Provisional Protein Sequences

packages/components/releaseNotes/components.md

@@ -1,6 +1,12 @@
 # @labkey/components
 Components, models, actions, and utility functions for LabKey applications and pages
 
+### version 7.??.?
+*Released*: ? March 2026
+- SchemaQuery.isEqual: add optional includeViewName argument, defaults to true
+- UnidentifiedPill: add schemaQuery prop
+- EMPTY_SEQUENCE_WARNING renamed to EMPTY_NS_SEQUENCE_WARNING
+
 ### version 7.23.1
 *Released*: 11 March 2026
 - Merge from release26.3-SNAPSHOT to develop

packages/components/src/index.ts

@@ -248,7 +248,7 @@ import {
     AssayUploadTabs,
     DataViewInfoTypes,
     EDIT_METHOD,
-    EMPTY_SEQUENCE_WARNING,
+    EMPTY_NS_SEQUENCE_WARNING,
     EXPORT_TYPES,
     GRID_CHECKBOX_OPTIONS,
     IMPORT_DATA_FORM_TYPES,
@@ -1266,7 +1266,7 @@ export {
     EditInlineField,
     EditorMode,
     EditorModel,
-    EMPTY_SEQUENCE_WARNING,
+    EMPTY_NS_SEQUENCE_WARNING,
     encodeFormDataQuote,
     encodePart,
     ensureAllFieldsInAllRows,

packages/components/src/internal/UnidentifiedPill.tsx

@@ -3,18 +3,28 @@ import { createPortal } from 'react-dom';
 import { generateId } from './util/utils';
 import { useOverlayTriggerState } from './OverlayTrigger';
 import { Popover } from './Popover';
-import { EMPTY_SEQUENCE_WARNING } from './constants';
+import { EMPTY_PS_SEQUENCE_WARNING, EMPTY_NS_SEQUENCE_WARNING } from './constants';
+import { SchemaQuery } from '../public/SchemaQuery';
+import { SCHEMAS } from './schemas';
 
-export const UnidentifiedPill: FC = () => {
+interface Props {
+    schemaQuery: SchemaQuery;
+}
+
+// TODO: take schemaQuery property and use that to determine the appropriate popover content
+export const UnidentifiedPill: FC<Props> = ({ schemaQuery }) => {
     const id = useMemo(() => generateId('unidentified-sequence-overlay-trigger'), []);
     // Note: we use useOverlayTriggerState instead of OverlayTrigger because the wrapping div from OverlayTrigger
     // causes layout problems.
     const { onMouseEnter, onMouseLeave, portalEl, show, targetRef } = useOverlayTriggerState(id, true, false);
+    const message = schemaQuery.isEqual(SCHEMAS.DATA_CLASSES.PROTEIN_SEQUENCE, false)
+        ? EMPTY_PS_SEQUENCE_WARNING
+        : EMPTY_NS_SEQUENCE_WARNING;
 
     const popover = useMemo(
         () => (
             <Popover id="unidentified-sequence-popover" placement="top" targetRef={targetRef}>
-                <div className="unidentified-sequence-popover">{EMPTY_SEQUENCE_WARNING}</div>
+                <div className="unidentified-sequence-popover">{message}</div>
             </Popover>
         ),
         [targetRef]

packages/components/src/internal/components/lineage/node/NodeDetailHeader.tsx

@@ -59,7 +59,7 @@ export const NodeDetailHeader: FC<NodeDetailHeaderProps> = memo(({ model, node,
     return (
         <DetailHeader header={header} iconSrc={node.iconProps.iconURL}>
             {/* Triple eq is important here; we only want false, not falsey values */}
-            {identified === false && <UnidentifiedPill />}
+            {identified === false && <UnidentifiedPill schemaQuery={model.schemaQuery} />}
             {displayType && <div>{displayType}</div>}
         </DetailHeader>
     );

packages/components/src/internal/constants.ts

@@ -34,8 +34,8 @@ export const MAX_EDITABLE_GRID_ROWS = MAX_SELECTION_ACTION_ROWS;
 export const LOOKUP_DEFAULT_SIZE = 25;
 
