🚨 Update peristence module tests to pass within springboot framework

cBioPortal · Sep 1, 2023 · 5a150a6 · 5a150a6
1 parent d60076f
commit 5a150a6
Show file tree

Hide file tree

Showing 11 changed files with 67 additions and 104 deletions.
diff --git a/...sistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java b/...sistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/ClinicalDataMapper.java
@@ -15,7 +15,7 @@ List<ClinicalData> getSampleClinicalData(List<String> studyIds, List<String> sam
     BaseMeta getMetaSampleClinicalData(List<String> studyIds, List<String> sampleIds, List<String> attributeIds);
 
     List<ClinicalData> getPatientClinicalData(List<String> studyIds, List<String> patientIds, List<String> attributeIds,
-                                              String projection, Integer limit, Integer offset, String sortby,
+                                              String projection, Integer limit, Integer offset, String sortBy,
                                               String direction);
 
     List<ClinicalData> getSampleClinicalTable(List<String> studyIds, List<String> sampleIds, String projection,

diff --git a/...-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml b/...-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/AlterationCountsMapper.xml
@@ -87,7 +87,7 @@
         INNER JOIN cancer_study ON cancer_study.CANCER_STUDY_ID = genetic_profile.CANCER_STUDY_ID
         INNER JOIN reference_genome_gene ON reference_genome_gene.ENTREZ_GENE_ID = cna_event.ENTREZ_GENE_ID
         INNER JOIN sample ON sample_cna_event.SAMPLE_ID = sample.INTERNAL_ID
-        AND reference_genome_gene.reference_genome_id = cancer_study.reference_genome_id
+        AND reference_genome_gene.REFERENCE_GENOME_ID = cancer_study.REFERENCE_GENOME_ID
         <where>
             <choose>
                 <when test="cnaTypes.hasNone()">NULL</when>
@@ -401,11 +401,11 @@
 	        gene.HUGO_GENE_SYMBOL,
 	        mutation_event.MUTATION_TYPE
         FROM mutation
-        INNER JOIN mutation_event ON mutation_event.mutation_event_id = mutation.mutation_event_id
-        INNER JOIN gene ON mutation.entrez_gene_id = gene.entrez_gene_id
-        INNER JOIN genetic_profile ON mutation.genetic_profile_id = genetic_profile.genetic_profile_id
-        INNER JOIN sample ON sample.internal_id = mutation.sample_id
-        INNER JOIN patient ON sample.patient_id = patient.internal_id
+        INNER JOIN mutation_event ON mutation_event.MUTATION_EVENT_ID = mutation.MUTATION_EVENT_ID
+        INNER JOIN gene ON mutation.ENTREZ_GENE_ID = gene.ENTREZ_GENE_ID
+        INNER JOIN genetic_profile ON mutation.GENETIC_PROFILE_ID = genetic_profile.GENETIC_PROFILE_ID
+        INNER JOIN sample ON sample.INTERNAL_ID = mutation.SAMPLE_ID
+        INNER JOIN patient ON sample.PATIENT_ID = patient.INTERNAL_ID
         <include refid="fromIncludeCustomAnnotationsMutation"/>
         <where>
             <choose>

diff --git a/...ence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml b/...ence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalDataMapper.xml
@@ -3,23 +3,6 @@
 
