← Files NGS Analysis WorkbenchARCHIVED FILE
src/inline/RunReviewApp.stories.tsx
18.8 KB · Oct 3, 2026 · 06:16 UTC
import type { Meta, StoryObj } from "@storybook/react-vite";
import { RunReviewSurface } from "./RunReviewApp";
import type { ReviewPlan, ReviewRun } from "./types";
import { snakemakeLogObservation } from "../fixtures/executionObservation";
const meta = {
title: "NGS/Inline Plan and Live Receipt",
parameters: { layout: "fullscreen" },
} satisfies Meta;
export default meta;
type Story = StoryObj<typeof meta>;
const readyPlan: ReviewPlan = {
binding: "snakemake",
planName: "S10 FASTQ intake",
planId: "ngs-plan-fae9e40d3f6c279f",
planChecksum: "sha256:fae9e40d3f6c279f8a6b58f0a9f673067bfabcb06d019f490af85775da0bf182",
runnable: true,
request: {
pipeline: "fastq_qc",
target: { target_id: "local", provider: "ngs-analysis-workbench" },
display_name: "S10 FASTQ intake",
workflow: "workflows/fastq_qc/workflow/Snakefile",
run_dir: "/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10",
config_file: "/tmp/test-qc/fastq-qc-config.json",
config_sha256: "sha256:48729a01c6a60779bbacb7bc5520621df0d6ddd2e49702e26a6922b82397a739",
workflow_sha256: "sha256:c2db94d21f4d0e84759f7e665c78bf41e970d554dbf6ac6067bf025a0d7025ee",
cores: 4,
run_id: "snakemake-fastq-qc-s10",
},
command: [
"/opt/homebrew/bin/snakemake",
"--snakefile",
"/tmp/test-qc/ngs_runs/snakemake/fastq_qc/snakemake-fastq-qc-s10/workflow/Snakefile",
"--configfile",
"/tmp/test-qc/ngs_runs/snakemake/fastq_qc/snakemake-fastq-qc-s10/config/fastq-qc-config.json",
"--directory",
"/tmp/test-qc/ngs_runs/snakemake/fastq_qc/snakemake-fastq-qc-s10",
"--cores",
"4",
],
readiness: {
ok: true,
scope: "local PATH",
commands: [
{ name: "snakemake", path: "/opt/homebrew/bin/snakemake", state: "ready", version: "9.24.0" },
],
blockers: [],
warnings: [],
},
effects: {
runDir: "/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10",
outputDir: "/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10/results",
workDir: "/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10/work",
launchLog: "/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10/launch.log",
localWrites: [
"/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10",
"/tmp/test-qc/ngs_runs/snakemake/snakemake-fastq-qc-s10/results",
],
downloads: [
"https://raw.githubusercontent.com/nf-core/test-datasets/pinned/sample1_R1.fastq.gz",
"https://raw.githubusercontent.com/nf-core/test-datasets/pinned/sample1_R2.fastq.gz",
],
networkAccess: ["verified HTTPS download from raw.githubusercontent.com"],
},
preparation: {
destinationDir: "/tmp/test-qc",
downloadBytes: 6_412_688,
writes: [
"/tmp/test-qc/inputs/sample1_R1.fastq.gz",
"/tmp/test-qc/inputs/sample1_R2.fastq.gz",
"/tmp/test-qc/fastq-qc-config.json",
],
operations: [
{
operation: "download_verified_file",
path: "/tmp/test-qc/inputs/sample1_R1.fastq.gz",
role: "SAMPLE1 read 1",
url: "https://raw.githubusercontent.com/nf-core/test-datasets/pinned/sample1_R1.fastq.gz",
bytes: 3_356_344,
sha256: "sha256:b7469350e3167dcdeab6a498984030b09af4bbf17e5b5a9e8f95dc3ee352b031",
},
{
operation: "download_verified_file",
path: "/tmp/test-qc/inputs/sample1_R2.fastq.gz",
role: "SAMPLE1 read 2",
url: "https://raw.githubusercontent.com/nf-core/test-datasets/pinned/sample1_R2.fastq.gz",
bytes: 3_056_344,
sha256: "sha256:1fcbddf6dbb6d6508755477859161fa63be14246a85d4a4f75683da3f461e153",
},
{
operation: "write_generated_file",
path: "/tmp/test-qc/fastq-qc-config.json",
bytes: 412,
sha256: "sha256:48729a01c6a60779bbacb7bc5520621df0d6ddd2e49702e26a6922b82397a739",
mediaType: "application/json",
},
],
},
blockers: [],
warnings: ["Reads will be inspected only; trimming is disabled."],
monitoring: {
terminal_statuses: ["completed", "failed", "canceled", "orphaned"],
log_paths: ["/tmp/test-qc/logs/nextflow.log"],
artifact_paths: ["/tmp/test-qc/results"],
},
};
const scrnaPlan: ReviewPlan = {
binding: "snakemake",
planName: "PBMC single-cell smoke test",
planId: "ngs-plan-2b35103408851039",
planChecksum: "sha256:2b351034088510398a237c91fc4f842196b6e088888a767169ef689d48fd34df",
runnable: true,
request: {