 export enum AssayUploadTabs {
-    Files = 2,
     Grid = 1,
+    Files = 2,
 }
 
 export enum EXPORT_TYPES {
@@ -61,84 +61,85 @@ export enum EDIT_METHOD {
 }
 
 export enum KEYS {
-    Backspace = 8,
-    Tab = 9,
-    Enter = 13,
-    Shift = 16,
-    Ctrl = 17,
+    A = 65,
+    Add = 107,
     Alt = 18,
-    PauseBreak = 19,
-    CapsLock = 20,
-    Escape = 27,
-    Space = 32,
-    PageUp = 33,
-    PageDown = 34,
-    End = 35,
-    Home = 36,
-
-    LeftArrow = 37,
-    UpArrow = 38,
-    RightArrow = 39,
-    DownArrow = 40,
-
-    Insert = 45,
-    Delete = 46,
-
-    Zero = 48,
-    ClosedParen = Zero,
-    One = 49,
-    ExclamationMark = One,
-    Two = 50,
-    AtSign = Two,
-    Three = 51,
-    PoundSign = Three,
-    Hash = PoundSign,
-    Four = 52,
-    DollarSign = Four,
-    Five = 53,
-    PercentSign = Five,
-    Six = 54,
-    Caret = Six,
-    Hat = Caret,
     Seven = 55,
     Ampersand = Seven,
     Eight = 56,
     Star = Eight,
     Asterik = Star,
-    Nine = 57,
-    OpenParen = Nine,
-
-    A = 65,
+    Two = 50,
+    AtSign = Two,
     B = 66,
+    Backspace = 8,
     C = 67,
+    CapsLock = 20,
+
+    Six = 54,
+    Caret = Six,
+    ClosedBracket = 221,
+    Zero = 48,
+
+    ClosedParen = Zero,
+    Comma = 188,
+
+    Ctrl = 17,
     D = 68,
+    Dash = 189,
+    DecimalPoint = 110,
+    Delete = 46,
+    Divide = 111,
+    Four = 52,
+    DollarSign = Four,
+    DownArrow = 40,
     E = 69,
+    End = 35,
+    Enter = 13,
+    Equals = 187,
+    Escape = 27,
+    One = 49,
+    ExclamationMark = One,
     F = 70,
+    F1 = 112,
+    F2 = 113,
+    F3 = 114,
+    F4 = 115,
+    F5 = 116,
+    F6 = 117,
+
+    F7 = 118,
+    F8 = 119,
+    F9 = 120,
+    F10 = 121,
+    F11 = 122,
+    F12 = 123,
+    FFLeftMetaKey = 224, // Firefox
+    Five = 53,
+    ForwardSlash = 191,
     G = 71,
+    Tilde = 192,
+    GraveAccent = Tilde,
     H = 72,
+    Three = 51,
+    PoundSign = Three,
+    Hash = PoundSign,
+    Hat = Caret,
+    Home = 36,
     I = 73,
+    Insert = 45,
     J = 74,
     K = 75,
     L = 76,
+    LeftArrow = 37,
+    LeftMetaKey = 91,
     M = 77,
-    N = 78,
-    O = 79,
-    P = 80,
-    Q = 81,
-    R = 82,
-    S = 83,
-    T = 84,
-    U = 85,
-    V = 86,
-    W = 87,
-    X = 88,
-    Y = 89,
-    Z = 90,
 
-    LeftMetaKey = 91,
-    RightMetaKey = 92,
-    SelectKey = 93,
+    Multiply = 106,
+    N = 78,
+    Nine = 57,
 
+    NumLock = 144,
     Numpad0 = 96,
     Numpad1 = 97,
     Numpad2 = 98,
@@ -148,46 +149,45 @@ export enum KEYS {
     Numpad6 = 102,
     Numpad7 = 103,
     Numpad8 = 104,
-    Numpad9 = 105,
 
-    Multiply = 106,
-    Add = 107,
-    Subtract = 109,
-    DecimalPoint = 110,
-    Divide = 111,
+    Numpad9 = 105,
+    O = 79,
+    OpenBracket = 219,
+    OpenParen = Nine,
+    P = 80,
 
