1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/4d554f1875eb/ Changeset: 4d554f1875eb User: jmchilton Date: 2014-04-28 16:53:07 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #378)

Allow specification of environment variables for job destinations Affected #: 9 files

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -74,6 +74,23 @@ <param id="Resource_List">walltime=72:00:00</param></destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/> + <destination id="java_cluster" runner="drmaa"> + <!-- set arbitrary environment variables at runtime - like metrics + doesn't yet work with local or CLI runners. But should work with + DRMAA/SLURM, PBS, Condor, and LWR. General dependencies for tools + should be configured via tool_depednency_dir and package options + and these options should be reserved for defining cluster specific + options. + --> + <env id="_JAVA_OPTIONS">-Xmx=6GB</env> + <env id="ANOTHER_OPTION" raw="true">'5'</env><!-- raw disables auto quoting --> + <env file="/mnt/java_cluster/environment_setup.sh" /><!-- will be sourced --> + <env exec="module load javastuff/2.10" /><!-- will be sourced --> + <!-- files to source and exec statements will be handled on remote + clusters. These don't need to be available on the Galaxy server + itself. + --> + </destination><destination id="real_user_cluster" runner="drmaa"><!-- TODO: The real user options should maybe not be considered runner params. --><param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -179,6 +179,7 @@ job_metrics.set_destination_conf_element( id, metrics_elements[ 0 ] ) job_destination = JobDestination(**dict(destination.items())) job_destination['params'] = self.__get_params(destination) + job_destination['env'] = self.__get_envs(destination) self.destinations[id] = (job_destination,) if job_destination.tags is not None: for tag in job_destination.tags: @@ -350,6 +351,25 @@ rval[param.get('id')] = param.text return rval

+ def __get_envs(self, parent): + """Parses any child <env> tags in to a dictionary suitable for persistence. + + :param parent: Parent element in which to find child <param> tags. + :type parent: ``xml.etree.ElementTree.Element`` + + :returns: dict + """ + rval = [] + for param in parent.findall('env'): + rval.append( dict( + name=param.get('id'), + file=param.get('file'), + execute=param.get('exec'), + value=param.text, + raw=util.asbool(param.get('raw', 'false')) + ) ) + return rval + @property def default_job_tool_configuration(self): """The default JobToolConfiguration, used if a tool does not have an explicit defintion in the configuration. It consists of a reference to the default handler and default destination.

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -17,6 +17,7 @@ from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size from galaxy.util import in_directory from galaxy.jobs.runners.util.job_script import job_script +from galaxy.jobs.runners.util.env import env_to_statement

log = logging.getLogger( __name__ )

@@ -253,10 +254,17 @@ def get_job_file(self, job_wrapper, **kwds): job_metrics = job_wrapper.app.job_metrics job_instrumenter = job_metrics.job_instrumenters[ job_wrapper.job_destination.id ] + + env_setup_commands = kwds.get( 'env_setup_commands', [] ) + env_setup_commands.append( job_wrapper.get_env_setup_clause() or '' ) + destination = job_wrapper.job_destination or {} + envs = destination.get( "env", [] ) + for env in envs: + env_setup_commands.append( env_to_statement( env ) ) options = dict( job_instrumenter=job_instrumenter, galaxy_lib=job_wrapper.galaxy_lib_dir, - env_setup_commands=job_wrapper.get_env_setup_clause(), + env_setup_commands=env_setup_commands, working_directory=os.path.abspath( job_wrapper.working_directory ), command=job_wrapper.runner_command_line, )

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -134,6 +134,7 @@ tool=job_wrapper.tool, config_files=job_wrapper.extra_filenames, requirements=requirements, + env=client.env, rewrite_paths=rewrite_paths, arbitrary_files=unstructured_path_rewrites, ) @@ -222,14 +223,15 @@ for key, value in params.iteritems(): if value: params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) - return self.get_client( params, job_id ) + env = getattr( job_wrapper.job_destination, "env", [] ) + return self.get_client( params, job_id, env )

def get_client_from_state(self, job_state): job_destination_params = job_state.job_destination.params job_id = job_state.job_id return self.get_client( job_destination_params, job_id )

