コード例 #1
0
 def manage_repository_reviews_of_revision(self, trans, **kwd):
     # The value of the received id is the encoded repository id.
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.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 = suc.get_reviews_by_repository_id_changeset_revision(
         trans, repository_id, changeset_revision)
     return trans.fill_template(
         '/webapps/community/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)
コード例 #2
0
ファイル: upload.py プロジェクト: cidvbi/PathogenPortal
 def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ):
     # Upload a tar archive of files.
     repo_dir = repository.repo_path( trans.app )
     repo = hg.repository( suc.get_configured_ui(), repo_dir )
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
     ok, message = self.__check_archive( tar )
     if not ok:
         tar.close()
         uploaded_file.close()
         return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed
     else:
         if upload_point is not None:
             full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) )
         else:
             full_path = os.path.abspath( repo_dir )
         filenames_in_archive = []
         for tarinfo_obj in tar.getmembers():
             ok = os.path.basename( tarinfo_obj.name ) not in undesirable_files
             if ok:
                 for file_path_item in tarinfo_obj.name.split( '/' ):
                     if file_path_item in undesirable_dirs:
                         undesirable_dirs_removed += 1
                         ok = False
                         break
             else:
                 undesirable_files_removed += 1
             if ok:
                 filenames_in_archive.append( tarinfo_obj.name )
         # Extract the uploaded tar to the load_point within the repository hierarchy.
         tar.extractall( path=full_path )
         tar.close()
         uploaded_file.close()
         return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed)
コード例 #3
0
ファイル: upload.py プロジェクト: cidvbi/PathogenPortal
 def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ):
     repo_dir = repository.repo_path( trans.app )
     repo = hg.repository( suc.get_configured_ui(), repo_dir )
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
     if upload_point is not None:
         full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) )
     else:
         full_path = os.path.abspath( repo_dir )
     filenames_in_archive = []
     for root, dirs, files in os.walk( uploaded_directory ):
         for uploaded_file in files:
             relative_path = os.path.normpath(os.path.join(os.path.relpath(root, uploaded_directory), uploaded_file))
             ok = os.path.basename( uploaded_file ) not in undesirable_files
             if ok:
                 for file_path_item in relative_path.split( '/' ):
                     if file_path_item in undesirable_dirs:
                         undesirable_dirs_removed += 1
                         ok = False
                         break
             else:
                 undesirable_files_removed += 1
             if ok:
                 repo_path = os.path.join(full_path, relative_path)
                 repo_basedir = os.path.normpath(os.path.join(repo_path, os.path.pardir))
                 if not os.path.exists(repo_basedir):
                     os.makedirs(repo_basedir)
                 if os.path.exists(repo_path):
                     if os.path.isdir(repo_path):
                         shutil.rmtree(repo_path)
                     else:
                         os.remove(repo_path)
                 shutil.move(os.path.join(uploaded_directory, relative_path), repo_path)
                 filenames_in_archive.append( relative_path )
     return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed)
コード例 #4
0
 def manage_repository_reviews(self, trans, mine=False, **kwd):
     # The value of the received id is the encoded repository id.
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.get('status', 'done')
     repository_id = kwd.get('id', None)
     if repository_id:
         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)
         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 suc.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 = suc.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 = suc.get_reviews_by_repository_id_changeset_revision(
                         trans, 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, 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/community/repository_review/reviews_of_repository.mako',
         repository=repository,
         reviews_dict=reviews_dict,
         mine=mine,
         message=message,
         status=status)
コード例 #5
0
ファイル: admin.py プロジェクト: iamciera/galaxy-dist
 def get_value(self, trans, grid, repository_metadata):
     repository = repository_metadata.repository
     repo = hg.repository(suc.get_configured_ui(),
                          repository.repo_path(trans.app))
     ctx = suc.get_changectx_for_changeset(
         repo, repository_metadata.changeset_revision)
     return "%s:%s" % (str(
         ctx.rev()), repository_metadata.changeset_revision)
コード例 #6
0
ファイル: upload.py プロジェクト: iamciera/galaxy-dist
 def __handle_directory_changes(self, trans, repository, full_path,
                                filenames_in_archive,
                                remove_repo_files_not_in_tar,
                                new_repo_alert, commit_message,
                                undesirable_dirs_removed,
                                undesirable_files_removed):
     repo_dir = repository.repo_path(trans.app)
     repo = hg.repository(suc.get_configured_ui(), repo_dir)
     content_alert_str = ''
     files_to_remove = []
     filenames_in_archive = [
         os.path.join(full_path, name) for name in filenames_in_archive
     ]
     if remove_repo_files_not_in_tar and not repository.is_new(trans.app):
