@gen-epix/ui 1.15.1 → 1.16.0

package/src/test/integration/lib/render.tsx

@@ -1,33 +0,0 @@
-import { render } from 'vitest-browser-react';
-import { CacheProvider } from '@emotion/react';
-import { QueryClientProvider } from '@tanstack/react-query';
-import type { PropsWithChildren } from 'react';
-import {
-  CssBaseline,
-  ThemeProvider,
-} from '@mui/material';
-
-import { ConfigManager } from '../../../classes/managers/ConfigManager';
-import { EmotionCacheManager } from '../../../classes/managers/EmotionCacheManager';
-import { QueryClientManager } from '../../../classes/managers/QueryClientManager';
-
-const queryQueryManager = QueryClientManager.instance;
-const emotionCacheManager = EmotionCacheManager.instance;
-
-// eslint-disable-next-line react-refresh/only-export-components
-const AllTheProviders = ({ children }: PropsWithChildren<unknown>) => {
-  return (
-    <QueryClientProvider client={queryQueryManager.queryClient}>
-      <CacheProvider value={emotionCacheManager.emotionCache}>
-        <ThemeProvider theme={ConfigManager.instance.config.theme}>
-          <CssBaseline />
-          { children }
-        </ThemeProvider>
-      </CacheProvider>
-    </QueryClientProvider>
-  );
-};
-
-export const customRender = async (...[ui, options]: Parameters<typeof render>) => {
-  return render(ui, { wrapper: AllTheProviders, ...options });
-};

package/src/test/integration/tests/integration-example/HelloWorld.test.tsx

@@ -1,14 +0,0 @@
-import {
-  expect,
-  test,
-} from 'vitest';
-import { render } from 'vitest-browser-react';
-
-import { HelloWorld } from './HelloWorld.tsx';
-
-test('renders name', async () => {
-  const { getByText } = await render(
-    <HelloWorld name={'GenEpix'} />,
-  );
-  await expect.element(getByText('Hello GenEpix!')).toBeInTheDocument();
-});

package/src/test/integration/tests/integration-example/HelloWorld.tsx

@@ -1,9 +0,0 @@
-export const HelloWorld = ({ name }: { readonly name: string }) => {
-  return (
-    <div>
-      <h1>
-        {`Hello ${name}!`}
-      </h1>
-    </div>
-  );
-};

package/src/test/setup-browser.ts

@@ -1,3 +0,0 @@
-import { setupTestEnvironment } from './setup';
-
-setupTestEnvironment();

package/src/test/setup-jsdom.ts

@@ -1,6 +0,0 @@
-import { setupTestEnvironment } from './setup';
-
-global.TextEncoder = TextEncoder;
-global.TextDecoder = TextDecoder;
-
-setupTestEnvironment();

package/src/test/setup.ts

@@ -1,9 +0,0 @@
-import { setup } from '../setup/setup';
-
-export const setupTestEnvironment = () => {
-  setup();
-
-  vi.setConfig({
-    testTimeout: 10000,
-  });
-};

package/src/utils/AbacUtil/AbacUtil.ts

@@ -1,21 +0,0 @@
-import type { CaseTypeAccessAbac } from '../../api';
-
-export class AbacUtil {
-  public static createEffectieveColumnAccessRights(
-    caseTypeAccessAbacs: CaseTypeAccessAbac[],
-  ): Map<string, { read: boolean; write: boolean }> {
-    const effectiveColumnAccessRights = new Map<string, { read: boolean; write: boolean }>();
-    caseTypeAccessAbacs.forEach((caseTypeAccessAbac) => {
-      caseTypeAccessAbac.read_col_ids.forEach(colId => {
-        const currentRights = effectiveColumnAccessRights.get(colId) ?? { read: false, write: false };
-        effectiveColumnAccessRights.set(colId, { ...currentRights, read: true });
-      });
-      caseTypeAccessAbac.write_col_ids.forEach(colId => {
-        const currentRights = effectiveColumnAccessRights.get(colId) ?? { read: false, write: false };
-        effectiveColumnAccessRights.set(colId, { ...currentRights, write: true });
-      });
-    });
-
-    return effectiveColumnAccessRights;
-  }
-}

package/src/utils/AbacUtil/index.ts

@@ -1 +0,0 @@
-export * from './AbacUtil';

