Merge pull request #554 from bcgsc/release/v6.31.0

Release/v6.31.0

Author: kttkjl

app/components/PrintTable/index.tsx

@@ -20,6 +20,8 @@ export type PrintTableProps = {
   collapseableCols?: string[];
   noRowsText?: string;
   fullWidth?: boolean;
+  outerRowOrderByInternalCol?: string[];
+  innerRowOrderByInternalCol?: string[];
 };
 
 /**
@@ -33,6 +35,8 @@ function PrintTable({
   noRowsText = '',
   collapseableCols = null,
   fullWidth = false,
+  outerRowOrderByInternalCol = null,
+  innerRowOrderByInternalCol = null,
 }: PrintTableProps): JSX.Element {
   const sortedColDefs = useMemo(() => columnDefs
     .filter((col) => (col.headerName && col.hide !== true && col.headerName !== 'Actions'))
@@ -84,12 +88,63 @@ function PrintTable({
       const colIdxsToCombine = {};
       const rowIdxsToSkip = {};
       const rowIdxsToExpand = {};
+      let outerRowsRank = {};
+
+      if (outerRowOrderByInternalCol) {
+        outerRowsRank = data.reduce((acc, row) => {
+          const rowkey = JSON.stringify(collapseableCols.map((val) => row[val]));
+          if (!acc[rowkey]) {
+            acc[rowkey] = {};
+          }
+          Object.keys(row).forEach((key) => {
+            if (outerRowOrderByInternalCol.includes(key)) {
+              if (!acc[rowkey][key]) {
+                acc[rowkey][key] = [];
+              }
+              acc[rowkey][key].push(row[key]);
+            }
+          });
+          return acc;
+        }, {});
+
+        Object.keys(outerRowsRank).forEach((key) => {
+          Object.keys(outerRowsRank[key]).forEach((subkey) => {
+            outerRowsRank[key][subkey] = JSON.stringify(outerRowsRank[key][subkey].sort()); // Sort and stringify
+          });
+        });
+      }
 
       (collapseableCols?.length > 0 ? [...data].sort((aRow, bRow) => {
-        const aKey = collapseableCols.map((val) => aRow[val]);
-        const bKey = collapseableCols.map((val) => bRow[val]);
-        if (aKey === bKey) return 0;
-        return aKey > bKey ? 1 : -1;
+        const aKey = JSON.stringify(collapseableCols.map((val) => aRow[val]));
+        const bKey = JSON.stringify(collapseableCols.map((val) => bRow[val]));
+        // ordering inner rows (rows with matching aKey/bKey)
+        if (aKey === bKey) {
+          // order by 'innerRowOrderByInternalCol' index 0 if possible, then index 1, etc
+          if (innerRowOrderByInternalCol) {
+            for (let i = 0; i < innerRowOrderByInternalCol.length; i++) {
+              const col = innerRowOrderByInternalCol[i];
+              // if the current column values are equal, move to next column
+              // otherwise return rank based on these columns
+              if (!(aRow[col] === bRow[col])) {
+                return aRow[col] > bRow[col] ? 1 : -1;
+              }
+            }
+          }
+          return 0;
+        }
+        // ordering outer rows (rows with different aKey/bKey)
+        if (outerRowOrderByInternalCol) {
+          // order by 'outerRowOrderByInternalCol' if possible, then by outer row key if necessary
+          for (let i = 0; i < outerRowOrderByInternalCol.length; i++) {
+            const rankA = outerRowsRank[aKey][outerRowOrderByInternalCol[i]];
+            const rankB = outerRowsRank[bKey][outerRowOrderByInternalCol[i]];
+            if (!(rankA === rankB)) {
+              return rankA > rankB ? 1 : -1;
+            }
+          }
+          return aKey > bKey ? 1 : -1;
+        }
+        return 0;
       }) : data).forEach((dataRow, rowIdx) => {
         const rowData = [];
         currRowKey = '';
@@ -178,7 +233,7 @@ function PrintTable({
       }
     }
     return component;
-  }, [sortedColDefs, noRowsText, data, collapseableCols]);
+  }, [sortedColDefs, noRowsText, data, collapseableCols, outerRowOrderByInternalCol, innerRowOrderByInternalCol]);
 
   const tableId = useMemo(() => {
     if (data?.length) {

app/components/SignatureCard/__tests__/SignatureCard.test.tsx

@@ -1,14 +1,21 @@
 import React from 'react';
-import { render, screen, fireEvent } from '@testing-library/react';
+import {
+  render, screen, fireEvent, waitFor,
+} from '@testing-library/react';
 
