diff --git a/assay/api-src/org/labkey/api/assay/plate/Plate.java b/assay/api-src/org/labkey/api/assay/plate/Plate.java index c754bdcd7e2..ea0c8973633 100644 --- a/assay/api-src/org/labkey/api/assay/plate/Plate.java +++ b/assay/api-src/org/labkey/api/assay/plate/Plate.java @@ -66,11 +66,11 @@ public interface Plate extends PropertySet, Identifiable @Nullable WellGroup getWellGroup(int rowId); - @NotNull List getWellGroups(); + @NotNull List getWellGroups(); - @NotNull List getWellGroups(Position position); + @NotNull List getWellGroups(Position position); - @NotNull List getWellGroups(WellGroup.Type type); + @NotNull List getWellGroups(WellGroup.Type type); @NotNull Map> getWellGroupMap(); diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateService.java b/assay/api-src/org/labkey/api/assay/plate/PlateService.java index 5021f606c33..b55634aa859 100644 --- a/assay/api-src/org/labkey/api/assay/plate/PlateService.java +++ b/assay/api-src/org/labkey/api/assay/plate/PlateService.java @@ -156,7 +156,7 @@ static PlateService get() */ @Nullable Plate getPlate(ContainerFilter cf, Long plateSetId, Object plateIdentifier); - @NotNull List getPlates(Container container); + @NotNull List getPlates(Container container); /** * Gets the plate set by ID diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateSet.java b/assay/api-src/org/labkey/api/assay/plate/PlateSet.java index 8e06e1c4c77..8dc659afa4d 100644 --- a/assay/api-src/org/labkey/api/assay/plate/PlateSet.java +++ b/assay/api-src/org/labkey/api/assay/plate/PlateSet.java @@ -26,7 +26,7 @@ public interface PlateSet extends Identifiable boolean isTemplate(); - List getPlates(); + List getPlates(); PlateSetType getType(); diff --git a/assay/package-lock.json b/assay/package-lock.json index 3833d904a1c..f501dd2d16f 100644 --- a/assay/package-lock.json +++ b/assay/package-lock.json @@ -14,7 +14,12 @@ "@labkey/build": "9.1.1", "@types/jest": "30.0.0", "@types/react": "18.3.27", - "@types/react-dom": "18.3.7" + 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+ "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", + "dev": true, + "license": "ISC" + }, + "node_modules/write-file-atomic": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-5.0.1.tgz", + "integrity": "sha512-+QU2zd6OTD8XWIJCbffaiQeH9U73qIqafo1x6V1snCWYGJf6cVE0cDR4D8xRzcEnfI21IFrUPzPGtcPf8AC+Rw==", + "dev": true, + "license": "ISC", + "dependencies": { + "imurmurhash": "^0.1.4", + "signal-exit": "^4.0.1" + }, + "engines": { + "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + } + }, + "node_modules/write-file-atomic/node_modules/signal-exit": { + "version": "4.1.0", + "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-4.1.0.tgz", + "integrity": "sha512-bzyZ1e88w9O1iNJbKnOlvYTrWPDl46O1bG0D3XInv+9tkPrxrN8jUUTiFlDkkmKWgn1M6CfIA13SuGqOa9Korw==", + "dev": true, + "license": "ISC", + "engines": { + "node": ">=14" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/ws": { "version": "8.20.0", "resolved": "https://registry.npmjs.org/ws/-/ws-8.20.0.tgz", @@ -10808,6 +14673,33 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/xml-name-validator": { + "version": "5.0.0", + "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-5.0.0.tgz", + "integrity": "sha512-EvGK8EJ3DhaHfbRlETOWAS5pO9MZITeauHKJyb8wyajUfQUenkIg2MvLDTZ4T/TgIcm3HU0TFBgWWboAZ30UHg==", + "dev": true, + "license": "Apache-2.0", + "engines": { + "node": ">=18" + } + }, + "node_modules/xmlchars": { + "version": "2.2.0", + "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz", + "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==", + "dev": true, + "license": "MIT" + }, + "node_modules/y18n": { + "version": "5.0.8", + "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", + "integrity": 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"integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", + "dev": true, + "license": "ISC", + "engines": { + "node": ">=12" + } + }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", diff --git a/assay/package.json b/assay/package.json index 7e67a515ade..e4b0b40973e 100644 --- a/assay/package.json +++ b/assay/package.json @@ -9,7 +9,42 @@ "start-link": "cross-env LINK=true npm run start", "build-dev": "npm run clean && cross-env NODE_ENV=development webpack --config node_modules/@labkey/build/webpack/dev.config.js --color", "build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map webpack --config node_modules/@labkey/build/webpack/prod.config.js --color --progress --profile", - "clean": "rimraf resources/web/assay/gen && rimraf resources/views/gen && rimraf resources/web/gen" + "clean": "rimraf resources/web/assay/gen && rimraf resources/views/gen && rimraf resources/web/gen", + "test": "cross-env NODE_ENV=test jest" + }, + "jest": { + "globals": { + "LABKEY": { + "container": { + "formats": { + "dateFormat": "yyyy-MM-dd" + } + }, + "user": { + "id": 1004 + }, + "project": {}, + "moduleContext": {} + } + }, + "moduleNameMapper": { + "\\.(scss|css)$": "/test/js/fileMock.js" + }, + "moduleFileExtensions": ["tsx", "ts", "js"], + "preset": "ts-jest", + "setupFilesAfterEnv": ["/test/js/setup.ts"], + "testEnvironment": "jsdom", + "testMatch": null, + "testRegex": "(\\.(test))\\.(ts|tsx)$", + "testResultsProcessor": "jest-teamcity-reporter", + "transform": { + "^.+\\.tsx?$": [ + "ts-jest", + { + "tsconfig": "node_modules/@labkey/build/webpack/tsconfig.test.json" + } + ] + } }, "dependencies": { "@labkey/components": "7.31.1" @@ -18,6 +53,11 @@ "@labkey/build": "9.1.1", "@types/jest": "30.0.0", "@types/react": "18.3.27", - "@types/react-dom": "18.3.7" + "@types/react-dom": "18.3.7", + "jest": "30.3.0", + "jest-cli": "30.3.0", + "jest-environment-jsdom": "30.3.0", + "jest-teamcity-reporter": "0.9.0", + "ts-jest": "29.4.6" } } diff --git a/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.scss b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.scss new file mode 100644 index 00000000000..f814107cf20 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.scss @@ -0,0 +1,732 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +/* + * ────────────────────────────────────────────────────────────────────────────── + * Overall layout (vertical stack): + * + * ┌──────────────────────────────────────────────────────────┐ + * │ .status-bar (Save & Close | Save | Cancel | status) │ + * ├──────────────────────────────────────────────────────────┤ + * │ .plate-template-designer__header (Plate Name input) │ + * ├──────────────────────────────────────────────────────────┤ + * │ .plate-template-designer__body (horizontal flex) │ + * │ ┌──────────────────────────────┐ ┌───────────────────┐ │ + * │ │ __left (flex: 0 0 auto) │ │ __right (flex:1) │ │ + * │ │ .group-types-panel │ │ right-panel-tabs │ │ + * │ │ ├─ tab strip │ │ + WellGroupProps │ │ + * │ │ └─ tab-body (flex row) │ │ or WarningPanel│ │ + * │ │ ├─ group list │ │ │ │ + * │ │ └─ .plate-grid-area │ │ │ │ + * │ │ ├─ TemplateGrid │ │ │ │ + * │ │ └─ ShiftPanel │ │ │ │ + * │ └──────────────────────────────┘ └───────────────────┘ │ + * └──────────────────────────────────────────────────────────┘ + * + * The left column is sized to its content (fixed width); the right column grows + * to fill remaining space with a minimum width so it doesn't collapse. + * ────────────────────────────────────────────────────────────────────────────── + */ + +// Visually-hidden utility — renders only to assistive technology +.sr-only { + position: absolute; + width: 1px; + height: 1px; + padding: 0; + margin: -1px; + overflow: hidden; + clip: rect(0, 0, 0, 0); + white-space: nowrap; + border: 0; +} + +// Root container +.plate-template-designer { + padding: 12px 16px; + font-size: 0.8125rem; + + &__error { + color: #c00; + padding: 16px; + } + + &__loading { + padding: 16px; + color: #666; + } + + &__header { + margin: 10px 0; + } + + &__name-label { + font-weight: bold; + } + + &__name-input { + margin-left: 8px; + padding: 4px 6px; + border: 1px solid #ccc; + border-radius: 3px; + font-size: 0.8125rem; + width: 280px; + } + + // Horizontal flex: left (group panel + grid) | right (properties / warnings) + &__body { + display: flex; + gap: 16px; + align-items: flex-start; + } + + // Shrinks/grows to fit GroupTypesPanel content; does not flex + &__left { + flex: 0 0 auto; + } + + // Fills remaining width; min-width prevents collapse when the window is narrow + &__right { + flex: 1; + min-width: 200px; + + // Guarantee hidden tabpanels (properties / warnings) take no space even if + // the framework's CSS reset omits the [hidden]{display:none} UA rule. + [hidden] { + display: none; + } + } +} + +// ── StatusBar ───────────────────────────────────────────────────────────────── +// Pinned above the plate header; uses flex to space buttons and status text. +.status-bar { + display: flex; + align-items: center; + gap: 8px; + padding: 6px 0 10px; + border-bottom: 1px solid #ddd; + margin-bottom: 8px; + + &__btn { + padding: 5px 14px; + border: 1px solid #aaa; + border-radius: 3px; + background: #f5f5f5; + cursor: pointer; + font-size: 0.8125rem; + + &:hover:not(:disabled) { + background: #e8e8e8; + } + + &:disabled { + opacity: 0.5; + cursor: default; + } + + &--primary { + background: #337ab7; + border-color: #2e6da4; + color: #fff; + + &:hover:not(:disabled) { + background: #286090; + } + } + } + + // Unsaved-changes indicator — uses role="status" in JSX for screen reader announcements + &__dirty { + color: #7a5800; + font-style: italic; + } + + // Transient save status ("Saving…", "Saved.") — auto-clears after 5 s + &__status { + color: #555; + } + + // Validation error message (e.g., empty plate name) — uses role="alert" in JSX + &__error { + color: #c00; + font-weight: bold; + margin-left: 12px; + } +} + +// ── GroupTypesPanel ─────────────────────────────────────────────────────────── +// Outer panel with a tab strip and a two-column flex body: +// left column: scrollable group list + create controls +// right column: TemplateGrid + ShiftPanel (passed as children) +.group-types-panel { + border: 1px solid #ccc; + border-radius: 3px; + + &__tabs { + display: flex; + flex-wrap: wrap; + border-bottom: 1px solid #ccc; + background: #f0f0f0; + } + + &__tab { + padding: 5px 10px; + border: none; + background: transparent; + cursor: pointer; + font-size: 0.75rem; + border-right: 1px solid #ddd; + + &:hover { + background: #e0e0e0; + } + + &--active { + background: #fff; + font-weight: bold; + border-bottom: 2px solid #337ab7; + } + } + + // Flex row: [group list] [grid area] — keeps the grid visually docked to the panel + &__tab-body { + display: flex; + align-items: flex-start; + gap: 12px; + padding: 8px; + + // Some CSS frameworks omit the UA-stylesheet [hidden]{display:none} rule. + // The higher specificity (class + attribute) ensures this wins over display:flex. + &[hidden] { + display: none; + } + } + + // Group list column — min-width prevents short lists from collapsing + &__groups { + flex-shrink: 0; + min-width: 280px; + min-height: 60px; + } + + // Individual group row — clickable to select; keyboard-accessible via tabIndex + onKeyDown + &__group { + display: flex; + align-items: center; + gap: 6px; + padding: 4px 6px; + margin-bottom: 3px; + border-radius: 3px; + cursor: pointer; + border: 1px solid transparent; + min-width: 0; + + &:hover { + background: #f0f0f0; + } + + &--active { + border-color: #337ab7; + background: #e8f0fb; + } + } + + // Colour indicator matching the group's colour on the grid + &__color-swatch { + display: inline-block; + width: 12px; + height: 12px; + border-radius: 2px; + border: 1px solid rgba(0, 0, 0, 0.2); + flex-shrink: 0; + } + + &__group-name { + flex: 1; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; + min-width: 0; + } + + // In-place rename input (replaces group-name span when renaming is active) + &__rename-input { + flex: 1; + padding: 1px 4px; + border: 1px solid #337ab7; + border-radius: 3px; + font-size: 0.75rem; + min-width: 0; + + &--error { + border-color: #c00; + } + } + + // Validation error shown below the create row or the rename input + &__name-error { + color: #c00; + font-size: 0.75rem; + margin-top: 2px; + } + + // Rename + delete buttons; always rendered to keep row height uniform. + // Inactive rows get --hidden: visibility:hidden preserves layout space while + // pointer-events:none blocks mouse interaction. + &__group-actions { + display: flex; + gap: 2px; + margin-left: auto; + flex-shrink: 0; + + &--hidden { + visibility: hidden; + pointer-events: none; + } + } + + &__action-btn { + padding: 5px 7px; + min-height: 24px; + min-width: 24px; + border: 1px solid #ccc; + border-radius: 2px; + background: transparent; + cursor: pointer; + font-size: 0.6875rem; + line-height: 1; + color: #555; + + &:hover { + background: #e0e0e0; + } + + &--delete { + color: #c00; + + &:hover { + background: #ffe0e0; + } + } + } + + // Inline "Delete?" prompt label shown before the Yes / No confirmation buttons. + &__confirm-text { + font-size: 0.75rem; + color: #333; + margin-right: 2px; + white-space: nowrap; + } + + // Row that holds the new-group name input + Create / Create multiple buttons + &__create-row { + display: flex; + align-items: center; + gap: 4px; + margin-top: 6px; + } + + // Shared by both the (free-text) variants + &__new-name-input { + flex: 1; + padding: 3px 5px; + border: 1px solid #ccc; + border-radius: 3px; + font-size: 0.75rem; + min-width: 0; + } + + &__add-btn { + padding: 3px 8px; + font-size: 0.75rem; + border: 1px solid #aaa; + border-radius: 3px; + background: #f5f5f5; + cursor: pointer; + color: #333; + white-space: nowrap; + + &:hover:not(:disabled) { + background: #e8e8e8; + } + + &:disabled { + opacity: 0.5; + cursor: default; + } + + &--primary { + background: #337ab7; + border-color: #2e6da4; + color: #fff; + + &:hover:not(:disabled) { + background: #286090; + } + } + } +} + +// ── Multi-create dialog ─────────────────────────────────────────────────────── +// Modal dialog for batch-creating N numbered groups. +// Uses the native element with showModal() for top-layer placement, focus +// restoration on close, and a browser-managed backdrop. Focus is trapped inside the +// dialog while open (see MultiCreateDialog focus-trap effect). +.multi-create-dialog { + background: #fff; + border: 1px solid #ccc; + border-radius: 4px; + box-shadow: 0 4px 16px rgba(0, 0, 0, 0.2); + padding: 20px; + min-width: 300px; + + &::backdrop { + background: rgba(0, 0, 0, 0.3); + } + + &__title { + font-weight: bold; + font-size: 0.875rem; + margin-bottom: 14px; + } + + // Flex column container replacing the old layout table + &__form { + display: flex; + flex-direction: column; + gap: 10px; + } + + // Each label + input row + &__field { + display: flex; + align-items: flex-start; + gap: 16px; + } + + // Label cells carry id attributes and are referenced via aria-labelledby on the inputs + &__label { + padding-top: 5px; + white-space: nowrap; + font-size: 0.8125rem; + min-width: 80px; + } + + // Wrapper for count input + error message (stacked vertically) + &__count-area { + display: flex; + flex-direction: column; + } + + &__input { + padding: 3px 5px; + border: 1px solid #ccc; + border-radius: 3px; + font-size: 0.8125rem; + width: 100%; + box-sizing: border-box; + + &--count { + width: 80px; + } + } + + &__error { + color: #c00; + font-size: 0.75rem; + margin-top: 2px; + } + + &__buttons { + display: flex; + gap: 6px; + justify-content: flex-end; + } +} + +// ── Plate grid area ─────────────────────────────────────────────────────────── +// Centres the TemplateGrid and ShiftPanel as a vertical column inside GroupTypesPanel. +.plate-grid-area { + display: flex; + flex-direction: column; + align-items: center; + gap: 8px; +} + +// ── ShiftPanel ──────────────────────────────────────────────────────────────── +// 3×3 CSS grid with arrow buttons at compass positions and a label in the centre. +// Empty corners use placeholders to maintain grid alignment. +.shift-panel { + &__grid { + display: grid; + grid-template-columns: repeat(3, 26px); + grid-template-rows: repeat(3, 26px); + gap: 2px; + align-items: center; + justify-items: center; + } + + &__btn { + width: 26px; + height: 26px; + padding: 0; + border: 1px solid #aaa; + border-radius: 3px; + background: #f5f5f5; + cursor: pointer; + font-size: 0.875rem; + line-height: 1; + + &:hover { + background: #e8e8e8; + } + } + + &__label { + font-size: 0.625rem; + color: #666; + text-align: center; + line-height: 1; + } +} + +// ── TemplateGrid ────────────────────────────────────────────────────────────── +// HTML table where each is a well. The user paints groups by clicking or dragging. +// Background colour comes from the colorMap for the active tab's groups (inline style). +// The --active modifier draws an outline around wells belonging to the selected group. +.template-grid { + user-select: none; // Prevents text selection during drag painting + + &__table { + border-collapse: collapse; + border: 1px solid #aaa; + } + + &__corner { + width: 24px; + height: 24px; + } + + &__col-header { + text-align: center; + font-size: 0.6875rem; + font-weight: bold; + width: 28px; + height: 22px; + background: #f0f0f0; + border: 1px solid #ccc; + } + + &__row-header { + text-align: center; + font-size: 0.6875rem; + font-weight: bold; + width: 22px; + background: #f0f0f0; + border: 1px solid #ccc; + } + + &__cell { + width: 28px; + height: 28px; + border: 1px solid #ccc; + cursor: crosshair; + transition: filter 0.1s; + + &:hover { + filter: brightness(0.88); + } + + // Indicates cells belonging to the currently active group + &--active { + outline: 2px solid #333; + outline-offset: -2px; + } + } +} + +// ── Right panel tabs ────────────────────────────────────────────────────────── +// Tab strip shown in the right column when showWarningPanel is true. +// --warn colours the Warnings tab amber; --active+--warn shifts the indicator colour too. +.right-panel-tabs { + display: flex; + border-bottom: 1px solid #ccc; + margin-bottom: 8px; + + &__tab { + padding: 5px 10px; + border: none; + background: transparent; + cursor: pointer; + font-size: 0.75rem; + border-bottom: 2px solid transparent; + margin-bottom: -1px; + + &:hover { + background: #f0f0f0; + } + + &--active { + font-weight: bold; + border-bottom-color: #337ab7; + background: #fff; + } + + &--warn { + color: #7a5800; + } + + &--active#{&}--warn { + border-bottom-color: #7a5800; + } + } +} + +// ── WellGroupProperties ─────────────────────────────────────────────────────── +// Table-based key/value editor for the active group's property bag. +// The --empty modifier styles the "no group selected" placeholder. +.well-group-properties { + border: 1px solid #ccc; + border-radius: 3px; + padding: 10px; + min-height: 60px; + + &--empty { + color: #767676; + font-style: italic; + } + + &__title { + font-weight: bold; + margin-bottom: 8px; + } + + &__no-props { + color: #767676; + font-style: italic; + font-size: 0.75rem; + } + + &__table { + width: 100%; + border-collapse: collapse; + } + + // Key column — fixed at 40% width, non-wrapping + &__key { + font-weight: bold; + padding: 3px 6px 3px 0; + white-space: nowrap; + width: 40%; + } + + &__value-cell { + padding: 2px 4px 2px 0; + } + + &__action-cell { + padding: 2px 0 2px 6px; + white-space: nowrap; + width: 1%; // Shrink-wraps to button content + } + + &__value { + padding: 3px 4px; + border: 1px solid #ccc; + border-radius: 3px; + font-size: 0.75rem; + width: 100%; + box-sizing: border-box; + } + + &__delete-btn { + padding: 5px 7px; + min-height: 24px; + min-width: 24px; + border: 1px solid #ccc; + border-radius: 2px; + background: transparent; + cursor: pointer; + font-size: 0.6875rem; + line-height: 1; + color: #c00; + + &:hover { + background: #ffe0e0; + } + } + + // Footer row — Add new property; separated visually from existing entries + &__add-row td { + border-top: 1px solid #eee; + padding-top: 6px; + } + + &__new-key { + padding: 3px 5px; + border: 1px solid #ccc; + border-radius: 3px; + font-size: 0.75rem; + width: 100%; + box-sizing: border-box; + } + + &__new-value { + padding: 3px 5px; + border: 1px solid #ccc; + border-radius: 3px; + font-size: 0.75rem; + width: 100%; + box-sizing: border-box; + } + + &__add-btn { + padding: 3px 8px; + border: 1px solid #aaa; + border-radius: 3px; + background: #f5f5f5; + cursor: pointer; + font-size: 0.75rem; + white-space: nowrap; + + &:hover:not(:disabled) { + background: #e8e8e8; + } + + &:disabled { + opacity: 0.5; + cursor: default; + } + } +} + +// ── WarningPanel ────────────────────────────────────────────────────────────── +// Amber-tinted panel listing validation warnings from computeWarnings(). +// Only rendered when plate.showWarningPanel is true (assay-type controlled). +.warning-panel { + border: 1px solid #e8a000; + border-radius: 3px; + padding: 10px; + background: #fffbe6; + + &__none { + color: #767676; + font-style: italic; + font-size: 0.75rem; + } + + &__list { + margin: 0; + padding-left: 18px; + } + + &__item { + color: #7a5800; + font-size: 0.75rem; + margin-bottom: 3px; + } +} diff --git a/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.test.tsx b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.test.tsx new file mode 100644 index 00000000000..eadbde173c6 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.test.tsx @@ -0,0 +1,141 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { act, render, screen } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; +import { Ajax } from '@labkey/api'; + +import { PlateTemplateDesigner } from './PlateTemplateDesigner'; +import { PlateTemplate } from './models'; + +jest.mock('@labkey/api', () => ({ + ActionURL: { + getParameter: jest.fn().mockReturnValue(null), + buildURL: jest.fn().mockReturnValue('/mock-url'), + }, + Ajax: { + request: jest.fn(), + }, + Utils: { + // Pass the callback through unchanged so tests can invoke it directly. + getCallbackWrapper: (fn: any) => fn, + }, +})); + +const mockPlate: PlateTemplate = { + rowId: 1, + name: 'Test Plate', + type: 'assay', + rows: 4, + cols: 4, + groupTypes: ['SPECIMEN', 'CONTROL'], + canCreateGroupsByType: { SPECIMEN: true, CONTROL: true }, + groups: [], + plateProperties: {}, + typesToDefaultGroups: {}, + showWarningPanel: false, + existingTemplateNames: [], + copyMode: false, + defaultPlateName: '', +}; + +describe('PlateTemplateDesigner', () => { + let successCallback: ((response: any) => void) | undefined; + let failureCallback: ((response: any) => void) | undefined; + + beforeEach(() => { + jest.clearAllMocks(); + (Ajax.request as jest.Mock).mockImplementation(({ success, failure }) => { + successCallback = success; + failureCallback = failure; + }); + }); + + afterEach(() => { + successCallback = undefined; + failureCallback = undefined; + }); + + describe('initial load', () => { + test('shows loading state before data arrives', () => { + render(); + expect(screen.getByText('Loading...')).toBeInTheDocument(); + }); + + test('calls Ajax.request on mount', () => { + render(); + expect(Ajax.request).toHaveBeenCalledTimes(1); + }); + + test('renders the plate name input after a successful load', () => { + render(); + act(() => successCallback?.