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gebbing12gebbing12
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Write backend and frontend for variant recommendation page
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19 files changed

+964
-5
lines changed

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

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

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

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

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

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

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

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@@ -91,6 +91,7 @@ public void configure(HttpSecurity http) throws Exception {
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.antMatchers("/api/authenticate").permitAll()
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.antMatchers("/api/auth-info").permitAll()
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.antMatchers("/api/logout").permitAll()
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.antMatchers("/api/variant-recommendation/**").permitAll()
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.antMatchers("/api/admin/**").hasAuthority(AuthoritiesConstants.ADMIN)
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.antMatchers("/api/audit/**").hasAuthority(AuthoritiesConstants.ADMIN)
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.antMatchers("/api/account/firebase-token").hasAnyAuthority(AuthoritiesConstants.CURATOR)

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

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

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

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package org.mskcc.oncokb.curation.web.rest;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import org.json.simple.JSONObject;
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import org.mskcc.oncokb.curation.config.Constants;
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import org.mskcc.oncokb.curation.service.S3Service;
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import org.mskcc.oncokb.curation.web.rest.errors.BadRequestAlertException;
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import org.mskcc.oncokb.curation.web.rest.errors.ResourceNotFoundException;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.http.ResponseEntity;
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import org.springframework.web.bind.annotation.GetMapping;
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import org.springframework.web.bind.annotation.PathVariable;
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import org.springframework.web.bind.annotation.RequestMapping;
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import org.springframework.web.bind.annotation.RestController;
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import software.amazon.awssdk.core.ResponseInputStream;
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import software.amazon.awssdk.services.s3.model.GetObjectResponse;
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@RestController
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@RequestMapping("/api")
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public class VariantRecommendController {
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private final Logger log = LoggerFactory.getLogger(VariantRecommendController.class);
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private static final String ENTITY_NAME = "variant-recommendation";
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@Autowired
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private S3Service s3Service;
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@GetMapping("/variant-recommendation/{file}")
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public ResponseEntity<List<JSONObject>> requestData(@PathVariable String file) throws IOException {
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Optional<ResponseInputStream<GetObjectResponse>> s3object = s3Service.getObject(Constants.ONCOKB_S3_BUCKET, file);
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if (s3object.isPresent()) {
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BufferedReader reader = new BufferedReader(new InputStreamReader(s3object.get(), StandardCharsets.UTF_8));
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String headerLine = reader.readLine();
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if (headerLine == null) {
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throw new BadRequestAlertException("File is empty", ENTITY_NAME, "fileempty");
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}
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String[] headers = headerLine.split("\t");
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List<JSONObject> jsonList = new ArrayList<>();
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String line;
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while ((line = reader.readLine()) != null) {
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String[] data = line.split("\t");
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JSONObject jsonObject = new JSONObject();
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for (int i = 0; i < headers.length; i++) {
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jsonObject.put(headers[i], "n/a".equals(data[i]) ? null : data[i]);
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}
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jsonList.add(jsonObject);
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}
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return ResponseEntity.ok(jsonList);
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} else {
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throw new ResourceNotFoundException();
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}
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}
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}

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

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

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

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package org.mskcc.oncokb.curation.web.rest.errors;
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import org.zalando.problem.AbstractThrowableProblem;
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import org.zalando.problem.Status;
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public class ResourceNotFoundException extends AbstractThrowableProblem {
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private static final long serialVersionUID = 1L;
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public ResourceNotFoundException() {
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super(ErrorConstants.RESOURCE_NOT_FOUND, "Resource Not Found", Status.NOT_FOUND);
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}
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}

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

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@@ -107,9 +107,8 @@ export enum FEATURE_PAGE_ROUTE {
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ACCOUNT = '/account',
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OAUTH = '/oauth2/authorization/oidc',
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SEARCH = '/search',
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/* Below are variant related paths */
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/* Below are variant recommendation related paths */
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VARIANR_REC = '/variant-recommendation',
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VARIANR_MERGE_DATA = '/variant-recommendation/:hugoSymbol}/:variantName',
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/* Below are curation related paths */
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CURATION = '/curation',
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CURATION_GENE = '/curation/:hugoSymbol/somatic',
@@ -427,3 +426,8 @@ export const DEFAULT_TOAST_ERROR_OPTIONS: ToastOptions = {
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export const KEYCLOAK_LOGOUT_REDIRECT_PARAM = 'post_logout_redirect_uri';
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export const KEYCLOAK_SESSION_TERMINATED_PARAM = 'session_terminated';
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export const KEYCLOAK_UNAUTHORIZED_PARAM = 'unauthorized';
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/* Files name in S3 bucket */
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export const ALL_FREQUENCY_FILE = 'msk_impact_2017_all_frequency.txt';
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export const TYPE_FREQUENCY_FILE = 'msk_impact_2017_type_frequency.txt';
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export const DETAILED_FREQUENCY_FILE = 'msk_impact_2017_detailed_frequency.txt';

‎src/main/webapp/app/oncokb-commons/components/twoRangeSlider/TwoRangeSlider.tsx

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/* eslint-disable no-console */
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import React, { useState } from 'react';
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import formatPercentage from 'app/pages/variantRecommendation/FormatPercentage';
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import classnames from 'classnames';
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import * as styles from './styles.module.scss';
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interface RangeSliderProps {
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min: number;
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max: number;
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range: [number, number];
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step: number;
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onChange: (newRange: [number, number]) => void;
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}
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export const TwoRangeSlider = ({ min, max, range, step, onChange }: RangeSliderProps) => {
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const [minValue, setMinValue] = useState(range ? range[0] : min);
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const [maxValue, setMaxValue] = useState(range ? range[1] : max);
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const handleMinChange = e => {
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e.preventDefault();
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const newMinVal = Math.min(+e.target.value, maxValue);
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setMinValue(newMinVal);
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onChange([newMinVal, maxValue]);
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};
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const handleMaxChange = e => {
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e.preventDefault();
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const newMaxVal = Math.max(+e.target.value, minValue);
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setMaxValue(newMaxVal);
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onChange([minValue, newMaxVal]);
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};
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const minPos = ((minValue - min) / ((max ?? 100) - min)) * 100;
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const maxPos = ((maxValue - min) / ((max ?? 100) - min)) * 100;
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return (
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<div className={styles.wrapper}>
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<div className={styles['range-slider']}>
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<div className={styles['range-labels']}>
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<span className={classnames(styles['range-label'], styles['range-label-start'])}>{formatPercentage(minValue)}</span>
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<span className={classnames(styles['range-label'], styles['range-label-end'])}>{formatPercentage(maxValue)}</span>
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</div>
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<input type="range" value={minValue} min={min} max={max} step={step} onChange={handleMinChange} />
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<input type="range" value={maxValue} min={min} max={max} step={step} onChange={handleMaxChange} />
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<div className={styles['track-wrapper']}>
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<div className={styles['track']} />
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<div className={styles['range-between']} style={{ left: `${minPos}%`, right: `${100 - maxPos}%` }} />
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<div className={styles['control']} style={{ left: `${minPos}%` }} />
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<div className={styles['control']} style={{ left: `${maxPos}%` }} />
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</div>
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</div>
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</div>
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);
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};
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export default TwoRangeSlider;

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