Python shed_util_common.get_repository_in_tool_shed函数代码示例

 def delete_repository( self, trans, **kwd ):
     message = kwd.get( 'message', ''  )
     status = kwd.get( 'status', 'done' )
     id = kwd.get( 'id', None )
     if id:
         # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. 
         ids = util.listify( id )
         count = 0
         deleted_repositories = ""
         for repository_id in ids:
             repository = suc.get_repository_in_tool_shed( trans, repository_id )
             if repository:
                 if not repository.deleted:
                     # Mark all installable repository_metadata records as not installable.
                     for repository_metadata in repository.downloadable_revisions:
                         repository_metadata.downloadable = False
                         trans.sa_session.add( repository_metadata )
                     repository.deleted = True
                     trans.sa_session.add( repository )
                     trans.sa_session.flush()
                     count += 1
                     deleted_repositories += " %s " % repository.name
         if count:
             message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), deleted_repositories )
         else:
             message = "All selected repositories were already marked deleted."
     else:
         message = "No repository ids received for deleting."
         status = 'error'
     trans.response.send_redirect( web.url_for( controller='admin',
                                                action='browse_repositories',
                                                message=util.sanitize_text( message ),
                                                status=status ) )

def get_repo_info_dicts( trans, tool_shed_url, repository_id, changeset_revision ):
    repository = suc.get_repository_in_tool_shed( trans, repository_id )
    repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
    # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
    repository_dependencies = \
        repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans,
                                                                                       repository=repository,
                                                                                       repository_metadata=repository_metadata,
                                                                                       toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ),
                                                                                       key_rd_dicts_to_be_processed=None,
                                                                                       all_repository_dependencies=None,
                                                                                       handled_key_rd_dicts=None )
    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
    repo_info_dict = {}
    # Cast unicode to string.
    repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),
                                                 suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ),
                                                 str( changeset_revision ),
                                                 str( ctx.rev() ),
                                                 str( repository.user.username ),
                                                 repository_dependencies,
                                                 None )
    all_required_repo_info_dict = common_install_util.get_required_repo_info_dicts( trans, tool_shed_url, [ repo_info_dict ] )
    all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] )
    return all_repo_info_dicts

    def show( self, trans, id, **kwd ):
        """
        GET /api/repositories/{encoded_repository_id}
        Returns information about a repository in the Tool Shed.

        Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135

        :param id: the encoded id of the Repository object
        :type  id: encoded str

        :returns:   detailed repository information
        :rtype:     dict

        :raises:  ObjectNotFound, MalformedId
        """
        try:
            trans.security.decode_id( id )
        except Exception:
            raise MalformedId( 'The given id is invalid.' )

        repository = suc.get_repository_in_tool_shed( trans.app, id )
        if repository is None:
            raise ObjectNotFound( 'Unable to locate repository for the given id.' )
        repository_dict = repository.to_dict( view='element',
                                              value_mapper=self.__get_value_mapper( trans ) )
        # TODO the following property would be better suited in the to_dict method
        repository_dict[ 'category_ids' ] = \
            [ trans.security.encode_id( x.category.id ) for x in repository.categories ]
        return repository_dict

 def upload( self, trans, **kwd ):
     message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     commit_message = escape( kwd.get( 'commit_message', 'Uploaded'  ) )
     category_ids = util.listify( kwd.get( 'category_id', '' ) )
     categories = suc.get_categories( trans.app )
     repository_id = kwd.get( 'repository_id', '' )
     repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
     repo_dir = repository.repo_path( trans.app )
     repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
     uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
     remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) )
     uploaded_file = None
     upload_point = commit_util.get_upload_point( repository, **kwd )
     tip = repository.tip( trans.app )
     file_data = kwd.get( 'file_data', '' )
     url = kwd.get( 'url', '' )
     # Part of the upload process is sending email notification to those that have registered to
     # receive them.  One scenario occurs when the first change set is produced for the repository.
     # See the suc.handle_email_alerts() method for the definition of the scenarios.
     new_repo_alert = repository.is_new( trans.app )
     uploaded_directory = None
     if kwd.get( 'upload_button', False ):
         if file_data == '' and url == '':
             message = 'No files were entered on the upload form.'
             status = 'error'
             uploaded_file = None
         elif url and url.startswith( 'hg' ):
             # Use mercurial clone to fetch repository, contents will then be copied over.
             uploaded_directory = tempfile.mkdtemp()
             repo_url = 'http%s' % url[ len( 'hg' ): ]
             repo_url = repo_url.encode( 'ascii', 'replace' )
             try:
                 commands.clone( hg_util.get_configured_ui(), repo_url, uploaded_directory )
             except Exception, e:
                 message = 'Error uploading via mercurial clone: %s' % basic_util.to_html_string( str( e ) )
                 status = 'error'
                 basic_util.remove_dir( uploaded_directory )
                 uploaded_directory = None
         elif url:
             valid_url = True
             try:
                 stream = urllib.urlopen( url )
             except Exception, e:
                 valid_url = False
                 message = 'Error uploading file via http: %s' % str( e )
                 status = 'error'
                 uploaded_file = None
             if valid_url:
                 fd, uploaded_file_name = tempfile.mkstemp()
                 uploaded_file = open( uploaded_file_name, 'wb' )
                 while 1:
                     chunk = stream.read( util.CHUNK_SIZE )
                     if not chunk:
                         break
                     uploaded_file.write( chunk )
                 uploaded_file.flush()
                 uploaded_file_filename = url.split( '/' )[ -1 ]
                 isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0

