Merge pull request #1 from platforma-open/chore/sdk-upgrade-silicon-docker

SDK toolchain upgrade + raw-file download, configurable scan limit, aligned randomize

Author: mizraelson

.changeset/fastq-reader-downloads-scan-limit-aligned-randomize.md

@@ -0,0 +1,18 @@
+---
+'@platforma-open/milaboratories.fastq-reader.model': minor
+'@platforma-open/milaboratories.fastq-reader.ui': minor
+'@platforma-open/milaboratories.fastq-reader.workflow': minor
+'@platforma-open/milaboratories.fastq-reader.software': minor
+'@platforma-open/milaboratories.fastq-reader': minor
+---
+
+Upgrade the SDK toolchain (enables building the linux/amd64 software image on Apple Silicon) and add:
+
+- **Download raw files without a Run** — the selected sample's original files are exposed by the pre-run, so they can be downloaded as soon as a dataset + sample are chosen. The download streams on demand from the backend and never stages the file to a workdir.
+- **Configurable scan limit** (default 2,000,000 reads) for the read-numbers, headers, pattern, and randomized-range modes. If it exceeds the file's read count, the whole file is scanned.
+- **Mate-aligned randomize** — randomized range now keeps paired R1/R2 aligned for both gzipped and uncompressed input (seeded reservoir sampling picks the same read ordinals on both sides).
+
+Fixes:
+
+- Read-header matching tooltip corrected (matches the full header or read id exactly, not as a prefix).
+- Removed the incorrect "R1/R2 are not mates" warning for randomized gzipped input, where pairs are in fact aligned.

.github/workflows/build.yaml

@@ -11,67 +11,68 @@ on:
   workflow_dispatch: {}
 jobs:
   init:
-    if: github.repository != 'milaboratory/platforma-block-boilerplate'
-    runs-on: ubuntu-latest
+    runs-on: hz-ubuntu-dind
     steps:
       - uses: milaboratory/github-ci/actions/context/init@v4
         with:
           version-canonize: false
           branch-versioning: main
   run:
-    if: github.repository != 'milaboratory/platforma-block-boilerplate'
     needs:
       - init
-
     uses: milaboratory/github-ci/.github/workflows/node-simple-pnpm.yaml@v4
     with:
-      app-name: 'Block: block-boilerplate'
-      app-name-slug: 'block-block-boilerplate'
-
+      app-name: 'Block: Fastq Reader'
+      app-name-slug: 'block-fastq-reader'
       node-version: '20.x'
-      build-script-name: 'build'
+      gha-runner-label: hz-ubuntu-dind
+      build-script-name: 'build:dev-local'
+      build-before-publish-script-name: 'build:release'
       pnpm-recursive-build: false
 
-      test: false
+      test: true
       test-script-name: 'test'
       pnpm-recursive-tests: false
       team-id: 'ciplopen'
 
+      publish-to-public: 'true'
       package-path: 'block'
-      publish-to-public: true
-      create-tag: true
+      create-tag: 'true'
 
       npmrc-config: |
         {
           "registries": {
             "https://registry.npmjs.org/": {
-              "scopes": ["milaboratories", "platforma-open", "platforma-sdk"],
+              "scopes": ["milaboratories", "platforma-sdk", "platforma-open"],
               "tokenVar": "NPMJS_TOKEN"
-            },
-            "https://npm.pkg.github.com/": {
-              "scopes": ["milaboratory"],
-              "tokenVar": "NODE_AUTH_TOKEN"
             }
           }
         }
-
     secrets:
       env: |
         { "PL_LICENSE": ${{ toJSON(secrets.MI_LICENSE) }},
           "MI_LICENSE": ${{ toJSON(secrets.MI_LICENSE) }},
-
           "NPMJS_TOKEN": ${{ toJSON(secrets.NPMJS_TOKEN) }},
           "PL_CI_TEST_USER": ${{ toJSON(secrets.PL_CI_TEST_USER) }},
           "PL_CI_TEST_PASSWORD": ${{ toJSON(secrets.PL_CI_TEST_PASSWORD) }},
 
