[Chore] Bulk - Fix experiment design's memory issue (#203)

* Remove experiment design field from Experiment

Temporary leave experimentDesign field on Experiment entity to pass the test. I am going to remove it in the last commit

* Refactor ExperimentsConditionsDetailsController

* Refactor BaselineExperimentAssayGroupsLines

* Refactor BaselineExperimentPageService

* Refactor HeatmapGroupingsService

* Refactor DifferentialExperimentPageService

* Refactor EvidenceService

* Refactor EvidenceService - left over

* Refactor ContrastSummaryController

* Refactor ExperimentPageContentService

* update with the latest atlas-web-core module changes

* Remove experimentDesign field from Experiment entity (latest core changes)

* Update to the latest atlas-web-core module changes

* Refactor getExperimentDesign method usage

app/src/main/java/uk/ac/ebi/atlas/controllers/rest/DASFeaturesController.java

@@ -60,10 +60,9 @@ public String getDifferentialJsonResults(
         SetMultimap<String, String> factorValuesByType = HashMultimap.create();
         for (DiffAnalytics dbe : diffAnalyticsList) {
             AssayGroup testAssayGroup = dbe.getContrastTestAssayGroup();
-            Experiment experiment = experimentTrader.getPublicExperiment(dbe.getExperimentAccession());
 
             FactorSet factorsForAssayGroup =
-                    FactorSet.create(experiment.getExperimentDesign()
+                    FactorSet.create(experimentTrader.getExperimentDesign(dbe.getExperimentAccession())
                              .getFactorValues(testAssayGroup.getFirstAssayId()));
             for (Factor factor : factorsForAssayGroup) {
                 factorValuesByType.put(factor.getType(), factor.getValue());

app/src/main/java/uk/ac/ebi/atlas/ebeyedump/BaselineExperimentAssayGroupsLines.java

@@ -2,13 +2,16 @@
 
 import com.google.common.collect.ImmutableList;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import uk.ac.ebi.atlas.model.experiment.ExperimentDesign;
 import uk.ac.ebi.atlas.model.experiment.sample.AssayGroup;
 import uk.ac.ebi.atlas.model.OntologyTerm;
 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.baseline.BaselineExperiment;
 import uk.ac.ebi.atlas.model.experiment.sdrf.Factor;
 
+import java.util.Collection;
 import java.util.Iterator;
 import java.util.LinkedHashSet;
 import java.util.Set;
@@ -18,9 +21,12 @@
 public class BaselineExperimentAssayGroupsLines implements Iterable<String[]> {
     private final LinkedHashSet<ImmutableList<String>> result = new LinkedHashSet<>();
     private final LinkedHashSet<ImmutableList<String>> assayGroupsDetails;
+    private final ExperimentDesign experimentDesign;
 
-    public BaselineExperimentAssayGroupsLines(BaselineExperiment experiment) {
-        assayGroupsDetails = buildAssayGroupsDetails(experiment);
+    public BaselineExperimentAssayGroupsLines(BaselineExperiment experiment,
+                                              ExperimentDesign experimentDesign) {
+        this.experimentDesign = experimentDesign;
+        this.assayGroupsDetails = buildAssayGroupsDetails(experiment);
     }
 
     private LinkedHashSet<ImmutableList<String>> buildAssayGroupsDetails(BaselineExperiment experiment) {
@@ -35,7 +41,9 @@ private LinkedHashSet<ImmutableList<String>> buildAssayGroupsDetails(BaselineExp
     }
 
     private void populateSamples(BaselineExperiment experiment, String assayAccession, AssayGroup assayGroup) {
-        for (SampleCharacteristic sample : experiment.getExperimentDesign().getSampleCharacteristics(assayAccession)) {
+        final String experimentAccession = experiment.getAccession();
+
+        for (SampleCharacteristic sample : getSampleCharacteristics(assayAccession, experimentAccession)) {
             ImmutableList<String> line =
                     ImmutableList.of(
                             experiment.getAccession(),
@@ -49,16 +57,26 @@ private void populateSamples(BaselineExperiment experiment, String assayAccessio
     }
 
