[Bugfix] Alternative view refactoring (#183)

* Fix test runners

* Upgrade Mockito to 5.2.0

* Add ontology related files to the local Docker env

* Remove large experiments from local env

* Implement ExperimentCellCountDao interface

* Remove experiment design tab from the experiment page

* Remove unused stubbing

* Add null check

* Adjust test to code changes that happened in February 2022

Unfortunately test code was not adjusted when the `download` endpoint has been changed in February 2022 and probably the tests were not executed before the PR as merged. :-(

* Add back E-MTAB-5214 to the experiment's fixtures

* Add E-MTAB-5555 as a private experiment

* Fix experiment fixture for GxaExperimentCrudIT

* Remove E-MTAB-5200 from the small-experiment-fixture.sql as we don't have it local

* Fix DASFeaturesControllerWIT's featuresURLGeneWithoutExpressions method

* Add temporary folders to .gitignore

* Fix port related issue for gradle task

* New section - How to add a private experiment into our local env

* Add known build issue to the README.md

* Improve the README.md

* Fix anchor in the README

* Change property source to git.properties

git.properties is being generated by the plugin

* Define folder name to git.properties

* Remove the definition of the folder for git.properties

* Change the path and name of the generated git props file

* Refactor how we handle the alternative views of an experiment

* Update with the latest atlas-web-core module

app/src/main/java/uk/ac/ebi/atlas/trader/GxaExperimentRepository.java

@@ -106,4 +106,9 @@ public Experiment getExperiment(String experimentAccession) {
                         + ": experiment type " + experimentDto.getExperimentType() + " is not supported");
         }
     }
+
+    @Override
+    public String getExperimentType(String experimentAccession) {
+        return experimentCrudDao.getExperimentType(experimentAccession);
+    }
 }

app/src/test/java/uk/ac/ebi/atlas/trader/GxaExperimentRepositoryIT.java

@@ -100,4 +100,22 @@ void baselineProteomicsDiaExperiments() {
                 .isInstanceOf(BaselineExperiment.class)
                 .hasNoNullFieldsOrProperties();
     }
+
+    @Test
+    void whenExperimentDoesNotExists_ThrowsException() {
+        assertThatExceptionOfType(ResourceNotFoundException.class)
+                .isThrownBy(
+                        () -> subject.getExperimentType(
+                                jdbcUtils.fetchRandomExperimentAccession() + "_NOT_EXIST")
+                );
+    }
+
+    @Test
+    void whenExperimentExists_thenReturnsExperimentType() {
+        var experimentAccession = jdbcUtils.fetchRandomExperimentAccession();
+        var originalExperimentType = jdbcUtils.fetchExperimentTypeByAccession(experimentAccession);
+        var experimentType = subject.getExperimentType(experimentAccession);
+
+        assertThat(experimentType).isEqualTo(originalExperimentType);
+    }
 }

app/src/test/java/uk/ac/ebi/atlas/trader/GxaExperimentRepositoryTest.java

@@ -7,11 +7,13 @@
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
+import uk.ac.ebi.atlas.controllers.ResourceNotFoundException;
 import uk.ac.ebi.atlas.experimentimport.ExperimentCrudDao;
 import uk.ac.ebi.atlas.experimentimport.ExperimentDto;
 import uk.ac.ebi.atlas.experimentimport.idf.IdfParser;
 import uk.ac.ebi.atlas.experimentimport.idf.IdfParserOutput;
 import uk.ac.ebi.atlas.model.experiment.ExperimentDesign;
+import uk.ac.ebi.atlas.model.experiment.ExperimentType;
 import uk.ac.ebi.atlas.trader.factory.BaselineExperimentFactory;
 import uk.ac.ebi.atlas.trader.factory.MicroarrayExperimentFactory;
 import uk.ac.ebi.atlas.trader.factory.ProteomicsDifferentialExperimentFactory;
@@ -24,6 +26,8 @@
 import java.util.concurrent.ThreadLocalRandom;
 
 import static org.apache.commons.lang3.RandomStringUtils.randomAlphanumeric;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatExceptionOfType;
 import static org.assertj.core.api.Assertions.assertThatIllegalArgumentException;
 import static org.mockito.Mockito.when;
 import static uk.ac.ebi.atlas.model.experiment.ExperimentType.SINGLE_CELL_RNASEQ_MRNA_BASELINE;
@@ -59,6 +63,9 @@ class GxaExperimentRepositoryTest {
 
     private GxaExperimentRepository subject;
 
+    private String experimentAccession;
+    private ExperimentDto experimentDto;
+
     @BeforeEach
     void setUp() {
         subject =
@@ -70,23 +77,25 @@ void setUp() {
                         rnaSeqDifferentialExperimentFactoryMock,
                         microarrayExperimentFactoryMock,
                         proteomicsDifferentialExperimentFactoryMock);
+
+        experimentAccession = generateRandomExperimentAccession();
+        experimentDto = new ExperimentDto(
+                experimentAccession,
+                SINGLE_CELL_RNASEQ_MRNA_BASELINE,
+                generateRandomSpecies().getName(),
+                ImmutableList.of(generateRandomPubmedId()),
+                ImmutableList.of(generateRandomDoi()),
+                new Timestamp(new Date().getTime()),
+                new Timestamp(new Date().getTime()),
+                RNG.nextBoolean(),
+                UUID.randomUUID().toString());
+
     }
 
     @Test
     void cannotBuildNonBulkExperiments() {
-        var experimentAccession = generateRandomExperimentAccession();
-
         when(experimentCrudDaoMock.readExperiment(experimentAccession))
-                .thenReturn(new ExperimentDto(
-                        experimentAccession,
-                        SINGLE_CELL_RNASEQ_MRNA_BASELINE,
-                        generateRandomSpecies().getName(),
-                        ImmutableList.of(generateRandomPubmedId()),
-                        ImmutableList.of(generateRandomDoi()),
-                        new Timestamp(new Date().getTime()),
-                        new Timestamp(new Date().getTime()),
-                        RNG.nextBoolean(),
-                        UUID.randomUUID().toString()));
+                .thenReturn(experimentDto);
 
         when(experimentDesignParserMock.parse(experimentAccession))
                 .thenReturn(new ExperimentDesign());
@@ -102,4 +111,30 @@ void cannotBuildNonBulkExperiments() {
         assertThatIllegalArgumentException()
                 .isThrownBy(() -> subject.getExperiment(experimentAccession));
     }
+
+    @Test
+    void whenExperimentDoesNotExists_ThrowsException() {
+        var experimentAccession = generateRandomExperimentAccession();
+
+        when(experimentCrudDaoMock.getExperimentType(experimentAccession))
+                .thenThrow(ResourceNotFoundException.class);
+
+        assertThatExceptionOfType(ResourceNotFoundException.class)
+                .isThrownBy(
+                        () -> subject.getExperimentType(experimentAccession)
+                );
+    }
+
+    @Test
+    void whenExperimentExists_thenReturnsExperimentType() {
+        final String originalExperimentType = experimentDto.getExperimentType().name();
+
+        when(experimentCrudDaoMock.getExperimentType(experimentAccession))
+                .thenReturn(originalExperimentType);
+
+        var experimentType = subject.getExperimentType(experimentAccession);
+
+        assertThat(experimentType).isEqualTo(originalExperimentType);
+        assertThat(ExperimentType.valueOf(experimentType)).isEqualTo(experimentDto.getExperimentType());
+    }
 }