Exemplo n.º 1
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 def test_0065_verify_filtering_repository(self):
     '''Verify the new tool versions and repository metadata.'''
     repository = test_db_util.get_repository_by_name_and_owner(
         repository_name, common.test_user_1_name)
     category = test_db_util.get_category_by_name(
         'Test 0000 Basic Repository Features 1')
     tip = self.get_repository_tip(repository)
     self.check_for_valid_tools(repository)
     strings_displayed = ['Select a revision']
     self.display_manage_repository_page(
         repository, strings_displayed=strings_displayed)
     self.check_count_of_metadata_revisions_associated_with_repository(
         repository, metadata_count=2)
     tool_guid = '%s/repos/user1/filtering_0000/Filter1/2.2.0' % self.url.replace(
         'http://', '').rstrip('/')
     tool_metadata_strings_displayed = [
         tool_guid,
         '2.2.0',  # The tool version.
         'Filter1',  # The tool ID.
         'Filter',  # The tool name.
         'data on any column using simple expressions'
     ]  # The tool description.
     tool_page_strings_displayed = ['Filter (version 2.2.0)']
     self.check_repository_tools_for_changeset_revision(
         repository,
         tip,
         tool_metadata_strings_displayed=tool_metadata_strings_displayed,
         tool_page_strings_displayed=tool_page_strings_displayed)
     self.check_repository_metadata(repository, tip_only=False)
Exemplo n.º 2
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 def test_0005_create_datatypes_repository(self):
     '''Create and populate the emboss_datatypes_0460 repository'''
     '''
     This is step 1 - Create and populate emboss_datatypes_0460.
     '''
     self.create_category(name=category_name,
                          description=category_description)
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name=datatypes_repository_name,
         description=datatypes_repository_description,
         long_description=datatypes_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     self.upload_file(
         repository,
         filename='emboss/datatypes/datatypes_conf.xml',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate emboss_datatypes_0460 with datatype definitions.',
         strings_displayed=[],
         strings_not_displayed=[])
Exemplo n.º 3
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 def test_0050_create_repositories_for_simple_dependencies(self):
     '''Create repositories for testing simple dependency generation.'''
     '''
     This is step 10 - Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460,
     repository_dependency_test_4_0460, repository_dependency_test_4_0460.. Each of these repositories will be populated in a way
     that tests a different way to achieve the same resulting dependency structure using complex tool dependencies.
     The different methods being tested are:
     - Upload an uncompressed repository_dependencies.xml to the root of the repository.
     - Upload a repository_dependencies.xml in a tarball, not in a subfolder.
     - Upload a repository_dependencies.xml in a subfolder within a tarball.
     - Upload via url, with the repository_dependencies.xml in the root of another repository.
     - Upload via url, with the repository_dependencies.xml in a subfolder within another repository.
     '''
     category = test_db_util.get_category_by_name(category_name)
     repository_base_name = 'repository_dependency_test_%d_0460'
     repository_base_description = 'Test #%d for repository dependency definitions.'
     repository_base_long_description = 'Test #%d for repository dependency definitions.'
     for number in range(1, 6):
         repository = self.get_or_create_repository(
             name=repository_base_name % number,
             description=repository_base_description % number,
             long_description=repository_base_long_description % number,
             owner=common.test_user_1_name,
             category_id=self.security.encode_id(category.id),
             strings_displayed=[])
 def test_0005_create_lapack_repository( self ):
     '''Create and populate package_lapack_3_4_1420.'''
     '''
     This is step 1 - Create repository package_lapack_3_4_1420.
     
     All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
     filesystem and install them into the path specified by $INSTALL_DIR.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=package_lapack_repository_name, 
                                                 description=package_lapack_repository_description, 
                                                 long_description=package_lapack_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     # Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
     # actual system path where the binary tarball is found.
     tool_dependency_path = self.generate_temp_path( '1420_tool_dependency', additional_paths=[ 'package_lapack_3_4_1420' ] )
     precompiled_binary_tarball = self.get_filename( '1420_files/binary_tarballs/lapack.tar' )
     edited_tool_dependency_filename = self.get_filename( filepath=tool_dependency_path, filename='tool_dependencies.xml' )
     original_tool_dependency = self.get_filename( '1420_files/package_lapack_3_4_1420/tool_dependencies.xml' )
     tool_dependency_definition = file( original_tool_dependency, 'r' ).read().replace( '__PATH__', precompiled_binary_tarball )
     file( edited_tool_dependency_filename, 'w' ).write( tool_dependency_definition )
     # Upload the edited tool dependency definition to the package_lapack_3_4_1420 repository.
     self.upload_file( repository, 
                       filename='tool_dependencies.xml', 
                       filepath=tool_dependency_path,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate package_lapack_3_4_1420 with tool dependency definitions.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
Exemplo n.º 5
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 def test_0005_create_libx11_repository(self):
     '''Create and populate package_x11_client_1_5_proto_7_0_0470.'''
