text: from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
  import tool_shed.base.test_db_util as test_db_util
  
  bwa_base_repository_name = 'bwa_base_repository_0100'
  bwa_base_repository_description = "BWA Base"
  bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
  
  bwa_package_repository_name = 'package_bwa_0_5_9_0100'
  bwa_package_repository_description = "BWA Tool"
  bwa_package_repository_long_description = "BWA repository with a package tool dependency defined to compile and install BWA 0.5.9."
  
  category_name = 'Test 0100 Complex Repository Dependencies'
  category_description = 'Test 0100 Complex Repository Dependencies'
  running_standalone = False
  
  
  class TestInstallingComplexRepositoryDependencies( ShedTwillTestCase ):
      '''Test features related to installing repositories with complex repository dependencies.'''
  
      def test_0000_initiate_users( self ):
          """Create necessary user accounts."""
          self.logout()
          self.login( email=common.test_user_1_email, username=common.test_user_1_name )
          test_user_1 = test_db_util.get_user( common.test_user_1_email )
          assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
          test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
          self.logout()
          self.login( email=common.admin_email, username=common.admin_username )
          admin_user = test_db_util.get_user( common.admin_email )
          assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
          admin_user_private_role = test_db_util.get_private_role( admin_user )
  
      def test_0005_create_bwa_package_repository( self ):
          '''Create and populate bwa_tool_0100.'''
          global running_standalone
          category = 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 )
          repository = self.get_or_create_repository( name=bwa_package_repository_name, 
                                                      description=bwa_package_repository_description, 
                                                      long_description=bwa_package_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
              old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'tool_dependencies.xml' ) )
              new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] )
              xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) )
              file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' )
                                       .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) )
              self.upload_file( repository, 
                                filename=xml_filename,
                                filepath=new_tool_dependency_path,
                                valid_tools_only=True,
                                uncompress_file=False,
                                remove_repo_files_not_in_tar=False, 
                                commit_message='Uploaded tool_dependencies.xml.',
                                strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], 
                                strings_not_displayed=[] )
              self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] )
  
      def test_0010_create_bwa_base_repository( self ):
          '''Create and populate bwa_base_0100.'''
          global running_standalone
          if running_standalone:
              category = 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 )
              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=[] )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              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_base.tar with tool wrapper XML, but without tool dependency XML.',
                                strings_displayed=[], 
                                strings_not_displayed=[] )
  
      def test_0015_generate_complex_repository_dependency_invalid_shed_url( self ):
          '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.'''
          global running_standalone
          if running_standalone:
              dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
              xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
              base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              url = 'http://http://this is not an url!'
              name = tool_repository.name
              owner = tool_repository.user.username
              changeset_revision = self.get_repository_tip( tool_repository )
              strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] 
              repository_tuple = ( url, name, owner, changeset_revision )
              self.create_repository_dependency( repository=base_repository, 
                                                 filepath=dependency_path, 
                                                 repository_tuples=[ repository_tuple ],
                                                 strings_displayed=strings_displayed,
                                                 complex=True,
                                                 package='bwa',
                                                 version='0.5.9' )
  
      def test_0020_generate_complex_repository_dependency_invalid_repository_name( self ):
          '''Generate and upload a complex repository definition that specifies an invalid repository name.'''
          global running_standalone
          if running_standalone:
              dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
              xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
              base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              url = self.url
              name = 'invalid_repository!?'
              owner = tool_repository.user.username
              changeset_revision = self.get_repository_tip( tool_repository )
              strings_displayed = [ 'because the name is invalid.' ]
              repository_tuple = ( url, name, owner, changeset_revision )
              self.create_repository_dependency( repository=base_repository, 
                                                 filepath=dependency_path, 
                                                 repository_tuples=[ repository_tuple ],
                                                 strings_displayed=strings_displayed,
                                                 complex=True,
                                                 package='bwa',
                                                 version='0.5.9' )
  
      def test_0025_generate_complex_repository_dependency_invalid_owner_name( self ):
          '''Generate and upload a complex repository definition that specifies an invalid owner.'''
          global running_standalone
          if running_standalone:
              dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
              xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
              base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              url = self.url
              name = tool_repository.name
              owner = 'invalid_owner!?'
              changeset_revision = self.get_repository_tip( tool_repository )
              strings_displayed = [ 'because the owner is invalid.' ]
              repository_tuple = ( url, name, owner, changeset_revision )
              self.create_repository_dependency( repository=base_repository, 
                                                 filepath=dependency_path, 
                                                 repository_tuples=[ repository_tuple ],
                                                 strings_displayed=strings_displayed,
                                                 complex=True,
                                                 package='bwa',
                                                 version='0.5.9' )
   
      def test_0030_generate_complex_repository_dependency_invalid_changeset_revision( self ):
          '''Generate and upload a complex repository definition that specifies an invalid changeset revision.'''
          global running_standalone
          if running_standalone:
              dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'shed' ] )
              xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
              base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              url = self.url
              name = tool_repository.name
              owner = tool_repository.user.username
              changeset_revision = '1234abcd'
              strings_displayed = [ 'because the changeset revision is invalid.' ]
              repository_tuple = ( url, name, owner, changeset_revision )
              self.create_repository_dependency( repository=base_repository, 
                                                 filepath=dependency_path, 
                                                 repository_tuples=[ repository_tuple ],
                                                 strings_displayed=strings_displayed,
                                                 complex=True,
                                                 package='bwa',
                                                 version='0.5.9' )
    
