Merge pull request #990 from DouglasNeuroInformatics/upload-feature

Author: joshunrau

apps/api/src/instrument-records/dto/upload-instrument-record.dto.ts

@@ -0,0 +1,14 @@
+import { ValidationSchema } from '@douglasneuroinformatics/libnest/core';
+import type { Json } from '@opendatacapture/schemas/core';
+import { $UploadInstrumentRecordsData } from '@opendatacapture/schemas/instrument-records';
+
+@ValidationSchema($UploadInstrumentRecordsData)
+export class UploadInstrumentRecordsDto {
+  groupId?: string;
+  instrumentId: string;
+  records: {
+    data: Json;
+    date: Date;
+    subjectId: string;
+  }[];
+}

apps/api/src/instrument-records/instrument-records.controller.ts

@@ -10,6 +10,7 @@ import { RouteAccess } from '@/core/decorators/route-access.decorator';
 import type { AppAbility } from '@/core/types';
 
 import { CreateInstrumentRecordDto } from './dto/create-instrument-record.dto';
+import { UploadInstrumentRecordsDto } from './dto/upload-instrument-record.dto';
 import { InstrumentRecordsService } from './instrument-records.service';
 
 @ApiTags('Instrument Records')
@@ -24,6 +25,13 @@ export class InstrumentRecordsController {
     return this.instrumentRecordsService.create(data, { ability });
   }
 
+  @ApiOperation({ summary: 'Upload Multiple Instrument Records' })
+  @Post('upload')
+  @RouteAccess({ action: 'create', subject: 'InstrumentRecord' })
+  upload(@Body() data: UploadInstrumentRecordsDto, @CurrentUser('ability') ability: AppAbility) {
+    return this.instrumentRecordsService.upload(data, { ability });
+  }
+
   @ApiOperation({ summary: 'Get Records for Instrument ' })
   @Get()
   @RouteAccess({ action: 'read', subject: 'InstrumentRecord' })

apps/api/src/instrument-records/instrument-records.service.ts

@@ -1,15 +1,16 @@
 import { yearsPassed } from '@douglasneuroinformatics/libjs';
 import { linearRegression } from '@douglasneuroinformatics/libstats';
-import { Injectable, UnprocessableEntityException } from '@nestjs/common';
+import { Injectable, NotFoundException, UnprocessableEntityException } from '@nestjs/common';
 import type { ScalarInstrument } from '@opendatacapture/runtime-core';
 import type {
   CreateInstrumentRecordData,
   InstrumentRecord,
   InstrumentRecordQueryParams,
   InstrumentRecordsExport,
-  LinearRegressionResults
+  LinearRegressionResults,
+  UploadInstrumentRecordsData
 } from '@opendatacapture/schemas/instrument-records';
-import type { InstrumentRecordModel, Prisma } from '@prisma/generated-client';
+import type { InstrumentRecordModel, Prisma, SessionModel } from '@prisma/generated-client';
 import { isNumber, pickBy } from 'lodash-es';
 
 import { accessibleQuery } from '@/ability/ability.utils';
@@ -19,6 +20,7 @@ import { InstrumentsService } from '@/instruments/instruments.service';
 import { InjectModel } from '@/prisma/prisma.decorators';
 import type { Model } from '@/prisma/prisma.types';
 import { SessionsService } from '@/sessions/sessions.service';
+import type { CreateSubjectDto } from '@/subjects/dto/create-subject.dto';
 import { SubjectsService } from '@/subjects/subjects.service';
 import { VirtualizationService } from '@/virtualization/virtualization.service';
 
