react-science 10.0.0 → 11.0.0

package/src/app-data/loaders/utility/index.ts

@@ -1,3 +0,0 @@
-export * from './getMeasurementInfoFromFile.js';
-export * from './measurementLoader.js';
-export * from './parserLog.js';

package/src/app-data/loaders/utility/measurementLoader.ts

@@ -1,26 +0,0 @@
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-
-import { assert } from '../../../components/index.js';
-import type { MeasurementBase, Measurements } from '../../index.js';
-
-export type MeasurementsLoader = (
-  fileCollection: FileCollection,
-  logger?: FifoLogger,
-) => Promise<Partial<Measurements>>;
-
-export function mergeMeasurements(
-  measurements: Partial<Measurements>,
-  newMeasurements: Partial<Measurements>,
-) {
-  //fixes for putting type "string" to key
-  let kind: keyof typeof newMeasurements;
-  for (kind in newMeasurements) {
-    if (!measurements[kind]) {
-      measurements[kind] = { entries: [] };
-    }
-    assert(measurements[kind], 'Error while loading, kind is not defined');
-    const entries: MeasurementBase[] = newMeasurements[kind]?.entries || [];
-    measurements[kind]?.entries.push(...entries);
-  }
-}

package/src/app-data/loaders/utility/parserLog.ts

@@ -1,39 +0,0 @@
-export interface ParserLog {
-  kind: 'error' | 'warn' | 'info' | 'debug' | 'summary';
-  /* name of the parser or converter*/
-  parser: string;
-  message: string;
-  /* if the parser has branches for text, binary, etc. */
-  branch?: string;
-  /* from FileCollectionItem or other*/
-  relativePath?: string;
-  error?: Error;
-}
-
-export function createLogEntry(info: Partial<ParserLog>): ParserLog {
-  const {
-    parser = 'biologic-converter',
-    branch,
-    kind = 'error',
-    message = 'Error parsing biologic experiment.',
-    error,
-    relativePath,
-  } = info;
-
-  const log: ParserLog = {
-    parser,
-    kind,
-    message,
-  };
-
-  if (error) {
-    log.error = error;
-  }
-  if (relativePath) {
-    log.relativePath = relativePath;
-  }
-  if (branch) {
-    log.branch = branch;
-  }
-  return log;
-}