 <mapper namespace="org.cbioportal.persistence.mybatis.ClinicalDataMapper">
 
-    <!--    TODO duplicate of select in ClinicalAttributeMapper - remove-->
-    <!--    somehow the namespace mechanism does not work for this mapper xml-->
-    <sql id="selectClinicalAttribute">
-        clinical_attribute_meta.ATTR_ID AS "${prefix}attrId",
-        cancer_study.CANCER_STUDY_IDENTIFIER AS "${prefix}cancerStudyIdentifier",
-        clinical_attribute_meta.CANCER_STUDY_ID AS "${prefix}cancerStudyId",
-        clinical_attribute_meta.PATIENT_ATTRIBUTE AS "${prefix}patientAttribute",
-        clinical_attribute_meta.DISPLAY_NAME AS "${prefix}displayName"
-        <if test="projection == 'SUMMARY' || projection == 'DETAILED'">
-            ,
-            clinical_attribute_meta.DESCRIPTION AS "${prefix}description",
-            clinical_attribute_meta.DATATYPE AS "${prefix}datatype",
-            clinical_attribute_meta.PRIORITY AS "${prefix}priority"
-        </if>
-    </sql>
-
-
     <sql id="selectSample">
         clinical_sample.INTERNAL_ID AS "${prefix}internalId",
         sample.STABLE_ID AS "${prefix}sampleId",
@@ -32,7 +15,7 @@
             </if>
             <if test="projection == 'DETAILED'">
                 ,
-                <include refid="selectClinicalAttribute">
+                <include refid="org.cbioportal.persistence.mybatis.ClinicalAttributeMapper.select">
                     <property name="prefix" value="${prefix}clinicalAttribute."/>
                 </include>
             </if>
@@ -50,12 +33,12 @@
             </if>
             <if test="projection == 'DETAILED'">
                 ,
-                <include refid="selectClinicalAttribute">
+                <include refid="org.cbioportal.persistence.mybatis.ClinicalAttributeMapper.select">
                     <property name="prefix" value="${prefix}clinicalAttribute."/>
                 </include>
             </if>
         </if>
-     </sql>
+    </sql>
 
     <sql id="fromSample">
         FROM clinical_sample
@@ -149,7 +132,7 @@
             INNER JOIN type_of_cancer ON cancer_study.TYPE_OF_CANCER_ID = type_of_cancer.TYPE_OF_CANCER_ID
         </if>
         <include refid="whereSample"/>
-        <if test="_parameter.containsKey('sortBy') and sortBy != null and projection != 'ID'">
+        <if test="sortBy != null and projection != 'ID'">
             ORDER BY "${sortBy}" ${direction}
         </if>
         <if test="projection == 'ID'">
@@ -179,7 +162,7 @@
             INNER JOIN type_of_cancer ON cancer_study.TYPE_OF_CANCER_ID = type_of_cancer.TYPE_OF_CANCER_ID
         </if>
         <include refid="wherePatient"/>
-        <if test="_parameter.containsKey('sortBy') and sortBy != null and projection != 'ID'">
+        <if test="sortBy != null and projection != 'ID'">
             ORDER BY ${sortBy} ${direction}
         </if>
         <if test="projection == 'ID'">
@@ -261,7 +244,7 @@
     <sql id="whereSampleSearchAndPagination">
         INNER JOIN (
             SELECT DISTINCT clinical_sample.INTERNAL_ID
-            <if test="_parameter.containsKey('sortBy') and sortBy != null">
+            <if test="sortBy != null">
                 <if test="sortBy == 'sampleId'">
                   , sample.STABLE_ID AS SORT_BY
                 </if>
@@ -280,11 +263,11 @@
             </if>
             <include refid="fromSampleAndClinicalPatient"/>
             <include refid="whereSample"/>
-            <if test="_parameter.containsKey('searchTerm') and searchTerm != null and not searchTerm.isBlank()">
+            <if test="searchTerm != null and not searchTerm.isBlank()">
                 AND
                 clinical_sample.ATTR_VALUE LIKE CONCAT('%', #{searchTerm}, '%')
             </if>
-            <if test="_parameter.containsKey('sortBy') and sortBy != null">
+            <if test=" sortBy != null">
                 <!-- Put 'NULL samples' last: -->
                 <choose>
                     <when test="_databaseId == 'mysql'">

diff --git a/...nce-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml b/...nce-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml
@@ -105,7 +105,7 @@
         from sample
         Inner Join patient on sample.PATIENT_ID = patient.INTERNAL_ID
         Inner join clinical_event on clinical_event.PATIENT_ID = patient.INTERNAL_ID
-        Inner Join cancer_study on cancer_study.CANCER_STUDY_ID = patient.cancer_STUDY_ID
+        Inner Join cancer_study on cancer_study.CANCER_STUDY_ID = patient.CANCER_STUDY_ID
         <where>
             <if test="sampleIds == null and studyIds != null">
                 cancer_study.CANCER_STUDY_IDENTIFIER IN

diff --git a/...-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml b/...-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MolecularProfileMapper.xml
@@ -3,26 +3,6 @@
 