     '''
     This is step 1 - Create and populate a repository named package_x11_client_1_5_proto_7_0.
     
     Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml.
     Keep the repository type as the default "Unrestricted".
     '''
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name=package_libx11_repository_name,
         description=package_libx11_repository_description,
         long_description=package_libx11_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
     self.upload_file(
         repository,
         filename=
         'emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.',
         strings_displayed=[],
         strings_not_displayed=[])
 def test_0010_create_repositories( self ):
     '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes_0030, and emboss_0030 repositories and populate the emboss_datatypes repository.'''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
     emboss_5_repository = self.get_or_create_repository( name=emboss_5_repository_name, 
                                                          description=emboss_repository_description, 
                                                          long_description=emboss_repository_long_description, 
                                                          owner=common.test_user_1_name,
                                                          category_id=self.security.encode_id( category.id ) )
     emboss_6_repository = self.get_or_create_repository( name=emboss_6_repository_name, 
                                                          description=emboss_repository_description, 
                                                          long_description=emboss_repository_long_description, 
                                                          owner=common.test_user_1_name,
                                                          category_id=self.security.encode_id( category.id ) )
     datatypes_repository = self.get_or_create_repository( name=datatypes_repository_name, 
                                                           description=emboss_repository_description, 
                                                           long_description=emboss_repository_long_description, 
                                                           owner=common.test_user_1_name,
                                                           category_id=self.security.encode_id( category.id ) )
     emboss_repository = self.get_or_create_repository( name=emboss_repository_name, 
                                                        description=emboss_repository_description, 
                                                        long_description=emboss_repository_long_description, 
                                                        owner=common.test_user_1_name,
                                                        category_id=self.security.encode_id( category.id ) )
     self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
     self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
     self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
     self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
Exemplo n.º 7
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 def test_0010_create_emboss_5_0_0_repository(self):
     '''Create and populate package_emboss_5_0_0_0470.'''
     '''
     This is step 2 - Create a repository named package_emboss_5_0_0 of type "Unrestricted".
     
     Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the
     above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision
     defined so it will get automatically populated.
     '''
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name=package_emboss_repository_name,
         description=package_emboss_repository_description,
         long_description=package_emboss_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository.
     self.upload_file(
         repository,
         filename=
         'emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate package_emboss_5_0_0_0470 with tool dependency definitions.',
         strings_displayed=[],
         strings_not_displayed=[])
Exemplo n.º 8
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 def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
     '''Create and populate the emboss_datatypes repository.'''
     global running_standalone
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name=datatypes_repository_name,
         description=datatypes_repository_description,
         long_description=datatypes_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     if self.repository_is_new(repository):
         running_standalone = True
         self.upload_file(repository,
                          filename='emboss/datatypes/datatypes_conf.xml',
                          filepath=None,
                          valid_tools_only=True,
                          uncompress_file=True,
                          remove_repo_files_not_in_tar=False,
                          commit_message='Uploaded datatypes_conf.xml.',
                          strings_displayed=[],
                          strings_not_displayed=[])
Exemplo n.º 9
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 def test_0015_create_emboss_5_repository(self):
     '''Create and populate emboss_5_0470.'''
     '''
     This is step 3 - Create a repository named emboss_5 of type "Unrestricted".
     
     Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency
     on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined 
     so it will get automatically populated.
     '''
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name=emboss_repository_name,
         description=emboss_repository_description,
         long_description=emboss_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     # Populate emboss_5 with tool and dependency definitions.
     self.upload_file(
         repository,
         filename='emboss/0470_files/emboss_complex_dependency.tar',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=True,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate emboss_5 with tool and dependency definitions.',
         strings_displayed=[],
         strings_not_displayed=[])
Exemplo n.º 10
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 def test_0005_create_repository(self):
     '''Create and populate the filtering repository'''
     '''
     This is step 1 - Create and populate a repository so that it has a single metadata revision.
