CLI Reference

Run these commands from the product root unless noted otherwise.

In preflight_v2 and exported customer bundles, the chart path is chart/preflight. Some standalone bundle copies also mirror the same chart at helm/glassbox-preflight. Only the chart path changes.

Shared defaults

Helm release name: glassbox-preflight
Namespace examples in this page: glassbox-preflight
service.type=ClusterIP
service.port=8080
app.authDisabled=false
storage.type=pvc
storage.pvc.size=20Gi
storage.pvc.accessMode=ReadWriteOnce
default runner image: us-docker.pkg.dev/glassbox-bio-public/glassbox-bio-molecular-audit/glassbox-mol-audit:1.0.0

`helm template glassbox-preflight chart/preflight`

Syntax:

helm template glassbox-preflight chart/preflight [options]

Arguments:

glassbox-preflight: release name used for rendered object names
chart/preflight: chart path in preflight_v2 and exported bundles
-f <values-file>: optional values overlay
--set key=value: optional inline override

Defaults:

renders the chart with the values declared in chart/preflight/values.yaml
use ./helm/glassbox-preflight instead of chart/preflight only when working from a standalone bundle that keeps that alternate path

Example:

helm template glassbox-preflight chart/preflight

`helm upgrade --install glassbox-preflight chart/preflight`

Syntax:

helm upgrade --install glassbox-preflight chart/preflight --namespace <ns> --create-namespace [options]

Arguments:

--namespace <ns>: target namespace
--create-namespace: create the namespace if missing
--set app.authToken=<token>: optional explicit API token
--set image.repository=<repo>: optional image repo override
--set image.tag=<tag> or --set image.digest=<digest>: optional image version override
--set storage.type=pvc|gcs: optional storage mode override
--set storage.pvc.size=<size>: optional PVC size override
--set storage.pvc.accessMode=ReadWriteOnce|ReadWriteMany: optional access mode override
--set app.runnerImage=<image>: optional core runner image override
--set app.runnerServiceAccount=<ksa>: optional runtime Job service account override
--set billing.enabled=true: optional metering enablement

Defaults:

if app.authToken is omitted, the chart preserves an existing auth secret or generates a new one on first install
the default service is ClusterIP on port 8080
the default shared storage contract is PVC-backed

Example:

export GBX_PREFLIGHT_TOKEN="change-me-before-real-use"

helm upgrade --install glassbox-preflight chart/preflight \
  --namespace glassbox-preflight \
  --create-namespace \
  --set app.authToken="$GBX_PREFLIGHT_TOKEN"

`kubectl get secret ... K8S_API_TOKENS`

Syntax:

kubectl -n <ns> get secret <release>-preflight-auth -o jsonpath='{.data.K8S_API_TOKENS}' | base64 -d

Arguments:

<ns>: namespace used at install time
<release>: Helm release name; with the default release it resolves to glassbox-preflight-preflight-auth

Defaults:

use this only when app.authToken was not supplied explicitly

Example:

kubectl -n glassbox-preflight get secret glassbox-preflight-preflight-auth \
  -o jsonpath='{.data.K8S_API_TOKENS}' | base64 -d | jq -r '.[0].token'

`kubectl rollout status deployment/glassbox-preflight-preflight`

Syntax:

kubectl -n <ns> rollout status deployment/<release>-preflight

Arguments:

<ns>: namespace used at install time
<release>: Helm release name; default examples use glassbox-preflight

Defaults:

with the default release name, the Deployment name is glassbox-preflight-preflight

Example:

kubectl -n glassbox-preflight rollout status deployment/glassbox-preflight-preflight

`kubectl port-forward svc/glassbox-preflight-preflight 8080:8080`

Syntax:

kubectl -n <ns> port-forward svc/<release>-preflight 8080:8080

Arguments:

<ns>: namespace used at install time
<release>: Helm release name; default examples use glassbox-preflight

Defaults:

forwards local port 8080 to the in-cluster service port 8080

Example:

kubectl -n glassbox-preflight port-forward svc/glassbox-preflight-preflight 8080:8080

`curl /api/health`

Syntax:

curl -fsSL http://127.0.0.1:8080/api/health

Arguments:

none

Defaults:

unauthenticated health probe
expected response includes {"status":"ok"}

Example:

curl -fsSL http://127.0.0.1:8080/api/health

`curl /api/config`

Syntax:

curl -fsSL http://127.0.0.1:8080/api/config

Arguments:

none

Defaults:

unauthenticated config probe
expected response includes the current runtime wiring such as inCluster, storage mode, and runner integration fields

Example:

curl -fsSL http://127.0.0.1:8080/api/config

`curl /api/modules`

Syntax:

curl -fsSL http://127.0.0.1:8080/api/modules

Arguments:

none

Defaults:

unauthenticated module registry read
expected response includes the built-in computational module

Example:

curl -fsSL http://127.0.0.1:8080/api/modules

`curl /api/runs/check`

Syntax:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/runs/check?runId=<run_id>[&paths=<relpath1>,<relpath2>]"

Arguments:

runId: required
paths: optional comma-separated list of relative output paths to require

Defaults:

requires auth unless the deployment explicitly disables token auth
when paths is omitted, checks:
- results/combined_unified_computational_outputs.json
- results/summary.json

Example:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/runs/check?runId=smoke-test"

`curl POST /api/modules/computational/smoke`

Syntax:

curl -fsSL -X POST \
  -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"namespace":"<ns>"}' \
  "http://127.0.0.1:8080/api/modules/computational/smoke"

Arguments:

namespace: required JSON body field

Defaults:

launches a short-lived Kubernetes Job
with the shipped registry, the smoke command resolves to python3 -m app.gbx_core_runner_v3 --help
verifies image pull, interpreter startup, and module CLI wiring without launching a scientific run

