test: add Pharmacogenomics Junit tests, #TASK-4769, #TASK-4761

cellbase-lib/src/test/java/org/opencb/cellbase/lib/GenericMongoDBAdaptorTest.java

@@ -60,7 +60,7 @@ public class GenericMongoDBAdaptorTest {
 
     protected String cellBaseName;
 
-    private static final String DATASET_BASENAME = "cellbase-v5.6-dr4";
+    private static final String DATASET_BASENAME = "cellbase-v5.7-dr6";
     private static final String DATASET_EXTENSION = ".tar.gz";
     private static final String DATASET_URL = "http://reports.test.zettagenomics.com/cellbase/test-data/";
     private static final String DATASET_TMP_DIR = "/tmp/cb";
@@ -135,7 +135,9 @@ private void downloadAndPopulate() throws IOException, ExecutionException, Class
         Path tmpPath = Paths.get(DATASET_TMP_DIR);
         tmpPath.toFile().mkdirs();
 
+        logger.info("Downloading " + url + " into " + tmpPath);
         URLUtils.download(url, tmpPath);
+
         Path tmpFile = tmpPath.resolve(DATASET_BASENAME + DATASET_EXTENSION);
         String commandline = "tar -xvzf " + tmpFile.toAbsolutePath() + " -C " + tmpPath;
         logger.info("Running: " + commandline);
@@ -206,6 +208,12 @@ private void downloadAndPopulate() throws IOException, ExecutionException, Class
         // clinical_variants.full.json.gz
         loadData("clinical_variants", "clinical_variants", baseDir.resolve("clinical_variants.full.json.gz"));
 
+        // pharmacogenomics.json.gz
+        loadData("pharmacogenomics", "pharmacogenomics", baseDir.resolve("pharmacogenomics/pharmacogenomics.json.gz"));
+
+        // pubmed.json.gz
+        loadData("pubmed", "pubmed", baseDir.resolve("pubmed/pubmed.json.gz"));
+
         // Clean temporary dir
     }
 

cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java

@@ -0,0 +1,83 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.cellbase.lib.impl.core;
+
+import org.hamcrest.CoreMatchers;
+import org.junit.jupiter.api.Test;
+import org.opencb.biodata.models.core.Gene;
+import org.opencb.biodata.models.pharma.PharmaChemical;
+import org.opencb.biodata.models.variant.avro.Constraint;
+import org.opencb.biodata.models.variant.avro.Expression;
+import org.opencb.biodata.models.variant.avro.ExpressionCall;
+import org.opencb.cellbase.core.api.GeneQuery;
+import org.opencb.cellbase.core.api.PharmaChemicalQuery;
+import org.opencb.cellbase.core.api.query.AbstractQuery;
+import org.opencb.cellbase.core.api.query.LogicalList;
+import org.opencb.cellbase.core.result.CellBaseDataResult;
+import org.opencb.cellbase.lib.GenericMongoDBAdaptorTest;
+import org.opencb.cellbase.lib.managers.GeneManager;
+import org.opencb.cellbase.lib.managers.PharmacogenomicsManager;
+
+import java.io.IOException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+/**
+ * Created by jtarraga on 08/21/23.
+ */
+public class PharmacogenomicsMongoDBAdaptorTest extends GenericMongoDBAdaptorTest {
+
+    public PharmacogenomicsMongoDBAdaptorTest() throws IOException {
+        super();
+    }
+
+    @Test
+    public void testQueryName() throws Exception {
+        PharmacogenomicsManager pharmacogenomicsManager = cellBaseManagerFactory.getPharmacogenomicsManager(SPECIES, ASSEMBLY);
+
+        Map<String, String> paramMap = new HashMap<>();
+        paramMap.put("name", "galantamine");
+        paramMap.put("include", "id,name");
+        paramMap.put(AbstractQuery.DATA_RELEASE, String.valueOf(dataRelease));
+
+        PharmaChemicalQuery chemicalQuery = new PharmaChemicalQuery(paramMap);
+        chemicalQuery.setCount(Boolean.TRUE);
+
+        CellBaseDataResult<PharmaChemical> cellBaseDataResult = pharmacogenomicsManager.search(chemicalQuery);
+
+        assertEquals(1, cellBaseDataResult.getNumMatches());
+        assertEquals("PA449726", cellBaseDataResult.first().getId());
+    }
+
+    @Test
+    public void testQuery() throws Exception {
+        PharmacogenomicsManager pharmacogenomicsManager = cellBaseManagerFactory.getPharmacogenomicsManager(SPECIES, ASSEMBLY);
+
+        PharmaChemicalQuery chemicalQuery = new PharmaChemicalQuery();
+        chemicalQuery.setGeneNames(Collections.singletonList("PRKCE"));
+        chemicalQuery.setDataRelease(dataRelease);
+        chemicalQuery.setCount(Boolean.TRUE);
+
+        CellBaseDataResult<PharmaChemical> cellBaseDataResult = pharmacogenomicsManager.search(chemicalQuery);
+
+        assertEquals(6, cellBaseDataResult.getNumMatches());
+    }
+}