Fix stubbings of experiment object as they’re used by the client

ebi-gene-expression-group · Oct 3, 2023 · dd8e575 · dd8e575
1 parent e6fb583
commit dd8e575
Showing 1 changed file with 23 additions and 21 deletions.
diff --git a/app/src/test/java/uk/ac/ebi/atlas/ebeyedump/BaselineExperimentAssayGroupsLinesTest.java b/app/src/test/java/uk/ac/ebi/atlas/ebeyedump/BaselineExperimentAssayGroupsLinesTest.java
@@ -9,12 +9,11 @@
 import uk.ac.ebi.atlas.model.experiment.sample.AssayGroup;
 import uk.ac.ebi.atlas.model.experiment.sample.BiologicalReplicate;
 import uk.ac.ebi.atlas.model.OntologyTerm;
+import uk.ac.ebi.atlas.model.experiment.sdrf.Factor;
+import uk.ac.ebi.atlas.model.experiment.sdrf.FactorSet;
 import uk.ac.ebi.atlas.model.experiment.sdrf.SampleCharacteristic;
-import uk.ac.ebi.atlas.model.experiment.ExperimentDesign;
 import uk.ac.ebi.atlas.model.experiment.baseline.BaselineExperiment;
 
-import java.util.Iterator;
-
 import static org.hamcrest.core.Is.is;
 import static org.junit.Assert.assertThat;
 import static org.mockito.Mockito.when;
@@ -64,31 +63,34 @@ public class BaselineExperimentAssayGroupsLinesTest {
 
     @Test
     public void lines() {
-        ExperimentDesign experimentDesign = new ExperimentDesign();
-
-        SampleCharacteristic sampleCharacteristic1 =
-                SampleCharacteristic.create(SAMPLE_HEADER, SAMPLE_VALUE1, SAMPLE_ONTOLOGY_TERM1);
-        SampleCharacteristic sampleCharacteristic2 =
-                SampleCharacteristic.create(SAMPLE_HEADER, SAMPLE_VALUE2, SAMPLE_ONTOLOGY_TERM2);
-
+        when(baselineExperiment.getAccession())
+                .thenReturn(EXPERIMENT_ACCESSION);
+        when(baselineExperiment.getDataColumnDescriptors())
+                .thenReturn(ImmutableList.of(ASSAY_GROUP1, ASSAY_GROUP2, ASSAY_GROUP3));
 
-        experimentDesign.putSampleCharacteristic(ASSAY1, SAMPLE_HEADER, sampleCharacteristic1);
-        experimentDesign.putFactor(ASSAY1, FACTOR_HEADER, FACTOR_VALUE1, FACTOR_ONTOLOGY_TERM1);
+        var sampleCharacteristic1 = SampleCharacteristic.create(SAMPLE_HEADER, SAMPLE_VALUE1, SAMPLE_ONTOLOGY_TERM1);
+        when(baselineExperiment.getSampleCharacteristics(ASSAY1)).thenReturn(ImmutableList.of(sampleCharacteristic1));
 
-        experimentDesign.putSampleCharacteristic(ASSAY2, SAMPLE_HEADER, sampleCharacteristic2);
-        experimentDesign.putFactor(ASSAY2, FACTOR_HEADER, FACTOR_VALUE2, FACTOR_ONTOLOGY_TERM2);
+        var sampleCharacteristic2 = SampleCharacteristic.create(SAMPLE_HEADER, SAMPLE_VALUE2, SAMPLE_ONTOLOGY_TERM2);
+        when(baselineExperiment.getSampleCharacteristics(ASSAY2)).thenReturn(ImmutableList.of(sampleCharacteristic2));
 
-        experimentDesign.putSampleCharacteristic(ASSAY3, SAMPLE_HEADER, SAMPLE_VALUE3);
-        experimentDesign.putFactor(ASSAY3, FACTOR_HEADER, FACTOR_VALUE3);
+        var sampleCharacteristic3 = SampleCharacteristic.create(SAMPLE_HEADER, SAMPLE_VALUE3);
+        when(baselineExperiment.getSampleCharacteristics(ASSAY3)).thenReturn(ImmutableList.of(sampleCharacteristic3));
 
+        var factorSet1 = new FactorSet();
+        factorSet1.add(new Factor(FACTOR_HEADER, FACTOR_VALUE1, FACTOR_ONTOLOGY_TERM1));
+        when(baselineExperiment.getFactors(ASSAY1)).thenReturn(factorSet1);
 
-        when(baselineExperiment.getAccession()).thenReturn(EXPERIMENT_ACCESSION);
-        when(baselineExperiment.getDataColumnDescriptors()).thenReturn(ImmutableList.of(ASSAY_GROUP1, ASSAY_GROUP2,
-                ASSAY_GROUP3));
+        var factorSet2 = new FactorSet();
+        factorSet2.add(new Factor(FACTOR_HEADER, FACTOR_VALUE2, FACTOR_ONTOLOGY_TERM2));
+        when(baselineExperiment.getFactors(ASSAY2)).thenReturn(factorSet2);
 
-        BaselineExperimentAssayGroupsLines subject = new BaselineExperimentAssayGroupsLines(baselineExperiment);
+        var factorSet3 = new FactorSet();
+        factorSet3.add(new Factor(FACTOR_HEADER, FACTOR_VALUE3));
+        when(baselineExperiment.getFactors(ASSAY3)).thenReturn(factorSet3);
 
-        Iterator<String[]> lines = subject.iterator();
+        var subject = new BaselineExperimentAssayGroupsLines(baselineExperiment);
+        var lines = subject.iterator();
 
         assertThat(
                 lines.next(),