Merge branch 'develop' into reduce_memory_metrics

CHANGELOG.md

@@ -5,6 +5,8 @@ All notable changes to Pantools will be documented in this file.
 ### Fixed
 - Clearer error message for homology group identifiers that could not by found by `group_info` (!253).
 - Prevent NullPointerException in `gene_classification` (!254).
+- Updated gene-ontology (GO) endpoint to HTTPS-protocol (!258).
+- Throw RuntimeException if empty homology-selection file in `msa` (!256).
 
 ## [4.3.2] - 20-12-2024
 

src/main/java/nl/wur/bif/pantools/construction/functions/add_functions/AddFunctions.java

@@ -318,7 +318,7 @@ public class AddFunctions {
                                    boolean tigrfamDatabaseExists) {
         if (!goDatabaseExists) {
             try {
-                downloadDatabase(functionalDatabasesPath, "go-basic.obo", "http://purl.obolibrary.org/obo/go/go-basic.obo");
+                downloadDatabase(functionalDatabasesPath, "go-basic.obo", "https://purl.obolibrary.org/obo/go/go-basic.obo");
             } catch (IOException e) {
                 Pantools.logger.error("Error while downloading GO database.");
             }

src/main/java/nl/wur/bif/pantools/utils/cli/mixins/SelectHmGroups.java

@@ -9,6 +9,7 @@ import static picocli.CommandLine.*;
 
 import java.io.IOException;
 import java.nio.file.Path;
+import java.util.ArrayList;
 import java.util.List;
 
 /**
@@ -32,6 +33,16 @@ public class SelectHmGroups {
 
     public List<Long> getHomologyGroups() throws IOException, NumberFormatException {
         if (homologyGroups != null) return homologyGroups;
-        return (homologyGroupsFile == null) ? null : Utils.parseHmFile(homologyGroupsFile);
+
+        if (homologyGroupsFile != null) {
+            List<Long> hmGroups = Utils.parseHmFile(homologyGroupsFile);
+
+            if (hmGroups.isEmpty()) {
+                throw new RuntimeException("Homology file does not contain any homology groups");
+            }
+
+            return hmGroups;
+        }
+        return null;
     }
 }