Allow textarea with CPL syntax to be previewed

package.json

@@ -61,6 +61,7 @@
     "test:watch": "yarn run jest -- --watch",
     "updateAPI": "openapi-generator-cli generate -i http://localhost:9090/v3/api-docs -g typescript-axios -o src/main/webapp/app/shared/api/generated/curation --type-mappings set=Array",
     "updateCoreAPI": "curl http://localhost:8000/oncokb/api/v1/v2/api-docs?group=Private%20APIs | jq '.definitions.ResponseEntity.properties.statusCode.enum |= unique' > /tmp/updateCoreAPI.json && openapi-generator-cli generate -i /tmp/updateCoreAPI.json -g typescript-axios -o src/main/webapp/app/shared/api/generated/core --type-mappings List=any",
+    "updateDefaultCoreAPI": "curl 'http://localhost:8080/app/api/v1/v2/api-docs?group=default' > /tmp/updateDefaultCoreAPI.json && openapi-generator-cli generate -i /tmp/updateDefaultCoreAPI.json -g typescript-axios -o src/main/webapp/app/shared/api/generated/defaultCore --type-mappings List=any",
     "wdio": "cross-env TS_NODE_PROJECT=src/test/javascript/tsconfig.json wdio run ./wdio.conf.ts",
     "webapp:build": "yarn run clean-www && yarn run webapp:build:dev --",
     "webapp:build:dev": "webpack --config webpack/webpack.dev.js --env stats=minimal",

src/main/java/org/mskcc/oncokb/curation/config/security/SecurityConfigurationOAuth.java

@@ -94,6 +94,7 @@ public SecurityFilterChain oauthFilterChain(HttpSecurity http, MvcRequestMatcher
                     .requestMatchers(mvc.pattern("/websocket/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER)
                     .requestMatchers(mvc.pattern("/api/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER, AuthoritiesConstants.ADMIN)
                     .requestMatchers(mvc.pattern("/legacy-api/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER, AuthoritiesConstants.ADMIN)
+                    .requestMatchers(mvc.pattern("/core/**")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER, AuthoritiesConstants.ADMIN)
                     .requestMatchers(mvc.pattern("/v3/api-docs/**")).hasAuthority(AuthoritiesConstants.ADMIN)
                     .requestMatchers(mvc.pattern("/management/**")).hasAuthority(AuthoritiesConstants.ADMIN)
             )

src/main/java/org/mskcc/oncokb/curation/web/rest/ApiProxy.java

@@ -20,7 +20,7 @@
 import org.springframework.web.server.ResponseStatusException;
 
 @RestController
-@RequestMapping({ "/legacy-api" })
+@RequestMapping({ "/legacy-api", "/api/v1/utils" })
 public class ApiProxy {
 
     private final ApiProxyService apiProxyService;

src/main/webapp/app/pages/curation/CurationPage.tsx

@@ -13,7 +13,7 @@ import OncoKBSidebar from 'app/components/sidebar/OncoKBSidebar';
 import CurationHistoryTab from 'app/components/tabs/CurationHistoryTab';
 import CurationToolsTab from 'app/components/tabs/CurationToolsTab';
 import Tabs from 'app/components/tabs/tabs';
-import { RealtimeCheckedInputGroup, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
+import { RealtimeCheckedInputGroup, RealtimeMultiTabTextAreaInput, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
 import GeneHeader from './header/GeneHeader';
 import VusTable from 'app/shared/table/VusTable';
 import * as styles from './styles.module.scss';