@@ -61,7 +63,11 @@ export class InstrumentRecordsService {
 
     await this.subjectsService.findById(subjectId);
     await this.sessionsService.findById(sessionId);
-
+    if (!instrument.validationSchema.safeParse(data).success) {
+      throw new UnprocessableEntityException(
+        `Data received does not pass validation schema of instrument '${instrument.id}'`
+      );
+    }
     return this.instrumentRecordModel.create({
       data: {
         computedMeasures: instrument.measures
@@ -243,4 +249,108 @@ export class InstrumentRecordsService {
     }
     return results;
   }
+
+  async upload(
+    { groupId, instrumentId, records }: UploadInstrumentRecordsData,
+    options?: EntityOperationOptions
+  ): Promise<InstrumentRecordModel[]> {
+    if (groupId) {
+      await this.groupsService.findById(groupId, options);
+    }
+
+    const instrument = await this.instrumentsService.findById(instrumentId);
+    if (instrument.kind === 'SERIES') {
+      throw new UnprocessableEntityException(
+        `Cannot create instrument record for series instrument '${instrument.id}'`
+      );
+    }
+
+    const createdRecordsArray: InstrumentRecordModel[] = [];
+    const createdSessionsArray: SessionModel[] = [];
+
+    try {
+      for (let i = 0; i < records.length; i++) {
+        const { data, date, subjectId } = records[i]!;
+        await this.createSubjectIfNotFound(subjectId);
+
+        const session = await this.sessionsService.create({
+          date: date,
+          groupId: groupId ? groupId : null,
+          subjectData: {
+            id: subjectId
+          },
+          type: 'RETROSPECTIVE'
+        });
+
+        createdSessionsArray.push(session);
+
+        const sessionId = session.id;
+
+        if (!instrument.validationSchema.safeParse(data).success) {
+          throw new UnprocessableEntityException(
+            `Data received for record at index '${i}' does not pass validation schema of instrument '${instrument.id}'`
+          );
+        }
+
+        const createdRecord = await this.instrumentRecordModel.create({
+          data: {
+            computedMeasures: instrument.measures
+              ? this.instrumentMeasuresService.computeMeasures(instrument.measures, data)
+              : null,
+            data,
+            date,
+            group: groupId
+              ? {
+                  connect: { id: groupId }
+                }
+              : undefined,
+            instrument: {
+              connect: {
+                id: instrumentId
+              }
+            },
+            session: {
+              connect: {
+                id: sessionId
+              }
+            },
+            subject: {
+              connect: {
+                id: subjectId
+              }
+            }
+          }
+        });
+
+        createdRecordsArray.push(createdRecord);
+      }
+    } catch (err) {
+      await this.instrumentRecordModel.deleteMany({
+        where: {
+          id: {
+            in: createdRecordsArray.map((record) => record.id)
+          }
+        }
+      });
+      await this.sessionsService.deleteByIds(createdSessionsArray.map((session) => session.id));
+      throw err;
+    }
+
+    return createdRecordsArray;
+  }
+
+  private async createSubjectIfNotFound(subjectId: string) {
+    try {
+      await this.subjectsService.findById(subjectId);
+    } catch (exception) {
+      if (exception instanceof NotFoundException) {
+        const addedSubject: CreateSubjectDto = {
+          id: subjectId
+        };
+        await this.subjectsService.create(addedSubject);
+      } else {
+        throw exception;
+      }
+    }
+  }
 }

apps/api/src/sessions/sessions.service.ts

@@ -56,6 +56,23 @@ export class SessionsService {
     }))!;
   }
 
+  async deleteById(id: string, { ability }: EntityOperationOptions = {}) {
+    return this.sessionModel.delete({
+      where: { AND: [accessibleQuery(ability, 'delete', 'Session')], id }
+    });
+  }
+
+  async deleteByIds(ids: string[], { ability }: EntityOperationOptions = {}) {
+    return this.sessionModel.deleteMany({
+      where: {
+        AND: [accessibleQuery(ability, 'delete', 'Session')],
+        id: {
+          in: ids
+        }
+      }
+    });
+  }
+
   async findById(id: string, { ability }: EntityOperationOptions = {}) {
     const session = await this.sessionModel.findFirst({
       where: { AND: [accessibleQuery(ability, 'read', 'Session')], id }

apps/web/src/Routes.tsx

@@ -13,6 +13,7 @@ import { datahubRoute } from './features/datahub';
 import { groupRoute } from './features/group';
 import { instrumentsRoute } from './features/instruments';
 import { sessionRoute } from './features/session';
+import { uploadRoute } from './features/upload';
 import { userRoute } from './features/user';
 import { DisclaimerProvider } from './providers/DisclaimerProvider';
 import { WalkthroughProvider } from './providers/WalkthroughProvider';
@@ -45,7 +46,8 @@ const protectedRoutes: RouteObject[] = [
       groupRoute,
       instrumentsRoute,
       sessionRoute,
-      userRoute
+      userRoute,
+      uploadRoute
     ]
   }
 ];

apps/web/src/components/Sidebar/Sidebar.tsx

@@ -13,7 +13,6 @@ import { useAppStore } from '@/store';
 import { NavButton } from '../NavButton';
 import { UserDropup } from '../UserDropup';
 