({ data: mockPlate })); + expect(screen.getByDisplayValue('Test Plate')).toBeInTheDocument(); + }); + + test('renders group type tabs after a successful load', () => { + render(); + act(() => successCallback?.({ data: mockPlate })); + expect(screen.getByRole('tab', { name: 'SPECIMEN' })).toBeInTheDocument(); + expect(screen.getByRole('tab', { name: 'CONTROL' })).toBeInTheDocument(); + }); + + test('uses defaultPlateName as the initial plate name when provided', () => { + render(); + act(() => successCallback?.({ + data: { ...mockPlate, defaultPlateName: 'Copy of Test Plate', name: 'Test Plate' }, + })); + expect(screen.getByDisplayValue('Copy of Test Plate')).toBeInTheDocument(); + }); + + test('starts in dirty state when copyMode is true', () => { + render(); + act(() => successCallback?.({ data: { ...mockPlate, copyMode: true } })); + expect(screen.getByText('Unsaved changes')).toBeInTheDocument(); + }); + }); + + describe('load failure', () => { + test('renders the server exception message on failure', () => { + render(); + act(() => failureCallback?.({ exception: 'Server error' })); + expect(screen.getByText('Server error')).toBeInTheDocument(); + }); + + test('renders a fallback message when exception is missing', () => { + render(); + act(() => failureCallback?.({})); + expect(screen.getByText('Failed to load plate template.')).toBeInTheDocument(); + }); + }); + + describe('plate name editing', () => { + async function renderLoaded() { + render(); + act(() => successCallback?.({ data: mockPlate })); + return screen.getByDisplayValue('Test Plate'); + } + + test('changing the plate name marks the form dirty', async () => { + const input = await renderLoaded(); + await userEvent.clear(input); + await userEvent.type(input, 'My Plate'); + expect(screen.getByText('Unsaved changes')).toBeInTheDocument(); + }); + + test('Save button is disabled when form is clean', async () => { + await renderLoaded(); + expect(screen.getByRole('button', { name: 'Save' })).toBeDisabled(); + }); + + test('Save button is enabled after a name change', async () => { + const input = await renderLoaded(); + await userEvent.clear(input); + await userEvent.type(input, 'My Plate'); + expect(screen.getByRole('button', { name: 'Save' })).toBeEnabled(); + }); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.tsx b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.tsx new file mode 100644 index 00000000000..5025beb9a56 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.tsx @@ -0,0 +1,504 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React, { useCallback, useEffect, useMemo, useRef, useState } from 'react'; +import { ActionURL, Ajax, Utils } from '@labkey/api'; + +import { PlateTemplate, Position, WellGroup, computeWarnings } from './models'; +import { StatusBar } from './components/StatusBar'; +import { GroupTypesPanel } from './components/GroupTypesPanel'; +import { RIGHT_TAB_PROPERTIES, RightPanel, RightTab } from './components/RightPanel'; +import { ShiftPanel } from './components/ShiftPanel'; +import { TemplateGrid } from './components/TemplateGrid'; + +import './PlateTemplateDesigner.scss'; + +/** + * Root component of the Plate Template Designer. + * + * ─── User workflow ────────────────────────────────────────────────────────────── + * 1. On mount, URL parameters are read (templateName, plateId, assayType, rowCount, + * colCount, copy) and the plate definition is fetched from the server. + * 2. The user selects a group type tab (e.g. CONTROL, SPECIMEN, REPLICATE). + * 3. Within that type, the user selects or creates a named group. + * 4. The user clicks or drags wells on the grid to paint them onto the active group. + * 5. The user optionally edits well group properties in the right panel. + * 6. "Save" persists without leaving; "Save & Close" saves then navigates to returnURL + * (or the plate list). "Cancel" navigates away without saving. + * + * ─── State architecture ───────────────────────────────────────────────────────── + * `plate` is the single source of truth for all template data. All mutations go + * through `setPlate` with functional updaters to avoid stale-closure bugs. + * + * `activeGroup` is a denormalized mirror of the currently selected group, kept in + * sync with `plate` via the sync effect below. It exists separately because: + * - Callbacks that use `setPlate(prev => ...)` don't have access to the current + * group data inside the updater; they use `activeGroup` from their closure. + * - Components that show the active group (WellGroupProperties, TemplateGrid + * cell highlighting) need a stable reference that doesn't require traversing + * `plate.groups` on every access. + * + * ─── ID conventions ───────────────────────────────────────────────────────────── + * Server-assigned group IDs are positive integers. Client-side created groups + * receive temporary negative IDs (nextGroupIdRef counts down from -1). This ensures + * new groups never collide with existing ones before the first save. The server + * replaces all IDs with permanent values on save; the client does not update + * individual group IDs — only the top-level `plate.rowId` is updated after save. + * + * ─── Cell interaction ─────────────────────────────────────────────────────────── + * Two cell callbacks are distinguished: + * `handleDragRect` — paints a rectangle; also evicts those cells from sibling + * groups of the same type (one cell can only belong to one group per type). + * Used during drag operations. + * `handleCellToggle` — toggle: if the cell is already in the active group, remove + * it; otherwise add it and evict it from any sibling group of the same type. + * Used for single-click (no drag movement). + */ + +const COLORS = [ + '#4e79a7', '#f28e2b', '#e15759', '#76b7b2', '#59a14f', + '#ecb830', '#9b59b6', '#e84878', '#7a4222', '#888888', + '#30c068', '#ccd828', '#4848cc', '#d04018', '#18a8c0', + '#c030a8', '#8caa28', '#583848', '#c8d8e8', '#204888', +]; + +export function assignColors(groups: WellGroup[]): Map { + const map = new Map(); + groups.forEach((g, i) => { + map.set(g.rowId, COLORS[i % COLORS.length]); + }); + return map; +} + +/** + * Toggles a single cell in the active group: + * - If the cell is already in the active group → remove it (no sibling changes). + * - If the cell is absent → add it to the active group and evict it from any + * other group of the same type so a cell never belongs to two groups of one type. + */ +export function toggleCell(groups: WellGroup[], activeGroupRowId: number, row: number, col: number): WellGroup[] { + const activeGroup = groups.find(g => g.rowId === activeGroupRowId); + if (!activeGroup) return groups; + const isInActiveGroup = activeGroup.positions.some(p => p.row === row && p.col === col); + const activeType = activeGroup.type; + return groups.map(g => { + if (g.rowId === activeGroupRowId) { + if (isInActiveGroup) { + return { ...g, positions: g.positions.filter(p => !(p.row === row && p.col === col)) }; + } + return { ...g, positions: [...g.positions, { row, col }] }; + } + // When adding: evict the cell from every sibling group of the same type + if (!isInActiveGroup && g.type === activeType) { + return { ...g, positions: g.positions.filter(p => !(p.row === row && p.col === col)) }; + } + return g; + }); +} + +export function isSameOrigin(url: string): boolean { + try { + return new URL(url, window.location.origin).origin === window.location.origin; + } catch { + return false; + } +} + +export function PlateTemplateDesigner(): JSX.Element { + const [plate, setPlate] = useState(null); + const [activeGroup, setActiveGroup] = useState(null); + const [activeTab, setActiveTab] = useState(''); + const [rightTab, setRightTab] = useState(RIGHT_TAB_PROPERTIES); + const [isDirty, setIsDirty] = useState(false); + const [status, setStatus] = useState(''); + const [colorMap, setColorMap] = useState>(new Map()); + const [error, setError] = useState(null); + const plateNameRef = useRef(''); // Mirrors plate.name; used in save-success to update URL without stale closure + const statusTimerRef = useRef | null>(null); + const nextGroupIdRef = useRef(-1); // Temporary negative IDs for client-created groups (see ID conventions above) + // Always-current ref so callbacks can read the latest activeGroup without stale-closure bugs. + const activeGroupRef = useRef(null); + activeGroupRef.current = activeGroup; + const nextColorIndexRef = useRef(0); // Monotonically increasing; never decrements on delete so colors stay unique + // Capture returnURL once at mount; handleSave strips query params via replaceState, so reading from the URL later would return null. + const returnURLRef = useRef(ActionURL.getParameter('returnUrl')); + + useEffect(() => { + const templateName = ActionURL.getParameter('templateName'); + const plateIdStr = ActionURL.getParameter('plateId'); + const assayType = ActionURL.getParameter('assayType'); + const templateType = ActionURL.getParameter('templateType'); + const rowCountStr = ActionURL.getParameter('rowCount'); + const colCountStr = ActionURL.getParameter('colCount'); + const copy = ActionURL.getParameter('copy') === 'true' || ActionURL.getParameter('copyTemplate') === 'true'; + + const params: Record = {}; + if (templateName) params.templateName = templateName; + if (plateIdStr) params.plateId = parseInt(plateIdStr, 10); + if (assayType) params.assayType = assayType; + if (templateType) params.templateType = templateType; + if (rowCountStr) params.rowCount = parseInt(rowCountStr, 10); + if (colCountStr) params.colCount = parseInt(colCountStr, 10); + params.copy = copy; + + Ajax.request({ + url: ActionURL.buildURL('plate', 'getDesignerTemplateDefinition.api'), + method: 'GET', + params, + success: Utils.getCallbackWrapper((response: { data: PlateTemplate }) => { + const plate = response.data; + plateNameRef.current = plate.defaultPlateName || plate.name || ''; + setPlate({ ...plate, name: plateNameRef.current }); + setColorMap(assignColors(plate.groups)); + nextColorIndexRef.current = plate.groups.length; + // Initialize below the minimum server rowId to avoid collisions. + // Server IDs should be positive, but guard against zero or negative values. + const minRowId = plate.groups.reduce((min, g) => Math.min(min, g.rowId), 0); + nextGroupIdRef.current = Math.min(-1, minRowId - 1); + setActiveTab(plate.groupTypes[0] ?? ''); + if (plate.copyMode) setIsDirty(true); + }), + failure: Utils.getCallbackWrapper((response: any) => { + setError(response?.exception ?? 'Failed to load plate template.'); + }, null, true), + }); + }, []); + + const handleNameChange = useCallback((name: string) => { + plateNameRef.current = name; + setPlate(prev => prev ? { ...prev, name } : null); + setIsDirty(true); + }, []); + + const handleGroupSelect = useCallback((group: WellGroup) => { + setActiveGroup(group); + }, []); + + // Called on every mouseenter during a drag with the rectangle defined by the + // mousedown cell and the current cell. preDragPositions is the snapshot of the + // active group's positions taken at mousedown (in TemplateGrid), before any drag + // events can modify state. + // + // Select mode (drag started on an empty cell): adds the rectangle to the group's + // pre-drag positions, so existing wells outside the rectangle are preserved. + // Also evicts rectangle cells from sibling groups of the same type. + // + // Unselect mode (drag started on a cell already in the group): removes all + // rectangle cells from the pre-drag positions without affecting other groups. + const handleDragRect = useCallback((r1: number, c1: number, r2: number, c2: number, isUnselect: boolean, preDragPositions: Position[]) => { + const activeGroup = activeGroupRef.current; + if (!activeGroup) return; + const minRow = Math.min(r1, r2); + const maxRow = Math.max(r1, r2); + const minCol = Math.min(c1, c2); + const maxCol = Math.max(c1, c2); + const rectPositions: Position[] = []; + for (let r = minRow; r <= maxRow; r++) { + for (let c = minCol; c <= maxCol; c++) { + rectPositions.push({ row: r, col: c }); + } + } + const rectKeys = new Set(rectPositions.map(p => `${p.row},${p.col}`)); + setPlate(prev => { + if (!prev) return null; + // Look up the active group's current type from prev to avoid stale-closure issues. + const currentType = prev.groups.find(g => g.rowId === activeGroup.rowId)?.type; + const updatedGroups = prev.groups.map(g => { + if (g.rowId === activeGroup.rowId) { + if (isUnselect) { + // Remove rect from pre-drag snapshot + return { ...g, positions: preDragPositions.filter(p => !rectKeys.has(`${p.row},${p.col}`)) }; + } + // Add rect to pre-drag snapshot (union, deduped) + const preDragKeys = new Set(preDragPositions.map(p => `${p.row},${p.col}`)); + const added = rectPositions.filter(p => !preDragKeys.has(`${p.row},${p.col}`)); + return { ...g, positions: [...preDragPositions, ...added] }; + } + if (!isUnselect && currentType !== undefined && g.type === currentType) { + // Evict rectangle cells from sibling groups of the same type + return { ...g, positions: g.positions.filter(p => !rectKeys.has(`${p.row},${p.col}`)) }; + } + return g; + }); + return { ...prev, groups: updatedGroups }; + }); + setIsDirty(true); + }, []); + + const handleCellToggle = useCallback((row: number, col: number) => { + const activeGroup = activeGroupRef.current; + if (!activeGroup) return; + setPlate(prev => prev ? { ...prev, groups: toggleCell(prev.groups, activeGroup.rowId, row, col) } : null); + setIsDirty(true); + }, []); + + const handleAddGroup = useCallback((type: string, name: string) => { + const rowId = nextGroupIdRef.current--; + const colorIndex = nextColorIndexRef.current++; + setPlate(prev => { + if (!prev) return null; + const newGroup: WellGroup = { + rowId, + type, + name, + positions: [], + properties: {}, + allowNewGroups: prev.canCreateGroupsByType?.[type] ?? false, + }; + return { ...prev, groups: [...prev.groups, newGroup] }; + }); + setColorMap(prev => { + const next = new Map(prev); + next.set(rowId, COLORS[colorIndex % COLORS.length]); + return next; + }); + // allowNewGroups is a stub here; the plate-sync effect re-derives it from the updated plate. + setActiveGroup({ rowId, type, name, positions: [], properties: {}, allowNewGroups: false }); + setIsDirty(true); + }, []); + + const handleShift = useCallback((verticalShift: number, horizontalShift: number) => { + setPlate(prev => { + if (!prev) return null; + const { rows, cols } = prev; + const updatedGroups = prev.groups.map(g => { + if (g.type !== activeTab) return g; + return { + ...g, + positions: g.positions.map(p => ({ + row: ((p.row - verticalShift) % rows + rows) % rows, + col: ((p.col - horizontalShift) % cols + cols) % cols, + })), + }; + }); + return { ...prev, groups: updatedGroups }; + }); + setIsDirty(true); + }, [activeTab]); + + const handleDeleteGroup = useCallback((rowId: number) => { + setPlate(prev => prev ? { ...prev, groups: prev.groups.filter(g => g.rowId !== rowId) } : null); + setColorMap(prev => { const next = new Map(prev); next.delete(rowId); return next; }); + setActiveGroup(prev => prev?.rowId === rowId ? null : prev); + setIsDirty(true); + }, []); + + const handleRenameGroup = useCallback((rowId: number, newName: string) => { + setPlate(prev => prev ? { ...prev, groups: prev.groups.map(g => g.rowId === rowId ? { ...g, name: newName } : g) } : null); + setActiveGroup(prev => prev?.rowId === rowId ? { ...prev, name: newName } : prev); + setIsDirty(true); + }, []); + + const handlePropertyChange = useCallback((groupRowId: number, key: string, value: string) => { + setPlate(prev => { + if (!prev) return null; + const updatedGroups = prev.groups.map(g => + g.rowId === groupRowId ? { ...g, properties: { ...g.properties, [key]: value } } : g + ); + return { ...prev, groups: updatedGroups }; + }); + setActiveGroup(prev => prev?.rowId === groupRowId ? { ...prev, properties: { ...prev.properties, [key]: value } } : prev); + setIsDirty(true); + }, []); + + const handleDeleteProperty = useCallback((groupRowId: number, key: string) => { + setPlate(prev => { + if (!prev) return null; + const updatedGroups = prev.groups.map(g => { + if (g.rowId !== groupRowId) return g; + const { [key]: _removed, ...rest } = g.properties; + return { ...g, properties: rest }; + }); + return { ...prev, groups: updatedGroups }; + }); + setActiveGroup(prev => { + if (prev?.rowId !== groupRowId) return prev; + const { [key]: _removed, ...rest } = prev.properties; + return { ...prev, properties: rest }; + }); + setIsDirty(true); + }, []); + + const warnings = useMemo(() => { + if (!plate?.showWarningPanel) return []; + return computeWarnings(plate); + }, [plate]); + + const navigateAway = useCallback(() => { + const returnURL = returnURLRef.current; + window.location.href = (returnURL && isSameOrigin(returnURL)) ? returnURL : ActionURL.buildURL('plate', 'plateList'); + }, []); + + /** + * Shared Ajax save logic. Takes the plate snapshot and a success callback to avoid + * duplicating the request setup and failure handler in handleSave / handleSaveAndClose. + * The plate is passed as a parameter (rather than closed over) so callers can pass the + * latest snapshot without worrying about stale state. + */ + const requestSave = useCallback((currentPlate: PlateTemplate, onSuccess: (response: { data: { rowId: number } }) => void) => { + setStatus('Saving...'); + Ajax.request({ + url: ActionURL.buildURL('plate', 'saveDesignerTemplate.api'), + method: 'POST', + jsonData: currentPlate, + success: Utils.getCallbackWrapper(onSuccess), + failure: Utils.getCallbackWrapper((response: any) => { + setStatus('Save failed: ' + (response?.exception ?? 'unknown error')); + }, null, true), + }); + }, []); + + const handleSave = useCallback(() => { + if (!plate) return; + requestSave(plate, (response) => { + const rowId = response.data.rowId; + setIsDirty(false); + setPlate(prev => prev ? { ...prev, rowId } : null); + // Update URL to canonical form so a refresh reloads this plate + const url = new URL(window.location.href); + url.search = ''; + url.searchParams.set('templateName', plateNameRef.current); + url.searchParams.set('plateId', String(rowId)); + window.history.replaceState(null, '', url.toString()); + setStatus('Saved.'); + if (statusTimerRef.current) clearTimeout(statusTimerRef.current); + statusTimerRef.current = setTimeout(() => setStatus(''), 5000); + }); + }, [plate, requestSave]); + + const handleSaveAndClose = useCallback(() => { + if (!plate) return; + if (!isDirty) { + navigateAway(); + return; + } + requestSave(plate, () => { + setIsDirty(false); + navigateAway(); + }); + }, [plate, isDirty, navigateAway, requestSave]); + + const handleCancel = useCallback(() => { + navigateAway(); + }, [navigateAway]); + + const handleTabChange = useCallback((tab: string) => { + setActiveTab(tab); + setActiveGroup(null); + }, []); + + // Clear pending status timer on unmount to prevent setState on an unmounted component. + useEffect(() => { + return () => { + if (statusTimerRef.current) clearTimeout(statusTimerRef.current); + }; + }, []); + + // Warn on unsaved navigation + useEffect(() => { + const handler = (e: BeforeUnloadEvent) => { + if (isDirty) { + e.preventDefault(); + e.returnValue = ''; + } + }; + window.addEventListener('beforeunload', handler); + return () => window.removeEventListener('beforeunload', handler); + }, [isDirty]); + + // Keep activeGroup in sync when plate changes. + // + // Most plate mutations go through setPlate(prev => ...) updaters which don't have + // access to the current activeGroup. After each plate update, this effect finds the + // matching group by rowId and refreshes activeGroup so downstream components (e.g. + // WellGroupProperties, TemplateGrid cell highlight) see the latest data. + // + // activeGroup is intentionally excluded from the deps array: adding it would cause + // an infinite loop (effect sets activeGroup → triggers effect → sets activeGroup …). + // handleDeleteGroup handles the "group no longer exists" case by explicitly setting + // activeGroup to null before this effect can run. + useEffect(() => { + if (!plate) return; + if (activeGroup) { + const updated = plate.groups.find(g => g.rowId === activeGroup.rowId); + if (updated) { + setActiveGroup(updated); + } + } + }, [plate]); // eslint-disable-line react-hooks/exhaustive-deps + + if (error) { + return
{error}
; + } + + if (!plate) { + return
Loading...