 def view_or_manage_repository( self, trans, **kwd ):
     repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
     if trans.user_is_admin() or repository.user == trans.user:
         return trans.response.send_redirect( web.url_for( controller='repository',
                                                           action='manage_repository',
                                                           **kwd ) )
     else:
         return trans.response.send_redirect( web.url_for( controller='repository',
                                                           action='view_repository',
                                                           **kwd ) )

def get_repo_info_dict( app, user, repository_id, changeset_revision ):
    repository = suc.get_repository_in_tool_shed( app, repository_id )
    repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
    repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository )
    repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
                                                                             repository_id,
                                                                             changeset_revision )
    if not repository_metadata:
        # The received changeset_revision is no longer installable, so get the next changeset_revision
        # in the repository's changelog.  This generally occurs only with repositories of type
        # repository_suite_definition or tool_dependency_definition.
        next_downloadable_changeset_revision = \
            suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
        if next_downloadable_changeset_revision:
            repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
                                                                                     repository_id,
                                                                                     next_downloadable_changeset_revision )
    if repository_metadata:
        # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
        # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
        # returned repo_info_dict.
        metadata = repository_metadata.metadata
        if 'tools' in metadata:
            includes_tools = True
        else:
            includes_tools = False
        includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel
        repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
        repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
            suc.get_repository_dependency_types( repository_dependencies )
        if 'tool_dependencies' in metadata:
            includes_tool_dependencies = True
        else:
            includes_tool_dependencies = False
    else:
        # Here's where we may have to handle enhancements to the callers. See above comment.
        includes_tools = False
        has_repository_dependencies = False
        has_repository_dependencies_only_if_compiling_contained_td = False
        includes_tool_dependencies = False
        includes_tools_for_display_in_tool_panel = False
    ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
    repo_info_dict = create_repo_info_dict( app=app,
                                            repository_clone_url=repository_clone_url,
                                            changeset_revision=changeset_revision,
                                            ctx_rev=str( ctx.rev() ),
                                            repository_owner=repository.user.username,
                                            repository_name=repository.name,
                                            repository=repository,
                                            repository_metadata=repository_metadata,
                                            tool_dependencies=None,
                                            repository_dependencies=None )
    return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \
        has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td

 def load_tool_from_changeset_revision( self, repository_id, changeset_revision, tool_config_filename ):
     """
     Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value
     of tool_config_filename.  The value of changeset_revision is a valid (downloadable)
     changeset revision.  The tool config will be located in the repository manifest between
     the received valid changeset revision and the first changeset revision in the repository,
     searching backwards.
     """
     original_tool_data_path = self.app.config.tool_data_path
     repository = suc.get_repository_in_tool_shed( self.app, repository_id )
     repo_files_dir = repository.repo_path( self.app )
     repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_files_dir, create=False )
     message = ''
     tool = None
     can_use_disk_file = False
     tool_config_filepath = suc.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename )
     work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ltfcr" )
     can_use_disk_file = self.can_use_tool_config_disk_file( repository,
                                                             repo,
                                                             tool_config_filepath,
                                                             changeset_revision )
     if can_use_disk_file:
         self.app.config.tool_data_path = work_dir
         tool, valid, message, sample_files = \
             self.handle_sample_files_and_load_tool_from_disk( repo_files_dir,
                                                               repository_id,
                                                               tool_config_filepath,
                                                               work_dir )
         if tool is not None:
             invalid_files_and_errors_tups = \
                 self.check_tool_input_params( repo_files_dir,
                                               tool_config_filename,
                                               tool,
                                               sample_files )
             if invalid_files_and_errors_tups:
                 message2 = tool_util.generate_message_for_invalid_tools( self.app,
                                                                          invalid_files_and_errors_tups,
                                                                          repository,
                                                                          metadata_dict=None,
                                                                          as_html=True,
                                                                          displaying_invalid_tool=True )
                 message = self.concat_messages( message, message2 )
     else:
         tool, message, sample_files = \
             self.handle_sample_files_and_load_tool_from_tmp_config( repo,
                                                                     repository_id,
                                                                     changeset_revision,
                                                                     tool_config_filename,
                                                                     work_dir )
     basic_util.remove_dir( work_dir )
     self.app.config.tool_data_path = original_tool_data_path
     # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
     self.tdtm.reset_tool_data_tables()
     return repository, tool, message