     private void populateFactors(BaselineExperiment experiment, String assayAccession, AssayGroup assayGroup) {
-        FactorSet factorSet = experiment.getExperimentDesign().getFactors(assayAccession);
+        final String experimentAccession = experiment.getAccession();
+
+        FactorSet factorSet = getFactors(assayAccession);
         if (factorSet != null) {
             for (Factor factor : factorSet) {
-                ImmutableList<String> line = ImmutableList.of(experiment.getAccession(), assayGroup.getId(), "factor",
+                ImmutableList<String> line = ImmutableList.of(experimentAccession, assayGroup.getId(), "factor",
                         factor.getHeader(), factor.getValue(), joinURIs(factor.getValueOntologyTerms()));
                 result.add(line);
             }
         }
     }
 
+    private Collection<SampleCharacteristic> getSampleCharacteristics(String assayAccession, String experimentAccession) {
+        return experimentDesign.getSampleCharacteristics(assayAccession);
+    }
+
+    private @Nullable FactorSet getFactors(String assayAccession) {
+        return experimentDesign.getFactors(assayAccession);
+    }
+
     private static String joinURIs(Set<OntologyTerm> ontologyTerms) {
         return ontologyTerms.stream().map(OntologyTerm::uri).collect(joining(" "));
     }

app/src/main/java/uk/ac/ebi/atlas/ebeyedump/DifferentialExperimentContrastLines.java

@@ -3,6 +3,7 @@
 import com.google.common.collect.ImmutableList;
 import org.jetbrains.annotations.NotNull;
 import uk.ac.ebi.atlas.model.OntologyTerm;
+import uk.ac.ebi.atlas.model.experiment.ExperimentDesign;
 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.sdrf.Factor;
@@ -18,9 +19,11 @@
 public class DifferentialExperimentContrastLines implements Iterable<String[]> {
     private final LinkedHashSet<ImmutableList<String>> contrastDetails;
     private final LinkedHashSet<ImmutableList<String>> result = new LinkedHashSet<>();
+    private final ExperimentDesign experimentDesign;
 
-    public DifferentialExperimentContrastLines(DifferentialExperiment experiment) {
+    public DifferentialExperimentContrastLines(DifferentialExperiment experiment, ExperimentDesign experimentDesign) {
         this.contrastDetails = buildContrastDetails(experiment);
+        this.experimentDesign = experimentDesign;
     }
 
     private LinkedHashSet<ImmutableList<String>> buildContrastDetails(DifferentialExperiment experiment) {
@@ -43,10 +46,11 @@ private void populateSamples(DifferentialExperiment experiment,
                                  String assayAccession,
                                  Contrast contrast,
                                  String value) {
-        for (SampleCharacteristic sample : experiment.getExperimentDesign().getSampleCharacteristics(assayAccession)) {
+        final String experimentAccession = experiment.getAccession();
+        for (SampleCharacteristic sample : experimentDesign.getSampleCharacteristics(assayAccession)) {
             ImmutableList<String> line =
                     ImmutableList.of(
-                            experiment.getAccession(),
+                            experimentAccession,
                             contrast.getId(),
                             value,
                             "characteristic",
@@ -61,12 +65,13 @@ private void populateFactors(DifferentialExperiment experiment,
                                  String assayAccession,
                                  Contrast contrast,
                                  String value) {
-        FactorSet factorSet = experiment.getExperimentDesign().getFactors(assayAccession);
+        final String experimentAccession = experiment.getAccession();
+        FactorSet factorSet = experimentDesign.getFactors(assayAccession);
         if (factorSet != null) {
             for (Factor factor : factorSet) {
                 ImmutableList<String> line =
                         ImmutableList.of(
-                                experiment.getAccession(),
+                                experimentAccession,
                                 contrast.getId(),
                                 value,
                                 "factor",

app/src/main/java/uk/ac/ebi/atlas/ebeyedump/ExperimentsConditionsDetailsController.java