      def test_0035_generate_valid_complex_repository_dependency( self ):
          '''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.'''
          global running_standalone
          if running_standalone:
              base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] )
              xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path )
              url = self.url
              name = tool_repository.name
              owner = tool_repository.user.username
              changeset_revision = self.get_repository_tip( tool_repository )
              repository_tuple = ( url, name, owner, changeset_revision )
              self.create_repository_dependency( repository=base_repository, 
                                                 filepath=dependency_path, 
                                                 repository_tuples=[ repository_tuple ],
                                                 complex=True,
                                                 package='bwa',
                                                 version='0.5.9' )
              self.check_repository_dependency( base_repository, tool_repository )
              self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] )
   
      def test_0040_update_tool_repository( self ):
          '''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.'''
          global running_standalone
          if running_standalone:
              base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
              tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
              previous_changeset = self.get_repository_tip( tool_repository )
              old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) )
              new_tool_dependency_path = self.generate_temp_path( 'test_1100', additional_paths=[ 'tool_dependency' ] )
              xml_filename = os.path.abspath( os.path.join( new_tool_dependency_path, 'tool_dependencies.xml' ) )
              file( xml_filename, 'w' ).write( file( old_tool_dependency, 'r' )
                                       .read().replace( '__PATH__', self.get_filename( 'bwa/complex' ) ) )
              self.upload_file( tool_repository, 
                                filename=xml_filename,
                                filepath=new_tool_dependency_path, 
                                valid_tools_only=True,
                                uncompress_file=False,
                                remove_repo_files_not_in_tar=False, 
                                commit_message='Uploaded new tool_dependencies.xml.',
                                strings_displayed=[], 
                                strings_not_displayed=[] )
              # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
              self.display_manage_repository_page( base_repository, 
                                                   strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ],
                                                   strings_not_displayed=[ previous_changeset ] )
   
      def test_0045_install_base_repository( self ):
          '''Verify installation of the repository with complex repository dependencies.'''
          self.galaxy_logout()
          self.galaxy_login( email=common.admin_email, username=common.admin_username )
          base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name )
          tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name )
          preview_strings_displayed = [ tool_repository.name, self.get_repository_tip( tool_repository ) ]
          self.install_repository( bwa_base_repository_name, 
                                   common.test_user_1_name, 
                                   category_name,
                                   install_tool_dependencies=True, 
                                   preview_strings_displayed=preview_strings_displayed,
                                   post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'new' ],
                                   includes_tools_for_display_in_tool_panel=True )
   
      def test_0050_verify_installed_repositories( self ):
          '''Verify that the installed repositories are displayed properly.'''
          base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
          tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name )
          strings_displayed = [ 'bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision ]
          strings_displayed.extend( [ 'package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision ] )
          strings_displayed.append( self.url.replace( 'http://', '' ) )
          self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] )
          strings_displayed = [ 'package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision ]
          strings_not_displayed = [ 'Missing tool dependencies' ]
          self.display_installed_repository_manage_page( tool_repository, 
                                                         strings_displayed=strings_displayed, 
                                                         strings_not_displayed=strings_not_displayed )
          strings_displayed = [ 'bwa_base_repository_0100',
                                'user1', 
                                'package_bwa_0_5_9_0100', 
                                base_repository.installed_changeset_revision, 
                                tool_repository.installed_changeset_revision ]
          strings_not_displayed = [ 'Missing tool dependencies' ]
          self.display_installed_repository_manage_page( base_repository, 
                                                         strings_displayed=strings_displayed, 
                                                         strings_not_displayed=strings_not_displayed )
    
      def test_0055_verify_complex_tool_dependency( self ):
          '''Verify that the generated env.sh contains the right data.'''
          base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
          tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name )
          env_sh_path = self.get_env_sh_path( tool_dependency_name='bwa', 
                                              tool_dependency_version='0.5.9', 
                                              repository=base_repository )
          assert os.path.exists( env_sh_path ), 'env.sh was not generated in %s for this dependency.' % env_sh_path
          contents = file( env_sh_path, 'r' ).read()
          if tool_repository.installed_changeset_revision not in contents:
              raise AssertionError( 'Installed changeset revision %s not found in env.sh.\nContents of env.sh: %s' % \
                                    ( tool_repository.installed_changeset_revision, contents ) )
          if 'package_bwa_0_5_9_0100' not in contents:
              raise AssertionError( 'Repository name package_bwa_0_5_9_0100 not found in env.sh.\nContents of env.sh: %s' % contents )
          
      def test_0060_verify_tool_dependency_uninstallation( self ):
          '''Uninstall the package_bwa_0_5_9_0100 repository.'''
          '''
          Uninstall the repository that defines an orphan tool dependency on BWA 0.5.9, and verify
          that this results in the compiled binary package also being removed.
          '''
          base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
          tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_package_repository_name, common.test_user_1_name )
          self.uninstall_repository( tool_repository, remove_from_disk=True )
          env_sh_path = os.path.join( self.galaxy_tool_dependency_dir, 
                                      'bwa', 
                                      '0.5.9', 
                                      tool_repository.owner, 
                                      tool_repository.name, 
                                      tool_repository.installed_changeset_revision, 
                                      'env.sh' )
          if os.path.exists( env_sh_path ):
              raise AssertionError( 'Path %s exists after uninstalling the repository that generated it.' % env_sh_path )
         
  