microbiomedata / nmdc-edge

Web-based interface to the NMDC EDGE platform
https://nmdc-edge.org
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Store Mongo configuration file in Git repository (Jetstream2) #233

Open eecavanna opened 1 week ago

eecavanna commented 1 week ago

Background

@mflynn-lanl created a Mongo configuration file named mongod.conf.

$ docker compose exec mongo bash
root@65279d9b27dc:~# pwd
/data/db
root@65279d9b27dc:~# ls -l | grep conf
-rw-r--r-- 1 root    root       462 Jul  3 18:09 mongod.conf
root@65279d9b27dc:~# cat mongod.conf

Here's what it contains (as of July 4, 2024):

# mongod.conf

# for documentation of all options, see:
#   http://docs.mongodb.org/manual/reference/configuration-options/

# Where and how to store data.
storage:
  dbPath: /data/db
#  engine:
#  wiredTiger:

# where to write logging data.
systemLog:
  destination: file
  logAppend: true
  path: /data/db/log/mongod.log

# network interfaces
net:
  port: 27017
  bindIp: 0.0.0.0

# how the process runs
processManagement:
  timeZoneInfo: /usr/share/zoneinfo

Task

eecavanna commented 1 week ago

A different one of my action items from this week's Jetstream2 squad meeting was to update the docker-compose.prod.yml file (currently in the docs folder in this repo) so that the mongo service has a custom entrypoint that runs mongod with the --config CLI option (whose value is the path to this config file) and also the --setParameter CLI option (whose value is: "logComponentVerbosity={query: {verbosity: 2}}").

In other words, define the entrypoint to be:

[
  "mongod",
  "--config",
  "/data/db/mongod.conf",
  "--setParameter",
  "logComponentVerbosity={query: {verbosity: 2}}"
]

For now, I am going to document that task here in this issue comment instead of creating a separate Issue. Rationale:

ssarrafan commented 2 days ago

I don't see any status on the sprint or Jetstream squad board. What's the status of this issue? Is it still active? @eecavanna @mflynn-lanl

eecavanna commented 2 days ago

I created the issue, but never assigned a status to it (or started working on it). I will move it to the next sprint (I do plan to either do it—or close it—next sprint).