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

import logging
import os
import stat

from six import string_types

log = logging.getLogger(__name__)


[docs]class EnvFileBuilder(object):

[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 = '%s:$%s' % (env_var_value, env_var_name)
            elif env_var_action == 'set_to':
                changed_value = '%s' % env_var_value
            elif env_var_action == 'append_to':
                changed_value = '$%s:%s' % (env_var_name, env_var_value)
            line = "%s=%s; export %s" % (env_var_name, changed_value, env_var_name)
        elif env_var_action == "source":
            line = "if [ -f %s ] ; then . %s ; fi" % (env_var_value, env_var_value)
        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, 'r').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, int('111', base=8) | os.stat(file_path)[stat.ST_MODE])
            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, string_types):
            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)