fix(central): schema names with - should be allowed (#4391)

molgenis · Oct 29, 2024 · 282d6d1 · 282d6d1
1 parent 90565b5
commit 282d6d1
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Showing 8 changed files with 30 additions and 14 deletions.
diff --git a/apps/central/src/components/SchemaCreateModal.vue b/apps/central/src/components/SchemaCreateModal.vue
@@ -168,7 +168,7 @@ export default {
   },
   methods: {
     validate(name) {
-      const simpleName = constants.TABLE_NAME_REGEX;
+      const simpleName = constants.SCHEMA_NAME_REGEX;
       if (name === null) {
         return undefined;
       }
@@ -179,7 +179,7 @@ export default {
       ) {
         return undefined;
       } else {
-        return "Table name must start with a letter, followed by zero or more letters, numbers, spaces or underscores. A space immediately before or after an underscore is not allowed. The character limit is 31.";
+        return "Table name must start with a letter, followed by zero or more letters, numbers, spaces, dash or underscores. A space immediately before or after an underscore is not allowed. The character limit is 31.";
       }
     },
     executeCreateSchema() {

diff --git a/apps/molgenis-components/src/components/constants.ts b/apps/molgenis-components/src/components/constants.ts
@@ -3,6 +3,7 @@ export default {
   CODE_9: 57,
   CODE_PERIOD: 46,
   CODE_MINUS: 45,
+  SCHEMA_NAME_REGEX: /^(?!.* _|.*_ )[a-zA-Z][-a-zA-Z0-9 _]{0,62}$/,
   TABLE_NAME_REGEX: /^(?!.* _|.*_ )[a-zA-Z][a-zA-Z0-9 _]{0,30}$/,
   COLUMN_NAME_REGEX: /^(?!.* _|.*_ )[a-zA-Z][a-zA-Z0-9 _]{0,62}$/,
   EMAIL_REGEX:

diff --git a/backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestImportExportAllExamples.java b/backend/molgenis-emx2-io/src/test/java/org/molgenis/emx2/io/TestImportExportAllExamples.java
@@ -24,49 +24,51 @@ public class TestImportExportAllExamples {
 
   static Database db;
 
+  static String prefix = TestImportExportAllExamples.class.getSimpleName();
+
   @BeforeAll
   public static void setup() {
     db = TestDatabaseFactory.getTestDatabase();
   }
 
   @Test
   public void testArrayTypeTestExample() throws IOException {
-    SchemaMetadata schema1 = new SchemaMetadata("1");
+    SchemaMetadata schema1 = new SchemaMetadata(prefix + "1");
     ArrayTypeTestExample.createSimpleTypeTest(schema1);
     executeCompare(schema1);
   }
 
   @Test
   public void testRefAndRefArrayExample() throws IOException {
-    SchemaMetadata schema1 = new SchemaMetadata("4");
+    SchemaMetadata schema1 = new SchemaMetadata(prefix + "4");
     RefAndRefArrayTestExample.createRefAndRefArrayTestExample(schema1);
     executeCompare(schema1);
   }
 
   @Test
   public void testSimpleTypeTestExample() throws IOException {
-    SchemaMetadata schema1 = new SchemaMetadata("5");
+    SchemaMetadata schema1 = new SchemaMetadata(prefix + "5");
     SimpleTypeTestExample.createSimpleTypeTest(schema1);
     executeCompare(schema1);
   }
 
   @Test
   public void testProductComponentPartsExample() throws IOException {
-    SchemaMetadata schema1 = new SchemaMetadata("6");
+    SchemaMetadata schema1 = new SchemaMetadata(prefix + "6");
     ProductComponentPartsExample.create(schema1);
     executeCompare(schema1);
   }
 
   @Test
   public void testPetStoreExample() throws IOException {
-    SchemaMetadata schema1 = new SchemaMetadata("7");
+    SchemaMetadata schema1 = new SchemaMetadata(prefix + "7");
     schema1.create(PetStoreLoader.getSchemaMetadata().getTables().toArray(new TableMetadata[0]));
     executeCompare(schema1);
   }
 
   @Test
   public void testDefaultValuesMetadata() throws IOException {
-    SchemaMetadata schema1 = new SchemaMetadata("8");
+    SchemaMetadata schema1 = new SchemaMetadata(prefix + "8");
     schema1.create(table("test", column("id").setDefaultValue("bla")));
     Schema result = executeCompare(schema1);
     assertEquals(
@@ -85,7 +87,7 @@ public Schema executeCompare(SchemaMetadata schema1) throws IOException, Molgeni
 
       CompareTools.assertEquals(schema1, schema2);
 