package/src/app-data/loaders/wdfLoader.ts

@@ -1,140 +0,0 @@
-import type { MeasurementVariable } from 'cheminfo-types';
-import type { FifoLogger } from 'fifo-logger';
-import type { FileCollection } from 'filelist-utils';
-import type { Wdf } from 'wdf-parser';
-import { parse } from 'wdf-parser';
-
-import type { MeasurementBase, Measurements } from '../index.js';
-
-import { getMeasurementInfoFromFile } from './utility/index.js';
-
-/**
- *
- * @param fileCollection - the dragged file/files
- * @param logger - whether to log to console or not
- * @returns - new measurements object to be merged
- */
-export async function wdfLoader(
-  fileCollection: FileCollection,
-  logger?: FifoLogger,
-): Promise<Partial<Measurements>> {
-  const measurements: Partial<Measurements> = {};
-  const entries: MeasurementBase[] = [];
-
-  for (const file of fileCollection) {
-    if (/\.wdf$/i.test(file.name)) {
-      try {
-        // TODO: load in parallel
-        // eslint-disable-next-line no-await-in-loop
-        const parsed = parse(await file.arrayBuffer());
-        entries.push({
-          meta: parsed.fileHeader,
-          ...getMeasurementInfoFromFile(file, parsed.fileHeader.title),
-          data: normalizeSpectra(parsed.blocks),
-        });
-      } catch (error) {
-        if (error instanceof Error) {
-          if (logger) {
-            logger.error(error);
-          } else {
-            throw error;
-          }
-        }
-      }
-    }
-  }
-
-  measurements.raman = { entries };
-  return measurements;
-}
-
-function normalizeSpectra(blocks: Wdf['blocks']) {
-  const yVariables = getYVariables(blocks);
-  const origins = getOrigins(blocks);
-
-  const results: MeasurementBase['data'] = [];
-
-  for (let i = 0; i < yVariables.length; i++) {
-    const yVariable = yVariables[i];
-    const origin = origins[i] || {};
-
-    results.push({
-      variables: { x: getXVariable(blocks), y: yVariable },
-      meta: { ...origin },
-    });
-  }
-  return results;
-}
-
-function getXVariable(blocks: Wdf['blocks']) {
-  const xBlock = blocks.find(
-    (block) => block.blockType === 'WDF_BLOCKID_XLIST',
-  );
-
-  const xList = xBlock?.xList;
-  const groups = xList?.units.match(/(?<label>.*) \((?<units>.*)\)/)?.groups;
-
-  if (!xList) {
-    throw new Error('no xList data found in wdf file');
-  }
-
-  const xVariable: MeasurementVariable = {
-    label: groups?.label || 'Arbitrary Units',
-    units: groups?.units || '',
-    data: Array.from(xList.values),
-  };
-  return xVariable;
-}
-
-function getYVariables(blocks: Wdf['blocks']) {
-  const dataBlock = blocks.find(
-    (block) => block.blockType === 'WDF_BLOCKID_DATA',
-  );
-
-  if (!dataBlock?.spectra) {
-    throw new Error('no spectrum found in data block of wdf file');
-  }
-
-  const yVariables: MeasurementVariable[] = [];
-  for (const spectrum of dataBlock.spectra) {
-    yVariables.push({
-      data: Array.from(spectrum),
-      units: '',
-      label: 'Arbitrary Intensity',
-    });
-  }
-
-  return yVariables;
-}
-
-interface Origin {
-  xPositionUnits: string;
-  yPositionUnits: string;
-  xPosition: number | bigint;
-  yPosition: number | bigint;
-}
-function getOrigins(blocks: Wdf['blocks']) {
-  const originBlock = blocks.find(
-    (block) => block.blockType === 'WDF_BLOCKID_ORIGIN',
-  );
-  if (!originBlock) return [];
-
-  const xPositions = originBlock.origins?.find((entry) => entry.label === 'X');
-  const yPositions = originBlock.origins?.find((entry) => entry.label === 'Y');
-  const xOrigins = xPositions?.axisOrigins;
-  const yOrigins = yPositions?.axisOrigins;
-
-  const origins: Origin[] = [];
-  if (xOrigins && yOrigins) {
-    for (let i = 0; i < xOrigins.length; i++) {
-      // we should add some xIndex and yIndex based on https://github.com/cheminfo/raman-spectrum/blob/1d3bc62ebe2930f8c35fcf65689b090f5b22ba9e/src/utils/surfaceAnalysis.js#L15-L70
-      origins.push({
-        xPositionUnits: xPositions.unit,
-        yPositionUnits: yPositions.unit,
-        xPosition: xOrigins[i],
-        yPosition: yOrigins[i],
-      });
-    }
-  }
-  return origins;
-}

package/src/app-data/state/app_state.actions.ts

@@ -1,49 +0,0 @@
-import type { AppState } from './app_state.js';
-import type {
-  MeasurementKind,
-  MeasurementKindAndId,
-  Measurements,
-} from './data/index.js';
-import type { MeasurementAppView, Plot2DZoom } from './view/index.js';
-
-type ActionType<Action, Payload = void> = Payload extends void
-  ? { type: Action }
-  : { type: Action; payload: Payload };
-
-export type AppStateAction =
-  | ActionType<'LOAD_START'>
-  | ActionType<'LOAD_STOP'>
-  | ActionType<'ADD_MEASUREMENTS', Partial<Measurements>>
-  | ActionType<'LOAD_FULL_STATE', AppState>
-  | ActionType<'PLOT_ZOOM', { kind: MeasurementKind; zoom: Plot2DZoom }>
-  | ActionType<'PLOT_ZOOM_OUT', { kind: MeasurementKind }>
-  | ActionType<
-      'SELECT_MEASUREMENT',
-      MeasurementKindAndId & { acc: 'add' | 'remove' | 'replace' }
-    >
-  | ActionType<
-      'SELECT_ALL_MEASUREMENTS',
-      { select: boolean; kind: MeasurementKind }
-    >
-  | ActionType<'SELECT_MEASUREMENT_KIND', MeasurementKind>
-  | ActionType<'SET_MEASUREMENT_VISIBILITY', { id: string; isVisible: boolean }>
-  | ActionType<
-      'SET_SELECTED_MEASUREMENTS_VISIBILITY',
-      { kind: MeasurementKind; isVisible: boolean }
-    >
-  | ActionType<
-      'CHANGE_MEASUREMENTS_DISPLAY',
-      { display: Partial<MeasurementAppView> }
-    >
-  | ActionType<
-      'CHANGE_MEASUREMENT_DISPLAY',
-      {
-        measurement: MeasurementKindAndId;
-        display: Partial<MeasurementAppView>;
-      }
-    >
-  | ActionType<'REMOVE_SELECTED_MEASUREMENTS', { kind: MeasurementKind }>
-  | ActionType<
-      'IV_PLOT_SELECT_VARIABLE',
-      { axis: 'x' | 'y'; variable: string }
-    >;

