Support DMS antibody modality

.changeset/migrate-to-structurer.md

@@ -0,0 +1,27 @@
+---
+'@platforma-open/milaboratories.sequence-properties': minor
+'@platforma-open/milaboratories.sequence-properties.model': minor
+'@platforma-open/milaboratories.sequence-properties.ui': patch
+'@platforma-open/milaboratories.sequence-properties.workflow': patch
+'@platforma-open/milaboratories.sequence-properties.software': patch
+---
+
+Migrate onto the structurer and upgrade the SDK
+
+The block now follows the canonical `block-tools structure` layout on
+block-tools 2.14.3, with the SDK bumped to model/ui-vue 1.83.x, workflow-tengo
+6.8.3, tengo-builder 4.0.23 and test 1.83.2.
+
+Two changes are visible outside the block:
+
+- **A new `kind` component** declares the block's identity and its init-params
+  contract. `BlockParams` is `{ inputAnchor?: PlRef }`, so a project template
+  can seed a new instance with the dataset to analyse. Every other field in the
+  block's data is view state and still defaults.
+- **`block` is now a slim facade.** It publishes with no dependencies, bundles
+  the whole block into `dist/` plus `block-pack/`, and exports
+  `SequencePropertiesBlockPointer` for consumers that add the block from code.
+
+`@platforma-sdk/ui-vue` is on 1.83.3, which publishes the component
+declaration files its own type entry re-exports again — 1.83.1 had dropped
+them and broke the facade build.

.changeset/read-declared-modality.md

@@ -0,0 +1,27 @@
+---
+'@platforma-open/milaboratories.sequence-properties': minor
+'@platforma-open/milaboratories.sequence-properties.workflow': minor
+---
+
+Read the input's declared `pl7.app/modality` instead of guessing from the run-id key
+
+`synthetic-repertoire-profiler` runs one pipeline over both antibody/TCR parents and designed
+libraries, and everything it emits sits on the modality-neutral `pl7.app/variantKey` axis. It
+keeps the same `pl7.app/repertoire/extractionRunId` key in both cases, so a VDJ run used to be
+read as amplicon and scanned as one whole sequence — its FR1–FR4 regions, CDR3 included, were
+never used.
+
+The profiler now declares which kind of repertoire it produced in the entity-axis domain, and
+this block reads that declaration: `vdj` takes the per-region antibody/TCR path, `amplicon` the
+whole-sequence path. A VDJ run therefore gets CDR3 charge and hydrophobicity, and full-chain
+properties, the same as MiXCR input does.
+
+Datasets with no declaration keep the previous behaviour exactly, so projects made before the
+declaration landed are unaffected.
+
+Two smaller things follow from it. A declared VDJ input carries no receptor — the profiler has
+none to emit, since germline auto-detect builds its reference from the user's own parent
+sequences — so the "receptor not detected" notice no longer tells those users to pick a MiXCR
+preset they never used; it says the labels defaulted to the antibody convention and that only
+labels are affected. And modality detection moved into its own workflow module so it could be
+unit-tested; `pnpm test` on the workflow package now runs those tests.

.github/workflows/build.yaml

@@ -11,67 +11,73 @@ on:
   workflow_dispatch: {}
 jobs:
   init:
-    if: github.repository != 'milaboratory/platforma-sequence-properties'
-    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-sequence-properties'
     needs:
       - init
-
     uses: milaboratory/github-ci/.github/workflows/node-simple-pnpm.yaml@v4
     with:
-      app-name: 'Block: sequence-properties'
+      app-name: 'Block: Sequence Properties'
       app-name-slug: 'block-sequence-properties'
-
-      node-version: '20.x'
-      build-script-name: 'build'
+      node-version: '22.x'
+      gha-runner-label: hz-ubuntu-dind
+      build-script-name: 'build:dev-local'
+      build-before-publish-script-name: 'build:release'
       pnpm-recursive-build: 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'
+
+      # Require the published `block` package to be bumped by a changeset on
+      # PRs (empty changeset or the `skip-changelog` label waives it). Needs
+      # the input to exist on the pinned `@v4` reusable workflow.
+      require-package-path-bump: 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

@@ -3,21 +3,19 @@ on:
   workflow_dispatch: {}
 jobs:
   init:
-    if: github.repository != 'milaboratory/platforma-sequence-properties'
     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-sequence-properties'
     needs:
       - init
     uses: milaboratory/github-ci/.github/workflows/block-mark-stable.yaml@v4
     with:
-      app-name: 'Block: sequence-properties - Mark Stable'
-      node-version: '20.x'
+      app-name: 'Block: Sequence Properties - Mark Stable'
+      node-version: '22.x'
       npmrc-config: |
         {
           "registries": {
@@ -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 }}

.structure

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

.vscode/settings.json

@@ -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"
 }

block/package.json

@@ -1,22 +1,42 @@
 {
   "name": "@platforma-open/milaboratories.sequence-properties",
   "version": "1.5.2",
+  "files": [
+    "dist",
+    "block-pack"
+  ],
+  "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": "shx rm -rf ./block-pack && block-tools pack",
+    "build": "ts-builder build --target block-facade && 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 --unstable -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 *.tgz && block-tools pack && pnpm pack && shx mv *.tgz package.tgz"
+    "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"
   },
-  "files": [
-    "index.d.ts",
-    "index.js"
-  ],
-  "dependencies": {
-    "@platforma-sdk/model": "catalog:",
-    "@platforma-open/milaboratories.sequence-properties.workflow": "workspace:*",
+  "dependencies": {},
+  "devDependencies": {
+    "@milaboratories/ts-builder": "catalog:",
+    "@milaboratories/ts-configs": "catalog:",
+    "@platforma-open/milaboratories.sequence-properties.kind": "workspace:*",
     "@platforma-open/milaboratories.sequence-properties.model": "workspace:*",
-    "@platforma-open/milaboratories.sequence-properties.ui": "workspace:*"
+    "@platforma-open/milaboratories.sequence-properties.ui": "workspace:*",
+    "@platforma-open/milaboratories.sequence-properties.workflow": "workspace:*",
+    "@platforma-sdk/block-tools": "catalog:",
+    "@platforma-sdk/model": "catalog:",
+    "shx": "catalog:",
+    "typescript": "catalog:"
   },
+  "packageManager": "pnpm@9.15.0",
   "block": {
     "components": {
       "workflow": "@platforma-open/milaboratories.sequence-properties.workflow/dist/tengo/tpl/main.plj.gz",
@@ -43,9 +63,5 @@
         "logo": "file:../logos/organization-logo.png"
       }
     }
-  },
-  "devDependencies": {
-    "@platforma-sdk/block-tools": "catalog:"
-  },
-  "packageManager": "pnpm@9.15.0"
+  }
 }

block/src/AGENTS.ts

@@ -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-extra.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/block-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.