     '''
     self.create_category(name=category_name,
                          description=category_description)
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     category = test_db_util.get_category_by_name(category_name)
     strings_displayed = [
         'Repository %s' % "'%s'" % repository_name,
         'Repository %s has been created' % "'%s'" % repository_name
     ]
     repository = self.get_or_create_repository(
         name=repository_name,
         description=repository_description,
         long_description=repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=strings_displayed)
     self.upload_file(
         repository,
         filename='filtering/filtering_1.1.0.tar',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message='Populate filtering_0450 with version 1.1.0',
         strings_displayed=[],
         strings_not_displayed=[])
Exemplo n.º 11
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 def test_0010_create_convert_chars_repository(self):
     '''Create and populate a repository named convert_chars_0440.'''
     '''
     We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0.
     '''
     category = test_db_util.get_category_by_name(
         'Test 0440 Deleted Dependency Definitions')
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     strings_displayed = [
         "Repository 'convert_chars_0440' has been created"
     ]
     repository = self.get_or_create_repository(
         name=convert_repository_name,
         description=convert_repository_description,
         long_description=convert_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=strings_displayed)
     self.upload_file(repository,
                      filename='convert_chars/convert_chars.tar',
                      filepath=None,
                      valid_tools_only=True,
                      uncompress_file=True,
                      remove_repo_files_not_in_tar=False,
                      commit_message='Uploaded convert chars tool tarball.',
                      strings_displayed=[],
                      strings_not_displayed=[])
 def test_0035_create_bwa_base_repository( self ):
     '''Create and populate the bwa_base_0440 repository.'''
     '''
     We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0.
     This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440.
     '''
     category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' )
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     strings_displayed = [ "Repository 'bwa_base_0440' has been created"  ]
     repository = self.get_or_create_repository( name=bwa_base_repository_name, 
                                                 description=bwa_base_repository_description, 
                                                 long_description=bwa_base_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=strings_displayed )
     self.upload_file( repository, 
                       filename='bwa/complex/bwa_base.tar',
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False, 
                       commit_message='Uploaded BWA nucleotide space mapping tool tarball.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
Exemplo n.º 13
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 def test_0010_create_freebayes_repository_and_upload_tool_xml( self ):
     '''Create freebayes repository and upload only freebayes.xml.'''
     '''
     We are at step 1 - Create repository freebayes_0020 and upload only the tool XML.
     Uploading only the tool XML file should result in an invalid tool and an error message on 
     upload, as well as on the manage repository page. 
     '''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' )
     repository = self.get_or_create_repository( name=repository_name, 
                                                 description=repository_description, 
                                                 long_description=repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     self.upload_file( repository, 
                       filename='freebayes/freebayes.xml', 
                       filepath=None,
                       valid_tools_only=False,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Uploaded the tool xml.',
                       strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ], 
                       strings_not_displayed=[] )
     self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] )
     tip = self.get_repository_tip( repository )
     strings_displayed = [ 'requires an entry', 'tool_data_table_conf.xml' ]
     self.check_repository_invalid_tools_for_changeset_revision( repository, tip, strings_displayed=strings_displayed )
 def test_0010_create_emboss_5_0_0_repository( self ):
     '''Create and populate package_emboss_5_0_0_0470.'''
     '''
     This is step 2 - Create a repository named package_emboss_5_0_0 of type "Unrestricted".
     
     Create a repository named package_emboss_5_0_0 of type "Unrestricted" that has a repository dependency definition that defines the
     above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision
     defined so it will get automatically populated.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=package_emboss_repository_name, 
                                                 description=package_emboss_repository_description, 
                                                 long_description=package_emboss_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository.
     self.upload_file( repository, 
                       filename='emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate package_emboss_5_0_0_0470 with tool dependency definitions.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0015_create_emboss_5_repository( self ):
     '''Create and populate emboss_5_0470.'''
     '''
     This is step 3 - Create a repository named emboss_5 of type "Unrestricted".
     
     Create a repository named emboss_5 of type "Unrestricted" that has a tool-dependencies.xml file defining a complex repository dependency
     on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined 
     so it will get automatically populated.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=emboss_repository_name, 
                                                 description=emboss_repository_description, 
                                                 long_description=emboss_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     # Populate emboss_5 with tool and dependency definitions.
     self.upload_file( repository, 
                       filename='emboss/0470_files/emboss_complex_dependency.tar', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate emboss_5 with tool and dependency definitions.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0055_create_bwa_tool_dependency_repository( self ):
     '''Create and populate the bwa_tool_dependency_0440 repository.'''