pipeline: "scrnaseq",
target: { target_id: "local", provider: "ngs-analysis-workbench" },
display_name: "PBMC single-cell smoke test",
workflow: "workflows/scrnaseq_fastq_to_count/workflow/Snakefile",
run_dir: "/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke",
config_file: "/tmp/ngs-scrnaseq-smoke/snakemake-config.json",
config_sha256: "sha256:999fb57ee3837af3f9cbaa8707e4bbc2944bdf7b8ad2a1765041eb6d59c6d25e",
workflow_sha256: "sha256:adc751413464799180a2b6b2f769bdbf251106721da68eebf2c79b127e2fc2eb",
cores: 4,
run_id: "snakemake-scrnaseq-smoke",
},
command: [
"/tmp/ngs-runtime/bin/snakemake",
"--snakefile",
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/workflow/Snakefile",
"--configfile",
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/config/snakemake-config.json",
"--directory",
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke",
"--cores",
"4",
],
readiness: {
ok: true,
scope: "executable_presence_only",
commands: [
{ name: "snakemake", path: "/tmp/ngs-runtime/bin/snakemake", state: "ready", version: "9.24.0" },
],
blockers: [],
warnings: [],
},
effects: {
runDir: "/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke",
outputDir: "/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke",
workDir: "/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke",
launchLog: "/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/logs/snakemake.log",
localWrites: [
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/workflow",
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/config/snakemake-config.json",
],
downloads: [],
networkAccess: [],
},
blockers: [],
warnings: ["Workflow-specific effects are owned by the Snakefile and supplied config."],
monitoring: {
terminal_statuses: ["completed", "failed", "canceled", "orphaned"],
log_paths: [
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/logs/snakemake.log",
],
artifact_paths: [
"/tmp/ngs-scrnaseq-smoke/ngs_runs/snakemake/scrnaseq/snakemake-scrnaseq-smoke/results",
],
},
};
const bulkRnaSnakemakePlan: ReviewPlan = {
binding: "snakemake",
planName: "Bulk RNA-seq QC · public example",
planId: "ngs-plan-97f3e6946c25fbf9",
planChecksum: "sha256:97f3e6946c25fbf9179fd245ff31ad47a09a2281f746bf8bc84fb933addb28d3",
runnable: true,
request: {
pipeline: "rnaseq",
target: { target_id: "local", provider: "ngs-analysis-workbench" },
display_name: "GSE110004 counts QC",
workflow: "workflows/bulk_rnaseq_counts_qc/workflow/Snakefile",
run_dir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2",
config_file: "/tmp/ngs-bulk-rnaseq-smoke-20260806/snakemake-config.json",
config_sha256: "sha256:1f223b846818b7a1517fef4af7d90114944284bcd1c68adfd7943420eb9b52db",
workflow_sha256: "sha256:24c9bc287c4db718cf49209f6af05f8bbf19ebf5a33ae277b948cc31fb740bae",
cores: 4,
run_id: "snakemake-rnaseq-gse110004-smoke-2",
},
command: [
"/tmp/ngs-scrnaseq-runtime-20260806/venv/bin/snakemake",
"--snakefile",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/workflow/Snakefile",
"--configfile",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/config/snakemake-config.json",
"--directory",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2",
"--cores",
"4",
"--printshellcmds",
"--shared-fs-usage",
"input-output",
"persistence",
"software-deployment",
"software-deployment-cache",
"sources",
"storage-local-copies",
],
readiness: {
ok: true,
scope: "executable_presence_only",
commands: [{
name: "snakemake",
path: "/tmp/ngs-scrnaseq-runtime-20260806/venv/bin/snakemake",
state: "ready",
version: "9.24.0",
}],
blockers: [],
warnings: [],
},
effects: {
runDir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2",
outputDir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2",
workDir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2",
launchLog: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/logs/snakemake.log",
localWrites: [
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/workflow",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/config/snakemake-config.json",
],
downloads: [],
networkAccess: [],
},
blockers: [],
warnings: ["Tool and output effects are owned by the approved Snakefile and reviewed config."],
