1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/4412842dc738/ changeset: 4412842dc738 user: greg date: 2011-11-15 20:50:08 summary: A tool shed admin will now receive content alerts (as part of the alert message) for each file uploaded to a repository that contains either image content or html content if the admin has chosen to receive email alerts for changes to the repository. affected #: 3 files

diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -26,6 +26,8 @@ Change description: ${description}

+${content_alert_str} + ----------------------------------------------------------------------------- This change alert was sent from the Galaxy tool shed hosted on the server "${host}" @@ -520,7 +522,7 @@ def get_user( trans, id ): """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def handle_email_alerts( trans, repository ): +def handle_email_alerts( trans, repository, content_alert_str='' ): repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) smtp_server = trans.app.config.smtp_server @@ -541,14 +543,25 @@ username = ctx.user().split()[0] except: username = ctx.user() - # Build the email message + # We'll use 2 template bodies because we only want to send content + # alerts to tool shed admin users. + admin_body = string.Template( email_alert_template ) \ + .safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str=content_alert_str ) body = string.Template( email_alert_template ) \ .safe_substitute( host=trans.request.host, repository_name=repository.name, revision='%s:%s' %( str( ctx.rev() ), ctx ), display_date=display_date, description=ctx.description(), - username=username ) + username=username, + content_alert_str='' ) + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) frm = email_from subject = "Galaxy tool shed repository update alert" email_alerts = from_json_string( repository.email_alerts ) @@ -556,7 +569,10 @@ to = email.strip() # Send it try: - util.send_mail( frm, to, subject, body, trans.app.config ) + if to in admin_users: + util.send_mail( frm, to, subject, admin_body, trans.app.config ) + else: + util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): @@ -567,30 +583,20 @@ repo = hg.repository( get_configured_ui(), repo_dir ) # The following will delete the disk copy of only the files in the repository. #os.system( 'hg update -r null > /dev/null 2>&1' ) - repo.ui.pushbuffer() files_to_remove_from_disk = [] files_to_commit = [] - commands.status( repo.ui, repo, all=True ) - status_and_file_names = repo.ui.popbuffer().strip().split( "\n" ) - if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]: - # status_and_file_names looks something like: - # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] - # The codes used to show the status of files are: - # M = modified - # A = added - # R = removed - # C = clean - # ! = deleted, but still tracked - # ? = not tracked - # I = ignored - for status_and_file_name in status_and_file_names: - if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): - files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): - files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) # We may have files on disk in the repo directory that aren't being tracked, so they must be removed. - # We'll use mercurial's purge extension to do this. Using this extension requires the following entry - # in the repository's hgrc file which was not required for some time, so we'll add it if it's missing. + # The codes used to show the status of files are as follows. + # M = modified + # A = added + # R = removed + # C = clean + # ! = deleted, but still tracked + # ? = not tracked + # I = ignored + # We'll use mercurial's purge extension to remove untracked file. Using this extension requires the + # following entry in the repository's hgrc file which was not required for some time, so we'll add it + # if it's missing. # [extensions] # hgext.purge= lines = repo.opener( 'hgrc', 'rb' ).readlines() @@ -624,9 +630,14 @@ commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit ) repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) + cmd = 'hg update > /dev/null 2>&1' os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() os.chdir( current_working_dir ) + if return_code != 0: + output = proc.stdout.read( 32768 ) + log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) def load_tool( trans, config_file ): """ Load a single tool from the file named by `config_file` and return

diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -101,12 +101,12 @@ 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 ) ) - # TODO: enhance this method to set a flag and alert an admin to review content since - # the hard checks are too restrictive. - #ok, message = self.__check_file_content( uploaded_file_name ) - #if ok: # Move the uploaded file to the load_point within the repository hierarchy. shutil.move( uploaded_file_name, full_path ) + if 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 ) try: commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) @@ -128,7 +128,7 @@ # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. copy_sample_loc_file( trans, full_path ) - handle_email_alerts( trans, repository ) + handle_email_alerts( trans, repository, content_alert_str=content_alert_str ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -194,18 +194,7 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() - """ - # TODO: enhance this method to set a flag and alert an admin to review content since - # the hard checks are too restrictive. - for filename_in_archive in filenames_in_archive: - if os.path.isfile( filename_in_archive ): - ok, message = self.__check_file_content( filename_in_archive ) - if not ok: - # Refresh the repository files for browsing. - current_working_dir = os.getcwd() - update_for_browsing( trans, repository, current_working_dir ) - return False, message, [] - """ + content_alert_str = '' if remove_repo_files_not_in_tar and not repository.is_new: # 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. @@ -250,6 +239,9 @@ # The directory is not empty pass for filename_in_archive in filenames_in_archive: + # Check file content to ensure it is appropriate. + if os.path.isfile( filename_in_archive ): + content_alert_str += self.__check_file_content( filename_in_archive ) commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ): # Handle the special case where a tool_data_table_conf.xml.sample @@ -271,7 +263,7 @@ # exception. If this happens, we'll try the following. repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) - handle_email_alerts( trans, repository ) + handle_email_alerts( trans, repository, content_alert_str ) return True, '', files_to_remove def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: @@ -349,15 +341,9 @@ return False, message return True, '' def __check_file_content( self, file_path ): - return True, '' message = '' - ok = True - head, tail = os.path.split( file_path ) if check_html( file_path ): - message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail ) - ok = False + message = 'The file "%s" contains HTML content.\n' % str( file_path ) elif check_image( file_path ): - # For now we won't allow images to be uploaded. - message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail ) - ok = False - return ok, message + message = 'The file "%s" contains image content.\n' % str( file_path ) + return message

diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -64,7 +64,13 @@ <div class="toolForm"><div class="toolFormTitle">Upload a single file or a tarball</div><div class="toolFormBody"> - ## TODO: nginx + <div class="form-row"> + <div class="warningmessage"> + Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your + browser after clicking the <b>Upload</b> button below. + </div> + <div style="clear: both"></div> + </div><form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post"><div class="form-row"><label>File:</label>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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