Add variant recommendation page

pom.xml

@@ -343,6 +343,11 @@
             <version>${jsonwebtoken.version}</version>
             <scope>runtime</scope>
         </dependency>
+        <dependency>
+            <groupId>software.amazon.awssdk</groupId>
+            <artifactId>aws-sdk-java</artifactId>
+            <version>2.22.7</version>
+        </dependency>
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
@@ -1257,4 +1262,4 @@
             </build>
         </profile>
     </profiles>
-</project>
+</project>

src/main/java/org/mskcc/oncokb/curation/config/Constants.java

@@ -22,5 +22,7 @@ public final class Constants {
 
     public static final String DEFAULT_GENE_SYNONMN_SOURCE = "cBioPortal";
 
+    public static final String ONCOKB_S3_BUCKET = "oncokb-bucket";
+
     private Constants() {}
 }

src/main/java/org/mskcc/oncokb/curation/config/application/ApplicationProperties.java

@@ -19,12 +19,22 @@ public class ApplicationProperties extends org.mskcc.oncokb.meta.model.applicati
 
     private FirebaseProperties firebase;
 
+    private AwsProperties aws;
+
     private String oncokbDataRepoDir;
 
     private OncoKbCoreConfig oncokbCore;
 
     private String nihEutilsToken;
 
+    public AwsProperties getAws() {
+        return aws;
+    }
+
+    public void setAws(AwsProperties aws) {
+        this.aws = aws;
+    }
+
     public OncoKbCoreConfig getOncokbCore() {
         return oncokbCore;
     }

src/main/java/org/mskcc/oncokb/curation/config/application/AwsProperties.java

@@ -0,0 +1,33 @@
+package org.mskcc.oncokb.curation.config.application;
+
+public class AwsProperties {
+
+    // Copy from oncoKb-Public
+    private String accessKeyId;
+    private String secretAccessKey;
+    private String region;
+
+    public String getAccessKeyId() {
+        return this.accessKeyId;
+    }
+
+    public void setAccessKeyId(String accessKeyId) {
+        this.accessKeyId = accessKeyId;
+    }
+
+    public String getSecretAccessKey() {
+        return this.secretAccessKey;
+    }
+
+    public void setSecretAccessKey(String secretAccessKey) {
+        this.secretAccessKey = secretAccessKey;
+    }
+
+    public String getRegion() {
+        return this.region;
+    }
+
+    public void setRegion(String region) {
+        this.region = region;
+    }
+}

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

@@ -88,6 +88,7 @@ public SecurityFilterChain oauthFilterChain(HttpSecurity http, MvcRequestMatcher
                     .requestMatchers(mvc.pattern("/api/authenticate")).permitAll()
                     .requestMatchers(mvc.pattern("/api/auth-info")).permitAll()
                     .requestMatchers(mvc.pattern("/api/logout")).permitAll()
+                    .requestMatchers("/api/variant-recommendation/**").permitAll()
                     .requestMatchers(mvc.pattern("/api/admin/**")).hasAuthority(AuthoritiesConstants.ADMIN)
                     .requestMatchers(mvc.pattern("/api/audit/**")).hasAuthority(AuthoritiesConstants.ADMIN)
                     .requestMatchers(mvc.pattern("/api/account/firebase-token")).hasAnyAuthority(AuthoritiesConstants.CURATOR, AuthoritiesConstants.USER)

src/main/java/org/mskcc/oncokb/curation/service/S3Service.java

@@ -0,0 +1,58 @@
+package org.mskcc.oncokb.curation.service;
+
+import java.util.Optional;
+import org.mskcc.oncokb.curation.config.application.ApplicationProperties;
+import org.mskcc.oncokb.curation.config.application.AwsProperties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Service;
+import software.amazon.awssdk.auth.credentials.AwsBasicCredentials;
+import software.amazon.awssdk.auth.credentials.StaticCredentialsProvider;
+import software.amazon.awssdk.core.ResponseInputStream;
+import software.amazon.awssdk.core.sync.ResponseTransformer;
+import software.amazon.awssdk.regions.Region;
+import software.amazon.awssdk.services.s3.S3Client;
+import software.amazon.awssdk.services.s3.model.GetObjectRequest;
+import software.amazon.awssdk.services.s3.model.GetObjectResponse;
+
+@Service
+public class S3Service {
+
+    private final Logger log = LoggerFactory.getLogger(S3Service.class);
+    private final ApplicationProperties applicationProperties;
+    private S3Client s3Client;
+
+    public S3Service(ApplicationProperties applicationProperties) {
+        this.applicationProperties = applicationProperties;
+        AwsProperties awsProperties = applicationProperties.getAws();
+        if (awsProperties != null) {
+            String accessKeyId = awsProperties.getAccessKeyId();
+            String secretAccessKey = awsProperties.getSecretAccessKey();
+            String region = awsProperties.getRegion();
+            AwsBasicCredentials awsCreds = AwsBasicCredentials.create(accessKeyId, secretAccessKey);
+            s3Client = S3Client.builder().region(Region.of(region)).credentialsProvider(StaticCredentialsProvider.create(awsCreds)).build();
+            log.info("S3 Client successfully initialized");
+        } else {
+            log.error("AWS credentials not configured properly");
+        }
+    }
+
+    /**
+     * Get an object from aws s3
+     * @param bucket s3 bucket name
+     * @param objectPath the path of the object
+     * @return a S3 object
+     */
+    public Optional<ResponseInputStream<GetObjectResponse>> getObject(String bucket, String objectPath) {
+        try {
+            ResponseInputStream<GetObjectResponse> s3object = s3Client.getObject(
+                GetObjectRequest.builder().bucket(bucket).key(objectPath).build(),
+                ResponseTransformer.toInputStream()
+            );
+            return Optional.of(s3object);
+        } catch (Exception e) {
+            log.error(e.getMessage(), e);
+            return Optional.empty();
+        }
+    }
+}

