Merge branch 'main' into 190-advanced-map-marker-config

packages/libs/components/src/map/SemanticMarkers.tsx

@@ -211,7 +211,7 @@ function constrainLongitudeToMainWorld({
   // but we need to make sure that west is slightly greater than east
   // so that they "wrap around" the whole globe
   // (if west was slightly less than east, it would represent a very tiny sliver)
-  if (newWest === newEast) newWest = newWest + 1e-8;
+  if (Math.abs(newEast - newWest) < 1e-8) newWest = newEast + 1e-8;
 
   return {
     southWest: { lat: south, lng: newWest },

packages/libs/eda/src/index.tsx

@@ -39,7 +39,6 @@ import { wrapWdkDependencies } from '@veupathdb/study-data-access/lib/shared/wra
 import {
   disableRestriction,
   enableRestriction,
-  reduxMiddleware,
 } from '@veupathdb/study-data-access/lib/data-restriction/DataRestrictionUtils';
 
 import { edaEndpoint, wdkEndpoint, rootElement, rootUrl } from './constants';
@@ -224,7 +223,6 @@ initialize({
     },
   }),
   endpoint: wdkEndpoint,
-  additionalMiddleware: [reduxMiddleware],
 } as any);
 
 // If you want to start measuring performance in your app, pass a function

packages/libs/eda/src/lib/core/components/visualizations/Visualizations.scss

@@ -165,6 +165,7 @@
       font-weight: 500;
       text-align: center;
       font-size: 1.2em;
+      max-width: 200px;
     }
   }
   &-FullScreenContainer {

packages/libs/eda/src/lib/core/components/visualizations/implementations/LineplotVisualization.tsx

@@ -651,14 +651,14 @@ function LineplotViz(props: VisualizationProps<Options>) {
     [options, providedOverlayVariable, providedOverlayVariableDescriptor]
   );
 
-  // define showMarginalHistogram
-  const showMarginalHistogram = options?.showMarginalHistogram ?? false;
   // check banner condition
   const showIndependentAxisBanner =
     vizConfig.independentAxisLogScale && vizConfig.useBinning;
   const showDependentAxisBanner =
     vizConfig.dependentAxisLogScale && vizConfig.showErrorBars;
 
+  const showMarginalHistogram = options?.showMarginalHistogram ?? false;
+
   const data = usePromise(
     useCallback(async (): Promise<LinePlotDataWithCoverage | undefined> => {
       if (

packages/libs/eda/src/lib/core/hooks/workspace.ts

@@ -130,11 +130,11 @@ export function useStudyEntities(filters?: Filter[]) {
                             min:
                               filter.type === 'numberRange'
                                 ? filter.min
-                                : filter.min.split('T00:00:00Z')[0],
+                                : filter.min.split(/T00:00:00(?:\.000)?Z?/)[0],
                             max:
                               filter.type === 'numberRange'
                                 ? filter.max
-                                : filter.max.split('T00:00:00Z')[0],
+                                : filter.max.split(/T00:00:00(?:\.000)?Z?/)[0],
                           }
                         : undefined;
 

packages/libs/eda/src/lib/map/analysis/hooks/standaloneVizPlugins.ts

@@ -23,6 +23,8 @@ import { barplotRequest } from './plugins/barplot';
 import { lineplotRequest } from './plugins/lineplot';
 import { histogramRequest } from './plugins/histogram';
 import { scatterplotRequest } from './plugins/scatterplot';
+//TO DO import timeline SVGIcon
+import LineSVG from '../../../core/components/visualizations/implementations/selectorIcons/LineSVG';
 
 interface Props {
   selectedOverlayConfig?: OverlayConfig;
@@ -40,10 +42,6 @@ export function useStandaloneVizPlugins({
       return visualization.withOptions({
         hideFacetInputs: true, // will also enable table-only mode for mosaic
         hideShowMissingnessToggle: true,
-        // TODO: need to distinguish lineplot from lineplot with marginal histogram?
-        // perhaps need to make another function only for lineplot with marginal histogram
-        // or define xxx.withOptions({}) directly at corresponding visualizationPlugins below
-        showMarginalHistogram: false,
         layoutComponent: FloatingLayout,
         // why are we providing three functions to access the properties of
         // one object? Because in the pre-SAM world, getOverlayVariable was already
@@ -108,6 +106,17 @@ export function useStandaloneVizPlugins({
             vizWithOptions(lineplotVisualization),
             lineplotRequest
           ),
+          // activate timeline Viz
+          timeseries: vizWithCustomizedGetRequest(
+            vizWithOptions(
+              lineplotVisualization
+                .withOptions({
+                  showMarginalHistogram: true,
+                })
+                .withSelectorIcon(LineSVG)
+            ),
+            lineplotRequest
+          ),
         },
       },
       'standalone-map-distributions': {

packages/libs/study-data-access/src/data-restriction/DataRestrictionUtils.js

@@ -1,30 +1,28 @@
-import { get, isPlainObject } from 'lodash';
 import React from 'react';
-import { BasketActions, ResultPanelActions, ResultTableSummaryViewActions } from '@veupathdb/wdk-client/lib/Actions';
-import {getResultTypeDetails} from '@veupathdb/wdk-client/lib/Utils/WdkResult';
 