; + } + + return ( +
+ +
+ +
+
+
+ + {/* The grid and shift panel are passed as children so they render + inside GroupTypesPanel's flex row, visually adjacent to the group list. */} +
+ + +
+ +
+ {/* Right panel: WellGroupProperties and (if enabled) a Warnings tab. + The tab strip only renders when showWarningPanel is true; otherwise + WellGroupProperties fills the full right column without tabs. */} + +
+
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.utils.test.ts b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.utils.test.ts new file mode 100644 index 00000000000..ca49ffc27dd --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/PlateTemplateDesigner.utils.test.ts @@ -0,0 +1,152 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import { WellGroup } from './models'; +import { assignColors, isSameOrigin, toggleCell } from './PlateTemplateDesigner'; + +function makeGroup(rowId: number): WellGroup { + return { rowId, type: 'SPECIMEN', name: `Group ${rowId}`, positions: [], properties: {}, allowNewGroups: false }; +} + +function makeGroupAt(rowId: number, type: string, coords: Array<[number, number]>): WellGroup { + return { rowId, type, name: `Group ${rowId}`, positions: coords.map(([row, col]) => ({ row, col })), properties: {}, allowNewGroups: false }; +} + +describe('assignColors', () => { + test('returns an empty map for an empty group list', () => { + expect(assignColors([])).toEqual(new Map()); + }); + + test('assigns a color entry for each group', () => { + const groups = [makeGroup(1), makeGroup(2), makeGroup(3)]; + const map = assignColors(groups); + expect(map.size).toBe(3); + expect(map.get(1)).toBeDefined(); + expect(map.get(2)).toBeDefined(); + expect(map.get(3)).toBeDefined(); + }); + + test('uses group rowId as the map key, not the array index', () => { + const groups = [makeGroup(10), makeGroup(20)]; + const map = assignColors(groups); + expect(map.has(10)).toBe(true); + expect(map.has(20)).toBe(true); + expect(map.has(0)).toBe(false); + }); + + test('assigns distinct colors to the first 20 groups', () => { + const groups = Array.from({ length: 20 }, (_, i) => makeGroup(i + 1)); + const map = assignColors(groups); + const colors = Array.from(map.values()); + expect(new Set(colors).size).toBe(20); + }); + + test('wraps color assignment after 20 groups (21st group gets same color as 1st)', () => { + const groups = Array.from({ length: 21 }, (_, i) => makeGroup(i + 1)); + const map = assignColors(groups); + expect(map.get(21)).toBe(map.get(1)); + }); + + test('assigns colors in array order, not by rowId value', () => { + // rowId 99 comes first in the array, so it gets the first color + const groups = [makeGroup(99), makeGroup(1)]; + const map = assignColors(groups); + const firstColor = assignColors([makeGroup(1)]).get(1); + expect(map.get(99)).toBe(firstColor); + }); +}); + +describe('toggleCell', () => { + test('adds cell to active group when the cell is absent', () => { + const groups = [makeGroupAt(1, 'SPECIMEN', [])]; + const result = toggleCell(groups, 1, 0, 0); + expect(result[0].positions).toEqual([{ row: 0, col: 0 }]); + }); + + test('removes cell from active group when the cell is already present', () => { + const groups = [makeGroupAt(1, 'SPECIMEN', [[0, 0]])]; + const result = toggleCell(groups, 1, 0, 0); + expect(result[0].positions).toEqual([]); + }); + + test('evicts cell from a sibling group of the same type when adding', () => { + const groups = [ + makeGroupAt(1, 'SPECIMEN', []), // active — does not have the cell + makeGroupAt(2, 'SPECIMEN', [[0, 0]]), // sibling — owns the cell + ]; + const result = toggleCell(groups, 1, 0, 0); + expect(result[0].positions).toEqual([{ row: 0, col: 0 }]); // added to active + expect(result[1].positions).toEqual([]); // evicted from sibling + }); + + test('does not evict from a group of a different type when adding', () => { + const groups = [ + makeGroupAt(1, 'SPECIMEN', []), + makeGroupAt(2, 'CONTROL', [[0, 0]]), // different type — must be untouched + ]; + const result = toggleCell(groups, 1, 0, 0); + expect(result[0].positions).toEqual([{ row: 0, col: 0 }]); + expect(result[1].positions).toEqual([{ row: 0, col: 0 }]); // unchanged + }); + + test('does not evict from sibling groups when removing (toggle off)', () => { + const groups = [ + makeGroupAt(1, 'SPECIMEN', [[0, 0]]), // active — owns the cell + makeGroupAt(2, 'SPECIMEN', [[0, 0]]), // sibling — also owns the cell (edge case) + ]; + const result = toggleCell(groups, 1, 0, 0); + expect(result[0].positions).toEqual([]); // removed from active + expect(result[1].positions).toEqual([{ row: 0, col: 0 }]); // sibling unchanged + }); + + test('leaves unrelated cells in the sibling group intact', () => { + const groups = [ + makeGroupAt(1, 'SPECIMEN', []), + makeGroupAt(2, 'SPECIMEN', [[0, 0], [1, 1]]), // sibling owns (0,0) and (1,1) + ]; + const result = toggleCell(groups, 1, 0, 0); + expect(result[0].positions).toEqual([{ row: 0, col: 0 }]); + expect(result[1].positions).toEqual([{ row: 1, col: 1 }]); // only (0,0) evicted + }); + + test('returns groups unchanged when activeGroupRowId is not found', () => { + const groups = [makeGroupAt(1, 'SPECIMEN', [])]; + expect(toggleCell(groups, 99, 0, 0)).toEqual(groups); + }); +}); + +describe('isSameOrigin', () => { + // jsdom sets window.location.origin to 'http://localhost' + + test('returns true for a URL on the same origin', () => { + expect(isSameOrigin('http://localhost/some/path')).toBe(true); + }); + + test('returns true for a root-relative URL (same origin by construction)', () => { + expect(isSameOrigin('/labkey/plate/plateList.view')).toBe(true); + }); + + test('returns false for a different hostname', () => { + expect(isSameOrigin('http://evil.com/path')).toBe(false); + }); + + test('returns false for a different scheme', () => { + expect(isSameOrigin('https://localhost/path')).toBe(false); + }); + + test('returns false for a different port', () => { + expect(isSameOrigin('http://localhost:8080/path')).toBe(false); + }); + + test('returns false for a javascript: URL (XSS guard)', () => { + expect(isSameOrigin('javascript:alert(1)')).toBe(false); + }); + + test('returns false for an absolute URL with an invalid host (throws during construction)', () => { + // 'http://a b' has a space in the hostname which is invalid; the URL constructor throws, + // and the catch block returns false. + expect(isSameOrigin('http://a b/path')).toBe(false); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/app.tsx b/assay/src/client/PlateTemplateDesigner/app.tsx new file mode 100644 index 00000000000..03276e83aa1 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/app.tsx @@ -0,0 +1,20 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { createRoot } from 'react-dom/client'; +import { getServerContext } from '@labkey/api'; +import { ServerContextProvider, withAppUser } from '@labkey/components'; + +import { PlateTemplateDesigner } from './PlateTemplateDesigner'; + +// Need to wait for container element to be available in labkey wrapper before render +window.addEventListener('DOMContentLoaded', () => { + createRoot(document.getElementById('app')).render( + + + + ); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/GroupTypesPanel.test.tsx b/assay/src/client/PlateTemplateDesigner/components/GroupTypesPanel.test.tsx new file mode 100644 index 00000000000..71f463a3db7 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/GroupTypesPanel.test.tsx @@ -0,0 +1,340 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { fireEvent, render, screen, within } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { PlateTemplate, WellGroup } from '../models'; +import { GroupTypesPanel } from './GroupTypesPanel'; + +function makeGroup(overrides: Partial = {}): WellGroup { + return { + rowId: 1, + type: 'SPECIMEN', + name: 'Group A', + positions: [], + properties: {}, + allowNewGroups: true, + ...overrides, + }; +} + +function makePlate(overrides: Partial = {}): PlateTemplate { + return { + rowId: 0, + name: 'Test Plate', + type: 'assay', + rows: 8, + cols: 12, + groupTypes: ['SPECIMEN', 'CONTROL'], + canCreateGroupsByType: { SPECIMEN: true, CONTROL: true }, + groups: [], + plateProperties: {}, + typesToDefaultGroups: {}, + showWarningPanel: false, + existingTemplateNames: [], + copyMode: false, + defaultPlateName: '', + ...overrides, + }; +} + +function renderPanel(overrides: Partial> = {}) { + const props = { + plate: makePlate(), + activeGroup: null, + activeTab: 'SPECIMEN', + colorMap: new Map(), + onGroupSelect: jest.fn(), + onTabChange: jest.fn(), + onAddGroup: jest.fn(), + onDeleteGroup: jest.fn(), + onRenameGroup: jest.fn(), + ...overrides, + }; + const result = render(); + return { ...result, props }; +} + +describe('GroupTypesPanel — create row: select vs input', () => { + test('shows a contains only the unused defaults', () => { + renderPanel({ + plate: makePlate({ + typesToDefaultGroups: { SPECIMEN: ['Virus', 'Cell Control'] }, + groups: [makeGroup({ name: 'Virus' })], // 'Virus' already used + }), + }); + const select = screen.getByRole('combobox', { name: 'Group name' }); + const options = Array.from(select.querySelectorAll('option')).map(o => o.textContent); + expect(options).toEqual(['Cell Control']); + }); + + test('shows a text when all defaults are used', () => { + renderPanel({ + plate: makePlate({ + typesToDefaultGroups: { SPECIMEN: ['Virus'] }, + groups: [makeGroup({ name: 'Virus' })], + }), + }); + expect(screen.getByRole('textbox', { name: 'Group name' })).toBeInTheDocument(); + expect(screen.queryByRole('combobox', { name: 'Group name' })).toBeNull(); + }); + + test('shows a text when no defaults are configured for the type', () => { + renderPanel({ plate: makePlate({ typesToDefaultGroups: {} }) }); + expect(screen.getByRole('textbox', { name: 'Group name' })).toBeInTheDocument(); + }); +}); + +describe('GroupTypesPanel — create row: name conflict detection', () => { + test('Create button is enabled for a unique name', async () => { + renderPanel({ plate: makePlate({ groups: [makeGroup({ name: 'Existing' })] }) }); + await userEvent.type(screen.getByRole('textbox', { name: 'Group name' }), 'New Group'); + expect(screen.getByRole('button', { name: 'Create' })).toBeEnabled(); + }); + + test('Create button is disabled and error shown when name conflicts', async () => { + renderPanel({ plate: makePlate({ groups: [makeGroup({ name: 'Existing' })] }) }); + await userEvent.type(screen.getByRole('textbox', { name: 'Group name' }), 'Existing'); + expect(screen.getByRole('button', { name: 'Create' })).toBeDisabled(); + expect(screen.getByText(/already exists in this type/i)).toBeInTheDocument(); + }); + + test('conflict only checks groups of the same type', async () => { + // A group named 'Shared Name' in CONTROL should not conflict with SPECIMEN create input + renderPanel({ + plate: makePlate({ + groups: [makeGroup({ rowId: 2, type: 'CONTROL', name: 'Shared Name' })], + }), + }); + await userEvent.type(screen.getByRole('textbox', { name: 'Group name' }), 'Shared Name'); + expect(screen.getByRole('button', { name: 'Create' })).toBeEnabled(); + expect(screen.queryByText(/already exists/i)).toBeNull(); + }); + + test('clicking Create calls onAddGroup with the trimmed name', async () => { + const { props } = renderPanel(); + await userEvent.type(screen.getByRole('textbox', { name: 'Group name' }), ' My Group '); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(props.onAddGroup).toHaveBeenCalledWith('SPECIMEN', 'My Group'); + }); + + test('pressing Enter in the name input calls onAddGroup', async () => { + const { props } = renderPanel(); + await userEvent.type(screen.getByRole('textbox', { name: 'Group name' }), 'My Group{Enter}'); + expect(props.onAddGroup).toHaveBeenCalledWith('SPECIMEN', 'My Group'); + }); + + test('Create button is disabled when name is empty', () => { + renderPanel(); + expect(screen.getByRole('button', { name: 'Create' })).toBeDisabled(); + }); +}); + +describe('GroupTypesPanel — inline rename', () => { + function renderWithActiveGroup() { + const group1 = makeGroup({ rowId: 1, name: 'Group A' }); + const group2 = makeGroup({ rowId: 2, name: 'Group B' }); + return renderPanel({ + plate: makePlate({ groups: [group1, group2] }), + activeGroup: group1, + }); + } + + test('rename button is visible for the active group when allowNewGroups is true', () => { + renderWithActiveGroup(); + expect(screen.getByRole('button', { name: 'Rename Group A' })).toBeInTheDocument(); + }); + + test('clicking rename shows an inline input', async () => { + renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Rename Group A' })); + expect(screen.getByRole('textbox', { name: 'Rename Group A' })).toBeInTheDocument(); + }); + + test('pressing Enter with a non-conflicting name calls onRenameGroup', async () => { + const { props } = renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Rename Group A' })); + const input = screen.getByRole('textbox', { name: 'Rename Group A' }); + await userEvent.clear(input); + await userEvent.type(input, 'Group C{Enter}'); + expect(props.onRenameGroup).toHaveBeenCalledWith(1, 'Group C'); + }); + + test('pressing Enter with a conflicting name shows an error and does not rename', async () => { + const { props } = renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Rename Group A' })); + const input = screen.getByRole('textbox', { name: 'Rename Group A' }); + await userEvent.clear(input); + await userEvent.type(input, 'Group B{Enter}'); + expect(props.onRenameGroup).not.toHaveBeenCalled(); + expect(screen.getByText(/"Group B" is already used/i)).toBeInTheDocument(); + }); + + test('blurring with a conflicting name reverts silently (no error, no rename)', async () => { + const { props } = renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Rename Group A' })); + const input = screen.getByRole('textbox', { name: 'Rename Group A' }); + await userEvent.clear(input); + await userEvent.type(input, 'Group B'); + await userEvent.tab(); // blur the input + expect(props.onRenameGroup).not.toHaveBeenCalled(); + expect(screen.queryByText(/"Group B" is already used/i)).toBeNull(); + expect(screen.queryByRole('textbox', { name: 'Rename Group A' })).toBeNull(); + }); + + test('pressing Escape cancels rename without calling onRenameGroup', async () => { + const { props } = renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Rename Group A' })); + const input = screen.getByRole('textbox', { name: 'Rename Group A' }); + await userEvent.clear(input); + await userEvent.type(input, 'Something{Escape}'); + expect(props.onRenameGroup).not.toHaveBeenCalled(); + expect(screen.queryByRole('textbox', { name: 'Rename Group A' })).toBeNull(); + }); +}); + +describe('GroupTypesPanel — tab switching resets create input', () => { + test('switching activeTab resets the create name to empty (no defaults)', async () => { + const { rerender, props } = renderPanel({ + plate: makePlate({ canCreateGroupsByType: { SPECIMEN: true, CONTROL: true } }), + activeTab: 'SPECIMEN', + }); + await userEvent.type(screen.getByRole('textbox', { name: 'Group name' }), 'In Progress'); + expect(screen.getByRole('textbox', { name: 'Group name' })).toHaveValue('In Progress'); + + rerender( + + ); + expect(screen.getByRole('textbox', { name: 'Group name' })).toHaveValue(''); + }); + + test('switching activeTab resets to the first unused default of the new tab', () => { + const plate = makePlate({ + canCreateGroupsByType: { SPECIMEN: true, CONTROL: true }, + typesToDefaultGroups: { CONTROL: ['Positive', 'Negative'] }, + }); + const { rerender, props } = renderPanel({ plate, activeTab: 'SPECIMEN' }); + + rerender(); + + const select = screen.getByRole('combobox', { name: 'Group name' }); + expect(select).toHaveValue('Positive'); + }); +}); + +describe('GroupTypesPanel — tab click', () => { + test('clicking a tab calls onTabChange with the tab key', async () => { + const { props } = renderPanel({ activeTab: 'SPECIMEN' }); + await userEvent.click(screen.getByRole('tab', { name: 'CONTROL' })); + expect(props.onTabChange).toHaveBeenCalledWith('CONTROL'); + }); +}); + +describe('GroupTypesPanel — group selection', () => { + function renderWithGroup() { + const group = makeGroup({ rowId: 1, name: 'Group A' }); + return renderPanel({ + plate: makePlate({ groups: [group] }), + activeGroup: null, + }); + } + + test('clicking a group row calls onGroupSelect with that group', async () => { + const { props } = renderWithGroup(); + await userEvent.click(screen.getByRole('option', { name: 'Group A' })); + expect(props.onGroupSelect).toHaveBeenCalledWith( + expect.objectContaining({ rowId: 1, name: 'Group A' }) + ); + }); + + test('pressing Enter on a group row calls onGroupSelect', () => { + const { props } = renderWithGroup(); + fireEvent.keyDown(screen.getByRole('option', { name: 'Group A' }), { key: 'Enter' }); + expect(props.onGroupSelect).toHaveBeenCalledWith( + expect.objectContaining({ rowId: 1, name: 'Group A' }) + ); + }); + + test('pressing Space on a group row calls onGroupSelect', () => { + const { props } = renderWithGroup(); + fireEvent.keyDown(screen.getByRole('option', { name: 'Group A' }), { key: ' ' }); + expect(props.onGroupSelect).toHaveBeenCalledWith( + expect.objectContaining({ rowId: 1, name: 'Group A' }) + ); + }); +}); + +describe('GroupTypesPanel — delete group', () => { + function renderWithActiveGroup() { + const group = makeGroup({ rowId: 1, name: 'Group A' }); + return renderPanel({ + plate: makePlate({ groups: [group] }), + activeGroup: group, + }); + } + + test('delete button calls onDeleteGroup when user confirms', async () => { + const { props } = renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Delete Group A' })); + // First click shows inline confirmation; click Yes to confirm + await userEvent.click(screen.getByRole('button', { name: 'Confirm delete Group A' })); + expect(props.onDeleteGroup).toHaveBeenCalledWith(1); + }); + + test('delete button does not call onDeleteGroup when user cancels', async () => { + const { props } = renderWithActiveGroup(); + await userEvent.click(screen.getByRole('button', { name: 'Delete Group A' })); + // First click shows inline confirmation; click No to cancel + await userEvent.click(screen.getByRole('button', { name: 'Cancel delete Group A' })); + expect(props.onDeleteGroup).not.toHaveBeenCalled(); + }); +}); + +describe('GroupTypesPanel — multi-create dialog', () => { + // Give the SPECIMEN type a default name so newGroupName starts as 'Virus', + // which becomes the dialog's initialBaseName. + function renderWithDefault() { + return renderPanel({ + plate: makePlate({ typesToDefaultGroups: { SPECIMEN: ['Virus'] } }), + }); + } + + test('clicking "Create multiple..." opens the dialog', async () => { + renderWithDefault(); + await userEvent.click(screen.getByRole('button', { name: 'Create multiple...' })); + expect(screen.getByRole('dialog')).toBeInTheDocument(); + }); + + test('confirming multi-create calls onAddGroup for each generated name', async () => { + const { props } = renderWithDefault(); + await userEvent.click(screen.getByRole('button', { name: 'Create multiple...' })); + // Dialog opens with initialBaseName='Virus', default count=2 + await userEvent.click(within(screen.getByRole('dialog')).getByRole('button', { name: 'Create' })); + expect(props.onAddGroup).toHaveBeenCalledWith('SPECIMEN', 'Virus 1'); + expect(props.onAddGroup).toHaveBeenCalledWith('SPECIMEN', 'Virus 2'); + }); + + test('closing the dialog with Cancel hides it', async () => { + renderWithDefault(); + await userEvent.click(screen.getByRole('button', { name: 'Create multiple...' })); + expect(screen.getByRole('dialog')).toBeInTheDocument(); + await userEvent.click(within(screen.getByRole('dialog')).getByRole('button', { name: 'Cancel' })); + expect(screen.queryByRole('dialog')).toBeNull(); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/GroupTypesPanel.tsx b/assay/src/client/PlateTemplateDesigner/components/GroupTypesPanel.tsx new file mode 100644 index 00000000000..b397e149783 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/GroupTypesPanel.tsx @@ -0,0 +1,385 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React, { useEffect, useMemo, useState } from 'react'; +import classNames from 'classnames'; + +import { PlateTemplate, WellGroup } from '../models'; +import { MultiCreateDialog } from './MultiCreateDialog'; +import { TabButton } from './TabButton'; + +interface GroupTypesPanelProps { + plate: PlateTemplate; + activeGroup: WellGroup | null; + activeTab: string; + colorMap: Map; + onGroupSelect: (group: WellGroup) => void; + onTabChange: (tab: string) => void; + onAddGroup: (type: string, name: string) => void; + onDeleteGroup: (rowId: number) => void; + onRenameGroup: (rowId: number, newName: string) => void; + children?: React.ReactNode; +} + +/** + * Left-hand panel that manages group types (tabs) and individual well groups. + * + * ─── Layout ──────────────────────────────────────────────────────────────────── + * The panel is split into two side-by-side areas via a flex row: + * Left column – the group list + create controls (fixed width) + * Right area – children (the TemplateGrid + ShiftPanel), passed in from the parent + * + * This composition pattern keeps the grid visually anchored inside the panel boundary + * while letting the tab strip and group list scroll independently. + * + * ─── Tab switching ───────────────────────────────────────────────────────────── + * Each tab corresponds to a group type key (e.g. "CONTROL", "SPECIMEN", "REPLICATE"). + * Switching tabs: + * - Clears the active group selection (the parent sets activeGroup to null). + * - Updates the grid to show only that type's colour layout. + * - Resets the create-name input to the first unused default for the new type. + * + * ─── Group selection ─────────────────────────────────────────────────────────── + * Clicking a group row makes it the "active group". Once active, clicking or + * dragging cells on the TemplateGrid paints them onto that group. The active group + * is highlighted with a blue border and shows inline rename/delete actions. + * + * ─── Creating groups ─────────────────────────────────────────────────────────── + * Some group types come with predefined slot names (`typesToDefaultGroups`), e.g. + * "Virus" and "Cell Control" for certain assay types. While unused defaults remain, + * a + * appears for custom names. + * + * "Create multiple…" opens a modal dialog that batch-creates N numbered groups + * (e.g. "Sample 1" through "Sample 8") from a base name and count. Useful for + * assays with many specimens or replicates. + * + * ─── Renaming ────────────────────────────────────────────────────────────────── + * The pencil button activates an inline rename input in place of the group name. + * Blur or Enter commits the change; Escape discards it. + * + * ─── Modal focus trap ────────────────────────────────────────────────────────── + * When the multi-create dialog opens, a useEffect traps Tab/Shift-Tab focus inside + * the dialog and moves initial focus to the first focusable element. Escape closes + * the dialog from anywhere within it. + */ +export function GroupTypesPanel({ + plate, + activeGroup, + activeTab, + colorMap, + onGroupSelect, + onTabChange, + onAddGroup, + onDeleteGroup, + onRenameGroup, + children, +}: GroupTypesPanelProps): JSX.Element { + const [newGroupName, setNewGroupName] = useState(''); + const [renamingId, setRenamingId] = useState(null); + const [renameValue, setRenameValue] = useState(''); + const [renameError, setRenameError] = useState(null); + const [multiCreateOpen, setMultiCreateOpen] = useState(false); + // rowId of the group awaiting inline delete confirmation; null when no confirmation is pending. + const [confirmDeleteId, setConfirmDeleteId] = useState(null); + + // Stable derived list — memoized so useMemo and useEffect deps are stable. + const groupsOfType = useMemo(() => plate.groups.filter(g => g.type === activeTab), [plate, activeTab]); + const canAdd = plate.canCreateGroupsByType?.[activeTab] ?? false; + + // True when the current create-input value is already taken by a group of this type. + const createNameConflicts = newGroupName.trim() !== '' && groupsOfType.some(g => g.name === newGroupName.trim()); + + // Predefined slot names not yet occupied by an existing group of this type. + // Drives the toggle in the create row. + const unusedDefaults = useMemo(() => { + const defaults = plate.typesToDefaultGroups[activeTab] ?? []; + return defaults.filter(d => !groupsOfType.some(g => g.name === d)); + }, [plate, activeTab, groupsOfType]); + + // Reset create-input and transient UI state when tab changes + useEffect(() => { + setNewGroupName(unusedDefaults[0] ?? ''); + setRenamingId(null); + setConfirmDeleteId(null); + }, [activeTab]); // eslint-disable-line react-hooks/exhaustive-deps + + // Advance to next unused default when the current one gets used + useEffect(() => { + if (unusedDefaults.length > 0 && !unusedDefaults.includes(newGroupName)) { + setNewGroupName(unusedDefaults[0]); + } + }, [unusedDefaults]); // eslint-disable-line react-hooks/exhaustive-deps + + const handleCreate = () => { + const trimmed = newGroupName.trim(); + if (!trimmed || createNameConflicts) return; + onAddGroup(activeTab, trimmed); + setNewGroupName(''); + }; + + const handleDeleteClick = (e: React.MouseEvent, group: WellGroup) => { + e.stopPropagation(); + setConfirmDeleteId(group.rowId); + }; + + const handleDeleteConfirm = (e: React.MouseEvent, rowId: number) => { + e.stopPropagation(); + onDeleteGroup(rowId); + setConfirmDeleteId(null); + }; + + const handleDeleteCancel = (e: React.MouseEvent) => { + e.stopPropagation(); + setConfirmDeleteId(null); + }; + + const handleRenameClick = (e: React.MouseEvent, group: WellGroup) => { + e.stopPropagation(); + setRenamingId(group.rowId); + setRenameValue(group.name); + setRenameError(null); + }; + + // revertOnConflict=true: silently discard (used on blur so moving focus away doesn't leave the input frozen). + // revertOnConflict=false: show an inline error and keep the input open (used on Enter so the user sees feedback). + const handleRenameCommit = (rowId: number, revertOnConflict: boolean) => { + const trimmed = renameValue.trim(); + if (trimmed && groupsOfType.some(g => g.rowId !== rowId && g.name === trimmed)) { + if (revertOnConflict) { + setRenamingId(null); + setRenameError(null); + } else { + setRenameError(`"${trimmed}" is already used by another group of this type.`); + } + return; + } + if (trimmed) onRenameGroup(rowId, trimmed); + setRenamingId(null); + setRenameError(null); + }; + + return ( +
+
) => { + if (e.key !== 'ArrowLeft' && e.key !== 'ArrowRight') return; + const tabs = Array.from(e.currentTarget.querySelectorAll('[role="tab"]')); + const currentIndex = tabs.findIndex(t => t === document.activeElement); + if (currentIndex === -1) return; + e.preventDefault(); + const next = e.key === 'ArrowLeft' + ? (currentIndex - 1 + tabs.length) % tabs.length + : (currentIndex + 1) % tabs.length; + tabs[next].click(); + tabs[next].focus(); + }} + > + {plate.groupTypes.map(type => ( + onTabChange(type)} + > + {type} + + ))} +
+ {plate.groupTypes.map(type => ( + + ))} + {multiCreateOpen && ( + g.name))} + onClose={() => setMultiCreateOpen(false)} + onConfirm={names => { + names.forEach(name => onAddGroup(activeTab, name)); + setMultiCreateOpen(false); + }} + /> + )} +
