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Fix: default db for packing remote configs#332

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rugeli merged 1 commit intostaging/cellpack-serverfrom
fix/default-db
May 7, 2025
Merged

Fix: default db for packing remote configs#332
rugeli merged 1 commit intostaging/cellpack-serverfrom
fix/default-db

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@rugeli
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@rugeli rugeli commented May 1, 2025

Problem

What is the problem this work solves, including
we need to set the default db to staging when running batch jobs

Solution

What I/we did to solve this problem

  • similar to how we did to recipe, added default db to config file packings
    with @alli

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)

Steps to Verify:

  1. upload a config to firebase: upload -c [CONFIG-LOCAL-PATH] to staging
  2. pack a firebase recipe with a firebase config files: pack -r [RECIPE-FIREBASE-PATH] -c [CONFIG-FIREBASE-PATH] -d
  3. verify if it uses staging db

@rugeli rugeli requested a review from ascibisz May 1, 2025 21:45
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github-actions bot commented May 1, 2025

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name Encapsulating radius Average number packed
ext_A 25 236.0

Packing image

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

@rugeli
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rugeli commented May 1, 2025

@ascibisz Alli you may see the credential error again raise S3UploadFailedError( boto3.exceptions.S3UploadFailedError: Failed to upload out/one_sphere/jitter/results_one_sphere_default-run_1.0.0_seed_0.simularium to cellpack-results/simularium/results_one_sphere_default-run_1.0.0_seed_0.simularium: An error occurred (ExpiredToken) when calling the PutObject operation: The provided token has expired. WARNING: All log messages before absl::InitializeLog() is called are written to STDERR E0000 00:00:1746136053.744972 25009560 init.cc:232] grpc_wait_for_shutdown_with_timeout() timed out.

I did the unsetting steps and run aws sts assume-role --role-arn arn:aws:iam::771753870375:role/batch --role-session-name Test. It went through.

@rugeli rugeli changed the base branch from main to staging/cellpack-server May 5, 2025 17:43
@rugeli rugeli merged commit 3ee623f into staging/cellpack-server May 7, 2025
7 checks passed
@rugeli rugeli deleted the fix/default-db branch May 7, 2025 22:44
ascibisz added a commit that referenced this pull request Jun 17, 2025
* Feature/aws cli in docker (#280)

* Add basic Dockerfile and docker-entrypoint file

* draft aws cli inside of docker container

* access aws s3 with saved cred

* update readme

* update docker commands

* update readme

* update readme

---------

Co-authored-by: ascibisz <alli.scibisz@alleninstitute.org>

* Feature/pass recipe to docker (#285)

* draft aws cli inside of docker container

* access aws s3 with saved cred

* update readme

* update docker commands

* update readme

* update readme

* add parameter for when we're using docker to default to using the staging firebase db

* read recipe and config in from docker run params

* use dockerignore file to prevent bloat in docker image

* add `batch_job_id` to result metadata (#295)

* retrieve job id

* formatting

* add a bucket for batch jobs

* formatting

* remove print statement and add comments

---------

Co-authored-by: Ruge Li <rugeli0605@gmail.com>
Co-authored-by: Ruge Li <91452427+rugeli@users.noreply.github.com>

* pull changes for firebase configs handling

* add docker option to config (#332)

* Bug Fix: keep grid_file_path when loading recipe from firebase (#334)

* keep grid_file_path when loading recipe from firebase

* only add grid_file_path if it's in the firebase recipe

* Feature/docker file for ecs (#336)

* Add Dockerfile.ecs for our ECS image and rename old Dockerfile to Dockerfile.batch

* add intentional error handling for if packing fails

* change messaging from /hello endpoint

* send response json using camelCase

* add healthcheck endpoint and use port 80 instead of 8443 for load balancer requirements

* add way for running ECS docker image locally without trying to publish results to cellpack-demo/

---------

Co-authored-by: ascibisz <alli.scibisz@alleninstitute.org>
Co-authored-by: Alli <111383930+ascibisz@users.noreply.github.com>
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2 participants