     '''
     We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid orphan tool 
     dependency definition and an installable revision 0.
     '''
     category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' )
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     strings_displayed = [ "Repository 'bwa_tool_dependency_0440' has been created"  ]
     repository = self.get_or_create_repository( name=bwa_tool_dependency_repository_name, 
                                                 description=bwa_tool_dependency_repository_description, 
                                                 long_description=bwa_tool_dependency_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=strings_displayed )
     self.upload_file( repository, 
                       filename='bwa/complex/tool_dependencies.xml',
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False, 
                       commit_message='Uploaded package tool dependency definition.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0005_create_libx11_repository( self ):
     '''Create and populate package_x11_client_1_5_proto_7_0_0470.'''
     '''
     This is step 1 - Create and populate a repository named package_x11_client_1_5_proto_7_0.
     
     Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml.
     Keep the repository type as the default "Unrestricted".
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=package_libx11_repository_name, 
                                                 description=package_libx11_repository_description, 
                                                 long_description=package_libx11_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
     self.upload_file( repository, 
                       filename='emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate package_x11_client_1_5_proto_7_0_0470 with tool dependency definitions.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0005_create_repository( self ):
     '''Create and populate the filtering repository'''
     '''
     This is step 1 - Create and populate a repository so that it has a single metadata revision.
     '''
     self.create_category( name=category_name, description=category_description )
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( category_name )
     strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, 
                           'Repository %s has been created' % "'%s'" % repository_name ]
     repository = self.get_or_create_repository( name=repository_name, 
                                                 description=repository_description, 
                                                 long_description=repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=strings_displayed )
     self.upload_file( repository, 
                       filename='filtering/filtering_1.1.0.tar', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate filtering_0450 with version 1.1.0',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
Exemplo n.º 19
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 def test_0005_ensure_existence_of_repository_and_category( self ):
     '''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.'''
     self.create_category( name=category_name, description=category_description )
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=repository_name, 
                                                 description=repository_description, 
                                                 long_description=repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     if self.repository_is_new( repository ):
         self.upload_file( repository, 
                           filename='bismark/bismark.tar',
                           filepath=None,
                           valid_tools_only=False,
                           uncompress_file=True,
                           remove_repo_files_not_in_tar=False, 
                           commit_message='Uploaded bismark tarball.',
                           strings_displayed=[], 
                           strings_not_displayed=[] )
         self.upload_file( repository, 
                           filename='bismark/bismark_methylation_extractor.xml',
                           filepath=None,
                           valid_tools_only=False,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False, 
                           commit_message='Uploaded an updated tool xml.',
                           strings_displayed=[], 
                           strings_not_displayed=[] )
Exemplo n.º 20
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 def test_0055_create_bwa_tool_dependency_repository(self):
     '''Create and populate the bwa_tool_dependency_0440 repository.'''
     '''
     We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid orphan tool 
     dependency definition and an installable revision 0.
     '''
     category = test_db_util.get_category_by_name(
         'Test 0440 Deleted Dependency Definitions')
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     strings_displayed = [
         "Repository 'bwa_tool_dependency_0440' has been created"
     ]
     repository = self.get_or_create_repository(
         name=bwa_tool_dependency_repository_name,
         description=bwa_tool_dependency_repository_description,
         long_description=bwa_tool_dependency_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=strings_displayed)
     self.upload_file(
         repository,
         filename='bwa/complex/tool_dependencies.xml',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=True,
         remove_repo_files_not_in_tar=False,
         commit_message='Uploaded package tool dependency definition.',
         strings_displayed=[],
         strings_not_displayed=[])
Exemplo n.º 21
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 def test_0035_create_bwa_base_repository(self):
     '''Create and populate the bwa_base_0440 repository.'''
     '''
     We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0.
     This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440.
