@datagrok/hit-triage 1.9.2 → 1.10.0

package/CLAUDE.md

@@ -0,0 +1,199 @@
+# CLAUDE.md
+
+## Overview
+
+**HitTriage** (`@datagrok/hit-triage`) is a Datagrok plugin for chemists to assess hit compound quality and manage
+molecule campaigns. It bundles **three applications** in one package:
+
+- **Hit Triage** — Upload a molecule dataset, filter/compute properties, submit results to a chosen function, share campaigns.
+- **Hit Design** — Sketch molecules in a spreadsheet, calculate properties, organize into stages, share campaigns.
+- **PeptiHit** — Like Hit Design but for peptides (HELM notation). Converts sequences to atomic level via the Bio package.
+
+Category: **Cheminformatics**. Browse paths: `Chem` (Hit Triage, Hit Design), `Peptides` (PeptiHit).
+
+## Architecture
+
+### Entry Point — `src/package.ts`
+
+- Defines `HTPackage` extending `DG.Package` with an LRU SMILES cache and campaigns cache.
+- `PackageFunctions` class registers all platform-visible functions via `@grok.decorators`:
+  - Three `@app` entries: Hit Triage, Hit Design, PeptiHit
+  - Three `@treeBrowser` entries for Browse panel integration
+  - Demo data source functions (`hitTriageDataSource` role)
+  - Demo submit function (`hitTriageSubmitFunction` role)
+  - `registerMoleculesToViD` — batch-registers all campaign molecules to V-iD dictionary
+  - `Hit Design V-iD` panel — semantic value panel for `HIT_DESIGN_VID` semtype
+  - `gasteigerRenderer` — custom grid cell renderer for Gasteiger PNG images
+  - Package settings editor widget
+
+### App Classes (in `src/app/`)
+
+| File | Class | Purpose |
+|---|---|---|
+| `hit-app-base.ts` | `HitAppBase<T>` | Abstract base for all three apps. Handles compute functions discovery, permissions, dataframe union/join, campaign locking, CSV download |
+| `hit-triage-app.ts` | `HitTriageApp` | Hit Triage flow: InfoView → PickView (filter) → SubmitView. Uses `DG.MultiView` |
+| `hit-design-app.ts` | `HitDesignApp<T>` | Hit Design flow: InfoView → DesignView (grid + sketching) → SubmitView. Handles molecule joining, single-cell calculations, V-iD registration, tile viewer, auto-save |
+| `pepti-hit-app.ts` | `PeptiHitApp` | Extends `HitDesignApp` for HELM/peptide molecules. Converts HELM→atomic level via `Bio:toAtomicLevel` |
+| `base-view.ts` | `HitBaseView<T,A>` | Base view class extending `DG.ViewBase` with campaign deletion and template access |
+
+### Types — `src/app/types.ts`
+
+Key types:
+- `AppName` = `'Hit Triage' | 'Hit Design' | 'PeptiHit'`
+- `HitTriageCampaign` — campaign state: name, template, status, filters, ingest config, save path, permissions, layout, column types
+- `HitDesignCampaign` — like HitTriageCampaign but without filters/ingest; has tile viewer sketch state
+- `HitTriageTemplate` / `HitDesignTemplate` — template definitions with compute config, submit config, campaign fields, stages, layout
+- `TriagePermissions` — `{edit: string[], view: string[]}` storing group IDs
+
+### Constants — `src/app/consts.ts`
+
+Important constants and their roles:
+- `HitTriageComputeFunctionTag` / `HitDesignerFunctionTag` — tags for discoverable compute functions
+- `HitTriageDataSourceTag` / `HitTriageSubmitTag` — tags for data source and submit functions
+- `ViDColName = 'V-iD'`, `ViDSemType = 'HIT_DESIGN_VID'` — virtual ID column
+- `TileCategoriesColName = 'Stage'` — column used for tile viewer lanes
+- `HitDesignMolColName = 'Molecule'`, `PeptiHitHelmColName = 'Helm'`
+- `i18n` — UI label strings
+- `CampaignGrouping` enum — None, Template, Status, Author, Last Modified User
+
+### Views (per app)
+
+**Hit Triage views** (`src/app/hit-triage-views/`):
+- `info-view.ts` — Landing page: list campaigns, create new campaign/template
+- `submit-view.ts` — Submit filtered results to a configured function
+
+**Hit Design views** (`src/app/hit-design-views/`):
+- `info-view.ts` — Landing page with campaign table, grouping, sorting, create/continue campaigns
+- `submit-view.ts` — Submit results
+- `tiles-view.ts` — Tile/Kanban viewer for stage-based molecule organization
+
+**PeptiHit views** (`src/app/pepti-hits-views/`):
+- `info-view.ts` — Extends Hit Design info view for peptide context
+
+### Accordions (`src/app/accordeons/`)
+
+UI accordions for creating new campaigns and templates:
+
+| File | Purpose |
+|---|---|
+| `new-campaign-accordeon.ts` | Hit Triage new campaign form: file/query data source, campaign fields |
+| `new-template-accordeon.ts` | Hit Triage template creator: name, key, compute config, submit function, layout, campaign fields |
+| `new-hit-design-campaign-accordeon.ts` | Hit Design/PeptiHit new campaign: creates initial DataFrame with Molecule, Stage, V-iD columns |
+| `new-hit-design-template-accordeon.ts` | Hit Design/PeptiHit template creator with stages editor |
+| `layout-input.ts` | Reusable layout file input that parses `.layout` files into `DG.ViewLayout` |
+
+### Dialogs (`src/app/dialogs/`)
+
+| File | Purpose |
+|---|---|
+| `functions-dialog.ts` | Compute configuration dialog: descriptor tree selection + tagged compute functions/scripts/queries with their parameter editors |
+| `save-campaign-dialog.ts` | Simple dialog to name a campaign before saving |
+| `permissions-dialog.ts` | Edit view/edit group permissions for a campaign. Default: All Users |
+
+### Utilities
+