         # We have a repository that is not new (it contains files), so discover
         # those files that are in the repository, but not in the uploaded archive.
         for root, dirs, files in os.walk(full_path):
             if root.find('.hg') < 0 and root.find('hgrc') < 0:
                 for undesirable_dir in undesirable_dirs:
                     if undesirable_dir in dirs:
                         dirs.remove(undesirable_dir)
                         undesirable_dirs_removed += 1
                 for undesirable_file in undesirable_files:
                     if undesirable_file in files:
                         files.remove(undesirable_file)
                         undesirable_files_removed += 1
                 for name in files:
                     full_name = os.path.join(root, name)
                     if full_name not in filenames_in_archive:
                         files_to_remove.append(full_name)
         for repo_file in files_to_remove:
             # Remove files in the repository (relative to the upload point) that are not in the uploaded archive.
             try:
                 commands.remove(repo.ui, repo, repo_file, force=True)
             except Exception, e:
                 log.debug(
                     "Error removing files using the mercurial API, so trying a different approach, the error was: %s"
                     % str(e))
                 relative_selected_file = selected_file.split(
                     'repo_%d' % repository.id)[1].lstrip('/')
                 repo.dirstate.remove(relative_selected_file)
                 repo.dirstate.write()
                 absolute_selected_file = os.path.abspath(selected_file)
                 if os.path.isdir(absolute_selected_file):
                     try:
                         os.rmdir(absolute_selected_file)
                     except OSError, e:
                         # The directory is not empty
                         pass
                 elif os.path.isfile(absolute_selected_file):
                     os.remove(absolute_selected_file)
                     dir = os.path.split(absolute_selected_file)[0]
                     try:
                         os.rmdir(dir)
                     except OSError, e:
                         # The directory is not empty
                         pass
コード例 #7
0
 def get_value( self, trans, grid, repository ):
     # Restrict to revisions that have been reviewed.
     if repository.reviews:
         rval = ''
         repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         for review in repository.reviews:
             changeset_revision = review.changeset_revision
             rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision )
             rval += '<a href="manage_repository_reviews_of_revision'
             rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label )
         return rval
     return ''
コード例 #8
0
 def browse_review( self, trans, **kwd ):
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.get( 'status', 'done' )
     review = suc.get_review( trans, kwd[ 'id' ] )
     repository = review.repository
     repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
     return trans.fill_template( '/webapps/community/repository_review/browse_review.mako',
                                 repository=repository,
                                 changeset_revision_label=changeset_revision_label,
                                 review=review,
                                 message=message,
                                 status=status )
コード例 #9
0
 def get_value(self, trans, grid, repository):
     # Restrict to revisions that have been reviewed.
     if repository.reviews:
         rval = ''
         repo = hg.repository(suc.get_configured_ui(),
                              repository.repo_path(trans.app))
         for review in repository.reviews:
             changeset_revision = review.changeset_revision
             rev, label = suc.get_rev_label_from_changeset_revision(
                 repo, changeset_revision)
             rval += '<a href="manage_repository_reviews_of_revision'
             rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % (
                 trans.security.encode_id(
                     repository.id), changeset_revision, label)
         return rval
     return ''
コード例 #10
0
ファイル: upload.py プロジェクト: cidvbi/PathogenPortal
 def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ):    
     repo_dir = repository.repo_path( trans.app )
     repo = hg.repository( suc.get_configured_ui(), repo_dir )
     content_alert_str = ''
     files_to_remove = []
     filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ]
     if remove_repo_files_not_in_tar and not repository.is_new( trans.app ):
         # We have a repository that is not new (it contains files), so discover
         # those files that are in the repository, but not in the uploaded archive.
         for root, dirs, files in os.walk( full_path ):
             if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
                 for undesirable_dir in undesirable_dirs:
                     if undesirable_dir in dirs:
                         dirs.remove( undesirable_dir )
                         undesirable_dirs_removed += 1
                 for undesirable_file in undesirable_files:
                     if undesirable_file in files:
                         files.remove( undesirable_file )
                         undesirable_files_removed += 1
                 for name in files:
                     full_name = os.path.join( root, name )
                     if full_name not in filenames_in_archive:
                         files_to_remove.append( full_name )
         for repo_file in files_to_remove:
