Fix: Handle empty network parameters on session startup

cytoscape · Jul 8, 2022 · 1440ccb · 1440ccb
1 parent f3f2664
commit 1440ccb
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Showing 3 changed files with 29 additions and 10 deletions.
diff --git a/src/main/java/org/nrnb/gsoc/enrichment/tasks/FilterEnrichmentTableTask.java b/src/main/java/org/nrnb/gsoc/enrichment/tasks/FilterEnrichmentTableTask.java
@@ -26,7 +26,10 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
 
 
 public class FilterEnrichmentTableTask extends AbstractTask implements ObservableTask {
@@ -38,28 +41,28 @@ public class FilterEnrichmentTableTask extends AbstractTask implements Observabl
             gravity = 1.0)
     public ListMultipleSelection<TermSource> categories = new ListMultipleSelection<>(TermSource.getValues());
 
-    @Tunable(description = "Select evidence code.",
+    @Tunable(description = "Select evidence code",
             tooltip = "Select the evidence codes to show in the table. If multiple codes are selected, those terms which " +
-                    "contains all the selected codes will be present in result.",
+                    "contains all the selected codes will be present in result",
             exampleStringValue = "GO:0005737",
             gravity = 1.0
     )
     public ListMultipleSelection<String> evidenceCodes;
 
     @Tunable(description = "Remove redundant terms",
-            tooltip = "Removes terms whose enriched genes significantly overlap with already selected terms.",
-            longDescription = "Removes terms whose enriched genes significantly overlap with already selected terms.",
+            tooltip = "Removes terms whose enriched genes significantly overlap with already selected terms",
+            longDescription = "Removes terms whose enriched genes significantly overlap with already selected terms",
             exampleStringValue = "true",
             gravity = 8.0)
     public boolean removeOverlapping;
 
     @Tunable(description = "Redundancy cutoff",
             tooltip = "<html>This is the maximum Jaccard similarity that will be allowed <br/>"
                     + "between a less significant term and a more significant term such that <br/>"
-                    + "the less significant term is kept in the list.</html>",
+                    + "the less significant term is kept in the list</html>",
             longDescription = "This is the maximum Jaccard similarity that will be allowed "
                     + "between a less significant term and a more significant term such that "
-                    + "the less significant term is kept in the list.",
+                    + "the less significant term is kept in the list",
             exampleStringValue="0.5",
             params="slider=true", dependsOn="removeOverlapping=true", gravity = 9.0)
     public BoundedDouble overlapCutoff = new BoundedDouble(0.0, 0.5, 1.0, false, false);
@@ -77,6 +80,7 @@ public FilterEnrichmentTableTask(final CyServiceRegistrar registrar, EnrichmentC
         this.applicationManager = registrar.getService(CyApplicationManager.class);
         this.network = applicationManager.getCurrentNetwork();
         this.enrichmentPanel = panel;
+        this.setCategoriesAndEvidenceCodesAtStartup();
         List<String> evidenceCodesEnum = EVIDENCE_CODES.stringValue();
         categories.setSelectedValues(ModelUtils.getNetSelectedCategories(network));
         this.evidenceCodes = new ListMultipleSelection<>(evidenceCodesEnum);
@@ -85,6 +89,21 @@ public FilterEnrichmentTableTask(final CyServiceRegistrar registrar, EnrichmentC
         overlapCutoff.setValue(ModelUtils.getNetRedundantCutoff(network));
     }
 
+    private void setCategoriesAndEvidenceCodesAtStartup() {
+        List<TermSource> selectedCategories = ModelUtils.getNetSelectedCategories(network);
+        if (!selectedCategories.isEmpty()) {
+            TermSource termSource = selectedCategories.get(0);
+            if (Objects.isNull(termSource)) ModelUtils.setNetSelectedCategories(network, Collections.emptyList());
+        }
+        List<String> selectedEvidenceCodes = ModelUtils.getNetSelectedEvidenceCode(network);
+        if (!selectedEvidenceCodes.isEmpty()) {
+            String termSource = selectedEvidenceCodes.get(0);
+            System.out.println("Filer evi: " + termSource);
+            if (Objects.isNull(termSource) || termSource.isEmpty())
+                ModelUtils.setNetSelectedEvidenceCodes(network, Collections.emptyList());
+        }
+    }
+
 
     @Override
     public void run(TaskMonitor monitor) throws Exception {

diff --git a/src/main/java/org/nrnb/gsoc/enrichment/ui/EnrichmentTableModel.java b/src/main/java/org/nrnb/gsoc/enrichment/ui/EnrichmentTableModel.java
@@ -229,7 +229,7 @@ public void filter(List<TermSource> sources, List<String> evidenceList, boolean
                        double cutoff) {
         filterBySource(sources);
         int length = filterByEvidenceCode(evidenceList);
-        if (removeOverlapping) {
+        if (removeOverlapping && length > 0) {
             rowNames = removeRedundancy(length, cutoff);
         }
         fireTableDataChanged();

diff --git a/src/main/java/org/nrnb/gsoc/enrichment/utils/ModelUtils.java b/src/main/java/org/nrnb/gsoc/enrichment/utils/ModelUtils.java
@@ -762,7 +762,7 @@ public static void setNetSelectedEvidenceCodes(CyNetwork network, List<String> s
 
     public static List<String> getNetSelectedEvidenceCode(CyNetwork network) {
         if (network.getDefaultNetworkTable().getColumn(NET_SELECTED_EVIDENCE_CODES) == null) {
-            return new ArrayList<>();
+            return Collections.emptyList();
         };
         return network.getRow(network).getList(NET_SELECTED_EVIDENCE_CODES, String.class);
     }
@@ -776,10 +776,10 @@ public static void setNetSelectedCategories(CyNetwork network, List<TermSource>
     public static List<TermSource> getNetSelectedCategories(CyNetwork network) {
         CyColumn column = network.getDefaultNetworkTable().getColumn(NET_SELECTED_CATEGORIES);
         if (column == null) {
-            return new ArrayList<>();
+            return Collections.emptyList();
         };
         List<String> categoriesString = network.getRow(network).getList(NET_SELECTED_CATEGORIES, String.class);
-        if (categoriesString == null || categoriesString.isEmpty()) return new ArrayList<>();
+        if (categoriesString == null || categoriesString.isEmpty()) return Collections.emptyList();
         return categoriesString.stream().map(TermSource::getByKey).collect(Collectors.toList());
     }