Exemple #1
0
 def set_peek(self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=True):
     """
     Set the peek.  This method is used by various subclasses of Text.
     """
     if not dataset.dataset.purged:
         # The file must exist on disk for the get_file_peek() method
         dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap)
         if line_count is None:
             # See if line_count is stored in the metadata
             if dataset.metadata.data_lines:
                 dataset.blurb = "%s %s" % (util.commaify(str(dataset.metadata.data_lines)), inflector.cond_plural(dataset.metadata.data_lines, self.line_class))
             else:
                 # Number of lines is not known ( this should not happen ), and auto-detect is
                 # needed to set metadata
                 # This can happen when the file is larger than max_optional_metadata_filesize.
                 if int(dataset.get_size()) <= 1048576:
                     # Small dataset, recount all lines and reset peek afterward.
                     lc = self.count_data_lines(dataset)
                     dataset.metadata.data_lines = lc
                     dataset.blurb = "%s %s" % (util.commaify(str(lc)), inflector.cond_plural(lc, self.line_class))
                 else:
                     est_lines = self.estimate_file_lines(dataset)
                     dataset.blurb = "~%s %s" % (util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class))
         else:
             dataset.blurb = "%s %s" % (util.commaify(str(line_count)), inflector.cond_plural(line_count, self.line_class))
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'
Exemple #2
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 def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ):
     """
     Set the peek.  This method is used by various subclasses of Text.
     """
     if not dataset.dataset.purged:
         # The file must exist on disk for the get_file_peek() method
         dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars )
         if line_count is None:
             # See if line_count is stored in the metadata
             if dataset.metadata.data_lines:
                 dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, self.line_class) )
             else:
                 # Number of lines is not known ( this should not happen ), and auto-detect is
                 # needed to set metadata
                 # This can happen when the file is larger than max_optional_metadata_filesize.
                 if int(dataset.get_size()) <= 1048576:
                     #Small dataset, recount all lines and reset peek afterward.
                     lc = self.count_data_lines(dataset)
                     dataset.metadata.data_lines = lc
                     dataset.blurb = "%s %s" % ( util.commaify( str(lc) ), inflector.cond_plural(lc, self.line_class) )
                 else:
                     est_lines = self.estimate_file_lines(dataset)
                     dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) )
         else:
             dataset.blurb = "%s %s" % ( util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) )
     else:
         dataset.peek = 'file does not exist'
         dataset.blurb = 'file purged from disk'
Exemple #3
0
 def delete_repository_metadata(self, trans, **kwd):
     message = escape(kwd.get("message", ""))
     status = kwd.get("status", "done")
     id = kwd.get("id", None)
     if id:
         ids = util.listify(id)
         count = 0
         for repository_metadata_id in ids:
             repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
             trans.sa_session.delete(repository_metadata)
             trans.sa_session.flush()
             count += 1
         if count:
             message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record"))
     else:
         message = "No repository metadata ids received for deleting."
         status = "error"
     trans.response.send_redirect(
         web.url_for(
             controller="admin",
             action="browse_repository_metadata",
             message=util.sanitize_text(message),
             status=status,
         )
     )
 def delete_repository_metadata(self, trans, **kwd):
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.get('status', 'done')
     id = kwd.get('id', None)
     if id:
         ids = util.listify(id)
         count = 0
         for repository_metadata_id in ids:
             repository_metadata = get_repository_metadata_by_id(
                 trans, repository_metadata_id)
             trans.sa_session.delete(repository_metadata)
             trans.sa_session.flush()
             count += 1
         if count:
             message = "Deleted %d repository metadata %s" % (
                 count, inflector.cond_plural(len(ids), "record"))
     else:
         message = "No repository metadata ids received for deleting."
