Merge branch 'main' and resolve conflicts

VEuPathDB · Jun 28, 2024 · 3300405 · 3300405
2 parents c15d9f7 + 8493062
commit 3300405
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Showing 31 changed files with 598 additions and 350 deletions.
diff --git a/packages/libs/components/src/components/plotControls/MultiSelect.tsx b/packages/libs/components/src/components/plotControls/MultiSelect.tsx
@@ -1,5 +1,5 @@
 import { useState, useRef } from 'react';
-import { default as ReactSelect, components, InputAction } from 'react-select';
+import { default as ReactSelect, components } from 'react-select';
 
 export interface Option {
   value: number | string | undefined;
@@ -67,10 +67,7 @@ const MultiSelect = (props: any) => {
     (value !== '*' && label?.toLowerCase().includes(input.toLowerCase())) ||
     (value === '*' && filteredOptions?.length > 0);
 
-  const onInputChange = (
-    inputValue: string,
-    event: { action: InputAction }
-  ) => {
+  const onInputChange = (inputValue: string, event: { action: any }) => {
     if (event.action === 'input-change') setSelectInput(inputValue);
     else if (event.action === 'menu-close' && selectInput !== '')
       setSelectInput('');

diff --git a/packages/libs/eda/src/lib/core/api/DataClient/types.ts b/packages/libs/eda/src/lib/core/api/DataClient/types.ts
@@ -15,7 +15,6 @@ import {
   keyof,
   boolean,
   literal,
-  any,
 } from 'io-ts';
 import { Filter } from '../../types/filter';
 import {
@@ -396,6 +395,11 @@ export const NodeIdList = type({
 // The network types are all built from nodes and links. Currently we've defined specific
 // flavors of networks, called "correlation" networks, that have extra information
 // about them based on their context.
+
+// NOTE tech debt below! The `sourece` and `target` of the NetworkData links should be
+// NodeData, but the backend is sending us strings. At this point it is unlikely the backend
+// will change for a while to fix this issue. If it does, we can simplify the below and let
+// BipartiteNetworkData extend NetworkData.
 const NodeData = intersection([
   type({
     id: string,
@@ -425,7 +429,7 @@ export const NetworkData = type({
 });
 
 const NetworkConfig = partial({
-  variables: any,
+  variables: unknown,
   correlationCoefThreshold: number,
   significanceThreshold: number,
 });

diff --git a/packages/libs/eda/src/lib/core/components/computations/plugins/selfCorrelation.tsx b/packages/libs/eda/src/lib/core/components/computations/plugins/selfCorrelation.tsx
@@ -1,4 +1,3 @@
-import { useMemo } from 'react';
 import { useFindEntityAndVariableCollection } from '../../..';
 import { ComputationConfigProps, ComputationPlugin } from '../Types';
 import { partial } from 'lodash';
@@ -127,11 +126,10 @@ export function SelfCorrelationConfiguration(props: ComputationConfigProps) {
     visualizationId,
   } = props;
 
-  const configuration = computation.descriptor
-    .configuration as SelfCorrelationConfig;
-
   assertComputationWithConfig(computation, SelfCorrelationConfig);
 
+  const { configuration } = computation.descriptor;
+
   const changeConfigHandler = useConfigChangeHandler(
     analysisState,
     computation,
@@ -212,17 +210,11 @@ export function SelfCorrelationConfiguration(props: ComputationConfigProps) {
     </div>
   );
 
-  const correlationMethodSelectorText = useMemo(() => {
-    if (configuration.correlationMethod) {
-      return (
-        CORRELATION_METHODS.find(
-          (method) => method.value === configuration.correlationMethod
-        )?.displayName ?? 'Select a method'
-      );
-    } else {
-      return 'Select a method';
-    }
-  }, [configuration.correlationMethod]);
+  const correlationMethodSelectorText = configuration.correlationMethod
+    ? CORRELATION_METHODS.find(
+        (method) => method.value === configuration.correlationMethod
+      )?.displayName ?? 'Select a method'
+    : 'Select a method';
 