src/main/webapp/app/pages/curation/collapsible/CancerTypeCollapsible.tsx

@@ -12,7 +12,7 @@ import ModifyCancerTypeModal from 'app/shared/modal/ModifyCancerTypeModal';
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
 import { getLevelDropdownOptions } from 'app/shared/util/firebase/firebase-level-utils';
 import { DIAGNOSTIC_LEVELS_ORDERING, READABLE_FIELD, PROGNOSTIC_LEVELS_ORDERING } from 'app/config/constants/firebase';
-import { RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
+import { RealtimeMultiTabTextAreaInput, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
 import RealtimeLevelDropdownInput, { LevelOfEvidenceType } from 'app/shared/firebase/input/RealtimeLevelDropdownInput';
 import CommentIcon from 'app/shared/icons/CommentIcon';
 import { DeleteSectionButton } from '../button/DeleteSectionButton';
@@ -141,11 +141,13 @@ function CancerTypeCollapsible({
         badge={<BadgeGroup firebasePath={cancerTypePath} showDeletedBadge={cancerTypesReview?.removed || false} />}
         isPendingDelete={cancerTypesReview?.removed || false}
       >
-        <RealtimeTextAreaInput
+        <RealtimeMultiTabTextAreaInput
           disabled={readOnly}
           firebasePath={`${cancerTypePath}/summary`}
           inputClass={styles.summaryTextarea}
           label="Therapeutic Summary (Optional)"
+          mutationName={mutationName}
+          cancerTypeName={cancerTypeName}
           labelIcon={
             <GeneHistoryTooltip
               historyData={parsedHistoryList}
@@ -155,11 +157,13 @@ function CancerTypeCollapsible({
           }
           name="txSummary"
         />
-        <RealtimeTextAreaInput
+        <RealtimeMultiTabTextAreaInput
           disabled={readOnly}
           firebasePath={`${cancerTypePath}/diagnosticSummary`}
           inputClass={styles.summaryTextarea}
           label="Diagnostic Summary (Optional)"
+          mutationName={mutationName}
+          cancerTypeName={cancerTypeName}
           labelIcon={
             <GeneHistoryTooltip
               historyData={parsedHistoryList}
@@ -169,11 +173,13 @@ function CancerTypeCollapsible({
           }
           name="dxSummary"
         />
-        <RealtimeTextAreaInput
+        <RealtimeMultiTabTextAreaInput
           disabled={readOnly}
           firebasePath={`${cancerTypePath}/prognosticSummary`}
           inputClass={styles.summaryTextarea}
           label="Prognostic Summary (Optional)"
+          mutationName={mutationName}
+          cancerTypeName={cancerTypeName}
           labelIcon={
             <GeneHistoryTooltip
               historyData={parsedHistoryList}
@@ -224,11 +230,13 @@ function CancerTypeCollapsible({
             name="diagnosticLevel"
             options={getLevelDropdownOptions(DIAGNOSTIC_LEVELS_ORDERING)}
           />
-          <RealtimeTextAreaInput
+          <RealtimeMultiTabTextAreaInput
             disabled={readOnly}
             firebasePath={`${cancerTypePath}/diagnostic/description`}
             inputClass={styles.textarea}
             label="Description of Evidence"
+            mutationName={mutationName}
+            cancerTypeName={cancerTypeName}
             name="evidenceDescription"
             parseRefs
           />
@@ -255,11 +263,13 @@ function CancerTypeCollapsible({
             name="prognosticLevel"
             options={getLevelDropdownOptions(PROGNOSTIC_LEVELS_ORDERING)}
           />
-          <RealtimeTextAreaInput
+          <RealtimeMultiTabTextAreaInput
             disabled={readOnly}
             firebasePath={`${cancerTypePath}/prognostic/description`}
             inputClass={styles.textarea}
             label="Description of Evidence"
+            mutationName={mutationName}
+            cancerTypeName={cancerTypeName}
             name="evidenceDescription"
             parseRefs
           />

src/main/webapp/app/pages/curation/collapsible/MutationCollapsible.tsx

@@ -11,7 +11,7 @@ import {
 } from 'app/config/constants/firebase';
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
 import { AlterationAnnotationStatus, HotspotDTO, ProteinExonDTO } from 'app/shared/api/generated/curation';
-import { RealtimeCheckedInputGroup, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
+import { RealtimeCheckedInputGroup, RealtimeMultiTabTextAreaInput, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
 import CommentIcon from 'app/shared/icons/CommentIcon';
 import EditIcon from 'app/shared/icons/EditIcon';
 import HotspotIcon from 'app/shared/icons/HotspotIcon';
@@ -355,10 +355,11 @@ const MutationCollapsible = ({
         }
         isPendingDelete={isMutationPendingDelete}
       >
-        <RealtimeTextAreaInput
+        <RealtimeMultiTabTextAreaInput
           firebasePath={`${mutationPath}/summary`}
           inputClass={styles.summaryTextarea}
           label="Mutation Summary (Optional)"
+          mutationName={mutationName}
           labelIcon={
             <GeneHistoryTooltip
               historyData={parsedHistoryList}
@@ -474,11 +475,12 @@ const MutationCollapsible = ({
               />
             </>
           )}
-          <RealtimeTextAreaInput
+          <RealtimeMultiTabTextAreaInput
             disabled={readOnly}
             firebasePath={`${mutationPath}/mutation_effect/description`}
             inputClass={styles.textarea}
             label="Description of Evidence"
+            mutationName={mutationName}
             labelIcon={
               <GeneHistoryTooltip
                 historyData={parsedHistoryList}

