Merge pull request #10039 from BasLee/custom_data_binning_endpoint

Binning of custom data
cBioPortal · Mar 17, 2023 · ca13827 · ca13827
2 parents f375e62 + bae8b2b
commit ca13827
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Showing 46 changed files with 1,979 additions and 687 deletions.
diff --git a/model/src/main/java/org/cbioportal/model/Binnable.java b/model/src/main/java/org/cbioportal/model/Binnable.java
@@ -0,0 +1,13 @@
+package org.cbioportal.model;
+
+/**
+ * Data that can be binned, clinical or custom
+ */
+public interface Binnable {
+    String getAttrId();
+    String getAttrValue();
+    String getSampleId();
+    String getPatientId();
+    String getStudyId();
+    Boolean isPatientAttribute();
+}
diff --git a/model/src/main/java/org/cbioportal/model/ClinicalData.java b/model/src/main/java/org/cbioportal/model/ClinicalData.java
@@ -2,7 +2,7 @@
 
 import javax.validation.constraints.NotNull;
 
-public class ClinicalData extends UniqueKeyBase {
+public class ClinicalData extends UniqueKeyBase implements Binnable  {
 
     private Integer internalId;
     private String sampleId;
@@ -51,6 +51,13 @@ public String getAttrId() {
         return attrId;
     }
 
+    public Boolean isPatientAttribute() {
+        if(clinicalAttribute == null) {
+            return null;
+        }
+        return this.clinicalAttribute.getPatientAttribute();
+    }
+
     public void setAttrId(String attrId) {
         this.attrId = attrId;
     }

diff --git a/service/pom.xml b/service/pom.xml
@@ -24,6 +24,29 @@
             <groupId>org.mskcc.cbio</groupId>
             <artifactId>permission-evaluator</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.github.cbioportal</groupId>
+            <artifactId>session-service</artifactId>
+            <classifier>model</classifier>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-to-slf4j</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>ch.qos.logback</groupId>
+                    <artifactId>logback-classic</artifactId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>spring-boot-starter-web</artifactId>
+                    <groupId>org.springframework.boot</groupId>
+                </exclusion>
+                <exclusion>
+                    <artifactId>spring-boot-starter-data-mongodb</artifactId>
+                    <groupId>org.springframework.boot</groupId>
+                </exclusion>
+            </exclusions>
+        </dependency>
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-test</artifactId>
@@ -57,6 +80,10 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
         </dependency>
+        <dependency>
+            <groupId>commons-codec</groupId>
+            <artifactId>commons-codec</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.mockito</groupId>
             <artifactId>mockito-core</artifactId>

diff --git a/service/src/main/java/org/cbioportal/service/AttributeByStudyService.java b/service/src/main/java/org/cbioportal/service/AttributeByStudyService.java
@@ -0,0 +1,9 @@
+package org.cbioportal.service;
+
+import org.cbioportal.model.ClinicalAttribute;
+
+import java.util.List;
+
+public interface AttributeByStudyService {
+    List<ClinicalAttribute> getClinicalAttributesByStudyIdsAndAttributeIds(List<String> studyIds, List<String> attributeIds);
+}
diff --git a/service/src/main/java/org/cbioportal/service/ClinicalAttributeService.java b/service/src/main/java/org/cbioportal/service/ClinicalAttributeService.java
@@ -8,7 +8,7 @@
 
 import java.util.List;
 
-public interface ClinicalAttributeService {
+public interface ClinicalAttributeService extends AttributeByStudyService {
 
     List<ClinicalAttribute> getAllClinicalAttributes(String projection, Integer pageSize, Integer pageNumber,
                                                      String sortBy, String direction);
@@ -31,5 +31,4 @@ List<ClinicalAttribute> getAllClinicalAttributesInStudy(String studyId, String p
 
     List<ClinicalAttributeCount> getClinicalAttributeCountsBySampleListId(String sampleListId);
 