             # Remove files in the repository (relative to the upload point) that are not in the uploaded archive.
             try:
                 commands.remove( repo.ui, repo, repo_file, force=True )
             except Exception, e:
                 log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e ))
                 relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' )
                 repo.dirstate.remove( relative_selected_file )
                 repo.dirstate.write()
                 absolute_selected_file = os.path.abspath( selected_file )
                 if os.path.isdir( absolute_selected_file ):
                     try:
                         os.rmdir( absolute_selected_file )
                     except OSError, e:
                         # The directory is not empty
                         pass
                 elif os.path.isfile( absolute_selected_file ):
                     os.remove( absolute_selected_file )
                     dir = os.path.split( absolute_selected_file )[0]
                     try:
                         os.rmdir( dir )
                     except OSError, e:
                         # The directory is not empty
                         pass
コード例 #11
0
ファイル: upload.py プロジェクト: iamciera/galaxy-dist
 def upload_directory(self, trans, repository, uploaded_directory,
                      upload_point, remove_repo_files_not_in_tar,
                      commit_message, new_repo_alert):
     repo_dir = repository.repo_path(trans.app)
     repo = hg.repository(suc.get_configured_ui(), repo_dir)
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
     if upload_point is not None:
         full_path = os.path.abspath(os.path.join(repo_dir, upload_point))
     else:
         full_path = os.path.abspath(repo_dir)
     filenames_in_archive = []
     for root, dirs, files in os.walk(uploaded_directory):
         for uploaded_file in files:
             relative_path = os.path.normpath(
                 os.path.join(os.path.relpath(root, uploaded_directory),
                              uploaded_file))
             ok = os.path.basename(uploaded_file) not in undesirable_files
             if ok:
                 for file_path_item in relative_path.split('/'):
                     if file_path_item in undesirable_dirs:
                         undesirable_dirs_removed += 1
                         ok = False
                         break
             else:
                 undesirable_files_removed += 1
             if ok:
                 repo_path = os.path.join(full_path, relative_path)
                 repo_basedir = os.path.normpath(
                     os.path.join(repo_path, os.path.pardir))
                 if not os.path.exists(repo_basedir):
                     os.makedirs(repo_basedir)
                 if os.path.exists(repo_path):
                     if os.path.isdir(repo_path):
                         shutil.rmtree(repo_path)
                     else:
                         os.remove(repo_path)
                 shutil.move(
                     os.path.join(uploaded_directory, relative_path),
                     repo_path)
                 filenames_in_archive.append(relative_path)
     return self.__handle_directory_changes(trans, repository, full_path,
                                            filenames_in_archive,
                                            remove_repo_files_not_in_tar,
                                            new_repo_alert, commit_message,
                                            undesirable_dirs_removed,
                                            undesirable_files_removed)
コード例 #12
0
 def browse_review(self, trans, **kwd):
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.get('status', 'done')
     review = suc.get_review(trans, kwd['id'])
     repository = review.repository
     repo = hg.repository(suc.get_configured_ui(),
                          repository.repo_path(trans.app))
     rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision(
         repo, review.changeset_revision)
     return trans.fill_template(
         '/webapps/community/repository_review/browse_review.mako',
         repository=repository,
         changeset_revision_label=changeset_revision_label,
         review=review,
         message=message,
         status=status)
コード例 #13
0
 def select_previous_review( self, trans, **kwd ):
     # The value of the received id is the encoded repository id.
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.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 = suc.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/community/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 )
コード例 #14
0
 def manage_repository_reviews( self, trans, mine=False, **kwd ):
     # The value of the received id is the encoded repository id.
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.get( 'status', 'done' )
     repository_id = kwd.get( 'id', None )
     if repository_id:
         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 )
         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 suc.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 = suc.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 = suc.get_reviews_by_repository_id_changeset_revision( trans, 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, 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/community/repository_review/reviews_of_repository.mako',
                                 repository=repository,
                                 reviews_dict=reviews_dict,
                                 mine=mine,
                                 message=message,
                                 status=status )
コード例 #15
0
ファイル: upload.py プロジェクト: iamciera/galaxy-dist
 def upload_tar(self, trans, repository, tar, uploaded_file, upload_point,
                remove_repo_files_not_in_tar, commit_message,
                new_repo_alert):
     # Upload a tar archive of files.
     repo_dir = repository.repo_path(trans.app)
     repo = hg.repository(suc.get_configured_ui(), repo_dir)
     undesirable_dirs_removed = 0
     undesirable_files_removed = 0
     ok, message = self.__check_archive(tar)
     if not ok:
         tar.close()
         uploaded_file.close()
         return ok, message, [], '', undesirable_dirs_removed, undesirable_files_removed
     else:
         if upload_point is not None:
             full_path = os.path.abspath(
                 os.path.join(repo_dir, upload_point))
         else:
             full_path = os.path.abspath(repo_dir)
         filenames_in_archive = []
         for tarinfo_obj in tar.getmembers():
             ok = os.path.basename(
                 tarinfo_obj.name) not in undesirable_files
             if ok:
                 for file_path_item in tarinfo_obj.name.split('/'):
                     if file_path_item in undesirable_dirs:
                         undesirable_dirs_removed += 1
                         ok = False
                         break
             else:
                 undesirable_files_removed += 1
             if ok:
                 filenames_in_archive.append(tarinfo_obj.name)