     '''
     category = test_db_util.get_category_by_name(
         'Test 0440 Deleted Dependency Definitions')
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     strings_displayed = ["Repository 'bwa_base_0440' has been created"]
     repository = self.get_or_create_repository(
         name=bwa_base_repository_name,
         description=bwa_base_repository_description,
         long_description=bwa_base_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=strings_displayed)
     self.upload_file(repository,
                      filename='bwa/complex/bwa_base.tar',
                      filepath=None,
                      valid_tools_only=True,
                      uncompress_file=True,
                      remove_repo_files_not_in_tar=False,
                      commit_message=
                      'Uploaded BWA nucleotide space mapping tool tarball.',
                      strings_displayed=[],
                      strings_not_displayed=[])
Exemplo n.º 22
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 def test_0010_browse_tool_shed( self ):
     """Browse the available tool sheds in this Galaxy instance and preview the bismark repository."""
     self.galaxy_logout()
     self.galaxy_login( email=common.admin_email, username=common.admin_username )
     self.browse_tool_shed( url=self.url, strings_displayed=[ category_name ] )
     category = test_db_util.get_category_by_name( category_name )
     self.browse_category( category, strings_displayed=[ repository_name ] )
     self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[ repository_name ] )
Exemplo n.º 23
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 def test_0010_browse_tool_shed( self ):
     """Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
     self.galaxy_logout()
     self.galaxy_login( email=common.admin_email, username=common.admin_username )
     self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0030 Repository Dependency Revisions' ] )
     category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
     self.browse_category( category, strings_displayed=[ 'emboss_0030' ] )
     self.preview_repository_in_tool_shed( 'emboss_0030', common.test_user_1_name, strings_displayed=[ 'emboss_0030', 'Valid tools' ] )
 def test_0090_verify_reserved_repository_name_handling( self ):
     '''Check that reserved repository names are handled correctly.'''
     category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
     self.get_or_create_repository( name='repos', 
                                    description=repository_description, 
                                    long_description=repository_long_description, 
                                    owner=common.test_user_1_name,
                                    category_id=self.security.encode_id( category.id ), 
                                    strings_displayed=[ 'The term <b>repos</b> is a reserved word in the tool shed, so it cannot be used as a repository name.' ] )
 def test_0020_create_emboss_5_repository_and_upload_files( self ):
     '''Create and populate the emboss_5_0020 repository.'''
     category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' )
     repository = self.get_or_create_repository( name=emboss_repository_name, 
                                          description=emboss_repository_description, 
                                          long_description=emboss_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
 def test_0020_create_emboss_5_repository_and_upload_files( self ):
     '''Create and populate the emboss_5_0110 repository.'''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=emboss_repository_name, 
                                          description=emboss_repository_description, 
                                          long_description=emboss_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
 def test_0065_verify_filtering_repository( self ):
     '''Verify the new tool versions and repository metadata.'''
     repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
     tip = self.get_repository_tip( repository )
     self.check_for_valid_tools( repository )
     strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' )
     self.display_manage_repository_page( repository, strings_displayed=strings_displayed )
     self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 )
     self.check_repository_tools_for_changeset_revision( repository, tip )
     self.check_repository_metadata( repository, tip_only=False )
Exemplo n.º 28
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 def test_0090_verify_reserved_repository_name_handling(self):
     '''Check that reserved repository names are handled correctly.'''
     category = test_db_util.get_category_by_name(
         'Test 0000 Basic Repository Features 1')
     error_message = 'The term <b>repos</b> is a reserved word in the tool shed, so it cannot be used as a repository name.'
     self.get_or_create_repository(
         name='repos',
         description=repository_description,
         long_description=repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[error_message])
 def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ):
     '''Create and populate the emboss_datatypes repository.'''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=datatypes_repository_name, 
                                          description=datatypes_repository_description, 
                                          long_description=datatypes_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
 def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ):
     '''Create and populate the emboss_datatypes repository.'''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' )
     repository = self.get_or_create_repository( name=datatypes_repository_name, 
                                          description=datatypes_repository_description, 
                                          long_description=datatypes_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
 def test_0010_create_repository( self ):
     """Create the filtering repository"""
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
     strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, 
                           'Repository %s has been created' % "'%s'" % repository_name ]
     self.get_or_create_repository( name=repository_name, 
                                    description=repository_description, 
                                    long_description=repository_long_description, 
                                    owner=common.test_user_1_name,
                                    category_id=self.security.encode_id( category.id ), 
                                    strings_displayed=strings_displayed )
 def test_0010_browse_tool_shed(self):
     """Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
     self.galaxy_logout()
     self.galaxy_login(email=common.admin_email,
                       username=common.admin_username)
     self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
     category = test_db_util.get_category_by_name(category_name)
     self.browse_category(category, strings_displayed=[repository_name])
     strings_displayed = [
         repository_name, 'Valid tools', 'Tool dependencies'
     ]
     self.preview_repository_in_tool_shed(
         repository_name,
         common.test_user_1_name,
         strings_displayed=strings_displayed)
Exemplo n.º 33
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 def test_0065_verify_filtering_repository(self):
     '''Verify the new tool versions and repository metadata.'''
