon( BaseController, Us # on which to perform the action. continue request_sample = request.samples[ sample_index ] - bc_message = self.__validate_barcode( trans, request_sample, current_sample[ 'barcode' ] ) - if bc_message: - #status = 'error' - message += bc_message - kwd[ 'message' ] = message - del kwd[ 'save_samples_button' ] - handle_error( **kwd ) + bar_code = current_sample[ 'bar_code' ] + if bar_code: + # If the sample has a new bar_code, make sure it is unique. + bc_message = self.__validate_bar_code( trans, request_sample, bar_code ) + if bc_message: + message += bc_message + kwd[ 'message' ] = message + del kwd[ 'save_samples_button' ] + handle_error( **kwd ) self.update_sample_state( trans, cntrller, encoded_selected_sample_ids, new_state, comment=sample_event_comment ) return trans.response.send_redirect( web.url_for( controller='requests_common', cntrller=cntrller, @@ -1088,18 +1093,22 @@ class RequestsCommon( BaseController, Us elif sample_operation == 'Select data library and folder': # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id - # and sample_operation-folder_id because the name sample_0_library_id should belong to the + # and sample_operation_folder_id because the name sample_0_library_id should belong to the # first sample since all other form field values are named like this. The library and folder # are skewed to be named +1 resulting in the forced use of id_index everywhere... library_id = params.get( 'sample_0_library_id', 'none' ) folder_id = params.get( 'sample_0_folder_id', 'none' ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) + for sample_index in range( len( samples ) ): + current_sample = samples[ sample_index ] + current_sample[ 'library' ] = library + current_sample[ 'folder' ] = folder self.__update_samples( trans, cntrller, request, samples, **kwd ) # Samples will not have an associated SampleState until the request is submitted, at which # time all samples of the request will be set to the first SampleState configured for the # request's RequestType defined by the admin. if request.is_submitted: - # See if all the samples' barcodes are in the same state, and if so send email if configured to. + # See if all the samples' bar_codes are in the same state, and if so send email if configured to. common_state = request.samples_have_common_state if common_state and common_state.id == request.type.states[1].id: comment = "All samples of this request are in the (%s) sample state. " % common_state.name @@ -1136,10 +1145,12 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) def __update_samples( self, trans, cntrller, request, sample_widgets, **kwd ): - # Determine if the values in kwd require updating the request's samples. The list of - # sample_widgets must have the same number of objects as request.samples, but some of - # the objects can be None. Those that are not None correspond to samples selected by - # the user for performing an action on multiple samples simultaneously. + # The list of sample_widgets must have the same number of objects as request.samples, + # but some of the objects can be None. Those that are not None correspond to samples + # selected by the user for performing an action on multiple samples simultaneously. + # The items in the sample_widgets list have already been populated with any changed + # param values (changed implies the value in kwd is different from the attribute value + # in the database) in kwd before this method is reached. def handle_error( **kwd ): kwd[ 'status' ] = 'error' return trans.response.send_redirect( web.url_for( controller='requests_common', @@ -1147,12 +1158,6 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, **kwd ) ) params = util.Params( kwd ) - sample_operation = params.get( 'sample_operation', 'none' ) - if sample_operation != 'none': - # These values will be in kwd if the user checked 1 or more checkboxes for performing this action - # on a set of samples. - library_id = params.get( 'sample_0_library_id', 'none' ) - folder_id = params.get( 'sample_0_folder_id', 'none' ) for index, sample_widget in enumerate( sample_widgets ): if sample_widget is not None: # sample_widget will be None if the user checked sample check boxes and selected an action @@ -1161,21 +1166,16 @@ class RequestsCommon( BaseController, Us # Get the sample's form values to see if they have changed. form_values = trans.sa_session.query( trans.model.FormValues ).get( sample.values.id ) if sample.name != sample_widget[ 'name' ] or \ - sample.bar_code != sample_widget[ 