-    List<ClinicalAttribute> getClinicalAttributesByStudyIdsAndAttributeIds(List<String> studyIds, List<String> attributeIds);
 }
diff --git a/service/src/main/java/org/cbioportal/service/CustomDataService.java b/service/src/main/java/org/cbioportal/service/CustomDataService.java
@@ -0,0 +1,10 @@
+package org.cbioportal.service;
+
+import org.cbioportal.service.util.CustomDataSession;
+
+import java.util.List;
+import java.util.Map;
+
+public interface CustomDataService {
+    Map<String, CustomDataSession> getCustomDataSessions(List<String> attributes);
+}
diff --git a/service/src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java b/service/src/main/java/org/cbioportal/service/impl/CustomDataServiceImpl.java
@@ -0,0 +1,58 @@
+package org.cbioportal.service.impl;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.cbioportal.service.CustomDataService;
+import org.cbioportal.service.util.CustomDataSession;
+import org.cbioportal.service.util.SessionServiceRequestHandler;
+import org.cbioportal.session_service.domain.SessionType;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.CompletableFuture;
+import java.util.stream.Collectors;
+
+@Service
+public class CustomDataServiceImpl implements CustomDataService {
+    @Autowired
+    private SessionServiceRequestHandler sessionServiceRequestHandler;
+
+    @Autowired
+    private ObjectMapper sessionServiceObjectMapper;
+
+    /**
+     * Retrieve CustomDataSession from session service for custom data attributes. 
+     * @param customAttributeIds - attribute id/hash of custom data used as session service key.
+     * @return Map of custom data attribute id to the CustomDataSession
+     */
+    @Override
+    public Map<String, CustomDataSession> getCustomDataSessions(List<String> customAttributeIds) {
+        Map<String, CompletableFuture<CustomDataSession>> postFuturesMap = customAttributeIds.stream()
+            .collect(Collectors.toMap(
+                attributeId -> attributeId,
+                attributeId -> CompletableFuture.supplyAsync(() -> {
+                    try {
+                        String customDataSessionJson = sessionServiceRequestHandler.getSessionDataJson(
+                            SessionType.custom_data,
+                            attributeId
+                        );
+                        return sessionServiceObjectMapper.readValue(customDataSessionJson, CustomDataSession.class);
+                    } catch (Exception e) {
+                        return null;
+                    }
+                })
+            ));
+
+        CompletableFuture.allOf(postFuturesMap.values().toArray(new CompletableFuture[postFuturesMap.size()])).join();
+
+        Map<String, CustomDataSession> customDataSessions = postFuturesMap.entrySet().stream()
+            .filter(entry -> entry.getValue().join() != null)
+            .collect(Collectors.toMap(
+                entry -> entry.getKey(),
+                entry -> entry.getValue().join()
+            ));
+
+        return customDataSessions;
+    }
+}
diff --git a/service/src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java b/service/src/main/java/org/cbioportal/service/util/BinnableCustomDataValue.java
@@ -0,0 +1,49 @@
+package org.cbioportal.service.util;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import org.cbioportal.model.Binnable;
+
+import java.io.Serializable;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class BinnableCustomDataValue implements Binnable, Serializable {
+
+    private final CustomDataValue customDataValue;
+    private final String attrId;
+    private final Boolean patientAttribute;
+
+    public BinnableCustomDataValue(
+        CustomDataValue customDataValue,
+        String attributeId,
+        Boolean patientAttribute
+    ) {
+        this.customDataValue = customDataValue;
+        this.attrId = attributeId;
+        this.patientAttribute = patientAttribute;
+    }
+
+    public String getSampleId() {
+        return customDataValue.getSampleId();
+    }
+
+    public String getPatientId() {
+        return customDataValue.getPatientId();
+    }
+
+    public String getStudyId() {
+        return customDataValue.getStudyId();
+    }
+
+    public String getAttrId() {
+        return attrId;
+    }
+
+    public Boolean isPatientAttribute() {
+        return patientAttribute;
+    }
+
+    public String getAttrValue() {
+        return customDataValue.getValue();
+    }
+
+}
diff --git a/service/src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java b/service/src/main/java/org/cbioportal/service/util/ClinicalAttributeUtil.java
@@ -11,17 +11,24 @@
 
 @Component
 public class ClinicalAttributeUtil {
-    public void extractCategorizedClinicalAttributes(List<ClinicalAttribute> clinicalAttributes,
-            List<String> sampleAttributeIds, List<String> patientAttributeIds,
-            List<String> conflictingPatientAttributeIds) {
-
+
+    public void extractCategorizedClinicalAttributes(
+        List<ClinicalAttribute> clinicalAttributes,
+        List<String> sampleAttributeIds, 
+        List<String> patientAttributeIds,
+        List<String> conflictingPatientAttributeIds
+    ) {
+
         Set<String> sampleAttributeIdsSet = new HashSet<String>();
         Set<String> patientAttributeIdsSet = new HashSet<String>();
         Set<String> conflictingPatientAttributeIdsSet = new HashSet<String>();
 
-        Map<String, Map<Boolean, List<ClinicalAttribute>>> groupedAttributesByIdAndType = clinicalAttributes.stream()
-                .collect(Collectors.groupingBy(ClinicalAttribute::getAttrId,
-                        Collectors.groupingBy(ClinicalAttribute::getPatientAttribute)));
+        Map<String, Map<Boolean, List<ClinicalAttribute>>> groupedAttributesByIdAndType = clinicalAttributes
+            .stream()
+            .collect(Collectors.groupingBy(
+                ClinicalAttribute::getAttrId,
+                Collectors.groupingBy(ClinicalAttribute::getPatientAttribute)
+            ));
 
         groupedAttributesByIdAndType.entrySet().forEach(entry -> {
             if (entry.getValue().keySet().size() == 1) {
@@ -42,7 +49,7 @@ public void extractCategorizedClinicalAttributes(List<ClinicalAttribute> clinica
                 });
             }
         });
-        
+
         sampleAttributeIds.addAll(sampleAttributeIdsSet);
         patientAttributeIds.addAll(patientAttributeIdsSet);
         conflictingPatientAttributeIds.addAll(conflictingPatientAttributeIdsSet);

diff --git a/...ioportal/web/CustomAttributeWithData.java → ...service/util/CustomAttributeWithData.java b/...ioportal/web/CustomAttributeWithData.java → ...service/util/CustomAttributeWithData.java
@@ -1,18 +1,18 @@
-package org.cbioportal.web;
+package org.cbioportal.service.util;
 
