Merge pull request #281 from bcgsc/release/v6.16.0

Release/v6.16.0

Author: kttkjl

app/common.d.ts

@@ -104,36 +104,15 @@ type GeneType = {
   tumourSuppressor: boolean;
 };
 
-type KbMatchVariantType = {
-  gene: GeneType;
-  transcript: string;
-  proteinChange: string;
-  chromosome: string;
-  startPosition: number;
-  endPosition: number;
-  refSeq: string;
-  altSeq: string;
-  zygosity: string;
-  tumourAltCount: number;
-  tumourRefCount: number;
-  tumourDepth: number;
-  rnaAltCount: number;
-  rnaRefCount: number;
-  rnaDepth: number;
-  normalAltCount: number;
-  normalRefCount: number;
-  normalDepth: number;
-  hgvsProtein: string;
-  hgvsCds: string;
-  hgvsGenomic: string;
-  ncbiBuild: string;
-  germline: boolean;
-  tumourAltCopies: number;
-  tumourRefCopies: number;
-  library: string;
-} & RecordDefaults;
+type VariantType = keyof VariantMap;
 
-type KbMatchType = {
+type VariantMap = {
+  'cnv': CopyNumberType
+  'mut': SmallMutationType
+  'sv': StructuralVariantType
+};
+
+type KbMatchType<T extends VariantType = VariantType> = {
   category: string;
   approvedTherapy: boolean;
   kbVariant: string;
@@ -148,7 +127,7 @@ type KbMatchType = {
   iprEvidenceLevel: string;
   matchedCancer: boolean;
   pmidRef: string;
-  variantType: string;
+  variantType: T;
   kbVariantId: string;
   kbStatementId: string;
   kbData: {
@@ -157,7 +136,7 @@ type KbMatchType = {
   externalSource: string;
   externalStatementId: string;
   reviewStatus: string;
-  variant: KbMatchVariantType;
+  variant: VariantMap[T];
 } & RecordDefaults;
 
 type CopyNumberType = {
@@ -185,8 +164,8 @@ type StructuralVariantType = {
   exon1: string | null;
   exon2: string | null;
   frame: string | null;
-  gene1: Record<string, unknown> | null;
-  gene2: Record<string, unknown> | null;
+  gene1: GeneType | null;
+  gene2: GeneType | null;
   highQuality: boolean;
   kbMatches: null | KbMatchType[];
   mavis_product_id: number | null;
@@ -202,11 +181,13 @@ type SmallMutationType = {
   altSeq: string | null;
   chromosome: number | null;
   endPosition: number | null;
-  gene: Record<string, unknown>;
+  gene: GeneType;
   germline: string | null;
   hgvsCds: string | null;
+  hgvsGenomic: string | null;
   hgvsProtein: string | null;
   kbMatches: KbMatchType[];
+  library: string | null;
   ncbiBuild: string | null;
   normalAltCount: number | null;
   normalDepth: number | null;
@@ -218,8 +199,10 @@ type SmallMutationType = {
   rnaRefCount: number | null;
   startPosition: number | null;
   transcript: string | null;
+  tumourAltCopies: number | null;
   tumourAltCount: number | null;
   tumourDepth: number | null;
+  tumourRefCopies: number | null;
   tumourRefCount: number | null;
   zygosity: string | null;
 } & RecordDefaults;

app/components/PrintTable/index.scss

@@ -4,6 +4,10 @@
   border-collapse: collapse;
   margin: 8px;
 
+  &--full-width {
+    width: 100%;
+  }
+
   &__header {
     font-size: 9pt;
     text-align: left;

app/components/PrintTable/index.tsx

@@ -15,6 +15,7 @@ export type PrintTableProps = {
   /* string of fieldNames for columns to be collapsed */
   collapseableCols?: string[];
   noRowsText?: string;
+  fullWidth?: boolean;
 };
 
 /**
@@ -27,6 +28,7 @@ const PrintTable = ({
   order = [],
   noRowsText = '',
   collapseableCols = null,
+  fullWidth = false,
 }: PrintTableProps): JSX.Element => {
   const sortedColDefs = useMemo(() => columnDefs
     .filter((col) => (col.headerName && col.hide !== true && col.headerName !== 'Actions'))
@@ -177,7 +179,7 @@ const PrintTable = ({
   return (
     <div className="table-container">
       {Boolean(columnDefs.length) && (
-        <table className="table">
+        <table className={`table ${fullWidth ? 'table--full-width' : ''}`}>
           <thead className="table__header">
             <tr>
               {sortedColDefs.map((col) => (

app/services/api/ApiCallSet.tsx

@@ -19,7 +19,10 @@ class ApiCallSet {
     this.calls.forEach((controller) => controller.abort());
   }
 
