Commit 985faf41 authored by Olivier Sallou's avatar Olivier Sallou
Browse files

New upstream version 3.0.15

parent 219928da

CHANGES.txt

+6 −0
Original line number Diff line number Diff line 
3.0.15:

  Add proc name in logs for waiting and result

3.0.14:

  Add env var BIOMAJ_HOST_DATA_DIR to use with *docker* process executor to specify data.dir location if different between host and container (if BIOMAJ_DATA_DIR not a subdirectory of BIOMAJ_DIR for example)

    If variable is not set, container wil mount data.dir between host and container,

    else will mount BIOMAJ_HOST_DATA_DIR:data.dir

3.0.13:

  Fix traefik prefix

3.0.12:

README.md

+2 −0
Original line number Diff line number Diff line 
# About



[![PyPI version](https://badge.fury.io/py/biomaj-process.svg)](https://badge.fury.io/py/biomaj-process)



Microservice to manage the process execution of biomaj.



A protobuf interface is available in biomaj_process/message/message_pb2.py to exchange messages between BioMAJ and the download service.

biomaj_process/process.py

+10 −7
Original line number Diff line number Diff line
@@ -224,9 +224,10 @@ class DockerProcess(Process): 
                    depends.append(value)

        # docker run with data.dir env as shared volume

        # forwarded env variables

        data_dir = self.bank_env['datadir'] + '/' + self.bank_env['dirversion']

        if 'BIOMAJ_DIR' in os.environ and os.environ['BIOMAJ_DIR'] and not os.environ['BIOMAJ_DIR'].startswith('local'):

            data_dir = os.environ['BIOMAJ_DIR'] + '/' + self.bank_env['dirversion']

        container_data_dir = self.bank_env['datadir'] + '/' + self.bank_env['dirversion']

        host_data_dir = container_data_dir

        if 'BIOMAJ_HOST_DATA_DIR' in os.environ and os.environ['BIOMAJ_HOST_DATA_DIR'] and not os.environ['BIOMAJ_HOST_DATA_DIR'].startswith('local'):

            host_data_dir = os.environ['BIOMAJ_HOST_DATA_DIR'] + '/' + self.bank_env['dirversion']



        depends_vol = ''

        for vol in depends:
@@ -236,13 +237,14 @@ class DockerProcess(Process): 
            cmd = '''uid={uid}

        gid={gid}

        {sudo} docker {docker_url} pull {container_id}

        {sudo} docker {docker_url}  run --rm -w {bank_dir} {depends_vol}  -v {data_dir}:{data_dir} {env} {container_id} \

        {sudo} docker {docker_url}  run --rm -w {bank_dir} {depends_vol}  -v {host_data_dir}:{container_data_dir} {env} {container_id} \

        bash -c "groupadd --gid {gid} {group_biomaj} && useradd --uid {uid} --gid {gid} {user_biomaj}; \

        {exe} {args}; \

        chown -R {uid}:{gid} {bank_dir}"'''.format(

                uid=os.getuid(),

                gid=os.getgid(),

                data_dir=data_dir,

                host_data_dir=host_data_dir,

                container_data_dir=container_data_dir,

                env=env,

                container_id=self.docker,

                group_biomaj='biomaj',
@@ -257,12 +259,13 @@ class DockerProcess(Process): 
        else:

            cmd = '''

        {sudo} docker {docker_url} pull {container_id}

        {sudo} docker {docker_url} run --rm -w {bank_dir} {depends_vol} -v {data_dir}:{data_dir} {env} {container_id} \

        {sudo} docker {docker_url} run --rm -w {bank_dir} {depends_vol} -v {host_data_dir}:{container_data_dir} {env} {container_id} \

        {exe} {args} \

        '''.format(

                uid=os.getuid(),

                gid=os.getgid(),

                data_dir=data_dir,

                host_data_dir=host_data_dir,

                container_data_dir=container_data_dir,

                env=env,

                container_id=self.docker,

                group_biomaj='biomaj',

biomaj_process/process_client.py

+3 −4
Original line number Diff line number Diff line
@@ -49,6 +49,7 @@ class ProcessServiceClient(object): 
        raise Exception('Failed to connect to the process proxy')



    def execute_process(self, biomaj_process):

        self.biomaj_process = biomaj_process

        if self.remote:

            self.channel.basic_publish(

                exchange='',
@@ -58,14 +59,12 @@ class ProcessServiceClient(object): 
                    # make message persistent

                    delivery_mode=2

                ))

        else:

            self.biomaj_process = biomaj_process



    def wait_for_process(self):

        over = False

        exitcode = -1

        info = None

        logging.info("Process:RemoteProcess:Waiting")

        logging.info("Process:RemoteProcess:Waiting:" + str(self.biomaj_process.process.name))

        errors = 0

        while not over:

            if errors >= 3:
@@ -89,7 +88,7 @@ class ProcessServiceClient(object): 
                over = True

                if result['exitcode'] > 0:

                    info = result['info']

                    self.logger.error('Process:RemoteProcess:Error:' + str(result['info']))

                    self.logger.error('Process:RemoteProcess:Error:' + str(self.biomaj_process.process.name) + ': ' + str(result['info']))

            else:

                time.sleep(10)

        return (exitcode, info)

setup.py

+1 −1
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@@ -21,7 +21,7 @@ config = { 
    'url': 'http://biomaj.genouest.org',

    'download_url': 'http://biomaj.genouest.org',

    'author_email': 'olivier.sallou@irisa.fr',

    'version': '3.0.13',

    'version': '3.0.15',

     'classifiers': [

        # How mature is this project? Common values are

        #   3 - Alpha