[2] | 1 | from base.twilltestcase import * |
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| 2 | from base.test_db_util import * |
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| 3 | |
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| 4 | class TestLibraryFeatures( TwillTestCase ): |
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| 5 | def test_000_initiate_users( self ): |
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| 6 | """Ensuring all required user accounts exist""" |
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| 7 | self.logout() |
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| 8 | self.login( email='test1@bx.psu.edu', username='regular-user1' ) |
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| 9 | global regular_user1 |
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| 10 | regular_user1 = get_user( 'test1@bx.psu.edu' ) |
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| 11 | assert regular_user1 is not None, 'Problem retrieving user with email "test1@bx.psu.edu" from the database' |
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| 12 | global regular_user1_private_role |
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| 13 | regular_user1_private_role = get_private_role( regular_user1 ) |
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| 14 | self.logout() |
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| 15 | self.login( email='test2@bx.psu.edu', username='regular-user2' ) |
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| 16 | global regular_user2 |
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| 17 | regular_user2 = get_user( 'test2@bx.psu.edu' ) |
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| 18 | assert regular_user2 is not None, 'Problem retrieving user with email "test2@bx.psu.edu" from the database' |
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| 19 | global regular_user2_private_role |
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| 20 | regular_user2_private_role = get_private_role( regular_user2 ) |
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| 21 | self.logout() |
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| 22 | self.login( email='test3@bx.psu.edu', username='regular-user3' ) |
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| 23 | global regular_user3 |
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| 24 | regular_user3 = get_user( 'test3@bx.psu.edu' ) |
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| 25 | assert regular_user3 is not None, 'Problem retrieving user with email "test3@bx.psu.edu" from the database' |
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| 26 | global regular_user3_private_role |
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| 27 | regular_user3_private_role = get_private_role( regular_user3 ) |
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| 28 | self.logout() |
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| 29 | self.login( email='test@bx.psu.edu', username='admin-user' ) |
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| 30 | global admin_user |
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| 31 | admin_user = get_user( 'test@bx.psu.edu' ) |
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| 32 | assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database' |
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| 33 | global admin_user_private_role |
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| 34 | admin_user_private_role = get_private_role( admin_user ) |
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| 35 | def test_005_create_library_templates( self ): |
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| 36 | """Testing creating several LibraryInformationTemplate form definitions""" |
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| 37 | # Logged in as admin_user |
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| 38 | for type in [ 'AddressField', 'CheckboxField', 'SelectField', 'TextArea', 'TextField', 'WorkflowField' ]: |
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| 39 | form_desc = '%s description' % type |
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| 40 | num_options = 0 |
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| 41 | if type == 'SelectField': |
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| 42 | # Pass number of options we want in our SelectField |
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| 43 | num_options = 2 |
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| 44 | # Create form for library template |
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| 45 | self.create_form( name=type, |
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| 46 | desc=form_desc, |
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| 47 | form_type=galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE, |
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| 48 | field_type=type, |
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| 49 | num_options=num_options ) |
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| 50 | # Get all of the new form definitions for later use |
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| 51 | global AddressField_form |
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| 52 | AddressField_form = get_form( 'AddressField' ) |
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| 53 | global CheckboxField_form |
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| 54 | CheckboxField_form = get_form( 'CheckboxField' ) |
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| 55 | global SelectField_form |
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| 56 | SelectField_form = get_form( 'SelectField' ) |
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| 57 | global TextArea_form |
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| 58 | TextArea_form = get_form( 'TextArea' ) |
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| 59 | global TextField_form |
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| 60 | TextField_form = get_form( 'TextField' ) |
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| 61 | global WorkflowField_form |
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| 62 | WorkflowField_form = get_form( 'WorkflowField' ) |
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| 63 | def test_010_create_libraries( self ): |
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| 64 | """Testing creating a new library for each template""" |
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| 65 | # Logged in as admin_user |
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| 66 | # library1 -> AddressField |
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| 67 | # library2 -> CheckboxField |
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| 68 | # library3 -> SelectField |
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| 69 | # library4 -> TextArea |
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| 70 | # library5 -> TextField |
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| 71 | # library6 -> WorkflowField |
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| 72 | for index, form in enumerate( [ AddressField_form, CheckboxField_form, SelectField_form, TextArea_form, TextField_form, WorkflowField_form ] ): |
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| 73 | name = 'library%s' % str( index + 1 ) |
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| 74 | description = '%s description' % name |