package/src/utils/AxiosUtil/AxiosUtil.test.ts

@@ -1,66 +0,0 @@
-import {
-  describe,
-  it,
-  expect,
-} from 'vitest';
-import type { AxiosError } from 'axios';
-import { CanceledError } from 'axios';
-import type { DeepPartial } from 'react-hook-form';
-
-import { AxiosUtil } from './AxiosUtil';
-
-describe('AxiosUtil', () => {
-  const createAxiosError = (status: number): DeepPartial<AxiosError> => ({
-    isAxiosError: true,
-    response: { status },
-    config: {},
-    name: '',
-    message: '',
-    toJSON: () => ({}),
-  });
-
-  it('should identify a canceled error', () => {
-    const error = new CanceledError();
-    expect(AxiosUtil.isAxiosCanceledError(error)).toBe(true);
-  });
-
-  it('should identify an unauthorized error', () => {
-    const error = createAxiosError(401);
-    expect(AxiosUtil.isAxiosUnauthorizedError(error)).toBe(true);
-  });
-
-  it('should identify a forbidden error', () => {
-    const error = createAxiosError(403);
-    expect(AxiosUtil.isAxiosForbiddenError(error)).toBe(true);
-  });
-
-  it('should identify an unprocessable entity error', () => {
-    const error = createAxiosError(422);
-    expect(AxiosUtil.isAxiosUnprocessableEntityError(error)).toBe(true);
-  });
-
-  it('should identify a not found error', () => {
-    const error = createAxiosError(404);
-    expect(AxiosUtil.isAxiosNotFoundError(error)).toBe(true);
-  });
-
-  it('should identify a bad request error', () => {
-    const error = createAxiosError(400);
-    expect(AxiosUtil.isAxiosBadRequestError(error)).toBe(true);
-  });
-
-  it('should identify an internal server error', () => {
-    const error = createAxiosError(500);
-    expect(AxiosUtil.isAxiosInternalServerError(error)).toBe(true);
-  });
-
-  it('should not identify an error with a different status code', () => {
-    const error = createAxiosError(418); // I'm a teapot
-    expect(AxiosUtil.isAxiosUnauthorizedError(error)).toBe(false);
-    expect(AxiosUtil.isAxiosForbiddenError(error)).toBe(false);
-    expect(AxiosUtil.isAxiosUnprocessableEntityError(error)).toBe(false);
-    expect(AxiosUtil.isAxiosNotFoundError(error)).toBe(false);
-    expect(AxiosUtil.isAxiosBadRequestError(error)).toBe(false);
-    expect(AxiosUtil.isAxiosInternalServerError(error)).toBe(false);
-  });
-});

package/src/utils/AxiosUtil/AxiosUtil.ts

@@ -1,47 +0,0 @@
-import type { AxiosError } from 'axios';
-import {
-  CanceledError,
-  isAxiosError,
-} from 'axios';
-
-export class AxiosUtil {
-  public static isAxiosTimeoutError(error: unknown): error is AxiosError<unknown> {
-    return isAxiosError(error) && !AxiosUtil.isAxiosCanceledError(error) && error.code === 'ECONNABORTED';
-  }
-
-  public static isAxiosCanceledError(error: unknown): error is CanceledError<unknown> {
-    return error instanceof CanceledError;
-  }
-
-  public static isAxiosUnauthorizedError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 401);
-  }
-
-  public static isAxiosForbiddenError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 403);
-  }
-
-  public static isAxiosUnprocessableEntityError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 422);
-  }
-
-  public static isAxiosNotFoundError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 404);
-  }
-
-  public static isAxiosBadRequestError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 400);
-  }
-
-  public static isAxiosInternalServerError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 500);
-  }
-
-  public static isAxiosConflictError(error: unknown): error is AxiosError<unknown> {
-    return AxiosUtil.isAxiosRequestErrorWithCode(error, 409);
-  }
-
-  public static isAxiosRequestErrorWithCode(error: unknown, status: number): error is AxiosError<unknown> {
-    return isAxiosError(error) && error.response?.status === status;
-  }
-}

package/src/utils/AxiosUtil/index.ts

@@ -1 +0,0 @@
-export * from './AxiosUtil';

package/src/utils/CaseSelectionUtil/CaseSelectionUtil.ts

@@ -1,32 +0,0 @@
-import intersection from 'lodash/intersection';
-
-export class CaseSelectionUtil {
-  public static addComponentCaseIdsToSelection(componentCaseIds: string[], selectedIds: string[]): string[] {
-    const caseIds = [...selectedIds, ...componentCaseIds];
-    return Array.from(new Set(caseIds));
-  }
-
-  public static removeComponentCaseIdsFromSelection(componentCaseIds: string[], selectedIds: string[]): string[] {
-    return selectedIds.filter(caseId => !componentCaseIds.includes(caseId));
-  }
-
-  public static refineSelectionWithComponentCaseIds(componentCaseIds: string[], selectedIds: string[]): string[] {
-    return componentCaseIds.filter(caseId => selectedIds.includes(caseId));
-  }
-
-  public static canAddToSelection(componentCaseIds: string[], selectedIds: string[]): boolean {
-    const intersectedCaseIds = intersection(componentCaseIds, selectedIds);
-    return intersectedCaseIds.length !== componentCaseIds.length;
-  }
-
-  public static canRemoveFromSelection(componentCaseIds: string[], selectedIds: string[]): boolean {
-    const intersectedCaseIds = intersection(componentCaseIds, selectedIds);
-    return intersectedCaseIds.length > 0;
-  }
-
-  public static canRefineSelection(componentCaseIds: string[], selectedIds: string[]): boolean {
-    const intersectedCaseIds = intersection(componentCaseIds, selectedIds);
-    const negationResult = intersectedCaseIds.length === 0 || (intersectedCaseIds.length === componentCaseIds.length && intersectedCaseIds.length === selectedIds.length);
-    return !negationResult;
-  }
-}

