Comments (3)
dnil
commented on June 13, 2024
1
That looks very familiar! 😅
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northwestwitch
commented on June 13, 2024
1
That looks very familiar! 😅
I guess this service and the beacon were not restarted in a while.. 😄
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northwestwitch
commented on June 13, 2024
This was actually my fault 😌 : when starting the service I typed the name wrong. Now I've started it and it performs fine on stage:
[hiseq.clinical@cg-vm1 ~]$ podman logs cf863fd468ee
[2023-11-14 09:51:27 +0100] [2] [DEBUG] Current configuration:
config: ./gunicorn.conf.py
wsgi_app: None
bind: ['0.0.0.0:8000']
backlog: 2048
workers: 4
worker_class: sync
threads: 4
worker_connections: 1000
max_requests: 0
max_requests_jitter: 0
timeout: 400
graceful_timeout: 30
keepalive: 2
limit_request_line: 4094
limit_request_fields: 100
limit_request_field_size: 8190
reload: False
reload_engine: auto
reload_extra_files: []
spew: False
check_config: False
print_config: False
preload_app: False
sendfile: None
reuse_port: False
chdir: /home/worker/app
daemon: False
raw_env: []
pidfile: None
worker_tmp_dir: None
user: 1000
group: 1000
umask: 0
initgroups: False
tmp_upload_dir: None
secure_scheme_headers: {'X-FORWARDED-PROTOCOL': 'ssl', 'X-FORWARDED-PROTO': 'https', 'X-FORWARDED-SSL': 'on'}
forwarded_allow_ips: ['10.0.2.100', '127.0.0.1']
accesslog: -
disable_redirect_access_to_syslog: False
access_log_format: %(h)s %(l)s %(u)s %(t)s "%(r)s" %(s)s %(b)s "%(f)s" "%(a)s"
errorlog: -
loglevel: debug
capture_output: False
logger_class: gunicorn.glogging.Logger
logconfig: None
logconfig_dict: {}
logconfig_json: None
syslog_addr: udp://localhost:514
syslog: True
syslog_prefix: None
syslog_facility: user
enable_stdio_inheritance: False
statsd_host: None
dogstatsd_tags:
statsd_prefix:
proc_name: None
default_proc_name: patientMatcher.server.auto:app
pythonpath: None
paste: None
on_starting: <function OnStarting.on_starting at 0x7f84b07fd8b0>
on_reload: <function OnReload.on_reload at 0x7f84b07fd9d0>
when_ready: <function WhenReady.when_ready at 0x7f84b07fdaf0>
pre_fork: <function Prefork.pre_fork at 0x7f84b07fdc10>
post_fork: <function Postfork.post_fork at 0x7f84b07fdd30>
post_worker_init: <function PostWorkerInit.post_worker_init at 0x7f84b07fde50>
worker_int: <function WorkerInt.worker_int at 0x7f84b07fdf70>
worker_abort: <function WorkerAbort.worker_abort at 0x7f84b08100d0>
pre_exec: <function PreExec.pre_exec at 0x7f84b08101f0>
pre_request: <function PreRequest.pre_request at 0x7f84b0810310>
post_request: <function PostRequest.post_request at 0x7f84b08103a0>
child_exit: <function ChildExit.child_exit at 0x7f84b08104c0>
worker_exit: <function WorkerExit.worker_exit at 0x7f84b08105e0>
nworkers_changed: <function NumWorkersChanged.nworkers_changed at 0x7f84b0810700>
on_exit: <function OnExit.on_exit at 0x7f84b0810820>
ssl_context: <function NewSSLContext.ssl_context at 0x7f84b0810940>
proxy_protocol: True
proxy_allow_ips: ['127.0.0.1']
keyfile: None
certfile: None
ssl_version: 2
cert_reqs: 0
ca_certs: None
suppress_ragged_eofs: True
do_handshake_on_connect: False
ciphers: None
raw_paste_global_conf: []
strip_header_spaces: False
[2023-11-14 09:51:27 +0100] [2] [INFO] Starting gunicorn 21.2.0
[2023-11-14 09:51:27 +0100] [2] [DEBUG] Arbiter booted
[2023-11-14 09:51:27 +0100] [2] [INFO] Listening at: http://0.0.0.0:8000 (2)
[2023-11-14 09:51:27 +0100] [2] [INFO] Using worker: gthread
[2023-11-14 09:51:27 +0100] [4] [INFO] Booting worker with pid: 4
[2023-11-14 09:51:27 +0100] [5] [INFO] Booting worker with pid: 5
[2023-11-14 09:51:27 +0100] [6] [INFO] Booting worker with pid: 6
[2023-11-14 09:51:27 +0100] [7] [INFO] Booting worker with pid: 7
[2023-11-14 09:51:27 +0100] [2] [DEBUG] 4 workers
PMATCHER_CONFIG env variable not found, configuring from instance file + env vars.
PMATCHER_CONFIG env variable not found, configuring from instance file + env vars.