+**`src/app/utils.ts`** — General helpers:
+- `loadCampaigns()` — loads campaign JSONs from `files/` storage, checks view permissions
+- `modifyUrl()` — updates URL query params without page reload
+- `checkEditPermissions()` / `checkViewPermissions()` — group-based permission checks
+- `addBreadCrumbsToRibbons()` — navigation breadcrumbs in ribbon
+- `joinQueryResults()` — joins query result dataframe back into main dataframe by molecule column
+- Campaign grouping/sorting helpers for info view tables
+
+**`src/app/utils/calculate-single-cell.ts`** — Runs compute pipeline (descriptors, functions, scripts, queries) on molecule values. Used for both batch column calculations and single-cell recalculations in Hit Design.
+
+**`src/app/utils/molreg.ts`** — V-iD (Virtual ID) molecule registration:
+- `obfuscateSmiles()` / `deobfuscateSmiles()` — XOR + base64 obfuscation using package secret key (`meta.sok`)
+- `registerMol()` — registers one molecule, returns V-iD string (e.g., `V000001`)
+- `registerMolsBatch()` — batch registration in groups of 50
+- `registerAllCampaignMols()` — scans all Hit Design campaigns and registers unregistered molecules
+
+**`src/packageSettingsEditor.ts`** — Custom settings editor widget. Settings:
+- Default sharing groups (view/edit) for new campaigns
+- Default campaign storage folder (default: `System.AppData/HitTriage`)
+
+**`src/pngRenderers.ts`** — `GasteigerPngRenderer`: custom `DG.GridCellRenderer` for base64 PNG images in grid cells.
+
+## Database Schema (`databases/hitdesign/`)
+
+PostgreSQL schema `hitdesign` with two migrations:
+
+**0000_init.sql** — Lock tables:
+- `campaign_locks(app_name, campaign_id, expires_at, locked_by)` — 30-second TTL campaign locks for concurrent edit protection
+- `update_logs(app_name, campaign_id, updated_at)` — tracks last save time
+
+**0001_dict.sql** — V-iD dictionary:
+- `vid_dictionary(id SERIAL, vid VARCHAR(15) GENERATED AS 'V' || LPAD(id, 6, '0'), mh_string TEXT UNIQUE)` — canonical SMILES → auto-generated V-iD
+- `campaign_vids(app_name, vid, campaign_id, created_by)` — tracks which V-iDs appear in which campaigns
+
+## SQL Queries (`queries/`)
+
+**vid.sql** (connection: `HitTriage:hitdesign`):
+- `addMolecule` — upsert single molecule, return V-iD
+- `addMolecules` — batch upsert via `UNNEST`, preserves input order
+- `getMoleculeByVid` — lookup canonical SMILES by V-iD
+- `getCampaignsByVid` — find all campaigns containing a V-iD
+
+**locks.sql** (connection: `HitTriage:hitdesign`):
+- `acquireCampaignLock` — acquire 30-second lock (auto-cleans expired)
+- `releaseCampaignLock` — release lock and log update timestamp
+- `getLastModified` — get last save timestamp for a campaign
+
+## Files Storage (`files/`)
+
+Campaign and template data stored in `System.AppData/HitTriage/`:
+
+```
+files/
+  Hit Triage/campaigns/{ID}/campaign.json + enriched_table.csv
+  Hit Triage/templates/{Name}.json
+  Hit Design/campaigns/{ID}/campaign.json + enriched_table.csv
+  Hit Design/templates/{Name}.json
+  PeptiHit/campaigns/{ID}/campaign.json + enriched_table.csv
+  PeptiHit/templates/{Name}.json
+```
+
+Each campaign has a `campaign.json` (metadata, template snapshot, permissions, layout) and `enriched_table.csv` (the molecule data).
+
+## Extension Points
+
+The package discovers external functions via tagged roles:
+
+| Tag/Role | Purpose | Expected Signature |
+|---|---|---|
+| `HitTriageFunction` | Compute function for property calculation | `(df: DataFrame, molCol: Column, ...args) → void` (mutates df) |
+| `HitDesignerFunction` | Same but specific to Hit Design context | Same as above |
+| `hitTriageDataSource` | Data source for Hit Triage campaigns | `(...args) → DataFrame` (with molecule column) |
+| `hitTriageSubmitFunction` | Submit handler called on campaign submission | `(df: DataFrame, molecules: string) → void` |
+
+## Package Settings (in `package.json`)
+
+- `properties.view` / `properties.edit` — default user group IDs for new campaign sharing
+- `properties.defaultCampaignFolder` — storage path (default: `System.AppData/HitTriage`)
+- `meta.sok` — secret key for SMILES obfuscation in V-iD dictionary
+
+## Key Dependencies
+
+- `@datagrok-libraries/compute-utils` — compute pipeline utilities
+- `@datagrok-libraries/utils` — `u2.appHeader`, `ItemsGrid` UI components
+- `uuid` — campaign ID generation
+- `typeahead-standalone` — autocomplete UI
+
+## Quick Lookups
+
+| Looking for... | Check first |
+|---|---|
+| App registration, tree browsers, demo functions | `src/package.ts` |
+| Campaign types, template types | `src/app/types.ts` |
+| UI labels, column names, tag constants | `src/app/consts.ts` |
+| Hit Triage campaign flow | `src/app/hit-triage-app.ts` |
+| Hit Design campaign flow (+ PeptiHit base) | `src/app/hit-design-app.ts` |
+| Peptide-specific logic | `src/app/pepti-hit-app.ts` |
+| Campaign load/save, permissions, URL management | `src/app/utils.ts` |
+| Molecule registration (V-iD) | `src/app/utils/molreg.ts` |
+| Property calculation pipeline | `src/app/utils/calculate-single-cell.ts` |
+| Compute function picker dialog | `src/app/dialogs/functions-dialog.ts` |
+| Campaign creation UI | `src/app/accordeons/` |
+| Database schema | `databases/hitdesign/` |
+| SQL queries (V-iD, locks) | `queries/` |
+| Package settings editor | `src/packageSettingsEditor.ts` |