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| 75 | synopsis = '%s synopsis' % name |
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| 76 | self.create_library( name=name, description=description, synopsis=synopsis ) |
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| 77 | # Get the libraries for later use |
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| 78 | global library1 |
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| 79 | library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' ) |
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| 80 | global library2 |
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| 81 | library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' ) |
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| 82 | global library3 |
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| 83 | library3 = get_library( 'library3', 'library3 description', 'library3 synopsis' ) |
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| 84 | global library4 |
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| 85 | library4 = get_library( 'library4', 'library4 description', 'library4 synopsis' ) |
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| 86 | global library5 |
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| 87 | library5 = get_library( 'library5', 'library5 description', 'library5 synopsis' ) |
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| 88 | global library6 |
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| 89 | library6 = get_library( 'library6', 'library6 description', 'library6 synopsis' ) |
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| 90 | def test_015_add_template_to_library1( self ): |
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| 91 | """Testing add an inheritable template containing an AddressField to library1""" |
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| 92 | # Logged in as admin_user |
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| 93 | # Add a template containing an AddressField to library1 |
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| 94 | self.add_library_template( 'library_admin', |
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| 95 | 'library', |
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| 96 | self.security.encode_id( library1.id ), |
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| 97 | self.security.encode_id( AddressField_form.id ), |
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| 98 | AddressField_form.name ) |
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| 99 | def test_020_add_folder_to_library1( self ): |
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| 100 | """Testing adding a folder to library1""" |
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| 101 | # Logged in as admin_user |
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| 102 | # Add a folder to library1 |
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| 103 | folder = library1.root_folder |
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| 104 | name = "folder" |
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| 105 | description = "folder description" |
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| 106 | self.add_folder( 'library_admin', |
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| 107 | self.security.encode_id( library1.id ), |
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| 108 | self.security.encode_id( folder.id ), |
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| 109 | name=name, |
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| 110 | description=description ) |
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| 111 | global folder1 |
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| 112 | folder1 = get_folder( folder.id, name, description ) |
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| 113 | def test_025_check_library1( self ): |
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| 114 | """Checking library1 and its root folder""" |
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| 115 | # Logged in as admin_user |
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| 116 | self.browse_library( 'library_admin', |
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| 117 | self.security.encode_id( library1.id ), |
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| 118 | strings_displayed=[ folder1.name, folder1.description ] ) |
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| 119 | # Make sure the template and contents were inherited to folder1 |
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| 120 | self.folder_info( 'library_admin', |
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| 121 | self.security.encode_id( folder1.id ), |
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| 122 | self.security.encode_id( library1.id ), |
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| 123 | strings_displayed=[ AddressField_form.name, |
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| 124 | 'This is an inherited template and is not required to be used with this folder' ] ) |
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| 125 | def test_030_add_dataset_to_folder1( self ): |
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| 126 | """Testing adding a ldda1 to folder1, and adding a new UserAddress on the upload form.""" |
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| 127 | # Logged in as admin_user |
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| 128 | # The AddressField template should be inherited to the library dataset upload form. Passing |
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| 129 | # the value 'new' should submit the form via refresh_on_change and allow new UserAddress information |
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| 130 | # to be posted as part of the upload. |
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| 131 | filename = '1.bed' |
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| 132 | ldda_message = '1.bed message' |
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| 133 | short_desc = 'Office' |
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| 134 | self.upload_library_dataset( cntrller='library_admin', |
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| 135 | library_id=self.security.encode_id( library1.id ), |
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| 136 | folder_id=self.security.encode_id( folder1.id ), |
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| 137 | filename=filename, |
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| 138 | file_type='bed', |
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| 139 | dbkey='hg18', |
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| 140 | ldda_message=ldda_message, |
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| 141 | template_refresh_field_contents='new', |
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| 142 | template_fields=[ ( 'field_0_short_desc', short_desc ), |
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| 143 | ( 'field_0_name', 'Dick' ), |
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| 144 | ( 'field_0_institution', 'PSU' ), |
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| 145 | ( 'field_0_address', '32 O Street' ), |
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| 146 | ( 'field_0_city', 'Anywhere' ), |
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| 147 | ( 'field_0_state', 'AK' ), |