 <mapper namespace="org.cbioportal.persistence.mybatis.MolecularProfileMapper">
 
-    <!--    TODO duplicate of select in StudyMapper - remove-->
-    <!--    somehow the namespace import mechanism does not work for this mapper xml-->
-    <sql id="selectStudy">
-        cancer_study.CANCER_STUDY_ID AS "${prefix}cancerStudyId",
-        cancer_study.CANCER_STUDY_IDENTIFIER AS "${prefix}cancerStudyIdentifier"
-        <if test="projection == 'SUMMARY' || projection == 'DETAILED'">
-            ,
-            cancer_study.TYPE_OF_CANCER_ID AS "${prefix}typeOfCancerId",
-            cancer_study.NAME AS "${prefix}name",
-            cancer_study.DESCRIPTION AS "${prefix}description",
-            cancer_study.PUBLIC AS "${prefix}publicStudy",
-            cancer_study.PMID AS "${prefix}pmid",
-            cancer_study.CITATION AS "${prefix}citation",
-            cancer_study.GROUPS AS "${prefix}groups",
-            cancer_study.STATUS AS "${prefix}status",
-            cancer_study.IMPORT_DATE AS "${prefix}importDate",
-            reference_genome.NAME AS "${prefix}referenceGenome"
-        </if>
-    </sql>
-
     <sql id="select">
         genetic_profile.GENETIC_PROFILE_ID AS "${prefix}molecularProfileId",
         genetic_profile.STABLE_ID AS "${prefix}stableId",
@@ -42,7 +22,7 @@
         </if>
         <if test="projection == 'DETAILED'">
             ,
-            <include refid="selectStudy">
+            <include refid="org.cbioportal.persistence.mybatis.StudyMapper.select">
                 <property name="prefix" value="${prefix}cancerStudy."/>
             </include>
         </if>

diff --git a/...batis/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml b/...batis/src/main/resources/org/cbioportal/persistence/mybatis/ReferenceGenomeGeneMapper.xml
@@ -10,7 +10,7 @@
         reference_genome_gene.REFERENCE_GENOME_ID AS "${prefix}referenceGenomeId"
         <if test="projection == 'SUMMARY' || projection == 'DETAILED'">
             ,
-            gene.hugo_gene_symbol AS "${prefix}hugoGeneSymbol",
+            gene.HUGO_GENE_SYMBOL AS "${prefix}hugoGeneSymbol",
             reference_genome_gene.CHR AS "${prefix}chromosome",
             reference_genome_gene.CYTOBAND AS "${prefix}cytoband",
             reference_genome_gene.START AS "${prefix}start",
@@ -24,7 +24,7 @@
             <property name="prefix" value=""/>
         </include>
         FROM reference_genome_gene
-        INNER JOIN gene on gene.entrez_gene_id = reference_genome_gene.entrez_gene_id
+        INNER JOIN gene on gene.ENTREZ_GENE_ID = reference_genome_gene.ENTREZ_GENE_ID
         <if test="genomeName != null">
             INNER JOIN reference_genome ON reference_genome.REFERENCE_GENOME_ID = reference_genome_gene.REFERENCE_GENOME_ID
             WHERE reference_genome.NAME = #{genomeName}
@@ -38,7 +38,7 @@
         </include>
         FROM reference_genome_gene
         INNER JOIN reference_genome ON reference_genome.REFERENCE_GENOME_ID = reference_genome_gene.REFERENCE_GENOME_ID
-        INNER JOIN gene ON gene.entrez_gene_id = reference_genome_gene.entrez_gene_id
+        INNER JOIN gene ON gene.ENTREZ_GENE_ID = reference_genome_gene.ENTREZ_GENE_ID
         <where>
             <if test="geneIds != null and !geneIds.isEmpty() and genomeName != null">
                 gene.HUGO_GENE_SYMBOL IN
@@ -60,7 +60,7 @@
         </include>
         FROM reference_genome_gene
         INNER JOIN reference_genome ON reference_genome.REFERENCE_GENOME_ID = reference_genome_gene.REFERENCE_GENOME_ID
-        INNER JOIN gene ON gene.entrez_gene_id = reference_genome_gene.entrez_gene_id
+        INNER JOIN gene ON gene.ENTREZ_GENE_ID = reference_genome_gene.ENTREZ_GENE_ID
         <where>
             <if test="geneIds != null and !geneIds.isEmpty() and genomeName != null">
                 gene.ENTREZ_GENE_ID IN
@@ -82,7 +82,7 @@
         </include>
         FROM reference_genome_gene
         INNER JOIN reference_genome ON reference_genome.REFERENCE_GENOME_ID = reference_genome_gene.REFERENCE_GENOME_ID
-        INNER JOIN gene ON gene.entrez_gene_id = reference_genome_gene.entrez_gene_id
+        INNER JOIN gene ON gene.ENTREZ_GENE_ID = reference_genome_gene.ENTREZ_GENE_ID
         <where>
             <if test="genomeName != null and geneId != null">
                 reference_genome.NAME = #{genomeName} AND gene.ENTREZ_GENE_ID = #{geneId}
@@ -95,11 +95,11 @@
             <property name="prefix" value=""/>
         </include>
         FROM reference_genome_gene
-        INNER JOIN gene on gene.entrez_gene_id = reference_genome_gene.entrez_gene_id
+        INNER JOIN gene on gene.ENTREZ_GENE_ID = reference_genome_gene.ENTREZ_GENE_ID
         INNER JOIN reference_genome ON reference_genome.REFERENCE_GENOME_ID = reference_genome_gene.REFERENCE_GENOME_ID
         <where>
             <if test="genomeName != null and geneticEntityId != null">
-                reference_genome.NAME = #{genomeName} AND gene.genetic_entity_id = #{geneticEntityId}
+                reference_genome.NAME = #{genomeName} AND gene.GENETIC_ENTITY_ID = #{geneticEntityId}
             </if>
             <if test="genomeName == null or geneticEntityId == null">
                 FALSE