-  async request(): Promise<RequestReturnType[]> {
+  async request(settled = false): Promise<PromiseSettledResult<RequestReturnType>[] | RequestReturnType[]> {
+    if (settled) {
+      return Promise.allSettled(this.calls.map((call) => call.request()));
+    }
     return Promise.all(this.calls.map((call) => call.request()));
   }
 }

app/views/AdminView/components/Users/components/AddEditUserDialog/index.tsx

@@ -18,6 +18,7 @@ import {
 import { useForm, Controller } from 'react-hook-form';
 import api, { ApiCallSet } from '@/services/api';
 import { UserType, GroupType } from '@/common';
+import snackbar from '@/services/SnackbarUtils';
 import {
   ProjectType,
 } from '../../../../types';
@@ -124,43 +125,62 @@ const AddEditUserDialog = ({
         username,
         type,
       };
-      // User Section
-      const addEditResp = editData
-        ? await api.put(`/user/${editData.ident}`, userReq).request()
-        : await api.post('/user', userReq).request();
 
-      // Project Section
-      if (dirtyFields.projects) {
-        const existingProjects = editData.projects.map(({ ident }) => ident);
+      try {
+        const addEditResp = editData
+          ? await api.put(`/user/${editData.ident}`, userReq).request()
+          : await api.post('/user', userReq).request();
 
-        const toAddProjs = projects.filter((projectId) => !existingProjects.includes(projectId));
-        const toRemoveProjs = existingProjects.filter((projectId) => !projects.includes(projectId));
+        // Project Section
+        if (dirtyFields.projects && editData) {
+          const existingProjects = editData.projects.map(({ ident }) => ident);
 
-        const callSet = new ApiCallSet([
-          ...toAddProjs.map((projectId) => api.post(`/project/${projectId}/user`, { user: addEditResp.ident }, {})),
-          ...toRemoveProjs.map((projectId) => api.del(`/project/${projectId}/user`, { user: addEditResp.ident }, {})),
-        ]);
-        await callSet.request();
-      }
+          const toAddProjs = projects.filter((projectId) => !existingProjects.includes(projectId));
+          const toRemoveProjs = existingProjects.filter((projectId) => !projects.includes(projectId));
+
+          const callSet = new ApiCallSet([
+            ...toAddProjs.map((projectId) => api.post(`/project/${projectId}/user`, { user: addEditResp.ident }, {})),
+            ...toRemoveProjs.map((projectId) => api.del(`/project/${projectId}/user`, { user: addEditResp.ident }, {})),
+          ]);
+          try {
+            await callSet.request();
+          } catch (e) {
+            throw { ...e, errorType: 'project' };
+          }
+        }
 
-      // Groups Section
-      if (dirtyFields.groups) {
-        const existingGroups = editData.groups.map(({ ident }) => ident);
+        // Groups Section
+        if (dirtyFields.groups && editData) {
+          const existingGroups = editData.groups.map(({ ident }) => ident);
 
-        const toAddGroups = groups.filter((groupId) => !existingGroups.includes(groupId));
-        const toRemoveGroups = existingGroups.filter((groupId) => !groups.includes(groupId));
+          const toAddGroups = groups.filter((groupId) => !existingGroups.includes(groupId));
+          const toRemoveGroups = existingGroups.filter((groupId) => !groups.includes(groupId));
 
-        const callSet = new ApiCallSet([
-          ...toAddGroups.map((groupId) => api.post(`/user/group/${groupId}/member`, { user: addEditResp.ident }, {})),
-          ...toRemoveGroups.map((groupId) => api.del(`/user/group/${groupId}/member`, { user: addEditResp.ident }, {})),
-        ]);
-        await callSet.request();
-      }
+          const callSet = new ApiCallSet([
+            ...toAddGroups.map((groupId) => api.post(`/user/group/${groupId}/member`, { user: addEditResp.ident }, {})),
+            ...toRemoveGroups.map((groupId) => api.del(`/user/group/${groupId}/member`, { user: addEditResp.ident }, {})),
+          ]);
+          try {
+            await callSet.request();
+          } catch (e) {
+            throw { ...e, errorType: 'group' };
+          }
+        }
+        addEditResp.projects = projectOptions.filter(({ ident }) => projects.includes(ident));
+        addEditResp.groups = groupOptions.filter(({ ident }) => groups.includes(ident));
 
