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159 changes: 123 additions & 36 deletions
159
...-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/ExportCommandExecutor.java
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84 changes: 84 additions & 0 deletions
84
...b/src/test/java/org/opencb/cellbase/lib/impl/core/PharmacogenomicsMongoDBAdaptorTest.java
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| /* | ||
| * 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; | ||
|
|
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| import static org.hamcrest.MatcherAssert.assertThat; | ||
| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
| import static org.opencb.cellbase.core.ParamConstants.DATA_RELEASE_PARAM; | ||
|
|
||
| /** | ||
| * Created by jtarraga on 08/21/23. | ||
| */ | ||
| public class PharmacogenomicsMongoDBAdaptorTest extends GenericMongoDBAdaptorTest { | ||
|
|
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| public PharmacogenomicsMongoDBAdaptorTest() throws IOException { | ||
| super(); | ||
| } | ||
|
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| @Test | ||
| public void testQueryName() throws Exception { | ||
| PharmacogenomicsManager pharmacogenomicsManager = cellBaseManagerFactory.getPharmacogenomicsManager(SPECIES, ASSEMBLY); | ||
|
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| Map<String, String> paramMap = new HashMap<>(); | ||
| paramMap.put("name", "galantamine"); | ||
| paramMap.put("include", "id,name"); | ||
| paramMap.put(DATA_RELEASE_PARAM, String.valueOf(dataRelease)); | ||
|
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| PharmaChemicalQuery chemicalQuery = new PharmaChemicalQuery(paramMap); | ||
| chemicalQuery.setCount(Boolean.TRUE); | ||
|
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| CellBaseDataResult<PharmaChemical> cellBaseDataResult = pharmacogenomicsManager.search(chemicalQuery); | ||
|
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| assertEquals(1, cellBaseDataResult.getNumMatches()); | ||
| assertEquals("PA449726", cellBaseDataResult.first().getId()); | ||
| } | ||
|
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| @Test | ||
| public void testQuery() throws Exception { | ||
| PharmacogenomicsManager pharmacogenomicsManager = cellBaseManagerFactory.getPharmacogenomicsManager(SPECIES, ASSEMBLY); | ||
|
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| PharmaChemicalQuery chemicalQuery = new PharmaChemicalQuery(); | ||
| chemicalQuery.setGeneNames(Collections.singletonList("PRKCE")); | ||
| chemicalQuery.setDataRelease(dataRelease); | ||
| chemicalQuery.setCount(Boolean.TRUE); | ||
|
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| CellBaseDataResult<PharmaChemical> cellBaseDataResult = pharmacogenomicsManager.search(chemicalQuery); | ||
|
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| assertEquals(6, cellBaseDataResult.getNumMatches()); | ||
| } | ||
| } |
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