-// eslint-disable-next-line max-lines-per-function
 export const Sidebar = () => {
   const navItems = useNavItems();
   const currentSession = useAppStore((store) => store.currentSession);

apps/web/src/features/about/components/TimeValue.tsx

@@ -9,6 +9,7 @@ export type TimeValueProps = {
 
 export const TimeValue = ({ value }: TimeValueProps) => {
   const format = useCallback((uptime: number) => {
+    // eslint-disable-next-line prefer-const
     let { days, hours, minutes, seconds } = parseDuration(uptime * 1000);
     hours += days * 24;
     return [hours, minutes, seconds].map((value) => (value < 10 ? '0' + value : value)).join(':');

apps/web/src/features/admin/pages/ManageGroupsPage.tsx

@@ -1,11 +1,12 @@
-import { useEffect, useState } from 'react';
+import { useState } from 'react';
 
 import { Button, ClientTable, Heading, SearchBar, Sheet } from '@douglasneuroinformatics/libui/components';
 import { useTranslation } from '@douglasneuroinformatics/libui/hooks';
 import type { Group } from '@opendatacapture/schemas/group';
 import { Link } from 'react-router-dom';
 
 import { PageHeader } from '@/components/PageHeader';
+import { useSearch } from '@/hooks/useSearch';
 
 import { useDeleteGroupMutation } from '../hooks/useDeleteGroupMutation';
 import { useGroupsQuery } from '../hooks/useGroupsQuery';
@@ -15,12 +16,7 @@ export const ManageGroupsPage = () => {
   const groupsQuery = useGroupsQuery();
   const deleteGroupMutation = useDeleteGroupMutation();
   const [selectedGroup, setSelectedGroup] = useState<Group | null>(null);
-  const [groups, setGroups] = useState<Group[]>(groupsQuery.data ?? []);
-  const [searchTerm, setSearchTerm] = useState('');
-
-  useEffect(() => {
-    setGroups((groupsQuery.data ?? []).filter((group) => group.name.toLowerCase().includes(searchTerm.toLowerCase())));
-  }, [groupsQuery.data, searchTerm]);
+  const { filteredData, searchTerm, setSearchTerm } = useSearch(groupsQuery.data ?? [], 'name');
 
   return (
     <Sheet open={Boolean(selectedGroup)} onOpenChange={() => setSelectedGroup(null)}>
@@ -69,7 +65,7 @@ export const ManageGroupsPage = () => {
             label: t('common.groupType')
           }
         ]}
-        data={groups}
+        data={filteredData}
         entriesPerPage={15}
         minRows={15}
         onEntryClick={setSelectedGroup}

apps/web/src/features/admin/pages/ManageUsersPage.tsx

@@ -1,4 +1,4 @@
-import { useEffect, useState } from 'react';
+import { useState } from 'react';
 
 import { snakeToCamelCase } from '@douglasneuroinformatics/libjs';
 import { Button, ClientTable, Heading, SearchBar, Sheet } from '@douglasneuroinformatics/libui/components';
@@ -7,24 +7,19 @@ import type { User } from '@opendatacapture/schemas/user';
 import { Link } from 'react-router-dom';
 
 import { PageHeader } from '@/components/PageHeader';
+import { useSearch } from '@/hooks/useSearch';
 import { useAppStore } from '@/store';
 
 import { useDeleteUserMutation } from '../hooks/useDeleteUserMutation';
 import { useUsersQuery } from '../hooks/useUsersQuery';
 
-// eslint-disable-next-line max-lines-per-function
 export const ManageUsersPage = () => {
   const currentUser = useAppStore((store) => store.currentUser);
   const { t } = useTranslation();
   const usersQuery = useUsersQuery();
   const deleteUserMutation = useDeleteUserMutation();
-  const [users, setUsers] = useState<User[]>(usersQuery.data ?? []);
   const [selectedUser, setSelectedUser] = useState<null | User>(null);
-  const [searchTerm, setSearchTerm] = useState('');
-
-  useEffect(() => {
-    setUsers((usersQuery.data ?? []).filter((user) => user.username.toLowerCase().includes(searchTerm.toLowerCase())));
-  }, [usersQuery.data, searchTerm]);
+  const { filteredData, searchTerm, setSearchTerm } = useSearch(usersQuery.data ?? [], 'username');
 
   const currentUserIsSelected = selectedUser?.username === currentUser?.username;
 
@@ -76,7 +71,7 @@ export const ManageUsersPage = () => {
             label: t('common.basePermissionLevel')
           }
         ]}
-        data={users}
+        data={filteredData}
         entriesPerPage={15}
         minRows={15}
         onEntryClick={setSelectedUser}

apps/web/src/features/datahub/components/MasterDataTable.tsx

@@ -15,7 +15,7 @@ export const MasterDataTable = ({ data, onSelect }: MasterDataTableProps) => {
     <ClientTable<Subject>
       columns={[
         {
-          field: (subject) => removeSubjectIdScope(subject.id).slice(0, 7),
+          field: (subject) => removeSubjectIdScope(subject.id).slice(0, 9),
           label: t('datahub.index.table.subject')
         },
         {