Merge branch 'TASK-5663' of github.com:opencb/opencga into TASK-5663

opencb · Feb 22, 2024 · 328a8bb · 328a8bb
2 parents 565693f + f4e9aa5
commit 328a8bb
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Showing 2 changed files with 25 additions and 23 deletions.
diff --git a/opencga-analysis/src/test/java/org/opencb/opencga/analysis/family/FamilyAnalysisTest.java b/opencga-analysis/src/test/java/org/opencb/opencga/analysis/family/FamilyAnalysisTest.java
@@ -170,15 +170,17 @@ public void test2Member2GenerationFamilyTest() throws CatalogException {
     public void updateTest() throws CatalogException {
         FamilyUpdateParams updateParams = new FamilyUpdateParams();
 
+        Family prevFamily = catalogManager.getFamilyManager().get(studyId, family.getId(), null, sessionIdUser).first();
+        assertEquals(prevFamily.getPedigreeGraph().getBase64(), family.getPedigreeGraph().getBase64());
+
         QueryOptions queryOptions = new QueryOptions()
                 .append(ParamConstants.FAMILY_UPDATE_ROLES_PARAM, true)
                 .append(ParamConstants.INCLUDE_RESULT_PARAM, true);
         Family updatedFamily = catalogManager.getFamilyManager().update(studyId, family.getId(), updateParams, queryOptions, sessionIdUser)
                 .first();
 
-        PedigreeGraph pedigreeGraph = updatedFamily.getPedigreeGraph();
-        MatcherAssert.assertThat(pedigreeGraph.getBase64(), CoreMatchers.startsWith("iVBORw0KGgoAAAANSUhEUgAAAeAAAAHg="));
-        MatcherAssert.assertThat(pedigreeGraph.getBase64(), CoreMatchers.endsWith("5UIf81hI8AAAAASUVORK5CYII="));
+        assertEquals(prevFamily.getPedigreeGraph().getBase64(), updatedFamily.getPedigreeGraph().getBase64());
+        assertEquals(prevFamily.getVersion() + 1, updatedFamily.getVersion());
     }
 
     @Test

diff --git a/...talog/src/main/java/org/opencb/opencga/catalog/db/mongodb/converters/FamilyConverter.java b/...talog/src/main/java/org/opencb/opencga/catalog/db/mongodb/converters/FamilyConverter.java
@@ -16,17 +16,16 @@
 
 package org.opencb.opencga.catalog.db.mongodb.converters;
 
+import org.apache.commons.collections4.CollectionUtils;
 import org.bson.Document;
 import org.opencb.biodata.models.clinical.Phenotype;
-import org.opencb.commons.utils.ListUtils;
 import org.opencb.opencga.catalog.db.api.FamilyDBAdaptor;
 import org.opencb.opencga.core.models.family.Family;
-import org.opencb.opencga.core.models.individual.Individual;
 import org.opencb.opencga.core.models.study.VariableSet;
 
-import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 /**
@@ -55,40 +54,41 @@ public Document convertToStorageType(Family object, List<VariableSet> variableSe
     }
 
     public void validateDocumentToUpdate(Document document) {
-        List<Document> memberList = (List) document.get("members");
+        List<Document> memberList = document.getList("members", Document.class);
         if (memberList != null) {
             // We make sure we don't store duplicates
-            Map<Long, Individual> individualMap = new HashMap<>();
+            Set<Long> individualSet = new HashSet<>();
             for (Document individual : memberList) {
-                long id = individual.getInteger("uid").longValue();
-                int version = individual.getInteger("version");
-                if (id > 0) {
-                    Individual tmpIndividual = new Individual()
-                            .setVersion(version);
-                    tmpIndividual.setUid(id);
-                    individualMap.put(id, tmpIndividual);
+                long uid = individual.get("uid", Number.class).longValue();
+                if (uid <= 0) {
+                    throw new IllegalArgumentException("Missing uid value for member '" + individual.getString("id") + "'.");
                 }
+                if (individualSet.contains(uid)) {
+                    throw new IllegalArgumentException("Duplicated member '" + individual.getString("id") + " (" + uid + ")' found.");
+                }
+                individualSet.add(uid);
             }
 
             document.put("members",
-                    individualMap.entrySet().stream()
+                    memberList.stream()
                             .map(entry -> new Document()
-                                    .append("uid", entry.getValue().getUid())
-                                    .append("version", entry.getValue().getVersion()))
+                                    .append("uid", entry.get("uid", Number.class).longValue())
+                                    .append("version", entry.get("version", Number.class).intValue())
+                            )
                             .collect(Collectors.toList()));
         }
 
-        List<Document> disorderList = (List) document.get("disorders");
+        List<Document> disorderList = document.getList("disorders", Document.class);
         if (disorderList != null) {
             for (Document disorder : disorderList) {
-                fixPhenotypeFields((List) disorder.get("evidences"));
+                fixPhenotypeFields(disorder.getList("evidences", Document.class));
             }
         }
-        fixPhenotypeFields((List) document.get("phenotypes"));
+        fixPhenotypeFields(document.getList("phenotypes", Document.class));
     }
 
     private void fixPhenotypeFields(List<Document> phenotypeList) {
-        if (ListUtils.isNotEmpty(phenotypeList)) {
+        if (CollectionUtils.isNotEmpty(phenotypeList)) {
             for (Document phenotype : phenotypeList) {
                 phenotype.put("status", Phenotype.Status.UNKNOWN.name());
                 phenotype.put("ageOfOnset", "-1");