Spike/migrations direct

apps/build.gradle

@@ -43,6 +43,11 @@ subprojects { subproject ->
         with nodeSpec
     }
 
+    task movePyFiles(type: Copy) {
+        from "migrations"
+        into "${parent.buildDir}/generated/main/resources/" + project.name + "/migration"
+    }
+
     task format(type: YarnTask, dependsOn: parent.yarn_install) {
         if (!isCI) {
             args = ['run', 'format']

apps/nuxt3-ssr/migrations/requirements.txt

@@ -0,0 +1,13 @@
+certifi==2024.7.4
+charset-normalizer==2.1.1
+idna==3.7
+numpy==1.26.3
+pandas==2.2.2
+python-dateutil==2.8.2
+python-decouple==3.8
+pytz==2022.7.1
+requests==2.32.3
+setuptools==70.0.0
+six==1.16.0
+molgenis_emx2_pyclient
+urllib3==1.26.19

apps/nuxt3-ssr/migrations/version1/migrate.py

@@ -0,0 +1,11 @@
+from molgenis_emx2_pyclient import Client
+
+username = 'admin'
+password = 'admin'
+
+# Initialize the client as a context manager
+with Client(url='http://localhost:8080') as client:
+    # Apply the 'signin' method with the username and password
+    client.signin(username, password)
+
+    # Perform other tasks

apps/yarn.lock

@@ -7034,15 +7034,6 @@ handlebars@^4.7.7, handlebars@^4.7.8:
   optionalDependencies:
     uglify-js "^3.1.4"
 
-happy-dom@15.10.1:
-  version "15.10.1"
-  resolved "https://registry.yarnpkg.com/happy-dom/-/happy-dom-15.10.1.tgz#db49321a7af97d8c18c45622de2817b382ac7595"
-  integrity sha512-FuGnj/qIB4QnBL6fWmD7Wnh6STxevLgOVWB6+nopDGgWG1+t9CXkNB2ldZ+iqwD2UKxD2D0SU8el8A6AX6Q1+g==
-  dependencies:
-    entities "^4.5.0"
-    webidl-conversions "^7.0.0"
-    whatwg-mimetype "^3.0.0"
-
 happy-dom@15.10.2:
   version "15.10.2"
   resolved "https://registry.yarnpkg.com/happy-dom/-/happy-dom-15.10.2.tgz#14ae6652d1a80d2611e3f5832cb61ab5e2d1b539"
@@ -7052,15 +7043,6 @@ happy-dom@15.10.2:
     webidl-conversions "^7.0.0"
     whatwg-mimetype "^3.0.0"
 
-happy-dom@15.7.4:
-  version "15.7.4"
-  resolved "https://registry.yarnpkg.com/happy-dom/-/happy-dom-15.7.4.tgz#05aade59c1d307336001b7004c76dfc6a829f220"
-  integrity sha512-r1vadDYGMtsHAAsqhDuk4IpPvr6N8MGKy5ntBo7tSdim+pWDxus2PNqOcOt8LuDZ4t3KJHE+gCuzupcx/GKnyQ==
-  dependencies:
-    entities "^4.5.0"
-    webidl-conversions "^7.0.0"
-    whatwg-mimetype "^3.0.0"
-
 has-ansi@^2.0.0:
   version "2.0.0"
   resolved "https://registry.yarnpkg.com/has-ansi/-/has-ansi-2.0.0.tgz#34f5049ce1ecdf2b0649af3ef24e45ed35416d91"

backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/RunMolgenisEmx2.java

@@ -3,6 +3,9 @@
 import static org.molgenis.emx2.ColumnType.BOOL;
 import static org.molgenis.emx2.ColumnType.INT;
 
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
 import org.molgenis.emx2.datamodels.BiobankDirectoryLoader;
 import org.molgenis.emx2.datamodels.DataModels;
 import org.molgenis.emx2.datamodels.PetStoreLoader;
@@ -28,7 +31,7 @@ public class RunMolgenisEmx2 {
       (Boolean)
           EnvironmentProperty.getParameter(Constants.MOLGENIS_EXCLUDE_PETSTORE_DEMO, false, BOOL);
 
-  public static void main(String[] args) {
+  public static void main(String[] args) throws IOException {
     logger.info("Starting MOLGENIS EMX2 Software Version=" + Version.getVersion());
 
     Integer port =
@@ -64,6 +67,54 @@ public static void main(String[] args) {
         });
 
     // start
+    logger.info("Before start");
     MolgenisWebservice.start(port);
+
+    logger.info("After start");
+
+    String relativeMigrationFilePath = "./apps/nuxt3-ssr/migrations/version1/migrate.py";
+    String relativeRequirementsFilePath = "./apps/nuxt3-ssr/migrations/requirements.txt";
+    String migrationFilePathString = "/nuxt3-ssr/migration/version1/migrate.py";
+
+    // define commands (given tempDir as working directory)
+    String createVenvCommand = "python3 -m venv venv";
+    String activateCommand = "source venv/bin/activate";
+    String pipUpgradeCommand = "pip3 install --upgrade pip";
+    String installRequirementsCommand = "pip3 install -r " + relativeRequirementsFilePath;
+    String runScriptCommand = "python3 -u " + relativeMigrationFilePath;
+    String command =
+        String.join(
+            " && ",
+            createVenvCommand,
+            activateCommand,
+            pipUpgradeCommand,
+            installRequirementsCommand,
+            runScriptCommand);
+    logger.debug("Running migration script with command: {}", command);
+
+    // String runScriptCommand = "pwd";
+    ProcessBuilder builder = new ProcessBuilder("bash", "-c", command);
+    builder.redirectErrorStream(true);
+    Process process = builder.start();
+
+    // Read the process output
+    try (BufferedReader reader =
+        new BufferedReader(new InputStreamReader(process.getInputStream()))) {
+      String line;
+      while ((line = reader.readLine()) != null) {
+        // Log each line of output
+        logger.info("Process output: {}", line);
+      }
+    }
+
+    // Wait for the process to complete
+    int exitCode = 0;
+    try {
+      exitCode = process.waitFor();
+    } catch (InterruptedException e) {
+      logger.error("Error waiting for migration process to complete", e);
+      throw new RuntimeException(e);
+    }
+    logger.info("Migration process exited with code: {}", exitCode);
   }
 }