-import { getStudyId, getStudyPolicyUrl, getStudyRequestNeedsApproval } from '../shared/studies';
-import { isUserApprovedForAction, isUserFullyApprovedForStudy } from '../study-access/permission';
-
-import { attemptAction } from './DataRestrictionActionCreators';
 import {
-  Action,
-  strictActions,
-} from './DataRestrictionUiActions';
+  getStudyId,
+  getStudyPolicyUrl,
+  getStudyRequestNeedsApproval,
+} from '../shared/studies';
+import {
+  isUserApprovedForAction,
+  isUserFullyApprovedForStudy,
+} from '../study-access/permission';
+
+import { Action, strictActions } from './DataRestrictionUiActions';
 
 // Getters!   =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
 
-export function getPolicyUrl (study = {}) {
-  return !study
-    ? null
-    : getStudyPolicyUrl(study);
+export function getPolicyUrl(study = {}) {
+  return !study ? null : getStudyPolicyUrl(study);
 }
 
-export function getRequestNeedsApproval (study = {}) {
+export function getRequestNeedsApproval(study = {}) {
   return getStudyRequestNeedsApproval(study);
 }
 
-export function getActionVerb (action) {
+export function getActionVerb(action) {
   if (typeof action !== 'string') return null;
   switch (action) {
     case Action.search:
@@ -43,28 +41,33 @@ export function getActionVerb (action) {
     case Action.download:
       return 'download data';
     case Action.basket:
-      return 'add to your basket'
-    default: 
+      return 'add to your basket';
+    default:
       return action;
   }
 }
 
-export function getRequirement ({ action, permissions, study, user }) {
+export function getRequirement({ action, permissions, study, user }) {
   //if (actionRequiresLogin({ action, study })) return 'login or create an account';
-  if ( getRequestNeedsApproval(study)=="0" ) return 'submit an access request';
-  if (actionRequiresApproval({ action, permissions, study, user })) return 'acquire research approval';
+  if (getRequestNeedsApproval(study) == '0') return 'submit an access request';
+  if (actionRequiresApproval({ action, permissions, study, user }))
+    return 'acquire research approval';
   return 'contact us';
 }
 
-export function getRestrictionMessage ({ action, permissions, study, user }) {
+export function getRestrictionMessage({ action, permissions, study, user }) {
   const intention = getActionVerb(action);
   const requirement = getRequirement({ action, permissions, study, user });
-  return <span>Please <b>{requirement}</b> in order to {intention}.</span>;
+  return (
+    <span>
+      Please <b>{requirement}</b> in order to {intention}.
+    </span>
+  );
 }
 
 // CHECKERS! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
 
-export function isAllowedAccess ({ permissions, action, study }) {
+export function isAllowedAccess({ permissions, action, study }) {
   const id = getStudyId(study);
   if (sessionStorage.getItem('restriction_override') === 'true') return true;
   if (isUserApprovedForAction(permissions, id, action)) return true;
@@ -75,141 +78,42 @@ export function isAllowedAccess ({ permissions, action, study }) {
 // the UI in (1) home page study card, (2) study menu, (3) study record page is different when
 // - the study.access is prerelease
 // - the user doesnt have access
-export function isPrereleaseStudy (access, studyId, permissions) {
+export function isPrereleaseStudy(access, studyId, permissions) {
   return (
     access === 'prerelease' &&
     !isUserFullyApprovedForStudy(permissions, studyId)
   );
 }
 
 // we will request the user to request approval if explicit approval needed (guest or not)
-export function actionRequiresApproval ({ action, permissions, study, user }) {
+export function actionRequiresApproval({ action, permissions, study, user }) {
   const datasetId = getStudyId(study);
 
-  return isUserApprovedForAction(
-    permissions,
-    datasetId,
-    action
-  ) === false;
+  return isUserApprovedForAction(permissions, datasetId, action) === false;
 }
 
-export function disableRestriction () {
+export function disableRestriction() {
   sessionStorage.setItem('restriction_override', true);
 }
 window._disableRestriction = disableRestriction;
 