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| 148 | ( 'field_0_postal_code', '0000000' ), |
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| 149 | ( 'field_0_country', 'USA' ) ], |
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| 150 | strings_displayed=[ 'Upload files' ] ) |
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| 151 | global user_address1 |
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| 152 | user_address1 = get_user_address( admin_user, short_desc ) |
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| 153 | assert user_address1 is not None, 'Problem retrieving user_address1 from the database' |
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| 154 | global ldda1 |
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| 155 | ldda1 = get_latest_ldda_by_name( filename ) |
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| 156 | assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database' |
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| 157 | self.browse_library( 'library_admin', |
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| 158 | self.security.encode_id( library1.id ), |
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| 159 | strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] ) |
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| 160 | # Make sure the library template contents were correctly saved |
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| 161 | self.ldda_edit_info( 'library_admin', |
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| 162 | self.security.encode_id( library1.id ), |
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| 163 | self.security.encode_id( folder1.id ), |
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| 164 | self.security.encode_id( ldda1.id ), |
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| 165 | ldda1.name, |
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| 166 | strings_displayed=[ 'Dick' ] ) |
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| 167 | def test_035_edit_contents_of_ldda1_tempplate( self ): |
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| 168 | """Testing editing the contents of ldda1 AddressField template by adding a new user_address""" |
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| 169 | short_desc = 'Home' |
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| 170 | # Now add a new user_address to ldda1 |
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| 171 | self.ldda_edit_info( 'library_admin', |
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| 172 | self.security.encode_id( library1.id ), |
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| 173 | self.security.encode_id( folder1.id ), |
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| 174 | self.security.encode_id( ldda1.id ), |
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| 175 | ldda1.name, |
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| 176 | template_refresh_field_contents='new', |
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| 177 | template_fields=[ ( 'field_0_short_desc', short_desc ), |
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| 178 | ( 'field_0_name', 'Richard' ), |
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| 179 | ( 'field_0_institution', 'PSU' ), |
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| 180 | ( 'field_0_address', '32 O Street' ), |
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| 181 | ( 'field_0_city', 'Anywhere' ), |
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| 182 | ( 'field_0_state', 'AK' ), |
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| 183 | ( 'field_0_postal_code', '0000000' ), |
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| 184 | ( 'field_0_country', 'USA' ) ], |
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| 185 | strings_displayed=[ short_desc ] ) |
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| 186 | global user_address2 |
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| 187 | user_address2 = get_user_address( admin_user, short_desc ) |
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| 188 | assert user_address2 is not None, 'Problem retrieving user_address2 from the database' |
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| 189 | def test_040_edit_contents_of_folder1_template( self ): |
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| 190 | """Testing editing the contents of folder1 AddressField template""" |
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| 191 | # Make sure the template and contents were inherited to folder1 |
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| 192 | self.folder_info( 'library_admin', |
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| 193 | self.security.encode_id( folder1.id ), |
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| 194 | self.security.encode_id( library1.id ), |
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| 195 | template_refresh_field_contents=str( user_address2.id ), |
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| 196 | strings_displayed=[ AddressField_form.name, |
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| 197 | 'This is an inherited template and is not required to be used with this folder' ], |
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| 198 | strings_displayed_after_submit=[ 'Richard' ] ) |
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| 199 | def test_045_add_dataset_to_folder1( self ): |
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| 200 | """Testing adding another ldda to folder1""" |
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| 201 | # The upload form should now inherit user_address2 on the upload form |
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| 202 | filename = '2.bed' |
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| 203 | ldda_message = '2.bed message' |
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| 204 | self.upload_library_dataset( cntrller='library_admin', |
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| 205 | library_id=self.security.encode_id( library1.id ), |
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| 206 | folder_id=self.security.encode_id( folder1.id ), |
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| 207 | filename=filename, |
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| 208 | file_type='bed', |
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| 209 | dbkey='hg18', |
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| 210 | ldda_message=ldda_message, |
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| 211 | strings_displayed=[ 'Upload files' ] ) |
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| 212 | # Make sure user_address2 is associated with ldda. |
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| 213 | self.ldda_edit_info( 'library_admin', |
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| 214 | self.security.encode_id( library1.id ), |
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| 215 | self.security.encode_id( folder1.id ), |
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| 216 | self.security.encode_id( ldda1.id ), |
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| 217 | ldda1.name, |
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| 218 | strings_displayed=[ user_address2.desc ] ) |
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| 219 | def test_050_add_template_to_library2( self ): |
