caltech-curation-services

aCeDB

run aCeDB using docker on your local computer (works on Linux only)

You can specify the location of a local directory that will be mounted from your computer to the aCeDB docker container by modifying the following variables in the .env file:

CALTECH_CURATION_FILES_INTERNAL_PATH= CALTECH_CURATION_FILES_EXTERNAL_PATH=

Once these variables are set, start the docker container with the following command:

$ make start-acedb

Setup

Grafana

Create grafana/grafana.ini file and modify it with custom config. For example, modify the smtp section to be able to send out email alert notifications.

grafana/grafana_original.ini contains the original default settings.

Email (AWS SES)

All outgoing mail - form confirmations, curator notifications, cron job error reports, the webinar and community curation mailings - goes through Jex::mailer in curation/scripts/perl_modules/Jex.pm, which talks to AWS SES over SMTP.

Set these two in the .env file that ENV_FILE_PATH points at, using the SES SMTP credentials from the textpresso AWS account:

EMAIL_SMTP_USER=<SES smtp username>
EMAIL_PASSWD=<SES smtp password>

EMAIL_SMTP_USER is an opaque SES credential, not an address, so the visible sender comes from EMAIL_FROM instead. EMAIL_HOST, EMAIL_PORT and EMAIL_FROM are optional; when empty, Jex.pm uses email-smtp.us-east-1.amazonaws.com, port 465 and WormBase Curation <no-reply@caltech-curation.textpressolab.com>. EMAIL_FROM has to be an SES-verified identity - textpressolab.com is verified as a parent domain, so any subdomain of it works without further DNS setup.

Because that From is a no-reply@ address, mailer always sets a Reply-To, and by default it is every address the message went to - the form submitter plus the curators in To and Cc - so a submitter hitting reply reaches all the curators on the thread, which is how these forms have always been read. Leaving the Reply-To off is not an option: the old From was outreach@wormbase.org, a mailbox somebody watches, so a plain reply used to arrive somewhere. With a no-reply From and no Reply-To it would go nowhere. Set EMAIL_REPLY_TO only to pin every reply to one fixed mailbox instead; an individual call can also pass its own, as the community curation tracker and mass mailer do with curation@wormbase.org.

Jex.pm is copied into the image by curation/Dockerfile, it is not bind mounted, so a change to the mailer needs a rebuild rather than a restart:

docker compose up -d --build curation

To check the credentials, send a test message through the same code path the forms use:

make test-mailer TO=you@example.org                        # on the server
make test-mailer TO=you@example.org COMPOSE_ARGS='--env-file .env.local'   # on a laptop

make test-mailer uses run --rm --no-deps, so it works whether or not the curation service is up. The equivalent by hand, and the way to reproduce the shape a form actually sends - submitter in To, curators in Cc, reply reaching all of them. -e, -c and -r each take a list: repeat the flag, pass one comma separated value, or mix the two.

docker compose run --rm --no-deps \
  curation /usr/lib/scripts/test_mailer.pl \
    -e submitter@example.org \
    -c cgrove@caltech.edu -c garys@caltech.edu -H

test_mailer.pl -h lists the rest. TO= on the make target also accepts a comma separated list.

To try credentials without editing the env file first, pass them straight in. Dotenv does not overwrite variables that are already in the environment, so these win over the file:

docker compose exec -e EMAIL_SMTP_USER -e EMAIL_PASSWD \
  curation /usr/lib/scripts/test_mailer.pl -e you@example.org

Do not add the EMAIL_* variables to the curation service's environment: block in docker-compose.yml. Because Dotenv yields to whatever is already set, an empty value there would shadow the real one in the env file.

Every send is logged to the apache or cron log with a mailer: prefix, whether it succeeded or failed, so an outage is visible instead of silent.