package/src/app-data/state/app_state.provider.tsx

@@ -1,24 +0,0 @@
-import type { ReactNode } from 'react';
-import { useReducer } from 'react';
-
-import {
-  appDispatchContext,
-  appReducer,
-  appStateContext,
-  getEmptyAppState,
-} from './app_state.js';
-
-export function AppStateProvider(props: { children: ReactNode }) {
-  const [appState, appDispatch] = useReducer(
-    appReducer,
-    null,
-    getEmptyAppState,
-  );
-  return (
-    <appDispatchContext.Provider value={appDispatch}>
-      <appStateContext.Provider value={appState}>
-        {props.children}
-      </appStateContext.Provider>
-    </appDispatchContext.Provider>
-  );
-}

package/src/app-data/state/app_state.ts

@@ -1,70 +0,0 @@
-import { produce } from 'immer';
-import type { Dispatch } from 'react';
-import { createContext, useContext } from 'react';
-
-import type { AppStateAction } from './app_state.actions.js';
-import type { AppData } from './data/index.js';
-import { getEmptyAppData } from './data/index.js';
-import { appStateProducer } from './producers/index.js';
-import type { AppSettings } from './settings/index.js';
-import { getEmptyAppSettings } from './settings/index.js';
-import type { AppView } from './view/index.js';
-import { getEmptyAppView } from './view/index.js';
-
-export interface AppState {
-  load: AppLoad;
-  data: AppData;
-  view: AppView;
-  settings: AppSettings;
-}
-
-export interface AppLoad {
-  isLoading: boolean;
-}
-
-export function getEmptyAppState(): AppState {
-  return {
-    load: {
-      isLoading: false,
-    },
-    data: getEmptyAppData(),
-    view: getEmptyAppView(),
-    settings: getEmptyAppSettings(),
-  };
-}
-
-export const appStateContext = createContext<AppState | null>(null);
-
-export function useAppState(): AppState {
-  const appState = useContext(appStateContext);
-  if (!appState) {
-    throw new Error('useAppState must be used within an AppStateProvider');
-  }
-  return appState;
-}
-
-export type AppDispatch = Dispatch<AppStateAction>;
-
-export const appDispatchContext = createContext<AppDispatch | null>(null);
-
-export function useAppDispatch(): AppDispatch {
-  const appDispatch = useContext(appDispatchContext);
-  if (!appDispatch) {
-    throw new Error('useAppDispatch must be used within an AppStateProvider');
-  }
-  return appDispatch;
-}
-
-export function useAppData(): AppData {
-  return useAppState().data;
-}
-
-export function useAppView(): AppView {
-  return useAppState().view;
-}
-
-export function useAppSettings(): AppSettings {
-  return useAppState().settings;
-}
-
-export const appReducer = produce(appStateProducer);

package/src/app-data/state/data/AppData.ts

@@ -1,77 +0,0 @@
-import type { Instrument, MeasurementVariable } from 'cheminfo-types';
-
-import type { IrMeasurement, IvMeasurement } from '../../index.js';
-
-export interface AppData {
-  measurements: Measurements;
-}
-
-/**
- * When we have a simple measurement like uv, ir, etc, data should only contain one element
- * Sometimes measurements are more complex like in GC / MS, GC / MS / MS, raman images, etc. In this case we will add the meta and info properties
- * to differentiate each measurement
- * If we have isotherm with gaz absorption / desorption this format should also be used.
- * The 'info'for each 'Measurement' should be normalized.
- */
-
-type UUID = string;
-
-export interface MeasurementBase {
-  id: UUID;
-  info: MeasurementBaseInfo;
-  // Unstructured object
-  meta: Record<string, any>;
-  data: Array<{
-    info?: Record<string, any>;
-    meta?: Record<string, any>;
-    variables: Record<string, MeasurementVariable>;
-  }>;
-}
-
-export interface MeasurementBaseInfo {
-  title: string;
-  file?: MeasurementFile;
-  instrument?: Instrument;
-}
-
-export interface MeasurementFile {
-  name: string;
-  path?: string;
-  size?: number;
-  lastModified?: number;
-}
-
-export interface Measurements {
-  ir: {
-    entries: IrMeasurement[];
-  };
-  iv: {
-    entries: IvMeasurement[];
-  };
-  raman: {
-    entries: MeasurementBase[];
-  };
-  uv: {
-    entries: MeasurementBase[];
-  };
-  uvvis: {
-    entries: MeasurementBase[];
-  };
-  gclc: {
-    entries: MeasurementBase[];
-  };
-  gclcms: {
-    entries: MeasurementBase[];
-  };
-  nmr: {
-    entries: MeasurementBase[];
-  };
-  mass: {
-    entries: MeasurementBase[];
-  };
-  other: {
-    entries: MeasurementBase[];
-  };
-}
-
-export type MeasurementKind = keyof Measurements;