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/MultiCreateDialog.test.tsx b/assay/src/client/PlateTemplateDesigner/components/MultiCreateDialog.test.tsx new file mode 100644 index 00000000000..395716da0bd --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/MultiCreateDialog.test.tsx @@ -0,0 +1,219 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { fireEvent, render, screen, within } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { MultiCreateDialog } from './MultiCreateDialog'; + +function renderDialog(overrides: Partial> = {}) { + const props = { + initialBaseName: 'Sample', + existingNames: new Set(), + onClose: jest.fn(), + onConfirm: jest.fn(), + ...overrides, + }; + render(); + return props; +} + +describe('MultiCreateDialog', () => { + describe('initial state', () => { + test('pre-populates base name from initialBaseName', () => { + renderDialog({ initialBaseName: 'Virus' }); + expect(screen.getByLabelText(/Base Name/i)).toHaveValue('Virus'); + }); + + test('defaults count to 2', () => { + renderDialog(); + expect(screen.getByLabelText(/Count/i)).toHaveValue(2); + }); + + test('Create button is disabled when base name is empty', () => { + renderDialog({ initialBaseName: '' }); + expect(screen.getByRole('button', { name: 'Create' })).toBeDisabled(); + }); + + test('Create button is enabled when base name is non-empty', () => { + renderDialog({ initialBaseName: 'Sample' }); + expect(screen.getByRole('button', { name: 'Create' })).toBeEnabled(); + }); + }); + + describe('successful creation', () => { + test('calls onConfirm with generated names using base name and count', async () => { + const { onConfirm } = renderDialog({ initialBaseName: 'Sample', existingNames: new Set() }); + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), '3'); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(onConfirm).toHaveBeenCalledWith(['Sample 1', 'Sample 2', 'Sample 3']); + }); + + test('trims whitespace from base name before generating names', async () => { + const { onConfirm } = renderDialog({ initialBaseName: ' Sample ' }); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(onConfirm).toHaveBeenCalledWith(['Sample 1', 'Sample 2']); + }); + + test('filters out names already in existingNames', async () => { + const { onConfirm } = renderDialog({ + initialBaseName: 'Sample', + existingNames: new Set(['Sample 1', 'Sample 3']), + }); + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), '3'); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + // Sample 1 and Sample 3 are already taken; only Sample 2 is new + expect(onConfirm).toHaveBeenCalledWith(['Sample 2']); + }); + }); + + describe('validation errors', () => { + test('shows error and does not call onConfirm when count is not a number', async () => { + const { onConfirm } = renderDialog(); + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), 'abc'); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(onConfirm).not.toHaveBeenCalled(); + expect(screen.getByText(/not a valid count/i)).toBeInTheDocument(); + }); + + test('shows error when count is less than 1', async () => { + const { onConfirm } = renderDialog(); + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), '0'); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(onConfirm).not.toHaveBeenCalled(); + expect(screen.getByText(/not a valid count/i)).toBeInTheDocument(); + }); + + test('shows error and does not call onConfirm when all generated names already exist', async () => { + const { onConfirm } = renderDialog({ + initialBaseName: 'Sample', + existingNames: new Set(['Sample 1', 'Sample 2']), + }); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(onConfirm).not.toHaveBeenCalled(); + expect(screen.getByText(/already exist/i)).toBeInTheDocument(); + }); + + test('count error clears when count input is changed', async () => { + renderDialog(); + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), '0'); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(screen.getByText(/not a valid count/i)).toBeInTheDocument(); + + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), '3'); + expect(screen.queryByText(/not a valid count/i)).toBeNull(); + }); + }); + + describe('cancel / close', () => { + test('clicking Cancel calls onClose', async () => { + const { onClose } = renderDialog(); + await userEvent.click(screen.getByRole('button', { name: 'Cancel' })); + expect(onClose).toHaveBeenCalledTimes(1); + }); + + test('clicking the overlay calls onClose', async () => { + const { onClose } = renderDialog(); + await userEvent.click(document.querySelector('.multi-create-dialog__overlay')); + expect(onClose).toHaveBeenCalledTimes(1); + }); + + test('clicking inside the dialog does not call onClose', async () => { + const { onClose } = renderDialog(); + await userEvent.click(document.querySelector('.multi-create-dialog')); + expect(onClose).not.toHaveBeenCalled(); + }); + + test('pressing Escape on the base name input calls onClose', async () => { + const { onClose } = renderDialog(); + await userEvent.type(screen.getByLabelText(/Base Name/i), '{Escape}'); + // Both the input's onKeyDown and the dialog's focus-trap listener fire on Escape + // (the event bubbles), so onClose is called twice. Both calls are idempotent. + expect(onClose).toHaveBeenCalled(); + }); + + test('pressing Escape on the count input calls onClose', async () => { + const { onClose } = renderDialog(); + await userEvent.type(screen.getByLabelText(/Count/i), '{Escape}'); + expect(onClose).toHaveBeenCalled(); + }); + }); + + describe('keyboard submit', () => { + test('pressing Enter in the base name input submits', async () => { + const { onConfirm } = renderDialog({ initialBaseName: 'Sample' }); + await userEvent.type(screen.getByLabelText(/Base Name/i), '{Enter}'); + expect(onConfirm).toHaveBeenCalledWith(['Sample 1', 'Sample 2']); + }); + + test('pressing Enter in the count input submits', async () => { + const { onConfirm } = renderDialog({ initialBaseName: 'Sample' }); + await userEvent.type(screen.getByLabelText(/Count/i), '{Enter}'); + expect(onConfirm).toHaveBeenCalledWith(['Sample 1', 'Sample 2']); + }); + }); + + describe('focus trap', () => { + // Focusable order: Base Name → Count → Cancel → Create. + // userEvent.tab() fires Tab keydown events that bubble to the dialog's native listener. + test('Tab from last focusable element (Create) wraps focus to first (Base Name)', async () => { + renderDialog({ initialBaseName: 'Sample' }); // Create button enabled + // After mount the useEffect focuses the first element (Base Name); tab forward to Create. + await userEvent.tab(); // → Count + await userEvent.tab(); // → Cancel + await userEvent.tab(); // → Create (last) + await userEvent.tab(); // → focus trap wraps back to Base Name + expect(document.activeElement).toBe(screen.getByLabelText(/Base Name/i)); + }); + + test('Shift+Tab from first focusable element (Base Name) wraps focus to last (Create)', async () => { + renderDialog({ initialBaseName: 'Sample' }); // Create button enabled + // After mount, Base Name is focused (first focusable). Shift+Tab wraps to Create (last). + await userEvent.keyboard('{Shift>}{Tab}{/Shift}'); + expect(document.activeElement).toBe( + within(screen.getByRole('dialog')).getByRole('button', { name: 'Create' }) + ); + }); + }); + + describe('base name input', () => { + test('typing in the base name input updates its value', async () => { + renderDialog({ initialBaseName: '' }); + expect(screen.getByRole('button', { name: 'Create' })).toBeDisabled(); + await userEvent.type(screen.getByLabelText(/Base Name/i), 'NewName'); + expect(screen.getByLabelText(/Base Name/i)).toHaveValue('NewName'); + expect(screen.getByRole('button', { name: 'Create' })).toBeEnabled(); + }); + + test('pressing Enter in count input with empty base name does not submit', async () => { + // The count input's onKeyDown calls handleCreate() without guarding baseName. + // handleCreate's own guard (if (!trimmedBase) return) must prevent submission. + const { onConfirm } = renderDialog({ initialBaseName: '' }); + await userEvent.type(screen.getByLabelText(/Count/i), '{Enter}'); + expect(onConfirm).not.toHaveBeenCalled(); + }); + }); + + describe('singular error message', () => { + test('uses singular "name" when count is 1 and that name already exists', async () => { + // Exercises the parsedCount === 1 branch of the ternary in the "all names exist" error. + renderDialog({ + initialBaseName: 'Sample', + existingNames: new Set(['Sample 1']), + }); + await userEvent.clear(screen.getByLabelText(/Count/i)); + await userEvent.type(screen.getByLabelText(/Count/i), '1'); + await userEvent.click(screen.getByRole('button', { name: 'Create' })); + expect(screen.getByText(/all 1 generated name already exist/i)).toBeInTheDocument(); + }); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/MultiCreateDialog.tsx b/assay/src/client/PlateTemplateDesigner/components/MultiCreateDialog.tsx new file mode 100644 index 00000000000..edb2b7456e6 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/MultiCreateDialog.tsx @@ -0,0 +1,135 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React, { useEffect, useRef, useState } from 'react'; + +interface MultiCreateDialogProps { + initialBaseName: string; + existingNames: Set; + onClose: () => void; + onConfirm: (names: string[]) => void; +} + +export function MultiCreateDialog({ initialBaseName, existingNames, onClose, onConfirm }: MultiCreateDialogProps): JSX.Element { + const [baseName, setBaseName] = useState(initialBaseName); + const [count, setCount] = useState('2'); + const [countError, setCountError] = useState(''); + const dialogRef = useRef(null); + + useEffect(() => { + const dialog = dialogRef.current; + if (!dialog) return; + + // Open as a modal (top layer + native backdrop; also restores focus on close). + dialog.showModal(); + + // Focus trap: cycle Tab/Shift-Tab within the dialog. + const focusableSelectors = 'button, input, select, textarea, [tabindex]:not([tabindex="-1"])'; + const getFocusable = () => Array.from(dialog.querySelectorAll(focusableSelectors)); + + const handleKeyDown = (e: KeyboardEvent) => { + if (e.key !== 'Tab') return; + const focusable = getFocusable(); + const first = focusable[0]; + const last = focusable[focusable.length - 1]; + if (e.shiftKey) { + if (document.activeElement === first) { e.preventDefault(); last?.focus(); } + } else { + if (document.activeElement === last) { e.preventDefault(); first?.focus(); } + } + }; + + // The native fires a `cancel` event on Escape before closing itself. + // Prevent the browser's default close so we control the unmounting via onClose. + const handleCancel = (e: Event) => { + e.preventDefault(); + onClose(); + }; + + dialog.addEventListener('keydown', handleKeyDown); + dialog.addEventListener('cancel', handleCancel); + + // Move focus to the first focusable element inside the dialog. + getFocusable()[0]?.focus(); + + return () => { + dialog.removeEventListener('keydown', handleKeyDown); + dialog.removeEventListener('cancel', handleCancel); + if (dialog.open) dialog.close(); + }; + }, []); // eslint-disable-line react-hooks/exhaustive-deps + + const handleCreate = () => { + const parsedCount = parseInt(count, 10); + if (isNaN(parsedCount) || parsedCount < 1) { + setCountError(`"${count}" is not a valid count.`); + return; + } + const trimmedBase = baseName.trim(); + if (!trimmedBase) return; + const namesToCreate = Array.from({ length: parsedCount }, (_, i) => `${trimmedBase} ${i + 1}`) + .filter(name => !existingNames.has(name)); + if (namesToCreate.length === 0) { + setCountError(`All ${parsedCount} generated name${parsedCount === 1 ? '' : 's'} already exist in this type.`); + return; + } + onConfirm(namesToCreate); + }; + + return ( + +
e.stopPropagation()}> +
Create Multiple Groups
+
+
+ Base Name + setBaseName(e.target.value)} + onKeyDown={e => { if (e.key === 'Enter') handleCreate(); if (e.key === 'Escape') onClose(); }} + /> +
+
+ Count +
+ { setCount(e.target.value); setCountError(''); }} + onKeyDown={e => { if (e.key === 'Enter') handleCreate(); if (e.key === 'Escape') onClose(); }} + /> + {countError &&
{countError}
} +
+
+
+ + +
+
+
+ + ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/RightPanel.test.tsx b/assay/src/client/PlateTemplateDesigner/components/RightPanel.test.tsx new file mode 100644 index 00000000000..c7cffcb5936 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/RightPanel.test.tsx @@ -0,0 +1,116 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { render, screen } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { RIGHT_TAB_PROPERTIES, RIGHT_TAB_WARNINGS, RightPanel } from './RightPanel'; + +function renderPanel(overrides: Partial> = {}) { + const props = { + showWarningPanel: false, + rightTab: RIGHT_TAB_PROPERTIES, + onRightTabChange: jest.fn(), + warnings: [], + activeGroup: null, + onPropertyChange: jest.fn(), + onDeleteProperty: jest.fn(), + ...overrides, + }; + render(); + return props; +} + +describe('RightPanel — without warning panel', () => { + test('renders WellGroupProperties with no tab strip', () => { + renderPanel({ showWarningPanel: false }); + expect(screen.queryByRole('tablist')).toBeNull(); + expect(screen.queryByRole('tabpanel')).toBeNull(); + // WellGroupProperties empty-state text is present + expect(screen.getByText(/select a well group/i)).toBeInTheDocument(); + }); + + test('properties div has no role or aria-labelledby when showWarningPanel is false', () => { + renderPanel({ showWarningPanel: false }); + // The wrapper div around WellGroupProperties should have no role + const tabpanels = document.querySelectorAll('[role="tabpanel"]'); + expect(tabpanels).toHaveLength(0); + }); +}); + +describe('RightPanel — with warning panel, properties tab', () => { + test('renders a tablist with two tabs', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES }); + expect(screen.getByRole('tablist')).toBeInTheDocument(); + expect(screen.getAllByRole('tab')).toHaveLength(2); + }); + + test('properties tab is aria-selected, warnings tab is not', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES }); + expect(screen.getByRole('tab', { name: 'Well Group Properties' })).toHaveAttribute('aria-selected', 'true'); + expect(screen.getByRole('tab', { name: 'Warnings' })).toHaveAttribute('aria-selected', 'false'); + }); + + test('properties tabpanel is rendered with correct id and aria-labelledby', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES }); + const panel = document.getElementById('right-panel-properties'); + expect(panel).toBeInTheDocument(); + expect(panel).toHaveAttribute('role', 'tabpanel'); + expect(panel).toHaveAttribute('aria-labelledby', 'right-tab-properties'); + }); + + test('warnings tabpanel is hidden when rightTab is "properties"', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES }); + expect(document.getElementById('right-panel-warnings')).toHaveAttribute('hidden'); + }); + + test('warnings tab label shows count badge when warnings exist', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES, warnings: ['w1', 'w2', 'w3'] }); + expect(screen.getByRole('tab', { name: 'Warnings (3)' })).toBeInTheDocument(); + }); + + test('warnings tab label shows plain "Warnings" when list is empty', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES, warnings: [] }); + expect(screen.getByRole('tab', { name: 'Warnings' })).toBeInTheDocument(); + }); + + test('clicking warnings tab calls onRightTabChange with "warnings"', async () => { + const { onRightTabChange } = renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_PROPERTIES }); + await userEvent.click(screen.getByRole('tab', { name: 'Warnings' })); + expect(onRightTabChange).toHaveBeenCalledWith(RIGHT_TAB_WARNINGS); + }); + + test('clicking properties tab calls onRightTabChange with "properties"', async () => { + const { onRightTabChange } = renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_WARNINGS }); + await userEvent.click(screen.getByRole('tab', { name: 'Well Group Properties' })); + expect(onRightTabChange).toHaveBeenCalledWith(RIGHT_TAB_PROPERTIES); + }); +}); + +describe('RightPanel — with warning panel, warnings tab', () => { + test('renders warnings tabpanel; properties tabpanel is hidden', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_WARNINGS, warnings: ['A1: warning'] }); + expect(document.getElementById('right-panel-warnings')).toBeInTheDocument(); + expect(document.getElementById('right-panel-properties')).toHaveAttribute('hidden'); + }); + + test('warnings tab is aria-selected, properties tab is not', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_WARNINGS }); + expect(screen.getByRole('tab', { name: 'Warnings' })).toHaveAttribute('aria-selected', 'true'); + expect(screen.getByRole('tab', { name: 'Well Group Properties' })).toHaveAttribute('aria-selected', 'false'); + }); + + test('warnings tabpanel has correct aria-labelledby', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_WARNINGS }); + const panel = document.getElementById('right-panel-warnings'); + expect(panel).toHaveAttribute('aria-labelledby', 'right-tab-warnings'); + }); + + test('WarningPanel content is visible in warnings tab', () => { + renderPanel({ showWarningPanel: true, rightTab: RIGHT_TAB_WARNINGS, warnings: [] }); + expect(screen.getByText('No warnings.')).toBeInTheDocument(); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/RightPanel.tsx b/assay/src/client/PlateTemplateDesigner/components/RightPanel.tsx new file mode 100644 index 00000000000..9e8e55579eb --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/RightPanel.tsx @@ -0,0 +1,95 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; + +import { WellGroup } from '../models'; +import { TabButton } from './TabButton'; +import { WellGroupProperties } from './WellGroupProperties'; +import { WarningPanel } from './WarningPanel'; + +export const RIGHT_TAB_PROPERTIES = 'properties' as const; +export const RIGHT_TAB_WARNINGS = 'warnings' as const; +export type RightTab = typeof RIGHT_TAB_PROPERTIES | typeof RIGHT_TAB_WARNINGS; + +interface RightPanelProps { + showWarningPanel: boolean; + rightTab: RightTab; + onRightTabChange: (tab: RightTab) => void; + warnings: string[]; + activeGroup: WellGroup | null; + onPropertyChange: (groupRowId: number, key: string, value: string) => void; + onDeleteProperty: (groupRowId: number, key: string) => void; +} + +export function RightPanel(props: RightPanelProps): JSX.Element { + const { showWarningPanel, rightTab, onRightTabChange, warnings, activeGroup, onPropertyChange, onDeleteProperty } = props; + const warningCount = warnings.length; + + return ( +
+ {showWarningPanel && ( // Only show the tabs if we are showing the warnings too. Otherwise, just show the properties +
) => { + if (e.key !== 'ArrowLeft' && e.key !== 'ArrowRight') return; + const tabs = Array.from(e.currentTarget.querySelectorAll('[role="tab"]')); + const currentIndex = tabs.findIndex(t => t === document.activeElement); + if (currentIndex === -1) return; + e.preventDefault(); + const next = e.key === 'ArrowLeft' + ? (currentIndex - 1 + tabs.length) % tabs.length + : (currentIndex + 1) % tabs.length; + tabs[next].click(); + tabs[next].focus(); + }} + > + onRightTabChange(RIGHT_TAB_PROPERTIES)} + > + Well Group Properties + + 0 ? 'right-panel-tabs__tab--warn' : undefined} + onClick={() => onRightTabChange(RIGHT_TAB_WARNINGS)} + > + {warningCount > 0 ? `Warnings (${warningCount})` : 'Warnings'} + +
+ )} + + {showWarningPanel && ( + + )} +
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/ShiftPanel.test.tsx b/assay/src/client/PlateTemplateDesigner/components/ShiftPanel.test.tsx new file mode 100644 index 00000000000..75b2c242f40 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/ShiftPanel.test.tsx @@ -0,0 +1,55 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { render, screen } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { ShiftPanel } from './ShiftPanel'; + +describe('ShiftPanel', () => { + test('renders four directional buttons', () => { + render(); + expect(screen.getByRole('button', { name: 'Shift up' })).toBeInTheDocument(); + expect(screen.getByRole('button', { name: 'Shift down' })).toBeInTheDocument(); + expect(screen.getByRole('button', { name: 'Shift left' })).toBeInTheDocument(); + expect(screen.getByRole('button', { name: 'Shift right' })).toBeInTheDocument(); + }); + + test('Shift up calls onShift(1, 0) — moves cells up (decreases row index)', async () => { + const onShift = jest.fn(); + render(); + await userEvent.click(screen.getByRole('button', { name: 'Shift up' })); + expect(onShift).toHaveBeenCalledWith(1, 0); + }); + + test('Shift down calls onShift(-1, 0) — moves cells down (increases row index)', async () => { + const onShift = jest.fn(); + render(); + await userEvent.click(screen.getByRole('button', { name: 'Shift down' })); + expect(onShift).toHaveBeenCalledWith(-1, 0); + }); + + test('Shift left calls onShift(0, 1) — moves cells left (decreases col index)', async () => { + const onShift = jest.fn(); + render(); + await userEvent.click(screen.getByRole('button', { name: 'Shift left' })); + expect(onShift).toHaveBeenCalledWith(0, 1); + }); + + test('Shift right calls onShift(0, -1) — moves cells right (increases col index)', async () => { + const onShift = jest.fn(); + render(); + await userEvent.click(screen.getByRole('button', { name: 'Shift right' })); + expect(onShift).toHaveBeenCalledWith(0, -1); + }); + + test('each button only fires once per click', async () => { + const onShift = jest.fn(); + render(); + await userEvent.click(screen.getByRole('button', { name: 'Shift up' })); + expect(onShift).toHaveBeenCalledTimes(1); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/ShiftPanel.tsx b/assay/src/client/PlateTemplateDesigner/components/ShiftPanel.tsx new file mode 100644 index 00000000000..08b1d913eb3 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/ShiftPanel.tsx @@ -0,0 +1,42 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; + +interface ShiftPanelProps { + onShift: (verticalShift: number, horizontalShift: number) => void; +} + +/** + * A compass-rose control that shifts all wells of the currently active group type one step in any + * cardinal direction. The shift wraps around plate edges (toroidal), so wells that fall off the + * bottom reappear at the top, etc. + * + * Sign convention (matches the modular arithmetic in PlateTemplateDesigner.handleShift): + * verticalShift > 0 → cells move UP (row index decreases: row = (row - shift + rows) % rows) + * verticalShift < 0 → cells move DOWN + * horizontalShift > 0 → cells move LEFT (col index decreases) + * horizontalShift < 0 → cells move RIGHT + * + * Shifts apply to every group of the active type simultaneously, preserving relative layout + * between groups. Only the active tab's type is affected; other types are unchanged. + */ +export function ShiftPanel({ onShift }: ShiftPanelProps): JSX.Element { + return ( +
+
+ + + + + Shift + + + + +
+
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/StatusBar.test.tsx b/assay/src/client/PlateTemplateDesigner/components/StatusBar.test.tsx new file mode 100644 index 00000000000..9ca66dba283 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/StatusBar.test.tsx @@ -0,0 +1,133 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { render, screen } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { StatusBar } from './StatusBar'; + +function renderStatusBar(overrides: Partial> = {}) { + const props = { + isDirty: false, + status: '', + plateName: 'My Plate', + onSaveAndClose: jest.fn(), + onSave: jest.fn(), + onCancel: jest.fn(), + ...overrides, + }; + render(); + return props; +} + +describe('StatusBar', () => { + describe('button states', () => { + test('Save button is disabled when plate is not dirty', () => { + renderStatusBar({ isDirty: false }); + expect(screen.getByRole('button', { name: 'Save' })).toBeDisabled(); + }); + + test('Save button is enabled when plate is dirty', () => { + renderStatusBar({ isDirty: true }); + expect(screen.getByRole('button', { name: 'Save' })).toBeEnabled(); + }); + + test('Save & Close and Cancel are always enabled', () => { + renderStatusBar({ isDirty: false }); + expect(screen.getByRole('button', { name: /Save & Close/i })).toBeEnabled(); + expect(screen.getByRole('button', { name: 'Cancel' })).toBeEnabled(); + }); + }); + + describe('dirty indicator', () => { + test('shows "Unsaved changes" when dirty', () => { + renderStatusBar({ isDirty: true }); + expect(screen.getByText('Unsaved changes')).toBeInTheDocument(); + }); + + test('shows nothing in dirty indicator when clean', () => { + renderStatusBar({ isDirty: false }); + // The element is present but empty + const statuses = document.querySelectorAll('.status-bar__dirty'); + expect(statuses).toHaveLength(1); + expect(statuses[0]).toHaveTextContent(''); + }); + + test('displays transient status text', () => { + renderStatusBar({ status: 'Saved.' }); + expect(screen.getByText('Saved.')).toBeInTheDocument(); + }); + }); + + describe('validation', () => { + test('clicking Save with empty plate name shows error and does not call onSave', async () => { + const { onSave } = renderStatusBar({ plateName: '', isDirty: true }); + await userEvent.click(screen.getByRole('button', { name: 'Save' })); + expect(onSave).not.toHaveBeenCalled(); + expect(screen.getByRole('alert')).toHaveTextContent(/plate name/i); + }); + + test('clicking Save with whitespace-only plate name shows error', async () => { + const { onSave } = renderStatusBar({ plateName: ' ', isDirty: true }); + await userEvent.click(screen.getByRole('button', { name: 'Save' })); + expect(onSave).not.toHaveBeenCalled(); + expect(screen.getByRole('alert')).toBeInTheDocument(); + }); + + test('clicking Save with valid plate name calls onSave and shows no error', async () => { + const { onSave } = renderStatusBar({ plateName: 'My Plate', isDirty: true }); + await userEvent.click(screen.getByRole('button', { name: 'Save' })); + expect(onSave).toHaveBeenCalledTimes(1); + expect(screen.queryByRole('alert')).toBeNull(); + }); + + test('clicking Save & Close with empty name shows error and does not call onSaveAndClose', async () => { + const { onSaveAndClose } = renderStatusBar({ plateName: '', isDirty: true }); + await userEvent.click(screen.getByRole('button', { name: /Save & Close/i })); + expect(onSaveAndClose).not.toHaveBeenCalled(); + expect(screen.getByRole('alert')).toBeInTheDocument(); + }); + + test('clicking Save & Close with valid name calls onSaveAndClose', async () => { + const { onSaveAndClose } = renderStatusBar({ plateName: 'My Plate' }); + await userEvent.click(screen.getByRole('button', { name: /Save & Close/i })); + expect(onSaveAndClose).toHaveBeenCalledTimes(1); + }); + + test('error clears on a subsequent successful save', async () => { + // First render with empty name to trigger error + const { rerender } = render( + + ); + await userEvent.click(screen.getByRole('button', { name: 'Save' })); + expect(screen.getByRole('alert')).toBeInTheDocument(); + + // Re-render with a valid name — the error clears on the next successful validate + const onSave = jest.fn(); + rerender( + + ); + await userEvent.click(screen.getByRole('button', { name: 'Save' })); + expect(onSave).toHaveBeenCalledTimes(1); + expect(screen.queryByRole('alert')).toBeNull(); + }); + }); + + describe('Cancel', () => { + test('clicking Cancel calls onCancel', async () => { + const { onCancel } = renderStatusBar(); + await userEvent.click(screen.getByRole('button', { name: 'Cancel' })); + expect(onCancel).toHaveBeenCalledTimes(1); + }); + + test('Cancel does not call onSave or onSaveAndClose', async () => { + const { onSave, onSaveAndClose } = renderStatusBar(); + await userEvent.click(screen.getByRole('button', { name: 'Cancel' })); + expect(onSave).not.toHaveBeenCalled(); + expect(onSaveAndClose).not.toHaveBeenCalled(); + }); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/StatusBar.tsx b/assay/src/client/PlateTemplateDesigner/components/StatusBar.tsx new file mode 100644 index 00000000000..80a539bd161 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/StatusBar.tsx @@ -0,0 +1,70 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React, { useEffect, useState } from 'react'; + +interface StatusBarProps { + isDirty: boolean; + status: string; + plateName: string; + onSaveAndClose: () => void; + onSave: () => void; + onCancel: () => void; +} + +/** + * Persistent action bar pinned to the top of the designer. + * + * Button behavior: + * - "Save & Close": saves if dirty, then navigates to the returnURL (or plate list). + * Always enabled so users can leave even when clean. + * - "Save": persists the current state and updates the page URL to the canonical + * ?templateName=...&plateId=... form so a browser refresh reloads the same plate. + * Disabled when the plate is clean to prevent redundant requests. + * - "Cancel": navigates away without saving. The browser's beforeunload handler + * will prompt if there are unsaved changes. + * + * The "Unsaved changes" indicator and transient status text ("Saving…", "Saved.") + * use `role="status"` so screen readers announce them as they appear. + */ +export function StatusBar({ isDirty, status, plateName, onSaveAndClose, onSave, onCancel }: StatusBarProps): JSX.Element { + const [error, setError] = useState(null); + + // Clear stale validation error once the user has filled in the plate name + useEffect(() => { + if (plateName.trim()) setError(null); + }, [plateName]); + + const validate = (): boolean => { + if (!plateName.trim()) { + setError('Please enter a plate name before saving.'); + return false; + } + setError(null); + return true; + }; + + const validateAndSave = () => { if (validate()) onSave(); }; + + // Skip validation when there is nothing to save — the parent will navigate away without writing. + const validateAndSaveAndClose = () => { if (!isDirty || validate()) onSaveAndClose(); }; + + return ( +
