From b15fc09beff203a81d622c49707a175ce75a92bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Thu, 25 Jan 2024 21:36:15 +0100
Subject: [PATCH 1/2] catalog: fix clinical analysis creation, #TASK-5538,
 #TASK-5516

---
 .../managers/ClinicalAnalysisManager.java     | 24 ++++++++++++-------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java
index 351ff17a184..5fb26ec5367 100644
--- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java
+++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ClinicalAnalysisManager.java
@@ -342,14 +342,20 @@ public OpenCGAResult<ClinicalAnalysis> create(String studyStr, ClinicalAnalysis
                 // Validate users
                 Set<String> userIds = new HashSet<>();
                 for (ClinicalAnalyst analyst : clinicalAnalysis.getAnalysts()) {
-                    userIds.add(analyst.getId());
+                    if (StringUtils.isNotEmpty(analyst.getId())) {
+                        userIds.add(analyst.getId());
+                    }
                 }
-                Query query = new Query(UserDBAdaptor.QueryParams.ID.key(), userIds);
-                OpenCGAResult<User> result = userDBAdaptor.get(query, userInclude);
-                if (result.getNumResults() < userIds.size()) {
-                    throw new CatalogException("Some clinical analysts could not be found.");
+                if (CollectionUtils.isNotEmpty(userIds)) {
+                    Query query = new Query(UserDBAdaptor.QueryParams.ID.key(), userIds);
+                    OpenCGAResult<User> result = userDBAdaptor.get(query, userInclude);
+                    if (result.getNumResults() < userIds.size()) {
+                        throw new CatalogException("Some clinical analysts could not be found.");
+                    }
+                    userList = result.getResults();
+                } else {
+                    userList = userDBAdaptor.get(userId, userInclude).getResults();
                 }
-                userList = result.getResults();
             }
             List<ClinicalAnalyst> clinicalAnalystList = new ArrayList<>(userList.size());
             for (User user : userList) {
@@ -663,7 +669,7 @@ public ClinicalAnalysisLoadResult load(String studyStr, Path filePath, String to
                     counter++;
                 } catch (Exception e) {
                     logger.error("Error loading clinical analysis" + (clinicalAnalysis != null ? (": " + clinicalAnalysis.getId()) : "")
-                    + ": " + e.getMessage());
+                            + ": " + e.getMessage());
                     result.getFailures().put(clinicalAnalysis.getId(), e.getMessage());
                 }
             }
@@ -2328,8 +2334,8 @@ public OpenCGAResult groupBy(@Nullable String studyStr, Query query, List<String
     }
 
     public OpenCGAResult<ClinicalAnalysis> updateAnnotations(String studyStr, String clinicalStr, String annotationSetId,
-                                                   Map<String, Object> annotations, ParamUtils.CompleteUpdateAction action,
-                                                   QueryOptions options, String token) throws CatalogException {
+                                                             Map<String, Object> annotations, ParamUtils.CompleteUpdateAction action,
+                                                             QueryOptions options, String token) throws CatalogException {
         if (annotations == null || annotations.isEmpty()) {
             throw new CatalogException("Missing array of annotations.");
         }

From 23224a3fafd41d9cdf940518c2c37f7a95552b6f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Thu, 25 Jan 2024 22:03:10 +0100
Subject: [PATCH 2/2] pom: workaround for SonarCloud issue on CI/CD, #TASK-5516

---
 pom.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pom.xml b/pom.xml
index 0de0a7fdc99..8079976c15f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -147,6 +147,13 @@
         <servlet-api.version>2.5-20081211</servlet-api.version>
 
         <kryo.version>2.23.0</kryo.version>
+        
+        <!--TO REMOVE:
+            The version of Java (11.0.21) used to run this analysis is deprecated, and SonarCloud no longer supports it. Please upgrade to Java 17 or later.
+            As a temporary measure, you can set the property 'sonar.scanner.force-deprecated-java-version' to 'true' to continue using Java 11.0.21
+            This workaround will only be effective until January 28, 2024. After this date, all scans using the deprecated Java 11 will fail.
+        -->
+        <sonar.scanner.force-deprecated-java-version>true</sonar.scanner.force-deprecated-java-version>
     </properties>
 
     <scm>