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| 220 | """ Testing add an inheritable template containing an CheckboxField to library2""" |
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| 221 | # Add a template containing an CheckboxField to library1 |
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| 222 | self.add_library_template( 'library_admin', |
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| 223 | 'library', |
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| 224 | self.security.encode_id( library2.id ), |
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| 225 | self.security.encode_id( CheckboxField_form.id ), |
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| 226 | CheckboxField_form.name ) |
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| 227 | # Check the CheckboxField to make sure the template contents are inherited |
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| 228 | self.library_info( 'library_admin', |
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| 229 | self.security.encode_id( library2.id ), |
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| 230 | template_fields = [ ( 'field_0', '1' ) ] ) |
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| 231 | def test_055_add_folder2_to_library2( self ): |
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| 232 | """Testing adding a folder to library2""" |
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| 233 | # Logged in as admin_user |
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| 234 | # Add a folder to library2 |
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| 235 | folder = library2.root_folder |
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| 236 | name = "folder" |
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| 237 | description = "folder description" |
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| 238 | self.add_folder( 'library_admin', |
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| 239 | self.security.encode_id( library2.id ), |
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| 240 | self.security.encode_id( folder.id ), |
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| 241 | name=name, |
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| 242 | description=description ) |
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| 243 | global folder2 |
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| 244 | folder2 = get_folder( folder.id, name, description ) |
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| 245 | def test_060_check_library2( self ): |
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| 246 | """Checking library2 and its root folder""" |
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| 247 | # Logged in as admin_user |
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| 248 | self.browse_library( 'library_admin', |
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| 249 | self.security.encode_id( library2.id ), |
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| 250 | strings_displayed=[ folder2.name, folder2.description ] ) |
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| 251 | def test_065_save_folder2_inherited_template( self ): |
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| 252 | """Saving the inherited template for folder2""" |
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| 253 | # Logged in as admin_user |
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| 254 | # Save the inherited template |
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| 255 | self.folder_info( cntrller='library_admin', |
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| 256 | folder_id=self.security.encode_id( folder2.id ), |
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| 257 | library_id=self.security.encode_id( library2.id ), |
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| 258 | template_fields=[ ( "field_0", '1' ) ], |
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| 259 | strings_displayed=[ CheckboxField_form.name, |
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| 260 | 'This is an inherited template and is not required to be used with this folder' ] ) |
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| 261 | def test_070_add_ldda_to_folder2( self ): |
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| 262 | """ |
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| 263 | Testing adding a new library dataset to library2's folder, making sure the CheckboxField is |
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| 264 | checked on the upload form. |
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| 265 | """ |
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| 266 | # Logged in as admin_user |
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| 267 | filename = '1.bed' |
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| 268 | ldda_message = '1.bed message' |
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| 269 | self.upload_library_dataset( cntrller='library_admin', |
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| 270 | library_id=self.security.encode_id( library2.id ), |
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| 271 | folder_id=self.security.encode_id( folder2.id ), |
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| 272 | filename=filename, |
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| 273 | file_type='bed', |
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| 274 | dbkey='hg18', |
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| 275 | ldda_message=ldda_message, |
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| 276 | strings_displayed=[ 'CheckboxField', 'checked' ] ) |
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| 277 | ldda = get_latest_ldda_by_name( filename ) |
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| 278 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
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| 279 | self.browse_library( 'library_admin', |
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| 280 | self.security.encode_id( library2.id ), |
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| 281 | strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) |
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| 282 | # Make sure the library template contents were correctly saved |
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| 283 | self.ldda_edit_info( 'library_admin', |
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| 284 | self.security.encode_id( library2.id ), |
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| 285 | self.security.encode_id( folder2.id ), |
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| 286 | self.security.encode_id( ldda.id ), |
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| 287 | ldda.name, |
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| 288 | strings_displayed=[ 'CheckboxField', 'checked' ] ) |
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| 289 | def test_080_add_template_to_library3( self ): |
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| 290 | """ Testing add an inheritable template containing an SelectField to library3""" |
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| 291 | # Logged in as admin_user |
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| 292 | self.add_library_template( 'library_admin', |
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| 293 | 'library', |