diff --git a/...ersistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml b/...ersistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/SampleMapper.xml
@@ -13,13 +13,12 @@
             sample.SAMPLE_TYPE AS "${prefix}sampleType",
             sample.PATIENT_ID AS "${prefix}patientId"
         </if>
-        <!--TODO: This causes an error while referencing another sql statement. Need to fix -->
-<!--        <if test="projection == 'DETAILED'">-->
-<!--            ,-->
-<!--            <include refid="org.cbioportal.persistence.mybatis.PatientMapper.select">-->
-<!--                <property name="prefix" value="${prefix}patient."/>-->
-<!--            </include>-->
-<!--        </if>-->
+        <if test="projection == 'DETAILED'">
+            ,
+            <include refid="org.cbioportal.persistence.mybatis.PatientMapper.select">
+                <property name="prefix" value="${prefix}patient."/>
+            </include>
+        </if>
     </sql>
 
     <sql id="from">

diff --git a/...persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml b/...persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/StudyMapper.xml
@@ -21,17 +21,6 @@
         </if>
     </sql>
 
-    <!--TODO fix duplicate -->
-    <sql id="CancerTypeMapperSelect">
-        type_of_cancer.TYPE_OF_CANCER_ID AS "${prefix}typeOfCancerId"
-        <if test="projection == 'SUMMARY' || projection == 'DETAILED'">
-            ,
-            type_of_cancer.NAME AS "${prefix}name",
-            type_of_cancer.DEDICATED_COLOR AS "${prefix}dedicatedColor",
-            type_of_cancer.SHORT_NAME AS "${prefix}shortName",
-            type_of_cancer.PARENT AS "${prefix}parent"
-        </if>
-    </sql>
 
     <sql id="selectDetailed">
         ,
@@ -45,8 +34,8 @@
         COUNT(CASE WHEN sample_list.STABLE_ID = CONCAT(cancer_study.CANCER_STUDY_IDENTIFIER,'_rppa') THEN 1 ELSE NULL END) AS rppaSampleCount,
         COUNT(CASE WHEN sample_list.STABLE_ID = CONCAT(cancer_study.CANCER_STUDY_IDENTIFIER,'_protein_quantification') THEN 1 ELSE NULL END) AS massSpectrometrySampleCount,
         COUNT(CASE WHEN sample_list.STABLE_ID = CONCAT(cancer_study.CANCER_STUDY_IDENTIFIER,'_3way_complete') THEN 1 ELSE NULL END) AS completeSampleCount,
-        IFNULL(treatment.count, 0 ) as treatmentCount, 
-        <include refid="CancerTypeMapperSelect">
+        IFNULL(treatment.count, 0 ) as treatmentCount,
+        <include refid="org.cbioportal.persistence.mybatis.CancerTypeMapper.select">
             <property name="prefix" value="typeOfCancer."/>
         </include>
     </sql>

diff --git a/...tis/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java b/...tis/src/test/java/org/cbioportal/persistence/mybatis/AlterationMyBatisRepositoryTest.java
@@ -1,5 +1,6 @@
 package org.cbioportal.persistence.mybatis;
 