           "AWS_CI_IAM_MONOREPO_SIMPLE_ROLE": ${{ toJSON(secrets.AWS_CI_IAM_MONOREPO_SIMPLE_ROLE) }},
           "AWS_CI_TURBOREPO_S3_BUCKET": ${{ toJSON(secrets.AWS_CI_TURBOREPO_S3_BUCKET) }},
+
+          "HZ_CI_TURBO_S3_BUCKET": ${{ toJSON(vars.HZ_CI_TURBO_S3_BUCKET) }},
+          "HZ_CI_TURBO_S3_ENDPOINT": ${{ toJSON(vars.HZ_CI_TURBO_S3_ENDPOINT) }},
+          "HZ_CI_TURBO_S3_REGION": ${{ toJSON(vars.HZ_CI_TURBO_S3_REGION) }},
+          "HZ_CI_TURBO_S3_ACCESS_KEY": ${{ toJSON(secrets.HZ_CI_TURBO_S3_ACCESS_KEY) }},
+          "HZ_CI_TURBO_S3_SECRET_KEY": ${{ toJSON(secrets.HZ_CI_TURBO_S3_SECRET_KEY) }},
+          "HZ_CI_CACHE_S3_ACCESS_KEY": ${{ toJSON(secrets.HZ_CI_CACHE_S3_ACCESS_KEY) }},
+          "HZ_CI_CACHE_S3_SECRET_KEY": ${{ toJSON(secrets.HZ_CI_CACHE_S3_SECRET_KEY) }},
+
           "PL_REGISTRY_PLATFORMA_OPEN_UPLOAD_URL": ${{ toJSON(secrets.PL_REGISTRY_PLOPEN_UPLOAD_URL) }},
           "QUAY_USERNAME": ${{ toJSON(secrets.QUAY_USERNAME) }},
           "QUAY_ROBOT_TOKEN": ${{ toJSON(secrets.QUAY_ROBOT_TOKEN) }} }
 
-      SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }}
       SLACK_CHANNEL: ${{ secrets.SLACK_BLOCKS_CI_CHANNEL }}
+      SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }}
 
       GH_ZEN_APP_ID: ${{ secrets.GH_ZEN_APP_ID }}
       GH_ZEN_APP_PRIVATE_KEY: ${{ secrets.GH_ZEN_APP_PRIVATE_KEY }}

.github/workflows/mark-stable.yaml

@@ -3,20 +3,18 @@ on:
   workflow_dispatch: {}
 jobs:
   init:
-    if: github.repository != 'milaboratory/platforma-block-boilerplate'
     runs-on: ubuntu-latest
     steps:
       - uses: milaboratory/github-ci/actions/context/init@v4
         with:
           version-canonize: false
           branch-versioning: main
   run:
-    if: github.repository != 'milaboratory/platforma-block-boilerplate'
     needs:
       - init
     uses: milaboratory/github-ci/.github/workflows/block-mark-stable.yaml@v4
     with:
-      app-name: 'Block: block-boilerplate - Mark Stable'
+      app-name: 'Block: Fastq Reader - Mark Stable'
       node-version: '20.x'
       npmrc-config: |
         {
@@ -32,5 +30,5 @@ jobs:
         { "NPMJS_TOKEN": ${{ toJSON(secrets.NPMJS_TOKEN) }},
           "AWS_CI_IAM_MONOREPO_SIMPLE_ROLE": ${{ toJSON(secrets.AWS_CI_IAM_MONOREPO_SIMPLE_ROLE) }} }
 
-      SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }}
       SLACK_CHANNEL: ${{ secrets.SLACK_BLOCKS_CI_CHANNEL }}
+      SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }}

.prettierrc

@@ -0,0 +1 @@
+{"version":2}

.structure

@@ -1,51 +1,3 @@
 {
-  "vitest.disableWorkspaceWarning": true,
-  "editor.defaultFormatter": "oxc.oxc-vscode",
-  "[typescript]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[vue]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "cSpell.words": [
-    "datasource",
-    "pframe",
-    "prerun"
-  ],
-  "editor.codeActionsOnSave": {
-    "source.fixAll.eslint": "always"
-  },
-  "eslint.enable": true,
-  "eslint.format.enable": true,
-  "[javascript]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[css]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[scss]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[html]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[yaml]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[markdown]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "[json]": {
-    "editor.defaultFormatter": "oxc.oxc-vscode",
-    "editor.tabSize": 2
-  },
-  "typescript.tsdk": "./node_modules/typescript/lib"
+  "typescript.tsdk": "node_modules/typescript/lib"
 }