         status = 'error'
     trans.response.send_redirect(
         web.url_for(controller='admin',
                     action='browse_repository_metadata',
                     message=util.sanitize_text(message),
                     status=status))
Exemple #5
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 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 undelete_repository(self, trans, **kwd):
     params = util.Params(kwd)
     message = util.restore_text(params.get('message', ''))
     status = params.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 = get_repository(trans, repository_id)
             if repository.deleted:
                 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'))
Exemple #7
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 def undelete_repository( self, trans, **kwd ):
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.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 = get_repository( trans, repository_id )
             if repository.deleted:
                 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' ) )
Exemple #8
0
 def reset_metadata_on_all_repositories( self, trans, **kwd ):
     params = util.Params( kwd )
     message = util.restore_text( params.get( 'message', ''  ) )
     status = params.get( 'status', 'done' )
     if 'reset_metadata_on_all_repositories_button' in kwd:
         successful_count = 0
         unsuccessful_count = 0
         for repository in trans.sa_session.query( trans.model.Repository ) \
                                           .filter( trans.model.Repository.table.c.deleted == False ):
             try:
                 error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) )
                 if status not in [ 'ok' ] and error_message:
                     log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, error_message ) )
                     unsuccessful_count += 1
                 elif status in [ 'ok' ] and error_message:
                     log.debug( "Successfully reset metadata on repository %s, but encountered this problem: %s" % ( repository.name, error_message ) )
                     successful_count += 1
                 else:
                     log.debug( "Successfully reset metadata on repository %s" % repository.name )
                     successful_count += 1
             except Exception, e:
                 log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) )
                 unsuccessful_count += 1
         message = "Successfully reset metadata on %d %s.  " % ( successful_count,
                                                                 inflector.cond_plural( successful_count, "repository" ) )            
         if unsuccessful_count:
             message += "Error setting metadata on %d %s - see the paster log for details.  " % ( unsuccessful_count,
                                                                                                  inflector.cond_plural( unsuccessful_count,
                                                                                                                         "repository" ) )
         trans.response.send_redirect( web.url_for( controller='admin',
                                                    action='browse_repository_metadata',
                                                    webapp='community',
                                                    message=util.sanitize_text( message ),
                                                    status=status ) )
Exemple #9
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 def reset_metadata_on_selected_repositories(self, user, **kwd):
     """
     Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
     This method is called from both Galaxy and the Tool Shed.
     """
     repository_ids = util.listify(kwd.get('repository_ids', None))
     message = ''
     status = 'done'
     if repository_ids:
         successful_count = 0
         unsuccessful_count = 0
         for repository_id in repository_ids:
             try:
                 repository = get_installed_tool_shed_repository(
                     self.app, repository_id)
                 self.set_repository(repository)
                 self.reset_all_metadata_on_installed_repository()
                 if self.invalid_file_tups:
                     message = generate_message_for_invalid_tools(
                         self.app,
                         self.invalid_file_tups,
                         repository,
                         None,
                         as_html=False)
                     log.debug(message)
                     unsuccessful_count += 1
                 else:
                     log.debug(
                         "Successfully reset metadata on repository %s owned by %s"
                         % (str(repository.name), str(repository.owner)))
                     successful_count += 1
             except Exception:
                 log.exception(
                     "Error attempting to reset metadata on repository %s",
                     str(repository.name))
                 unsuccessful_count += 1
         message = "Successfully reset metadata on %d %s.  " % \
             (successful_count, inflector.cond_plural(successful_count, "repository"))
         if unsuccessful_count:
             message += "Error setting metadata on %d %s - see the paster log for details.  " % \
                 (unsuccessful_count, inflector.cond_plural(unsuccessful_count, "repository"))
     else:
         message = 'Select at least one repository to on which to reset all metadata.'
         status = 'error'
     return message, status
 def reset_metadata_on_selected_repositories( self, user, **kwd ):
     """
     Inspect the repository changelog to reset metadata for all appropriate changeset revisions.
     This method is called from both Galaxy and the Tool Shed.
     """
     repository_ids = util.listify( kwd.get( 'repository_ids', None ) )
     message = ''
     status = 'done'
     if repository_ids:
         successful_count = 0
         unsuccessful_count = 0
         for repository_id in repository_ids:
             try:
                 repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id )
                 self.set_repository( repository )
                 self.reset_all_metadata_on_installed_repository()
                 if self.invalid_file_tups:
                     message = tool_util.generate_message_for_invalid_tools( self.app,
                                                                             self.invalid_file_tups,
                                                                             repository,
                                                                             None,
                                                                             as_html=False )
                     log.debug( message )
                     unsuccessful_count += 1
                 else:
                     log.debug( "Successfully reset metadata on repository %s owned by %s" %
                         ( str( repository.name ), str( repository.owner ) ) )
                     successful_count += 1
             except:
                 log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) )
                 unsuccessful_count += 1
         message = "Successfully reset metadata on %d %s.  " % \
             ( successful_count, inflector.cond_plural( successful_count, "repository" ) )
         if unsuccessful_count:
             message += "Error setting metadata on %d %s - see the paster log for details.  " % \
                 ( unsuccessful_count, inflector.cond_plural( unsuccessful_count, "repository" ) )
     else:
         message = 'Select at least one repository to on which to reset all metadata.'