monitoring: {
terminal_statuses: ["completed", "failed", "canceled", "orphaned"],
log_paths: [
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/logs/snakemake.log",
],
artifact_paths: [
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/snakemake/rnaseq/snakemake-rnaseq-gse110004-smoke-2/results",
],
},
};
const bulkRnaNfcorePlan: ReviewPlan = {
binding: "nextflow",
planName: "Bulk RNA-seq QC · nf-core alternative",
planId: "ngs-plan-dcebb40355863a07",
planChecksum: "sha256:dcebb40355863a0706f894264784591c238b7da25bb50cf09970808f8125b7c4",
runnable: true,
request: {
pipeline: "rnaseq",
target: { target_id: "local", provider: "ngs-analysis-workbench" },
display_name: "GSE110004 nf-core RNA-seq",
workflow: "nf-core/rnaseq",
run_dir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2",
profile: "test,docker",
sample_sheet: "/tmp/ngs-bulk-rnaseq-smoke-20260806/samplesheet.csv",
sample_sheet_sha256: "sha256:8bfd55084a46726a2005c8f38fd13f27b9f5ba7aab00c1b2bc8682276f831e36",
revision: "3.26.0",
params_file: "/tmp/ngs-bulk-rnaseq-smoke-20260806/nfcore-params.json",
params_file_sha256: "sha256:24863b0175ce24ad7885875f39a8768568919b869dd16aae8372d81c172e56e1",
trim: false,
runtime_snapshot_id: "runtime-0123456789abcdef0123456789abcdef",
run_id: "nfcore-rnaseq-gse110004-smoke-2",
},
command: [
"/tmp/ngs-scrnaseq-runtime-20260806/bin/nextflow",
"run",
"nf-core/rnaseq",
"-params-file",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/nfcore-params.json",
"-work-dir",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/work",
"-with-report",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/workflow/nextflow_report.html",
"-with-timeline",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/workflow/timeline.html",
"-with-trace",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/workflow/trace.txt",
"-with-dag",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/workflow/dag.html",
"-r",
"3.26.0",
"-profile",
"test,docker",
"--input",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/samplesheet.csv",
"--outdir",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/results",
],
readiness: {
ok: true,
scope: "local_runtime_snapshot",
snapshotId: "runtime-0123456789abcdef0123456789abcdef",
host: { os: "darwin", arch: "arm64" },
commands: [
{
name: "nextflow",
path: "/tmp/ngs-scrnaseq-runtime-20260806/bin/nextflow",
state: "ready",
version: "version 26.04.6 build 0",
},
{ name: "java", path: "/usr/bin/java", state: "ready", version: "openjdk version 26.0.1" },
{ name: "docker", path: "/usr/bin/docker", state: "ready", version: "Docker version 29.6.0" },
],
docker: {
path: "/usr/bin/docker",
context: "desktop-linux",
endpoint: "unix:///Users/scientist/.docker/run/docker.sock",
endpointIsLocal: true,
daemonReachable: true,
serverVersion: "29.6.1",
serverOs: "linux",
serverArch: "arm64",
},
blockers: [],
warnings: ["Container image architecture is verified only after images resolve."],
},
effects: {
runDir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2",
outputDir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/results",
workDir: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/work",
launchLog: "/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/logs/nextflow.log",
localWrites: [
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/results",
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/work",
],
downloads: [
"workflow source for nf-core/rnaseq at revision 3.26.0",
"container images referenced by the workflow if absent from the local cache",
"test-profile inputs referenced by the workflow if absent from the local cache",
],
networkAccess: [
"Nextflow workflow source resolution",
"container registry access for uncached images",
"remote test-data access declared by the workflow",
],
},
blockers: [],
warnings: [],
monitoring: {
terminal_statuses: ["completed", "failed", "canceled", "orphaned"],
log_paths: [
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/logs/nextflow.log",
],
artifact_paths: [
"/tmp/ngs-bulk-rnaseq-smoke-20260806/ngs_runs/nextflow/rnaseq/nfcore-rnaseq-gse110004-smoke-2/results",
