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 ) ) if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION: ok = os.path.basename( uploaded_file ) == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME else: ok = os.path.basename( uploaded_file ) not in commit_util.UNDESIRABLE_FILES if ok: for file_path_item in relative_path.split( '/' ): if file_path_item in commit_util.UNDESIRABLE_DIRS: undesirable_dirs_removed += 1 ok = False break else: undesirable_files_removed += 1 if ok: uploaded_file_name = os.path.abspath( os.path.join( root, uploaded_file ) ) if os.path.split( uploaded_file_name )[ -1 ] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name, unpopulate=False ) if error_message: return False, error_message, [], '', [], [] elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if error_message: return False, error_message, [], '', [], [] if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) 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 commit_util.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 )
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 = commit_util.check_archive( repository, 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 commit_util.UNDESIRABLE_FILES if ok: for file_path_item in tarinfo_obj.name.split( '/' ): if file_path_item in commit_util.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() for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) if os.path.split( uploaded_file_name )[ -1 ] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) return commit_util.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 )
def generate_repository_archive(trans, work_dir, tool_shed_url, repository, changeset_revision, file_type): file_type_str = suc.get_file_type_str(changeset_revision, file_type) file_name = "%s-%s" % (repository.name, file_type_str) return_code, error_message = archive_repository_revision(trans, ui, repository, work_dir, changeset_revision) if return_code: return None, error_message repository_archive_name = os.path.join(work_dir, file_name) # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files. repository_archive = tarfile.open(repository_archive_name, "w:%s" % file_type) for root, dirs, files in os.walk(work_dir): if root.find(".hg") < 0 and root.find("hgrc") < 0: for dir in dirs: if dir in commit_util.UNDESIRABLE_DIRS: dirs.remove(dir) for name in files: name = str(name) if str(name) in commit_util.UNDESIRABLE_FILES: continue full_path = os.path.join(root, name) relative_path = full_path.replace(work_dir, "").lstrip("/") # See if we have a repository dependencies defined. if name == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans, full_path, unpopulate=True ) if error_message: return None, error_message if altered: tmp_filename = xml_util.create_and_write_tmp_file(root_elem, use_indent=True) shutil.move(tmp_filename, full_path) elif name == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags. altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans, full_path, unpopulate=True ) if error_message: return None, error_message if altered: tmp_filename = xml_util.create_and_write_tmp_file(root_elem, use_indent=True) shutil.move(tmp_filename, full_path) repository_archive.add(full_path, arcname=relative_path) repository_archive.close() return repository_archive, error_message
def upload( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) commit_message = kwd.get( 'commit_message', 'Uploaded' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) categories = suc.get_categories( trans ) repository_id = kwd.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( kwd.get( 'uncompress_file', 'true' ) ) remove_repo_files_not_in_tar = util.string_as_bool( kwd.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None upload_point = commit_util.get_upload_point( repository, **kwd ) tip = repository.tip( trans.app ) file_data = kwd.get( 'file_data', '' ) url = kwd.get( 'url', '' ) # Part of the upload process is sending email notification to those that have registered to # receive them. One scenario occurs when the first change set is produced for the repository. # See the suc.handle_email_alerts() method for the definition of the scenarios. new_repo_alert = repository.is_new( trans.app ) uploaded_directory = None if kwd.get( 'upload_button', False ): if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' uploaded_file = None elif url and url.startswith( 'hg' ): # Use mercurial clone to fetch repository, contents will then be copied over. uploaded_directory = tempfile.mkdtemp() repo_url = 'http%s' % url[ len( 'hg' ): ] repo_url = repo_url.encode( 'ascii', 'replace' ) 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( util.CHUNK_SIZE ) if not chunk: break uploaded_file.write( chunk ) uploaded_file.flush() uploaded_file_filename = url.split( '/' )[ -1 ] isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 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 = commit_util.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip=isgzip, isbz2=isbz2 ) if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and uploaded_file_filename != suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: ok = False message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named <b>tool_dependencies.xml</b>.' if ok: 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 some version of the uploaded file to the load_point within the repository hierarchy. if uploaded_file_filename in [ suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name, unpopulate=False ) if error_message: ok = False message = error_message status = 'error' elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) elif uploaded_file_filename in [ suc.