src/main/webapp/app/pages/curation/collapsible/TherapyCollapsible.tsx

@@ -1,7 +1,7 @@
 import GeneHistoryTooltip from 'app/components/geneHistoryTooltip/GeneHistoryTooltip';
 import { READABLE_FIELD } from 'app/config/constants/firebase';
 import { notifyError } from 'app/oncokb-commons/components/util/NotificationUtils';
-import { RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
+import { RealtimeMultiTabTextAreaInput, RealtimeTextAreaInput } from 'app/shared/firebase/input/RealtimeInputs';
 import CommentIcon from 'app/shared/icons/CommentIcon';
 import EditIcon from 'app/shared/icons/EditIcon';
 import ModifyTherapyModal from 'app/shared/modal/ModifyTherapyModal';
@@ -128,10 +128,12 @@ function TherapyCollapsible({
         isPendingDelete={treatmentReview?.removed || false}
       >
         <TherapyDropdownGroup treatmentPath={therapyPath} />
-        <RealtimeTextAreaInput
+        <RealtimeMultiTabTextAreaInput
           disabled={readOnly}
           firebasePath={`${therapyPath}/description`}
           inputClass={styles.textarea}
+          mutationName={mutationName}
+          cancerTypeName={cancerTypeName}
           label="Description of Evidence"
           labelIcon={
             <GeneHistoryTooltip

src/main/webapp/app/pages/curation/tooltip/CPLHelpTooltip.tsx

@@ -0,0 +1,44 @@
+import DefaultTooltip from 'app/shared/tooltip/DefaultTooltip';
+import React from 'react';
+
+export default function CPLHelpTooltip(props) {
+  const tableData = [
+    ['[[tumor type]]', 'Tumor type', 'Melanoma'],
+    ['[[gene]]', 'Gene', 'BRAF'],
+    ['[[mutation]] [[[mutation]]]', 'Mutation + ‘mutation’', 'V600E mutation'],
+    ['[[mutation]] [[[mutant]]]', 'Mutation + ‘mutant’', 'V600E mutant'],
+    ['[[variant]]', 'Gene + Mutation + ‘mutant’ + Tumor Type', 'BRAF V600E mutant melanoma'],
+    ['[[mutation|singular]]', 'Singularize mutation', 'Oncogenic Mutation'],
+    ['[[mutation|plural]]', 'Pluralize mutation', 'Fusions'],
+  ];
+  return (
+    <DefaultTooltip
+      placement="top"
+      overlayInnerStyle={{ maxWidth: '450px' }}
+      overlay={
+        <table style={{ borderCollapse: 'collapse', width: '100%' }}>
+          <thead>
+            <tr style={{ borderBottom: '2px solid black' }}>
+              <th>OCPL Code</th>
+              <th>Output of Code from API</th>
+              <th>Example of output in an annotation</th>
+            </tr>
+          </thead>
+          <tbody>
+            {tableData.map((row, index) => (
+              <tr key={index} style={{ borderBottom: '1px solid #ccc' }}>
+                <td>
+                  <pre style={{ margin: 0 }}>{row[0]}</pre>
+                </td>
+                <td>{row[1]}</td>
+                <td>{row[2]}</td>
+              </tr>
+            ))}
+          </tbody>
+        </table>
+      }
+    >
+      {props.children}
+    </DefaultTooltip>
+  );
+}