+ + + + {isDirty ? 'Unsaved changes' : ''} + {status} + {error && {error}} +
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/TabButton.test.tsx b/assay/src/client/PlateTemplateDesigner/components/TabButton.test.tsx new file mode 100644 index 00000000000..c229a5ef014 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/TabButton.test.tsx @@ -0,0 +1,88 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { render, screen } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { TabButton } from './TabButton'; + +function renderTab(overrides: Partial> = {}) { + const props = { + id: 'my-tab', + panelId: 'my-panel', + isActive: false, + baseClass: 'my-tab', + onClick: jest.fn(), + children: 'Tab Label', + ...overrides, + }; + render(); + return props; +} + +describe('TabButton', () => { + test('renders with role="tab"', () => { + renderTab(); + expect(screen.getByRole('tab')).toBeInTheDocument(); + }); + + test('sets id on the button element', () => { + renderTab({ id: 'right-tab-properties' }); + expect(screen.getByRole('tab')).toHaveAttribute('id', 'right-tab-properties'); + }); + + test('sets aria-controls to panelId', () => { + renderTab({ panelId: 'right-panel-properties' }); + expect(screen.getByRole('tab')).toHaveAttribute('aria-controls', 'right-panel-properties'); + }); + + test('aria-selected is true when isActive is true', () => { + renderTab({ isActive: true }); + expect(screen.getByRole('tab', { selected: true })).toBeInTheDocument(); + }); + + test('aria-selected is false when isActive is false', () => { + renderTab({ isActive: false }); + expect(screen.getByRole('tab', { selected: false })).toBeInTheDocument(); + }); + + test('applies baseClass to the button', () => { + renderTab({ baseClass: 'my-tab' }); + expect(screen.getByRole('tab')).toHaveClass('my-tab'); + }); + + test('adds --active when isActive is true', () => { + renderTab({ baseClass: 'my-tab', isActive: true }); + expect(screen.getByRole('tab')).toHaveClass('my-tab--active'); + }); + + test('does not add --active when isActive is false', () => { + renderTab({ baseClass: 'my-tab', isActive: false }); + expect(screen.getByRole('tab')).not.toHaveClass('my-tab--active'); + }); + + test('applies extraClassName when provided', () => { + renderTab({ extraClassName: 'my-tab--warn' }); + expect(screen.getByRole('tab')).toHaveClass('my-tab--warn'); + }); + + test('does not add unexpected classes when extraClassName is omitted', () => { + renderTab({ baseClass: 'my-tab', isActive: false }); + expect(screen.getByRole('tab')).toHaveClass('my-tab'); + expect(screen.getByRole('tab').className.trim()).toBe('my-tab'); + }); + + test('renders children', () => { + renderTab({ children: 'Well Group Properties' }); + expect(screen.getByText('Well Group Properties')).toBeInTheDocument(); + }); + + test('calls onClick when clicked', async () => { + const { onClick } = renderTab(); + await userEvent.click(screen.getByRole('tab')); + expect(onClick).toHaveBeenCalledTimes(1); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/TabButton.tsx b/assay/src/client/PlateTemplateDesigner/components/TabButton.tsx new file mode 100644 index 00000000000..5809c4ea9f8 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/TabButton.tsx @@ -0,0 +1,37 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import classNames from 'classnames'; + +interface TabButtonProps { + id: string; + panelId: string; + isActive: boolean; + baseClass: string; + extraClassName?: string; + onClick: () => void; + children: React.ReactNode; +} + +/** + * A single ARIA tab button. Handles `role="tab"`, `aria-controls`, `aria-selected`, + * and the BEM `--active` modifier. Use inside a `role="tablist"` container. + */ +export function TabButton({ id, panelId, isActive, baseClass, extraClassName, onClick, children }: TabButtonProps): JSX.Element { + return ( + + ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/TemplateGrid.test.tsx b/assay/src/client/PlateTemplateDesigner/components/TemplateGrid.test.tsx new file mode 100644 index 00000000000..79add5b0c0e --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/TemplateGrid.test.tsx @@ -0,0 +1,286 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { fireEvent, render, screen } from '@testing-library/react'; + +import { PlateTemplate, WellGroup } from '../models'; +import { TemplateGrid } from './TemplateGrid'; + +function makePlate(rows = 4, cols = 4, groups: WellGroup[] = []): PlateTemplate { + return { + rowId: 1, + name: 'Test', + type: 'assay', + rows, + cols, + groupTypes: ['SPECIMEN'], + canCreateGroupsByType: {}, + groups, + plateProperties: {}, + typesToDefaultGroups: {}, + showWarningPanel: false, + existingTemplateNames: [], + copyMode: false, + defaultPlateName: '', + }; +} + +function renderGrid(overrides: Partial> = {}) { + const props = { + plate: makePlate(), + activeGroup: null, + activeTab: 'SPECIMEN', + colorMap: new Map(), + onDragRect: jest.fn(), + onCellToggle: jest.fn(), + ...overrides, + }; + render(); + return props; +} + +// Helpers for getting cells by their aria-label (e.g. "A1", "B3") +function getCell(label: string) { + return screen.getByLabelText(label); +} + +describe('TemplateGrid — rendering', () => { + test('renders the correct number of data cells', () => { + renderGrid({ plate: makePlate(3, 4) }); + // 3 rows × 4 cols = 12 cells, all labeled A1..C4 + expect(screen.getByLabelText('A1')).toBeInTheDocument(); + expect(screen.getByLabelText('C4')).toBeInTheDocument(); + }); + + test('renders column headers 1..cols', () => { + renderGrid({ plate: makePlate(2, 3) }); + expect(screen.getByText('1')).toBeInTheDocument(); + expect(screen.getByText('2')).toBeInTheDocument(); + expect(screen.getByText('3')).toBeInTheDocument(); + }); + + test('renders row headers A..H for 8 rows', () => { + renderGrid({ plate: makePlate(8, 1) }); + ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'].forEach(letter => { + expect(screen.getAllByText(letter)[0]).toBeInTheDocument(); + }); + }); + + test('cell aria-label includes group name when cell is assigned', () => { + const group: WellGroup = { + rowId: 1, type: 'SPECIMEN', name: 'Sample 1', + positions: [{ row: 0, col: 0 }], properties: {}, allowNewGroups: false, + }; + renderGrid({ + plate: makePlate(2, 2, [group]), + colorMap: new Map([[1, '#ff0000']]), + }); + expect(screen.getByLabelText('A1: Sample 1')).toBeInTheDocument(); + }); + + test('cell tooltip is just the location when unassigned', () => { + renderGrid({ plate: makePlate(2, 2) }); + expect(screen.getByLabelText('B2')).toBeInTheDocument(); + }); +}); + +describe('TemplateGrid — roving tabindex', () => { + test('cell (0,0) has tabIndex=0 before any focus interaction', () => { + renderGrid(); + expect(getCell('A1')).toHaveAttribute('tabindex', '0'); + expect(getCell('A2')).toHaveAttribute('tabindex', '-1'); + }); + + test('all other cells have tabIndex=-1 initially', () => { + renderGrid({ plate: makePlate(2, 2) }); + ['A2', 'B1', 'B2'].forEach(label => { + expect(getCell(label)).toHaveAttribute('tabindex', '-1'); + }); + }); + + test('focusing a cell updates the tab stop to that cell', () => { + renderGrid({ plate: makePlate(2, 2) }); + fireEvent.focus(getCell('B2')); + expect(getCell('B2')).toHaveAttribute('tabindex', '0'); + expect(getCell('A1')).toHaveAttribute('tabindex', '-1'); + }); +}); + +describe('TemplateGrid — keyboard navigation', () => { + test('ArrowRight moves focus from A1 to A2', () => { + renderGrid(); + fireEvent.keyDown(getCell('A1'), { key: 'ArrowRight' }); + expect(getCell('A2')).toHaveAttribute('tabindex', '0'); + expect(getCell('A1')).toHaveAttribute('tabindex', '-1'); + }); + + test('ArrowDown moves focus from A1 to B1', () => { + renderGrid(); + fireEvent.keyDown(getCell('A1'), { key: 'ArrowDown' }); + expect(getCell('B1')).toHaveAttribute('tabindex', '0'); + }); + + test('ArrowLeft moves focus from A2 to A1', () => { + renderGrid(); + fireEvent.focus(getCell('A2')); + fireEvent.keyDown(getCell('A2'), { key: 'ArrowLeft' }); + expect(getCell('A1')).toHaveAttribute('tabindex', '0'); + }); + + test('ArrowUp moves focus from B1 to A1', () => { + renderGrid(); + fireEvent.focus(getCell('B1')); + fireEvent.keyDown(getCell('B1'), { key: 'ArrowUp' }); + expect(getCell('A1')).toHaveAttribute('tabindex', '0'); + }); + + test('ArrowLeft at column 0 does nothing', () => { + renderGrid(); + fireEvent.keyDown(getCell('A1'), { key: 'ArrowLeft' }); + // A1 should remain the tab stop + expect(getCell('A1')).toHaveAttribute('tabindex', '0'); + }); + + test('ArrowUp at row 0 does nothing', () => { + renderGrid(); + fireEvent.keyDown(getCell('A1'), { key: 'ArrowUp' }); + expect(getCell('A1')).toHaveAttribute('tabindex', '0'); + }); + + test('ArrowDown at last row does nothing', () => { + renderGrid({ plate: makePlate(4, 4) }); + fireEvent.focus(getCell('D1')); + fireEvent.keyDown(getCell('D1'), { key: 'ArrowDown' }); + expect(getCell('D1')).toHaveAttribute('tabindex', '0'); + }); + + test('ArrowRight at last column does nothing', () => { + renderGrid({ plate: makePlate(4, 4) }); + fireEvent.focus(getCell('A4')); + fireEvent.keyDown(getCell('A4'), { key: 'ArrowRight' }); + expect(getCell('A4')).toHaveAttribute('tabindex', '0'); + }); +}); + +describe('TemplateGrid — keyboard cell toggle', () => { + test('Space key calls onCellToggle with the cell coordinates', () => { + const { onCellToggle } = renderGrid(); + fireEvent.keyDown(getCell('A1'), { key: ' ' }); + expect(onCellToggle).toHaveBeenCalledWith(0, 0); + }); + + test('Enter key calls onCellToggle with the cell coordinates', () => { + const { onCellToggle } = renderGrid(); + fireEvent.keyDown(getCell('B3'), { key: 'Enter' }); + expect(onCellToggle).toHaveBeenCalledWith(1, 2); + }); + + test('other keys do not call onCellToggle', () => { + const { onCellToggle } = renderGrid(); + fireEvent.keyDown(getCell('A1'), { key: 'Tab' }); + expect(onCellToggle).not.toHaveBeenCalled(); + }); +}); + +describe('TemplateGrid — mouse click (no drag)', () => { + test('mousedown + mouseup on the same cell calls onCellToggle', () => { + const { onCellToggle } = renderGrid(); + const cell = getCell('A1'); + fireEvent.mouseDown(cell, { button: 0 }); + fireEvent.mouseUp(cell); + expect(onCellToggle).toHaveBeenCalledWith(0, 0); + }); + + test('right-click (button !== 0) does not start a drag', () => { + const { onCellToggle, onDragRect } = renderGrid(); + const cell = getCell('A1'); + fireEvent.mouseDown(cell, { button: 2 }); + fireEvent.mouseUp(cell); + expect(onCellToggle).not.toHaveBeenCalled(); + expect(onDragRect).not.toHaveBeenCalled(); + }); +}); + +describe('TemplateGrid — mouse drag', () => { + test('mousedown then mouseenter a different cell calls onDragRect (not onCellToggle)', () => { + const { onDragRect, onCellToggle } = renderGrid(); + fireEvent.mouseDown(getCell('A1'), { button: 0 }); + fireEvent.mouseEnter(getCell('B2')); + expect(onDragRect).toHaveBeenCalledWith(0, 0, 1, 1, false, []); + expect(onCellToggle).not.toHaveBeenCalled(); + }); + + test('drag started on a cell already in the active group uses unselect mode', () => { + const activeGroup: WellGroup = { + rowId: 1, type: 'SPECIMEN', name: 'Sample 1', + positions: [{ row: 0, col: 0 }], properties: {}, allowNewGroups: false, + }; + const { onDragRect } = renderGrid({ activeGroup }); + fireEvent.mouseDown(getCell('A1'), { button: 0 }); + fireEvent.mouseEnter(getCell('B2')); + // isUnselect should be true since A1 is already in the active group + expect(onDragRect).toHaveBeenCalledWith(0, 0, 1, 1, true, activeGroup.positions); + }); + + test('drag started on an empty cell uses select mode', () => { + const activeGroup: WellGroup = { + rowId: 1, type: 'SPECIMEN', name: 'Sample 1', + positions: [], properties: {}, allowNewGroups: false, + }; + const { onDragRect } = renderGrid({ activeGroup }); + fireEvent.mouseDown(getCell('A1'), { button: 0 }); + fireEvent.mouseEnter(getCell('B2')); + expect(onDragRect).toHaveBeenCalledWith(0, 0, 1, 1, false, []); + }); + + test('mouseleave the grid resets drag state so subsequent mouseenter does not fire', () => { + const { onDragRect } = renderGrid(); + const grid = document.querySelector('.template-grid') as HTMLElement; + fireEvent.mouseDown(getCell('A1'), { button: 0 }); + fireEvent.mouseLeave(grid); // drag cancelled + fireEvent.mouseEnter(getCell('B2')); // should be ignored + expect(onDragRect).not.toHaveBeenCalled(); + }); + + test('mouseup after drag does not call onCellToggle', () => { + const { onCellToggle } = renderGrid(); + fireEvent.mouseDown(getCell('A1'), { button: 0 }); + fireEvent.mouseEnter(getCell('B2')); + fireEvent.mouseUp(getCell('B2')); + expect(onCellToggle).not.toHaveBeenCalled(); + }); +}); + +describe('TemplateGrid — colorMap fallback', () => { + test('cell gets #f5f5f5 background when its group rowId is not in colorMap', () => { + const group: WellGroup = { + rowId: 1, type: 'SPECIMEN', name: 'Sample 1', + positions: [{ row: 0, col: 0 }], properties: {}, allowNewGroups: false, + }; + renderGrid({ + plate: makePlate(2, 2, [group]), + colorMap: new Map(), // rowId 1 not in map → falls back to '#f5f5f5' + }); + const cell = screen.getByLabelText('A1: Sample 1'); + expect(cell).toBeInTheDocument(); + expect(cell).toHaveStyle({ backgroundColor: '#f5f5f5' }); + }); + + test('group of a type other than activeTab is excluded from position map', () => { + const controlGroup: WellGroup = { + rowId: 2, type: 'CONTROL', name: 'Virus', + positions: [{ row: 0, col: 0 }], properties: {}, allowNewGroups: false, + }; + renderGrid({ + plate: makePlate(2, 2, [controlGroup]), + colorMap: new Map([[2, '#00ff00']]), + activeTab: 'SPECIMEN', // CONTROL !== SPECIMEN → group is skipped + }); + // Cell is not labeled with the CONTROL group name since that type is inactive + expect(screen.getByLabelText('A1')).toBeInTheDocument(); + expect(screen.queryByLabelText('A1: Virus')).toBeNull(); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/TemplateGrid.tsx b/assay/src/client/PlateTemplateDesigner/components/TemplateGrid.tsx new file mode 100644 index 00000000000..7882dfd4771 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/TemplateGrid.tsx @@ -0,0 +1,216 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React, { useCallback, useMemo, useRef, useState } from 'react'; +import classNames from 'classnames'; + +import { PlateTemplate, Position, WellGroup } from '../models'; + +interface TemplateGridProps { + plate: PlateTemplate; + activeGroup: WellGroup | null; + activeTab: string; + colorMap: Map; + onDragRect: (r1: number, c1: number, r2: number, c2: number, isUnselect: boolean, preDragPositions: Position[]) => void; + onCellToggle: (row: number, col: number) => void; +} + +function getRowLabel(row: number): string { + return String.fromCharCode(65 + row); +} + +/** + * A scrollable well grid that lets the user paint cells onto the active well group. + * + * ─── Coloring ────────────────────────────────────────────────────────────────── + * Only wells belonging to groups of the *active tab type* are colored. Wells from + * other types are invisible in the current view. + * + * ─── Drag / click interaction ────────────────────────────────────────────────── + * Cell assignment uses a three-phase state machine tracked entirely via refs + * (no re-renders on drag): + * + * Phase 1 – mousedown on a cell: + * Enter drag mode. Record the start cell. Do NOT assign anything yet — we + * first need to know whether the user is clicking (toggle) or dragging (rect). + * + * Phase 2 – mouseenter a *different* cell while dragging: + * We now know it's a drag. Call onDragRect with the axis-aligned rectangle + * defined by the mousedown cell and the current cell, plus the drag mode + * (select vs unselect) determined at mousedown. The parent replaces or removes + * cells on every call, so the selection dynamically resizes as the mouse moves. + * + * Phase 3 – mouseup: + * If the pointer never left the start cell (hasMoved === false), treat the + * interaction as a click and toggle that cell (add if absent, remove if present). + * Either way, reset all drag state. + * + * Drag state is also cleaned up on mouseleave of the outer div, preventing stuck + * drag state when the pointer exits the grid. + */ +export function TemplateGrid({ plate, activeGroup, activeTab, colorMap, onDragRect, onCellToggle }: TemplateGridProps): JSX.Element { + const isDragging = useRef(false); + const hasMoved = useRef(false); + const startCell = useRef<{ row: number; col: number } | null>(null); + const dragIsUnselect = useRef(false); // true when the drag started on a cell already in the active group + const preDragPositions = useRef([]); // snapshot of activeGroup.positions at mousedown + + // Roving-tabindex state: tracks which cell holds tabIndex=0. Null means no cell has been + // focused yet, in which case (0,0) is the tab entry point. + const [focusedCell, setFocusedCell] = useState<{ row: number; col: number } | null>(null); + const cellRefs = useRef>(new Map()); + + // Pre-compute a "row,col" → {color, groupName} map for the active tab type. + // This lets each cell do an O(1) lookup rather than scanning all groups and + // positions on every render (which would be O(groups × positions) per cell). + const positionMap = useMemo(() => { + const map = new Map(); + for (const group of plate.groups) { + if (group.type !== activeTab) continue; + const color = colorMap.get(group.rowId) ?? '#f5f5f5'; + for (const p of group.positions) { + map.set(`${p.row},${p.col}`, { color, groupName: group.name }); + } + } + return map; + }, [plate, activeTab, colorMap]); + + // Pre-compute a Set of "row,col" keys for the active group's positions so each cell + // can do an O(1) membership check instead of scanning the positions array on every render. + const activeGroupPositionSet = useMemo(() => { + const set = new Set(); + if (activeGroup) { + for (const p of activeGroup.positions) { + set.add(`${p.row},${p.col}`); + } + } + return set; + }, [activeGroup]); + + const handleMouseDown = useCallback((row: number, col: number, e: React.MouseEvent) => { + if (e.button !== 0) return; + isDragging.current = true; + hasMoved.current = false; + startCell.current = { row, col }; + dragIsUnselect.current = activeGroup?.positions.some(p => p.row === row && p.col === col) ?? false; + // Snapshot the current positions NOW, from the prop, before any drag events can modify state. + preDragPositions.current = activeGroup?.positions ?? []; + // Note: text selection during drag is already prevented by `user-select: none` in CSS, + // so e.preventDefault() is not needed here and is intentionally omitted so the browser's + // default focus-on-mousedown behaviour is preserved. + }, [activeGroup]); + + const handleMouseEnter = useCallback((row: number, col: number) => { + if (!isDragging.current || !startCell.current) return; + hasMoved.current = true; + onDragRect(startCell.current.row, startCell.current.col, row, col, dragIsUnselect.current, preDragPositions.current); + }, [onDragRect]); + + // Called on mouseup over a specific cell — handles click-toggle + const handleCellMouseUp = useCallback((row: number, col: number) => { + if (isDragging.current && !hasMoved.current) { + // Explicitly move focus to the clicked cell so arrow-key navigation + // picks up from the correct position after a mouse interaction. + cellRefs.current.get(`${row},${col}`)?.focus(); + onCellToggle(row, col); + } + }, [onCellToggle]); + + // Called on the wrapper div — cleans up drag state + const handleDragEnd = useCallback(() => { + isDragging.current = false; + hasMoved.current = false; + startCell.current = null; + dragIsUnselect.current = false; + }, []); + + const handleCellFocus = useCallback((row: number, col: number) => { + setFocusedCell({ row, col }); + }, []); + + // Keyboard interaction for grid cells: + // Space / Enter → toggle the cell (same as a click with no drag) + // Arrow keys → move focus to the adjacent cell (wraps are intentionally prevented + // at plate edges to avoid confusing wrap-around focus jumps) + const handleCellKeyDown = useCallback((row: number, col: number, e: React.KeyboardEvent) => { + const moveFocus = (r: number, c: number) => { + e.preventDefault(); + setFocusedCell({ row: r, col: c }); + cellRefs.current.get(`${r},${c}`)?.focus(); + }; + switch (e.key) { + case ' ': + case 'Enter': + e.preventDefault(); + onCellToggle(row, col); + break; + case 'ArrowUp': + if (row > 0) moveFocus(row - 1, col); + break; + case 'ArrowDown': + if (row < plate.rows - 1) moveFocus(row + 1, col); + break; + case 'ArrowLeft': + if (col > 0) moveFocus(row, col - 1); + break; + case 'ArrowRight': + if (col < plate.cols - 1) moveFocus(row, col + 1); + break; + } + }, [onCellToggle, plate.rows, plate.cols]); + + return ( +
+ + + + + ))} + + + + {Array.from({ length: plate.rows }, (_, row) => ( + + + {Array.from({ length: plate.cols }, (_, col) => { + const entry = positionMap.get(`${row},${col}`); + const isActiveGroupCell = activeGroupPositionSet.has(`${row},${col}`); + const location = `${getRowLabel(row)}${col + 1}`; + const tooltip = entry ? `${location}: ${entry.groupName}` : location; + const isTabStop = focusedCell + ? focusedCell.row === row && focusedCell.col === col + : row === 0 && col === 0; + return ( + + ))} + +
+ {Array.from({ length: plate.cols }, (_, col) => ( + {col + 1}
{getRowLabel(row)} { + const key = `${row},${col}`; + if (el) cellRefs.current.set(key, el); + else cellRefs.current.delete(key); + }} + tabIndex={isTabStop ? 0 : -1} + className={classNames('template-grid__cell', { + 'template-grid__cell--active': isActiveGroupCell, + })} + style={{ backgroundColor: entry?.color ?? '#f5f5f5' }} + aria-label={tooltip} + onMouseDown={e => handleMouseDown(row, col, e)} + onMouseEnter={() => handleMouseEnter(row, col)} + onMouseUp={() => handleCellMouseUp(row, col)} + onFocus={() => handleCellFocus(row, col)} + onKeyDown={e => handleCellKeyDown(row, col, e)} + /> + ); + })} +
+
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/WarningPanel.test.tsx b/assay/src/client/PlateTemplateDesigner/components/WarningPanel.test.tsx new file mode 100644 index 00000000000..1a740ce48d5 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/WarningPanel.test.tsx @@ -0,0 +1,41 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { render, screen } from '@testing-library/react'; + +import { WarningPanel } from './WarningPanel'; + +describe('WarningPanel', () => { + test('shows "No warnings." and no list when warnings is empty', () => { + render(); + expect(screen.getByText('No warnings.')).toBeInTheDocument(); + expect(screen.queryByRole('list')).toBeNull(); + }); + + test('renders a list item for each warning', () => { + const warnings = ['A1: replicate with no specimen', 'B3: in both specimen and control']; + render(); + expect(screen.queryByText('No warnings.')).toBeNull(); + expect(screen.getAllByRole('listitem')).toHaveLength(2); + expect(screen.getByText('A1: replicate with no specimen')).toBeInTheDocument(); + expect(screen.getByText('B3: in both specimen and control')).toBeInTheDocument(); + }); + + test('renders a single warning without "No warnings."', () => { + render(); + expect(screen.getAllByRole('listitem')).toHaveLength(1); + expect(screen.queryByText('No warnings.')).toBeNull(); + }); + + test('switches from "No warnings." to a list when warnings change', () => { + const { rerender } = render(); + expect(screen.getByText('No warnings.')).toBeInTheDocument(); + + rerender(); + expect(screen.queryByText('No warnings.')).toBeNull(); + expect(screen.getByText('A1: some warning')).toBeInTheDocument(); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/WarningPanel.tsx b/assay/src/client/PlateTemplateDesigner/components/WarningPanel.tsx new file mode 100644 index 00000000000..dabb40c5998 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/WarningPanel.tsx @@ -0,0 +1,35 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; + +interface WarningPanelProps { + warnings: string[]; +} + +/** + * Displays the list of validation warnings for the current plate layout. + * + * Warnings are computed in the parent (PlateTemplateDesigner) and passed as a prop so the + * computation is not duplicated between the count badge and this panel. + * The panel is only shown when `plate.showWarningPanel` is true, which is controlled by the + * server-side assay type configuration (not all assay types use the REPLICATE/SPECIMEN/CONTROL + * group semantics that produce warnings). + */ +export function WarningPanel({ warnings }: WarningPanelProps): JSX.Element { + return ( +
+ {warnings.length === 0 ? ( +
No warnings.
