Merge branch 'develop' into 374-experiments-default-plot-option-is-no…

…t-correctly-displayed-in-scxa

app/src/test/java/uk/ac/ebi/atlas/configuration/TestConfigForHCA.java

@@ -0,0 +1,57 @@
+package uk.ac.ebi.atlas.configuration;
+
+import com.google.common.collect.ImmutableSet;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.ComponentScan.Filter;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.FilterType;
+import uk.ac.ebi.atlas.hcalandingpage.HcaHumanExperimentDao;
+import uk.ac.ebi.atlas.hcalandingpage.HcaHumanExperimentService;
+import uk.ac.ebi.atlas.solr.cloud.SolrCloudCollectionProxyFactory;
+import uk.ac.ebi.atlas.trader.ExperimentTrader;
+
+import java.util.Set;
+
+@Configuration
+// Enabling component scanning will also load BasePathsConfig, JdbcConfig and SolrConfig, so just using this class as
+// application context is enough in integration tests. It’s important to exclude CacheConfig, otherwise Spring will
+// complain if you want to inject classes such as ScxaExperimentTrader, since a proxy will be injected instead! As an
+// exercise, remove CacheConfig.class and run tests in ScxaExperimentTraderIT.
+@ComponentScan(basePackages = "uk.ac.ebi.atlas",
+               excludeFilters = @Filter(type = FilterType.ASSIGNABLE_TYPE,
+                                        value = {AppConfig.class, CacheConfig.class}))
+public class TestConfigForHCA extends TestConfig {
+
+    private static final String INVALID_CHARACTERISTIC_VALUE = "foo";
+    private static final String VALID_CHARACTERISTIC_VALUE = "pancreas";
+
+    private static final ImmutableSet<String> ALL_ACCESSION_IDS =
+            ImmutableSet.of("E-CURD-4", "E-EHCA-2", "E-GEOD-71585", "E-GEOD-81547", "E-GEOD-99058", "E-MTAB-5061",
+                    "E-ENAD-53");
+
+    @Bean
+    public HcaHumanExperimentDao hcaHumanExperimentDao(SolrCloudCollectionProxyFactory solrCloudCollectionProxyFactory) {
+
+        return new HcaHumanExperimentDao(solrCloudCollectionProxyFactory) {
+
+            @Override
+            public ImmutableSet<String> fetchExperimentAccessions(String characteristicName,
+                                                                  Set<String> characteristicValues) {
+                if (characteristicValues.contains(INVALID_CHARACTERISTIC_VALUE)) {
+                    return ImmutableSet.of();
+                } else if(characteristicValues.contains(VALID_CHARACTERISTIC_VALUE)) {
+                    return ImmutableSet.of("E-MTAB-5061");
+                } else {
+                    return ALL_ACCESSION_IDS;
+                }
+            }
+        };
+    }
+
+    @Bean
+    public HcaHumanExperimentService hcaHumanExperimentService(ExperimentTrader experimentTrader,
+                                                               HcaHumanExperimentDao hcaHumanExperimentDao) {
+        return new HcaHumanExperimentService(experimentTrader, hcaHumanExperimentDao);
+    }
+}

app/src/test/java/uk/ac/ebi/atlas/experimentimport/idf/IdfParserIT.java → app/src/test/java/uk/ac/ebi/atlas/experimentimport/idf/IdfParserForSingleCellIT.java

@@ -17,15 +17,14 @@
 
 import javax.inject.Inject;
 import javax.sql.DataSource;
-import java.nio.file.Path;
 
 import static org.assertj.core.api.Assertions.assertThat;
 
 @ExtendWith(SpringExtension.class)
 @ContextConfiguration(classes = TestConfig.class)
 @WebAppConfiguration
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
-class IdfParserIT {
+class IdfParserForSingleCellIT {
     @Inject
     private DataSource dataSource;
 

app/src/test/java/uk/ac/ebi/atlas/hcalandingpage/HcaHumanExperimentsControllerWIT.java

@@ -6,6 +6,7 @@
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.TestInstance;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.junit.jupiter.MockitoExtension;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.http.MediaType;
@@ -16,7 +17,7 @@
 import org.springframework.test.web.servlet.MockMvc;
 import org.springframework.test.web.servlet.setup.MockMvcBuilders;
 import org.springframework.web.context.WebApplicationContext;
-import uk.ac.ebi.atlas.configuration.TestConfig;
+import uk.ac.ebi.atlas.configuration.TestConfigForHCA;
 
 import javax.inject.Inject;
 import javax.sql.DataSource;
@@ -26,9 +27,9 @@
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
-@ExtendWith(SpringExtension.class)
+@ExtendWith({MockitoExtension.class, SpringExtension.class})
 @WebAppConfiguration
-@ContextConfiguration(classes = TestConfig.class)
+@ContextConfiguration(classes = TestConfigForHCA.class)
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
 class HcaHumanExperimentsControllerWIT {
     @Inject