   return (
     <ComputationStepContainer

diff --git a/.../libs/eda/src/lib/core/components/visualizations/implementations/NetworkVisualization.tsx b/.../libs/eda/src/lib/core/components/visualizations/implementations/NetworkVisualization.tsx
@@ -44,7 +44,6 @@ import { FacetedPlotLayout } from '../../layouts/FacetedPlotLayout';
 import { H6 } from '@veupathdb/coreui';
 import { CorrelationConfig } from '../../../types/apps';
 import { LabelPosition } from '@veupathdb/components/lib/plots/Node';
-
 import MultiSelect, {
   Option as NodeLabelProp,
 } from '@veupathdb/components/lib/components/plotControls/MultiSelect';

diff --git a/packages/libs/user-datasets/src/lib/Actions/UserDatasetsActions.ts b/packages/libs/user-datasets/src/lib/Actions/UserDatasetsActions.ts
@@ -12,7 +12,6 @@ import {
   EmptyAction,
   emptyAction,
 } from '@veupathdb/wdk-client/lib/Core/WdkMiddleware';
-import { ServiceError } from '@veupathdb/wdk-client/lib/Service/ServiceError';
 
 import { validateVdiCompatibleThunk } from '../Service';
 
@@ -25,6 +24,7 @@ import {
   UserQuotaMetadata,
   UserDatasetFileListing,
 } from '../Utils/types';
+import { FetchClientError } from '@veupathdb/http-utils';
 
 export type Action =
   | DetailErrorAction
@@ -91,12 +91,12 @@ export const LIST_ERROR_RECEIVED = 'user-dataset/list-error';
 export type ListErrorReceivedAction = {
   type: typeof LIST_ERROR_RECEIVED;
   payload: {
-    error: ServiceError;
+    error: FetchClientError;
   };
 };
 
 export function listErrorReceived(
-  error: ServiceError
+  error: FetchClientError
 ): ListErrorReceivedAction {
   return {
     type: LIST_ERROR_RECEIVED,
@@ -161,11 +161,11 @@ export const DETAIL_ERROR = 'user-datasets/detail-error';
 export type DetailErrorAction = {
   type: typeof DETAIL_ERROR;
   payload: {
-    error: ServiceError;
+    error: FetchClientError;
   };
 };
 
-export function detailError(error: ServiceError): DetailErrorAction {
+export function detailError(error: FetchClientError): DetailErrorAction {
   return {
     type: DETAIL_ERROR,
     payload: {
@@ -217,12 +217,12 @@ export const DETAIL_UPDATE_ERROR = 'user-datasets/detail-update-error';
 export type DetailUpdateErrorAction = {
   type: typeof DETAIL_UPDATE_ERROR;
   payload: {
-    error: ServiceError;
+    error: FetchClientError;
   };
 };
 
 export function detailUpdateError(
-  error: ServiceError
+  error: FetchClientError
 ): DetailUpdateErrorAction {
   return {
     type: DETAIL_UPDATE_ERROR,
@@ -275,12 +275,12 @@ export const DETAIL_REMOVE_ERROR = 'user-datasets/detail-remove-error';
 export type DetailRemoveErrorAction = {
   type: typeof DETAIL_REMOVE_ERROR;
   payload: {
-    error: ServiceError;
+    error: FetchClientError;
   };
 };
 
 export function detailRemoveError(
-  error: ServiceError
+  error: FetchClientError
 ): DetailRemoveErrorAction {
   return {
     type: DETAIL_REMOVE_ERROR,
@@ -485,8 +485,7 @@ export function loadUserDatasetDetailWithoutLoadingIndicator(id: string) {
         };
         return detailReceived(id, transformedResponse, fileListing);
       },
-      (error: ServiceError) =>
-        error.status === 404 ? detailReceived(id) : detailError(error)
+      (error: FetchClientError) => detailError(error)
     )
   );
 }
@@ -632,6 +631,7 @@ function transformVdiResponseToLegacyResponseHelper(
     created,
     status,
     importMessages,
+    visibility,
   } = ud;
   const { quota } = userQuotaMetadata;
   return {
@@ -647,6 +647,7 @@ function transformVdiResponseToLegacyResponseHelper(
       name,
       description: description ?? '',
       summary: summary ?? '',
+      visibility,
     },
     ownerUserId: owner.userId,
     age: Date.now() - Date.parse(created),

diff --git a/packages/libs/user-datasets/src/lib/Components/Detail/UserDatasetDetail.jsx b/packages/libs/user-datasets/src/lib/Components/Detail/UserDatasetDetail.jsx
@@ -1,4 +1,5 @@
 import React from 'react';
+import { Public } from '@material-ui/icons';
 