],
},
};
const blockedPlan: ReviewPlan = {
...readyPlan,
planName: "Blocked FASTQ QC",
planId: "ngs-plan-7ff89bfe1b71e51f",
planChecksum: "sha256:7ff89bfe1b71e51f9add0dc01d784e3d321324e4b5669a3a10d72801b6b352f8",
runnable: false,
readiness: {
...readyPlan.readiness,
ok: false,
commands: [
{ name: "snakemake", path: null, state: "missing" },
],
blockers: ["Snakemake is not available on PATH."],
},
blockers: [
"Snakemake is not available on PATH.",
"FastQC and MultiQC must be installed before this local plan can run.",
],
warnings: [],
};
const runningRun: ReviewRun = {
binding: "snakemake",
registryRunId: "ngs-run-snakemake-fastq-qc-example",
runId: "snakemake-fastq-qc-20260805-143501-a1b2c3d4",
revision: 2,
status: "running",
workflow: "Local FASTQ QC",
pid: 48172,
runDir: "/tmp/test-qc/ngs_runs/snakemake/fastq_qc/snakemake-fastq-qc-20260805-143501-a1b2c3d4",
command: readyPlan.command,
warnings: ["Workflow-specific effects are owned by the Snakefile and supplied config."],
logTail: [
"Building DAG of jobs...",
"[Tue Aug 5 14:35:04 2026]",
"rule fastqc:",
" input: S10_L001_R1_001.fastq.gz, S10_L001_R2_001.fastq.gz",
" output: results/fastqc/S10_R1_fastqc.html, results/fastqc/S10_R2_fastqc.html",
].join("\n"),
execution: snakemakeLogObservation,
};
const completedRun: ReviewRun = {
...runningRun,
status: "completed",
returncode: 0,
warnings: [],
logTail: `${runningRun.logTail}\nWorkflow completed successfully.`,
};
const failedRun: ReviewRun = {
...runningRun,
status: "failed",
returncode: 1,
warnings: ["MultiQC was not started because one FastQC task failed."],
logTail: `${runningRun.logTail}\nFastQC reported a truncated gzip stream for read 2.`,
};
const runActions = {
refreshing: false,
onRefresh: () => undefined,
};
export const Loading: Story = {
render: () => <RunReviewSurface state="loading" />,
};
export const PlanReady: Story = {
render: () => <RunReviewSurface state="plan" plan={readyPlan} />,
};
export const SingleCellPlanReady: Story = {
render: () => <RunReviewSurface state="plan" plan={scrnaPlan} />,
};
export const BulkRnaSnakemakePlanReady: Story = {
render: () => (
<RunReviewSurface state="plan" plan={bulkRnaSnakemakePlan} />
),
};
export const BulkRnaNfCorePlanReady: Story = {
render: () => <RunReviewSurface state="plan" plan={bulkRnaNfcorePlan} />,
};
export const PlanBlocked: Story = {
render: () => <RunReviewSurface state="plan" plan={blockedPlan} />,
};
export const Running: Story = {
render: () => (
<RunReviewSurface state="run" run={runningRun} {...runActions} />
),
};
export const Completed: Story = {
render: () => (
<RunReviewSurface state="run" run={completedRun} {...runActions} />
),
};
export const Failed: Story = {
render: () => (
<RunReviewSurface state="run" run={failedRun} {...runActions} />
),
};
export const Refreshing: Story = {
render: () => (
<RunReviewSurface state="run" run={runningRun} {...runActions} refreshing />
),
};
export const ReceiptError: Story = {
render: () => (
<RunReviewSurface
state="run"
run={runningRun}
{...runActions}
error="The approved execution response included an incomplete receipt."
/>
),
};
export const InvalidResponse: Story = {
render: () => (
<RunReviewSurface
state="error"
message="The execution response was incomplete."
payload={{ ok: true, status: "running" }}
/>
),
};
export const ExecutionBlocked: Story = {
render: () => (
<RunReviewSurface
state="blocked"
failure={{
message: "runtime snapshot is unknown to this server; call get_runtime_environment again",
recovery: "Refresh the runtime environment, then create and review a new execution plan.",
}}
payload={{
ok: false,
errors: ["runtime snapshot is unknown to this server; call get_runtime_environment again"],
}}
/>
),
};
export const Narrow: Story = {
parameters: { storyWidth: 390 },
render: () => <RunReviewSurface state="plan" plan={readyPlan} />,
};
export const DarkRunning: Story = {
parameters: { theme: "dark" },
render: () => (
<RunReviewSurface state="run" run={runningRun} {...runActions} />
),
};
SHA-256: b43c003f78bb8e0f51db4680d8e73617c8650e261bfaf98b7731f56a14f42989