Automated release-1.19.0 to rc merge

cBioPortal · Nov 27, 2018 · 9e294f5 · 9e294f5
2 parents 99a3afc + 15bcbd6
commit 9e294f5
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Showing 7 changed files with 16 additions and 7 deletions.
diff --git a/...mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml b/...mybatis/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalAttributeMapper.xml
@@ -60,6 +60,7 @@
                 SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
                 INNER JOIN sample_list ON sample_list_list.LIST_ID = sample_list.LIST_ID
                 WHERE sample_list.STABLE_ID = #{sampleListId}
+                AND sample_list_list.SAMPLE_ID = sample.INTERNAL_ID
             )
         </where>
     </sql>

diff --git a/...mybatis/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml b/...mybatis/src/main/resources/org/cbioportal/persistence/mybatis/CopyNumberSegmentMapper.xml
@@ -93,6 +93,7 @@
             SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
             INNER JOIN sample_list ON sample_list_list.LIST_ID = sample_list.LIST_ID
             WHERE sample_list.STABLE_ID = #{sampleListId}
+            AND sample_list_list.SAMPLE_ID = copy_number_seg.SAMPLE_ID
         )
     </select>
 </mapper>
diff --git a/...ybatis/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml b/...ybatis/src/main/resources/org/cbioportal/persistence/mybatis/DiscreteCopyNumberMapper.xml
@@ -60,6 +60,7 @@
                 SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
                 INNER JOIN sample_list ON sample_list_list.LIST_ID = sample_list.LIST_ID
                 WHERE sample_list.STABLE_ID = #{sampleListId}
+                AND sample_list_list.SAMPLE_ID = sample_cna_event.SAMPLE_ID
             )
             <if test="entrezGeneIds != null and !entrezGeneIds.isEmpty()">
                 AND cna_event.ENTREZ_GENE_ID IN
@@ -213,7 +214,9 @@
                 <foreach item="item" collection="molecularProfileIds" open="(" separator="," close=")">
                     #{item}
                 </foreach>
-            </if>)
+            </if>
+            AND sample.INTERNAL_ID = sample_cna_event.SAMPLE_ID 
+            AND genetic_profile.GENETIC_PROFILE_ID = sample_cna_event.GENETIC_PROFILE_ID)
         </if>
         <if test="entrezGeneIds != null">
             AND (cna_event.ENTREZ_GENE_ID, cna_event.ALTERATION) IN

diff --git a/...istence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml b/...istence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/GenePanelMapper.xml
@@ -101,6 +101,7 @@
             SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
             INNER JOIN sample_list ON sample_list_list.LIST_ID = sample_list.LIST_ID
             WHERE sample_list.STABLE_ID = #{sampleListId}
+            AND sample_list_list.SAMPLE_ID = sample_profile.SAMPLE_ID
         )
     </select>
 

diff --git a/...sistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml b/...sistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MutationMapper.xml
@@ -88,6 +88,7 @@
                 SELECT sample_list_list.SAMPLE_ID FROM sample_list_list
                 INNER JOIN sample_list ON sample_list_list.LIST_ID = sample_list.LIST_ID
                 WHERE sample_list.STABLE_ID = #{sampleListId}
+                AND sample_list_list.SAMPLE_ID = mutation.SAMPLE_ID
             )
             <if test="entrezGeneIds != null and !entrezGeneIds.isEmpty()">
                 AND mutation.ENTREZ_GENE_ID IN
@@ -126,7 +127,9 @@
                     <foreach item="item" collection="molecularProfileIds" open="(" separator="," close=")">
                         #{item}
                     </foreach>
-                </if>)
+                </if>
+                AND sample.INTERNAL_ID = mutation.SAMPLE_ID 
+                AND genetic_profile.GENETIC_PROFILE_ID = mutation.GENETIC_PROFILE_ID)
             </if>
             <if test="sampleIds == null">
                 genetic_profile.STABLE_ID IN

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
@@ -112,6 +112,7 @@
             <foreach item="item" collection="list" open="(" separator="," close=")">
                 #{item}
             </foreach>
+            AND sample_list_list.SAMPLE_ID = sample.INTERNAL_ID
         )
     </select>
 

diff --git a/...batis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java b/...batis/src/test/java/org/cbioportal/persistence/mybatis/MutationMyBatisRepositoryTest.java
@@ -12,7 +12,6 @@
 
 import java.math.BigDecimal;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 @RunWith(SpringJUnit4ClassRunner.class)
@@ -224,14 +223,14 @@ public void getMutationsInMultipleMolecularProfiles() throws Exception {
 
         Assert.assertEquals(3, result.size());
         Mutation mutation1 = result.get(0);
-        Assert.assertEquals("acc_tcga_mutations", mutation1.getMolecularProfileId());
-        Assert.assertEquals("TCGA-A1-B0SO-01", mutation1.getSampleId());
+        Assert.assertEquals("study_tcga_pub_mutations", mutation1.getMolecularProfileId());
+        Assert.assertEquals("TCGA-A1-A0SH-01", mutation1.getSampleId());
         Mutation mutation2 = result.get(1);
         Assert.assertEquals("study_tcga_pub_mutations", mutation2.getMolecularProfileId());
         Assert.assertEquals("TCGA-A1-A0SH-01", mutation2.getSampleId());
         Mutation mutation3 = result.get(2);
-        Assert.assertEquals("study_tcga_pub_mutations", mutation3.getMolecularProfileId());
-        Assert.assertEquals("TCGA-A1-A0SH-01", mutation3.getSampleId());
+        Assert.assertEquals("acc_tcga_mutations", mutation3.getMolecularProfileId());
+        Assert.assertEquals("TCGA-A1-B0SO-01", mutation3.getSampleId());
     }
 
     @Test