Paginated clinical table

model/src/main/java/org/cbioportal/model/ClinicalDataCollection.java

@@ -5,9 +5,16 @@
 
 public class ClinicalDataCollection {
 
+    /**
+     * Paginated resource
+     */
     private List<ClinicalData> sampleClinicalData = new ArrayList<>();
-    private List<ClinicalData> patientClinicalData = new ArrayList<>();
 
+    /**
+     * Patient info associated with paginated samples
+     */
+    private List<ClinicalData> patientClinicalData = new ArrayList<>();
+
     public List<ClinicalData> getSampleClinicalData() {
         return sampleClinicalData;
     }

persistence/persistence-api/src/main/java/org/cbioportal/persistence/ClinicalDataRepository.java

@@ -47,9 +47,13 @@ BaseMeta fetchMetaClinicalDataInStudy(String studyId, List<String> ids, List<Str
     List<ClinicalData> fetchClinicalData(List<String> studyIds, List<String> ids, List<String> attributeIds,
                                          String clinicalDataType, String projection);
 
-    List<ClinicalData> fetchSampleClinicalDataClinicalTable(List<String> studyIds, List<String> ids,
-                                                            Integer pageSize, Integer pageNumber, String searchTerm,
-                                                            String sortBy, String direction);
+    List<ClinicalData> fetchSampleClinicalTable(List<String> studyIds, List<String> ids,
+                                                Integer pageSize, Integer pageNumber, String searchTerm,
+                                                String sortBy, String direction);
+
+    @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
+    Integer fetchSampleClinicalTableCount(List<String> studyIds, List<String> ids, String searchTerm,
+                                          String sortBy, String direction);
 
     @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
     BaseMeta fetchMetaClinicalData(List<String> studyIds, List<String> ids, List<String> attributeIds,

persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java

@@ -18,9 +18,12 @@ List<ClinicalData> getPatientClinicalData(List<String> studyIds, List<String> pa
                                               String projection, Integer limit, Integer offset, String sortby,
                                               String direction);
 
-    List<ClinicalData> getSampleClinicalDataClinicalTable(List<String> studyIds, List<String> sampleIds, String projection, 
-                                                          Integer limit, Integer offset, String searchTerm,
-                                                          String sortBy, String direction);
+    List<ClinicalData> getSampleClinicalTable(List<String> studyIds, List<String> sampleIds, String projection,
+                                              Integer limit, Integer offset, String searchTerm,
+                                              String sortBy, String direction);
+
+    Integer getSampleClinicalTableCount(List<String> studyIds, List<String> sampleIds, String projection,
+                                        String searchTerm, String sortBy, String direction);
 
     BaseMeta getMetaPatientClinicalData(List<String> studyIds, List<String> patientIds, List<String> attributeIds);
 
@@ -33,5 +36,4 @@ List<ClinicalDataCount> fetchPatientClinicalDataCounts(List<String> studyIds, Li
     List<ClinicalData> getPatientClinicalDataDetailedToSample(List<String> studyIds, List<String> patientIds,
                                                               List<String> attributeIds, String projection, Integer limit,
                                                               Integer offset, String sortBy, String direction);
-
 }

persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepository.java

@@ -138,17 +138,24 @@ public List<ClinicalData> fetchClinicalData(List<String> studyIds, List<String>
     }
 
     @Override
-    public List<ClinicalData> fetchSampleClinicalDataClinicalTable(List<String> studyIds, List<String> ids,
-                                                                   Integer pageSize, Integer pageNumber, String searchTerm,
-                                                                   String sortBy, String direction) {
+    public List<ClinicalData> fetchSampleClinicalTable(List<String> studyIds, List<String> ids,
+                                                       Integer pageSize, Integer pageNumber, String searchTerm,
+                                                       String sortBy, String direction) {
         if (ids.isEmpty()) {
             return new ArrayList<>();
         }
         int offset = offsetCalculator.calculate(pageSize, pageNumber);
-        return clinicalDataMapper.getSampleClinicalDataClinicalTable(studyIds, ids,"SUMMARY", pageSize,
+        return clinicalDataMapper.getSampleClinicalTable(studyIds, ids,"SUMMARY", pageSize,
             offset, searchTerm, sortBy, direction);
     }
 
