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Source code for galaxy.jobs.runners.util.env

RAW_VALUE_BY_DEFAULT = False


[docs]def env_to_statement(env): ''' Return the abstraction description of an environment variable definition into a statement for shell script. >>> env_to_statement(dict(name='X', value='Y')) 'X="Y"; export X' >>> env_to_statement(dict(name='X', value='Y', raw=True)) 'X=Y; export X' >>> env_to_statement(dict(name='X', value='"A","B","C"')) 'X="\\\\"A\\\\",\\\\"B\\\\",\\\\"C\\\\""; export X' >>> env_to_statement(dict(file="Y")) '. "Y"' >>> env_to_statement(dict(file="'RAW $FILE'", raw=True)) ". 'RAW $FILE'" >>> # Source file takes precedence >>> env_to_statement(dict(name='X', value='"A","B","C"', file="S")) '. "S"' >>> env_to_statement(dict(execute="module load java/1.5.1")) 'module load java/1.5.1' ''' source_file = env.get('file', None) if source_file: return '. %s' % __escape(source_file, env) execute = env.get('execute', None) if execute: return execute name = env['name'] value = __escape(env['value'], env) return f'{name}={value}; export {name}'
def __escape(value, env): raw = env.get('raw', RAW_VALUE_BY_DEFAULT) if not raw: value = '"' + value.replace('"', '\\"') + '"' return value