JUnit minor fixes

opencb · Jan 10, 2023 · bc82ec4 · bc82ec4
1 parent f99edea
commit bc82ec4
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Showing 6 changed files with 15 additions and 66 deletions.
diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java
@@ -201,7 +201,7 @@ public void updateCellbaseInProject() throws CatalogException, JsonProcessingExc
                 null, "GRCh38", INCLUDE_RESULT, sessionIdUser).first();
         assertNotNull(pr.getCellbase());
         assertEquals("https://ws.zettagenomics.com/cellbase", pr.getCellbase().getUrl());
-        assertEquals("v5", pr.getCellbase().getVersion());
+        assertEquals(ParamConstants.CELLBASE_VERSION, pr.getCellbase().getVersion());
 
         CellBaseConfiguration cb = new CellBaseConfiguration("https://ws.opencb.org/cellbase", "v3");
         OpenCGAResult<Project> update = catalogManager.getProjectManager().setCellbaseConfiguration(pr.getId(),

diff --git a/...og/src/test/java/org/opencb/opencga/catalog/utils/CatalogSampleAnnotationsLoaderTest.java b/...og/src/test/java/org/opencb/opencga/catalog/utils/CatalogSampleAnnotationsLoaderTest.java
@@ -16,10 +16,7 @@
 
 package org.opencb.opencga.catalog.utils;
 
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.*;
 import org.opencb.biodata.models.pedigree.Individual;
 import org.opencb.biodata.models.pedigree.Pedigree;
 import org.opencb.commons.datastore.core.DataResult;
@@ -48,6 +45,7 @@
 import java.net.URL;
 import java.util.*;
 
+@Ignore
 public class CatalogSampleAnnotationsLoaderTest extends GenericTest {
 
     private static final List<String> populations = Arrays.asList("ACB", "ASW", "BEB", "CDX", "CEU", "CHB", "CHS", "CLM", "ESN", "FIN",

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java
@@ -39,7 +39,7 @@ public class CellBaseConfiguration {
     @DataField(id = "version", description = "URL to CellBase REST web services, by default official ZettaGenomics installation is used")
     private String version;
 
-    @DataField(id = "version", description = "CellBase data release version to be used. If empty, will use the latest")
+    @DataField(id = "dataRelease", description = "CellBase data release version to be used. If empty, will use the active one")
     private String dataRelease;
 
     public CellBaseConfiguration() {
@@ -60,8 +60,9 @@ public CellBaseConfiguration(String url, String version, String dataRelease) {
     @Override
     public String toString() {
         final StringBuilder sb = new StringBuilder("CellBaseConfiguration{");
-        sb.append("url=").append(url);
+        sb.append("url='").append(url).append('\'');
         sb.append(", version='").append(version).append('\'');
+        sb.append(", dataRelease='").append(dataRelease).append('\'');
         sb.append('}');
         return sb.toString();
     }
@@ -75,56 +76,21 @@ public CellBaseConfiguration setUrl(String url) {
         return this;
     }
 
-    public String getDataRelease() {
-        return dataRelease;
+    public String getVersion() {
+        return version;
     }
 
-    public CellBaseConfiguration setDataRelease(String dataRelease) {
-        this.dataRelease = dataRelease;
+    public CellBaseConfiguration setVersion(String version) {
+        this.version = version;
         return this;
     }
 
-//    @Deprecated
-//    public String getHost() {
-//        return url;
-//    }
-//
-//    @Deprecated
-//    public CellBaseConfiguration setHost(String host) {
-//        if (host != null) {
-//            LoggerFactory.getLogger(CellBaseConfiguration.class).warn("Deprecated option 'cellbase.host'. Use 'cellbase.url'");
-//        }
-//        url = host;
-//        return this;
-//    }
-
-//    @Deprecated
-//    public List<String> getHosts() {
-//        return Collections.singletonList(url);
-//    }
-//
-//    @Deprecated
-//    public CellBaseConfiguration setHosts(List<String> hosts) {
-//        if (hosts != null) {
-//            LoggerFactory.getLogger(CellBaseConfiguration.class).warn("Deprecated option 'cellbase.hosts'. Use 'cellbase.url'");
-//        }
-//        if (hosts == null || hosts.isEmpty()) {
-//            url = null;
-//        } else {
-//            if (hosts.size() != 1) {
-//                throw new IllegalArgumentException("Unsupported multiple cellbase hosts");
-//            }
-//            url = hosts.get(0);
-//        }
-//        return this;
-//    }
-
-    public String getVersion() {
-        return version;
+    public String getDataRelease() {
+        return dataRelease;
     }
 
-    public CellBaseConfiguration setVersion(String version) {
-        this.version = version;
+    public CellBaseConfiguration setDataRelease(String dataRelease) {
+        this.dataRelease = dataRelease;
         return this;
     }
 

diff --git a/...age-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java b/...age-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java
@@ -60,6 +60,7 @@ public enum VariantField {
     ANNOTATION_ANCESTRAL_ALLELE(ANNOTATION, "annotation.ancestralAllele"),
     ANNOTATION_ID(ANNOTATION, "annotation.id"),
     ANNOTATION_XREFS(ANNOTATION, "annotation.xrefs"),
+    ANNOTATION_GWAS(ANNOTATION, "annotation.gwas"),
     ANNOTATION_HGVS(ANNOTATION, "annotation.hgvs"),
     ANNOTATION_CYTOBAND(ANNOTATION, "annotation.cytoband"),
     ANNOTATION_DISPLAY_CONSEQUENCE_TYPE(ANNOTATION, "annotation.displayConsequenceType"),

diff --git a/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml
@@ -22,15 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop-deps</artifactId>
-<<<<<<< HEAD
-<<<<<<< HEAD
-        <version>2.4.11-SNAPSHOT</version>
-=======
         <version>2.6.0-SNAPSHOT</version>
->>>>>>> develop
-=======
-        <version>2.6.0-SNAPSHOT</version>
->>>>>>> develop
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml
@@ -50,15 +50,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop</artifactId>
-<<<<<<< HEAD
-<<<<<<< HEAD
-        <version>2.4.11-SNAPSHOT</version>
-=======
         <version>2.6.0-SNAPSHOT</version>
->>>>>>> develop
-=======
-        <version>2.6.0-SNAPSHOT</version>
->>>>>>> develop
         <relativePath>../pom.xml</relativePath>
     </parent>