-      Schema schema3 = db.dropCreateSchema(getClass().getSimpleName() + schema1.getName());
+      Schema schema3 = db.dropCreateSchema(schema1.getName() + "_copy");
       schema3.migrate(schema2);
       return schema3;
 

diff --git a/backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/TestSchemaCreateDestroy.java b/backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/TestSchemaCreateDestroy.java
@@ -16,7 +16,7 @@
 
 public class TestSchemaCreateDestroy {
   private static Database db;
-  private static final String name = TestSchemaCreateDestroy.class.getName() + "Desc";
+  private static final String name = TestSchemaCreateDestroy.class.getSimpleName() + "Desc";
 
   @BeforeAll
   public static void setUp() {

diff --git a/backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/TestSchemaUpdate.java b/backend/molgenis-emx2-sql/src/test/java/org/molgenis/emx2/sql/TestSchemaUpdate.java
@@ -13,15 +13,18 @@ public class TestSchemaUpdate {
   @BeforeAll
   public static void setUp() {
     db = TestDatabaseFactory.getTestDatabase();
-    db.dropCreateSchema(TestSchemaUpdate.class.getName(), desc);
+    db.dropCreateSchema(TestSchemaUpdate.class.getSimpleName(), desc);
   }
 
   @Test
   public void testUpdateDescription() {
     String descUpdate = "update me";
-    db.updateSchema(TestSchemaUpdate.class.getName(), descUpdate);
+    db.updateSchema(TestSchemaUpdate.class.getSimpleName(), descUpdate);
     assertTrue(
-        db.getSchemaInfo(TestSchemaUpdate.class.getName()).description().contains(descUpdate));
-    assertFalse(db.getSchemaInfo(TestSchemaUpdate.class.getName()).description().contains(desc));
+        db.getSchemaInfo(TestSchemaUpdate.class.getSimpleName())
+            .description()
+            .contains(descUpdate));
+    assertFalse(
+        db.getSchemaInfo(TestSchemaUpdate.class.getSimpleName()).description().contains(desc));
   }
 }
diff --git a/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Constants.java b/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Constants.java
@@ -79,6 +79,9 @@ public class Constants {
   };
   protected static final Operator[] EQUALITY_OPERATORS = {EQUALS, NOT_EQUALS};
 
+  // n.b. we allow _SYSTEM_
+  protected static final String SCHEMA_NAME_REGEX = "^(?!.* _|.*_ )[a-zA-Z][-a-zA-Z0-9 _]{0,62}$";
+
   protected static final String TABLE_NAME_REGEX = "^(?!.* _|.*_ )[a-zA-Z][a-zA-Z0-9 _]{0,30}$";
 
   protected static final String COLUMN_NAME_REGEX = "^(?!.* _|.*_ )[a-zA-Z][a-zA-Z0-9 _]{0,62}$";

diff --git a/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/SchemaMetadata.java b/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/SchemaMetadata.java
@@ -2,6 +2,7 @@
 
 import static org.molgenis.emx2.Constants.OIDC_CALLBACK_PATH;
 import static org.molgenis.emx2.Constants.OIDC_LOGIN_PATH;
+import static org.molgenis.emx2.TableMetadata.SCHEMA_NAME_MESSAGE;
 import static org.molgenis.emx2.utils.TypeUtils.convertToPascalCase;
 
 import java.util.*;
@@ -42,6 +43,10 @@ public SchemaMetadata(Database db, SchemaMetadata schema) {
   }
 
   private void validateSchemaName(String name) {
+    // we only allow _SYSTEM_
+    if (!name.matches(Constants.SCHEMA_NAME_REGEX) && !name.equals("_SYSTEM_")) {
+      throw new MolgenisException("Invalid schema name '" + name + SCHEMA_NAME_MESSAGE);
+    }
     if (name == null || name.isEmpty())
       throw new MolgenisException("Create schema failed: Schema name was null or empty");
     if (name.equalsIgnoreCase(OIDC_LOGIN_PATH) || name.equalsIgnoreCase(OIDC_CALLBACK_PATH))

diff --git a/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/TableMetadata.java b/backend/molgenis-emx2/src/main/java/org/molgenis/emx2/TableMetadata.java
@@ -16,6 +16,8 @@ public class TableMetadata extends HasLabelsDescriptionsAndSettings<TableMetadat
 
   public static final String TABLE_NAME_MESSAGE =
       ": Table name must start with a letter, followed by zero or more letters, numbers, spaces or underscores. A space immediately before or after an underscore is not allowed. The character limit is 31.";
+  public static final String SCHEMA_NAME_MESSAGE =
+      ": Schema name must start with a letter, followed by zero or more letters, numbers, spaces, dash or underscores. A space immediately before or after an underscore is not allowed. The character limit is 31.";
   // if a table extends another table (optional)
   public String inheritName = null;
   // to allow indicate that a table should be dropped