     repository = test_db_util.get_repository_by_name_and_owner(
         repository_name, common.test_user_1_name)
     category = test_db_util.get_category_by_name(
         'Test 0000 Basic Repository Features 1')
     tip = self.get_repository_tip(repository)
     self.check_for_valid_tools(repository)
     strings_displayed = self.get_repository_metadata_revisions(
         repository).append('Select a revision')
     self.display_manage_repository_page(
         repository, strings_displayed=strings_displayed)
     self.check_count_of_metadata_revisions_associated_with_repository(
         repository, metadata_count=2)
     self.check_repository_tools_for_changeset_revision(repository, tip)
     self.check_repository_metadata(repository, tip_only=False)
Exemplo n.º 34
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 def test_0010_create_repository(self):
     """Create the filtering repository"""
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     category = test_db_util.get_category_by_name(
         'Test 0000 Basic Repository Features 1')
     strings_displayed = [
         'Repository %s' % "'%s'" % repository_name,
         'Repository %s has been created' % "'%s'" % repository_name
     ]
     self.get_or_create_repository(
         name=repository_name,
         description=repository_description,
         long_description=repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=strings_displayed)
Exemplo n.º 35
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 def test_0020_create_emboss_5_repository_and_upload_files( self ):
     '''Create and populate the emboss_5_0110 repository.'''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=emboss_repository_name, 
                                          description=emboss_repository_description, 
                                          long_description=emboss_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 
                       filename='emboss/emboss.tar',
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False, 
                       commit_message='Uploaded emboss tool tarball.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0020_create_emboss_5_repository_and_upload_files( self ):
     '''Create and populate the emboss_5_0020 repository.'''
     category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' )
     repository = self.get_or_create_repository( name=emboss_repository_name, 
                                          description=emboss_repository_description, 
                                          long_description=emboss_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 
                       filename='emboss/emboss.tar', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Uploaded emboss.tar',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
Exemplo n.º 37
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 def test_0070_create_repositories_for_url_upload(self):
     '''Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.'''
     '''
     This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate
     with repository dependencies.
     '''
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name='hg_repository_dependency_0460',
         description=bwa_repository_description,
         long_description=bwa_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     self.upload_file(
         repository,
         filename='0460_files/repository_dependencies.xml',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate hg_repository_dependency_0460 with an orphan tool dependency definition.',
         strings_displayed=[],
         strings_not_displayed=[])
     repository = self.get_or_create_repository(
         name='hg_subfolder_repository_dependency_0460',
         description=bwa_repository_description,
         long_description=bwa_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     self.upload_file(
         repository,
         filename='0460_files/repository_dependencies_in_subfolder.tar',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate hg_subfolder_repository_dependency_0460 with an orphan tool dependency definition.',
         strings_displayed=[],
         strings_not_displayed=[])
Exemplo n.º 38
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 def test_0010_create_repositories(self):
     '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes_0030, and emboss_0030 repositories and populate the emboss_datatypes repository.'''
     self.logout()
     self.login(email=common.test_user_1_email,
                username=common.test_user_1_name)
     category = test_db_util.get_category_by_name(
         'Test 0030 Repository Dependency Revisions')
     emboss_5_repository = self.get_or_create_repository(
         name=emboss_5_repository_name,
         description=emboss_repository_description,
         long_description=emboss_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id))
     emboss_6_repository = self.get_or_create_repository(
         name=emboss_6_repository_name,
         description=emboss_repository_description,
         long_description=emboss_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id))
     datatypes_repository = self.get_or_create_repository(
         name=datatypes_repository_name,
         description=emboss_repository_description,
         long_description=emboss_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id))
     emboss_repository = self.get_or_create_repository(
         name=emboss_repository_name,
         description=emboss_repository_description,
         long_description=emboss_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id))
     self.upload_file(emboss_5_repository,
                      'emboss/emboss.tar',
                      commit_message='Uploaded tool tarball.')
     self.upload_file(emboss_6_repository,
                      'emboss/emboss.tar',
                      commit_message='Uploaded tool tarball.')
     self.upload_file(datatypes_repository,
                      'emboss/datatypes/datatypes_conf.xml',
                      commit_message='Uploaded datatypes_conf.xml.')
     self.upload_file(emboss_repository,
                      'emboss/emboss.tar',
                      commit_message='Uploaded tool tarball.')
