app: Fix NPE. Add appHome to OrganizationMigration. #TASK-7118

opencb · Oct 24, 2024 · bfe1925 · bfe1925
1 parent d2c8073
commit bfe1925
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/...pp/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java b/...pp/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java
@@ -70,7 +70,7 @@ private void runMigrationToV3() throws Exception {
         setCatalogDatabaseCredentials(options, options.commonOptions);
 
         OrganizationMigration organizationMigration = new OrganizationMigration(configuration, options.commonOptions.adminPassword,
-                options.user, options.organizationId);
+                options.user, options.organizationId, Paths.get(appHome));
         organizationMigration.execute();
     }
 

diff --git a/...-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/...-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java
@@ -9,6 +9,7 @@
 import org.bson.conversions.Bson;
 import org.opencb.commons.datastore.mongodb.MongoDataStore;
 import org.opencb.commons.utils.CryptoUtils;
+import org.opencb.commons.utils.FileUtils;
 import org.opencb.opencga.analysis.variant.manager.VariantStorageManager;
 import org.opencb.opencga.catalog.auth.authentication.CatalogAuthenticationManager;
 import org.opencb.opencga.catalog.db.api.StudyDBAdaptor;
@@ -45,6 +46,7 @@
 import java.lang.reflect.Modifier;
 import java.net.URL;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.security.NoSuchAlgorithmException;
 import java.util.*;
@@ -70,21 +72,25 @@ private enum MigrationStatus {
         ERROR
     }
 
-    public OrganizationMigration(Configuration configuration, String adminPassword, String userId, String organizationId)
-            throws CatalogException {
+    public OrganizationMigration(Configuration configuration, String adminPassword, String userId, String organizationId, Path appHome)
+            throws CatalogException, IOException {
         this.configuration = configuration;
         this.adminPassword = adminPassword;
         this.userId = userId;
         this.organizationId = organizationId;
+        this.appHome = appHome;
 
         this.status = checkAndInit();
     }
 
-    private MigrationStatus checkAndInit() throws CatalogException {
+    private MigrationStatus checkAndInit() throws CatalogException, IOException {
         this.oldDatabase = configuration.getDatabasePrefix() + "_catalog";
         this.mongoDBAdaptorFactory = new MongoDBAdaptorFactory(configuration);
         this.oldDatastore = mongoDBAdaptorFactory.getMongoManager().get(oldDatabase, mongoDBAdaptorFactory.getMongoDbConfiguration());
 
+        FileUtils.checkDirectory(appHome);
+        readStorageConfiguration();
+
         MongoCollection<Document> userCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION);
         FindIterable<Document> iterable = userCol.find(Filters.eq("id", ParamConstants.OPENCGA_USER_ID));
         try (MongoCursor<Document> cursor = iterable.cursor()) {