 def undelete_repository(self, trans, **kwd):
     message = escape(kwd.get("message", ""))
     id = kwd.get("id", None)
     if id:
         # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
         ids = util.listify(id)
         count = 0
         undeleted_repositories = ""
         for repository_id in ids:
             repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
             if repository:
                 if repository.deleted:
                     # Inspect all repository_metadata records to determine those that are installable, and mark
                     # them accordingly.
                     for repository_metadata in repository.metadata_revisions:
                         metadata = repository_metadata.metadata
                         if metadata:
                             if metadata_util.is_downloadable(metadata):
                                 repository_metadata.downloadable = True
                                 trans.sa_session.add(repository_metadata)
                     # Mark the repository admin role as not deleted.
                     repository_admin_role = repository.admin_role
                     if repository_admin_role is not None:
                         repository_admin_role.deleted = False
                         trans.sa_session.add(repository_admin_role)
                     repository.deleted = False
                     trans.sa_session.add(repository)
                     trans.sa_session.flush()
                     if not repository.deprecated:
                         # Update the repository registry.
                         trans.app.repository_registry.add_entry(repository)
                     count += 1
                     undeleted_repositories += " %s" % repository.name
         if count:
             message = "Undeleted %d %s: %s" % (
                 count,
                 inflector.cond_plural(count, "repository"),
                 undeleted_repositories,
             )
         else:
             message = "No selected repositories were marked deleted, so they could not be undeleted."
     else:
         message = "No repository ids received for undeleting."
     trans.response.send_redirect(
         web.url_for(
             controller="admin", action="browse_repositories", message=util.sanitize_text(message), status="done"
         )
     )

 def select_previous_review( self, trans, **kwd ):
     # The value of the received id is the encoded repository id.
     message = kwd.get( 'message', ''  )
     status = kwd.get( 'status', 'done' )
     repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] )
     changeset_revision = kwd.get( 'changeset_revision', None )
     repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     previous_reviews_dict = review_util.get_previous_repository_reviews( trans, repository, changeset_revision )
     rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
     return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako',
                                 repository=repository,
                                 changeset_revision=changeset_revision,
                                 changeset_revision_label=changeset_revision_label,
                                 previous_reviews_dict=previous_reviews_dict,
                                 message=message,
                                 status=status )

    def show(self, trans, id, **kwd):
        """
        GET /api/repositories/{encoded_repository_id}
        Returns information about a repository in the Tool Shed.

        :param id: the encoded id of the Repository object
        """
        # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
        repository = suc.get_repository_in_tool_shed(trans.app, id)
        if repository is None:
            log.debug("Unable to locate repository record for id %s." % (str(id)))
            return {}
        repository_dict = repository.to_dict(view="element", value_mapper=self.__get_value_mapper(trans))
        repository_dict["url"] = web.url_for(
            controller="repositories", action="show", id=trans.security.encode_id(repository.id)
        )
        return repository_dict

 def manage_repository_reviews( self, trans, mine=False, **kwd ):
     # The value of the received id is the encoded repository id.
     message = escape( kwd.get( 'message', '' ) )
     status = kwd.get( 'status', 'done' )
     repository_id = kwd.get( 'id', None )
     if repository_id:
         repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
         repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
         metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
         reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
         reviews_dict = odict()
         for changeset in hg_util.get_reversed_changelog_changesets( repo ):
             ctx = repo.changectx( changeset )
             changeset_revision = str( ctx )
             if changeset_revision in metadata_revision_hashes or changeset_revision in reviewed_revision_hashes:
                 rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
                 if changeset_revision in reviewed_revision_hashes:
                     # Find the review for this changeset_revision
                     repository_reviews = \
                         review_util.get_reviews_by_repository_id_changeset_revision( trans.app,
                                                                                      repository_id,
                                                                                      changeset_revision )
                     # Determine if the current user can add a review to this revision.
                     can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ]
                     repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
                     if repository_metadata:
                         repository_metadata_reviews = util.listify( repository_metadata.reviews )
                     else:
                         repository_metadata_reviews = []
                 else:
                     repository_reviews = []
                     repository_metadata_reviews = []
                     can_add_review = True
                 installable = changeset_revision in metadata_revision_hashes
                 revision_dict = dict( changeset_revision_label=changeset_revision_label,
                                       repository_reviews=repository_reviews,
                                       repository_metadata_reviews=repository_metadata_reviews,
                                       installable=installable,
                                       can_add_review=can_add_review )
                 reviews_dict[ changeset_revision ] = revision_dict
     return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_repository.mako',
                                 repository=repository,
                                 reviews_dict=reviews_dict,
                                 mine=mine,
                                 message=message,
                                 status=status )