Exemplo n.º 39
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 def test_0025_create_emboss_repository( self ):
     '''Create and populate the emboss_0030 repository.'''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
     repository = self.get_or_create_repository( name=emboss_repository_name, 
                                                 description=emboss_repository_description, 
                                                 long_description=emboss_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ) )
     self.upload_file( repository, 
                       filename='emboss/emboss.tar', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Uploaded the tool tarball.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ):
     '''Create and populate the emboss_datatypes repository.'''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=datatypes_repository_name, 
                                          description=datatypes_repository_description, 
                                          long_description=datatypes_repository_long_description, 
                                          owner=common.test_user_1_name,
                                          category_id=self.security.encode_id( category.id ), 
                                          strings_displayed=[] )
     self.upload_file( repository, 
                       filename='emboss/datatypes/datatypes_conf.xml',
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False, 
                       commit_message='Uploaded datatypes_conf.xml.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0010_create_freebayes_repository_and_upload_tool_xml( self ):
     '''Create freebayes repository and upload freebayes.xml without tool_data_table_conf.xml.sample. This should result in an error message and invalid tool.'''
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' )
     repository = self.get_or_create_repository( name=repository_name, 
                                                 description=repository_description, 
                                                 long_description=repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     self.upload_file( repository, 
                       'freebayes/freebayes.xml', 
                       valid_tools_only=False,
                       strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ], 
                       commit_message='Uploaded the tool xml.' )
     self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] )
     tip = self.get_repository_tip( repository )
     self.check_repository_invalid_tools_for_changeset_revision( repository, 
                                                                 tip, 
                                                                 strings_displayed=[ 'requires an entry', 'tool_data_table_conf.xml' ] )
 def test_0010_create_bwa_package_repository( self ):
     '''Create and populate the package_bwa_0_5_9_0460 repository.'''
     '''
     This is step 2 - Create and populate package_bwa_0_5_9_0460.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=bwa_repository_name, 
                                                 description=bwa_repository_description, 
                                                 long_description=bwa_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     self.upload_file( repository, 
                       filename='bwa/complex/tool_dependencies.xml', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate package_bwa_0_5_9_0460 with an orphan tool dependency definition.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0065_verify_filtering_repository( self ):
     '''Verify the new tool versions and repository metadata.'''
     repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
     category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
     tip = self.get_repository_tip( repository )
     self.check_for_valid_tools( repository )
     strings_displayed = [ 'Select a revision' ]
     self.display_manage_repository_page( repository, strings_displayed=strings_displayed )
     self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 )
     tool_guid = '%s/repos/user1/filtering_0000/Filter1/2.2.0' % self.url.replace( 'http://', '' ).rstrip( '/' )
     tool_metadata_strings_displayed = [ tool_guid,
                                         '2.2.0', # The tool version.
                                         'Filter1', # The tool ID.
                                         'Filter', # The tool name.
                                         'data on any column using simple expressions' ] # The tool description.
     tool_page_strings_displayed = [ 'Filter (version 2.2.0)' ]
     self.check_repository_tools_for_changeset_revision( repository,
                                                         tip,
                                                         tool_metadata_strings_displayed=tool_metadata_strings_displayed,
                                                         tool_page_strings_displayed=tool_page_strings_displayed )
     self.check_repository_metadata( repository, tip_only=False )
Exemplo n.º 44
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 def test_0010_create_column_repository( self ):
     '''Create and populate the column_1430 repository.'''
     '''
     This is step 2 - Create and populate the column_1430 repository.
     
     This repository will depend on the filter_1430 repository.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name=column_repository_name, 
                                                 description=column_repository_description, 
                                                 long_description=column_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     self.upload_file( repository, 
                       filename='column_maker/column_maker.tar', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate column_1430 with tool definitions.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0070_create_repositories_for_url_upload( self ):
     '''Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.'''
