Remove functionality unrelated to cna long format

core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java

@@ -59,8 +59,8 @@
  * <br>
  * @author Selcuk Onur Sumer
  */
-
 public class ImportExtendedMutationData{
+
     private File mutationFile;
     private int geneticProfileId;
     private boolean swissprotIsAccession;

core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java

@@ -33,14 +33,10 @@
 package org.mskcc.cbio.portal.scripts;
 
 import java.io.*;
-import java.util.ArrayList;
-import java.util.Date;
 import java.util.Set;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
 import joptsimple.*;
 
-import org.cbioportal.model.EntityType;
 import org.mskcc.cbio.portal.model.*;
 import org.mskcc.cbio.portal.util.*;
 
@@ -126,7 +122,7 @@ public void run() {
                 if (pdAnnotationsFilename != null && !"".equals(pdAnnotationsFilename)) {
                     importer.setPdAnnotationsFile(new File(dataFile.getParent(), pdAnnotationsFilename));
                 }
-                importer.importData(numLines);            
+                importer.importData(numLines);
             }
        }
        catch (Exception e) {

core/src/main/java/org/mskcc/cbio/portal/scripts/ImportStructuralVariantData.java

@@ -44,7 +44,7 @@
  */
 
 public class ImportStructuralVariantData {
-        
+
     // Initialize variables
     private File structuralVariantFile;
     private int geneticProfileId;

core/src/main/scripts/importer/cbioportal_common.py

@@ -45,7 +45,6 @@ class MetaFileTypes(object):
     SAMPLE_ATTRIBUTES = 'meta_clinical_sample'
     PATIENT_ATTRIBUTES = 'meta_clinical_patient'
     CNA_DISCRETE = 'meta_CNA'
-    CNA_DISCRETE_LONG = 'meta_CNA'
     CNA_LOG2 = 'meta_log2CNA'
     CNA_CONTINUOUS = 'meta_contCNA'
     SEG = 'meta_segment'
@@ -112,20 +111,7 @@ class MetaFileTypes(object):
         'profile_description': True,
         'data_filename': True,
         'gene_panel': False,
-        'pd_annotations_filename': False,
-        'namespaces': False
-    },
-    MetaFileTypes.CNA_DISCRETE_LONG: {
-        'cancer_study_identifier': True,
-        'genetic_alteration_type': True,
-        'datatype': True,
-        'stable_id': True,
-        'show_profile_in_analysis_tab': True,
-        'profile_name': True,
-        'profile_description': True,
-        'data_filename': True,
-        'gene_panel': False,
-        'namespaces': False
+        'pd_annotations_filename': False
     },
     MetaFileTypes.CNA_LOG2: {
         'cancer_study_identifier': True,
@@ -631,7 +617,6 @@ def get_meta_file_type(meta_dictionary, logger, filename):
         ("PROTEIN_LEVEL", "CONTINUOUS"): MetaFileTypes.PROTEIN,
         # cna
         ("COPY_NUMBER_ALTERATION", "DISCRETE"): MetaFileTypes.CNA_DISCRETE,
-        ("COPY_NUMBER_ALTERATION", "DISCRETE_LONG"): MetaFileTypes.CNA_DISCRETE,
         ("COPY_NUMBER_ALTERATION", "CONTINUOUS"): MetaFileTypes.CNA_CONTINUOUS,
         ("COPY_NUMBER_ALTERATION", "LOG2-VALUE"): MetaFileTypes.CNA_LOG2,
         ("COPY_NUMBER_ALTERATION", "SEG"): MetaFileTypes.SEG,

core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCnaDiscreteLongData.java

@@ -55,6 +55,7 @@
 import static java.util.stream.Collectors.joining;
 import static java.util.stream.Collectors.toList;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @ContextConfiguration(locations = {"classpath:/applicationContext-dao.xml"})
@@ -132,7 +133,7 @@ public void testImportCnaDiscreteLongDataAddsCnaEvents() throws Exception {
             .map(e -> e.getAlteration().getDescription())
             .collect(toList());
         assertEquals(2, cnaEvents.size());
-        assertEquals("Amplified,Homozygously deleted", String.join(",", cnaEvents));
+        assertTrue(newArrayList("Amplified", "Homozygously deleted").containsAll(cnaEvents));
 
