Feature/grip updates

[matthewpeterkort]

Adds gecko service for config wrangling. See https://github.com/ACED-IDP/gecko
Swaps mongo driver for grip grids driver, thus removing mongodb service.
Re configures ETL routing from /graphql to /writer so that /graphql can be used for grip graphql reader

nginx.ingress.kubernetes.io/proxy-body-size: 10240m
needs to be added to ingress to allow for larger body sizes.

this should be added to the annotations section with kubectl edit ingress revproxy-dev -n default

[quinnwai]

If we're planning to do a release using this gen3-helm PR, can we move the Kafka work to another branch? If I recall correctly, the Kafka work was a proof of concept anyways.

[lbeckman314]

Testing Steps (Creating Local K8s Cluster):

• Setting up Kind
• Kubernetes in Docker Setup Local deployment

1. Start Docker Desktop ✅

➜ open -a Docker

2. Create Kind Cluster ✅

kind-config.yaml

kind: Cluster
apiVersion: kind.x-k8s.io/v1alpha4
name:  kind-multi-node
networking:
  ipFamily: ipv4
  apiServerAddress: 127.0.0.1
nodes:
  - role: control-plane
    kubeadmConfigPatches:
      - |
        kind: InitConfiguration
        nodeRegistration:
          kubeletExtraArgs:
            node-labels: "ingress-ready=true"
    extraPortMappings:
      - containerPort: 80
        hostPort: 80
        protocol: TCP
      - containerPort: 443
        hostPort: 443
        protocol: TCP

kind create cluster --config kind-config.yaml

3. Create Ingress NGINX Controller ✅

kubectl apply --filename https://raw.githubusercontent.com/kubernetes/ingress-nginx/master/deploy/static/provider/kind/deploy.yaml

kubectl wait --namespace ingress-nginx \
  --for=condition=ready pod \
  --selector=app.kubernetes.io/component=controller \
  --timeout=90s

4. Update /etc/hosts ✅

Added to /etc/hosts:

127.0.0.1 calypr.ohsu.edu

5. Update Makefile ✅

# Update Makefile (replace 'rancher-desktop' with 'kind-kind-multi-node')
➜ sed -i '' 's/rancher-desktop/kind-kind-multi-node/g' Makefile

➜ make clean

[lbeckman314]

Note

Thanks @matthewpeterkort for unblocking the local SSL issue that allowed the local testing to continue!

Caution

Only a basic "Hello, World!" file was tested for upload and download (no rich metadata)

Warning

These steps were run with OHSU's fork of gen3-client to avoid the the mismatch issue between a file's uploaded path and it's GUID in Indexd

Overview

• Expected services up and running on local deployment (with minor image tag change above) ✅
• Data upload not yet tested (blocked by SSL issue with local K8s cluster) ⚠️

Testing Steps (Gecko + GRIP/GRIDS)

1. Update Secrets ✅

➜ scp -r <cbds-prod>:/cbds/gen3-helm/Secrets ./Secrets-local

➜ ln -s Secrets-local Secrets

# Enable Gecko Service
➜ echo "gecko:\n  enabled: true" >> Secrets/values.yaml

2. Update Dependencies ✅

➜ gh pr checkout 78
branch 'feature/grip-updates' set up to track 'origin/feature/grip-updates'.
Switched to a new branch 'feature/grip-updates'

➜ helm dependency build helm/gen3

➜ make update

3. Deploy ✅

➜ make local
Switched to context "kind-kind-multi-node".
Deploying local
...
NAMESPACE: default
STATUS: deployed
REVISION: 1

4. Verify calypr.ohsu.edu resolves to localhost ✅

➜ ping calypr.ohsu.edu
PING calypr.ohsu.edu (127.0.0.1): 56 data bytes
64 bytes from 127.0.0.1: icmp_seq=0 ttl=64 time=0.066 ms
...

5. Wait for Pods to be ready ✅

Wait ~20 Minutes from fresh install (mainly waiting for all images to be pulled)...

6. Verify Gecko Service ⚠️

Adds gecko service for config wrangling. See https://github.com/ACED-IDP/gecko

➜ kubectl get deployment/gecko-deployment
NAME               READY   UP-TO-DATE   AVAILABLE
gecko-deployment   0/1     1            0

➜ kubectl logs deployment/gecko-deployment
Failed to connect to database: dial tcp [::1]:5432: connect: connection refused ❌ 

Updating the image tag to latest resolves the Database Connection issue:

➜ kubectl delete jobs local-gecko-db-init

➜ make local

➜ kubectl get deployment/gecko-deployment
NAME               READY   UP-TO-DATE   AVAILABLE
gecko-deployment   1/1     1            1 ✅ 

➜ kubectl logs deployment/gecko-deployment
gecko serving at :80
server.go:201: INFO: Health check passed ✅ 

7. Verify GRIP + GRIDS Service ✅

Swaps mongo driver for grip grids driver, thus removing mongodb service.

