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Source code for galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder

import logging
import os
import stat

log = logging.getLogger(__name__)

[docs]class EnvFileBuilder:
[docs] def __init__(self, install_dir): self.install_dir = install_dir self.return_code = 0
[docs] def append_line(self, make_executable=True, **kwd): env_var_dict = dict(**kwd) env_entry, env_file = self.create_or_update_env_shell_file(self.install_dir, env_var_dict) return_code = self.file_append(env_entry, env_file, make_executable=make_executable) self.return_code = self.return_code or return_code return self.return_code
[docs] @staticmethod def create_or_update_env_shell_file(install_dir, env_var_dict): env_var_action = env_var_dict['action'] env_var_value = env_var_dict['value'] if env_var_action in ['prepend_to', 'set_to', 'append_to']: env_var_name = env_var_dict['name'] if env_var_action == 'prepend_to': changed_value = f'{env_var_value}:${env_var_name}' elif env_var_action == 'set_to': changed_value = '%s' % env_var_value elif env_var_action == 'append_to': changed_value = f'${env_var_name}:{env_var_value}' line = f"{env_var_name}={changed_value}; export {env_var_name}" elif env_var_action == "source": line = f"if [ -f {env_var_value} ] ; then . {env_var_value} ; fi" else: raise Exception("Unknown shell file action %s" % env_var_action) env_shell_file_path = os.path.join(install_dir, 'env.sh') return line, env_shell_file_path
[docs] def file_append(self, text, file_path, make_executable=True): """ Append a line to a file unless the line already exists in the file. This method creates the file if it doesn't exist. If make_executable is True, the permissions on the file are set to executable by the owner. """ file_dir = os.path.dirname(file_path) if not os.path.exists(file_dir): try: os.makedirs(file_dir) except Exception as e: log.exception(str(e)) return 1 if os.path.exists(file_path): try: new_env_file_contents = [] env_file_contents = open(file_path).readlines() # Clean out blank lines from the env.sh file. for line in env_file_contents: line = line.rstrip() if line: new_env_file_contents.append(line) env_file_contents = new_env_file_contents except Exception as e: log.exception(str(e)) return 1 else: env_file_handle = open(file_path, 'w') env_file_handle.close() env_file_contents = [] if make_executable: # Explicitly set the file's executable bits. try: os.chmod(file_path, os.stat(file_path).st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH) except Exception as e: log.exception(str(e)) return 1 # Convert the received text to a list, in order to support adding one or more lines to the file. if isinstance(text, str): text = [text] for line in text: line = line.rstrip() if line and line not in env_file_contents: env_file_contents.append(line) try: open(file_path, 'w').write('\n'.join(env_file_contents)) except Exception as e: log.exception(str(e)) return 1 return 0
[docs] def handle_action_shell_file_paths(self, action_dict): shell_file_paths = action_dict.get('action_shell_file_paths', []) for shell_file_path in shell_file_paths: self.append_line(action="source", value=shell_file_path)