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https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
More changes to sample tracking functional tests
- assign target data library, editing samples, assign sample barcode
This commit is contained in:
Ramkrishna Chakrabarty
@@ -4,7 +4,9 @@ from base.twilltestcase import *
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from base.test_db_util import *
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sample_states = [ ( 'New', 'Sample entered into the system' ),
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( 'Received', 'Sample tube received' ),
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( 'Received', 'Sample tube received' ),
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( 'Library Started', 'Sample library preparation' ),
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( 'Run Started', 'Sequence run in progress' ),
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( 'Done', 'Sequence run complete' ) ]
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address_dict = dict( short_desc="Office",
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name="James Bond",
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@@ -93,6 +95,49 @@ class TestFormsAndRequests( TwillTestCase ):
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global role2
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role2 = get_role_by_name( name )
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assert role2 is not None, 'Problem retrieving role named "Role2" from the database'
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def test_006_create_library_and_folder( self ):
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"""Testing creating the target data library and folder"""
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# Logged in as admin_user
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for index in range( 0, 2 ):
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name = 'library%s' % str( index + 1 )
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description = '%s description' % name
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synopsis = '%s synopsis' % name
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self.create_library( name=name, description=description, synopsis=synopsis )
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# Get the libraries for later use
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global library1
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library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' )
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assert library1 is not None, 'Problem retrieving library (library1) from the database'
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global library2
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library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' )
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assert library2 is not None, 'Problem retrieving library (library2) from the database'
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# setup add_library_item permission to regular_user1
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# Set permissions on the library, sort for later testing.
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permissions_in = [ 'LIBRARY_ACCESS' ]
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permissions_out = []
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# Role1 members are: admin_user, regular_user1, regular_user3.
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# Each of these users will be permitted for LIBRARY_ACCESS, LIBRARY_ADD on
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# library1 and library2.
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for library in [ library1, library2 ]:
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self.library_permissions( self.security.encode_id( library.id ),
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library.name,
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str( role1.id ),
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permissions_in,
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permissions_out )
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# adding a folder
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for library in [ library1, library2 ]:
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name = "%s_folder1" % library.name
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description = "%s description" % name
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self.add_folder( 'library_admin',
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self.security.encode_id( library.id ),
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self.security.encode_id( library.root_folder.id ),
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name=name,
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description=description )
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global library1_folder1
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library1_folder1 = get_folder( library1.root_folder.id, 'library1_folder1', 'library1_folder1 description' )
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assert library1_folder1 is not None, 'Problem retrieving library folder named "library1_folder1" from the database'
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global library2_folder1
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library2_folder1 = get_folder( library2.root_folder.id, 'library2_folder1', 'library2_folder1 description' )
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assert library2_folder1 is not None, 'Problem retrieving library folder named "library2_folder1" from the database'
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#
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# ====== Form definition test methods ================================================
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#
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@@ -283,25 +328,25 @@ class TestFormsAndRequests( TwillTestCase ):
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self.view_request( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=[ 'Sequencing request "%s"' % request1.name,
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'There are no samples.',
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sample_form_layout_grid_name ],
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'There are no samples.' ],
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strings_not_displayed=[ request1.states.SUBMITTED,
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request1.states.COMPLETE,
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request1.states.REJECTED ] )
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request1.states.REJECTED,
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'Submit request' ] ) # this button should NOT show up as there are no samples yet
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# check if the request is showing in the 'new' filter
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self.check_request_grid( cntrller='requests',
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state=request1.states.NEW,
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strings_displayed=[ request1.name ] )
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self.view_request_history( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=[ 'History of Sequencing Request "%s"' % request1.name,
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strings_displayed=[ 'History of sequencing request "%s"' % request1.name,
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request1.states.NEW,
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'Request created' ],
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strings_not_displayed=[ request1.states.SUBMITTED,
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request1.states.COMPLETE,
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request1.states.REJECTED ] )
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def test_030_edit_basic_request_info( self ):
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"""Testing editing the basic information of a sequencing request"""
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"""Testing editing the basic information and email settings of a sequencing request"""
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# logged in as regular_user1
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fields = [ 'option2', str( user_address1.id ), 'field3 value (edited)' ]
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new_name=request1.name + ' (Renamed)'
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@@ -315,43 +360,186 @@ class TestFormsAndRequests( TwillTestCase ):
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strings_displayed=[ 'Edit sequencing request "%s"' % request1.name ],
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strings_displayed_after_submit=[ new_name, new_desc ] )
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refresh( request1 )
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# now check email notification settings
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check_sample_states = [ ( request1.type.states[0].name, request1.type.states[0].id, True ),
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( request1.type.states[2].name, request1.type.states[2].id, True ),
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( request1.type.states[4].name, request1.type.states[4].id, True ) ]#[ ( state.id, True ) for state in request1.type.states ]
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strings_displayed = [ 'Edit sequencing request "%s"' % request1.name,
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'Email notification settings' ]
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additional_emails = [ 'test@.bx.psu.edu', 'test2@.bx.psu.edu' ]
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strings_displayed_after_submit = [ "The changes made to the email notification settings have been saved",