         // Test gene with partial deletion and amplification has two cna events:
         List<String> convertedCnaEvents = resultCnaEvents
@@ -141,7 +142,7 @@ public void testImportCnaDiscreteLongDataAddsCnaEvents() throws Exception {
             .map(e -> e.getAlteration().getDescription())
             .collect(toList());
         assertEquals(2, cnaEvents.size());
-        assertEquals("Amplified,Homozygously deleted", String.join(",", cnaEvents));
+        assertTrue( newArrayList("Amplified", "Homozygously deleted").containsAll(cnaEvents));
 
         // Test gene with homozygous deletion and amplification has no cna events:
         List<CnaEvent.Event> skippedCnaEvents = resultCnaEvents

core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCopyNumberSegmentData.java

@@ -19,7 +19,7 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
+*/
 
 package org.mskcc.cbio.portal.scripts;
 
@@ -62,45 +62,45 @@
 @Transactional
 public class TestImportCopyNumberSegmentData {
 
-    @Autowired
-    ApplicationContext applicationContext;
-
-    //To use in test cases where we expect an exception:
-    @Rule
-    public ExpectedException exception = ExpectedException.none();
-
-
-    @Before
-    public void setUp() throws DaoException
-    {
-        //set it, to avoid this being set to the runtime (not for testing) application context:
-        SpringUtil.setApplicationContext(applicationContext);
-    }
-
-    /**
+	@Autowired
+	ApplicationContext applicationContext;
+	
+	//To use in test cases where we expect an exception:
+	@Rule
+	public ExpectedException exception = ExpectedException.none();
+    
+	
+	@Before 
+	public void setUp() throws DaoException
+	{
+		//set it, to avoid this being set to the runtime (not for testing) application context:
+		SpringUtil.setApplicationContext(applicationContext);
+	}
+	
+	/**
      * Test importing of Clinical Data File.
      *
      * @throws DaoException Database Access Error.
      * @throws IOException  IO Error.
      */
-    @Test
+	@Test
     public void testImportSegmentDataNewStudy() throws Exception {
-        //new dummy study to simulate importing clinical data in empty study:
-        CancerStudy cancerStudy = new CancerStudy("testnewseg","testnewseg","testnewseg","brca",true);
+		//new dummy study to simulate importing clinical data in empty study:
+		CancerStudy cancerStudy = new CancerStudy("testnewseg","testnewseg","testnewseg","brca",true);
         cancerStudy.setReferenceGenome("hg19");
-        DaoCancerStudy.addCancerStudy(cancerStudy);
+		DaoCancerStudy.addCancerStudy(cancerStudy);
         addTestPatientAndSampleRecords(new File("src/test/resources/segment/data_cna_hg19.seg"), cancerStudy);
 
         String[] args = {
-            "--data","src/test/resources/segment/data_cna_hg19.seg",
-            "--meta","src/test/resources/segment/meta_cna_hg19_seg.txt",
-            "--loadMode", "bulkLoad"
-        };
+        		"--data","src/test/resources/segment/data_cna_hg19.seg",
+        		"--meta","src/test/resources/segment/meta_cna_hg19_seg.txt",
+        		"--loadMode", "bulkLoad"
+        		};
         ImportCopyNumberSegmentData runner = new ImportCopyNumberSegmentData(args);
-        runner.run();
+        runner.run(); 
         //TODO : fix test to actually store data and add some checks 
-
-    }
+       
+	}
 
     private void addTestPatientAndSampleRecords(File file, CancerStudy cancerStudy) throws FileNotFoundException, IOException, DaoException {
         // extract sample ids from first column
@@ -124,4 +124,4 @@ private void addTestPatientAndSampleRecords(File file, CancerStudy cancerStudy)
         }
         MySQLbulkLoader.flushAll();
     }
-}
+}

db-scripts/src/main/resources/cgds.sql

@@ -590,7 +590,6 @@ CREATE TABLE `cna_event` (
   `CNA_EVENT_ID` int(255) NOT NULL auto_increment,
   `ENTREZ_GENE_ID` int(11) NOT NULL,
   `ALTERATION` tinyint NOT NULL,
-  `ANNOTATION_JSON` JSON,
   PRIMARY KEY (`CNA_EVENT_ID`),
   UNIQUE (`ENTREZ_GENE_ID`, `ALTERATION`),
   FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`),
@@ -761,4 +760,4 @@ CREATE TABLE `resource_study` (
 );
 
