fix Patient Mapper select SQL prefix

Author: onursumer

src/main/resources/org/cbioportal/legacy/persistence/mybatis/PatientMapper.xml

@@ -3,25 +3,26 @@
 
 <mapper namespace="org.cbioportal.legacy.persistence.mybatis.PatientMapper">
 
+    <!-- TODO: we should eventually get rid of the ${prefix} and the quotes if possible -->
     <sql id="select">
         patient.internal_id AS "${prefix}internalId",
         patient.stable_id AS "${prefix}stableId",
         patient.cancer_study_id AS "${prefix}cancerStudyId",
         cancer_study.cancer_study_identifier AS "${prefix}cancerStudyIdentifier"
         <if test="projection == 'DETAILED'">
             ,
-            cancer_study.cancer_study_id         AS "cancerStudy.cancerStudyId",
-            cancer_study.cancer_study_identifier AS "cancerStudy.cancerStudyIdentifier",
-            cancer_study.type_of_cancer_id       AS "cancerStudy.typeOfCancerId",
-            cancer_study.name                   AS "cancerStudy.name",
-            cancer_study.description             AS "cancerStudy.description",
-            cancer_study.public                  AS "cancerStudy.publicStudy",
-            cancer_study.pmid                    AS "cancerStudy.pmid",
-            cancer_study.citation                AS "cancerStudy.citation",
-            cancer_study.groups                  AS "cancerStudy.groups",
-            cancer_study.status                  AS "cancerStudy.status",
-            cancer_study.import_date             AS "cancerStudy.importDate",
-            reference_genome.name                AS "cancerStudy.referenceGenome"
+            cancer_study.cancer_study_id         AS "${prefix}cancerStudy.cancerStudyId",
+            cancer_study.cancer_study_identifier AS "${prefix}cancerStudy.cancerStudyIdentifier",
+            cancer_study.type_of_cancer_id       AS "${prefix}cancerStudy.typeOfCancerId",
+            cancer_study.name                    AS "${prefix}cancerStudy.name",
+            cancer_study.description             AS "${prefix}cancerStudy.description",
+            cancer_study.public                  AS "${prefix}cancerStudy.publicStudy",
+            cancer_study.pmid                    AS "${prefix}cancerStudy.pmid",
+            cancer_study.citation                AS "${prefix}cancerStudy.citation",
+            cancer_study.groups                  AS "${prefix}cancerStudy.groups",
+            cancer_study.status                  AS "${prefix}cancerStudy.status",
+            cancer_study.import_date             AS "${prefix}cancerStudy.importDate",
+            reference_genome.name                AS "${prefix}cancerStudy.referenceGenome"
         </if>
     </sql>
 

src/test/java/org/cbioportal/legacy/persistence/mybatis/SampleMyBatisRepositoryTest.java

@@ -89,9 +89,9 @@ public void getAllSamplesInStudyDetailedProjection() throws Exception {
     Assert.assertEquals("brca", cancerStudy.getTypeOfCancerId());
     Assert.assertEquals("Breast Invasive Carcinoma (TCGA, Nature 2012)", cancerStudy.getName());
     Assert.assertEquals(
-        "<a href=\\\"http://cancergenome.nih.gov/\\\">The Cancer Genome Atlas (TCGA)</a> Breast"
-            + " Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href=\\\"http://tcga-data.nci."
-            + "nih.gov/tcga/\\\">Raw data via the TCGA Data Portal</a>.",
+        "<a href=\"http://cancergenome.nih.gov/\">The Cancer Genome Atlas (TCGA)</a> Breast"
+            + " Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href=\"http://tcga-data.nci."
+            + "nih.gov/tcga/\">Raw data via the TCGA Data Portal</a>.",
         cancerStudy.getDescription());
     Assert.assertEquals(true, cancerStudy.getPublicStudy());
     Assert.assertEquals("23000897,26451490", cancerStudy.getPmid());
@@ -162,9 +162,9 @@ public void getSampleInStudy() throws Exception {
     Assert.assertEquals("brca", cancerStudy.getTypeOfCancerId());
     Assert.assertEquals("Breast Invasive Carcinoma (TCGA, Nature 2012)", cancerStudy.getName());
     Assert.assertEquals(
-        "<a href=\\\"http://cancergenome.nih.gov/\\\">The Cancer Genome Atlas (TCGA)</a> Breast"
-            + " Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href=\\\"http://tcga-data.nci."
-            + "nih.gov/tcga/\\\">Raw data via the TCGA Data Portal</a>.",
+        "<a href=\"http://cancergenome.nih.gov/\">The Cancer Genome Atlas (TCGA)</a> Breast"
+            + " Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href=\"http://tcga-data.nci."
+            + "nih.gov/tcga/\">Raw data via the TCGA Data Portal</a>.",
         cancerStudy.getDescription());
     Assert.assertEquals(true, cancerStudy.getPublicStudy());
     Assert.assertEquals("23000897,26451490", cancerStudy.getPmid());
@@ -229,9 +229,9 @@ public void getAllSamplesOfPatientInStudyDetailedProjection() throws Exception {
     Assert.assertEquals("brca", cancerStudy.getTypeOfCancerId());
     Assert.assertEquals("Breast Invasive Carcinoma (TCGA, Nature 2012)", cancerStudy.getName());
     Assert.assertEquals(
-        "<a href=\\\"http://cancergenome.nih.gov/\\\">The Cancer Genome Atlas (TCGA)</a> Breast"
-            + " Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href=\\\"http://tcga-data.nci."
-            + "nih.gov/tcga/\\\">Raw data via the TCGA Data Portal</a>.",
+        "<a href=\"http://cancergenome.nih.gov/\">The Cancer Genome Atlas (TCGA)</a> Breast"
+            + " Invasive Carcinoma project. 825 cases.<br><i>Nature 2012.</i> <a href=\"http://tcga-data.nci."
+            + "nih.gov/tcga/\">Raw data via the TCGA Data Portal</a>.",
         cancerStudy.getDescription());
     Assert.assertEquals(true, cancerStudy.getPublicStudy());
     Assert.assertEquals("23000897,26451490", cancerStudy.getPmid());