test: improve JUnit tests, and exception management, #TASK-6020, #TAS…

…K-5789
opencb · Apr 17, 2024 · 30f167c · 30f167c
1 parent 1777ca2
commit 30f167c
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Showing 5 changed files with 35 additions and 13 deletions.
diff --git a/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/VariantClientTest.java b/cellbase-client/src/test/java/org/opencb/cellbase/client/rest/VariantClientTest.java
@@ -18,6 +18,7 @@
 
 import org.apache.avro.specific.SpecificRecordBase;
 import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.junit.jupiter.api.Assumptions;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
@@ -31,9 +32,12 @@
 import org.opencb.cellbase.client.config.ClientConfiguration;
 import org.opencb.cellbase.client.config.RestConfig;
 import org.opencb.cellbase.core.common.GitRepositoryState;
+import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.cellbase.core.result.CellBaseDataResponse;
+import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.utils.VersionUtils;
 
 import java.util.*;
 import java.util.stream.Collectors;
@@ -147,18 +151,23 @@ public void getAllConsequenceTypes(CellBaseClient cellBaseClient) throws Excepti
 
     @Test
     public void testSearchSnpBydbSnpId() throws Exception {
-        Assumptions.assumeTrue(GitRepositoryState.get().getBranch().equals("TASK-5789"));
-
+        int dataRelease = 7;
         ClientConfiguration clientConfiguration = new ClientConfiguration()
                 .setDefaultSpecies("hsapiens")
                 .setVersion("v5.8.3-SNAPSHOT")
                 .setRest(new RestConfig(Collections.singletonList("https://ws.zettagenomics.com/cellbase"), 2000));
 
         CellBaseClient client = new CellBaseClient(clientConfiguration);
 
+        // Assumptions before running the test
+        ObjectMap result = client.getMetaClient().about().firstResult();
+        Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8.3-SNAPSHOT", result.getString("Version")));
+        CellBaseDataResponse<DataRelease> dataReleaseResponse = client.getMetaClient().dataReleases();
+        Assumptions.assumeTrue(dataReleaseResponse.getResponses().get(0).getResults().stream().map(DataRelease::getRelease).collect(Collectors.toList()).contains(dataRelease));
+
         Query query = new Query();
         query.put("id", "rs1570391602,rs41278952");
-        query.put("dataRelease", 7);
+        query.put("dataRelease", dataRelease);
 
         CellBaseDataResponse<Snp> response = client.getVariantClient().searchSnp(query, new QueryOptions());
         assertEquals(2, response.getResponses().get(0).getNumResults());
@@ -168,20 +177,25 @@ public void testSearchSnpBydbSnpId() throws Exception {
 
     @Test
     public void testSearchSnpByPosition() throws Exception {
-        Assumptions.assumeTrue(GitRepositoryState.get().getBranch().equals("TASK-5789"));
-
+        int dataRelease = 7;
         ClientConfiguration clientConfiguration = new ClientConfiguration()
                 .setDefaultSpecies("hsapiens")
                 .setVersion("v5.8.3-SNAPSHOT")
                 .setRest(new RestConfig(Collections.singletonList("https://ws.zettagenomics.com/cellbase"), 2000));
 
         CellBaseClient client = new CellBaseClient(clientConfiguration);
 
+        // Assumptions before running the test
+        ObjectMap result = client.getMetaClient().about().firstResult();
+        Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8.3-SNAPSHOT", result.getString("Version")));
+        CellBaseDataResponse<DataRelease> dataReleaseResponse = client.getMetaClient().dataReleases();
+        Assumptions.assumeTrue(dataReleaseResponse.getResponses().get(0).getResults().stream().map(DataRelease::getRelease).collect(Collectors.toList()).contains(dataRelease));
+
         Query query = new Query();
         query.put("chromosome", "1");
         query.put("position", "56948509");
         query.put("reference", "T");
-        query.put("dataRelease", 7);
+        query.put("dataRelease", dataRelease);
 
         CellBaseDataResponse<Snp> response = client.getVariantClient().searchSnp(query, new QueryOptions());
         assertEquals(1, response.getResponses().get(0).getNumResults());
@@ -194,18 +208,23 @@ public void testSearchSnpByPosition() throws Exception {
 