+ ) : ( +
    + {warnings.map((w) => ( +
  • {w}
    • + ))} +
+ )} +
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/components/WellGroupProperties.test.tsx b/assay/src/client/PlateTemplateDesigner/components/WellGroupProperties.test.tsx new file mode 100644 index 00000000000..879bcd515ab --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/WellGroupProperties.test.tsx @@ -0,0 +1,164 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { fireEvent, render, screen } from '@testing-library/react'; +import { userEvent } from '@testing-library/user-event'; + +import { WellGroup } from '../models'; +import { WellGroupProperties } from './WellGroupProperties'; + +function makeGroup(overrides: Partial = {}): WellGroup { + return { + rowId: 1, + type: 'SPECIMEN', + name: 'Group A', + positions: [], + properties: {}, + allowNewGroups: true, + ...overrides, + }; +} + +function renderProps(activeGroup: WellGroup | null, overrides: Partial> = {}) { + const props = { + activeGroup, + onPropertyChange: jest.fn(), + onDeleteProperty: jest.fn(), + ...overrides, + }; + render(); + return props; +} + +describe('WellGroupProperties', () => { + describe('empty state', () => { + test('shows placeholder text when no group is selected', () => { + renderProps(null); + expect(screen.getByText(/select a well group/i)).toBeInTheDocument(); + }); + + test('does not render a table when no group is selected', () => { + renderProps(null); + expect(screen.queryByRole('table')).toBeNull(); + }); + }); + + describe('group display', () => { + test('renders the group name as a title', () => { + renderProps(makeGroup({ name: 'My Group' })); + expect(screen.getByText('My Group')).toBeInTheDocument(); + }); + + test('shows "No properties defined" when group has no properties', () => { + renderProps(makeGroup({ properties: {} })); + expect(screen.getByText(/No properties defined/i)).toBeInTheDocument(); + }); + + test('renders a row for each existing property', () => { + renderProps(makeGroup({ properties: { conc: '1.0', dilution: '2x' } })); + expect(screen.getByText('conc')).toBeInTheDocument(); + expect(screen.getByDisplayValue('1.0')).toBeInTheDocument(); + expect(screen.getByText('dilution')).toBeInTheDocument(); + expect(screen.getByDisplayValue('2x')).toBeInTheDocument(); + }); + + test('renders a delete button per property', () => { + renderProps(makeGroup({ properties: { a: '1', b: '2' } })); + expect(screen.getAllByRole('button', { name: /Delete property/i })).toHaveLength(2); + }); + }); + + describe('editing existing properties', () => { + test('changing a value input calls onPropertyChange with groupRowId, key, and new value', () => { + const group = makeGroup({ properties: { conc: '1.0' } }); + const { onPropertyChange } = renderProps(group); + // The input is controlled (value comes from activeGroup.properties), so use + // fireEvent.change to fire a single synthetic event without the re-render cycle + // that makes userEvent.type fight the controlled value. + fireEvent.change(screen.getByLabelText('conc'), { target: { value: '5.0' } }); + expect(onPropertyChange).toHaveBeenCalledWith(group.rowId, 'conc', '5.0'); + }); + + test('clicking the delete button calls onDeleteProperty with groupRowId and key', async () => { + const group = makeGroup({ properties: { conc: '1.0' } }); + const { onDeleteProperty } = renderProps(group); + await userEvent.click(screen.getByRole('button', { name: 'Delete property conc' })); + expect(onDeleteProperty).toHaveBeenCalledWith(group.rowId, 'conc'); + }); + }); + + describe('adding a new property', () => { + test('Add button is disabled when the key input is empty', () => { + renderProps(makeGroup()); + expect(screen.getByRole('button', { name: 'Add' })).toBeDisabled(); + }); + + test('Add button is enabled when a key is typed', async () => { + renderProps(makeGroup()); + await userEvent.type(screen.getByLabelText('Property name'), 'newKey'); + expect(screen.getByRole('button', { name: 'Add' })).toBeEnabled(); + }); + + test('clicking Add calls onPropertyChange with the new key and value then clears inputs', async () => { + const group = makeGroup(); + const { onPropertyChange } = renderProps(group); + await userEvent.type(screen.getByLabelText('Property name'), 'dose'); + await userEvent.type(screen.getByLabelText('Property value'), '10mg'); + await userEvent.click(screen.getByRole('button', { name: 'Add' })); + expect(onPropertyChange).toHaveBeenCalledWith(group.rowId, 'dose', '10mg'); + expect(screen.getByLabelText('Property name')).toHaveValue(''); + expect(screen.getByLabelText('Property value')).toHaveValue(''); + }); + + test('pressing Enter in the key input calls onPropertyChange', async () => { + const group = makeGroup(); + const { onPropertyChange } = renderProps(group); + await userEvent.type(screen.getByLabelText('Property name'), 'dose'); + await userEvent.type(screen.getByLabelText('Property value'), '10mg'); + await userEvent.type(screen.getByLabelText('Property name'), '{Enter}'); + expect(onPropertyChange).toHaveBeenCalledWith(group.rowId, 'dose', '10mg'); + }); + + test('pressing Enter in the value input calls onPropertyChange', async () => { + const group = makeGroup(); + const { onPropertyChange } = renderProps(group); + await userEvent.type(screen.getByLabelText('Property name'), 'dose'); + await userEvent.type(screen.getByLabelText('Property value'), '10mg'); + await userEvent.type(screen.getByLabelText('Property value'), '{Enter}'); + expect(onPropertyChange).toHaveBeenCalledWith(group.rowId, 'dose', '10mg'); + }); + + test('Add does not fire when key is whitespace-only', async () => { + const { onPropertyChange } = renderProps(makeGroup()); + await userEvent.type(screen.getByLabelText('Property name'), ' '); + await userEvent.click(screen.getByRole('button', { name: 'Add' })); + expect(onPropertyChange).not.toHaveBeenCalled(); + }); + + test('pressing Enter with a whitespace-only key does not call onPropertyChange', async () => { + // The Add button is disabled for whitespace, but the Enter key handler on the + // input calls handleAdd() directly, which must guard against empty trimmed keys. + const { onPropertyChange } = renderProps(makeGroup()); + await userEvent.type(screen.getByLabelText('Property name'), ' {Enter}'); + expect(onPropertyChange).not.toHaveBeenCalled(); + }); + }); + + describe('inputs reset when active group changes', () => { + test('newKey input is cleared when activeGroup prop changes', async () => { + const group1 = makeGroup({ rowId: 1, name: 'Group 1' }); + const group2 = makeGroup({ rowId: 2, name: 'Group 2' }); + const { rerender } = render( + + ); + await userEvent.type(screen.getByLabelText('Property name'), 'stale-key'); + rerender( + + ); + expect(screen.getByLabelText('Property name')).toHaveValue(''); + }); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/components/WellGroupProperties.tsx b/assay/src/client/PlateTemplateDesigner/components/WellGroupProperties.tsx new file mode 100644 index 00000000000..1e520886c77 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/components/WellGroupProperties.tsx @@ -0,0 +1,139 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React, { useEffect, useState } from 'react'; + +import { WellGroup } from '../models'; + +interface WellGroupPropertiesProps { + activeGroup: WellGroup | null; + onPropertyChange: (groupRowId: number, key: string, value: string) => void; + onDeleteProperty: (groupRowId: number, key: string) => void; +} + +/** + * Shows and edits the key/value property bag for the currently selected well group. + * + * Properties are assay-type-specific metadata attached to a group (e.g. concentration, + * dilution factor, sample ID). They are stored as plain strings and round-tripped through + * the server without interpretation by the designer. + * + * Interaction pattern: + * - Existing properties: each row has an inline text input for the value; changes propagate + * immediately to the parent (no separate submit step) via onPropertyChange. + * - Deleting: the trash button removes a property key entirely. + * - Adding: the footer row accepts a new key + value; "Add" (or Enter) commits the pair. + * The new-key input is the gate — the Add button stays disabled until a key is typed. + */ +export function WellGroupProperties({ activeGroup, onPropertyChange, onDeleteProperty }: WellGroupPropertiesProps): JSX.Element { + const [newKey, setNewKey] = useState(''); + const [newValue, setNewValue] = useState(''); + + // Reset draft inputs when the selected group changes so stale text from a + // previous group cannot accidentally be committed to the newly selected one. + useEffect(() => { + setNewKey(''); + setNewValue(''); + }, [activeGroup?.rowId]); + + if (!activeGroup) { + return ( +
+ Select a well group to view its properties. +
+ ); + } + + const propEntries = Object.entries(activeGroup.properties); + + const handleAdd = () => { + const key = newKey.trim(); + if (!key) return; + onPropertyChange(activeGroup.rowId, key, newValue); + setNewKey(''); + setNewValue(''); + }; + + return ( +
+
{activeGroup.name}
+ + + + + + + + + + {propEntries.length === 0 && ( + + + + )} + {propEntries.map(([key, value]) => ( + + + + + + ))} + + + + + + + + +
PropertyValueActions
No properties defined.
{key} + onPropertyChange(activeGroup.rowId, key, e.target.value)} + /> + + +
+ setNewKey(e.target.value)} + onKeyDown={e => { if (e.key === 'Enter' && newKey.trim()) handleAdd(); }} + /> + + setNewValue(e.target.value)} + onKeyDown={e => { if (e.key === 'Enter' && newKey.trim()) handleAdd(); }} + /> + + +
+
+ ); +} diff --git a/assay/src/client/PlateTemplateDesigner/dev.tsx b/assay/src/client/PlateTemplateDesigner/dev.tsx new file mode 100644 index 00000000000..d75b4201270 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/dev.tsx @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import React from 'react'; +import { createRoot } from 'react-dom/client'; +import { getServerContext } from '@labkey/api'; +import { ServerContextProvider, withAppUser } from '@labkey/components'; + +import { PlateTemplateDesigner } from './PlateTemplateDesigner'; + +createRoot(document.getElementById('app')).render( + + + +); diff --git a/assay/src/client/PlateTemplateDesigner/models.test.ts b/assay/src/client/PlateTemplateDesigner/models.test.ts new file mode 100644 index 00000000000..90872a9b1ae --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/models.test.ts @@ -0,0 +1,153 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +import { + PlateTemplate, + WellGroup, + computeWarnings, + GROUP_TYPE_CONTROL, + GROUP_TYPE_REPLICATE, + GROUP_TYPE_SPECIMEN, +} from './models'; + +function makePlate(groups: Partial[]): PlateTemplate { + return { + rowId: 1, + name: 'Test Plate', + type: 'assay', + rows: 8, + cols: 12, + groupTypes: [GROUP_TYPE_SPECIMEN, GROUP_TYPE_CONTROL, GROUP_TYPE_REPLICATE], + canCreateGroupsByType: {}, + groups: groups.map((g, i) => ({ + rowId: i + 1, + type: GROUP_TYPE_SPECIMEN, + name: `Group ${i + 1}`, + positions: [], + properties: {}, + allowNewGroups: false, + ...g, + })), + plateProperties: {}, + typesToDefaultGroups: {}, + showWarningPanel: true, + existingTemplateNames: [], + copyMode: false, + defaultPlateName: '', + }; +} + +describe('computeWarnings', () => { + test('returns no warnings for an empty plate', () => { + expect(computeWarnings(makePlate([]))).toEqual([]); + }); + + test('returns no warnings when no cells are assigned', () => { + const plate = makePlate([ + { type: GROUP_TYPE_REPLICATE, positions: [] }, + { type: GROUP_TYPE_SPECIMEN, positions: [] }, + ]); + expect(computeWarnings(plate)).toEqual([]); + }); + + test('warns when a REPLICATE cell has no SPECIMEN or CONTROL', () => { + const plate = makePlate([ + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }] }, + ]); + const warnings = computeWarnings(plate); + expect(warnings).toHaveLength(1); + expect(warnings[0]).toContain('A1'); + expect(warnings[0]).toContain('replicate'); + }); + + test('no warning when REPLICATE cell is also in a SPECIMEN group', () => { + const plate = makePlate([ + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }] }, + { type: GROUP_TYPE_SPECIMEN, positions: [{ row: 0, col: 0 }] }, + ]); + expect(computeWarnings(plate)).toEqual([]); + }); + + test('no warning when REPLICATE cell is also in a CONTROL group', () => { + const plate = makePlate([ + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }] }, + { type: GROUP_TYPE_CONTROL, positions: [{ row: 0, col: 0 }] }, + ]); + expect(computeWarnings(plate)).toEqual([]); + }); + + test('warns when a cell is in both SPECIMEN and CONTROL groups', () => { + const plate = makePlate([ + { type: GROUP_TYPE_SPECIMEN, positions: [{ row: 1, col: 2 }] }, + { type: GROUP_TYPE_CONTROL, positions: [{ row: 1, col: 2 }] }, + ]); + const warnings = computeWarnings(plate); + expect(warnings).toHaveLength(1); + expect(warnings[0]).toContain('B3'); + expect(warnings[0]).toContain('specimen'); + expect(warnings[0]).toContain('control'); + }); + + test('cell in SPECIMEN + CONTROL + REPLICATE produces only the specimen/control warning', () => { + // REPLICATE warning suppressed because CONTROL is present + const plate = makePlate([ + { type: GROUP_TYPE_SPECIMEN, positions: [{ row: 0, col: 0 }] }, + { type: GROUP_TYPE_CONTROL, positions: [{ row: 0, col: 0 }] }, + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }] }, + ]); + const warnings = computeWarnings(plate); + expect(warnings).toHaveLength(1); + expect(warnings[0]).toContain('specimen'); + expect(warnings[0]).toContain('control'); + }); + + test('cell in an unrelated group type produces no warning', () => { + const plate = makePlate([ + { type: 'UNKNOWN', positions: [{ row: 0, col: 0 }] }, + ]); + expect(computeWarnings(plate)).toEqual([]); + }); + + test('produces separate warnings for multiple problem cells', () => { + const plate = makePlate([ + // Two orphan replicates + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }, { row: 0, col: 1 }] }, + ]); + const warnings = computeWarnings(plate); + expect(warnings).toHaveLength(2); + }); + + test('uses correct spreadsheet cell labels', () => { + // row 0 col 0 → A1 + // row 1 col 11 → B12 + // row 7 col 11 → H12 + const plate = makePlate([ + { + type: GROUP_TYPE_REPLICATE, + positions: [ + { row: 0, col: 0 }, + { row: 1, col: 11 }, + { row: 7, col: 11 }, + ], + }, + ]); + const warnings = computeWarnings(plate); + const labels = warnings.map(w => w.split(':')[0]); + expect(labels).toContain('A1'); + expect(labels).toContain('B12'); + expect(labels).toContain('H12'); + }); + + test('a cell in the same group type twice (two groups, same type) still counts as one type', () => { + // Two REPLICATE groups covering the same cell — the cell is still only REPLICATE-typed + const plate = makePlate([ + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }] }, + { type: GROUP_TYPE_REPLICATE, positions: [{ row: 0, col: 0 }] }, + ]); + const warnings = computeWarnings(plate); + // Only one warning for the cell (not two) + expect(warnings).toHaveLength(1); + }); +}); diff --git a/assay/src/client/PlateTemplateDesigner/models.ts b/assay/src/client/PlateTemplateDesigner/models.ts new file mode 100644 index 00000000000..b8e120e63cd --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/models.ts @@ -0,0 +1,79 @@ +/* + * Copyright (c) 2024 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +export interface Position { + row: number; + col: number; +} + +export interface WellGroup { + rowId: number; // Positive = server-assigned; negative = client-side temp ID (see nextGroupIdRef) + type: string; // Group type key, e.g. "CONTROL", "SPECIMEN", "REPLICATE" + name: string; + positions: Position[]; + properties: Record; + allowNewGroups: boolean; // Whether the user can create/rename/delete groups of this type +} + +export interface PlateTemplate { + rowId: number; + name: string; + type: string; + rows: number; + cols: number; + groupTypes: string[]; // Ordered list of type keys; drives the tab strip + canCreateGroupsByType: Record; // Which types expose the create-group UI + groups: WellGroup[]; + plateProperties: Record; + typesToDefaultGroups: Record; // Predefined slot names per type (e.g. "Virus", "Cell Control") + showWarningPanel: boolean; // Set by the server based on assay type config + existingTemplateNames: string[]; + copyMode: boolean; // True when the plate was loaded as a copy; starts the editor in dirty state + defaultPlateName: string; +} + +/** + * Two conditions produce warnings: + * 1. A REPLICATE well that belongs to neither a SPECIMEN nor a CONTROL group is almost certainly + * a configuration error — replicates are only meaningful relative to a specimen or control. + * 2. A well assigned to both a SPECIMEN and a CONTROL group is contradictory; those roles are + * mutually exclusive in LabKey assay semantics. + * + * Notes: + * - Warnings are per-cell, not per-group. + * - A cell can appear in multiple groups of different types (e.g. SPECIMEN + REPLICATE together is fine). + * - Cell labels use spreadsheet notation: row → letter (A=0, B=1, …), col → 1-based number. + */ +export const GROUP_TYPE_REPLICATE = 'REPLICATE'; +export const GROUP_TYPE_SPECIMEN = 'SPECIMEN'; +export const GROUP_TYPE_CONTROL = 'CONTROL'; + +export function computeWarnings(plate: PlateTemplate): string[] { + // Build a map from cell position → set of group types that include it. + const cellTypes = new Map>(); + for (const group of plate.groups) { + for (const pos of group.positions) { + const key = `${pos.row},${pos.col}`; + if (!cellTypes.has(key)) cellTypes.set(key, new Set()); + cellTypes.get(key).add(group.type); + } + } + const warnings: string[] = []; + for (const [key, types] of cellTypes.entries()) { + const [row, col] = key.split(',').map(Number); + const cellLabel = `${String.fromCharCode(65 + row)}${col + 1}`; + const hasReplicate = types.has(GROUP_TYPE_REPLICATE); + const hasSpecimen = types.has(GROUP_TYPE_SPECIMEN); + const hasControl = types.has(GROUP_TYPE_CONTROL); + if (hasReplicate && !(hasSpecimen || hasControl)) { + warnings.push(`${cellLabel}: Well is a replicate, but is not part of a specimen or control group.`); + } + if (hasControl && hasSpecimen) { + warnings.push(`${cellLabel}: Well is in both a specimen and a control group.`); + } + } + return warnings; +} diff --git a/assay/src/client/PlateTemplateDesigner/typings/main.d.ts b/assay/src/client/PlateTemplateDesigner/typings/main.d.ts new file mode 100644 index 00000000000..b8a4a9133e6 --- /dev/null +++ b/assay/src/client/PlateTemplateDesigner/typings/main.d.ts @@ -0,0 +1,14 @@ +/** + * @deprecated Use getServerContext() from @labkey/api instead + */ +declare const LABKEY: import('@labkey/api').LabKey; + +/** + * Needed so we can use process.env.NODE_ENV, which is injected by webpack, but not included in the types declared in + * the browser environments. + */ +declare const process: { + env: { + NODE_ENV: string; + }; +}; diff --git a/assay/src/client/entryPoints.js b/assay/src/client/entryPoints.js index b11f0af9722..e0522e96d3c 100644 --- a/assay/src/client/entryPoints.js +++ b/assay/src/client/entryPoints.js @@ -9,5 +9,13 @@ module.exports = { title: 'New Assay Design', permissionClasses: ['org.labkey.api.assay.security.DesignAssayPermission'], path: './src/client/AssayTypeSelect' + }, { + name: 'plateTemplateDesigner', + title: 'Plate Template Designer', + permissionClasses: [ + 'org.labkey.api.security.permissions.InsertPermission', + 'org.labkey.api.assay.security.DesignAssayPermission' + ], + path: './src/client/PlateTemplateDesigner' }] }; \ No newline at end of file diff --git a/assay/src/org/labkey/assay/PlateController.java b/assay/src/org/labkey/assay/PlateController.java index e33db16cdd4..0e7ed1cc1a0 100644 --- a/assay/src/org/labkey/assay/PlateController.java +++ b/assay/src/org/labkey/assay/PlateController.java @@ -20,6 +20,7 @@ import org.json.JSONObject; import org.labkey.api.action.ApiJsonForm; import org.labkey.api.action.FormHandlerAction; +import org.labkey.api.action.JsonInputLimit; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.GWTServiceAction; import org.labkey.api.action.Marshal; @@ -32,9 +33,12 @@ import org.labkey.api.action.SpringActionController; import org.labkey.api.assay.plate.Plate; import org.labkey.api.assay.plate.PlateCustomField; +import org.labkey.api.assay.plate.PlateLayoutHandler; import org.labkey.api.assay.plate.PlateService; import org.labkey.api.assay.plate.PlateSet; import org.labkey.api.assay.plate.PlateType; +import org.labkey.api.assay.plate.Position; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.collections.RowMapFactory; import org.labkey.api.data.Container; @@ -62,6 +66,8 @@ import org.labkey.api.util.JsonUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.URLHelper; +import org.labkey.api.module.ModuleHtmlView; +import org.labkey.api.module.ModuleLoader; import org.labkey.api.util.logging.LogHelper; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataViewSnapshotSelectionForm; @@ -76,6 +82,7 @@ import org.labkey.assay.plate.PlateSetExport; import org.labkey.assay.plate.PlateUrls; import org.labkey.assay.plate.TsvPlateLayoutHandler; +import org.labkey.assay.plate.WellGroupImpl; import org.labkey.assay.plate.model.CreatePlateSetOptions; import org.labkey.assay.plate.model.ReformatOptions; import org.labkey.assay.view.AssayGWTView; @@ -91,6 +98,7 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; +import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Set; @@ -101,6 +109,45 @@ public class PlateController extends SpringActionController private static final SpringActionController.DefaultActionResolver _actionResolver = new DefaultActionResolver(PlateController.class); private static final Logger LOG = LogHelper.getLogger(PlateController.class, "Controller for plate related actions"); + public record SubmittedGroup(int rowId, String type, String name, List positions, Map properties) + { + public static SubmittedGroup from(JSONObject g) + { + int rowId = g.optInt("rowId", -1); + String type = g.getString("type"); + String name = g.getString("name"); + JSONArray posArr = g.optJSONArray("positions"); + List positions = new ArrayList<>(); + if (posArr != null) + { + for (int j = 0; j < posArr.length(); j++) + { + JSONObject p = posArr.getJSONObject(j); + positions.add(PlatePosition.from(p)); + } + } + JSONObject propsObj = g.optJSONObject("properties"); + Map props = new HashMap<>(); + if (propsObj != null) + { + for (String key : propsObj.keySet()) + { + Object val = propsObj.get(key); + props.put(key, val == JSONObject.NULL ? null : val); + } + } + return new SubmittedGroup(rowId, type, name, positions, props); + } + } + + record PlatePosition(int row, int col) + { + public static PlatePosition from(JSONObject p) + { + return new PlatePosition(p.getInt("row"), p.getInt("col")); + } + } + public PlateController() { setActionResolver(_actionResolver); @@ -122,7 +169,7 @@ public ActionURL getPlateDetailsURL(Container c) } @RequiresPermission(ReadPermission.class) - public static class BeginAction extends SimpleRedirectAction + public static class BeginAction extends SimpleRedirectAction { @Override public ActionURL getRedirectURL(Object o) @@ -154,7 +201,7 @@ public static class PlateListAction extends SimpleViewAction public ModelAndView getView(ReturnUrlForm form, BindException errors) { setHelpTopic("editPlateTemplate"); - List plateTemplates = PlateService.get().getPlates(getContainer()) + List plateTemplates = PlateService.get().getPlates(getContainer()) .stream() .filter(p -> !TsvPlateLayoutHandler.TYPE.equalsIgnoreCase(p.getAssayType())) .toList(); @@ -169,6 +216,7 @@ public void addNavTrail(NavTree root) } } + /** Delete soon! */ @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class}) public static class DesignerServiceAction extends GWTServiceAction { @@ -194,6 +242,134 @@ public void setRowId(int rowId) } } + @Marshal(Marshaller.JSONObject) + @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class}) + @JsonInputLimit(10 * 1024 * 1024) + public static class SaveDesignerTemplateAction extends MutatingApiAction + { + private PlateType _plateType; + + @Override + public Object execute(CreatePlateForm form, BindException errors) throws Exception + { + Long rowId = form.getRowId(); + String name = form.getName(); + boolean updateExisting = false; + PlateImpl plate; + + if (rowId != null && rowId > 0) + { + plate = PlateManager.get().getPlate(getContainer(), rowId); + if (plate == null) + throw new NotFoundException("Plate template not found: " + rowId); + Plate conflict = PlateManager.get().getPlateByName(getContainer(), name); + if (conflict != null && !conflict.getRowId().equals(plate.getRowId())) + throw new ValidationException("A plate template with name '" + name + "' already exists."); + if (!plate.getAssayType().equals(form.getAssayType())) + throw new ValidationException("Plate template type '" + plate.getAssayType() + "' cannot be changed for '" + name + "'"); + if (plate.getRows() != form.getRows() || plate.getColumns() != form.getCols()) + throw new ValidationException("Plate template dimensions cannot be changed for '" + name + "'"); + updateExisting = true; + } + else + { + if (PlateManager.get().getPlateByName(getContainer(), name) != null) + throw new ValidationException("A plate template with name '" + name + "' already exists."); + plate = PlateManager.get().createPlate(getContainer(), form.getAssayType(), _plateType); + plate.setTemplate(true); + } + + plate.setName(name); + plate.setProperties(form.getPlateProperties()); + + List submittedGroups = form.getGroups(); + Set