Example:

curl -fsSL -X POST \
  -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"namespace":"glassbox-preflight"}' \
  "http://127.0.0.1:8080/api/modules/computational/smoke"

`curl /api/modules/computational/status`

Syntax:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/modules/computational/status?namespace=<ns>"

Arguments:

namespace: required query parameter

Defaults:

returns the configured runner image, runner service account, and latest observed execution verification state for the module

Example:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/modules/computational/status?namespace=glassbox-preflight"

`curl POST /api/pipeline/run`

Syntax:

curl -fsSL -X POST \
  -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"projectId":"<project_id>","namespace":"<ns>"[,"runId":"<run_id>","moduleId":"computational","mode":"standard","gpuDocking":false]}' \
  "http://127.0.0.1:8080/api/pipeline/run"

Arguments:

projectId: required JSON body field
namespace: required JSON body field
runId: optional
moduleId: optional; defaults to computational
mode: optional; defaults to standard
gpuDocking: optional boolean; defaults to false

Defaults:

requires GBX_RUNNER_IMAGE and GBX_APP_FULLNAME to be configured on the preflight server
if runId is omitted, the server generates run_<timestamp>
GPU scheduling is enabled only when mode=deep and gpuDocking=true

Example:

curl -fsSL -X POST \
  -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{"projectId":"test","namespace":"glassbox-preflight","mode":"standard"}' \
  "http://127.0.0.1:8080/api/pipeline/run"

`curl /api/k8s/pods`

Syntax:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/k8s/pods?namespace=<ns>[&jobName=<job_name>][&label=<selector>][&context=<kubectl_context>]"

Arguments:

namespace: required query parameter
jobName: optional query parameter
label: optional query parameter
context: optional query parameter

Defaults:

returns pod names, phases, containers, and start times
use jobName when you want only the pods for one launched Job

Example:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/k8s/pods?namespace=glassbox-preflight"

`curl /api/outputs/list`

Syntax:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/outputs/list?runId=<run_id>[&prefix=<relative_prefix>]"

Arguments:

runId: required query parameter
prefix: optional relative output prefix

Defaults:

when prefix is omitted, the response prefers the well-known top-level directories:
- results/
- thresholds/
- seal/
- repro_pack/

Example:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  "http://127.0.0.1:8080/api/outputs/list?runId=run_20260325T010203"

`curl /api/outputs/download`

Syntax:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -o <local_file> \
  "http://127.0.0.1:8080/api/outputs/download?runId=<run_id>&path=<relative_path>"

Arguments:

runId: required query parameter
path: required relative path under the run output root
-o <local_file>: recommended local output filename

Defaults:

downloads a single file under GBX_OUTPUT_ROOT/<run_id>/

Example:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -o summary.json \
  "http://127.0.0.1:8080/api/outputs/download?runId=run_20260325T010203&path=results/summary.json"

`curl /api/outputs/repro-pack.tgz`

Syntax:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -o repro_pack_<run_id>.tgz \
  "http://127.0.0.1:8080/api/outputs/repro-pack.tgz?runId=<run_id>"

Arguments:

runId: required query parameter
-o repro_pack_<run_id>.tgz: recommended local filename

Defaults:

archives and streams the repro_pack/ directory for the run
returns 404 if that directory does not exist yet

Example:

curl -fsSL -H "Authorization: Bearer $GBX_PREFLIGHT_TOKEN" \
  -o repro_pack_run_20260325T010203.tgz \
  "http://127.0.0.1:8080/api/outputs/repro-pack.tgz?runId=run_20260325T010203"

`APP_BASE_URL=... ./apptest/tester/tester.sh`

Syntax:

APP_BASE_URL=http://127.0.0.1:8080 ./apptest/tester/tester.sh

Arguments:

APP_BASE_URL: required environment variable pointing at the running preflight app

Defaults:

checks /api/health
checks /api/config
checks /api/modules for the computational registry entry

Example:

APP_BASE_URL=http://127.0.0.1:8080 ./apptest/tester/tester.sh

Shared defaults​

helm template glassbox-preflight chart/preflight​

helm upgrade --install glassbox-preflight chart/preflight​

kubectl get secret ... K8S_API_TOKENS​

kubectl rollout status deployment/glassbox-preflight-preflight​

kubectl port-forward svc/glassbox-preflight-preflight 8080:8080​

curl /api/health​

curl /api/config​

curl /api/modules​

curl /api/runs/check​

curl POST /api/modules/computational/smoke​

curl /api/modules/computational/status​

curl POST /api/pipeline/run​

curl /api/k8s/pods​

curl /api/outputs/list​

curl /api/outputs/download​

curl /api/outputs/repro-pack.tgz​

APP_BASE_URL=... ./apptest/tester/tester.sh​

Shared defaults

`helm template glassbox-preflight chart/preflight`

`helm upgrade --install glassbox-preflight chart/preflight`

`kubectl get secret ... K8S_API_TOKENS`

`kubectl rollout status deployment/glassbox-preflight-preflight`

`kubectl port-forward svc/glassbox-preflight-preflight 8080:8080`

`curl /api/health`

`curl /api/config`

`curl /api/modules`

`curl /api/runs/check`

`curl POST /api/modules/computational/smoke`

`curl /api/modules/computational/status`

`curl POST /api/pipeline/run`

`curl /api/k8s/pods`

`curl /api/outputs/list`

`curl /api/outputs/download`

`curl /api/outputs/repro-pack.tgz`

`APP_BASE_URL=... ./apptest/tester/tester.sh`