 import ReportContext from '@/context/ReportContext';
 import SignatureCard, { SignatureType } from '..';
-import { mockNullData, mockNullObjectData, mockObjectData } from './mockData';
+import {
+  mockNullData, mockNullObjectData, mockObjectData, mockReportData,
+} from './mockData';
+
+jest.mock('@/services/SnackbarUtils');
+jest.mock('@/services/api');
 
 describe('SignatureCard', () => {
   test('Author and sign button are visible', async () => {
     render(
-      <ReportContext.Provider value={{ canEdit: true, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: true, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Author"
           type="author"
@@ -23,7 +30,7 @@ describe('SignatureCard', () => {
 
   test('Sign button is not visible without edit permissions', async () => {
     render(
-      <ReportContext.Provider value={{ canEdit: false, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: false, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Author"
           type="author"
@@ -36,25 +43,27 @@ describe('SignatureCard', () => {
   });
 
   test('Sign button calls onClick', async () => {
-    const handleClick = jest.fn();
+    const handleSign = jest.fn();
     render(
-      <ReportContext.Provider value={{ canEdit: true, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: true, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Author"
           type="author"
           signatures={null}
-          onClick={handleClick}
+          onClick={handleSign}
         />
       </ReportContext.Provider>,
     );
     fireEvent.click(await screen.findByRole('button', { name: 'Sign' }));
 
-    expect(handleClick).toHaveBeenCalledTimes(1);
+    waitFor(() => {
+      expect(handleSign).toHaveBeenCalledTimes(1);
+    });
   });
 
   test('Sign button is visible when reviewerSignature is null', async () => {
     render(
-      <ReportContext.Provider value={{ canEdit: true, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: true, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Reviewer"
           type="reviewer"
@@ -69,7 +78,7 @@ describe('SignatureCard', () => {
 
   test('Sign button is visible when reviewerSignature has null data', async () => {
     render(
-      <ReportContext.Provider value={{ canEdit: true, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: true, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Reviewer"
           type="reviewer"
@@ -84,7 +93,7 @@ describe('SignatureCard', () => {
 
   test('Reviewer name & remove signature button are visible', async () => {
     render(
-      <ReportContext.Provider value={{ canEdit: true, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: true, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Reviewer"
           type="reviewer"
@@ -94,13 +103,15 @@ describe('SignatureCard', () => {
       </ReportContext.Provider>,
     );
 
-    expect(screen.queryByRole('button', { name: 'Sign' })).not.toBeInTheDocument();
+    waitFor(() => {
+      expect(screen.queryByRole('button', { name: 'Sign' })).not.toBeInTheDocument();
+    });
     expect(await screen.findByRole('button', { name: /^((?!Sign).)*$/ })).toBeInTheDocument();
   });
 
   test('No buttons are visible in print view', async () => {
     render(
-      <ReportContext.Provider value={{ canEdit: true, report: null, setReport: () => {} }}>
+      <ReportContext.Provider value={{ canEdit: true, report: mockReportData, setReport: () => {} }}>
         <SignatureCard
           title="Reviewer"
           type="reviewer"

app/components/SignatureCard/__tests__/mockData.ts

@@ -48,8 +48,39 @@ const mockObjectData = {
   reviewerSignedAt: '2020',
 };
 
+const mockReportData = {
+  ident: 'mockIdent',
+  createdAt: '2020',
+  updatedAt: '2020',
+  alternateIdentifier: null,
+  pediatricIds: null,
+  analysisStartedAt: null,
+  biopsyName: null,
+  createdBy: null,
+  expression_matrix: null,
+  kbVersion: null,
+  patientId: null,
+  patientInformation: null,
+  ploidy: null,
+  projects: null,
+  reportVersion: null,
+  sampleInfo: null,
+  state: null,
+  subtyping: null,
+  template: null,
+  tumourContent: null,
+  type: null,
+  users: null,
+  oncotreeTumourType: null,
+  kbDiseaseMatch: null,
+  m1m2Score: null,
+  captiv8Score: null,
+  appendix: null,
+};
+
 export {
   mockNullData,
   mockNullObjectData,
   mockObjectData,
+  mockReportData,
 };

app/components/SignatureCard/index.tsx

@@ -1,17 +1,21 @@
 import React, {
   useState, useEffect, useMemo,
+  useCallback,
 } from 'react';
 import {
   Paper,
   Typography,
   IconButton,
   Button,
 } from '@mui/material';
+import api from '@/services/api';
 import GestureIcon from '@mui/icons-material/Gesture';
 import RemoveCircleIcon from '@mui/icons-material/RemoveCircle';
-
+import snackbar from '@/services/SnackbarUtils';
 import { UserType } from '@/common';
 import useReport from '@/hooks/useReport';
+import useResource from '@/hooks/useResource';
+import useSecurity from '@/hooks/useSecurity';
 import { formatDate } from '@/utils/date';
 import { SignatureType, SignatureUserType } from './types';
 