package/src/app-data/state/data/data.helpers.ts

@@ -1,192 +0,0 @@
-import { assertNotNull } from '../../../components/index.js';
-import type { AppState, AppView } from '../index.js';
-
-import type {
-  AppData,
-  MeasurementBase,
-  MeasurementKind,
-  Measurements,
-} from './AppData.js';
-import { measurementKinds } from './kinds.js';
-
-export function getMeasurement(
-  measurements: Measurements,
-  kind: MeasurementKind,
-  selected: string,
-) {
-  const measurement = measurements[kind].entries.find(
-    (entry) => entry.id === selected,
-  );
-  return measurement || null;
-}
-
-export function getMeasurementOrFail(
-  measurements: Measurements,
-  kind: MeasurementKind,
-  selected: string,
-) {
-  const result = getMeasurement(measurements, kind, selected);
-  assertNotNull(result);
-  return result;
-}
-
-export function getFirstMeasurement<Kind extends MeasurementKind>(
-  measurements: Measurements,
-  kind: Kind,
-): { kind: Kind; measurement: Measurements[Kind]['entries'][0] } | null {
-  const measurement = measurements[kind].entries[0];
-  if (measurement) return { kind, measurement };
-
-  return null;
-}
-export function getFirstMeasurementOrFail<Kind extends MeasurementKind>(
-  measurements: Measurements,
-  kind: Kind,
-) {
-  const result = getFirstMeasurement(measurements, kind);
-  assertNotNull(result);
-  return result;
-}
-
-export function getCurrentMeasurement(state: AppState) {
-  const selectedMeasurement = getSelectedMeasurement(state.view);
-  if (!selectedMeasurement) return null;
-  const measurements: MeasurementBase[] = [];
-  for (const id of selectedMeasurement.ids) {
-    const measurement = getMeasurement(
-      state.data.measurements,
-      selectedMeasurement.kind,
-      id,
-    );
-    if (!measurement) return null;
-    measurements.push(measurement);
-  }
-  return measurements;
-}
-
-export function getCurrentMeasurementData(state: AppState) {
-  const selectedMeasurement = getCurrentMeasurement(state);
-  if (!selectedMeasurement) return null;
-  const kindAndIds = getMeasurementKindAndIds(state.data, selectedMeasurement);
-  const display = selectedMeasurement.map(
-    ({ id }) => state.view.measurements[id],
-  );
-  return { data: selectedMeasurement, display, kindAndIds };
-}
-
-export function getFirstSelectedMeasurementData(state: AppState) {
-  const {
-    data,
-    view: {
-      selectedMeasurements,
-      selectedKind,
-      measurements: measurementsView,
-    },
-  } = state;
-  if (!selectedKind) return null;
-
-  const measurements = selectedMeasurements[selectedKind];
-  if (!measurements?.length) return null;
-  assertNotNull(measurements);
-
-  const measurementId = measurements[0];
-  const measurement = getMeasurement(
-    data.measurements,
-    selectedKind,
-    measurementId,
-  );
-
-  return { data: measurement, display: measurementsView[measurementId] };
-}
-
-export interface MeasurementKindAndId {
-  kind: MeasurementKind;
-  id: string;
-}
-export interface MeasurementKindAndIds {
-  kind: MeasurementKind;
-  ids: string[];
-}
-export function getMeasurementKindAndId(data: AppData, measurementId: string) {
-  for (const kind of measurementKinds) {
-    const measurement = getMeasurement(data.measurements, kind, measurementId);
-    if (measurement) return { kind, id: measurementId };
-  }
-  throw new Error(`Measurement kind for ${measurementId} not found`);
-}
-export function getMeasurementKindAndIds(
-  data: AppData,
-  measurementId: MeasurementBase[],
-) {
-  let found = false;
-  for (const kind of measurementKinds) {
-    for (const { id } of measurementId) {
-      const measurement = getMeasurement(data.measurements, kind, id);
-      if (measurement) found = true;
-      if (found && !measurement) {
-        throw new Error(
-          `Measurement kind for ${measurementId.join(', ')} not found`,
-        );
-      }
-    }
-    if (found) return { kind, ids: measurementId };
-  }
-  throw new Error(`Measurement kind for ${measurementId.join(', ')} not found`);
-}
-export function getSelectedMeasurement(
-  view: AppView,
-): MeasurementKindAndIds | null {
-  const { selectedKind, selectedMeasurements } = view;
-  if (!selectedKind) return null;
-  const kind = selectedKind;
-  const currentMeasurements = selectedMeasurements[kind];
-  if (!currentMeasurements || currentMeasurements.length === 0) return null;
-  const ids = currentMeasurements;
-  return { kind, ids };
-}
-
-export function getSelectedMeasurementOrFail(view: AppView) {
-  const selected = getSelectedMeasurement(view);
-  assertNotNull(selected);
-  return selected;
-}
-
-export function* iterateMeasurementEntries(
-  measurements: Partial<Measurements>,
-) {
-  for (const [measurementKind, measurementData] of Object.entries(
-    measurements,
-  )) {
-    for (const measurement of measurementData.entries) {
-      yield { kind: measurementKind as MeasurementKind, measurement };
-    }
-  }
-}
-
-export interface MeasurementAndView<Kind extends MeasurementKind> {
-  measurement: Measurements[Kind]['entries'][number];
-  view: AppView['measurements'][string];
-}
-
-export function* iterateKindMeasurementsAndView<Kind extends MeasurementKind>(
-  state: AppState,
-  kind: Kind,
-): IterableIterator<MeasurementAndView<Kind>> {
-  const measurements = state.data.measurements[kind];
-  const view = state.view.measurements;
-  for (const measurement of measurements.entries) {
-    yield { measurement, view: view[measurement.id] };
-  }
-}
-
-export function getExistingMeasurementKinds(
-  measurements: Partial<Measurements>,
-): MeasurementKind[] {
-  const result: MeasurementKind[] = [];
-  for (const [kind, { entries }] of Object.entries(measurements)) {
-    if (entries.length > 0) {
-      result.push(kind as MeasurementKind);
-    }
-  }
-  return result;
-}