 def delete_repository(self, trans, **kwd):
     message = escape(kwd.get("message", ""))
     status = kwd.get("status", "done")
     id = kwd.get("id", None)
     if id:
         # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
         ids = util.listify(id)
         count = 0
         deleted_repositories = ""
         for repository_id in ids:
             repository = suc.get_repository_in_tool_shed(trans.app, repository_id)
             if repository:
                 if not repository.deleted:
                     # Mark all installable repository_metadata records as not installable.
                     for repository_metadata in repository.downloadable_revisions:
                         repository_metadata.downloadable = False
                         trans.sa_session.add(repository_metadata)
                     # Mark the repository admin role as deleted.
                     repository_admin_role = repository.admin_role
                     if repository_admin_role is not None:
                         repository_admin_role.deleted = True
                         trans.sa_session.add(repository_admin_role)
                     repository.deleted = True
                     trans.sa_session.add(repository)
                     trans.sa_session.flush()
                     # Update the repository registry.
                     trans.app.repository_registry.remove_entry(repository)
                     count += 1
                     deleted_repositories += " %s " % repository.name
         if count:
             message = "Deleted %d %s: %s" % (
                 count,
                 inflector.cond_plural(len(ids), "repository"),
                 escape(deleted_repositories),
             )
         else:
             message = "All selected repositories were already marked deleted."
     else:
         message = "No repository ids received for deleting."
         status = "error"
     trans.response.send_redirect(
         web.url_for(
             controller="admin", action="browse_repositories", message=util.sanitize_text(message), status=status
         )
     )

 def manage_repository_reviews_of_revision( self, trans, **kwd ):
     # The value of the received id is the encoded repository id.
     message = kwd.get( 'message', ''  )
     status = kwd.get( 'status', 'done' )
     repository_id = kwd.get( 'id', None )
     changeset_revision = kwd.get( 'changeset_revision', None )
     repository = suc.get_repository_in_tool_shed( trans, repository_id )
     repo_dir = repository.repo_path( trans.app )
     repo = hg.repository( suc.get_configured_ui(), repo_dir )
     installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
     rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
     reviews = review_util.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision )
     return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako',
                                 repository=repository,
                                 changeset_revision=changeset_revision,
                                 changeset_revision_label=changeset_revision_label,
                                 reviews=reviews,
                                 installable=installable,
                                 message=message,
                                 status=status )

 def show( self, trans, id, **kwd ):
     """
     GET /api/repositories/{encoded_repository_id}
     Returns information about a repository in the Tool Shed.
     
     :param id: the encoded id of the Repository object
     """
     # Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
     try:
         repository = suc.get_repository_in_tool_shed( trans, id )
         repository_dict = repository.get_api_value( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
         repository_dict[ 'url' ] = web.url_for( controller='repositories',
                                                 action='show',
                                                 id=trans.security.encode_id( repository.id ) )
         return repository_dict
     except Exception, e:
         message = "Error in the Tool Shed repositories API in show: %s" % str( e )
         log.error( message, exc_info=True )
         trans.response.status = 500
         return message

 def undelete_repository( self, trans, **kwd ):
     message = kwd.get( 'message', ''  )
     status = kwd.get( 'status', 'done' )
     id = kwd.get( 'id', None )
     if id:
         # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
         ids = util.listify( id )
         count = 0
         undeleted_repositories = ""
         for repository_id in ids:
             repository = suc.get_repository_in_tool_shed( trans, repository_id )
             if repository:
                 if repository.deleted:
                     # Inspect all repository_metadata records to determine those that are installable, and mark them accordingly.
                     for repository_metadata in repository.metadata_revisions:
                         metadata = repository_metadata.metadata
                         if metadata:
                             if metadata_util.is_downloadable( metadata ):
                                 repository_metadata.downloadable = True
                                 trans.sa_session.add( repository_metadata )
                     repository.deleted = False
                     trans.sa_session.add( repository )
                     trans.sa_session.flush()
                     count += 1
                     undeleted_repositories += " %s" % repository.name
         if count:
             message = "Undeleted %d %s: %s" % ( count, inflector.cond_plural( count, "repository" ), undeleted_repositories )
         else:
             message = "No selected repositories were marked deleted, so they could not be undeleted."
     else:
         message = "No repository ids received for undeleting."
         status = 'error'
     trans.response.send_redirect( web.url_for( controller='admin',
                                                action='browse_repositories',
                                                message=util.sanitize_text( message ),
                                                status='done' ) )