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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.
This commit is contained in:
Greg Von Kuster
@@ -26,6 +26,8 @@ Revision: ${revision}
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Change description:
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${description}
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${content_alert_str}
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-----------------------------------------------------------------------------
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This change alert was sent from the Galaxy tool shed hosted on the server
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"${host}"
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@@ -520,7 +522,7 @@ def get_configured_ui():
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def get_user( trans, id ):
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"""Get a user from the database by id"""
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return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) )
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def handle_email_alerts( trans, repository ):
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def handle_email_alerts( trans, repository, content_alert_str='' ):
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repo_dir = repository.repo_path
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repo = hg.repository( get_configured_ui(), repo_dir )
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smtp_server = trans.app.config.smtp_server
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@@ -541,14 +543,25 @@ def handle_email_alerts( trans, repository ):
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username = ctx.user().split()[0]
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except:
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username = ctx.user()
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# Build the email message
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# We'll use 2 template bodies because we only want to send content
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# alerts to tool shed admin users.
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admin_body = string.Template( email_alert_template ) \
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.safe_substitute( host=trans.request.host,
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repository_name=repository.name,
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revision='%s:%s' %( str( ctx.rev() ), ctx ),
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display_date=display_date,
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description=ctx.description(),
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username=username,
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content_alert_str=content_alert_str )
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body = string.Template( email_alert_template ) \
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.safe_substitute( host=trans.request.host,
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repository_name=repository.name,
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revision='%s:%s' %( str( ctx.rev() ), ctx ),
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display_date=display_date,
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description=ctx.description(),
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username=username )
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username=username,
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content_alert_str='' )
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admin_users = trans.app.config.get( "admin_users", "" ).split( "," )
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frm = email_from
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subject = "Galaxy tool shed repository update alert"
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email_alerts = from_json_string( repository.email_alerts )
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@@ -556,7 +569,10 @@ def handle_email_alerts( trans, repository ):
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to = email.strip()
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# Send it
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try:
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util.send_mail( frm, to, subject, body, trans.app.config )
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if to in admin_users:
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util.send_mail( frm, to, subject, admin_body, trans.app.config )
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else:
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util.send_mail( frm, to, subject, body, trans.app.config )
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except Exception, e:
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log.exception( "An error occurred sending a tool shed repository update alert by email." )
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def update_for_browsing( trans, repository, current_working_dir, commit_message='' ):
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@@ -567,30 +583,20 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message=
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repo = hg.repository( get_configured_ui(), repo_dir )
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# The following will delete the disk copy of only the files in the repository.
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#os.system( 'hg update -r null > /dev/null 2>&1' )
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repo.ui.pushbuffer()
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files_to_remove_from_disk = []
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files_to_commit = []
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commands.status( repo.ui, repo, all=True )
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status_and_file_names = repo.ui.popbuffer().strip().split( "\n" )
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if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]:
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# status_and_file_names looks something like:
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# ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml']
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# The codes used to show the status of files are:
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# M = modified
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# A = added
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# R = removed
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# C = clean
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# ! = deleted, but still tracked
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# ? = not tracked
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# I = ignored
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for status_and_file_name in status_and_file_names:
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if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ):
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files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
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elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ):
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files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) )
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# We may have files on disk in the repo directory that aren't being tracked, so they must be removed.
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# We'll use mercurial's purge extension to do this. Using this extension requires the following entry
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# in the repository's hgrc file which was not required for some time, so we'll add it if it's missing.
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# The codes used to show the status of files are as follows.
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# M = modified
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# A = added
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# R = removed
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# C = clean
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# ! = deleted, but still tracked
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# ? = not tracked
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# I = ignored
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# We'll use mercurial's purge extension to remove untracked file. Using this extension requires the
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# following entry in the repository's hgrc file which was not required for some time, so we'll add it
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# if it's missing.