.vscode/settings.json

@@ -1,22 +1,40 @@
 {
   "name": "@platforma-open/milaboratories.fastq-reader",
   "version": "1.0.0",
-  "scripts": {
-    "build": "shx rm -rf ./block-pack && block-tools pack",
-    "mark-stable": "block-tools mark-stable -r 's3://milab-euce1-prod-pkgs-s3-block-registry/pub/releases/?region=eu-central-1'",
-    "prepublishOnly": "block-tools pack && block-tools publish -r 's3://milab-euce1-prod-pkgs-s3-block-registry/pub/releases/?region=eu-central-1'",
-    "do-pack": "shx rm -f *.tgz && block-tools pack && pnpm pack && shx mv *.tgz package.tgz"
-  },
   "files": [
-    "index.d.ts",
-    "index.js"
+    "dist",
+    "block-pack"
   ],
-  "dependencies": {
-    "@platforma-sdk/model": "catalog:",
-    "@platforma-open/milaboratories.fastq-reader.workflow": "workspace:*",
+  "type": "module",
+  "main": "./dist/index.js",
+  "module": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "sources": "./src/index.ts",
+      "types": "./dist/index.d.ts",
+      "default": "./dist/index.js"
+    }
+  },
+  "scripts": {
+    "build": "ts-builder build --target block-facade && block-tools pack",
+    "prepublishOnly": "block-tools publish -r s3://milab-euce1-prod-pkgs-s3-block-registry/pub/releases/?region=eu-central-1 --registry-serve-url https://blocks.pl-open.science",
+    "do-pack": "shx rm -f package.tgz && pnpm pack && shx mv *.tgz package.tgz",
+    "check": "ts-builder type-check --target block-facade"
+  },
+  "dependencies": {},
+  "devDependencies": {
+    "@milaboratories/ts-builder": "catalog:",
+    "@milaboratories/ts-configs": "catalog:",
     "@platforma-open/milaboratories.fastq-reader.model": "workspace:*",
-    "@platforma-open/milaboratories.fastq-reader.ui": "workspace:*"
+    "@platforma-open/milaboratories.fastq-reader.ui": "workspace:*",
+    "@platforma-open/milaboratories.fastq-reader.workflow": "workspace:*",
+    "@platforma-sdk/block-tools": "catalog:",
+    "@platforma-sdk/model": "catalog:",
+    "shx": "catalog:",
+    "typescript": "catalog:"
   },
+  "packageManager": "pnpm@9.12.0",
   "block": {
     "components": {
       "workflow": "@platforma-open/milaboratories.fastq-reader.workflow/dist/tengo/tpl/main.plj.gz",
@@ -31,16 +49,18 @@
       "description": "Inspect raw reads of an imported FASTQ/FASTA dataset, one sample at a time.",
       "longDescription": "file:../docs/description.md",
       "changelog": "file:../CHANGELOG.md",
-      "tags": ["fastq", "fasta", "reads", "qc", "viewer"],
+      "tags": [
+        "fastq",
+        "fasta",
+        "reads",
+        "qc",
+        "viewer"
+      ],
       "organization": {
         "name": "MiLaboratories Inc",
         "url": "https://milaboratories.com/",
         "logo": "file:../logos/organization-logo.png"
       }
     }
-  },
-  "devDependencies": {
-    "@platforma-sdk/block-tools": "catalog:"
-  },
-  "packageManager": "pnpm@9.12.0"
+  }
 }

block/package.json

@@ -0,0 +1,5 @@
+// This file is managed by `block-tools structure`. Do not edit by hand.
+// Narrow MCP / AI surface.
+
+export type { BlockContract, BlockOutputs, BlockData } from "./index";
+export * from "./agents-extra";

block/src/AGENTS.ts

@@ -0,0 +1,8 @@
+// Author-owned. `block-tools structure` does not modify this file.
+// MCP / AI extension surface. Add types and functions the agent
+// surface should expose.
+//
+// In the future this file will host JS functions the MCP runtime
+// can execute. The `.d.ts` declarations stay visible to the agent;
+// the JS bodies execute in the MCP code-execution context (the
+// agent sees the types but not the implementation).

block/src/agents-extra.ts

@@ -0,0 +1,9 @@
+// Author-owned. `block-tools structure` does not modify this file.
+// Add block-specific helper types or values the consumer surface
+// should expose. Anything you `export` here flows out via the
+// main entry (./index re-exports this file).
+//
+// Do NOT redefine: BlockContract, BlockOutputs, BlockData,
+// BlockPointer, platforma, or the block-named <PascalName>Block*
+// aliases — those names come from ./index and `export *` from this
+// file would shadow them.