package/css/hit-triage.css

@@ -3,31 +3,6 @@
     height: initial !important;
 }
 
-.hit-triage-compute-dialog-pane-header {
-    display: flex;
-    align-items: center;
-    justify-content: end;
-}
-
-.hit-triage-compute-dialog-host>.d4-tab-host.d4-tab-vertical>.d4-tab-header-stripe>.d4-tab-header.hit-triage-compute-dialog-pane-header {
-    border: none;
-    border-left: 4px solid transparent;
-    border-radius: 1px;
-    padding: 4px 8px;
-    min-height: 28px;
-    justify-content: flex-end;
-    flex-direction: row-reverse;
-}
-
-.hit-triage-compute-dialog-host>.d4-tab-host.d4-tab-vertical>.d4-tab-header-stripe>.d4-tab-header.hit-triage-compute-dialog-pane-header.selected {
-    border-left: 4px solid var(--blue-1);
-    background-color: #f2f2f5;
-}
-
-.hit-triage-compute-dialog-host>.d4-tab-host.d4-tab-vertical>.d4-tab-header-stripe>.d4-tab-header.hit-triage-compute-dialog-pane-header>span {
-    padding: 0 4px;
-}
-
 table.hit-triage-table {
     margin: 10px;
     width: calc(100% - 20px);
@@ -64,22 +39,6 @@ table.hit-triage-table {
     width: 100% !important;
 }
 
-.hit-triage-compute-dialog-host {
-    max-height: 550px;
-    max-width: 800px;
-    min-width: 550px;
-    overflow: clip;
-}
-
-.hit-triage-compute-dialog-descriptors-group {
-    margin-left: 16px;
-    overflow: hidden;
-}
-
-.oy-scroll {
-    overflow-y: scroll;
-}
-
 .d4-ribbon-name .ui-breadcrumbs {
 	overflow: hidden;
     white-space: nowrap;

package/dist/package-test.js

@@ -1,2 +1,2 @@
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