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| 294 | self.security.encode_id( library3.id ), |
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| 295 | self.security.encode_id( SelectField_form.id ), |
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| 296 | SelectField_form.name ) |
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| 297 | # Select the 2nd option in the SelectField to make sure the template contents are inherited |
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| 298 | # SelectField option names are zero-based |
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| 299 | self.library_info( 'library_admin', |
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| 300 | self.security.encode_id( library3.id ), |
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| 301 | template_fields=[ ( 'field_0', 'Option1' ) ] ) |
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| 302 | def test_085_add_folder3_to_library3( self ): |
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| 303 | """Testing adding a folder to library3""" |
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| 304 | # Logged in as admin_user |
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| 305 | # Add a folder to library3 |
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| 306 | folder = library3.root_folder |
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| 307 | name = "folder" |
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| 308 | description = "folder description" |
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| 309 | self.add_folder( 'library_admin', |
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| 310 | self.security.encode_id( library3.id ), |
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| 311 | self.security.encode_id( folder.id ), |
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| 312 | name=name, |
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| 313 | description=description ) |
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| 314 | global folder3 |
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| 315 | folder3 = get_folder( folder.id, name, description ) |
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| 316 | def test_090_check_library3( self ): |
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| 317 | """Checking library3 and its root folder""" |
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| 318 | # Logged in as admin_user |
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| 319 | self.browse_library( 'library_admin', |
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| 320 | self.security.encode_id( library3.id ), |
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| 321 | strings_displayed=[ folder3.name, folder3.description ] ) |
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| 322 | def test_095_save_folder3_inherited_template( self ): |
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| 323 | """Saving the inherited template for folder3""" |
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| 324 | # Logged in as admin_user |
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| 325 | # Save the inherited template |
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| 326 | self.folder_info( cntrller='library_admin', |
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| 327 | folder_id=self.security.encode_id( folder3.id ), |
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| 328 | library_id=self.security.encode_id( library3.id ), |
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| 329 | template_fields=[ ( "field_0", 'Option1' ) ], |
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| 330 | strings_displayed=[ SelectField_form.name, |
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| 331 | 'This is an inherited template and is not required to be used with this folder', |
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| 332 | 'Option1' ] ) |
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| 333 | def test_100_add_ldda_to_folder3( self ): |
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| 334 | """ |
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| 335 | Testing adding a new library dataset to library3's folder, |
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| 336 | making sure the SelectField setting is correct on the upload form. |
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| 337 | """ |
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| 338 | filename = '3.bed' |
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| 339 | ldda_message = '3.bed message' |
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| 340 | # Logged in as admin_user |
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| 341 | self.upload_library_dataset( cntrller='library_admin', |
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| 342 | library_id=self.security.encode_id( library3.id ), |
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| 343 | folder_id=self.security.encode_id( folder3.id ), |
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| 344 | filename=filename, |
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| 345 | file_type='bed', |
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| 346 | dbkey='hg18', |
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| 347 | ldda_message=ldda_message, |
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| 348 | strings_displayed=[ 'SelectField', 'selected>Option1' ] ) |
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| 349 | ldda = get_latest_ldda_by_name( filename ) |
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| 350 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
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| 351 | self.browse_library( 'library_admin', |
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| 352 | self.security.encode_id( library3.id ), |
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| 353 | strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) |
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| 354 | # Make sure the library template contents were correctly saved |
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| 355 | self.ldda_edit_info( 'library_admin', |
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| 356 | self.security.encode_id( library3.id ), |
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| 357 | self.security.encode_id( folder3.id ), |
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| 358 | self.security.encode_id( ldda.id ), |
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| 359 | ldda.name, |
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| 360 | strings_displayed=[ 'SelectField', 'Option1' ] ) |
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| 361 | # Import a dataset from the current history |
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| 362 | filename = '8.bed' |
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| 363 | self.new_history( name='import with SelectField' ) |
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| 364 | self.upload_file( filename ) |
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| 365 | hda = get_latest_hda() |
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| 366 | self.upload_library_dataset( cntrller='library_admin', |
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| 367 | library_id=self.security.encode_id( library3.id ), |
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| 368 | folder_id=self.security.encode_id( folder3.id ), |