package/src/app-data/state/data/getEmptyAppData.ts

@@ -1,18 +0,0 @@
-import type { AppData } from './AppData.js';
-
-export function getEmptyAppData(): AppData {
-  return {
-    measurements: {
-      ir: { entries: [] },
-      iv: { entries: [] },
-      raman: { entries: [] },
-      uv: { entries: [] },
-      uvvis: { entries: [] },
-      gclc: { entries: [] },
-      gclcms: { entries: [] },
-      nmr: { entries: [] },
-      mass: { entries: [] },
-      other: { entries: [] },
-    },
-  };
-}

package/src/app-data/state/data/index.ts

@@ -1,4 +0,0 @@
-export * from './data.helpers.js';
-export * from './AppData.js';
-export * from './getEmptyAppData.js';
-export * from './kinds.js';

package/src/app-data/state/data/kinds.ts

@@ -1,16 +0,0 @@
-import type { MeasurementKind } from './AppData.js';
-
-export const kindLabels: Record<MeasurementKind, string> = {
-  ir: 'IR',
-  iv: 'IV',
-  raman: 'Raman',
-  uv: 'UV',
-  uvvis: 'UV-VIS',
-  mass: 'Mass',
-  gclc: 'GC/LC',
-  gclcms: 'GC/LC MS',
-  nmr: 'NMR',
-  other: 'Other',
-};
-
-export const measurementKinds = Object.keys(kindLabels) as MeasurementKind[];

package/src/app-data/state/index.ts

@@ -1,14 +0,0 @@
-export {
-  type AppState,
-  type AppLoad,
-  useAppState,
-  type AppDispatch,
-  useAppDispatch,
-  useAppData,
-  useAppView,
-  useAppSettings,
-} from './app_state.js';
-export { AppStateProvider } from './app_state.provider.js';
-export * from './data/index.js';
-export * from './settings/index.js';
-export * from './view/index.js';