src/main/webapp/app/shared/api/clients.ts

@@ -12,6 +12,7 @@ import {
   ArticleResourceApi,
   AuditResourceApi,
 } from './generated/curation/api';
+import { UtilsApi } from './generated/defaultCore';
 import { DriveAnnotationApi } from './manual/drive-annotation-api';
 import { EvidenceApi } from './manual/evidence-api';
 import { GeneTypeApi } from './manual/gene-type-api';
@@ -34,3 +35,5 @@ export const evidenceClient = new EvidenceApi(undefined, '', axiosInstance);
 export const geneTypeClient = new GeneTypeApi(undefined, '', axiosInstance);
 export const driveAnnotationClient = new DriveAnnotationApi(undefined, '', axiosInstance);
 export const geneLegacyApi = new GeneApi(undefined, '', axiosInstance);
+
+export const utilsClient = new UtilsApi(undefined, 'api/v1', axiosInstance);

src/main/webapp/app/shared/api/generated/defaultCore/.gitignore

@@ -0,0 +1,4 @@
+wwwroot/*.js
+node_modules
+typings
+dist

src/main/webapp/app/shared/api/generated/defaultCore/.npmignore

@@ -0,0 +1 @@
+# empty npmignore to ensure all required files (e.g., in the dist folder) are published by npm

src/main/webapp/app/shared/api/generated/defaultCore/.openapi-generator-ignore

@@ -0,0 +1,23 @@
+# OpenAPI Generator Ignore
+# Generated by openapi-generator https://github.com/openapitools/openapi-generator
+
+# Use this file to prevent files from being overwritten by the generator.
+# The patterns follow closely to .gitignore or .dockerignore.
+
+# As an example, the C# client generator defines ApiClient.cs.
+# You can make changes and tell OpenAPI Generator to ignore just this file by uncommenting the following line:
+#ApiClient.cs
+
+# You can match any string of characters against a directory, file or extension with a single asterisk (*):
+#foo/*/qux
+# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux
+
+# You can recursively match patterns against a directory, file or extension with a double asterisk (**):
+#foo/**/qux
+# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux
+
+# You can also negate patterns with an exclamation (!).
+# For example, you can ignore all files in a docs folder with the file extension .md:
+#docs/*.md
+# Then explicitly reverse the ignore rule for a single file:
+#!docs/README.md

src/main/webapp/app/shared/api/generated/defaultCore/.openapi-generator/FILES

@@ -0,0 +1,61 @@
+.gitignore
+.npmignore
+.openapi-generator-ignore
+api.ts
+base.ts
+common.ts
+configuration.ts
+docs/Alteration.md
+docs/AnnotateMutationByGenomicChangeQuery.md
+docs/AnnotateMutationByHGVSgQuery.md
+docs/AnnotatedVariant.md
+docs/ApiHttpError.md
+docs/Article.md
+docs/ArticleAbstract.md
+docs/BiologicalVariant.md
+docs/CancerTypeCount.md
+docs/Citations.md
+docs/ClinicalVariant.md
+docs/CplAnnotationRequest.md
+docs/DownloadAvailability.md
+docs/Drug.md
+docs/DrugSynonym.md
+docs/DrugsApi.md
+docs/EnsemblGene.md
+docs/EnsemblTranscript.md
+docs/Evidence.md
+docs/Exon.md
+docs/Gene.md
+docs/GeneNumber.md
+docs/Geneset.md
+docs/GenomeNexusAnnotatedVariantInfo.md
+docs/Implication.md
+docs/IndicatorQueryTreatment.md
+docs/LevelNumber.md
+docs/MainNumber.md
+docs/MainNumberLevel.md
+docs/MainType.md
+docs/MatchVariant.md
+docs/MatchVariantRequest.md
+docs/MatchVariantResult.md
+docs/MutationEffectResp.md
+docs/PfamDomainRange.md
+docs/PortalAlteration.md
+docs/Query.md
+docs/RelevantCancerTypeQuery.md
+docs/SearchApi.md
+docs/TranscriptApi.md
+docs/TranscriptCoverageFilterResult.md
+docs/TranscriptResult.md
+docs/Treatment.md
+docs/TreatmentDrug.md
+docs/TreatmentDrugId.md
+docs/TumorType.md
+docs/TypeaheadSearchResp.md
+docs/UntranslatedRegion.md
+docs/UtilsApi.md
+docs/VariantAnnotation.md
+docs/VariantAnnotationTumorType.md
+docs/VariantConsequence.md
+git_push.sh
+index.ts

src/main/webapp/app/shared/api/generated/defaultCore/.openapi-generator/VERSION

@@ -0,0 +1 @@
+7.13.0