submittedGroupIds = new HashSet<>(); + for (SubmittedGroup g : submittedGroups) + if (g.rowId() > 0) + submittedGroupIds.add(g.rowId()); + + // Mark well groups absent from the submission for deletion + List existingWellGroups = plate.getWellGroups(); + for (WellGroup existingGroup : existingWellGroups) + if (existingGroup.getRowId() != null && !submittedGroupIds.contains(existingGroup.getRowId())) + plate.markWellGroupForDeletion(existingGroup); + + // Update existing or create new well groups + for (SubmittedGroup gm : submittedGroups) + { + WellGroup.Type groupType; + try + { + groupType = WellGroup.Type.valueOf(gm.type()); + } + catch (IllegalArgumentException e) + { + throw new ValidationException("Unknown well group type: '" + gm.type() + "'"); + } + + List positions = new ArrayList<>(); + for (PlatePosition p : gm.positions()) + { + if (p.row() < 0 || p.row() >= plate.getRows() || p.col() < 0 || p.col() >= plate.getColumns()) + throw new ValidationException("Position (" + p.row() + ", " + p.col() + ") is out of bounds for a " + plate.getRows() + " x " + plate.getColumns() + " plate."); + positions.add(plate.getPosition(p.row(), p.col())); + } + + WellGroupImpl group; + if (updateExisting && gm.rowId() > 0) + { + group = findExistingWellGroup(existingWellGroups, gm.rowId()); + if (group == null) + throw new ValidationException("Well group " + gm.rowId() + " was not found."); + if (group.getType() != groupType) + throw new ValidationException("Well group type cannot be changed: " + gm.name()); + group.setName(gm.name()); + group.setPositions(positions); + plate.storeWellGroup(group); + } + else + { + group = plate.addWellGroup(gm.name(), groupType, positions); + } + group.setProperties(gm.properties()); + } + + PlateLayoutHandler handler = PlateManager.get().getPlateLayoutHandler(plate.getAssayType()); + if (handler == null) + throw new NotFoundException("Invalid assay type"); + handler.validatePlate(getContainer(), getUser(), plate); + long savedRowId = PlateService.get().save(getContainer(), getUser(), plate); + return success(Map.of("rowId", savedRowId)); + } + + private WellGroupImpl findExistingWellGroup(List wellGroups, int rowId) + { + for (WellGroupImpl wg : wellGroups) + if (wg.getRowId() != null && wg.getRowId() == rowId) + return wg; + return null; + } + + @Override + public void validateForm(CreatePlateForm form, Errors errors) + { + if (form.getGroups() == null || form.getGroups().isEmpty()) + { + errors.reject(ERROR_REQUIRED, "At least one group is required."); + } + // Template designer (groups) path: plateType resolved by rowId lookup on update, + // or by rows×cols on create. + if (form.getRowId() == null || form.getRowId() <= 0) + { + _plateType = form.getPlateType() != null + ? PlateManager.get().getPlateType(form.getPlateType()) + : PlateService.get().getPlateType(form.getRows(), form.getCols()); + if (_plateType == null) + errors.reject(ERROR_REQUIRED, "The plate type (" + form.getRows() + " x " + form.getCols() + ") does not exist."); + } + } + } + @RequiresPermission(ReadPermission.class) public static class PlateDetailsAction extends SimpleRedirectAction { @@ -211,7 +387,162 @@ public ActionURL getRedirectURL(RowIdForm form) } @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class}) - public class DesignerAction extends SimpleViewAction + public class GetDesignerTemplateDefinitionAction extends ReadOnlyApiAction + { + @Override + public Object execute(DesignerForm form, BindException errors) throws Exception + { + String templateName = form.getTemplateName(); + Long plateId = form.getPlateId(); + boolean copyTemplate = form.isCopy(); + + if (templateName == null && plateId != null) + { + Plate plate = PlateManager.get().getPlate(getContainer(), plateId); + if (plate != null) + { + templateName = plate.getName(); + } + } + + Plate template; + PlateLayoutHandler handler; + + if (templateName != null) + { + if (plateId == null) + throw new NotFoundException("plateId is required when templateName is specified."); + template = PlateService.get().getPlate(getContainer(), plateId); + if (template == null) + throw new NotFoundException("Plate referenced by plateId does not exist."); + handler = PlateManager.get().getPlateLayoutHandler(template.getAssayType()); + if (handler == null) + throw new ValidationException("Plate template type '" + template.getAssayType() + "' does not exist."); + } + else + { + String assayTypeName = form.getAssayType(); + String templateTypeName = form.getTemplateType(); + int rowCount = form.getRowCount(); + int colCount = form.getColCount(); + + handler = PlateManager.get().getPlateLayoutHandler(assayTypeName); + if (handler == null) + throw new ValidationException("Plate template type '" + assayTypeName + "' does not exist."); + PlateType plateType = PlateService.get().getPlateType(rowCount, colCount); + if (plateType == null) + throw new ValidationException("The plate type (" + rowCount + " x " + colCount + ") does not exist."); + template = handler.createPlate(templateTypeName, getContainer(), plateType); + } + + // Build groups list + List groups = template.getWellGroups(); + List> groupList = new ArrayList<>(); + for (int i = 0; i < groups.size(); i++) + { + WellGroup group = groups.get(i); + List> positions = new ArrayList<>(); + for (Position position : group.getPositions()) + { + Map pos = new HashMap<>(); + pos.put("row", position.getRow()); + pos.put("col", position.getColumn()); + positions.add(pos); + } + Map groupProps = new HashMap<>(); + for (String propName : group.getPropertyNames()) + { + Object propValue = group.getProperty(propName); + groupProps.put(propName, (propValue == null || propValue == JSONObject.NULL) ? null : propValue.toString()); + } + + int wellGroupId = copyTemplate || group.getRowId() == null ? -1 * (i + 1) : group.getRowId(); + Map g = new HashMap<>(); + g.put("rowId", wellGroupId); + g.put("type", group.getType().name()); + g.put("name", group.getName()); + g.put("positions", positions); + g.put("properties", groupProps); + g.put("allowNewGroups", handler.canCreateNewGroups(group.getType())); + groupList.add(g); + } + + Map templateProperties = new HashMap<>(); + for (String propName : template.getPropertyNames()) + templateProperties.put(propName, template.getProperty(propName) == null ? null : template.getProperty(propName).toString()); + + // Build type list + List typeList = new ArrayList<>(); + for (WellGroup.Type type : handler.getWellGroupTypes()) + typeList.add(type.name()); + + // Build canCreateGroupsByType + Map canCreateGroupsByType = new LinkedHashMap<>(); + for (WellGroup.Type type : handler.getWellGroupTypes()) + canCreateGroupsByType.put(type.name(), handler.canCreateNewGroups(type)); + + // Build typesToDefaultGroups + Map> typesToDefaultGroups = handler.getDefaultGroupsForTypes(); + + // Existing template names in container + List existingTemplateNames = new ArrayList<>(); + for (Plate p : PlateService.get().getPlates(getContainer())) + existingTemplateNames.add(p.getName()); + + long responseRowId = copyTemplate || template.getRowId() == null ? -1 : template.getRowId(); + String defaultPlateName; + if (templateName != null) + { + defaultPlateName = copyTemplate ? getUniqueName(getContainer(), templateName) : templateName; + } + else + { + defaultPlateName = ""; + } + + Map result = new HashMap<>(); + result.put("rowId", responseRowId); + result.put("name", template.getName()); + result.put("type", template.getAssayType()); + result.put("rows", template.getRows()); + result.put("cols", template.getColumns()); + result.put("groupTypes", typeList); + result.put("canCreateGroupsByType", canCreateGroupsByType); + result.put("groups", groupList); + result.put("plateProperties", templateProperties); + result.put("typesToDefaultGroups", typesToDefaultGroups); + result.put("showWarningPanel", handler.showEditorWarningPanel()); + result.put("existingTemplateNames", existingTemplateNames); + result.put("copyMode", copyTemplate); + result.put("defaultPlateName", defaultPlateName); + + return success(result); + } + } + + @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class}) + public static class DesignerAction extends SimpleViewAction + { + @Override + public ModelAndView getView(DesignerForm form, BindException errors) + { + return ModuleHtmlView.get( + ModuleLoader.getInstance().getModule("assay"), + ModuleHtmlView.getGeneratedViewPath("plateTemplateDesigner") + ); + } + + @Override + public void addNavTrail(NavTree root) + { + setHelpTopic("editPlateTemplate"); + root.addChild("Plate Editor"); + } + } + + /** Delete soon! */ + @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class}) + public class DesignerGwtAction extends SimpleViewAction { @Override public ModelAndView getView(DesignerForm form, BindException errors) @@ -262,7 +593,7 @@ else if (form.getPlateId() != null) public void addNavTrail(NavTree root) { setHelpTopic("editPlateTemplate"); - root.addChild("Plate Editor"); + root.addChild("Plate Editor (GWT)"); } } @@ -295,7 +626,7 @@ public static class CopyTemplateBean private HtmlString _treeHtml; private Plate _plate; private String _selectedDestination; - private List _destinationTemplates; + private List _destinationTemplates; public CopyTemplateBean(final Container container, final User user, final Integer plateId, final String selectedDestination) { @@ -577,6 +908,13 @@ public static class CreatePlateForm implements ApiJsonForm private boolean _template; private Long _templateId; + // Template designer fields (groups path) + private Long _rowId; + private int _rows; + private int _cols; + private List _groups; // non-null activates the template-upsert path + private final Map _plateProperties = new HashMap<>(); + public String getDescription() { return _description; @@ -622,6 +960,31 @@ public Long getTemplateId() return _templateId; } + public Long getRowId() + { + return _rowId; + } + + public int getRows() + { + return _rows; + } + + public int getCols() + { + return _cols; + } + + public List getGroups() + { + return _groups; + } + + public Map getPlateProperties() + { + return _plateProperties; + } + @Override public void bindJson(JSONObject json) { @@ -649,6 +1012,33 @@ public void bindJson(JSONObject json) if (json.has("templateId")) _templateId = json.getLong("templateId"); + // Template designer fields + if (json.has("rowId")) + _rowId = json.getLong("rowId"); + // "type" is how the React designer sends assayType + if (json.has("type") && !json.has("assayType")) + _assayType = json.getString("type"); + if (json.has("rows")) + _rows = json.getInt("rows"); + if (json.has("cols")) + _cols = json.getInt("cols"); + if (json.has("plateProperties")) + { + JSONObject props = json.getJSONObject("plateProperties"); + for (String key : props.keySet()) + { + Object val = props.get(key); + _plateProperties.put(key, val == JSONObject.NULL ? null : val); + } + } + if (json.has("groups")) + { + _groups = new ArrayList<>(); + JSONArray arr = json.getJSONArray("groups"); + for (int i = 0; i < arr.length(); i++) + _groups.add(SubmittedGroup.from(arr.getJSONObject(i))); + } + if (json.has("data")) { _data = new ArrayList<>(); @@ -670,6 +1060,7 @@ public void bindJson(JSONObject json) @Marshal(Marshaller.JSONObject) @RequiresAnyOf({InsertPermission.class, DesignAssayPermission.class}) + @JsonInputLimit(10 * 1024 * 1024) public static class CreatePlateAction extends MutatingApiAction { private PlateType _plateType; @@ -679,6 +1070,8 @@ public void validateForm(CreatePlateForm form, Errors errors) { if (form.getPlateType() == null) errors.reject(ERROR_REQUIRED, "Plate \"plateType\" is required."); + if (form.getGroups() != null) + errors.reject(ERROR_REQUIRED, "Group values are not supported."); _plateType = PlateManager.get().getPlateType(form.getPlateType()); if (_plateType == null) @@ -714,7 +1107,7 @@ public Object execute(CreatePlateForm form, BindException errors) throws Excepti PlateImpl newPlate = new PlateImpl(getContainer(), form.getName(), form.getBarcode(), form.getAssayType(), _plateType); if (form.getData() == null && form.getTemplateId() != null && TsvPlateLayoutHandler.TYPE.equalsIgnoreCase(newPlate.getAssayType())) { - newPlate = (PlateImpl) PlateManager.get().copyPlate( + newPlate = PlateManager.get().copyPlate( getContainer(), getUser(), form.getTemplateId(), @@ -735,7 +1128,7 @@ public Object execute(CreatePlateForm form, BindException errors) throws Excepti if (form.isTemplate() && data == null) data = PlateManager.get().prepareEmptyPlateTemplateData(getContainer(), _plateType); - newPlate = (PlateImpl) PlateManager.get().createAndSavePlate(getContainer(), getUser(), newPlate, form.getPlateSetId(), data); + newPlate = PlateManager.get().createAndSavePlate(getContainer(), getUser(), newPlate, form.getPlateSetId(), data); } return success(newPlate); diff --git a/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java b/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java index b4d7635f972..1dca54939e2 100644 --- a/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java +++ b/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java @@ -238,7 +238,7 @@ public Map apply(Map row) }); } - private List getPlatesForPlateSet( + private List getPlatesForPlateSet( Container container, User user, Long plateSetId, @@ -270,7 +270,7 @@ public DataIteratorBuilder parsePlateData( ) throws ExperimentException { // get the ordered list of plates for the plate set - List plates = getPlatesForPlateSet(container, user, plateSetId, protocol); + List plates = getPlatesForPlateSet(container, user, plateSetId, protocol); if (plates.isEmpty()) throw new ExperimentException("No plates were found for the plate set (" + plateSetId + ")."); PlateSet plateSet = plates.get(0).getPlateSet(); @@ -297,7 +297,7 @@ private List> _parsePlateData( AssayProvider provider, ExpProtocol protocol, PlateSet plateSet, - List plates, + List plates, FileLike dataFile, DataLoaderSettings settings ) throws ExperimentException @@ -356,7 +356,7 @@ public DataIteratorBuilder mergeReRunData( ) throws ExperimentException { Long plateSetId = getPlateSetId(context, provider, protocol); - List plates = getPlatesForPlateSet(container, user, plateSetId, protocol); + List plates = getPlatesForPlateSet(container, user, plateSetId, protocol); if (plates.isEmpty()) throw new ExperimentException("No plates were found for the plate set (" + plateSetId + ")."); @@ -540,7 +540,7 @@ private boolean isGridFormat(List> data) private List> parsePlateRows( AssayProvider provider, ExpProtocol protocol, - List plates, + List plates, List> data ) throws ExperimentException { @@ -604,7 +604,7 @@ private List> parsePlateRows( } // Resolves a pre-calculated "plateIdField" to a plate rowId and furnishes new "data" rows with the plate rowId. - private List> resolvePlateIdentifier(List plates, List> data, String plateIdField) + private List> resolvePlateIdentifier(List plates, List> data, String plateIdField) { var newData = new ArrayList>(); var plateIdentifiers = new HashMap(); @@ -664,7 +664,7 @@ public PlateGridInfo(PlateUtils.GridInfo info, PlateSet plateSet, Set me // locate the plate in the plate set this grid is associated with plus an optional // measure name - List plates = PlateManager.get().getPlatesForPlateSet(plateSet); + List plates = PlateManager.get().getPlatesForPlateSet(plateSet); List annotations = getAnnotations(); // if the plate set only has one plate, then treat a single annotation as the measure @@ -694,7 +694,7 @@ public PlateGridInfo(PlateUtils.GridInfo info, PlateSet plateSet, Set me } } - private @NotNull Plate getPlateForId(String annotation, List platesetPlates) throws ExperimentException + private @NotNull Plate getPlateForId(String annotation, List platesetPlates) throws ExperimentException { Plate plate = platesetPlates.stream().filter(p -> p.isIdentifierMatch(annotation)).findFirst().orElse(null); if (plate == null) @@ -734,7 +734,7 @@ private List> parsePlateGrids( AssayProvider provider, ExpProtocol protocol, PlateSet plateSet, - List plates, + List plates, FileLike dataFile ) throws ExperimentException { @@ -1754,7 +1754,7 @@ public void testGridAnnotations() throws Exception ); PlateSet plateSet = PlateManager.get().createPlateSet(container, user, new PlateSetImpl(), plates, null, null); - List plateSetPlates = PlateManager.get().getPlatesForPlateSet(plateSet); + List plateSetPlates = PlateManager.get().getPlatesForPlateSet(plateSet); assertEquals("Expected two plates to be created.", 2, plateSetPlates.size()); Plate plate = plateSetPlates.get(0); diff --git a/assay/src/org/labkey/assay/plate/PlateCache.java b/assay/src/org/labkey/assay/plate/PlateCache.java index 9827c7cfb5c..828a9674ccf 100644 --- a/assay/src/org/labkey/assay/plate/PlateCache.java +++ b/assay/src/org/labkey/assay/plate/PlateCache.java @@ -32,15 +32,15 @@ public class PlateCache { private static final PlateLoader _loader = new PlateLoader(); - private static final Cache PLATE_CACHE = CacheManager.getBlockingStringKeyCache(CacheManager.UNLIMITED, CacheManager.DAY, "Plate Cache", _loader); + private static final Cache PLATE_CACHE = CacheManager.getBlockingStringKeyCache(CacheManager.UNLIMITED, CacheManager.DAY, "Plate Cache", _loader); private static final Logger LOG = LogManager.getLogger(PlateCache.class); - private static class PlateLoader implements CacheLoader + private static class PlateLoader implements CacheLoader { private final Map> _containerPlateMap = new HashMap<>(); // internal collection to help un-cache all plates for a container @Override - public Plate load(@NotNull String key, @Nullable Object argument) + public PlateImpl load(@NotNull String key, @Nullable Object argument) { // parse the cache key PlateCacheKey cacheKey = new PlateCacheKey(key); @@ -55,7 +55,7 @@ public Plate load(@NotNull String key, @Nullable Object argument) { PlateBean bean = plates.get(0); - Plate plate = PlateManager.get().populatePlate(bean); + PlateImpl plate = PlateManager.get().populatePlate(bean); LOG.debug(String.format("Caching plate \"%s\" for folder %s", plate.getName(), cacheKey._container.getPath())); // add all cache keys for this plate @@ -65,7 +65,7 @@ public Plate load(@NotNull String key, @Nullable Object argument) return null; } - private void addCacheKeys(PlateCacheKey cacheKey, Plate plate) + private void addCacheKeys(PlateCacheKey cacheKey, PlateImpl plate) { if (plate != null) { @@ -84,14 +84,14 @@ private void addCacheKeys(PlateCacheKey cacheKey, Plate plate) if (cacheKey._type != PlateCacheKey.Type.plateId) PLATE_CACHE.put(PlateCacheKey.getCacheKey(plate.getContainer(), plate.getPlateId()), plate); - _containerPlateMap.computeIfAbsent(cacheKey._container, k -> new HashSet<>()).add(plate.getRowId()); + _containerPlateMap.computeIfAbsent(cacheKey._container, _ -> new HashSet<>()).add(plate.getRowId()); } } } - public static @Nullable Plate getPlate(Container c, long rowId) + public static @Nullable PlateImpl getPlate(Container c, long rowId) { - Plate plate = PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, rowId)); + PlateImpl plate = PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, rowId)); // We allow plates to be mutated, return a copy of the cached object which still references the // original wells and well groups return plate != null ? plate.copy() : null; @@ -150,23 +150,23 @@ private void addCacheKeys(PlateCacheKey cacheKey, Plate plate) ).getArrayList(Long.class); } - private static @NotNull List getPlates(Container c, @Nullable SimpleFilter filter) + private static @NotNull List getPlates(Container c, @Nullable SimpleFilter filter) { List ids = getPlateIDs(c, filter); return ids.stream().map(id -> PLATE_CACHE.get(PlateCacheKey.getCacheKey(c, id))).toList(); } - public static @NotNull List getPlates(Container c) + public static @NotNull List getPlates(Container c) { return getPlates(c, null); } - public static @NotNull List getPlatesForPlateSet(Container c, Long plateSetRowId) + public static @NotNull List getPlatesForPlateSet(Container c, Long plateSetRowId) { return getPlates(c, new SimpleFilter(FieldKey.fromParts(PlateTable.Column.PlateSet.name()), plateSetRowId)); } - public static @NotNull List getPlateTemplates(Container c) + public static @NotNull List getPlateTemplates(Container c) { return getPlates(c, new SimpleFilter(FieldKey.fromParts(PlateTable.Column.Template.name()), true)); } diff --git a/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java b/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java index 9efbde2e7a1..af614c9465f 100644 --- a/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java +++ b/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java @@ -198,7 +198,7 @@ public long saveChanges(GWTPlate gwtPlate, boolean replaceIfExisting) throws Exc // first, mark well groups not submitted for saving as deleted Set groups = gwtPlate.getGroups(); - List existingWellGroups = plate.getWellGroups(); + List existingWellGroups = plate.getWellGroups(); for (WellGroup existingWellGroup : existingWellGroups) { if (groups.stream().noneMatch(g-> g.getRowId() == existingWellGroup.getRowId())) @@ -246,7 +246,7 @@ public long saveChanges(GWTPlate gwtPlate, boolean replaceIfExisting) throws Exc } } - private WellGroupImpl findExistingWellGroup(List wellGroups, int rowId) + private WellGroupImpl findExistingWellGroup(List wellGroups, int rowId) { for (WellGroup wellGroup : wellGroups) { diff --git a/assay/src/org/labkey/assay/plate/PlateImpl.java b/assay/src/org/labkey/assay/plate/PlateImpl.java index 5a255cf82ca..0cfbca7fb86 100644 --- a/assay/src/org/labkey/assay/plate/PlateImpl.java +++ b/assay/src/org/labkey/assay/plate/PlateImpl.java @@ -237,13 +237,16 @@ public WellGroup addWellGroup(WellGroupImpl group) } @JsonIgnore - protected WellGroupImpl storeWellGroup(WellGroupImpl group) + public WellGroupImpl storeWellGroup(WellGroupImpl group) { group.setPlate(this); if (_groups == null) _groups = new HashMap<>(); Map groupsByType = _groups.computeIfAbsent(group.getType(), k -> new LinkedHashMap<>()); + // If this group has a rowId, remove any stale entry keyed under the old name (rename case). + if (group.getRowId() != null) + groupsByType.values().removeIf(existing -> group.getRowId().equals(existing.getRowId())); groupsByType.put(group.getName(), group); if (!wellGroupsInOrder(groupsByType)) { @@ -281,14 +284,14 @@ private boolean wellGroupsInOrder(Map groups) @JsonIgnore @Override - public @NotNull List getWellGroups(Position position) + public @NotNull List getWellGroups(Position position) { - List wellGroups = getWellGroups(); + List wellGroups = getWellGroups(); if (wellGroups.isEmpty()) return Collections.emptyList(); - List groups = new ArrayList<>(); - for (WellGroup group : wellGroups) + List groups = new ArrayList<>(); + for (WellGroupImpl group : wellGroups) { if (group.contains(position)) groups.add(group); @@ -299,12 +302,12 @@ private boolean wellGroupsInOrder(Map groups) @JsonIgnore @Override - public @NotNull List getWellGroups() + public @NotNull List getWellGroups() { if (_groups == null) return Collections.emptyList(); - List allGroups = new ArrayList<>(); + List allGroups = new ArrayList<>(); for (Map groups : _groups.values()) allGroups.addAll(groups.values()); diff --git a/assay/src/org/labkey/assay/plate/PlateManager.java b/assay/src/org/labkey/assay/plate/PlateManager.java index 2512cdb4ea9..72138aeca1b 100644 --- a/assay/src/org/labkey/assay/plate/PlateManager.java +++ b/assay/src/org/labkey/assay/plate/PlateManager.java @@ -300,15 +300,15 @@ public List getWellGroupTypes() } @Override - public @NotNull Plate createPlate(Container container, String assayType, @NotNull PlateType plateType) + public @NotNull PlateImpl createPlate(Container container, String assayType, @NotNull PlateType plateType) { return new PlateImpl(container, null, null, assayType, plateType); } - public @NotNull Plate createAndSavePlate( + public @NotNull PlateImpl createAndSavePlate( @NotNull Container container, @NotNull User user, - @NotNull Plate plate, + @NotNull PlateImpl plate, @Nullable Long plateSetId, @Nullable List> data ) throws Exception @@ -316,10 +316,10 @@ public List getWellGroupTypes() return createAndSavePlate(container, user, plate, plateSetId, data, false); } - private @NotNull Plate createAndSavePlate( + private @NotNull PlateImpl createAndSavePlate( @NotNull Container container, @NotNull User user, - @NotNull Plate plate, + @NotNull PlateImpl plate, @Nullable Long plateSetId, @Nullable List> data, boolean skipAudit @@ -346,7 +346,7 @@ public List getWellGroupTypes() throw new ValidationException(String.format("Failed to create plate. Plate set \"%s\" is not a template plate set.", plateSet.getName())); if (!plate.isTemplate() && plateSet.isTemplate()) throw new ValidationException(String.format("Failed to create plate. Plate set \"%s\" is a template plate set.", plateSet.getName())); - ((PlateImpl) plate).setPlateSet(plateSet); + plate.setPlateSet(plateSet); } // Intentionally passing skipAudit=true, and not the passed in value for skipAudit, @@ -479,7 +479,7 @@ public Position createPosition(Container container, int row, int column) List plates = new TableSelector(AssayDbSchema.getInstance().getTableInfoPlate(), filter, null).getArrayList(PlateBean.class); // this should be 1 or 0, but don't blow up if there are more than one if (!plates.isEmpty()) - return populatePlate(plates.get(0)); + return populatePlate(plates.getFirst()); return null; } @@ -512,7 +512,7 @@ public List getMetadataColumns(@NotNull PlateSet plateSet, Container c } @NotNull - public List getPlateTemplates(Container container) + public List getPlateTemplates(Container