PMATCHER_CONFIG env variable not found, configuring from instance file + env vars.
PMATCHER_CONFIG env variable not found, configuring from instance file + env vars.
2023-11-14 09:51:28 cf863fd468ee patientMatcher.server[5] INFO Connecting to database 'pmatcher-stage' on Database(MongoClient(host=['cg-mongo-stage.scilifelab.se:27030'], document_class=dict, tz_aware=False, connect=True, serverselectiontimeoutms=30000), 'pmatcher-stage')
2023-11-14 09:51:28 cf863fd468ee patientMatcher.server[6] INFO Connecting to database 'pmatcher-stage' on Database(MongoClient(host=['cg-mongo-stage.scilifelab.se:27030'], document_class=dict, tz_aware=False, connect=True, serverselectiontimeoutms=30000), 'pmatcher-stage')
2023-11-14 09:51:28 cf863fd468ee patientMatcher.server[7] INFO Connecting to database 'pmatcher-stage' on Database(MongoClient(host=['cg-mongo-stage.scilifelab.se:27030'], document_class=dict, tz_aware=False, connect=True, serverselectiontimeoutms=30000), 'pmatcher-stage')
2023-11-14 09:51:28 cf863fd468ee patientMatcher.server[4] INFO Connecting to database 'pmatcher-stage' on Database(MongoClient(host=['cg-mongo-stage.scilifelab.se:27030'], document_class=dict, tz_aware=False, connect=True, serverselectiontimeoutms=30000), 'pmatcher-stage')
2023-11-14 09:51:28 cf863fd468ee patientMatcher.utils.hpo[5] INFO Parsed 17272 HPO terms into HPO nodes from resource file
2023-11-14 09:51:28 cf863fd468ee patientMatcher.utils.hpo[4] INFO Parsed 17272 HPO terms into HPO nodes from resource file
2023-11-14 09:51:28 cf863fd468ee patientMatcher.utils.hpo[7] INFO Parsed 17272 HPO terms into HPO nodes from resource file
2023-11-14 09:51:28 cf863fd468ee patientMatcher.utils.hpo[6] INFO Parsed 17272 HPO terms into HPO nodes from resource file
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.disease[6] INFO Parsed 22164 disease/phenotypes from resource file
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.disease[7] INFO Parsed 22164 disease/phenotypes from resource file
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[6] INFO Initializing the HPO information content
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[7] INFO Initializing the HPO information content
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.disease[5] INFO Parsed 22164 disease/phenotypes from resource file
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[5] INFO Initializing the HPO information content
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.disease[4] INFO Parsed 22164 disease/phenotypes from resource file
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[4] INFO Initializing the HPO information content
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[6] INFO Total term frequency mass: 1.0000000000000415
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[7] INFO Total term frequency mass: 1.0000000000000415
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[4] INFO Total term frequency mass: 1.0000000000000415
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[5] INFO Total term frequency mass: 1.0000000000000415
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[7] INFO IC calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[6] INFO IC calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[4] INFO IC calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[5] INFO IC calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[7] INFO Link strength calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[6] INFO Link strength calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[4] INFO Link strength calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[5] INFO Link strength calculated for 11743/17272 terms
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[7] INFO HPO information content initialized
2023-11-14 09:51:30 cf863fd468ee patientMatcher.server[7] DEBUG Configuring email error logging to notify server admins:['[email protected]']
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[6] INFO HPO information content initialized
2023-11-14 09:51:30 cf863fd468ee patientMatcher.server[6] DEBUG Configuring email error logging to notify server admins:['[email protected]']
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[4] INFO HPO information content initialized
2023-11-14 09:51:30 cf863fd468ee patientMatcher.server[4] DEBUG Configuring email error logging to notify server admins:['[email protected]']
2023-11-14 09:51:30 cf863fd468ee patientMatcher.utils.hpo[5] INFO HPO information content initialized
2023-11-14 09:51:30 cf863fd468ee patientMatcher.server[5] DEBUG Configuring email error logging to notify server admins:['[email protected]']
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Related Issues (20)
- Docs link doesn't work HOT 1
- Add this repo to Sonarcloud HOT 3
- Phenotype annotations link is not working any more
- Parsed 0 disease/phenotypes from resource file
- Deprecated Ubuntu version 18.04 in GitHub actions
- Can't download phenotype_annotation.tab HOT 2
- Do not start the server if resource files can't be parsed properly
- Broken badge on readme page
- Display connected details on landing page HOT 2
- Newest resource file not correctly parsed HOT 1
- Gunicorn workers not loading HOT 1
- Modify node documents to include link to institute
- How to use docker image to run commands for interacting with the database HOT 1
- Create a simple command to view connected nodes and available clients
- Option to rename a connected node to something else
- unfreeze PyMongo HOT 1
- Investigate why version >=4.5 is returning matching info with isodates instead of timestamps
- remove many info logs
- Build & Push to Docker Hub failing
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