package/src/utils/CaseSelectionUtil/index.ts

@@ -1 +0,0 @@
-export * from './CaseSelectionUtil';

package/src/utils/CaseSetUtil/CaseSetUtil.ts

@@ -1,13 +0,0 @@
-import { StringUtil } from '../StringUtil';
-import type { CaseSet } from '../../api';
-import { WindowManager } from '../../classes/managers/WindowManager';
-
-export class CaseSetUtil {
-  public static createCaseSetLink(caseSet: CaseSet, full?: boolean): string {
-    const path = `/events/${StringUtil.createSlug(caseSet.name)}/${caseSet.id}`;
-    if (full) {
-      return `${WindowManager.instance.window.location.origin}${path}`;
-    }
-    return path;
-  }
-}

package/src/utils/CaseSetUtil/index.ts

@@ -1 +0,0 @@
-export * from './CaseSetUtil';

package/src/utils/CaseTypeUtil/CaseTypeUtil.ts

@@ -1,178 +0,0 @@
-import uniq from 'lodash/uniq';
-
-import { StringUtil } from '../StringUtil';
-import type {
-  CaseType,
-  CompleteCaseType,
-  RefDim,
-  RefCol,
-  Col,
-  Dim,
-} from '../../api';
-import {
-  DimType,
-  ColType,
-} from '../../api';
-import { WindowManager } from '../../classes/managers/WindowManager';
-
-export const SELECTION_FILTER_GROUP = 'selection';
-export const TREE_FILTER_GROUP = 'tree';
-
-export class CaseTypeUtil {
-  public static createCaseTypeLink(caseType: CaseType | CompleteCaseType, full?: boolean): string {
-    const path = `/cases/${StringUtil.createSlug(caseType.name)}/${caseType.id}`;
-    if (full) {
-      return `${WindowManager.instance.window.location.origin}${path}`;
-    }
-    return path;
-  }
-
-  public static getInitialVisibleColIds(completeCaseType: CompleteCaseType): string[] {
-    const visibleColumnIds: string[] = [];
-
-    completeCaseType.ordered_dim_ids.map(x => completeCaseType.dims[x]).forEach((dim) => {
-      const refDims = completeCaseType.ref_dims[dim.ref_dim_id];
-
-      const cols = completeCaseType.ordered_col_ids_by_dim[dim.id].map(id => completeCaseType.cols[id]);
-      const refCols = cols.map(col => completeCaseType.ref_cols[col.ref_col_id]);
-
-      if (refDims.dim_type === DimType.GEO) {
-        visibleColumnIds.push(CaseTypeUtil.getPreferredGEOCol(cols).id);
-      } else if (refDims.dim_type === DimType.TIME || refDims.dim_type === DimType.NUMBER || CaseTypeUtil.isGeneticDistanceDim(refDims, refCols)) {
-        visibleColumnIds.push(CaseTypeUtil.getPreferredColInDimHavingHighestRank(cols, completeCaseType).id);
-      } else {
-        visibleColumnIds.push(...cols.filter(cc => {
-          const refCol = completeCaseType.ref_cols[cc.ref_col_id];
-          const hiddenColTypes: ColType[] = [ColType.GENETIC_READS, ColType.GENETIC_SEQUENCE];
-          return !hiddenColTypes.includes(refCol.col_type);
-        }).map(c => c.id));
-      }
-    });
-
-    return visibleColumnIds;
-  }
-
-  public static getDimLabel(completeCaseType: CompleteCaseType, dimId: string): string {
-    const dim = completeCaseType.dims[dimId];
-    return dim.code;
-  }
-
-  public static isGeneticDistanceDim(refDim: RefDim, refCols: RefCol[]): boolean {
-    return refDim.dim_type === DimType.OTHER && refCols.find(refCol => refCol.col_type === ColType.GENETIC_DISTANCE) !== undefined;
-  }
-
-  public static getPreferredGEOCol(cols: Col[]): Col {
-    return cols[Math.min(cols.length - 1, Math.floor((cols.length - 1) / 2))];
-  }
-
-  public static getPreferredColInDimHavingHighestRank(cols: Col[], completeCaseType: CompleteCaseType): Col {
-    return cols.find(col => completeCaseType.ref_cols[col.ref_col_id].rank === 1) ?? cols?.[0];
-  }
-
-  public static getDims(completeCaseType: CompleteCaseType, dimTypes?: DimType[]): Dim[] {
-    const dims = Object.values(completeCaseType.ordered_dim_ids).map(x => completeCaseType.dims[x]);
-    if (!dimTypes?.length) {