-    F1 = 112,
-    F2 = 113,
-    F3 = 114,
-    F4 = 115,
-    F5 = 116,
-    F6 = 117,
-    F7 = 118,
-    F8 = 119,
-    F9 = 120,
-    F10 = 121,
-    F11 = 122,
-    F12 = 123,
+    PageDown = 34,
+    PageUp = 33,
+    PauseBreak = 19,
+    PercentSign = Five,
+    Period = 190,
+    PlusSign = Equals,
+    Q = 81,
+    Quote = 222,
+    R = 82,
+    RightArrow = 39,
+    RightMetaKey = 92,
+    S = 83,
 
-    NumLock = 144,
     ScrollLock = 145,
+    SelectKey = 93,
 
     SemiColon = 186,
-    Equals = 187,
-    Comma = 188,
-    Dash = 189,
-    Period = 190,
+    Shift = 16,
+    Space = 32,
+    Subtract = 109,
+    T = 84,
+    Tab = 9,
+    U = 85,
     UnderScore = Dash,
-    PlusSign = Equals,
-    ForwardSlash = 191,
-    Tilde = 192,
-    GraveAccent = Tilde,
+    UpArrow = 38,
+    V = 86,
 
-    OpenBracket = 219,
-    ClosedBracket = 221,
-    Quote = 222,
+    W = 87,
+    X = 88,
+    Y = 89,
 
-    FFLeftMetaKey = 224, // Firefox
+    Z = 90,
 }
 
 // This is used for filtering search results.  Since we first check for search hits containing
@@ -261,5 +261,7 @@ export const APP_FIELD_CANNOT_BE_REMOVED_MESSAGE = 'This application field canno
 
 export const CELL_SELECTION_HANDLE_CLASSNAME = 'cell-selection-handle';
 
-export const EMPTY_SEQUENCE_WARNING =
+export const EMPTY_NS_SEQUENCE_WARNING =
     'Without a sequence, Protein sequence translations cannot be done automatically, and the system cannot prevent duplicates.';
+export const EMPTY_PS_SEQUENCE_WARNING =
+    'No sequence added. The structure format and physical properties of molecules using this sequence cannot be calculated.';

packages/components/src/internal/util/utils.ts

@@ -905,9 +905,8 @@ export const isTestEnv = (): boolean => IS_NODE_TEST_ENV || IS_TEST_ENV;
 
 export function hasIdentifiedCol(schemaQuery: SchemaQuery): boolean {
     // Drop the viewName from the schemaQuery so we can properly compare
-    const sqNoView = new SchemaQuery(schemaQuery.schemaName, schemaQuery.queryName);
-    const isNucSeq = sqNoView.isEqual(SCHEMAS.DATA_CLASSES.NUC_SEQUENCE);
-    const isProtSeq = sqNoView.isEqual(SCHEMAS.DATA_CLASSES.PROTEIN_SEQUENCE);
-    const isMolecule = sqNoView.isEqual(SCHEMAS.DATA_CLASSES.MOLECULE);
+    const isNucSeq = schemaQuery.isEqual(SCHEMAS.DATA_CLASSES.NUC_SEQUENCE, false);
+    const isProtSeq = schemaQuery.isEqual(SCHEMAS.DATA_CLASSES.PROTEIN_SEQUENCE, false);
+    const isMolecule = schemaQuery.isEqual(SCHEMAS.DATA_CLASSES.MOLECULE, false);
     return isNucSeq || isProtSeq || isMolecule;
 }

packages/components/src/public/SchemaQuery.ts

@@ -84,9 +84,9 @@ export class SchemaQuery {
         this.viewName = viewName;
     }
 
-    isEqual(sq: SchemaQuery): boolean {
+    isEqual(sq: SchemaQuery, includeViewName = true): boolean {
         if (!sq) return false;
-        return this.toString().toLowerCase() === sq.toString().toLowerCase();
+        return this.toString(includeViewName).toLowerCase() === sq.toString(includeViewName).toLowerCase();
     }
 
     hasSchema(schemaName: string): boolean {