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| 369 | upload_option='import_from_history', |
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| 370 | hda_ids=self.security.encode_id( hda.id ), |
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| 371 | strings_displayed=[ '<input type="hidden" name="field_0" value="Option1"/>' ] ) |
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| 372 | ldda = get_latest_ldda_by_name( filename ) |
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| 373 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
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| 374 | self.browse_library( 'library_admin', |
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| 375 | self.security.encode_id( library3.id ), |
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| 376 | strings_displayed=[ ldda.name, admin_user.email ] ) |
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| 377 | # Make sure the library template contents were correctly saved |
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| 378 | self.ldda_edit_info( 'library_admin', |
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| 379 | self.security.encode_id( library3.id ), |
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| 380 | self.security.encode_id( folder3.id ), |
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| 381 | self.security.encode_id( ldda.id ), |
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| 382 | ldda.name, |
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| 383 | strings_displayed=[ 'SelectField', 'Option1' ] ) |
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| 384 | def test_105_add_template_to_library4( self ): |
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| 385 | """ Testing add an inheritable template containing an TextArea to library4""" |
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| 386 | # Logged in as admin_user |
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| 387 | # Add an inheritable template to library4 |
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| 388 | self.add_library_template( 'library_admin', |
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| 389 | 'library', |
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| 390 | self.security.encode_id( library4.id ), |
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| 391 | self.security.encode_id( TextArea_form.id ), |
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| 392 | TextArea_form.name ) |
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| 393 | # Select the 2nd option in the SelectField to make sure the template contents are inherited |
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| 394 | self.library_info( 'library_admin', |
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| 395 | self.security.encode_id( library4.id ), |
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| 396 | template_fields=[ ('field_0', 'This text should be inherited' ) ] ) |
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| 397 | def test_110_add_folder4_to_library4( self ): |
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| 398 | """Testing adding a folder to library4""" |
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| 399 | # Logged in as admin_user |
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| 400 | # Add a folder to library4 |
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| 401 | folder = library4.root_folder |
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| 402 | name = "folder" |
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| 403 | description = "folder description" |
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| 404 | self.add_folder( 'library_admin', |
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| 405 | self.security.encode_id( library4.id ), |
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| 406 | self.security.encode_id( folder.id ), |
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| 407 | name=name, |
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| 408 | description=description ) |
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| 409 | global folder4 |
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| 410 | folder4 = get_folder( folder.id, name, description ) |
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| 411 | def test_115_save_folder4_inherited_template( self ): |
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| 412 | """Saving the inherited template for folder4""" |
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| 413 | # Logged in as admin_user |
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| 414 | # Save the inherited template |
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| 415 | self.folder_info( cntrller='library_admin', |
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| 416 | folder_id=self.security.encode_id( folder4.id ), |
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| 417 | library_id=self.security.encode_id( library4.id ), |
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| 418 | template_fields=[ ( "field_0", 'This text should be inherited' ) ], |
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| 419 | strings_displayed=[ TextArea_form.name, |
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| 420 | 'This is an inherited template and is not required to be used with this folder', |
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| 421 | 'This text should be inherited' ] ) |
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| 422 | def test_120_add_ldda_to_folder4( self ): |
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| 423 | """ |
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| 424 | Testing adding a new library dataset to library4's folder, |
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| 425 | making sure the TextArea setting is correct on the upload form. |
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| 426 | """ |
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| 427 | filename = '4.bed' |
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| 428 | ldda_message = '4.bed message' |
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| 429 | # Logged in as admin_user |
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| 430 | self.upload_library_dataset( cntrller='library_admin', |
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| 431 | library_id=self.security.encode_id( library4.id ), |
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| 432 | folder_id=self.security.encode_id( folder4.id ), |
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| 433 | filename=filename, |
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| 434 | file_type='bed', |
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| 435 | dbkey='hg18', |
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| 436 | ldda_message=ldda_message, |
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| 437 | strings_displayed=[ 'TextArea', 'This text should be inherited' ] ) |
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| 438 | ldda = get_latest_ldda_by_name( filename ) |
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| 439 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
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| 440 | self.browse_library( 'library_admin', |
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| 441 | self.security.encode_id( library4.id ), |