-      addEditResp.projects = projectOptions.filter(({ ident }) => projects.includes(ident));
-      addEditResp.groups = groupOptions.filter(({ ident }) => groups.includes(ident));
-      onClose(addEditResp);
+        snackbar.success(`User successfully ${editData ? 'updated' : 'created'}`);
+        onClose(addEditResp);
+      } catch (e) {
+        if (e.errorType) {
+          snackbar.error(`Error setting ${e.errorType}s related to user`);
+        } else {
+          snackbar.error(`Error ${editData ? 'editing' : 'creating'} user`);
+        }
+        console.error(e);
+      }
     }
+
     onClose(null);
   }, [dirtyFields, editData, onClose, projectOptions, groupOptions]);
 

app/views/AdminView/components/Users/index.tsx

@@ -56,13 +56,11 @@ const Users = (): JSX.Element => {
         const newUsers = [...users];
         newUsers[userIndex] = newData;
         setUsers(newUsers);
-        snackbar.enqueueSnackbar('User edited');
       } else {
         setUsers((prevVal) => [...prevVal, newData]);
-        snackbar.enqueueSnackbar('User added');
       }
     }
-  }, [snackbar, users]);
+  }, [users]);
 
   return (
     <div className="admin-table__container">

app/views/PrintView/index.tsx

@@ -33,8 +33,8 @@ const reducer = (state, action) => {
   switch (action.type) {
     case 'summary':
       return { ...state, summary: true };
-    case 'analyst':
-      return { ...state, analyst: true };
+    case 'analyst-comments':
+      return { ...state, 'analyst-comments': true };
     case 'pathway':
       return { ...state, pathway: true };
     case 'therapeutic':
@@ -46,7 +46,7 @@ const reducer = (state, action) => {
     default:
       return {
         summary: false,
-        analyst: false,
+        'analyst-comments': false,
         pathway: false,
         therapeutic: false,
         slides: false,
@@ -63,7 +63,7 @@ const Print = (): JSX.Element => {
   const [report, setReport] = useState<ReportType>(null);
   const [reportSectionsLoaded, dispatch] = useReducer(reducer, {
     summary: false,
-    analyst: false,
+    'analyst-comments': false,
     pathway: false,
     therapeutic: false,
     slides: false,

app/views/ReportView/components/AnalystComments/index.tsx

@@ -25,13 +25,15 @@ import './index.scss';
 type AnalystCommentsProps = {
   isPrint?: boolean;
   isSigned?: boolean;
+  loadedDispatch?: (type: Record<'type', string>) => void;
 } & WithLoadingInjectedProps;
 
 const AnalystComments = ({
   isPrint = false,
   isLoading,
   isSigned,
   setIsLoading,
+  loadedDispatch,
 }: AnalystCommentsProps): JSX.Element => {
   const { report } = useContext(ReportContext);
   const { setIsSigned } = useContext(ConfirmContext);
@@ -64,11 +66,14 @@ const AnalystComments = ({
           snackbar.error(`Network error: ${err}`);
         } finally {
           setIsLoading(false);
+          if (loadedDispatch) {
+            loadedDispatch({ type: 'analyst-comments' });
+          }
         }
       };
       getData();
     }
-  }, [report, setIsLoading]);
+  }, [report, setIsLoading, loadedDispatch]);
 
   const handleSign = useCallback(async (signed: boolean, role: SignatureUserType) => {
     let newSignature;

app/views/ReportView/components/GenomicSummary/index.scss

@@ -1,32 +1,18 @@
-.genomic-summary {
-  margin: 20px auto;
-  padding: 0 20px;
-
-  @media print {
-    margin: 0 auto;
-  }
-  
+// Shared styling between both versions
+.genomic-summary, .genomic-summary--print {
   &__patient-information {
     margin: 0 0 32px 0;
 
-    &-title {
-      @media print {
-        margin: 0 0 8px;
-      }
-    }
-
     &-content {
       padding: 0 16px;
     }
   }
 
-  &__analysis-summary {
+  &__tumour-summary, &__alterations {
     margin: 0 0 32px 0;
+  }
 
-    @media print {
-      margin: 32px 0;
-    }
-
+  &__analysis-summary {
     &-title {
       margin: 8px 0;
     }
@@ -35,12 +21,20 @@
       padding: 0 16px;
     }
   }
+}
 
-  &__tumour-summary {
-    margin: 0 0 32px 0;
-  }
+.genomic-summary {
+  margin: 20px auto;
+  padding: 0 20px;
+}
 
-  &__alterations {
-    margin: 0 0 32px 0;
+.genomic-summary--print {
+  margin: 0 auto;
+  padding: 0 20px;
+
+  &__patient-information {
+    &-title {
+      margin: 0 0 8px;
+    }
   }
-}
+}