         # Extract the uploaded tar to the load_point within the repository hierarchy.
         tar.extractall(path=full_path)
         tar.close()
         uploaded_file.close()
         return self.__handle_directory_changes(
             trans, repository, full_path, filenames_in_archive,
             remove_repo_files_not_in_tar, new_repo_alert, commit_message,
             undesirable_dirs_removed, undesirable_files_removed)
コード例 #16
0
 def manage_repository_reviews_of_revision( self, trans, **kwd ):
     # The value of the received id is the encoded repository id.
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.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 = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision )
     return trans.fill_template( '/webapps/community/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 )
コード例 #17
0
 def select_previous_review(self, trans, **kwd):
     # The value of the received id is the encoded repository id.
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.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 = suc.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/community/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)
コード例 #18
0
ファイル: admin.py プロジェクト: cidvbi/PathogenPortal
 def get_value( self, trans, grid, repository_metadata ):
     repository = repository_metadata.repository
     repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
     return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision )
コード例 #19
0
 def edit_review(self, trans, **kwd):
     # The value of the received id is the encoded review id.
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.get('status', 'done')
     review_id = kwd.get('id', None)
     review = suc.get_review(trans, review_id)
     components_dict = odict()
     for component in suc.get_components(trans):
         components_dict[component.name] = dict(component=component,
                                                component_review=None)
     repository = review.repository
     repo = hg.repository(suc.get_configured_ui(),
                          repository.repo_path(trans.app))
     for component_review in review.component_reviews:
         if component_review and component_review.component:
             component_name = component_review.component.name
             if component_name in components_dict:
                 component_review_dict = components_dict[component_name]
                 component_review_dict[
                     'component_review'] = component_review
                 components_dict[component_name] = component_review_dict
     # Handle a Save button click.
     save_button_clicked = False
     save_buttons = [
         '%s%sreview_button' % (component_name, STRSEP)
         for component_name in components_dict.keys()
     ]
     save_buttons.append('revision_approved_button')
     for save_button in save_buttons:
         if save_button in kwd:
             save_button_clicked = True
             break
     if save_button_clicked:
         # Handle the revision_approved_select_field value.
         revision_approved = kwd.get('revision_approved', None)
         revision_approved_setting_changed = False
         if revision_approved:
             revision_approved = str(revision_approved)
             if review.approved != revision_approved:
                 revision_approved_setting_changed = True
                 review.approved = revision_approved
                 trans.sa_session.add(review)
                 trans.sa_session.flush()
         saved_component_names = []
         for component_name in components_dict.keys():
             flushed = False
             # Retrieve the review information from the form.
             # The star rating form field is a radio button list, so it will not be received if it was not clicked in the form.
             # Due to this behavior, default the value to 0.
             rating = 0
             for k, v in kwd.items():
                 if k.startswith('%s%s' % (component_name, STRSEP)):
                     component_review_attr = k.replace(
                         '%s%s' % (component_name, STRSEP), '')
                     if component_review_attr == 'component_id':
                         component_id = str(v)
                     elif component_review_attr == 'comment':
                         comment = str(v)
                     elif component_review_attr == 'private':
                         private = CheckboxField.is_checked(v)
                     elif component_review_attr == 'approved':
                         approved = str(v)
                     elif component_review_attr == 'rating':
                         rating = int(str(v))
             component = suc.get_component(trans, component_id)
             component_review = suc.get_component_review_by_repository_review_id_component_id(
                 trans, review_id, component_id)
             if component_review:
                 # See if the existing component review should be updated.
                 if component_review.comment != comment or \
                 component_review.private != private or \
                 component_review.approved != approved or \
                 component_review.rating != rating:
                     component_review.comment = comment
                     component_review.private = private
                     component_review.approved = approved
                     component_review.rating = rating
                     trans.sa_session.add(component_review)
                     trans.sa_session.flush()
                     flushed = True
                     saved_component_names.append(component_name)
             else:
                 # See if a new component_review should be created.
                 if comment or private or approved != trans.model.ComponentReview.approved_states.NO or rating:
                     component_review = trans.model.ComponentReview(
                         repository_review_id=review.id,
                         component_id=component.id,
                         comment=comment,
                         approved=approved,
                         rating=rating)
                     trans.sa_session.add(component_review)
                     trans.sa_session.flush()
                     flushed = True
                     saved_component_names.append(component_name)
             if flushed:
                 # Update the repository rating value to be the average of all component review ratings.
                 average_rating = trans.sa_session.query( func.avg( trans.model.ComponentReview.table.c.rating ) ) \
                                                  .filter( trans.model.ComponentReview.table.c.repository_review_id == review.id ) \
                                                  .scalar()
                 review.rating = int(average_rating)
                 trans.sa_session.add(review)
                 trans.sa_session.flush()
                 # Update the information in components_dict.
                 if component_name in components_dict:
                     component_review_dict = components_dict[component_name]
                     component_review_dict[
                         'component_review'] = component_review
                     components_dict[component_name] = component_review_dict
         if revision_approved_setting_changed:
             message += 'Approved value <b>%s</b> saved for this revision.<br/>' % review.approved
         if saved_component_names:
             message += 'Reviews were saved for components: %s' % ', '.join(
                 saved_component_names)
         if not revision_approved_setting_changed and not saved_component_names:
             message += 'No changes were made to this review, so nothing was saved.'
     if review and review.approved:
         selected_value = review.approved
     else:
         selected_value = trans.model.ComponentReview.approved_states.NO
     revision_approved_select_field = build_approved_select_field(
         trans,
         name='revision_approved',
         selected_value=selected_value,
         for_component=False)
     rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision(
         repo, review.changeset_revision)
     return trans.fill_template(
         '/webapps/community/repository_review/edit_review.mako',
         repository=repository,
         review=review,
         changeset_revision_label=changeset_revision_label,
         revision_approved_select_field=revision_approved_select_field,
         components_dict=components_dict,
         message=message,
         status=status)
コード例 #20
0
 def edit_review( self, trans, **kwd ):
     # The value of the received id is the encoded review id.
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.get( 'status', 'done' )
     review_id = kwd.get( 'id', None )
     review = suc.get_review( trans, review_id )
     components_dict = odict()
     for component in suc.get_components( trans ):
         components_dict[ component.name ] = dict( component=component, component_review=None )
     repository = review.repository
     repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     for component_review in review.component_reviews:
         if component_review and component_review.component:
             component_name = component_review.component.name
             if component_name in components_dict:
                 component_review_dict = components_dict[ component_name ]
                 component_review_dict[ 'component_review' ] = component_review
                 components_dict[ component_name ] = component_review_dict
     # Handle a Save button click.
     save_button_clicked = False
     save_buttons = [ '%s%sreview_button' % ( component_name, STRSEP ) for component_name in components_dict.keys() ]
     save_buttons.append( 'revision_approved_button' )
     for save_button in save_buttons:
         if save_button in kwd:
             save_button_clicked = True
             break
     if save_button_clicked:
         # Handle the revision_approved_select_field value.
         revision_approved = kwd.get( 'revision_approved', None )
         revision_approved_setting_changed = False
         if revision_approved:
             revision_approved = str( revision_approved )
             if review.approved != revision_approved:
                 revision_approved_setting_changed = True
                 review.approved = revision_approved
                 trans.sa_session.add( review )
                 trans.sa_session.flush()
         saved_component_names = []
         for component_name in components_dict.keys():
             flushed = False
             # Retrieve the review information from the form.
             # The star rating form field is a radio button list, so it will not be received if it was not clicked in the form.
             # Due to this behavior, default the value to 0.
             rating = 0
             for k, v in kwd.items():
                 if k.startswith( '%s%s' % ( component_name, STRSEP ) ):
                     component_review_attr = k.replace( '%s%s' % ( component_name, STRSEP ), '' )
                     if component_review_attr == 'component_id':
                         component_id = str( v )
                     elif component_review_attr == 'comment':
                         comment = str( v )
                     elif component_review_attr == 'private':
                         private = CheckboxField.is_checked( v )
                     elif component_review_attr == 'approved':
                         approved = str( v )
                     elif component_review_attr == 'rating':
                         rating = int( str( v ) )
             component = suc.get_component( trans, component_id )
             component_review = suc.get_component_review_by_repository_review_id_component_id( trans, review_id, component_id )
             if component_review:
                 # See if the existing component review should be updated.
                 if component_review.comment != comment or \
                 component_review.private != private or \
                 component_review.approved != approved or \
                 component_review.rating != rating:
                     component_review.comment = comment
                     component_review.private = private
                     component_review.approved = approved
                     component_review.rating = rating
                     trans.sa_session.add( component_review )
                     trans.sa_session.flush()
                     flushed = True
                     saved_component_names.append( component_name )
             else:
                 # See if a new component_review should be created.
                 if comment or private or approved != trans.model.ComponentReview.approved_states.NO or rating:
                     component_review = trans.model.ComponentReview( repository_review_id=review.id,
                                                                     component_id=component.id,
                                                                     comment=comment,
                                                                     approved=approved,
                                                                     rating=rating )
                     trans.sa_session.add( component_review )
                     trans.sa_session.flush()
                     flushed = True
                     saved_component_names.append( component_name )
             if flushed:
                 # Update the repository rating value to be the average of all component review ratings.
                 average_rating = trans.sa_session.query( func.avg( trans.model.ComponentReview.table.c.rating ) ) \
                                                  .filter( trans.model.ComponentReview.table.c.repository_review_id == review.id ) \
                                                  .scalar()
                 review.rating = int( average_rating )
                 trans.sa_session.add( review )
                 trans.sa_session.flush()
                 # Update the information in components_dict.
                 if component_name in components_dict:
                     component_review_dict = components_dict[ component_name ]
                     component_review_dict[ 'component_review' ] = component_review
                     components_dict[ component_name ] = component_review_dict
         if revision_approved_setting_changed:
             message += 'Approved value <b>%s</b> saved for this revision.<br/>' % review.approved
         if saved_component_names:
             message += 'Reviews were saved for components: %s' % ', '.join( saved_component_names )
         if not revision_approved_setting_changed and not saved_component_names:
             message += 'No changes were made to this review, so nothing was saved.'
     if review and review.approved:
         selected_value = review.approved
     else:
         selected_value = trans.model.ComponentReview.approved_states.NO
     revision_approved_select_field = build_approved_select_field( trans,
                                                                   name='revision_approved',
                                                                   selected_value=selected_value,
                                                                   for_component=False )
     rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision )
     return trans.fill_template( '/webapps/community/repository_review/edit_review.mako',
                                 repository=repository,
                                 review=review,
                                 changeset_revision_label=changeset_revision_label,
                                 revision_approved_select_field=revision_approved_select_field,
                                 components_dict=components_dict,
                                 message=message,
                                 status=status )
コード例 #21
0
ファイル: upload.py プロジェクト: cidvbi/PathogenPortal
 def upload( self, trans, **kwd ):
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.get( 'status', 'done' )
     commit_message = util.restore_text( params.get( 'commit_message', 'Uploaded'  ) )
     category_ids = util.listify( params.get( 'category_id', '' ) )
     categories = suc.get_categories( trans )
     repository_id = params.get( 'repository_id', '' )
     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 )
     uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) )
     remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) )
     uploaded_file = None
     upload_point = self.__get_upload_point( repository, **kwd )
     tip = repository.tip( trans.app )
     file_data = params.get( 'file_data', '' )
     url = params.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 params.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' )
             commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory )
         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( 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
         elif file_data not in ( '', None ):
             uploaded_file = file_data.file
             uploaded_file_name = uploaded_file.name
             uploaded_file_filename = os.path.split( file_data.filename )[ -1 ]
             isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
         if uploaded_file or uploaded_directory:
             ok = True
             isgzip = False
             isbz2 = False
             if uploaded_file:
                 if uncompress_file:
                     isgzip = checkers.is_gzip( uploaded_file_name )
                     if not isgzip:
                         isbz2 = checkers.is_bz2( uploaded_file_name )
                 if isempty:
                     tar = None
                     istar = False
                 else:                
                     # Determine what we have - a single file or an archive
                     try:
                         if ( isgzip or isbz2 ) and uncompress_file:
                             # Open for reading with transparent compression.
                             tar = tarfile.open( uploaded_file_name, 'r:*' )
                         else:
                             tar = tarfile.open( uploaded_file_name )
                         istar = True
                     except tarfile.ReadError, e:
                         tar = None
                         istar = False
             else:
                 # Uploaded directory
                 istar = False
             if istar:
                 ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
             elif uploaded_directory:
                 ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     self.upload_directory( trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
             else:
                 if ( isgzip or isbz2 ) and uncompress_file:
                     uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 )
                 if upload_point is not None:
                     full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
                 else:
                     full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
                 # Move the uploaded file to the load_point within the repository hierarchy.
                 shutil.move( uploaded_file_name, full_path )