- def get_client( self, job_destination_params, job_id ): + def get_client( self, job_destination_params, job_id, env=[] ): # Cannot use url_for outside of web thread. #files_endpoint = url_for( controller="job_files", job_id=encoded_job_id )

@@ -243,6 +245,7 @@ get_client_kwds = dict( job_id=str( job_id ), files_endpoint=files_endpoint, + env=env ) return self.client_manager.get_client( job_destination_params, **get_client_kwds )

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -41,6 +41,7 @@ job_directory = None self.env = destination_params.get( "env", [] ) self.files_endpoint = destination_params.get("files_endpoint", None) + self.env = destination_params.get("env", []) self.job_directory = job_directory

self.default_file_action = self.destination_params.get("default_file_action", "transfer")

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -296,7 +296,7 @@ else: stage_commands = ''

- env_setup_commands = '%s\n%s' % (stage_commands, job_wrapper.get_env_setup_clause()) + env_setup_commands = [ stage_commands ] script = self.get_job_file(job_wrapper, exit_code_path=ecfile, env_setup_commands=env_setup_commands) job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id) fh = file(job_file, "w")

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/runners/util/env.py --- /dev/null +++ b/lib/galaxy/jobs/runners/util/env.py @@ -0,0 +1,40 @@ + +RAW_VALUE_BY_DEFAULT = False + + +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 '%s=%s; export %s' % (name, value, name) + + +def __escape(value, env): + raw = env.get('raw', RAW_VALUE_BY_DEFAULT) + if not raw: + value = '"' + value.replace('"', '\"') + '"' + return value

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee lib/galaxy/jobs/runners/util/job_script/__init__.py --- a/lib/galaxy/jobs/runners/util/job_script/__init__.py +++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py @@ -16,7 +16,7 @@ OPTIONAL_TEMPLATE_PARAMS = { 'galaxy_lib': None, 'headers': '', - 'env_setup_commands': '', + 'env_setup_commands': [], 'slots_statement': SLOTS_STATEMENT_CLUSTER_DEFAULT, 'instrument_pre_commands': '', 'instrument_post_commands': '', @@ -51,13 +51,15 @@ raise Exception("Failed to create job_script, a required parameter is missing.") job_instrumenter = kwds.get("job_instrumenter", None) if job_instrumenter: - del kwds[ "job_instrumenter" ] + del kwds["job_instrumenter"] working_directory = kwds["working_directory"] kwds["instrument_pre_commands"] = job_instrumenter.pre_execute_commands(working_directory) or '' kwds["instrument_post_commands"] = job_instrumenter.post_execute_commands(working_directory) or ''

template_params = OPTIONAL_TEMPLATE_PARAMS.copy() template_params.update(**kwds) + env_setup_commands_str = "\n".join(template_params["env_setup_commands"]) + template_params["env_setup_commands"] = env_setup_commands_str if not isinstance(template, Template): template = Template(template) return template.safe_substitute(template_params)

diff -r b0067c6e06274e80157496e034c9c7d0a083ffb6 -r 4d554f1875eb9e1dfc5fc156dbae86c79c2efbee test/unit/jobs/test_job_configuration.py --- a/test/unit/jobs/test_job_configuration.py +++ b/test/unit/jobs/test_job_configuration.py @@ -111,6 +111,20 @@ assert limits.concurrent_jobs[ "longjobs" ] == 1 assert limits.walltime_delta == datetime.timedelta( 0, 0, 0, 0, 0, 24 )

+ def test_env_parsing( self ): + self.__with_advanced_config() + env_dest = self.job_config.destinations[ "java_cluster" ][ 0 ] + assert len( env_dest.env ) == 4, len( env_dest.env ) + assert env_dest.env[ 0 ][ "name" ] == "_JAVA_OPTIONS" + assert env_dest.env[ 0 ][ "value" ] == '-Xmx=6GB' + + assert env_dest.env[ 1 ][ "name" ] == "ANOTHER_OPTION" + assert env_dest.env[ 1 ][ "raw" ] is True + + assert env_dest.env[ 2 ][ "file" ] == "/mnt/java_cluster/environment_setup.sh" + + assert env_dest.env[ 3 ][ "execute" ] == "module load javastuff/2.10" + # TODO: Add job metrics parsing test.

@property

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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