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# [extensions]
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# hgext.purge=
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lines = repo.opener( 'hgrc', 'rb' ).readlines()
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@@ -624,9 +630,14 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message=
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commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit )
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repo.dirstate.write()
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repo.commit( user=trans.user.username, text=commit_message )
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cmd = 'hg update > /dev/null 2>&1'
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os.chdir( repo_dir )
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os.system( 'hg update > /dev/null 2>&1' )
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proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
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return_code = proc.wait()
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os.chdir( current_working_dir )
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if return_code != 0:
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output = proc.stdout.read( 32768 )
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log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) )
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def load_tool( trans, config_file ):
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"""
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Load a single tool from the file named by `config_file` and return
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@@ -101,12 +101,12 @@ class UploadController( BaseUIController ):
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full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) )
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else:
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full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) )
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# TODO: enhance this method to set a flag and alert an admin to review content since
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# the hard checks are too restrictive.
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#ok, message = self.__check_file_content( uploaded_file_name )
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#if ok:
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# Move the uploaded file to the load_point within the repository hierarchy.
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shutil.move( uploaded_file_name, full_path )
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if os.path.isfile( full_path ):
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content_alert_str = self.__check_file_content( full_path )
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else:
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content_alert_str = ''
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commands.add( repo.ui, repo, full_path )
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try:
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commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
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@@ -128,7 +128,7 @@ class UploadController( BaseUIController ):
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# Handle the special case where a xxx.loc.sample file is
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# being uploaded by copying it to ~/tool-data/xxx.loc.
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copy_sample_loc_file( trans, full_path )
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handle_email_alerts( trans, repository )
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handle_email_alerts( trans, repository, content_alert_str=content_alert_str )
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if ok:
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# Update the repository files for browsing.
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update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message )
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@@ -194,18 +194,7 @@ class UploadController( BaseUIController ):
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tar.extractall( path=full_path )
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tar.close()
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uploaded_file.close()
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"""
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# TODO: enhance this method to set a flag and alert an admin to review content since
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# the hard checks are too restrictive.
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for filename_in_archive in filenames_in_archive:
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if os.path.isfile( filename_in_archive ):
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ok, message = self.__check_file_content( filename_in_archive )
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if not ok:
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# Refresh the repository files for browsing.
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current_working_dir = os.getcwd()
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update_for_browsing( trans, repository, current_working_dir )
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return False, message, []
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"""
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content_alert_str = ''
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if remove_repo_files_not_in_tar and not repository.is_new:
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# We have a repository that is not new (it contains files), so discover
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# those files that are in the repository, but not in the uploaded archive.
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@@ -250,6 +239,9 @@ class UploadController( BaseUIController ):
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# The directory is not empty
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pass
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for filename_in_archive in filenames_in_archive:
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# Check file content to ensure it is appropriate.
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if os.path.isfile( filename_in_archive ):
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content_alert_str += self.__check_file_content( filename_in_archive )
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commands.add( repo.ui, repo, filename_in_archive )
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if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ):
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# Handle the special case where a tool_data_table_conf.xml.sample
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@@ -271,7 +263,7 @@ class UploadController( BaseUIController ):
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# exception. If this happens, we'll try the following.
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repo.dirstate.write()
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repo.commit( user=trans.user.username, text=commit_message )
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handle_email_alerts( trans, repository )
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handle_email_alerts( trans, repository, content_alert_str )
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return True, '', files_to_remove
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def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ):
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if isgzip:
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@@ -349,15 +341,9 @@ class UploadController( BaseUIController ):
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return False, message
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return True, ''
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def __check_file_content( self, file_path ):
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return True, ''
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message = ''
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ok = True
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head, tail = os.path.split( file_path )
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if check_html( file_path ):
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message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail )
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ok = False
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message = 'The file "%s" contains HTML content.\n' % str( file_path )
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elif check_image( file_path ):
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# For now we won't allow images to be uploaded.
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message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail )
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ok = False
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return ok, message
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message = 'The file "%s" contains image content.\n' % str( file_path )
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return message
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@@ -64,7 +64,13 @@
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<div class="toolForm">
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<div class="toolFormTitle">Upload a single file or a tarball</div>
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<div class="toolFormBody">
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## TODO: nginx
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<div class="form-row">
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<div class="warningmessage">
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Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your
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browser after clicking the <b>Upload</b> button below.
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</div>
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<div style="clear: both"></div>
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</div>
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<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">
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<div class="form-row">
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<label>File:</label>
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