+    @Override
+    public Integer fetchSampleClinicalTableCount(List<String> studyIds, List<String> sampleIds,
+                                                 String searchTerm, String sortBy, String direction) {
+        return clinicalDataMapper.getSampleClinicalTableCount(studyIds, sampleIds,"SUMMARY", 
+            searchTerm, sortBy, direction);
+    }
+
     @Override
     public BaseMeta fetchMetaClinicalData(List<String> studyIds, List<String> ids, List<String> attributeIds,
                                           String clinicalDataType) {

persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml

@@ -47,6 +47,11 @@
         INNER JOIN cancer_study ON patient.CANCER_STUDY_ID = cancer_study.CANCER_STUDY_ID
     </sql>
 
+    <sql id="fromSampleAndClinicalPatient">
+        <include refid="fromSample"/>
+        LEFT JOIN clinical_patient ON clinical_patient.INTERNAL_ID = patient.INTERNAL_ID
+    </sql>
+
     <sql id="fromPatient">
         FROM clinical_patient
         INNER JOIN patient ON clinical_patient.INTERNAL_ID = patient.INTERNAL_ID
@@ -221,7 +226,7 @@
         GROUP BY clinical_patient.ATTR_ID, clinical_patient.ATTR_VALUE
     </select>
 
-    <select id="getSampleClinicalDataClinicalTable" resultType="org.cbioportal.model.ClinicalData">
+    <select id="getSampleClinicalTable" resultType="org.cbioportal.model.ClinicalData">
         SELECT
         <include refid="selectSample">
             <property name="prefix" value=""/>
@@ -230,28 +235,55 @@
         <include refid="whereSampleSearchAndPagination"/>
     </select>
 
+    <select id="getSampleClinicalTableCount" resultType="Integer">
+        SELECT count(DISTINCT clinical_sample.INTERNAL_ID)
+        <include refid="fromSample"/>
+        <include refid="whereSampleSearchAndPagination"/>
+    </select>
+
     <sql id="whereSampleSearchAndPagination">
-        INNER JOIN
-        (SELECT DISTINCT clinical_sample.INTERNAL_ID
+        INNER JOIN (
+            SELECT DISTINCT clinical_sample.INTERNAL_ID
             <if test="_parameter.containsKey('sortBy') and sortBy != null">
-                , clinical_sample.ATTR_ID, clinical_sample.ATTR_VALUE
+                <if test="sortBy == 'sampleId'">
+                  , sample.STABLE_ID AS SORT_BY
+                </if>
+                <if test="sortBy == 'patientId'">
+                  , patient.STABLE_ID AS SORT_BY
+                </if>
+                <!-- else: -->
+                <if test="sortBy != 'sampleId' and sortBy != 'patientId'">
+                  <!-- Mark samples without the sort attribute as NULL: -->
+                  , CASE 
+                        WHEN clinical_sample.ATTR_ID = #{sortBy} THEN clinical_sample.ATTR_VALUE 
+                        WHEN clinical_patient.ATTR_ID = #{sortBy} THEN clinical_patient.ATTR_VALUE 
+                        ELSE NULL 
+                    END AS SORT_BY
+                </if>
             </if>
-            <include refid="fromSample"/>
+            <include refid="fromSampleAndClinicalPatient"/>
             <include refid="whereSample"/>
             <if test="_parameter.containsKey('searchTerm') and searchTerm != null and not searchTerm.isBlank()">
                 AND
-                clinical_sample.ATTR_VALUE LIKE CONCAT('%','${searchTerm}', '%')
+                clinical_sample.ATTR_VALUE LIKE CONCAT('%', #{searchTerm}, '%')
             </if>
             <if test="_parameter.containsKey('sortBy') and sortBy != null">
-                AND 
-                clinical_sample.ATTR_ID = '${sortBy}'
-                ORDER BY clinical_sample.ATTR_VALUE ${direction}
+                <!-- Put 'NULL samples' last: -->
+                <choose>
+                    <when test="_databaseId == 'mysql'">
+                        ORDER BY ISNULL(SORT_BY), SORT_BY ${direction}
+                    </when>
+                    <when test="_databaseId == 'h2'">
+                        ORDER BY SORT_BY ${direction} NULLS LAST
+                    </when>
+                </choose>
             </if>
+
             <if test="_parameter.containsKey('limit') and limit != null and limit != 0">
                 LIMIT #{limit} OFFSET #{offset}
             </if>
-        ) as sample_id_subquery
-        ON clinical_sample.INTERNAL_ID = sample_id_subquery.INTERNAL_ID
+        ) AS sample_id_subquery
+          ON clinical_sample.INTERNAL_ID = sample_id_subquery.INTERNAL_ID
     </sql>
 