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

@@ -0,0 +1,63 @@
+package org.mskcc.oncokb.curation.web.rest;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import org.json.JSONArray;
+import org.json.JSONObject;
+import org.mskcc.oncokb.curation.config.Constants;
+import org.mskcc.oncokb.curation.service.S3Service;
+import org.mskcc.oncokb.curation.web.rest.errors.BadRequestAlertException;
+import org.mskcc.oncokb.curation.web.rest.errors.ResourceNotFoundException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+import software.amazon.awssdk.core.ResponseInputStream;
+import software.amazon.awssdk.services.s3.model.GetObjectResponse;
+
+@RestController
+@RequestMapping("/api")
+public class VariantRecommendController {
+
+    private final Logger log = LoggerFactory.getLogger(VariantRecommendController.class);
+
+    private static final String ENTITY_NAME = "variant-recommendation";
+
+    @Autowired
+    private S3Service s3Service;
+
+    @GetMapping("/variant-recommendation/{filename}")
+    public ResponseEntity<String> requestData(@PathVariable String filename) throws IOException {
+        Optional<ResponseInputStream<GetObjectResponse>> s3object = s3Service.getObject(Constants.ONCOKB_S3_BUCKET, filename);
+        if (s3object.isPresent()) {
+            BufferedReader reader = new BufferedReader(new InputStreamReader(s3object.orElseThrow(), StandardCharsets.UTF_8));
+            String headerLine = reader.readLine();
+            if (headerLine == null) {
+                throw new BadRequestAlertException("File is empty", ENTITY_NAME, "fileempty");
+            }
+            String[] headers = headerLine.split("\t");
+            JSONArray jsonArray = new JSONArray();
+            String line;
+            while ((line = reader.readLine()) != null) {
+                String[] data = line.split("\t");
+                JSONObject jsonObject = new JSONObject();
+                for (int i = 0; i < headers.length; i++) {
+                    jsonObject.put(headers[i], "n/a".equals(data[i]) ? null : data[i]);
+                }
+                jsonArray.put(jsonObject);
+            }
+            return ResponseEntity.ok(jsonArray.toString());
+        } else {
+            throw new ResourceNotFoundException("File not Found", ENTITY_NAME, "nofile");
+        }
+    }
+}

src/main/java/org/mskcc/oncokb/curation/web/rest/errors/ErrorConstants.java

@@ -12,6 +12,7 @@ public final class ErrorConstants {
     public static final URI USER_NOT_APPROVED = URI.create(PROBLEM_BASE_URL + "user-not-approved");
     public static final URI EMAIL_ALREADY_USED_TYPE = URI.create(PROBLEM_BASE_URL + "/email-already-used");
     public static final URI LOGIN_ALREADY_USED_TYPE = URI.create(PROBLEM_BASE_URL + "/login-already-used");
+    public static final URI RESOURCE_NOT_FOUND = URI.create(PROBLEM_BASE_URL + "/resource-not-found");
 
     public ErrorConstants() {}
 }

src/main/java/org/mskcc/oncokb/curation/web/rest/errors/ResourceNotFoundException.java

@@ -0,0 +1,38 @@
+package org.mskcc.oncokb.curation.web.rest.errors;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.ErrorResponseException;
+import tech.jhipster.web.rest.errors.ProblemDetailWithCause.ProblemDetailWithCauseBuilder;
+
+public class ResourceNotFoundException extends ErrorResponseException {
+
+    private static final long serialVersionUID = 1L;
+
+    private final String entityName;
+
+    private final String errorKey;
+
+    public ResourceNotFoundException(String defaultMessage, String entityName, String errorKey) {
+        super(
+            HttpStatus.NOT_FOUND,
+            ProblemDetailWithCauseBuilder.instance()
+                .withStatus(HttpStatus.NOT_FOUND.value())
+                .withType(ErrorConstants.RESOURCE_NOT_FOUND)
+                .withTitle(defaultMessage)
+                .withProperty("message", "error." + errorKey)
+                .withProperty("params", entityName)
+                .build(),
+            null
+        );
+        this.entityName = entityName;
+        this.errorKey = errorKey;
+    }
+
+    public String getEntityName() {
+        return entityName;
+    }
+
+    public String getErrorKey() {
+        return errorKey;
+    }
+}