 import Icon from '@veupathdb/wdk-client/lib/Components/Icon/IconAlt';
 import SaveableTextEditor from '@veupathdb/wdk-client/lib/Components/InputControls/SaveableTextEditor';
@@ -149,8 +150,8 @@ class UserDatasetDetail extends React.Component {
 
     return [
       {
-        className: classify('Name'),
         attribute: this.props.detailsPageTitle,
+        className: classify('Name'),
         value: (
           <SaveableTextEditor
             value={meta.name}
@@ -161,7 +162,6 @@ class UserDatasetDetail extends React.Component {
       },
       {
         attribute: 'Status',
-        className: classify('Status'),
         value: (
           <UserDatasetStatus
             linkToDataset={false}
@@ -173,6 +173,36 @@ class UserDatasetDetail extends React.Component {
           />
         ),
       },
+      {
+        attribute: 'Visibility',
+        value:
+          meta.visibility === 'public' ? (
+            <>
+              {' '}
+              <Public className="Community-visible" /> This{' '}
+              {dataNoun.singular.toLowerCase()} is visible to the community.
+            </>
+          ) : (
+            <>
+              This {dataNoun.singular.toLowerCase()} is only visble to the owner
+              and those they have shared it with.
+            </>
+          ),
+      },
+      !isOwner || !sharedWith || !sharedWith.length
+        ? null
+        : {
+            attribute: 'Shared with',
+            value: (
+              <ul>
+                {sharedWith.map((share, index) => (
+                  <li key={`${share.userDisplayName}-${index}`}>
+                    {share.userDisplayName}
+                  </li>
+                ))}
+              </ul>
+            ),
+          },
       {
         attribute: 'Owner',
         value: isOwner ? 'Me' : owner,
@@ -223,20 +253,6 @@ class UserDatasetDetail extends React.Component {
               quotaSize
             )}`,
           },
-      !isOwner || !sharedWith || !sharedWith.length
-        ? null
-        : {
-            attribute: 'Shared with',
-            value: (
-              <ul>
-                {sharedWith.map((share, index) => (
-                  <li key={`${share.userDisplayName}-${index}`}>
-                    {share.userDisplayName}
-                  </li>
-                ))}
-              </ul>
-            ),
-          },
       !questions || !questions.length || !isInstalled
         ? null
         : {
@@ -298,7 +314,9 @@ class UserDatasetDetail extends React.Component {
         {attributes.map(({ attribute, value, className }, index) => (
           <div
             className={
-              classify('AttributeRow') + (className ? ' ' + className : '')
+              classify('AttributeRow') +
+              ' ' +
+              (className ?? classify(attribute))
             }
             key={index}
           >
@@ -326,7 +344,9 @@ class UserDatasetDetail extends React.Component {
             onPress={this.openSharingModal}
           />
         )}
-        <ThemedDeleteButton buttonText="Delete" onPress={this.handleDelete} />
+        {isOwner ? (
+          <ThemedDeleteButton buttonText="Delete" onPress={this.handleDelete} />
+        ) : null}
       </div>
     );
   }
@@ -617,6 +637,8 @@ class UserDatasetDetail extends React.Component {
       sharingDatasetPending,
       shareSuccessful,
       shareError,
+      updateUserDatasetDetail,
+      enablePublicUserDatasets,
     } = this.props;
     const AllDatasetsLink = this.renderAllDatasetsLink;
     if (!userDataset)
@@ -644,6 +666,8 @@ class UserDatasetDetail extends React.Component {
             sharingDatasetPending={sharingDatasetPending}
             shareSuccessful={shareSuccessful}
             shareError={shareError}
+            updateUserDatasetDetail={updateUserDatasetDetail}
+            enablePublicUserDatasets={enablePublicUserDatasets}
           />
         )}
       </div>

diff --git a/packages/libs/user-datasets/src/lib/Components/Detail/UserDatasetDetail.scss b/packages/libs/user-datasets/src/lib/Components/Detail/UserDatasetDetail.scss
@@ -102,8 +102,8 @@
         flex: 1 1 auto;
       }
     }
-    .UserDatasetDetail-Status {
-      margin-bottom: 1em;
+    .UserDatasetDetail-Owner {
+      margin-top: 1em;
     }
   }
 }