 -- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml
-INSERT INTO info VALUES ('2.12.15', NULL);
+INSERT INTO info VALUES ('2.12.14', NULL);

db-scripts/src/main/resources/migration.sql

@@ -992,7 +992,3 @@ ALTER TABLE `structural_variant` DROP COLUMN `SITE2_EXON`;
 ALTER TABLE `structural_variant` DROP COLUMN `CENTER`;
 ALTER TABLE `structural_variant` DROP COLUMN `EXTERNAL_ANNOTATION`;
 UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.14";
-
-##version: 2.12.15
-ALTER TABLE `cna_event` ADD COLUMN `ANNOTATION_JSON` JSON AFTER `ALTERATION`;
-UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.15";

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

@@ -1,33 +1,18 @@
 package org.cbioportal.model;
 
-import com.fasterxml.jackson.annotation.JsonRawValue;
-import io.swagger.annotations.ApiModelProperty;
-
 import java.io.Serializable;
 import javax.validation.constraints.NotNull;
 
 public class DiscreteCopyNumberData extends Alteration implements Serializable {
+
     @NotNull
     private Integer alteration;
-
-    @JsonRawValue
-    @ApiModelProperty(dataType = "java.util.Map")
-    private String annotationJson;
-
+
     public Integer getAlteration() {
         return alteration;
     }
 
     public void setAlteration(Integer alteration) {
         this.alteration = alteration;
     }
-
-    public String getAnnotationJson() {
-        return annotationJson;
-    }
-
-    public void setAnnotationJson(String annotationJson) {
-        this.annotationJson = annotationJson;
-    }
-
 }

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

@@ -6,7 +6,6 @@
     <sql id="select">
         cna_event.ENTREZ_GENE_ID as entrezGeneId,
         cna_event.ALTERATION AS alteration,
-        cna_event.ANNOTATION_JSON as annotationJson,
         genetic_profile.STABLE_ID AS molecularProfileId,
         sample.STABLE_ID AS sampleId,
         patient.STABLE_ID AS patientId,

persistence/persistence-mybatis/src/test/resources/testSql.sql

@@ -417,9 +417,9 @@ INSERT INTO genetic_alteration (GENETIC_PROFILE_ID,GENETIC_ENTITY_ID,`VALUES`) V
 INSERT INTO genetic_alteration (GENETIC_PROFILE_ID,GENETIC_ENTITY_ID,`VALUES`) VALUES (2,2,'1.4146,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1146,0.3498,0.0349,0.4927,-0.8665,-0.4754,-0.7221,');
 INSERT INTO genetic_alteration (GENETIC_PROFILE_ID,GENETIC_ENTITY_ID,`VALUES`) VALUES (3,2,'-0.8097,0.7360,-1.0225,-0.8922,0.7247,0.3537,1.2702,-0.1419,');
 
-INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION,ANNOTATION_JSON) VALUES (1,207,-2, '{"columnName":{"fieldName":"fieldValue"}}');
-INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION,ANNOTATION_JSON) VALUES (2,208,2, '{"columnName":{"fieldName":"fieldValue"}}');
-INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION,ANNOTATION_JSON) VALUES (3,207,2, '{"columnName":{"fieldName":"fieldValue"}}');
+INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION) VALUES (1,207,-2);
+INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION) VALUES (2,208,2);
+INSERT INTO cna_event (CNA_EVENT_ID,ENTREZ_GENE_ID,ALTERATION) VALUES (3,207,2);
 
 INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID) VALUES (1,1,2);
 INSERT INTO sample_cna_event (CNA_EVENT_ID,SAMPLE_ID,GENETIC_PROFILE_ID) VALUES (2,1,2);

pom.xml

@@ -315,7 +315,7 @@
     <tomcat.session.timeout>720</tomcat.session.timeout>
 
     <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
-    <db.version>2.12.15</db.version>
+    <db.version>2.12.14</db.version>
   </properties>
 
   <modules>

service/src/test/java/org/cbioportal/service/impl/DiscreteCopyNumberServiceImplTest.java

@@ -64,65 +64,6 @@ public void getDiscreteCopyNumbersInMultipleMolecularProfilesHomdelOrAmp() {
         Assert.assertEquals(toStrings(returned), toStrings(actual));
     }
 