container) { return PlateCache.getPlateTemplates(container); } @@ -557,7 +557,7 @@ public int getRunCountUsingPlate(@NotNull Container c, @NotNull User user, @NotN * @return A map of plate rowId to total number of runs across all plate-based assay runs in the * container/user scope for the specified plates. */ - public Map getPlateRunCounts(@NotNull Container c, @NotNull User user, @NotNull Collection plates) + public Map getPlateRunCounts(@NotNull Container c, @NotNull User user, @NotNull Collection plates) { if (plates.isEmpty()) return emptyMap(); @@ -742,7 +742,7 @@ private int getRunCountUsingPlateInResults(@NotNull Container c, @NotNull User u } @Override - public @Nullable Plate getPlate(Container container, long rowId) + public @Nullable PlateImpl getPlate(Container container, long rowId) { return PlateCache.getPlate(container, rowId); } @@ -786,10 +786,10 @@ private int getRunCountUsingPlateInResults(@NotNull Container c, @NotNull User u Plate plate = null; if (plateIdentifier != null) { - List plates = getPlatesForPlateSet(plateSet); - List matchingPlates = plates.stream().filter(p -> p.isIdentifierMatch(plateIdentifier.toString())).toList(); + List plates = getPlatesForPlateSet(plateSet); + List matchingPlates = plates.stream().filter(p -> p.isIdentifierMatch(plateIdentifier.toString())).toList(); if (matchingPlates.size() == 1) - plate = matchingPlates.get(0); + plate = matchingPlates.getFirst(); else if (matchingPlates.isEmpty()) throw new IllegalArgumentException("The plate identifier \"" + plateIdentifier + "\" does not match any plate in the plate set \"" + plateSet.getName() + "\"."); else @@ -820,7 +820,7 @@ else if (matchingPlates.isEmpty()) throw new IllegalStateException("More than one " + tableInfo.getName() + " found that matches the filter."); if (containers.size() == 1) - return ContainerManager.getForId(containers.get(0)); + return ContainerManager.getForId(containers.getFirst()); return null; } @@ -952,7 +952,7 @@ public boolean isDuplicatePlateTemplateName(Container container, String name) } @Override - public @NotNull List getPlates(Container c) + public @NotNull List getPlates(Container c) { return PlateCache.getPlates(c); } @@ -962,7 +962,7 @@ public boolean isDuplicatePlateTemplateName(Container container, String name) return PlateSetCache.getPlateSets(c); } - public List getPlatesForPlateSet(PlateSet plateSet) + public List getPlatesForPlateSet(PlateSet plateSet) { return PlateCache.getPlatesForPlateSet(plateSet.getContainer(), plateSet.getRowId()); } @@ -1028,7 +1028,7 @@ private long save(Container container, User user, Plate plate, @Nullable List wellGroupIds = wellToWellGroups.computeIfAbsent(wellId, k -> new HashSet<>()); + Set wellGroupIds = wellToWellGroups.computeIfAbsent(wellId, _ -> new HashSet<>()); wellGroupIds.add(wellGroupId); } @@ -1070,7 +1070,7 @@ protected Plate populatePlate(PlateBean bean) { for (Integer wellGroupId : wellGroupIds) { - List groupPositions = groupIdToPositions.computeIfAbsent(wellGroupId, k -> new ArrayList<>()); + List groupPositions = groupIdToPositions.computeIfAbsent(wellGroupId, _ -> new ArrayList<>()); groupPositions.add(well); } } @@ -1213,9 +1213,9 @@ private long savePlateImpl( // create/update well groups QueryUpdateService wellGroupQus = getWellGroupUpdateService(container, user); - for (WellGroup group : plate.getWellGroups()) + for (WellGroupImpl wellgroup : plate.getWellGroups()) { - WellGroupImpl wellgroup = (WellGroupImpl) group; + assert !wellgroup._deleted; String wellGroupInstanceLsid = wellgroup.getLSID(); Map wellGroupRow; @@ -1239,8 +1239,8 @@ private long savePlateImpl( if (wellGroupErrors.hasErrors()) throw wellGroupErrors; - wellGroupInstanceLsid = (String) insertedRows.get(0).get(WellTable.Column.Lsid.name()); - wellgroup = ObjectFactory.Registry.getFactory(WellGroupImpl.class).fromMap(wellgroup, insertedRows.get(0)); + wellGroupInstanceLsid = (String) insertedRows.getFirst().get(WellTable.Column.Lsid.name()); + wellgroup = ObjectFactory.Registry.getFactory(WellGroupImpl.class).fromMap(wellgroup, insertedRows.getFirst()); savePropertyBag(container, user, wellGroupInstanceLsid, wellgroup.getProperties(), false); } } @@ -1274,7 +1274,7 @@ private long savePlateImpl( if (wellDataMap.containsKey(position.getDescription())) { wellDataMap.get(position.getDescription()).forEach( - (key, value) -> wellRow.merge(key, value, (v1, v2) -> v1) + (key, value) -> wellRow.merge(key, value, (v1, _) -> v1) ); } @@ -1398,7 +1398,7 @@ private long savePlateImpl( // return a list of wellId and wellGroupId pairs private List> getWellGroupPositions(Plate plate, Position position) { - List groups = plate.getWellGroups(position); + List groups = plate.getWellGroups(position); List> wellGroupPositions = new ArrayList<>(groups.size()); for (WellGroup group : groups) @@ -1583,7 +1583,7 @@ public void beforeDeleteWellGroup(Container container, Integer wellGroupId) DbScope scope = schema.getSchema().getScope(); assert scope.isTransactionActive(); - new SqlExecutor(scope).execute("" + + new SqlExecutor(scope).execute( "DELETE FROM " + schema.getTableInfoWellGroupPositions() + " WHERE wellGroupId = ?", wellGroupId); } @@ -1594,7 +1594,7 @@ private void deleteWellGroupPositions(Plate plate) DbScope scope = schema.getSchema().getScope(); assert scope.isTransactionActive(); - new SqlExecutor(scope).execute("" + + new SqlExecutor(scope).execute( "DELETE FROM " + schema.getTableInfoWellGroupPositions() + " WHERE wellId IN (SELECT rowId FROM " + schema.getTableInfoWell() + " WHERE plateId=?)", plate.getRowId()); } @@ -1956,7 +1956,7 @@ private void copyWellGroups(@NotNull Plate source, @NotNull Plate copy) } } - public Plate copyPlate( + public PlateImpl copyPlate( Container container, User user, Long sourcePlateRowId, @@ -2025,7 +2025,7 @@ else if (isDuplicatePlateName(container, user, name, destinationPlateSet)) // Save the plate long plateId = savePlateImpl(container, user, newPlate, true, null, true); - newPlate = (PlateImpl) getPlate(container, plateId); + newPlate = getPlate(container, plateId); if (newPlate == null) throw new IllegalStateException("Unexpected failure. Failed to retrieve plate after save (pre-commit)."); @@ -4541,7 +4541,7 @@ public record ReformatResult( Long plateSetRowId; String plateSetName; - List newPlates; + List newPlates; if (targetPlateSet.isNew()) { @@ -4846,7 +4846,7 @@ else if (!Objects.equals(sourcePlateSet.getRowId(), plateSet.getRowId())) return Pair.of(sourcePlateSet, sourcePlates); } - private @NotNull List getReformatTargetPlates(@NotNull PlateSetImpl targetPlateSet) + private @NotNull List getReformatTargetPlates(@NotNull PlateSetImpl targetPlateSet) { if (targetPlateSet.isNew()) return emptyList(); @@ -5079,7 +5079,7 @@ private record HydratedResult(List plateData, @Nullable Integer plate List sourcedWells = Arrays.stream(wellLayout.getWells()).filter(well -> well != null && well.sourcePlateId() > 0).toList(); if (!sourcedWells.isEmpty()) { - Long sourcePlateId = sourcedWells.get(0).sourcePlateId(); + Long sourcePlateId = sourcedWells.getFirst().sourcePlateId(); if (sourcedWells.stream().allMatch(w -> sourcePlateId.equals(w.sourcePlateId()))) templateId = sourcePlateId; } diff --git a/assay/src/org/labkey/assay/plate/PlateManagerTest.java b/assay/src/org/labkey/assay/plate/PlateManagerTest.java index b0df652dbb9..77efd75ea70 100644 --- a/assay/src/org/labkey/assay/plate/PlateManagerTest.java +++ b/assay/src/org/labkey/assay/plate/PlateManagerTest.java @@ -230,16 +230,16 @@ public void testCreatePlateTemplate() throws Exception assertNotNull(savedTemplate.getLSID()); assertEquals(plateType.getRowId(), savedTemplate.getPlateType().getRowId()); - List wellGroups = savedTemplate.getWellGroups(); + List wellGroups = savedTemplate.getWellGroups(); assertEquals(3, wellGroups.size()); // TsvPlateTypeHandler creates two CONTROL well groups "Positive" and "Negative" - List controlWellGroups = savedTemplate.getWellGroups(WellGroup.Type.CONTROL); + List controlWellGroups = savedTemplate.getWellGroups(WellGroup.Type.CONTROL); assertEquals(2, controlWellGroups.size()); - List sampleWellGroups = savedTemplate.getWellGroups(WellGroup.Type.SAMPLE); + List sampleWellGroups = savedTemplate.getWellGroups(WellGroup.Type.SAMPLE); assertEquals(1, sampleWellGroups.size()); - WellGroup savedWg1 = sampleWellGroups.get(0); + WellGroup savedWg1 = sampleWellGroups.getFirst(); assertEquals("wg1", savedWg1.getName()); assertEquals("100", savedWg1.getProperty("score")); @@ -292,11 +292,11 @@ public void testCreatePlateTemplate() throws Exception assertNotNull(updatedWg2); // verify deleted well group - List updatedControlWellGroups = updatedTemplate.getWellGroups(WellGroup.Type.CONTROL); + List updatedControlWellGroups = updatedTemplate.getWellGroups(WellGroup.Type.CONTROL); assertEquals(1, updatedControlWellGroups.size()); // verify added positions - assertEquals(2, updatedControlWellGroups.get(0).getPositions().size()); + assertEquals(2, updatedControlWellGroups.getFirst().getPositions().size()); // verify plate type information assertEquals(plateType.getRows().intValue(), updatedTemplate.getRows()); @@ -353,7 +353,7 @@ public void testAccessPlateByIdentifiers() throws Exception // Assert assertTrue("Expected plateSet to have been persisted and provided with a rowId", plateSet.getRowId() > 0); - List plates = plateSet.getPlates(); + List plates = plateSet.getPlates(); assertEquals("Expected plateSet to have 3 plates", 3, plates.size()); // verify access via plate rowId @@ -394,7 +394,7 @@ public void testCreatePlateTemplates() throws Exception createPlate(PLATE_TYPE_96_WELLS); // Verify only plate templates are returned - List templates = PlateManager.get().getPlateTemplates(container); + List templates = PlateManager.get().getPlateTemplates(container); assertFalse("Expected there to be a plate template", templates.isEmpty()); for (Plate t : templates) assertTrue("Expected saved plate to have the template field set to true", t.isTemplate()); @@ -704,7 +704,7 @@ public void testGetWorklistSingleSampleManyToMany() throws Exception { // Arrange ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(container, user); - ExpMaterial sample = createSamples(1).get(0); + ExpMaterial sample = createSamples(1).getFirst(); List> rows1 = List.of( wellWithMetdata(createWellRow("A1", "SAMPLE", sample.getRowId()), 2.25, "B1234"), @@ -732,7 +732,7 @@ public void testGetWorklistSingleSampleOneToOne() throws Exception { // Arrange ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(container, user); - ExpMaterial sample = createSamples(3).get(0); + ExpMaterial sample = createSamples(3).getFirst(); List> rows1 = List.of( wellWithMetdata(createWellRow("A1", "SAMPLE", sample.getRowId()), 2.25, "B1234"), @@ -769,7 +769,7 @@ public void testGetWorklistSingleSampleOneToMany() throws Exception { // Arrange ContainerFilter cf = ContainerFilter.Type.CurrentAndSubfolders.create(container, user); - ExpMaterial sample = createSamples(3).get(0); + ExpMaterial sample = createSamples(3).getFirst(); List> rows1 = List.of( wellWithMetdata(createWellRow("A1", "SAMPLE", sample.getRowId()), 2.25, "B1234") @@ -927,7 +927,7 @@ public void testReformatQuadrant() throws Exception assertNotNull(result.previewData()); assertEquals("Expected quadrant operation on 3 plates to generate 1 plate.", 1, result.previewData().size()); - var previewPlate = result.previewData().get(0); + var previewPlate = result.previewData().getFirst(); var wellData = previewPlate.data(); assertEquals("Expected 12 wells to have data", 12, wellData.size()); @@ -961,7 +961,7 @@ public void testReformatQuadrant() throws Exception assertTrue("Expected a new plate set to be created", result.plateSetRowId() > 0); assertEquals(1, result.plateRowIds().size()); - var newPlate = PlateManager.get().getPlate(container, result.plateRowIds().get(0)); + var newPlate = PlateManager.get().getPlate(container, result.plateRowIds().getFirst()); assertNotNull(newPlate); assertEquals(PLATE_TYPE_384_WELLS, newPlate.getPlateType()); @@ -1087,7 +1087,7 @@ public void testReformatCompressByColumn() throws Exception assertNotNull(result.previewData()); assertEquals("Expected column compress operation on a 384-well plate to generate 1 12-well plates.", 1, result.previewData().size()); - List> plateData = result.previewData().get(0).data(); + List> plateData = result.previewData().getFirst().data(); assertEquals("Expected well P12 to be dropped as it does not include a sample.", sourcePlateData.size() - 1, plateData.size()); assertEquals(sampleRowIds.get(0), plateData.get(0).get("sampleId")); @@ -1111,7 +1111,7 @@ public void testReformatCompressByColumn() throws Exception assertEquals("Expected target plate set to be used", targetPlateSetId, result.plateSetRowId()); assertEquals(1, result.plateRowIds().size()); - Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().get(0)); + Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().getFirst()); assertNotNull(newPlate); assertEquals(PLATE_TYPE_12_WELLS, newPlate.getPlateType()); @@ -1168,7 +1168,7 @@ public void testReformatCompressByRow() throws Exception assertNotNull(result.previewData()); assertEquals("Expected row compress operation on a 384-well plate to generate 1 12-well plates.", 1, result.previewData().size()); - List> plateData = result.previewData().get(0).data(); + List> plateData = result.previewData().getFirst().data(); assertEquals("Expected well P12 to be dropped as it does not include a sample.", sourcePlateData.size() - 1, plateData.size()); assertEquals(sampleRowIds.get(0), plateData.get(0).get("sampleId")); @@ -1192,7 +1192,7 @@ public void testReformatCompressByRow() throws Exception assertEquals("Expected target plate set to be used", targetPlateSetId, result.plateSetRowId()); assertEquals(1, result.plateRowIds().size()); - Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().get(0)); + Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().getFirst()); assertNotNull(newPlate); assertEquals(PLATE_TYPE_12_WELLS, newPlate.getPlateType()); @@ -1302,7 +1302,7 @@ public void testReformatArrayByColumn() throws Exception assertEquals("Expected target plate set to be used", context.targetPlateSetId, result.plateSetRowId()); assertEquals(2, result.plateRowIds().size()); - Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().get(0)); + Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().getFirst()); assertNotNull(newPlate); assertEquals(PLATE_TYPE_12_WELLS, newPlate.getPlateType()); List sampleRowIds = context.sampleRowIds; @@ -1368,7 +1368,7 @@ public void testReformatArrayByRow() throws Exception assertEquals("Expected target plate set to be used", context.targetPlateSetId, result.plateSetRowId()); assertEquals(2, result.plateRowIds().size()); - Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().get(0)); + Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().getFirst()); assertNotNull(newPlate); assertEquals(PLATE_TYPE_12_WELLS, newPlate.getPlateType()); List sampleRowIds = context.sampleRowIds; @@ -1454,7 +1454,7 @@ public void testReformatArrayFromTemplate() throws Exception assertEquals("Expected target plate set to be used", context.targetPlateSetId, result.plateSetRowId()); assertEquals(3, result.plateRowIds().size()); - Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().get(0)); + Plate newPlate = PlateManager.get().getPlate(container, result.plateRowIds().getFirst()); assertNotNull(newPlate); assertEquals(PLATE_TYPE_12_WELLS, newPlate.getPlateType()); List sampleRowIds = context.sampleRowIds; @@ -1505,7 +1505,7 @@ public void testReformatArrayFromTemplate() throws Exception switch (wellPosition) { - case "A1" -> assertEquals(sampleRowIds.get(0).intValue(), sampleId); // Group "S1" + case "A1" -> assertEquals(sampleRowIds.getFirst().intValue(), sampleId); // Group "S1" case "A2" -> assertEquals(sampleRowIds.get(11).intValue(), sampleId); case "A3" -> assertEquals(sampleRowIds.get(12).intValue(), sampleId); case "A4" -> assertEquals(0, sampleId); @@ -1516,7 +1516,7 @@ public void testReformatArrayFromTemplate() throws Exception case "C1" -> assertEquals(0, sampleId); // Control case "C2" -> assertEquals(0, sampleId); case "C3" -> assertEquals(0, sampleId); // Control - case "C4" -> assertEquals(sampleRowIds.get(0).intValue(), sampleId); // Group "S1" + case "C4" -> assertEquals(sampleRowIds.getFirst().intValue(), sampleId); // Group "S1" } var barcode = r.getString(FieldKey.fromParts(PlateMetadataFields.barcode.name())); @@ -1612,7 +1612,7 @@ public void testReplicateWellValidation() throws Exception assertCreatePlateThrows(expectedMessage, PLATE_TYPE_96_WELLS, plateName, null, sourcePlateData); // Fixup rows by making all rows the same and resubmit - sourcePlateData.forEach(row -> row.put("sampleId", sampleRowIds.get(0))); + sourcePlateData.forEach(row -> row.put("sampleId", sampleRowIds.getFirst())); // Act var newPlate = createPlate(PLATE_TYPE_96_WELLS, plateName, null, sourcePlateData); @@ -1668,8 +1668,8 @@ public void testReplicateCrossPlateValidation() throws Exception List sampleRowIds = createSamples(2).stream().map(ExpObject::getRowId).sorted().toList(); List> plate1Data = new ArrayList<>(); - plate1Data.add(createWellRow("A1", "SAMPLE", sampleRowIds.get(0), null, "R1")); - plate1Data.add(createWellRow("A2", "SAMPLE", sampleRowIds.get(0), null, "R1")); + plate1Data.add(createWellRow("A1", "SAMPLE", sampleRowIds.getFirst(), null, "R1")); + plate1Data.add(createWellRow("A2", "SAMPLE", sampleRowIds.getFirst(), null, "R1")); plate1Data.add(createWellRow("A3", "SAMPLE", sampleRowIds.get(0), null, "R1")); List> plate2Data = new ArrayList<>(); @@ -1679,8 +1679,8 @@ public void testReplicateCrossPlateValidation() throws Exception List> plate3Data = new ArrayList<>(); plate2Data.add(createWellRow("C1", "SAMPLE", sampleRowIds.get(0), null, "R2")); - plate2Data.add(createWellRow("C2", "SAMPLE", sampleRowIds.get(0), null, "R2")); - plate2Data.add(createWellRow("C3", "SAMPLE", sampleRowIds.get(0), null, "R2")); + plate2Data.add(createWellRow("C2", "SAMPLE", sampleRowIds.getFirst(), null, "R2")); + plate2Data.add(createWellRow("C3", "SAMPLE", sampleRowIds.getFirst(), null, "R2")); var plateData = List.of( new PlateManager.PlateData(null, plateType.getRowId(), null, null, plate1Data), @@ -1694,7 +1694,7 @@ public void testReplicateCrossPlateValidation() throws Exception assertCreatePlateSetThrows(expectedMessage, plateSetImpl, plateData, null); // Fixup rows by making all rows the same and resubmit - plate2Data.forEach(row -> row.put("sampleId", sampleRowIds.get(0))); + plate2Data.forEach(row -> row.put("sampleId", sampleRowIds.getFirst())); // Assert (expect no errors) createPlateSet(plateSetImpl, plateData, null); @@ -1721,12 +1721,12 @@ public void testControlValidation() throws Exception var plateData1 = List.of(new PlateManager.PlateData("PS1", plateType.getRowId(), null, null, PS1Data)); PlateSet plateSet1 = createPlateSet(plateSetImpl, plateData1, null); - List> dataPS2 = Arrays.asList(createWellRow("A1", "POSITIVE_CONTROL", sampleRowIds.get(0))); + List> dataPS2 = Arrays.asList(createWellRow("A1", "POSITIVE_CONTROL", sampleRowIds.getFirst())); var plateData2 = List.of(new PlateManager.PlateData("PS2", plateType.getRowId(), null, null, dataPS2)); // Act / Assert // Since the sample of index 0 is on PS1's plate, it is not a valid control for PS2's plate - String errorMsg = String.format("The sample \"%s\" is not a valid control.", sampleNames.get(0)); + String errorMsg = String.format("The sample \"%s\" is not a valid control.", sampleNames.getFirst()); assertCreatePlateSetThrows(errorMsg, plateSetImpl, plateData2, plateSet1.getRowId()); // Assert (expect no errors) @@ -1758,7 +1758,7 @@ public void testBuiltInColumns() throws Exception // Assert assertEquals(1, PPSPlateFields.size()); - assertEquals("SampleID", PPSPlateFields.get(0).getName()); + assertEquals("SampleID", PPSPlateFields.getFirst().getName()); assertEquals(4, APSPlateFields.size()); assertEquals("Type", APSPlateFields.get(0).getName()); @@ -1808,7 +1808,7 @@ public void testEnsureSampleWellTypeTriggerRespectsType() throws Exception List sampleRowIds = samples.stream().map(ExpObject::getRowId).sorted().toList(); List> data = List.of( - createWellRow("A1", "CONTROL", sampleRowIds.get(0)) + createWellRow("A1", "CONTROL", sampleRowIds.getFirst()) ); // Act @@ -1919,12 +1919,12 @@ public void testDeleteSampleWellReferencesUponSampleDelete() throws Exception var plateData = List.of(new PlateManager.PlateData(null, PLATE_TYPE_12_WELLS.getRowId(), null, null, wellData)); var PPS = createPlateSet(pps, plateData, null); - var ppsPlateRowId = PPS.getPlates().get(0).getRowId(); + var ppsPlateRowId = PPS.getPlates().getFirst().getRowId(); var aps = new PlateSetImpl(); aps.setType(PlateSetType.assay); var APS = createPlateSet(aps, plateData, PPS.getRowId()); - var apsPlateRowId = APS.getPlates().get(0).getRowId(); + var apsPlateRowId = APS.getPlates().getFirst().getRowId(); // Act // Formerly, this would result in a foreign key violation on the assay.well table diff --git a/assay/src/org/labkey/assay/plate/PlateSetImpl.java b/assay/src/org/labkey/assay/plate/PlateSetImpl.java index e17b57a09a7..7fe5db23cea 100644 --- a/assay/src/org/labkey/assay/plate/PlateSetImpl.java +++ b/assay/src/org/labkey/assay/plate/PlateSetImpl.java @@ -147,7 +147,7 @@ public boolean isStandalone() } @Override - public List getPlates() + public List getPlates() { if (isNew()) return Collections.emptyList(); diff --git a/assay/src/org/labkey/assay/plate/WellGroupImpl.java b/assay/src/org/labkey/assay/plate/WellGroupImpl.java index 857c6fb47d9..19c7e530c8b 100644 --- a/assay/src/org/labkey/assay/plate/WellGroupImpl.java +++ b/assay/src/org/labkey/assay/plate/WellGroupImpl.java @@ -209,7 +209,7 @@ public synchronized Set getOverlappingGroups() _overlappingGroups = new LinkedHashSet<>(); for (Position position : getPositions()) { - List groups = _plate.getWellGroups(position); + List groups = _plate.getWellGroups(position); for (WellGroup group : groups) { if (group != this) @@ -313,7 +313,7 @@ public Plate getPlate() { if (_plate == null && _plateId != null) { - _plate = (PlateImpl) PlateCache.getPlate(getContainer(), _plateId); + _plate = PlateCache.getPlate(getContainer(), _plateId); } return _plate; } diff --git a/assay/src/org/labkey/assay/plate/layout/LayoutEngine.java b/assay/src/org/labkey/assay/plate/layout/LayoutEngine.java index 75bced3f604..96bca37324f 100644 --- a/assay/src/org/labkey/assay/plate/layout/LayoutEngine.java +++ b/assay/src/org/labkey/assay/plate/layout/LayoutEngine.java @@ -19,7 +19,7 @@ public class LayoutEngine private final ReformatOptions _options; private Collection _sampleIds; private List _sourcePlates; - private List _targetPlates; + private List _targetPlates; private List _targetPlateData; private PlateType _targetPlateType; private Plate _targetTemplate; @@ -93,7 +93,7 @@ public void setSourcePlates(List sourcePlates) _sourcePlates = sourcePlates; } - public void setTargetPlates(List targetPlates) + public void setTargetPlates(List targetPlates) { _targetPlates = targetPlates; } diff --git a/assay/src/org/labkey/assay/plate/layout/LayoutOperation.java b/assay/src/org/labkey/assay/plate/layout/LayoutOperation.java index 2809df13514..cef436ec356 100644 --- a/assay/src/org/labkey/assay/plate/layout/LayoutOperation.java +++ b/assay/src/org/labkey/assay/plate/layout/LayoutOperation.java @@ -59,7 +59,7 @@ record ExecutionContext( PlateType targetPlateType, List sourcePlates, Plate targetTemplate, - List targetPlates, + List targetPlates, List targetPlateData, Collection sampleIds, WellData.Cache wellDataCache diff --git a/assay/src/org/labkey/assay/plate/query/PlateSetTable.java b/assay/src/org/labkey/assay/plate/query/PlateSetTable.java index dc5cd4927d7..42499ff0ab4 100644 --- a/assay/src/org/labkey/assay/plate/query/PlateSetTable.java +++ b/assay/src/org/labkey/assay/plate/query/PlateSetTable.java @@ -194,7 +194,7 @@ public DataIteratorBuilder createImportDIB(User user, Container container, DataI // generate a value for the lsid final TableInfo plateSetTable = getQueryTable(); lsidGenerator.addColumn(plateSetTable.getColumn(PlateTable.Column.Lsid.name()), - (Supplier) () -> PlateManager.get().getLsid(PlateSet.class, container)); + (Supplier) () -> PlateManager.get().getLsid(PlateSet.class, container)); SimpleTranslator nameExpressionTranslator = new SimpleTranslator(lsidGenerator, context); nameExpressionTranslator.setDebugName("nameExpressionTranslator"); @@ -252,7 +252,7 @@ protected Map deleteRow( if (plateSet == null) throw new QueryUpdateServiceException(String.format("Plate set could not be found for ID : %d", rowId)); - List plates = plateSet.getPlates(); + List plates = plateSet.getPlates(); if (!plates.isEmpty()) throw new QueryUpdateServiceException(String.format("Plate set has %d plates associated with it and cannot be deleted.", plates.size())); diff --git a/assay/test/js/fileMock.js b/assay/test/js/fileMock.js new file mode 100644 index 00000000000..f053ebf7976 --- /dev/null +++ b/assay/test/js/fileMock.js @@ -0,0 +1 @@ +module.exports = {}; diff --git a/assay/test/js/setup.ts b/assay/test/js/setup.ts new file mode 100644 index 00000000000..95ccacbca05 --- /dev/null +++ b/assay/test/js/setup.ts @@ -0,0 +1,10 @@ +import '@testing-library/jest-dom'; + +// jsdom does not implement HTMLDialogElement.showModal / .close. +// These stubs are enough for component tests to run. +HTMLDialogElement.prototype.showModal = function () { + this.setAttribute('open', ''); +}; +HTMLDialogElement.prototype.close = function () { + this.removeAttribute('open'); +};