@@ -24,7 +28,7 @@ const NON_BREAKING_SPACE = '\u00A0';
 export type SignatureCardProps = {
   title: string;
   signatures: SignatureType;
-  onClick: (isSigned: boolean, type: string) => void;
+  onClick: (isSigned: boolean, updatedSignature: SignatureType) => void;
   type: SignatureUserType;
   isPrint?: boolean;
 };
@@ -36,28 +40,75 @@ const SignatureCard = ({
   type,
   isPrint = false,
 }: SignatureCardProps): JSX.Element => {
-  const { canEdit } = useReport();
+  const { reportAssignmentAccess: canAddSignatures } = useResource();
+  const { canEdit, report, setReport } = useReport();
+  const { userDetails } = useSecurity();
+
   const [userSignature, setUserSignature] = useState<UserType>();
+  const [role, setRole] = useState('');
 
   useEffect(() => {
     if (signatures && type) {
       if (type === 'author') {
         setUserSignature(signatures.authorSignature);
+        setRole('author');
       } else if (type === 'reviewer') {
         setUserSignature(signatures.reviewerSignature);
+        setRole('reviewer');
       } else if (type === 'creator') {
         setUserSignature(signatures.creatorSignature);
+        setRole('bioinformatician');
+      }
+    }
+  }, [signatures, type, setRole]);
+
+  const handleSign = useCallback(async () => {
+    let newReport = null;
+
+    // Assign user
+    try {
+      newReport = await api.post(
+        `/reports/${report.ident}/user`,
+        // Hardcode analyst role here because report does not accept 'author'
+        { user: userDetails.ident, role: 'analyst' },
+        {},
+      ).request();
+    } catch (e) {
+      // If user already assigned, silent fail this add
+      if (e.content?.status !== 409) {
+        snackbar.error('Error assigning user to report: ', e.message);
       }
     }
-  }, [signatures, type]);
 
-  const handleSign = () => {
-    onClick(true, type);
-  };
+    // Do signature
+    try {
+      const newSignature = await api.put(
+        `/reports/${report.ident}/signatures/sign/${role}`,
+        {},
+      ).request();
 
-  const handleRevoke = () => {
-    onClick(false, type);
-  };
+      if (newReport) {
+        setReport(newReport);
+      }
+      onClick(true, newSignature);
+      snackbar.success('User assigned to report');
+    } catch (err) {
+      snackbar.error(`Error adding user: ${err}`);
+    }
+  }, [onClick, report.ident, role, setReport, userDetails.ident]);
+
+  const handleRevoke = useCallback(async () => {
+    try {
+      const newSignature = await api.put(
+        `/reports/${report.ident}/signatures/revoke/${role}`,
+        {},
+      ).request();
+      onClick(false, newSignature);
+      snackbar.success('User removed from report');
+    } catch (err) {
+      snackbar.error(`Error removing user: ${err}`);
+    }
+  }, [onClick, report.ident, role]);
 
   const renderDate = useMemo(() => {
     if (signatures?.ident) {
@@ -129,7 +180,7 @@ const SignatureCard = ({
             {userSignature.lastName}
           </Typography>
         )}
-        {!userSignature?.ident && canEdit && (
+        {!userSignature?.ident && (canEdit || canAddSignatures) && (
           <Button
             onClick={handleSign}
             variant="text"

app/context/ResourceContext/index.tsx

@@ -25,15 +25,27 @@ const REPORTS_BLOCK = [];
 const ADMIN_ACCESS = ['admin'];
 const ADMIN_BLOCK = [...ALL_ROLES, ...NO_GROUP_MATCH];
 
+/**
+ * Checks user permissions based on the groups they are assigned, nothing report-specific
+ */
 const useResources = (): ResourceContextType => {
   const { userDetails: { groups } } = useSecurity();
 
   const [germlineAccess, setGermlineAccess] = useState(false);
   const [reportsAccess, setReportsAccess] = useState(false);
+  /**
+   * Is the user allowed to edit the report
+   */
   const [reportEditAccess, setReportEditAccess] = useState(false);
+  /**
+   * Is the user allowed to assign users to the report
+   */
   const [reportAssignmentAccess, setReportAssignmentAccess] = useState(false);
   const [adminAccess, setAdminAccess] = useState(false);
   const [managerAccess, setManagerAccess] = useState(false);
+  /**
+   * Is the user allowed to see the settings page
+   */
   const [reportSettingAccess, setReportSettingAccess] = useState(false);
   const [unreviewedAccess, setUnreviewedAccess] = useState(false);
   const [nonproductionAccess, setNonproductionAccess] = useState(false);