TASK-4761

cellbase-core/src/main/java/org/opencb/cellbase/core/api/PharmaChemicalQuery.java

@@ -50,7 +50,7 @@ public class PharmaChemicalQuery extends AbstractQuery {
     @QueryParameter(id = "variants.haplotypes", alias = {"haplotype"})
     private List<String> hapolotypes;
 
-    @QueryParameter(id = "variants.geneNames", alias = {"geneName"})
+    @QueryParameter(id = "geneName")
     private List<String> geneNames;
 
     @QueryParameter(id = "variants.phenotypes", alias = {"phenotype"})

cellbase-core/src/main/java/org/opencb/cellbase/core/api/query/AbstractQuery.java

@@ -124,7 +124,9 @@ public void updateParams(Map<String, String> uriParams) {
         annotations = getAnnotations();
 
         try {
-            validateParams(uriParams, classAttributesToType, annotations);
+            // Skip this validation because some CellBase endpoint URL parameters are not included
+            // in the query (such as GeneQuery, VariantQuery,...)
+            //validateParams(uriParams, classAttributesToType, annotations);
 
             Map<String, Object> objectHashMap = new HashMap<>();
             for (Map.Entry<String, Class<?>> entry : classAttributesToType.entrySet()) {
@@ -175,7 +177,7 @@ public void updateParams(Map<String, String> uriParams) {
                 }
             }
             objectMapper.updateValue(this, objectHashMap);
-        } catch (JsonProcessingException | QueryException e) {
+        } catch (JsonProcessingException e) { // | QueryException e) {
             throw new IllegalArgumentException(e);
         }
     }

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptor.java

@@ -17,10 +17,12 @@
 package org.opencb.cellbase.lib.impl.core;
 
 import com.mongodb.client.model.Filters;
+import org.apache.commons.collections4.CollectionUtils;
 import org.bson.Document;
 import org.bson.conversions.Bson;
 import org.opencb.biodata.models.pharma.PharmaChemical;
 import org.opencb.cellbase.core.api.PharmaChemicalQuery;
+import org.opencb.cellbase.core.api.query.LogicalList;
 import org.opencb.cellbase.core.api.query.ProjectionQueryOptions;
 import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
@@ -108,7 +110,6 @@ public CellBaseDataResult<PharmaChemical> groupBy(PharmaChemicalQuery query) thr
 
     public Bson parseQuery(PharmaChemicalQuery pharmaQuery) {
         List<Bson> andBsonList = new ArrayList<>();
-        boolean visited = false;
         try {
             for (Map.Entry<String, Object> entry : pharmaQuery.toObjectMap().entrySet()) {
                 String dotNotationName = entry.getKey();
@@ -118,6 +119,12 @@ public Bson parseQuery(PharmaChemicalQuery pharmaQuery) {
                     case "token":
                         // do nothing
                         break;
+                    case "geneName":
+                        List<Bson> orBsonList = new ArrayList<>();
+                        orBsonList.add(getLogicalListFilter(new LogicalList<String>((List) value), "variants.geneNames"));
+                        orBsonList.add(getLogicalListFilter(new LogicalList<String>((List) value), "genes.xrefs.id"));
+                        andBsonList.add(Filters.or(orBsonList));
+                        break;
                     default:
                         createAndOrQuery(value, dotNotationName, QueryParam.Type.STRING, andBsonList);
                         break;
@@ -126,8 +133,8 @@ public Bson parseQuery(PharmaChemicalQuery pharmaQuery) {
         } catch (IllegalAccessException e) {
             e.printStackTrace();
         }
-        logger.debug("pharmacogenomics parsed query: " + andBsonList);
-        if (andBsonList.size() > 0) {
+        logger.debug("Pharmacogenomics parsed query: {}", andBsonList);
+        if (CollectionUtils.isNotEmpty(andBsonList)) {
             return Filters.and(andBsonList);
         } else {
             return new Document();

cellbase-lib/src/main/java/org/opencb/cellbase/lib/loader/LoadRunner.java

@@ -21,6 +21,7 @@
 import org.opencb.cellbase.core.config.CellBaseConfiguration;
 import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.models.DataRelease;
+import org.opencb.cellbase.lib.EtlCommons;
 import org.opencb.cellbase.lib.managers.DataReleaseManager;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -100,7 +101,9 @@ public void load(Path filePath, String data, int dataRelease, String field, Stri
         // protein_functional_prediction documents are extremely big. Increasing the batch size will probably
         // lead to an OutOfMemory error for this collection. Batch size can be much higher for the rest of
         // collections though
-        if (data.equals(PROTEIN_FUNCTIONAL_PREDICTION)) {
+        if (data.equals(PROTEIN_FUNCTIONAL_PREDICTION)
+                || data.equals(EtlCommons.PHARMACOGENOMICS_DATA)
+                || data.equals(EtlCommons.PUBMED_DATA)) {
             batchSize = 50;
         } else {
             batchSize = 200;

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

@@ -47,6 +47,8 @@
 import java.util.List;
 import java.util.concurrent.ExecutionException;
 
+import static org.opencb.cellbase.lib.EtlCommons.PHARMACOGENOMICS_DATA;
+import static org.opencb.cellbase.lib.EtlCommons.PUBMED_DATA;
 import static org.opencb.cellbase.lib.db.MongoDBManager.DBNAME_SEPARATOR;
 
 /**
@@ -60,7 +62,7 @@ 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 +137,9 @@ 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 +210,12 @@ 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_DATA, PHARMACOGENOMICS_DATA, baseDir.resolve("pharmacogenomics/pharmacogenomics.json.gz"));
+
+        // pubmed.json.gz
+        loadData(PUBMED_DATA, PUBMED_DATA, 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());
+    }
+}

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java

@@ -92,7 +92,8 @@ public PharmacogenomicsWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVe
                     + "please, call the endpoint endpoint pharmacogenomics/distinct?field=variants.haplotypes", dataType = "java.util.List",
                     paramType = "query"),
             @ApiImplicitParam(name = "geneName", value = "List of gene names, e.g.: NT5C2,VKORC1. In order to get the list of gene names,"
-                    + "please, call the endpoint endpoint pharmacogenomics/distinct?field=variants.geneNames", dataType = "java.util.List",
+                    + "please, call the endpoint endpoints pharmacogenomics/distinct?field=variants.geneNames and "
+                    + " pharmacogenomics/distinct?field=genes.xrefs.id", dataType = "java.util.List",
                     paramType = "query"),
             @ApiImplicitParam(name = "location", value = "List of chromosomic coordinates in the format: chromosome:position, e.g.:"
                     + " 10:103109774", dataType = "java.util.List", paramType = "query"),
@@ -125,6 +126,7 @@ public PharmacogenomicsWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVe
     public Response getAll() {
         try {
             PharmaChemicalQuery query = new PharmaChemicalQuery(uriParams);
+            query.setDataRelease(getDataRelease());
             CellBaseDataResult<PharmaChemical> queryResults = pharmacogenomicsManager.search(query);
 
             return createOkResponse(queryResults);
@@ -170,6 +172,7 @@ public Response getUniqueValues(@QueryParam("field") @ApiParam(name = "field", r
         try {
             copyToFacet("field", field);
             PharmaChemicalQuery query = new PharmaChemicalQuery(uriParams);
+            query.setDataRelease(getDataRelease());
             CellBaseDataResult<String> queryResults = pharmacogenomicsManager.distinct(query);
             return createOkResponse(queryResults);
         } catch (Exception e) {