Search result shows topLevelPathways as their own topLevelPathways. Updated iReactions.

Author: Luis Francisco Hernández Sánchez

src/no/uib/pap/methods/analysis/ora/AnalysisTest.java

@@ -3,10 +3,7 @@
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.ImmutableSetMultimap;
 import no.uib.pap.methods.search.Search;
-import no.uib.pap.model.MessageStatus;
-import no.uib.pap.model.Pathway;
-import no.uib.pap.model.Proteoform;
-import no.uib.pap.model.ProteoformFormat;
+import no.uib.pap.model.*;
 import org.apache.commons.lang3.tuple.MutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 import org.junit.jupiter.api.AfterEach;
@@ -30,7 +27,7 @@ class AnalysisTest {
     static HashSet<String> hitProteins = null;
     static HashSet<String> hitPathways = null;
 
-    private static ImmutableMap<String, String> iReactions; // Reaction stId to Reaction displayName
+    private static ImmutableMap<String, Reaction> iReactions; // Reaction stId to Reaction displayName
     private static ImmutableMap<String, Pathway> iPathways; // Pathway stId to Pathway instance
     private static ImmutableMap<String, String> iProteins; // Protein accession (UniProt) to name
     private static ImmutableSetMultimap<String, String> imapGenesToProteins = null;
@@ -48,7 +45,7 @@ class AnalysisTest {
 
     @BeforeAll
     static void loadStaticMapping() {
-        iReactions = (ImmutableMap<String, String>) getSerializedObject("iReactions.gz");
+        iReactions = (ImmutableMap<String, Reaction>) getSerializedObject("iReactions.gz");
         iPathways = (ImmutableMap<String, Pathway>) getSerializedObject("iPathways.gz");
         iProteins = (ImmutableMap<String, String>) getSerializedObject("iProteins.gz");
         imapGenesToProteins = (ImmutableSetMultimap<String, String>) getSerializedObject("imapGenesToProteins.gz");

src/no/uib/pap/methods/search/Search.java

@@ -31,7 +31,7 @@ class SearchTest {
     static HashSet<String> hitProteins = null;
     static HashSet<String> hitPathways = null;
 
-    private static ImmutableMap<String, String> iReactions; // Reaction stId to Reaction displayName
+    private static ImmutableMap<String, Reaction> iReactions; // Reaction stId to Reaction displayName
     private static ImmutableMap<String, Pathway> iPathways; // Pathway stId to Pathway instance
     private static ImmutableMap<String, String> iProteins; // Protein accession (UniProt) to name
     private static ImmutableSetMultimap<String, String> imapGenesToProteins = null;
@@ -49,7 +49,7 @@ class SearchTest {
 
     @BeforeAll
     static void loadStaticMapping() {
-        iReactions = (ImmutableMap<String, String>) getSerializedObject("iReactions.gz");
+        iReactions = (ImmutableMap<String, Reaction>) getSerializedObject("iReactions.gz");
         iPathways = (ImmutableMap<String, Pathway>) getSerializedObject("iPathways.gz");
         iProteins = (ImmutableMap<String, String>) getSerializedObject("iProteins.gz");
         imapGenesToProteins = (ImmutableSetMultimap<String, String>) getSerializedObject("imapGenesToProteins.gz");
@@ -61,9 +61,8 @@ static void loadStaticMapping() {
         imapProteoformsToReactions = (ImmutableSetMultimap<Proteoform, String>) getSerializedObject("imapProteoformsToReactions.gz");
 //        imapRsIdsToProteins = (ImmutableSetMultimap<String,String>) getSerializedObject("imapRsIdsToProteins.gz");
 //        imapChrBpToProteins = (ImmutableSetMultimap<String,String>) getSerializedObject("imapChrBpToProteins.gz");
-        imapReactionsToParticipants = (ImmutableSetMultimap<String, String>) getSerializedObject("imapReactionsToParticipants.gz");
         imapProteinsToComplexes = (ImmutableSetMultimap<String, String>) getSerializedObject("imapProteinsToComplexes.gz");
-        imapComplexesToParticipants = (ImmutableSetMultimap<String, String>) getSerializedObject("imapComplexesToParticipants.gz");
+        imapComplexesToParticipants = (ImmutableSetMultimap<String, String>) getSerializedObject("imapComplexesToComponents.gz");
     }
 
     @BeforeEach