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values # are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if error_message: ok = False message = error_message status = 'error' if ok: if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) else: shutil.move( uploaded_file_name, full_path ) if ok: # 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 = commit_util.check_file_contents_for_email_alerts( trans ) if check_contents and os.path.isfile( full_path ): content_alert_str = commit_util.check_file_content_for_html_and_images( 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 = tool_util.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 <b>%s</b> 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 metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) 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 str( repository.type ) != rt_util.TOOL_DEPENDENCY_DEFINITION: change_repository_type_message = tool_dependency_util.generate_message_for_repository_type_change( trans, repository ) if change_repository_type_message: message += change_repository_type_message status = 'warning' else: # 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. Tool dependency definitions can define orphan tool dependencies (no relationship to any tools contained in the repository), # so warning messages are important because orphans are always valid. The repository owner must be warned in case they did not intend to define an # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition. orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata_dict ) if orphan_message: message += orphan_message status = 'warning' # Handle messaging for invalid tool dependencies. invalid_tool_dependencies_message = tool_dependency_util.generate_message_for_invalid_tool_dependencies( metadata_dict ) if invalid_tool_dependencies_message: message += invalid_tool_dependencies_message status = 'error' # Handle messaging for invalid repository dependencies. invalid_repository_dependencies_message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict ) if invalid_repository_dependencies_message: message += invalid_repository_dependencies_message status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. tool_util.reset_tool_data_tables( trans.app ) if uploaded_directory: suc.remove_dir( uploaded_directory ) 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: if uploaded_directory: suc.remove_dir( uploaded_directory ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. tool_util.reset_tool_data_tables( trans.app )
altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name, unpopulate=False ) if error_message: ok = False message = error_message status = 'error' elif altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) elif uploaded_file_filename in [ suc.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values # are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if error_message: ok = False message = error_message status = 'error' if ok: if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, full_path ) else: shutil.move( uploaded_file_name, full_path ) else: shutil.move( uploaded_file_name, full_path ) if ok: # 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.
def import_repository_archive( trans, repository, repository_archive_dict ): """Import a repository archive contained within a repository capsule.""" archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] file_path = encoding_util.tool_shed_decode( encoded_file_path ) results_dict = dict( ok=True, error_message='' ) archive_file_path = os.path.join( file_path, archive_file_name ) archive = tarfile.open( archive_file_path, 'r:*' ) 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, error_message = commit_util.check_archive( repository, archive ) if ok: full_path = os.path.abspath( repo_dir ) filenames_in_archive = [] for tarinfo_obj in archive.getmembers(): # Check files and directories in the archive. ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES if ok: for file_path_item in tarinfo_obj.name.split( '/' ): if file_path_item in commit_util.UNDESIRABLE_DIRS: undesirable_dirs_removed += 1 error_message = 'Import failed: invalid file path <b>%s</b> in archive <b>%s</b>' % \ ( str( file_path_item ), str( archive_file_name ) ) results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message return results_dict filenames_in_archive.append( tarinfo_obj.name ) else: undesirable_files_removed += 1 # Extract the uploaded archive to the repository root. archive.extractall( path=full_path ) archive.close() for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) if os.path.split( uploaded_file_name )[ -1 ] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name, unpopulate=False ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) elif os.path.split( uploaded_file_name )[ -1 ] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem, error_message = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) commit_message = 'Imported from capsule %s' % str( capsule_file_name ) # Send email notification to those that have registered to receive alerts for new repositories in this Tool Shed. new_repo_alert = True # Since the repository is new, the following must be False. remove_repo_files_not_in_tar = False ok, error_message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \ commit_util.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 ) try: metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str ) except Exception, e: log.debug( "Error setting metadata on repository %s created from imported archive %s: %s" % \ ( str( repository.name ), str( archive_file_name ), str( e ) ) ) results_dict[ 'ok' ] = ok results_dict[ 'error_message' ] += error_message