'barcode' ] or \ + sample.bar_code != sample_widget[ 'bar_code' ] or \ sample.library != sample_widget[ 'library' ] or \ sample.folder != sample_widget[ 'folder' ] or \ form_values.content != sample_widget[ 'field_values' ]: # Information about this sample has been changed. sample.name = sample_widget[ 'name' ] - barcode = sample_widget[ 'barcode' ] - # The bar_code field requires special handling because after a request is submitted, the - # state of a sample cannot be changed without a bar_code associated with the sample. Bar - # codes can only be added to a sample after the request is submitted. Also, a samples will - # not have an associated SampleState until the request is submitted, at which time the sample - # is automatically associated with the first SamplesState configured by the admin for the - # request's RequestType. - if barcode: - bc_message = self.__validate_barcode( trans, sample, bar_code ) + bar_code = sample_widget[ 'bar_code' ] + # If the sample has a new bar_code, make sure it is unique. + if bar_code: + bc_message = self.__validate_bar_code( trans, sample, bar_code ) if bc_message: kwd[ 'message' ] = bc_message del kwd[ 'save_samples_button' ] @@ -1191,7 +1191,7 @@ class RequestsCommon( BaseController, Us 'Bar code associated with the sample' ) trans.sa_session.add( event ) trans.sa_session.flush() - sample.bar_code = barcode + sample.bar_code = bar_code sample.library = sample_widget[ 'library' ] sample.folder = sample_widget[ 'folder' ] form_values.content = sample_widget[ 'field_values' ] @@ -1281,7 +1281,7 @@ class RequestsCommon( BaseController, Us # Update the sample attributes from kwd sample_id = None name = util.restore_text( params.get( 'sample_%i_name' % index, sample.name ) ) - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, sample.bar_code ) ) + bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, sample.bar_code ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) if not library_id and sample.library: library_id = trans.security.encode_id( sample.library.id ) @@ -1303,7 +1303,7 @@ class RequestsCommon( BaseController, Us **kwd ) sample_widgets.append( dict( id=sample_id, name=name, - barcode=bar_code, + bar_code=bar_code, library=library, folder=folder, field_values=field_values, @@ -1317,7 +1317,7 @@ class RequestsCommon( BaseController, Us if not name: break id_index = index + 1 - bar_code = util.restore_text( params.get( 'sample_%i_barcode' % index, '' ) ) + bar_code = util.restore_text( params.get( 'sample_%i_bar_code' % index, '' ) ) library_id = util.restore_text( params.get( 'sample_%i_library_id' % id_index, '' ) ) folder_id = util.restore_text( params.get( 'sample_%i_folder_id' % id_index, '' ) ) library, folder = self.__get_library_and_folder( trans, library_id, folder_id ) @@ -1334,7 +1334,7 @@ class RequestsCommon( BaseController, Us **kwd ) sample_widgets.append( dict( id=None, name=name, - barcode=bar_code, + bar_code=bar_code, library=library, folder=folder, field_values=field_values, @@ -1492,31 +1492,24 @@ class RequestsCommon( BaseController, Us action='edit_samples', cntrller=cntrller, **kwd ) ) - def __validate_barcode( self, trans, sample, barcode ): + def __validate_bar_code( self, trans, sample, bar_code ): """ - Makes sure that the barcode about to be assigned to a sample is globally unique. - That is, barcodes must be unique across requests in Galaxy sample tracking. + Make sure that the bar_code about to be assigned to a sample is globally unique. + That is, bar_codes must be unique across requests in Galaxy sample tracking. + Bar codes are not required, but if used, they can only be added to a sample after + the request is submitted. """ message = '' unique = True for index in range( len( sample.request.samples ) ): - # Check for empty bar code - if not barcode.strip(): - if sample.state.id == sample.request.type.states[0].id: - # The user has not yet filled in the barcode value, but the sample is - # 'new', so all is well. - break - else: - message = "Fill in the barcode for sample (%s) before changing it's state." % sample.name - break # TODO: Add a unique constraint to sample.bar_code table column # Make sure bar code is unique - for sample_with_barcode in trans.sa_session.query( trans.model.Sample ) \ - .filter( trans.model.Sample.table.c.bar_code == barcode ): - if sample_with_barcode and sample_with_barcode.id != sample.id: + for sample_with_bar_code in trans.sa_session.query( trans.model.Sample ) \ + .filter( trans.model.Sample.table.c.bar_code == bar_code ): + if sample_with_bar_code and sample_with_bar_code.id != sample.id: message = '''The bar code (%s) associated with the sample (%s) belongs to another sample. Bar codes must be unique across all samples, so use a different bar code - for this sample.''' % ( barcode, sample.name ) + for this sample.''' % ( bar_code, sample.name ) unique = False break if not unique: --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -122,7 +122,7 @@ is_rejected = request.is_rejected is_submitted = sample.request.is_submitted is_unsubmitted = sample.request.is_unsubmitted - can_delete_samples = not is_complete + can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) @@ -153,10 +153,10 @@ %if display_bar_code: <td valign="top"> %if is_admin: - <input type="text" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}" size="10"/> + <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> %else: - ${sample_widget['barcode']} - <input type="hidden" name="sample_${sample_widget_index}_barcode" value="${sample_widget['barcode']}"/> + ${sample_widget['bar_code']} + <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> %endif </td> %endif @@ -234,7 +234,7 @@ is_submitted = request.is_submitted is_unsubmitted = request.is_unsubmitted can_add_samples = request.is_unsubmitted - can_delete_samples = editing_samples and request.samples and not is_complete + can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) can_edit_samples = request.samples and ( is_admin or not is_complete ) can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete ) can_transfer_datasets = is_admin and request.samples and not request.is_rejected @@ -280,14 +280,14 @@ <tbody><% trans.sa_session.refresh( request ) %> ## displayable_sample_widgets is a dictionary whose keys are: - ## id, name, barcode, library, folder, field_values, library_select_field, folder_select_field + ## id, name, bar_code, library, folder, field_values, library_select_field, folder_select_field ## A displayable_sample_widget will have an id == None if the widget's associated sample has not ## yet been saved (i.e., the use clicked the "Add sample" button but has not yet clicked the ## "Save" button. %for sample_widget_index, sample_widget in enumerate( displayable_sample_widgets ): <% sample_widget_name = sample_widget[ 'name' ] - sample_widget_barcode = sample_widget[ 'barcode' ] + sample_widget_bar_code = sample_widget[ 'bar_code' ] sample_widget_library = sample_widget[ 'library' ] if sample_widget_library: if cntrller == 'requests': @@ -309,7 +309,12 @@ <td> %if sample.state and ( can_select_datasets or can_transfer_datasets ): ## A sample will have a state only after the request has been submitted. - <% encoded_id = trans.security.encode_id( sample.id ) %> + <% + encoded_id = trans.security.encode_id( sample.id ) + transferred_dataset_files = sample.transferred_dataset_files + if not transferred_dataset_files: + transferred_dataset_files = [] + %><div style="float: left; margin-left: 2px;" class="menubutton split popup" id="sample-${sample.id}-popup"> ${sample.name} </div> @@ -317,8 +322,10 @@ %if can_select_datasets: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> %endif - %if sample.untransferred_dataset_files: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ): + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> + %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ): + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li> %endif </div> %else: @@ -326,7 +333,7 @@ %endif </td> %if display_bar_code: - <td>${sample_widget_barcode}</td> + <td>${sample_widget_bar_code}</td> %endif %if is_unsubmitted: <td>Unsubmitted</td> @@ -361,9 +368,8 @@ <td> %if is_admin: <% - if sample.transferred_dataset_files: - transferred_dataset_files = sample.transferred_dataset_files - else: + transferred_dataset_files = sample.transferred_dataset_files + if not transferred_dataset_files: transferred_dataset_files = [] %> %if not sample.datasets: --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1575,7 +1575,7 @@ class TwillTestCase( unittest.TestCase ) for index, field_value in enumerate( bar_codes ): sample_field_name = "sample_%i_name" % index sample_field_value = samples[ index ].name.replace( ' ', '+' ) - field_name = "sample_%i_barcode" % index + field_name = "sample_%i_bar_code" % index url += "&%s=%s" % ( field_name, field_value ) url += "&%s=%s" % ( sample_field_name, sample_field_value ) url += "&save_samples_button=Save"

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galaxy-commits November 2010