[med-svn] [Git][med-team/biomaj3-process][master] 3 commits: New upstream version 3.0.15
Olivier Sallou
gitlab at salsa.debian.org
Tue Nov 12 10:53:23 GMT 2019
Olivier Sallou pushed to branch master at Debian Med / biomaj3-process
Commits:
985faf41 by Olivier Sallou at 2019-11-12T10:32:00Z
New upstream version 3.0.15
- - - - -
2ac6bb5f by Olivier Sallou at 2019-11-12T10:32:00Z
Update upstream source from tag 'upstream/3.0.15'
Update to upstream version '3.0.15'
with Debian dir 7d24309f82429c3c7e52b8b3be0fc91fdd730e84
- - - - -
7fac5c6f by Olivier Sallou at 2019-11-12T10:32:28Z
new upstream 3.0.15
- - - - -
6 changed files:
- CHANGES.txt
- README.md
- biomaj_process/process.py
- biomaj_process/process_client.py
- debian/changelog
- setup.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,9 @@
+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
=====================================
@@ -1,5 +1,7 @@
# About
+[](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
=====================================
@@ -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
=====================================
@@ -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)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+biomaj3-process (3.0.15-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 12 Nov 2019 10:32:06 +0000
+
biomaj3-process (3.0.13-1) unstable; urgency=medium
* New upstream release
=====================================
setup.py
=====================================
@@ -21,7 +21,7 @@ config = {
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.0.13',
+ 'version': '3.0.15',
'classifiers': [
# How mature is this project? Common values are
# 3 - Alpha
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-process/compare/085f9f3c631ae0661f95004bba6a0b77e777492e...7fac5c6f01f2c4e886331e5943ad1debcb147ec7
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-process/compare/085f9f3c631ae0661f95004bba6a0b77e777492e...7fac5c6f01f2c4e886331e5943ad1debcb147ec7
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