 </mapper>

persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java

@@ -354,9 +354,9 @@ public void fetchClinicalDataNullAttributeSummaryProjection() {
     @Test
     public void fetchClinicalSampleDataClinicalTabPagingSuccess() {
 
-        List<ClinicalData> resultFirstPage = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(studyIds,
+        List<ClinicalData> resultFirstPage = clinicalDataMyBatisRepository.fetchSampleClinicalTable(studyIds,
             sampleIds, 1, 0, noSearch, noSort, "DESC");
-        List<ClinicalData> resultSecondPage = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(studyIds,
+        List<ClinicalData> resultSecondPage = clinicalDataMyBatisRepository.fetchSampleClinicalTable(studyIds,
             sampleIds, 1, 1, noSearch, noSort, "DESC");
 
         Assert.assertEquals(4, resultFirstPage.size());
@@ -380,7 +380,7 @@ public void fetchClinicalSampleDataClinicalTabPagingSuccess() {
     public void fetchClinicalSampleDataClinicalTablePagingHandleNoneExistingPage() {
 
         // There are only two patients in total. The second page (index 1) with pageSize 2 does not refer to any records.
-        List<ClinicalData> resultNonExistingPage = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(
+        List<ClinicalData> resultNonExistingPage = clinicalDataMyBatisRepository.fetchSampleClinicalTable(
             studyIds, sampleIds, 2, 1, noSearch, noSort, "DESC");
 
         Assert.assertEquals(0, resultNonExistingPage.size());
@@ -389,15 +389,15 @@ public void fetchClinicalSampleDataClinicalTablePagingHandleNoneExistingPage() {
     @Test
     public void fetchClinicalSampleDataClinicalTabSearchTermSuccess() {
 
-        List<ClinicalData> resultSample1 = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(
+        List<ClinicalData> resultSample1 = clinicalDataMyBatisRepository.fetchSampleClinicalTable(
             studyIds, sampleIds, noPaging, noPaging, "5C631CE8", noSort, "DESC");
 
         Assert.assertEquals(4, resultSample1.size());
         List<String> observedSampleIds = resultSample1.stream().map(s -> s.getSampleId()).distinct().collect(Collectors.toList());
         Assert.assertEquals(1, observedSampleIds.size());
         Assert.assertEquals("TCGA-A1-A0SB-01", observedSampleIds.get(0));
 
-        List<ClinicalData> resultSample2 = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(
+        List<ClinicalData> resultSample2 = clinicalDataMyBatisRepository.fetchSampleClinicalTable(
             studyIds, sampleIds, noPaging, noPaging, "F3408556-9259", noSort, "DESC");
 
         Assert.assertEquals(4, resultSample2.size());
@@ -409,7 +409,7 @@ public void fetchClinicalSampleDataClinicalTabSearchTermSuccess() {
     @Test
     public void fetchClinicalSampleDataEClinicalTabEmptyStringSearchTerm() {
 