@@ -4,6 +4,7 @@
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.GetMapping;
 import uk.ac.ebi.atlas.model.experiment.Experiment;
+import uk.ac.ebi.atlas.model.experiment.ExperimentDesign;
 import uk.ac.ebi.atlas.model.experiment.ExperimentType;
 import uk.ac.ebi.atlas.model.experiment.baseline.BaselineExperiment;
 import uk.ac.ebi.atlas.model.experiment.differential.DifferentialExperiment;
@@ -26,7 +27,7 @@
 @Controller
 @Scope("request")
 public class ExperimentsConditionsDetailsController {
-    private ExperimentTrader experimentTrader;
+    private final ExperimentTrader experimentTrader;
 
     public ExperimentsConditionsDetailsController(ExperimentTrader experimentTrader) {
         this.experimentTrader = experimentTrader;
@@ -36,7 +37,8 @@ public ExperimentsConditionsDetailsController(ExperimentTrader experimentTrader)
     public void generateTsvFormatBaseline(HttpServletResponse response) {
         writeTsvLinesToResponse(
                 response,
-                experiment -> new BaselineExperimentAssayGroupsLines((BaselineExperiment) experiment),
+                experiment -> new BaselineExperimentAssayGroupsLines(
+                        (BaselineExperiment) experiment, getExperimentDesign(experiment.getAccession())),
                 RNASEQ_MRNA_BASELINE,
                 PROTEOMICS_BASELINE,
                 PROTEOMICS_BASELINE_DIA);
@@ -46,13 +48,18 @@ public void generateTsvFormatBaseline(HttpServletResponse response) {
     public void generateTsvFormatDifferential(HttpServletResponse response) {
         writeTsvLinesToResponse(
                 response,
-                experiment -> new DifferentialExperimentContrastLines((DifferentialExperiment) experiment),
+                experiment -> new DifferentialExperimentContrastLines(
+                        (DifferentialExperiment) experiment, getExperimentDesign(experiment.getAccession())),
                 MICROARRAY_1COLOUR_MICRORNA_DIFFERENTIAL,
                 MICROARRAY_1COLOUR_MRNA_DIFFERENTIAL,
                 MICROARRAY_2COLOUR_MRNA_DIFFERENTIAL,
                 RNASEQ_MRNA_DIFFERENTIAL);
     }
 
+    private ExperimentDesign getExperimentDesign(String experimentAccession) {
+        return experimentTrader.getExperimentDesign(experimentAccession);
+    }
+
     private void writeTsvLinesToResponse(HttpServletResponse response,
                                          Function<Experiment, Iterable<String[]>> linesIteratorProducer,
                                          ExperimentType... experimentTypes) {

app/src/main/java/uk/ac/ebi/atlas/experimentpage/baseline/BaselineExperimentPageService.java

@@ -9,6 +9,7 @@
 import uk.ac.ebi.atlas.experimentpage.baseline.profiles.BaselineExperimentProfilesListSerializer;
 import uk.ac.ebi.atlas.experimentpage.baseline.profiles.BaselineExperimentProfilesService;
 import uk.ac.ebi.atlas.experimentpage.context.BaselineRequestContext;
+import uk.ac.ebi.atlas.model.experiment.ExperimentDesign;
 import uk.ac.ebi.atlas.model.experiment.sample.AssayGroup;
 import uk.ac.ebi.atlas.model.ExpressionUnit;
 import uk.ac.ebi.atlas.model.GeneProfilesList;
@@ -38,12 +39,13 @@ public BaselineExperimentPageService(BaselineExperimentProfilesService baselineE
     }
 
     public <U extends ExpressionUnit.Absolute> JsonObject getResultsForExperiment(
-            BaselineExperiment experiment, String accessKey, BaselineRequestPreferences<U> preferences) {
+            BaselineExperiment experiment, ExperimentDesign experimentDesign, String accessKey,
+            BaselineRequestPreferences<U> preferences) {
 
         BaselineRequestContext<U> requestContext = new BaselineRequestContext<>(preferences, experiment);
 