-export function enableRestriction () {
+export function enableRestriction() {
   sessionStorage.removeItem('restriction_override');
 }
 window._enableRestriction = enableRestriction;
 
-export function isActionStrict (action) {
+export function isActionStrict(action) {
   return strictActions.has(action);
 }
 
-export function getIdFromRecordClassName (recordClassName) {
+export function getIdFromRecordClassName(recordClassName) {
   if (typeof recordClassName !== 'string') return null;
-  if (recordClassName.length > 13) recordClassName = recordClassName.slice(0, 13);
+  if (recordClassName.length > 13)
+    recordClassName = recordClassName.slice(0, 13);
   const result = recordClassName.match(/^DS_[^_]+/g);
-  return result === null
-    ? null
-    : result[0];
+  return result === null ? null : result[0];
 }
 
 export function isStudyRecordClass(recordClass) {
   return recordClass == null || recordClass.fullName.startsWith('DS_');
 }
-
-
-// Redux Middleware
-// ----------------
-
-/**
- * Redux middleware for applying restrictions to specific redux actions.
- */
-export const reduxMiddleware = store => next => action => {
-  if (!isPlainObject(action) || action.type == null) return next(action);
-  const restrictedAction = getDataRestrictionActionAndRecordClass(
-    store.getState(),
-    action,
-    (dataRestrictionAction, recordClassName) =>
-      attemptAction(dataRestrictionAction,{
-        studyId: getIdFromRecordClassName(recordClassName),
-        onAllow: () => next(action)
-      })
-  );
-  return restrictedAction == null ? next(action) : store.dispatch(restrictedAction);
-}
-
-/**
- * Checks if a redux action should be restricted, and if so, calls `callback`
- * with the restriction Action, and the record class name associated with the
- * action.
- * 
- * Return null to indicate that the redux action does not need to be
- * restricted.
- */
-function getDataRestrictionActionAndRecordClass(state, action, callback) {
-  if (!isPlainObject(action)) return null;
-
-  switch(action.type || '') {
-    case ResultPanelActions.openTabListing.type:
-      return getRecordClassNameByResultType(action.payload.resultType, recordClassName =>
-        callback(Action.results, recordClassName));
-
-    case 'step-analysis/select-tab':
-    case 'step-analysis/create-new-tab': {
-      return  getRecordClassNameByStepId(state.stepAnalysis.stepId, recordClassName =>
-        callback(Action.analysis, recordClassName));
-    }
-
-    case BasketActions.requestUpdateBasket.type:
-      return callback(Action.basket, action.payload.recordClassName);
-
-    case BasketActions.requestAddStepToBasket.type:
-      return getRecordClassNameByStepId(action.payload.stepId, recordClassName =>
-        callback(Action.basket, recordClassName));
-
-    case ResultTableSummaryViewActions.requestPageSizeUpdate.type:
-    case ResultTableSummaryViewActions.requestSortingUpdate.type:
-      return getRecordClassNameByResultType(getResultTypeByViewId(action.payload.viewId, state), recordClassName =>
-        callback(Action.paginate, recordClassName));
-
-    case ResultTableSummaryViewActions.viewPageNumber.type:
-      return action.payload.page === 1
-        ? null
-        : getRecordClassNameByResultType(getResultTypeByViewId(action.payload.viewId, state), recordClassName =>
-            callback(Action.paginate, recordClassName));
-
-    default:
-        return null;
-  }
-}
-
-function getResultTypeByViewId(viewId, state) {
-  return get(state, ['resultTableSummaryView', viewId, 'resultType']);
-}
-
-function getRecordClassNameByStepId(stepId, callback) {
-  return async function run({ wdkService }) {
-    try {
-      const step = await wdkService.findStep(stepId);
-      return callback(step.recordClassName);
-    }
-    catch(error) {
-      return callback(null);
-    }
-  };
-}
-
-function getRecordClassNameByResultType(resultType, callback) {
-  return async function run({ wdkService }) {
-    try {
-      const { recordClassName } = await getResultTypeDetails(wdkService, resultType)
-      return callback(recordClassName);
-    }
-    catch(error) {
-      return callback(null);
-    }
-  };
-}

packages/libs/wdk-client/src/Actions/BasketActions.ts

@@ -43,7 +43,7 @@ export const fulfillUpdateBasket = makeActionCreator(
 
 export const requestAddStepToBasket = makeActionCreator(
   'requestAddStepToBasket',
-  (stepId: number) => ({ stepId })
+  (stepId: number, clearFirst: boolean) => ({ stepId, clearFirst })
 );
 
 export const fulfillAddStepToBasket = makeActionCreator(