-        List<ClinicalData> result = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(
+        List<ClinicalData> result = clinicalDataMyBatisRepository.fetchSampleClinicalTable(
             studyIds, sampleIds, noPaging, noPaging, "", noSort, "DESC");
 
         Assert.assertEquals(8, result.size());
@@ -418,9 +418,9 @@ public void fetchClinicalSampleDataEClinicalTabEmptyStringSearchTerm() {
     @Test
     public void fetchClinicalSampleDataClinicalTabSortSuccess() {
 
-        List<ClinicalData> resultSortAsc = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(studyIds,
+        List<ClinicalData> resultSortAsc = clinicalDataMyBatisRepository.fetchSampleClinicalTable(studyIds,
             sampleIds, 1, 0, noSearch, "SAMPLE_TYPE", "ASC");
-        List<ClinicalData> resultSortDesc = clinicalDataMyBatisRepository.fetchSampleClinicalDataClinicalTable(studyIds,
+        List<ClinicalData> resultSortDesc = clinicalDataMyBatisRepository.fetchSampleClinicalTable(studyIds,
             sampleIds, 1, 0, noSearch, "SAMPLE_TYPE", "DESC");
 
         Assert.assertEquals(4, resultSortAsc.size());

service/src/main/java/org/cbioportal/service/ClinicalDataService.java

@@ -52,6 +52,9 @@ BaseMeta fetchMetaClinicalData(List<String> studyIds, List<String> ids, List<Str
     List<ClinicalData> getPatientClinicalDataDetailedToSample(List<String> studyIds, List<String> patientIds,
             List<String> attributeIds);
 
-    List<ClinicalData> fetchSampleClinicalDataClinicalTable(List<String> studyIds, List<String> sampleIds, Integer pageSize,
-                                                            Integer pageNumber, String searchTerm, String sortBy, String direction);
+    List<ClinicalData> fetchSampleClinicalTable(List<String> studyIds, List<String> sampleIds, Integer pageSize,
+                                                Integer pageNumber, String searchTerm, String sortBy, String direction);
+
+    Integer fetchSampleClinicalTableCount(List<String> studyIds, List<String> sampleIds, String searchTerm,
+                                          String sortBy, String direction);
 }

service/src/main/java/org/cbioportal/service/impl/ClinicalDataServiceImpl.java

@@ -1,6 +1,5 @@
 package org.cbioportal.service.impl;
 
-import org.apache.commons.collections4.list.UnmodifiableList;
 import org.cbioportal.model.*;
 import org.cbioportal.model.meta.BaseMeta;
 import org.cbioportal.persistence.ClinicalDataRepository;
@@ -228,10 +227,17 @@ public List<ClinicalData> getPatientClinicalDataDetailedToSample(List<String> st
     }
 
     @Override
-    public List<ClinicalData> fetchSampleClinicalDataClinicalTable(List<String> studyIds, List<String> sampleIds, Integer pageSize,
-                                                                   Integer pageNumber, String searchTerm, String sortBy,
-                                                                   String direction) {
-        return clinicalDataRepository.fetchSampleClinicalDataClinicalTable(studyIds, sampleIds, pageSize, pageNumber, searchTerm,
+    public List<ClinicalData> fetchSampleClinicalTable(List<String> studyIds, List<String> sampleIds, Integer pageSize,
+                                                       Integer pageNumber, String searchTerm, String sortBy,
+                                                       String direction) {
+        return clinicalDataRepository.fetchSampleClinicalTable(studyIds, sampleIds, pageSize, pageNumber, searchTerm,
                                                                             sortBy, direction);
     }
+
+    @Override
+    public Integer fetchSampleClinicalTableCount(List<String> studyIds, List<String> sampleIds,
+                                                 String searchTerm, String sortBy, String direction) {
+        return clinicalDataRepository.fetchSampleClinicalTableCount(studyIds, sampleIds, searchTerm, 
+            sortBy, direction);
+    }
 }