     '''
     This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate
     with repository dependencies.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository = self.get_or_create_repository( name='hg_repository_dependency_0460', 
                                                 description=bwa_repository_description, 
                                                 long_description=bwa_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     self.upload_file( repository, 
                       filename='0460_files/repository_dependencies.xml', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate hg_repository_dependency_0460 with an orphan tool dependency definition.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
     repository = self.get_or_create_repository( name='hg_subfolder_repository_dependency_0460', 
                                                 description=bwa_repository_description, 
                                                 long_description=bwa_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=[] )
     self.upload_file( repository, 
                       filename='0460_files/repository_dependencies_in_subfolder.tar', 
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=False,
                       remove_repo_files_not_in_tar=False,
                       commit_message='Populate hg_subfolder_repository_dependency_0460 with an orphan tool dependency definition.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0050_create_repositories_for_simple_dependencies( self ):
     '''Create repositories for testing simple dependency generation.'''
     '''
     This is step 10 - Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460,
     repository_dependency_test_4_0460, repository_dependency_test_4_0460.. Each of these repositories will be populated in a way
     that tests a different way to achieve the same resulting dependency structure using complex tool dependencies.
     The different methods being tested are:
     - Upload an uncompressed repository_dependencies.xml to the root of the repository.
     - Upload a repository_dependencies.xml in a tarball, not in a subfolder.
     - Upload a repository_dependencies.xml in a subfolder within a tarball.
     - Upload via url, with the repository_dependencies.xml in the root of another repository.
     - Upload via url, with the repository_dependencies.xml in a subfolder within another repository.
     '''
     category = test_db_util.get_category_by_name( category_name )
     repository_base_name = 'repository_dependency_test_%d_0460'
     repository_base_description = 'Test #%d for repository dependency definitions.'
     repository_base_long_description = 'Test #%d for repository dependency definitions.'
     for number in range( 1, 6 ):
         repository = self.get_or_create_repository( name=repository_base_name % number, 
                                                     description=repository_base_description % number, 
                                                     long_description=repository_base_long_description % number, 
                                                     owner=common.test_user_1_name,
                                                     category_id=self.security.encode_id( category.id ), 
                                                     strings_displayed=[] )
Exemplo n.º 47
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 def test_0010_create_bwa_package_repository(self):
     '''Create and populate the package_bwa_0_5_9_0460 repository.'''
     '''
     This is step 2 - Create and populate package_bwa_0_5_9_0460.
     '''
     category = test_db_util.get_category_by_name(category_name)
     repository = self.get_or_create_repository(
         name=bwa_repository_name,
         description=bwa_repository_description,
         long_description=bwa_repository_long_description,
         owner=common.test_user_1_name,
         category_id=self.security.encode_id(category.id),
         strings_displayed=[])
     self.upload_file(
         repository,
         filename='bwa/complex/tool_dependencies.xml',
         filepath=None,
         valid_tools_only=True,
         uncompress_file=False,
         remove_repo_files_not_in_tar=False,
         commit_message=
         'Populate package_bwa_0_5_9_0460 with an orphan tool dependency definition.',
         strings_displayed=[],
         strings_not_displayed=[])
 def test_0010_create_convert_chars_repository( self ):
     '''Create and populate a repository named convert_chars_0440.'''
     '''
     We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0.
     '''
     category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' )
     self.logout()
     self.login( email=common.test_user_1_email, username=common.test_user_1_name )
     strings_displayed = [ "Repository 'convert_chars_0440' has been created"  ]
     repository = self.get_or_create_repository( name=convert_repository_name, 
                                                 description=convert_repository_description, 
                                                 long_description=convert_repository_long_description, 
                                                 owner=common.test_user_1_name,
                                                 category_id=self.security.encode_id( category.id ), 
                                                 strings_displayed=strings_displayed )
     self.upload_file( repository, 
                       filename='convert_chars/convert_chars.tar',
                       filepath=None,
                       valid_tools_only=True,
                       uncompress_file=True,
                       remove_repo_files_not_in_tar=False, 
                       commit_message='Uploaded convert chars tool tarball.',
                       strings_displayed=[], 
                       strings_not_displayed=[] )
 def test_0015_browse_test_0000_category(self):
     """Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test."""
     category = test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
     self.browse_category(category, strings_displayed=["filtering_0000"])
Exemplo n.º 50
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 def test_0015_browse_test_0000_category(self):
     '''Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test.'''
     category = test_db_util.get_category_by_name(
         'Test 0000 Basic Repository Features 1')
     self.browse_category(category, strings_displayed=['filtering_0000'])