         JsonObject result = new JsonObject();
-        result.add("columnHeaders", constructColumnHeaders(requestContext, experiment));
+        result.add("columnHeaders", constructColumnHeaders(requestContext, experiment, experimentDesign));
         result.add("columnGroupings", new JsonArray());
 
         GeneProfilesList<BaselineProfile> baselineProfilesList = fetchProfiles(experiment, preferences);
@@ -88,7 +90,8 @@ private GeneProfilesList<BaselineProfile> fetchProfiles(BaselineExperiment exper
         return baselineProfilesList;
     }
 
-    private JsonArray constructColumnHeaders(BaselineRequestContext<?> requestContext, BaselineExperiment experiment) {
+    private JsonArray constructColumnHeaders(BaselineRequestContext<?> requestContext, BaselineExperiment experiment,
+                                             ExperimentDesign experimentDesign) {
         JsonArray result = new JsonArray();
 
         for (AssayGroup dataColumnDescriptor : requestContext.getDataColumnsToReturn()) {
@@ -101,7 +104,7 @@ private JsonArray constructColumnHeaders(BaselineRequestContext<?> requestContex
             o.add("assayGroupSummary",
                     new AssayGroupSummaryBuilder()
                     .forAssayGroup(experiment.getDataColumnDescriptor(dataColumnDescriptor.getId()))
-                    .withExperimentDesign(experiment.getExperimentDesign())
+                    .withExperimentDesign(experimentDesign)
                     .build().toJson());
             result.add(o);
         }

app/src/main/java/uk/ac/ebi/atlas/experimentpage/content/ExperimentPageContentService.java

@@ -22,6 +22,7 @@
 import uk.ac.ebi.atlas.model.experiment.ExperimentType;
 import uk.ac.ebi.atlas.model.experiment.sample.ReportsGeneExpression;
 import uk.ac.ebi.atlas.resource.DataFileHub;
+import uk.ac.ebi.atlas.trader.ExperimentTrader;
 import uk.ac.ebi.atlas.utils.GsonProvider;
 
 import java.util.List;
@@ -39,10 +40,14 @@ public class ExperimentPageContentService {
 
     private final DataFileHub dataFileHub;
     private final ExpressionAtlasContentService expressionAtlasContentService;
+    private final ExperimentTrader experimentTrader;
 
-    public ExperimentPageContentService(DataFileHub dataFileHub, ExpressionAtlasContentService expressionAtlasContentService) {
+    public ExperimentPageContentService(DataFileHub dataFileHub,
+                                        ExpressionAtlasContentService expressionAtlasContentService,
+                                        ExperimentTrader experimentTrader) {
         this.dataFileHub = dataFileHub;
         this.expressionAtlasContentService = expressionAtlasContentService;
+        this.experimentTrader = experimentTrader;
     }
 
     @Cacheable(cacheNames = "experimentContent", key = "#experiment.getAccession()")
@@ -66,7 +71,8 @@ private JsonObject experimentPageContentForExperiment(final Experiment<? extends
         // everything wants to have a heatmap
         availableTabs.add(
                 heatmapTab(
-                        GSON.toJsonTree(getExperimentVariablesAsHeatmapFilterGroups(experiment)).getAsJsonArray(),
+                        GSON.toJsonTree(getExperimentVariablesAsHeatmapFilterGroups(experiment,
+                                experimentTrader.getExperimentDesign(experiment.getAccession()))).getAsJsonArray(),
                         JsonBaselineExperimentController.geneDistributionUrl(
                                 experiment.getAccession(),
                                 accessKey,
@@ -90,7 +96,7 @@ private JsonObject experimentPageContentForExperiment(final Experiment<? extends
 
         if (dataFileHub.getExperimentFiles(experiment.getAccession()).experimentDesign.exists()) {
             availableTabs.add(
-                    experimentDesignTab(new ExperimentDesignTable(experiment).asJson(),
+                    experimentDesignTab(new ExperimentDesignTable(experimentTrader, experiment).asJson(),
                             ExperimentDesignFile.makeUrl(experiment.getAccession(), accessKey)));
         }