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -16,6 +17,7 @@
 import org.cbioportal.model.QueryElement;
 import org.cbioportal.model.util.Select;
 import org.cbioportal.persistence.mybatis.config.TestConfig;
+import org.h2.tools.Server;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;

diff --git a/...s/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java b/...s/src/test/java/org/cbioportal/persistence/mybatis/ClinicalDataMyBatisRepositoryTest.java
@@ -59,11 +59,14 @@ public void getAllClinicalDataOfSampleInStudyNullAttributeSummaryProjection() {
             "TCGA-A1-A0SB-01", null, "SUMMARY", null, null, null, null);
 
         Assert.assertEquals(4, result.size());
-        ClinicalData data = result.get(0);
-        Assert.assertEquals("DAYS_TO_COLLECTION", data.getAttrId());
-        Assert.assertEquals("276", data.getAttrValue());
-        Assert.assertEquals((Integer) 1, data.getInternalId());
-        Assert.assertNull(data.getClinicalAttribute());
+        Optional<ClinicalData> clinicalDataOptional =
+            result.stream().filter(r -> r.getAttrId().equals("DAYS_TO_COLLECTION")).findAny();
+        Assert.assertTrue(clinicalDataOptional.isPresent());
+        ClinicalData clinicalAttribute = clinicalDataOptional.get();
+
+        Assert.assertEquals("276", clinicalAttribute.getAttrValue());
+        Assert.assertEquals((Integer) 1, clinicalAttribute.getInternalId());
+        Assert.assertNull(clinicalAttribute.getClinicalAttribute());
     }
 
     @Test
@@ -230,7 +233,10 @@ public void getAllClinicalDataInStudyNullAttributeSummaryProjection() {
             null, PersistenceConstants.SAMPLE_CLINICAL_DATA_TYPE, "SUMMARY", null, null, null, null);
 
         Assert.assertEquals(8, result.size());
-        ClinicalData data = result.get(0);
+        Optional<ClinicalData> clinicalDataOptional =
+            result.stream().filter(r -> r.getAttrId().equals("DAYS_TO_COLLECTION")).findAny();
+        Assert.assertTrue(clinicalDataOptional.isPresent());
+        ClinicalData data = clinicalDataOptional.get();
         Assert.assertEquals("DAYS_TO_COLLECTION", data.getAttrId());
         Assert.assertEquals("276", data.getAttrValue());
         Assert.assertEquals((Integer) 1, data.getInternalId());
@@ -325,14 +331,6 @@ public void fetchAllClinicalDataInStudy() {
             PersistenceConstants.SAMPLE_CLINICAL_DATA_TYPE, "SUMMARY");
 
         Assert.assertEquals(8, result.size());
-        ClinicalData data = result.get(0);
-        Assert.assertEquals("DAYS_TO_COLLECTION", data.getAttrId());
-        Assert.assertEquals("276", data.getAttrValue());
-        Assert.assertEquals((Integer) 1, data.getInternalId());
-        Assert.assertNull(data.getClinicalAttribute());
-        Assert.assertEquals(6, result.size());
-
-
         Optional<ClinicalData> clinicalDataOptional =
             result.stream().filter(r -> r.getAttrId().equals("DAYS_TO_COLLECTION")).findAny();
         Assert.assertTrue(clinicalDataOptional.isPresent());
@@ -359,13 +357,6 @@ public void fetchClinicalDataNullAttributeSummaryProjection() {
             PersistenceConstants.SAMPLE_CLINICAL_DATA_TYPE, "SUMMARY");
 
         Assert.assertEquals(8, result.size());
-        ClinicalData data = result.get(0);
-        Assert.assertEquals("DAYS_TO_COLLECTION", data.getAttrId());
-        Assert.assertEquals("276", data.getAttrValue());
-        Assert.assertEquals((Integer) 1, data.getInternalId());
-        Assert.assertNull(data.getClinicalAttribute());
-        Assert.assertEquals(6, result.size());
-
         Optional<ClinicalData> clinicalDataOptional =
             result.stream().filter(r -> r.getAttrId().equals("DAYS_TO_COLLECTION")).findAny();
         Assert.assertTrue(clinicalDataOptional.isPresent());