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'\r\n'.join( additional_emails ) ]
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self.edit_request_email_settings( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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check_request_owner=True,
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additional_emails='\r\n'.join( additional_emails ),
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check_sample_states=check_sample_states,
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strings_displayed=strings_displayed,
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strings_displayed_after_submit=strings_displayed_after_submit )
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# lastly check the details in the request page
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strings_displayed = [ 'Sequencing request "%s"' % new_name,
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new_desc ]
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for field in fields:
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strings_displayed.append( field )
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for state_name, id, is_checked in check_sample_states:
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strings_displayed.append( state_name )
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for email in additional_emails:
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strings_displayed.append( email )
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self.view_request( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=strings_displayed,
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strings_not_displayed=[] )
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def test_035_add_samples_to_request( self ):
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"""Testing adding samples to request"""
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# logged in as regular_user1
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# Sample fields - the tuple represents a sample name and a list of sample form field values
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sample_value_tuples = [ ( 'Sample1', [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ),
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( 'Sample2', [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ),
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( 'Sample3', [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ]
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target_library_info = dict(library=self.security.encode_id(library2.id),
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folder=self.security.encode_id(library2_folder1.id) )
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sample_value_tuples = \
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[ ( 'Sample1', target_library_info, [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ),
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( 'Sample2', target_library_info, [ 'option2', 'sample2 field2 value', 'sample2 field3 value' ] ),
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( 'Sample3', target_library_info, [ 'option1', 'sample3 field2 value', 'sample3 field3 value' ] ) ]
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strings_displayed_after_submit = [ 'Unsubmitted' ]
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for sample_name, field_values in sample_value_tuples:
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for sample_name, lib_info, field_values in sample_value_tuples:
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strings_displayed_after_submit.append( sample_name )
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# add the sample values too
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for values in field_values:
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strings_displayed_after_submit.append( values )
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# Add samples to the request
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self.add_samples( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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request_name=request1.name,
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sample_value_tuples=sample_value_tuples,
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strings_displayed=[ 'Add Samples to Request "%s"' % request1.name,
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'<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field
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strings_displayed_after_submit=strings_displayed_after_submit )
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# def test_040_edit_samples_of_new_request( self ):
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# """Testing editing the sample information of new request1"""
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# # logged in as regular_user1
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# pass
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# def test_035_submit_request( self ):
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# """Testing editing a sequence run request"""
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# # logged in as regular_user1
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# self.submit_request( cntrller='requests',
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# request_id=self.security.encode_id( request1.id ),
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# request_name=request1.name,
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# strings_displayed_after_submit=[ 'The request has been submitted.' ] )
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# refresh( request1 )
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# # Make sure the request is showing in the 'submitted' filter
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# self.check_request_grid( cntrller='requests',
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# state=request1.states.SUBMITTED,
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# strings_displayed=[ request1.name ] )
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# # Make sure the request's state is now set to 'submitted'
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# assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \
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# % ( request1.name, request1.states.SUBMITTED )
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# check the new sample field values on the request page
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strings_displayed = [ 'Sequencing request "%s"' % request1.name,
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'Submit request' ] # this button should appear now
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strings_displayed.extend( strings_displayed_after_submit )
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strings_displayed_count = []
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strings_displayed_count.append( ( library2.name, len( sample_value_tuples ) ) )
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strings_displayed_count.append( ( library2_folder1.name, len( sample_value_tuples ) ) )
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self.view_request( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=strings_displayed,
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strings_displayed_count=strings_displayed_count )
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def test_040_edit_samples_of_new_request( self ):
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"""Testing editing the sample information of new request1"""
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# logged in as regular_user1
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# target data library - change it to library1
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target_library_info = dict(library=self.security.encode_id(library1.id),
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folder=self.security.encode_id(library1_folder1.id) )
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new_sample_value_tuples = \
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[ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ),
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( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ),
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( 'Sample3_renamed', target_library_info, [ 'option2', 'sample3 field2 value edited', 'sample3 field3 value edited' ] ) ]
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strings_displayed_after_submit = [ 'Unsubmitted' ]
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for sample_name, lib_info, field_values in new_sample_value_tuples:
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strings_displayed_after_submit.append( sample_name )
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# add the sample values too
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for values in field_values:
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strings_displayed_after_submit.append( values )
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# Add samples to the request
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self.edit_samples( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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sample_value_tuples=new_sample_value_tuples,
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strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name,
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'<input type="text" name="sample_0_name" value="Sample1" size="10"/>' ], # sample name input field
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strings_displayed_after_submit=strings_displayed_after_submit )
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# check the changed sample field values on the request page
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strings_displayed = [ 'Sequencing request "%s"' % request1.name ]
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strings_displayed.extend( strings_displayed_after_submit )