src/main/webapp/app/components/sidebar/NavigationSidebar.tsx

@@ -248,6 +248,14 @@ export const NavigationSidebar: React.FunctionComponent<StoreProps> = ({ isNavSi
                 nav={<NavLink to={PAGE_ROUTE.CURATION} />}
               />
             )}
+            {props.isUser && (
+              <MenuItemCollapsible
+                isCollapsed={isNavSidebarCollapsed}
+                text="Variant Recommendation"
+                icon={<FiFileText size={DEFAULT_NAV_ICON_SIZE} />}
+                nav={<NavLink to={PAGE_ROUTE.VARIANR_REC} />}
+              />
+            )}
             {props.isUser && (
               <>
                 <MenuItemCollapsible

src/main/webapp/app/config/constants/constants.ts

@@ -108,6 +108,8 @@ export enum FEATURE_PAGE_ROUTE {
   OAUTH = '/oauth2/authorization/oidc',
   SEARCH = '/search',
   SWAGGER = '/swagger-ui/index.html',
+  /* Below are variant recommendation related paths */
+  VARIANR_REC = '/variant-recommendation',
   /* Below are curation related paths */
   CURATION = '/curation',
   CURATION_SOMATIC = '/curation/somatic',
@@ -441,3 +443,7 @@ export const KEYCLOAK_UNAUTHORIZED_PARAM = 'unauthorized';
  */
 export const PRIORITY_ENTITY_MENU_ITEM_KEY = 'oncokbCuration-entityMenuPriorityKey';
 export const SOMATIC_GERMLINE_SETTING_KEY = 'oncokbCuration-somaticGermlineSettingKey';
+/* Files name in S3 bucket */
+export const ALL_FREQUENCY_FILE = 'msk_impact_2017_all_frequency.txt';
+export const TYPE_FREQUENCY_FILE = 'msk_impact_2017_type_frequency.txt';
+export const DETAILED_FREQUENCY_FILE = 'msk_impact_2017_detailed_frequency.txt';

src/main/webapp/app/index.tsx

@@ -3,7 +3,6 @@ import ReactDOM from 'react-dom';
 import { Provider } from 'mobx-react';
 import { createStores } from 'app/stores';
 import { createBrowserHistory } from 'history';
-
 import setupAxiosInterceptors from './config/axios-interceptor';
 import ErrorBoundary from './shared/error/error-boundary';
 import AppComponent from './app';
@@ -94,7 +93,7 @@ const render = Component =>
         <Component />
       </Provider>
     </ErrorBoundary>,
-    rootEl
+    rootEl,
   );
 
 render(AppComponent);

src/main/webapp/app/oncokb-commons/components/twoThumbSlider/TwoThumbSlider.tsx

@@ -0,0 +1,55 @@
+import React, { useState } from 'react';
+import { formatPercentage } from 'app/shared/util/utils';
+import classnames from 'classnames';
+import * as styles from './styles.module.scss';
+
+interface RangeSliderProps {
+  min: number;
+  max: number;
+  range: [number, number];
+  step: number;
+  onChange: (newRange: [number, number]) => void;
+}
+
+export const TwoThumbSlider = ({ min, max, range, step, onChange }: RangeSliderProps) => {
+  const [minValue, setMinValue] = useState(range ? range[0] : min);
+  const [maxValue, setMaxValue] = useState(range ? range[1] : max);
+
+  const handleMinChange = e => {
+    e.preventDefault();
+    const newMinVal = Math.min(+e.target.value, maxValue);
+    setMinValue(newMinVal);
+    onChange([newMinVal, maxValue]);
+  };
+
+  const handleMaxChange = e => {
+    e.preventDefault();
+    const newMaxVal = Math.max(+e.target.value, minValue);
+    setMaxValue(newMaxVal);
+    onChange([minValue, newMaxVal]);
+  };
+
+  const minPos = ((minValue - min) / ((max ?? 100) - min)) * 100;
+  const maxPos = ((maxValue - min) / ((max ?? 100) - min)) * 100;
+
+  return (
+    <div className={styles.wrapper}>
+      <div className={styles['range-slider']}>
+        <div className={styles['range-labels']}>
+          <span className={classnames(styles['range-label'], styles['range-label-start'])}>{formatPercentage(minValue)}</span>
+          <span className={classnames(styles['range-label'], styles['range-label-end'])}>{formatPercentage(maxValue)}</span>
+        </div>
+        <input type="range" value={minValue} min={min} max={max} step={step} onChange={handleMinChange} />
+        <input type="range" value={maxValue} min={min} max={max} step={step} onChange={handleMaxChange} />
+        <div className={styles['track-wrapper']}>
+          <div className={styles['track']} />
+          <div className={styles['range-between']} style={{ left: `${minPos}%`, right: `${100 - maxPos}%` }} />
+          <div className={styles['control']} style={{ left: `${minPos}%` }} />
+          <div className={styles['control']} style={{ left: `${maxPos}%` }} />
+        </div>
+      </div>
+    </div>
+  );
+};
+
+export default TwoThumbSlider;