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| 442 | strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) |
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| 443 | # Make sure the library template contents were correctly saved |
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| 444 | self.ldda_edit_info( 'library_admin', |
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| 445 | self.security.encode_id( library4.id ), |
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| 446 | self.security.encode_id( folder4.id ), |
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| 447 | self.security.encode_id( ldda.id ), |
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| 448 | ldda.name, |
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| 449 | strings_displayed=[ 'TextArea', 'This text should be inherited' ] ) |
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| 450 | def test_125_add_template_to_library5( self ): |
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| 451 | """ Testing add an inheritable template containing an TextField to library5""" |
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| 452 | # Add an inheritable template to library5 |
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| 453 | self.add_library_template( 'library_admin', |
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| 454 | 'library', |
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| 455 | self.security.encode_id( library5.id ), |
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| 456 | self.security.encode_id( TextField_form.id ), |
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| 457 | TextField_form.name ) |
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| 458 | # Select the 2nd option in the SelectField to make sure the template contents are inherited |
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| 459 | self.library_info( 'library_admin', |
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| 460 | self.security.encode_id( library5.id ), |
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| 461 | template_fields=[ ( 'field_0', 'This text should be inherited' ) ] ) |
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| 462 | def test_130_add_folder5_to_library5( self ): |
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| 463 | """Testing adding a folder to library5""" |
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| 464 | # Logged in as admin_user |
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| 465 | # Add a folder to library5 |
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| 466 | folder = library5.root_folder |
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| 467 | name = "folder" |
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| 468 | description = "folder description" |
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| 469 | self.add_folder( 'library_admin', |
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| 470 | self.security.encode_id( library5.id ), |
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| 471 | self.security.encode_id( folder.id ), |
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| 472 | name=name, |
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| 473 | description=description ) |
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| 474 | global folder5 |
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| 475 | folder5 = get_folder( folder.id, name, description ) |
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| 476 | def test_135_save_folder5_inherited_template( self ): |
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| 477 | """Saving the inherited template for folder5""" |
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| 478 | # Logged in as admin_user |
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| 479 | # Save the inherited template |
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| 480 | self.folder_info( cntrller='library_admin', |
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| 481 | folder_id=self.security.encode_id( folder5.id ), |
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| 482 | library_id=self.security.encode_id( library5.id ), |
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| 483 | template_fields=[ ( "field_0", 'This text should be inherited' ) ], |
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| 484 | strings_displayed=[ TextField_form.name, |
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| 485 | 'This is an inherited template and is not required to be used with this folder', |
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| 486 | 'This text should be inherited' ] ) |
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| 487 | def test_140_add_ldda_to_folder5( self ): |
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| 488 | """ |
---|
| 489 | Testing adding a new library dataset to library5's folder, |
---|
| 490 | making sure the TextField setting is correct on the upload form. |
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| 491 | """ |
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| 492 | # Logged in as admin_user |
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| 493 | filename = '5.bed' |
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| 494 | ldda_message = '5.bed message' |
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| 495 | self.upload_library_dataset( cntrller='library_admin', |
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| 496 | library_id=self.security.encode_id( library5.id ), |
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| 497 | folder_id=self.security.encode_id( folder5.id ), |
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| 498 | filename=filename, |
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| 499 | file_type='bed', |
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| 500 | dbkey='hg18', |
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| 501 | ldda_message=ldda_message, |
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| 502 | strings_displayed=[ 'TextField', 'This text should be inherited' ] ) |
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| 503 | ldda = get_latest_ldda_by_name( filename ) |
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| 504 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
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| 505 | self.browse_library( 'library_admin', |
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| 506 | self.security.encode_id( library5.id ), |
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| 507 | strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) |
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| 508 | # Make sure the library template contents were correctly saved |
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| 509 | self.ldda_edit_info( 'library_admin', |
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| 510 | self.security.encode_id( library5.id ), |
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| 511 | self.security.encode_id( folder5.id ), |
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| 512 | self.security.encode_id( ldda.id ), |
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| 513 | ldda.name, |
---|
| 514 | strings_displayed=[ 'TextField', 'This text should be inherited' ] ) |
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| 515 | def test_145_edit_library5_template_layout( self ): |
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| 516 | """Test editing the layout of library5's template""" |