-      return dims;
-    }
-    return dims.filter(dim => {
-      const refDim = completeCaseType.ref_dims[dim.ref_dim_id];
-      return dimTypes.includes(refDim.dim_type);
-    });
-  }
-
-  public static getCols(completeCaseType: CompleteCaseType, dimId?: string): Col[] {
-    if (!dimId) {
-      return Object.values(completeCaseType.cols);
-    }
-    return completeCaseType.ordered_col_ids_by_dim[dimId].map(id => completeCaseType.cols[id]);
-  }
-
-
-  /**
-   * Get columns by their column type.
-   * @param completeCaseType The complete case type object.
-   * @param colType The column type to filter by.
-   * @returns An array of columns matching the specified column type.
-   */
-  public static getColsByType(completeCaseType: CompleteCaseType, colType: ColType[]): Col[] {
-    return Object.values(completeCaseType.cols).filter(col => {
-      const refCol = completeCaseType.ref_cols[col.ref_col_id];
-      return colType.includes(refCol?.col_type);
-    });
-  }
-
-
-  /**
-   * Find a unique column by its column ID or column ID.
-   * @param completeCaseType The complete case type object.
-   * @param id The ID of the column or column.
-   * @returns The unique column if found, otherwise null.
-   */
-  public static findUniqueColByColIdRefOrColId(completeCaseType: CompleteCaseType, id: string): Col {
-    const colId = Object.values(completeCaseType.cols).find(col => col.ref_col_id === id);
-    if (colId) {
-      return colId;
-    }
-    const colIds = Object.values(completeCaseType.ref_cols).filter(ref_col => ref_col.id === id);
-    if (colIds.length !== 1) {
-      return null;
-    }
-    const cols = Object.values(completeCaseType.cols).filter(col => col.ref_col_id === colIds[0].id);
-    if (cols.length !== 1) {
-      return null;
-    }
-    return cols[0];
-  }
-
-
-  /**
-   * Find paired FWD/REV columns in the same dimension.
-   * @param completeCaseType The complete case type object.
-   * @returns An array of paired FWD/REV columns.
-   */
-  public static findPairedReadsCols(completeCaseType: CompleteCaseType): { fwd: Col; rev: Col }[] {
-    const pairs: { fwd: Col; rev: Col }[] = [];
-
-    completeCaseType.ordered_dim_ids.forEach(dimId => {
-      const cols = completeCaseType.ordered_col_ids_by_dim[dimId].map(x => completeCaseType.cols[x]);
-      if (!cols) {
-        return;
-      }
-      const readsColumns = cols.filter(col => {
-        const refCol = completeCaseType.ref_cols[col.ref_col_id];
-        return refCol?.col_type === ColType.GENETIC_READS;
-      });
-
-      if (readsColumns.length === 2) {
-        pairs.push({ fwd: readsColumns[0], rev: readsColumns[1] });
-      }
-
-    });
-
-    return pairs;
-  }
-
-  public static getWritableColIds(completeCaseType: CompleteCaseType): string[] {
-    const writableColIds: string[] = [];
-    Object.values(completeCaseType.case_type_access_abacs).forEach((abac) => {
-      writableColIds.push(...abac.write_col_ids);
-    });
-    return uniq(writableColIds);
-  }
-
-  public static getWritableImportExportColIds(completeCaseType: CompleteCaseType): string[] {
-    const writableColIds = CaseTypeUtil.getWritableColIds(completeCaseType);
-    return Object.keys(completeCaseType.cols).filter(colId => {
-      if (!writableColIds.includes(colId)) {
-        return false;
-      }
-      const col = completeCaseType.cols[colId];
-      const refCol = completeCaseType.ref_cols[col.ref_col_id];
-      if (([ColType.GENETIC_DISTANCE, ColType.GENETIC_PROFILE, ColType.GENETIC_READS, ColType.GENETIC_SEQUENCE] as ColType[]).includes(refCol.col_type)) {
-        return false;
-      }
-      return true;
-    });
-  }
-
-}

package/src/utils/CaseTypeUtil/index.ts

@@ -1 +0,0 @@
-export * from './CaseTypeUtil';