-    @Test
-    public void getDiscreteCopyNumbersWithAnnotationJson() {
-        List<DiscreteCopyNumberData> returned = Arrays.asList(
-            discreteCopyNumberData("sample1", "study1", -2),
-            discreteCopyNumberData("sample2", "study2", 2)
-        );
-        returned.get(0).setAnnotationJson("{\"columnName\":{\"fieldName\":\"fieldValue\"}}");
-        List<String> profiles = Arrays.asList("profile1", "profile2");
-        List<String> samples = Arrays.asList("sample1", "sample2");
-        List<Integer> geneIds = Arrays.asList(0, 1);
-        List<Integer> alterationTypes = Arrays.asList(-2, 2);
-
-        Mockito.when(discreteCopyNumberRepository.getDiscreteCopyNumbersInMultipleMolecularProfiles(
-                profiles,
-                samples,
-                geneIds,
-                alterationTypes,
-                PROJECTION
-            ))
-            .thenReturn(
-                returned
-            );
-
-        List<DiscreteCopyNumberData> actual = discreteCopyNumberService.getDiscreteCopyNumbersInMultipleMolecularProfiles(
-            profiles, samples, geneIds, alterationTypes, PROJECTION
-        );
-
-        Assert.assertEquals(toStrings(returned), toStrings(actual));
-    }
-    @Test
-    public void getDiscreteCopyNumbersWithoutAnnotationJson() {
-        List<DiscreteCopyNumberData> returned = Arrays.asList(
-            discreteCopyNumberData("sample1", "study1", -2),
-            discreteCopyNumberData("sample2", "study2", 2)
-        );
-        // returned.get(0).setAnnotationJson("{\"columnName\":{\"fieldName\":\"fieldValue\"}}");
-        List<String> profiles = Arrays.asList("profile1", "profile2");
-        List<String> samples = Arrays.asList("sample1", "sample2");
-        List<Integer> geneIds = Arrays.asList(0, 1);
-        List<Integer> alterationTypes = Arrays.asList(-2, 2);
-
-        Mockito.when(discreteCopyNumberRepository.getDiscreteCopyNumbersInMultipleMolecularProfiles(
-                profiles,
-                samples,
-                geneIds,
-                alterationTypes,
-                PROJECTION
-            ))
-            .thenReturn(
-                returned
-            );
-
-        List<DiscreteCopyNumberData> actual = discreteCopyNumberService.getDiscreteCopyNumbersInMultipleMolecularProfiles(
-            profiles, samples, geneIds, alterationTypes, PROJECTION
-        );
-        Assert.assertNull(returned.get(0).getAnnotationJson());
-        Assert.assertEquals(toStrings(returned), toStrings(actual));
-    }
-
     @Test
     public void getDiscreteCopyNumbersInMultipleMolecularProfilesAllAlterationTypes() {
         List<GeneMolecularData> returned = Arrays.asList(

web/src/main/java/org/cbioportal/web/config/CustomObjectMapper.java

@@ -47,7 +47,6 @@
 import org.cbioportal.model.ClinicalEvent;
 import org.cbioportal.model.ClinicalEventData;
 import org.cbioportal.model.DataAccessToken;
-import org.cbioportal.model.DiscreteCopyNumberData;
 import org.cbioportal.model.CopyNumberSeg;
 import org.cbioportal.model.Gene;
 import org.cbioportal.model.GenePanel;
@@ -83,7 +82,6 @@
 import org.cbioportal.web.mixin.ClinicalEventMixin;
 import org.cbioportal.web.mixin.CopyNumberSegMixin;
 import org.cbioportal.web.mixin.DataAccessTokenMixin;
-import org.cbioportal.web.mixin.DiscreteCopyNumberDataMixin;
 import org.cbioportal.web.mixin.GeneMixin;
 import org.cbioportal.web.mixin.GenePanelMixin;
 import org.cbioportal.web.mixin.GenePanelToGeneMixin;
@@ -120,7 +118,6 @@ public CustomObjectMapper() {
         mixinMap.put(ClinicalEventData.class, ClinicalEventDataMixin.class);
         mixinMap.put(CopyNumberSeg.class, CopyNumberSegMixin.class);
         mixinMap.put(DataAccessToken.class, DataAccessTokenMixin.class);
-        mixinMap.put(DiscreteCopyNumberData.class, DiscreteCopyNumberDataMixin.class);
         mixinMap.put(Gene.class, GeneMixin.class);
         mixinMap.put(GenePanel.class, GenePanelMixin.class);
         mixinMap.put(GenePanelToGene.class, GenePanelToGeneMixin.class);