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| 517 | # Currently there is only a TextField, and we'll add a TextArea. |
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| 518 | self.edit_template( 'library_admin', |
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| 519 | 'library', |
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| 520 | self.security.encode_id( library5.id ), |
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| 521 | field_type='TextArea', |
---|
| 522 | field_name_1=TextArea_form.name, |
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| 523 | field_helptext_1='%s help' % TextArea_form.name, |
---|
| 524 | field_default_1='%s default' % TextArea_form.name ) |
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| 525 | def test_150_add_ldda_to_library5( self ): |
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| 526 | """ |
---|
| 527 | Testing adding a new library dataset to library5's folder, |
---|
| 528 | making sure the TextField and new TextArea settings are |
---|
| 529 | correct on the upload form. |
---|
| 530 | """ |
---|
| 531 | filename = '6.bed' |
---|
| 532 | ldda_message = '6.bed message' |
---|
| 533 | # Logged in as admin_user |
---|
| 534 | self.upload_library_dataset( cntrller='library_admin', |
---|
| 535 | library_id=self.security.encode_id( library5.id ), |
---|
| 536 | folder_id=self.security.encode_id( library5.root_folder.id ), |
---|
| 537 | filename=filename, |
---|
| 538 | file_type='bed', |
---|
| 539 | dbkey='hg18', |
---|
| 540 | ldda_message=ldda_message, |
---|
| 541 | strings_displayed=[ 'TextField', |
---|
| 542 | 'This text should be inherited', |
---|
| 543 | 'TextArea' ] ) |
---|
| 544 | ldda = get_latest_ldda_by_name( filename ) |
---|
| 545 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
---|
| 546 | self.browse_library( 'library_admin', |
---|
| 547 | self.security.encode_id( library5.id ), |
---|
| 548 | strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) |
---|
| 549 | # Make sure the library template contents were correctly saved |
---|
| 550 | self.ldda_edit_info( 'library_admin', |
---|
| 551 | self.security.encode_id( library5.id ), |
---|
| 552 | self.security.encode_id( library5.root_folder.id ), |
---|
| 553 | self.security.encode_id( ldda.id ), |
---|
| 554 | ldda.name, |
---|
| 555 | strings_displayed=[ 'TextField', |
---|
| 556 | 'This text should be inherited', |
---|
| 557 | 'TextArea' ] ) |
---|
| 558 | def test_155_add_template_to_library6( self ): |
---|
| 559 | """ Testing add an inheritable template containing an WorkflowField to library6""" |
---|
| 560 | # Add an inheritable template to library6 |
---|
| 561 | # We won't select an option since we have no workflow to select |
---|
| 562 | self.add_library_template( 'library_admin', |
---|
| 563 | 'library', |
---|
| 564 | self.security.encode_id( library6.id ), |
---|
| 565 | self.security.encode_id( WorkflowField_form.id ), |
---|
| 566 | WorkflowField_form.name ) |
---|
| 567 | def test_160_add_folder6_to_library6( self ): |
---|
| 568 | """Testing adding a folder to library6""" |
---|
| 569 | # Logged in as admin_user |
---|
| 570 | # Add a folder to library5 |
---|
| 571 | folder = library6.root_folder |
---|
| 572 | name = "folder" |
---|
| 573 | description = "folder description" |
---|
| 574 | self.add_folder( 'library_admin', |
---|
| 575 | self.security.encode_id( library6.id ), |
---|
| 576 | self.security.encode_id( folder.id ), |
---|
| 577 | name=name, |
---|
| 578 | description=description ) |
---|
| 579 | global folder6 |
---|
| 580 | folder6 = get_folder( folder.id, name, description ) |
---|
| 581 | def test_165_save_folder6_inherited_template( self ): |
---|
| 582 | """Saving the inherited template for folder6""" |
---|
| 583 | # Logged in as admin_user |
---|
| 584 | # Save the inherited template - we won't select an option since we have no workflow to select |
---|
| 585 | self.folder_info( cntrller='library_admin', |
---|
| 586 | folder_id=self.security.encode_id( folder6.id ), |
---|
| 587 | library_id=self.security.encode_id( library6.id ), |
---|
| 588 | template_fields=[ ( "field_0", 'none' ) ], |
---|
| 589 | strings_displayed=[ WorkflowField_form.name, |
---|
| 590 | 'This is an inherited template and is not required to be used with this folder', |
---|
| 591 | 'none' ] ) |
---|
| 592 | def test_170_add_ldda_to_folder6( self ): |
---|
| 593 | """ |
---|
| 594 | Testing adding a new library dataset to library6's folder, |
---|
| 595 | making sure the WorkflowField setting is correct on the upload form. |
---|
| 596 | """ |
---|
| 597 | # Logged in as admin_user |
---|
| 598 | filename = '7.bed' |
---|
| 599 | ldda_message = '7.bed message' |
---|
| 600 | self.upload_library_dataset( cntrller='library_admin', |
---|
| 601 | library_id=self.security.encode_id( library6.id ), |
---|
| 602 | folder_id=self.security.encode_id( folder6.id ), |
---|
| 603 | filename=filename, |
---|
| 604 | file_type='bed', |
---|
| 605 | dbkey='hg18', |
---|
| 606 | ldda_message=ldda_message, |
---|
| 607 | strings_displayed=[ 'WorkflowField', 'none' ] ) |
---|
| 608 | ldda = get_latest_ldda_by_name( filename ) |
---|
| 609 | assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' |
---|
| 610 | self.browse_library( 'library_admin', |
---|
| 611 | self.security.encode_id( library6.id ), |
---|
| 612 | strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) |
---|
| 613 | # Make sure the library template contents were correctly saved |
---|
| 614 | self.ldda_edit_info( 'library_admin', |
---|
| 615 | self.security.encode_id( library6.id ), |
---|
| 616 | self.security.encode_id( folder6.id ), |
---|
| 617 | self.security.encode_id( ldda.id ), |
---|
| 618 | ldda.name, |
---|
| 619 | strings_displayed=[ 'WorkflowField', 'none' ] ) |
---|
| 620 | def test_999_reset_data_for_later_test_runs( self ): |
---|
| 621 | """Reseting data to enable later test runs to pass""" |
---|
| 622 | # Logged in as admin_user |
---|
| 623 | ################## |
---|
| 624 | # Delete all form definitions |
---|
| 625 | ################## |
---|
| 626 | for form in [ AddressField_form, CheckboxField_form, SelectField_form, TextArea_form, TextField_form, WorkflowField_form ]: |
---|
| 627 | self.mark_form_deleted( self.security.encode_id( form.form_definition_current.id ) ) |
---|
| 628 | ################## |
---|
| 629 | # Mark all user_addresses deleted |
---|
| 630 | ################## |
---|
| 631 | for user_address in [ user_address1, user_address2 ]: |
---|
| 632 | mark_obj_deleted( user_address ) |
---|
| 633 | ################## |
---|
| 634 | # Purge all libraries |
---|
| 635 | ################## |
---|
| 636 | for library in [ library1, library2, library3, library4, library5, library6 ]: |
---|
| 637 | self.delete_library_item( 'library_admin', |
---|
| 638 | self.security.encode_id( library.id ), |
---|
| 639 | self.security.encode_id( library.id ), |
---|
| 640 | library.name, |
---|
| 641 | item_type='library' ) |
---|
| 642 | self.purge_library( self.security.encode_id( library.id ), library.name ) |
---|
| 643 | ################## |
---|
| 644 | # Make sure all users are associated only with their private roles |
---|
| 645 | ################## |
---|
| 646 | for user in [ admin_user, regular_user1, regular_user2, regular_user3 ]: |
---|
| 647 | refresh( user ) |
---|
| 648 | if len( user.roles) != 1: |
---|
| 649 | raise AssertionError( '%d UserRoleAssociations are associated with %s ( should be 1 )' % ( len( user.roles ), user.email ) ) |
---|
| 650 | self.logout() |
---|