     @Test
     public void testStarsWithSnp() throws Exception {
-        Assumptions.assumeTrue(GitRepositoryState.get().getBranch().equals("TASK-5789"));
-
+        int dataRelease = 7;
         ClientConfiguration clientConfiguration = new ClientConfiguration()
                 .setDefaultSpecies("hsapiens")
                 .setVersion("v5.8.3-SNAPSHOT")
                 .setRest(new RestConfig(Collections.singletonList("https://ws.zettagenomics.com/cellbase"), 2000));
 
         CellBaseClient client = new CellBaseClient(clientConfiguration);
 
+        // Assumptions before running the test
+        ObjectMap result = client.getMetaClient().about().firstResult();
+        Assumptions.assumeTrue(VersionUtils.isMinVersion("5.8.3-SNAPSHOT", result.getString("Version")));
+        CellBaseDataResponse<DataRelease> dataReleaseResponse = client.getMetaClient().dataReleases();
+        Assumptions.assumeTrue(dataReleaseResponse.getResponses().get(0).getResults().stream().map(DataRelease::getRelease).collect(Collectors.toList()).contains(dataRelease));
+
         Query query = new Query();
         query.put("id", "rs157039161");
-        query.put("dataRelease", 7);
+        query.put("dataRelease", dataRelease);
 
         CellBaseDataResponse<Snp> response = client.getVariantClient().startsWithSnp(query, new QueryOptions());
         assertEquals(9, response.getResponses().get(0).getNumResults());

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java
@@ -35,6 +35,8 @@
  */
 public class EtlCommons {
 
+    public static final String HOMO_SAPIENS_NAME ="Homo sapiens";
+
     public static final String GENOME_DATA = "genome";
     public static final String GENE_DATA = "gene";
     public static final String REFSEQ_DATA = "refseq";

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/VariationDownloadManager.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/VariationDownloadManager.java
@@ -19,6 +19,7 @@
 import org.opencb.cellbase.core.config.CellBaseConfiguration;
 import org.opencb.cellbase.core.config.DownloadProperties;
 import org.opencb.cellbase.core.exception.CellBaseException;
+import org.opencb.cellbase.lib.EtlCommons;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -45,7 +46,7 @@ public DownloadFile downloadDbSnp() throws IOException, InterruptedException {
         if (!speciesHasInfoToDownload(speciesConfiguration, VARIATION_DATA)) {
             return null;
         }
-        if (speciesConfiguration.getScientificName().equals("Homo sapiens")) {
+        if (speciesConfiguration.getScientificName().equals(EtlCommons.HOMO_SAPIENS_NAME)) {
             logger.info("Downloading dbSNP information ...");
 
             Path variation = downloadFolder.resolve(VARIATION_DATA);

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/SnpMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/SnpMongoDBAdaptor.java
@@ -122,7 +122,7 @@ public CellBaseDataResult<Snp> startsWith(String id, QueryOptions options, int d
         return new CellBaseDataResult<>(mongoDBCollection.find(regex, projection, CONVERTER, options));
     }
 
-    public Bson parseQuery(SnpQuery query) {
+    public Bson parseQuery(SnpQuery query) throws CellBaseException {
         List<Bson> andBsonList = new ArrayList<>();
         try {
             for (Map.Entry<String, Object> entry : query.toObjectMap().entrySet()) {
@@ -145,7 +145,7 @@ public Bson parseQuery(SnpQuery query) {
                 }
             }
         } catch (IllegalAccessException e) {
-            e.printStackTrace();
+            throw new CellBaseException("Error parsing SNP query: " + query, e);
         }
 
         logger.info("SnpMongoDBAdaptor parsed query: {}", andBsonList);

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptor.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptor.java
@@ -305,7 +305,7 @@ public Bson parseQuery(VariantQuery query) throws CellBaseException {
                 }
             }
         } catch (IllegalAccessException e) {
-            throw new CellBaseException(e.getMessage());
+            throw new CellBaseException("Error parsing variant query: " + query, e);
         }
 
         logger.debug("variant parsed query: {}", andBsonList);