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 = commit_util.check_archive(repository, 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 commit_util.UNDESIRABLE_FILES if ok: for file_path_item in tarinfo_obj.name.split('/'): if file_path_item in commit_util.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() for filename in filenames_in_archive: uploaded_file_name = os.path.join(full_path, filename) if os.path.split(uploaded_file_name)[ -1] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem) shutil.move(tmp_filename, uploaded_file_name) elif os.path.split(uploaded_file_name)[ -1] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem) shutil.move(tmp_filename, uploaded_file_name) return commit_util.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)
def upload(self, trans, **kwd): message = kwd.get('message', '') status = kwd.get('status', 'done') commit_message = kwd.get('commit_message', 'Uploaded') category_ids = util.listify(kwd.get('category_id', '')) categories = suc.get_categories(trans) repository_id = kwd.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( kwd.get('uncompress_file', 'true')) remove_repo_files_not_in_tar = util.string_as_bool( kwd.get('remove_repo_files_not_in_tar', 'true')) uploaded_file = None upload_point = commit_util.get_upload_point(repository, **kwd) tip = repository.tip(trans.app) file_data = kwd.get('file_data', '') url = kwd.get('url', '') # Part of the upload process is sending email notification to those that have registered to # receive them. One scenario occurs when the first change set is produced for the repository. # See the suc.handle_email_alerts() method for the definition of the scenarios. new_repo_alert = repository.is_new(trans.app) uploaded_directory = None if kwd.get('upload_button', False): if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' uploaded_file = None elif url and url.startswith('hg'): # Use mercurial clone to fetch repository, contents will then be copied over. uploaded_directory = tempfile.mkdtemp() repo_url = 'http%s' % url[len('hg'):] repo_url = repo_url.encode('ascii', 'replace') 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(util.CHUNK_SIZE) if not chunk: break uploaded_file.write(chunk) uploaded_file.flush() uploaded_file_filename = url.split('/')[-1] isempty = os.path.getsize( os.path.abspath(uploaded_file_name)) == 0 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 = commit_util.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2) if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and uploaded_file_filename != suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: ok = False message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named <b>tool_dependencies.xml</b>.' if ok: 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 some version of the uploaded file to the load_point within the repository hierarchy. if uploaded_file_filename in [ suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem) shutil.move(tmp_filename, full_path) else: shutil.move(uploaded_file_name, full_path) elif uploaded_file_filename in [ suc.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values # are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem) shutil.move(tmp_filename, full_path) else: shutil.move(uploaded_file_name, full_path) else: 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 = commit_util.check_file_contents_for_email_alerts( trans) if check_contents and os.path.isfile(full_path): content_alert_str = commit_util.check_file_content_for_html_and_images( 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 = tool_util.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 <b>%s</b> 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 metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd) 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 str(repository.type ) != rt_util.TOOL_DEPENDENCY_DEFINITION: # 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. Tool dependency definitions can define orphan tool dependencies (no relationship to any tools contained in the repository), # so warning messages are important because orphans are always valid. The repository owner must be warned in case they did not intend to define an # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition. # Handle messaging for orphan tool dependencies. orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata_dict) if orphan_message: message += orphan_message status = 'warning' # Handle messaging for invalid tool dependencies. invalid_tool_dependencies_message = tool_dependency_util.generate_message_for_invalid_tool_dependencies( metadata_dict) if invalid_tool_dependencies_message: message += invalid_tool_dependencies_message status = 'error' # Handle messaging for invalid repository dependencies. invalid_repository_dependencies_message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict) if invalid_repository_dependencies_message: message += invalid_repository_dependencies_message status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. tool_util.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. tool_util.reset_tool_data_tables(trans.app)
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)) if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION: ok = os.path.basename( uploaded_file ) == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME else: ok = os.path.basename( uploaded_file) not in commit_util.UNDESIRABLE_FILES if ok: for file_path_item in relative_path.split('/'): if file_path_item in commit_util.UNDESIRABLE_DIRS: undesirable_dirs_removed += 1 ok = False break else: undesirable_files_removed += 1 if ok: uploaded_file_name = os.path.abspath( os.path.join(root, uploaded_file)) if os.path.split( uploaded_file_name )[-1] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem) shutil.move(tmp_filename, uploaded_file_name) elif os.path.split(uploaded_file_name)[ -1] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem) shutil.move(tmp_filename, uploaded_file_name) 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 commit_util.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)