➜ kubectl get deployment/grip-deployment
NAME              READY   UP-TO-DATE   AVAILABLE
grip-deployment   1/1     1            1

➜ kubectl logs deployment/grip-deployment
{
  "data": 200,
  "graph": "",
  "level": "info",
  "msg": "[200] healthy _status",
  "status": 200,
}

8. Verify ETL Routing (/writer) ✅

Re configures ETL routing from /graphql to /writer so that /graphql can be used for grip graphql reader

➜ kubectl port-forward svc/grip-service 8201:8201
Forwarding from 127.0.0.1:8201 -> 8201
Forwarding from [::1]:8201 -> 8201

# Writer Endpoint
➜ curl localhost:8201/writer/
{
  "data": null,
  "message": " Not Found",
  "status": "404"
}

# GraphQL Endpoint
➜ curl localhost:8201/graphql/
<!DOCTYPE html>
<html>
  <head>
        <meta charset="utf-8">
        <title>GraphQL Playground</title>
        ...

9. Upload Basic File ✅

Download new Profile Credentials from https://calypr.ohsu.edu/Profile (~/Downloads/credentials.json)

➜ mv ~/Downloads/credentials.json ~/.gen3/credentials.json.local

➜ g3t --version
g3t, version 0.0.7rc12

➜ gen3-client configure --profile=local --cred=~/.gen3/credentials.json.local --apiendpoint=https://calypr.ohsu.edu
Profile 'local' has been configured successfully.

➜ export G3T_PROFILE=local

➜ g3t ping
Connected using profile:local'
endpoint: https://calypr.ohsu.edu
bucket_programs:                                                                                                                                                              cbds: cbds
  gdcdata: gdc
  get3test: fortera
  smmart-caliper-dev: smmart
your_access:
  /data_file: update,file_upload,create,write-storage,*,delete
  /mds_gateway: access
  /programs: create,read,update,*
  /programs/cbds: create,read,update,*
  /programs/cbds/projects: create,read,update,*
  /programs/cbds/projects/test: create,read,update,*
  /services/sheepdog/submission/program: '*'                                                                                                                                  /services/sheepdog/submission/project: '*'                                                                                                                                  /sower: create,access,read,update                                                                                                                                           /workspace: access,update,file_upload,create,write-storage,*,read,read-storage,delete

➜ mkdir cbds-test

➜ cd cbds-test

➜ g3t init cbds-testing
Approval needed. to approve the project, a privileged user must run `g3t collaborator approve --all`

➜ g3t collaborator approve --all
approved:
- policy_id: programs.cbds.projects.testing_writer
  status: SIGNED
- policy_id: programs.cbds.projects.testing_reader
  status: SIGNED
msg: OK

➜ echo 'Hello, World!' > hello-world.txt && date >> hello-world.txt

➜ cat hello-world.txt
Hello, World!
Mon May 12 16:51:00 PDT 2025

➜ g3t add hello-world.txt

➜ g3t meta init
Updated 2 metadata files.
resources={'summary': {'DocumentReference': 1, 'ResearchStudy': 1}} exceptions=[]

➜ g3t commit -m "add file"
[main fd298d8] add file
 4 files changed, 26 insertions(+)
 create mode 100644 MANIFEST/hello-world.txt.dvc
 create mode 100644 META/DocumentReference.ndjson
 create mode 100644 META/ResearchStudy.ndjson

➜ g3t push
{'summary': {'DocumentReference': 1, 'ResearchStudy': 1}}
Scanned new: 1, updated: 0 files
Published project. Logs found at logs/publish.log

10. Verify Data Upload in S3 ✅

➜ g3t ls
bucket:
...
- did: d70d5a79-2f88-5d0d-9ed0-fd0bb6ddd6fe
  file_name: hello-world.txt
  indexd_created_date: '2025-05-13T00:01:43.914352'
  meta:
    object_id: d70d5a79-2f88-5d0d-9ed0-fd0bb6ddd6fe
  urls:
  - s3://cbds/d70d5a79-2f88-5d0d-9ed0-fd0bb6ddd6fe/hello-world.txt
...

➜ mc ls cbds/cbds/d70d5a79-2f88-5d0d-9ed0-fd0bb6ddd6fe/hello-world.txt
[2025-05-12 17:01:46 PDT]    43B STANDARD hello-world.txt

➜ mc cat cbds/cbds/d70d5a79-2f88-5d0d-9ed0-fd0bb6ddd6fe/hello-world.txt
Hello, World!
Mon May 12 16:51:00 PDT 2025

11. Download Basic File ✅

➜ mkdir clone-test

➜ cd clone-test

➜ g3t clone cbds-testing
Cloned .g3t/work/cbds-testing.git.zip
On branch main
nothing to commit, working tree clean

➜ cd cbds-testing

➜ ls
MANIFEST META

➜ g3t pull
2025/05/12 17:05:51 File info prepared successfully
hello-world.txt  43 B / 43 B
2025/05/12 17:05:52 1 files downloaded.

➜ ls
MANIFEST        META            hello-world.txt

➜ cat hello-world.txt
Hello, World!
Mon May 12 16:51:00 PDT 2025