                 # See if any admin users have chosen to receive email alerts when a repository is
                 # updated.  If so, check every uploaded file to ensure content is appropriate.
                 check_contents = suc.check_file_contents( trans )
                 if check_contents and os.path.isfile( full_path ):
                     content_alert_str = self.__check_file_content( full_path )
                 else:
                     content_alert_str = ''
                 commands.add( repo.ui, repo, full_path )
                 # Convert from unicode to prevent "TypeError: array item must be char"
                 full_path = full_path.encode( 'ascii', 'replace' )
                 commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
                 if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
                     # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries
                     # to the in-memory trans.app.tool_data_tables dictionary.
                     error, error_message = suc.handle_sample_tool_data_table_conf_file( trans.app, full_path )
                     if error:
                         message = '%s<br/>%s' % ( message, error_message )
                 # See if the content of the change set was valid.
                 admin_only = len( repository.downloadable_revisions ) != 1
                 suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
             if ok:
                 # Update the repository files for browsing.
                 suc.update_repository( repo )
                 # Get the new repository tip.
                 if tip == repository.tip( trans.app ):
                     message = 'No changes to repository.  '
                     status = 'warning'
                 else:
                     if ( isgzip or isbz2 ) and uncompress_file:
                         uncompress_str = ' uncompressed and '
                     else:
                         uncompress_str = ' '
                     if uploaded_directory:
                         source_type = "repository"
                         source = url
                     else:
                         source_type = "file"
                         source = uploaded_file_filename
                     message = "The %s '%s' has been successfully%suploaded to the repository.  " % ( source_type, source, uncompress_str )
                     if istar and ( undesirable_dirs_removed or undesirable_files_removed ):
                         items_removed = undesirable_dirs_removed + undesirable_files_removed
                         message += "  %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive.  " % items_removed
                     if istar and remove_repo_files_not_in_tar and files_to_remove:
                         if upload_point is not None:
                             message += "  %d files were removed from the repository relative to the selected upload point '%s'.  " % ( len( files_to_remove ), upload_point )
                         else:
                             message += "  %d files were removed from the repository root.  " % len( files_to_remove )
                     kwd[ 'message' ] = message
                     suc.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd )
                 # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch
                 # or some other problem.
                 if suc.get_config_from_disk( 'tool_dependencies.xml', repo_dir ):
                     if repository.metadata_revisions:
                         # A repository's metadata revisions are order descending by update_time, so the zeroth revision will be the tip just after an upload.
                         metadata_dict = repository.metadata_revisions[0].metadata
                     else:
                         metadata_dict = {}
                     if suc.has_orphan_tool_dependencies_in_tool_shed( metadata_dict ):
                         message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", '
                         message += 'so one or more of the defined tool dependencies are considered orphans within this repository.'
                         status = 'warning'
                 # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
                 suc.reset_tool_data_tables( trans.app )
                 trans.response.send_redirect( web.url_for( controller='repository',
                                                            action='browse_repository',
                                                            id=repository_id,
                                                            commit_message='Deleted selected files',
                                                            message=message,
                                                            status=status ) )
             else:
                 status = 'error'
             # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
             suc.reset_tool_data_tables( trans.app )
コード例 #22
0
ファイル: upload.py プロジェクト: iamciera/galaxy-dist
 def upload(self, trans, **kwd):
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.get('status', 'done')
     commit_message = util.restore_text(
         params.get('commit_message', 'Uploaded'))
     category_ids = util.listify(params.get('category_id', ''))
     categories = suc.get_categories(trans)
     repository_id = params.get('repository_id', '')
     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)
     uncompress_file = util.string_as_bool(
         params.get('uncompress_file', 'true'))
     remove_repo_files_not_in_tar = util.string_as_bool(
         params.get('remove_repo_files_not_in_tar', 'true'))
     uploaded_file = None
     upload_point = self.__get_upload_point(repository, **kwd)
     tip = repository.tip(trans.app)
     file_data = params.get('file_data', '')
     url = params.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 params.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')
             commands.clone(suc.get_configured_ui(), repo_url,
                            uploaded_directory)
         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(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
         elif file_data not in ('', None):
             uploaded_file = file_data.file
             uploaded_file_name = uploaded_file.name
             uploaded_file_filename = os.path.split(file_data.filename)[-1]
             isempty = os.path.getsize(
                 os.path.abspath(uploaded_file_name)) == 0
         if uploaded_file or uploaded_directory:
             ok = True
             isgzip = False
             isbz2 = False
             if uploaded_file:
                 if uncompress_file:
                     isgzip = checkers.is_gzip(uploaded_file_name)
                     if not isgzip:
                         isbz2 = checkers.is_bz2(uploaded_file_name)
                 if isempty:
                     tar = None
                     istar = False
                 else:
                     # Determine what we have - a single file or an archive
                     try:
                         if (isgzip or isbz2) and uncompress_file:
                             # Open for reading with transparent compression.
                             tar = tarfile.open(uploaded_file_name, 'r:*')
                         else:
                             tar = tarfile.open(uploaded_file_name)
                         istar = True
                     except tarfile.ReadError, e:
                         tar = None
                         istar = False
             else:
                 # Uploaded directory
                 istar = False
             if istar:
                 ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     self.upload_tar( trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
             elif uploaded_directory:
                 ok,message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
                     self.upload_directory( trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert )
             else:
                 if (isgzip or isbz2) and uncompress_file:
                     uploaded_file_filename = self.uncompress(
                         repository, uploaded_file_name,
                         uploaded_file_filename, isgzip, isbz2)
                 if upload_point is not None:
                     full_path = os.path.abspath(
                         os.path.join(repo_dir, upload_point,
                                      uploaded_file_filename))
                 else:
                     full_path = os.path.abspath(
                         os.path.join(repo_dir, uploaded_file_filename))
                 # Move the uploaded file to the load_point within the repository hierarchy.
                 shutil.move(uploaded_file_name, full_path)
                 # See if any admin users have chosen to receive email alerts when a repository is
                 # updated.  If so, check every uploaded file to ensure content is appropriate.
                 check_contents = suc.check_file_contents(trans)
                 if check_contents and os.path.isfile(full_path):
                     content_alert_str = self.__check_file_content(
                         full_path)
                 else:
                     content_alert_str = ''
                 commands.add(repo.ui, repo, full_path)
                 # Convert from unicode to prevent "TypeError: array item must be char"
                 full_path = full_path.encode('ascii', 'replace')
                 commands.commit(repo.ui,
                                 repo,
                                 full_path,
                                 user=trans.user.username,
                                 message=commit_message)
                 if full_path.endswith('tool_data_table_conf.xml.sample'):
                     # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries
                     # to the in-memory trans.app.tool_data_tables dictionary.
                     error, error_message = suc.handle_sample_tool_data_table_conf_file(
                         trans.app, full_path)
                     if error:
                         message = '%s<br/>%s' % (message, error_message)
                 # See if the content of the change set was valid.
                 admin_only = len(repository.downloadable_revisions) != 1
                 suc.handle_email_alerts(
                     trans,
                     repository,
                     content_alert_str=content_alert_str,
                     new_repo_alert=new_repo_alert,
                     admin_only=admin_only)
             if ok:
                 # Update the repository files for browsing.
                 suc.update_repository(repo)
                 # Get the new repository tip.
                 if tip == repository.tip(trans.app):
                     message = 'No changes to repository.  '
                     status = 'warning'
                 else:
                     if (isgzip or isbz2) and uncompress_file:
                         uncompress_str = ' uncompressed and '
                     else:
                         uncompress_str = ' '
                     if uploaded_directory:
                         source_type = "repository"
                         source = url
                     else:
                         source_type = "file"
                         source = uploaded_file_filename
                     message = "The %s '%s' has been successfully%suploaded to the repository.  " % (
                         source_type, source, uncompress_str)
                     if istar and (undesirable_dirs_removed
                                   or undesirable_files_removed):
                         items_removed = undesirable_dirs_removed + undesirable_files_removed
                         message += "  %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive.  " % items_removed
                     if istar and remove_repo_files_not_in_tar and files_to_remove:
                         if upload_point is not None:
                             message += "  %d files were removed from the repository relative to the selected upload point '%s'.  " % (
                                 len(files_to_remove), upload_point)
                         else:
                             message += "  %d files were removed from the repository root.  " % len(
                                 files_to_remove)
                     kwd['message'] = message
                     suc.set_repository_metadata_due_to_new_tip(
                         trans,
                         repository,
                         content_alert_str=content_alert_str,
                         **kwd)
                 # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch
                 # or some other problem.
                 if suc.get_config_from_disk('tool_dependencies.xml',
                                             repo_dir):
                     if repository.metadata_revisions:
                         # A repository's metadata revisions are order descending by update_time, so the zeroth revision will be the tip just after an upload.
                         metadata_dict = repository.metadata_revisions[
                             0].metadata
                     else:
                         metadata_dict = {}
                     if suc.has_orphan_tool_dependencies_in_tool_shed(
                             metadata_dict):
                         message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", '
                         message += 'so one or more of the defined tool dependencies are considered orphans within this repository.'
                         status = 'warning'
                 # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
                 suc.reset_tool_data_tables(trans.app)
                 trans.response.send_redirect(
                     web.url_for(controller='repository',
                                 action='browse_repository',
                                 id=repository_id,
                                 commit_message='Deleted selected files',
                                 message=message,
                                 status=status))
             else:
                 status = 'error'
             # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
             suc.reset_tool_data_tables(trans.app)