         status = 'error'
     return message, status
 def undelete_repository(self, trans, **kwd):
     message = escape(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.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."
         status = 'error'
     trans.response.send_redirect(
         web.url_for(controller='admin',
                     action='browse_repositories',
                     message=util.sanitize_text(message),
                     status='done'))
Exemple #12
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 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 reset_user_password(self, trans, **kwd):
     user_id = kwd.get('id', None)
     if not user_id:
         message = "No users received for resetting passwords."
         trans.response.send_redirect(
             web.url_for(controller='admin',
                         action='users',
                         message=message,
                         status='error'))
     user_ids = util.listify(user_id)
     if 'reset_user_password_button' in kwd:
         message = ''
         status = ''
         for user_id in user_ids:
             user = get_user(trans, user_id)
             password = kwd.get('password', None)
             confirm = kwd.get('confirm', None)
             if len(password) < 6:
                 message = "Use a password of at least 6 characters."
                 status = 'error'
                 break
             elif password != confirm:
                 message = "Passwords do not match."
                 status = 'error'
                 break
             else:
                 user.set_password_cleartext(password)
                 trans.sa_session.add(user)
                 trans.sa_session.flush()
         if not message and not status:
             message = "Passwords reset for %d %s." % (len(
                 user_ids), inflector.cond_plural(len(user_ids), 'user'))
             status = 'done'
         trans.response.send_redirect(
             web.url_for(controller='admin',
                         action='users',
                         message=util.sanitize_text(message),
                         status=status))
     users = [get_user(trans, user_id) for user_id in user_ids]
     if len(user_ids) > 1:
         user_id = ','.join(user_ids)
     return trans.fill_template(
         '/webapps/tool_shed/admin/user/reset_password.mako',
         id=user_id,
         users=users,
         password='',
         confirm='')
Exemple #14
0
 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
         )
     )
Exemple #15
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 def reset_user_password(self, trans, **kwd):
     user_id = kwd.get('id', None)
     if not user_id:
         message = "No users received for resetting passwords."
         trans.response.send_redirect(web.url_for(controller='admin',
                                                  action='users',
                                                  message=message,
                                                  status='error'))
     user_ids = util.listify(user_id)
     if 'reset_user_password_button' in kwd:
         message = ''
         status = ''
         for user_id in user_ids:
             user = get_user(trans, user_id)
             password = kwd.get('password', None)
             confirm = kwd.get('confirm', None)
             if len(password) < 6:
                 message = "Use a password of at least 6 characters."
                 status = 'error'
                 break
             elif password != confirm:
                 message = "Passwords do not match."
                 status = 'error'
                 break
             else:
                 user.set_password_cleartext(password)
                 trans.sa_session.add(user)
                 trans.sa_session.flush()
         if not message and not status:
             message = "Passwords reset for %d %s." % (len(user_ids), inflector.cond_plural(len(user_ids), 'user'))
             status = 'done'
         trans.response.send_redirect(web.url_for(controller='admin',
                                                  action='users',
                                                  message=util.sanitize_text(message),
                                                  status=status))
     users = [get_user(trans, user_id) for user_id in user_ids]
     if len(user_ids) > 1:
         user_id = ','.join(user_ids)
     return trans.fill_template('/webapps/tool_shed/admin/user/reset_password.mako',
                                id=user_id,
                                users=users,
                                password='',
                                confirm='')
 def delete_repository_metadata( self, trans, **kwd ):
     message = kwd.get( 'message', ''  )
     status = kwd.get( 'status', 'done' )
     id = kwd.get( 'id', None )
     if id:
         ids = util.listify( id )
         count = 0
         for repository_metadata_id in ids:
             repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
             trans.sa_session.delete( repository_metadata )
             trans.sa_session.flush()
             count += 1
         if count:
             message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) )
     else:
         message = "No repository metadata ids received for deleting."
         status = 'error'
     trans.response.send_redirect( web.url_for( controller='admin',
                                                action='browse_repository_metadata',
                                                message=util.sanitize_text( message ),
                                                status=status ) )
Exemple #17
0
 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' ) )