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strings_displayed_count = []
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strings_displayed_count.append( ( library1.name, len( new_sample_value_tuples ) ) )
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strings_displayed_count.append( ( library1_folder1.name, len( new_sample_value_tuples ) ) )
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self.view_request( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=strings_displayed,
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strings_displayed_count=strings_displayed_count )
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def test_045_submit_request( self ):
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"""Testing submitting a sequencing request"""
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# logged in as regular_user1
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self.submit_request( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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request_name=request1.name,
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strings_displayed_after_submit=[ 'The request has been submitted.' ] )
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refresh( request1 )
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# Make sure the request is showing in the 'submitted' filter
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self.check_request_grid( cntrller='requests',
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state=request1.states.SUBMITTED,
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strings_displayed=[ request1.name ] )
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# Make sure the request's state is now set to 'submitted'
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assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \
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% ( request1.name, request1.states.SUBMITTED )
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# the sample state should appear once for each sample
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strings_displayed_count = [ ( request1.type.states[0].name, len( request1.samples ) ) ]
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# after submission, these buttons should not appear
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strings_not_displayed = [ 'Add sample', 'Submit request' ]
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# check the request page
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self.view_request( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=[ request1.states.SUBMITTED ],
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strings_displayed_count=strings_displayed_count,
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strings_not_displayed=strings_not_displayed )
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strings_displayed=[ 'History of sequencing request "%s"' % request1.name,
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'Request submitted by %s' % regular_user1.email,
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'Request created' ]
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strings_displayed_count = [ ( request1.states.SUBMITTED, 1 ) ]
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self.view_request_history( cntrller='requests',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=strings_displayed,
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strings_displayed_count=strings_displayed_count,
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strings_not_displayed=[ request1.states.COMPLETE,
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request1.states.REJECTED ] )
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#
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# ====== Sequencing request test methods - Admin perspective ================
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#
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def test_050_receive_request_as_admin( self ):
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"""Testing receiving a sequencing request and assigning it barcodes"""
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self.logout()
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self.login( email=admin_user.email )
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self.check_request_grid( cntrller='requests_admin',
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state=request1.states.SUBMITTED,
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strings_displayed=[ request1.name ] )
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strings_displayed = [ request1.states.SUBMITTED,
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'Reject this request' ]
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strings_not_displayed = [ 'Add sample' ]
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self.view_request( cntrller='requests_admin',
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request_id=self.security.encode_id( request1.id ),
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strings_not_displayed=strings_not_displayed )
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# Set bar codes for the samples
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bar_codes = [ '10001', '10002', '10003' ]
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strings_displayed_after_submit = [ 'Changes made to the samples have been saved.' ]
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strings_displayed_after_submit.extend( bar_codes )
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self.add_bar_codes( cntrller='requests_admin',
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request_id=self.security.encode_id( request1.id ),
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bar_codes=bar_codes,
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strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ],
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strings_displayed_after_submit=strings_displayed_after_submit )
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# the second sample state should appear once for each sample
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strings_displayed_count = [ ( request1.type.states[1].name, len( request1.samples ) ),
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( request1.type.states[0].name, 0 ) ]
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# check the request page
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self.view_request( cntrller='requests_admin',
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request_id=self.security.encode_id( request1.id ),
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strings_displayed=bar_codes,
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strings_displayed_count=strings_displayed_count )
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# the sample state descriptions of the future states should not appear
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# here the state names are not checked as all of them appear at the top of
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# the page like: state1 > state2 > state3
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strings_not_displayed=[ request1.type.states[2].desc,
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request1.type.states[3].desc,
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request1.type.states[4].desc ]
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# check history of each sample
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for sample in request1.samples:
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strings_displayed = [ 'Events for Sample "%s"' % sample.name,
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'Request submitted and sample state set to %s' % request1.type.states[0].name,
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request1.type.states[0].name,
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request1.type.states[1].name ]
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self.view_sample_history( cntrller='requests_admin',
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sample_id=self.security.encode_id( sample.id ),
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strings_displayed=strings_displayed,
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strings_not_displayed=strings_not_displayed )
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# def test_040_request_lifecycle( self ):
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# """Testing request life-cycle as it goes through all the states"""
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# # logged in as regular_user1
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@@ -477,6 +665,17 @@ class TestFormsAndRequests( TwillTestCase ):
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# Logged in as admin_user
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self.logout()
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self.login( email=admin_user.email )
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##################
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# Purge all libraries
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##################
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for library in [ library1, library2 ]:
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self.delete_library_item( 'library_admin',
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self.security.encode_id( library.id ),
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self.security.encode_id( library.id ),
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library.name,
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item_type='library' )
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self.purge_library( self.security.encode_id( library.id ), library.name )
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##################
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# Delete request_type permissions
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##################
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