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import javax.validation.constraints.NotNull;
 
-import org.cbioportal.web.parameter.CustomDataValue;
-
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 
 @JsonIgnoreProperties(ignoreUnknown = true)
-public class CustomAttributeWithData implements Serializable{
+public class CustomAttributeWithData implements Serializable {
 
     private String owner = "anonymous";
     private Set<String> origin = new HashSet<>();

diff --git a/...rtal/web/parameter/CustomDataSession.java → ...ortal/service/util/CustomDataSession.java b/...rtal/web/parameter/CustomDataSession.java → ...ortal/service/util/CustomDataSession.java
@@ -1,12 +1,11 @@
-package org.cbioportal.web.parameter;
+package org.cbioportal.service.util;
 
 import java.io.IOException;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.cbioportal.session_service.domain.Session;
 import org.cbioportal.session_service.domain.SessionType;
-import org.cbioportal.web.CustomAttributeWithData;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;

diff --git a/...portal/web/parameter/CustomDataValue.java → ...oportal/service/util/CustomDataValue.java b/...portal/web/parameter/CustomDataValue.java → ...oportal/service/util/CustomDataValue.java
@@ -1,4 +1,4 @@
-package org.cbioportal.web.parameter;
+package org.cbioportal.service.util;
 
 import java.io.Serializable;
 

diff --git a/service/src/main/java/org/cbioportal/service/util/SessionServiceConfig.java b/service/src/main/java/org/cbioportal/service/util/SessionServiceConfig.java
@@ -0,0 +1,16 @@
+package org.cbioportal.service.util;
+
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class SessionServiceConfig {
+
+    @Bean
+    public ObjectMapper sessionServiceObjectMapper() {
+        return new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+    }
+
+}
diff --git a/...eb/util/SessionServiceRequestHandler.java → ...ce/util/SessionServiceRequestHandler.java b/...eb/util/SessionServiceRequestHandler.java → ...ce/util/SessionServiceRequestHandler.java
@@ -1,15 +1,10 @@
-package org.cbioportal.web.util;
+package org.cbioportal.service.util;
 
 import java.nio.charset.Charset;
 
 import org.apache.commons.codec.binary.Base64;
 import org.apache.commons.lang3.StringUtils;
-import org.cbioportal.session_service.domain.Session;
 import org.cbioportal.session_service.domain.SessionType;
-import org.cbioportal.web.parameter.CustomDataSession;
-import org.cbioportal.web.parameter.CustomGeneList;
-import org.cbioportal.web.parameter.PageSettings;
-import org.cbioportal.web.parameter.VirtualStudy;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
@@ -18,9 +13,6 @@
 import org.springframework.stereotype.Component;
 import org.springframework.web.client.RestTemplate;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 @Component
 public class SessionServiceRequestHandler {
 
@@ -56,32 +48,16 @@ public HttpHeaders getHttpHeaders() {
         };
     }
 
-    public Session getSession(SessionType type, String id) throws Exception {
+    public String getSessionDataJson(SessionType type, String id) throws Exception {
 
         RestTemplate restTemplate = new RestTemplate();
 
         // add basic authentication in header
-        HttpEntity<String> headers = new HttpEntity<String>(getHttpHeaders());
+        HttpEntity<String> headers = new HttpEntity<>(getHttpHeaders());
         ResponseEntity<String> responseEntity = restTemplate.exchange(sessionServiceURL + type + "/" + id,
                 HttpMethod.GET, headers, String.class);
 
-        ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-
-        Session session;
-
-        if (type.equals(SessionType.virtual_study) || type.equals(SessionType.group)) {
-            session = mapper.readValue(responseEntity.getBody(), VirtualStudy.class);
-        } else if (type.equals(SessionType.settings)) {
-            session = mapper.readValue(responseEntity.getBody(), PageSettings.class);
-        } else if (type.equals(SessionType.custom_data)) {
-            session = mapper.readValue(responseEntity.getBody(), CustomDataSession.class);
-        } else if (type.equals(SessionType.custom_gene_list)) {
-            session = mapper.readValue(responseEntity.getBody(), CustomGeneList.class);
-        } else {
-            session = mapper.readValue(responseEntity.getBody(), Session.class);
-        }
-
-        return session;
+        return responseEntity.getBody();
     }
 
 }