Use openbis 20.10.x (#510)

* wip

* testable version

* cleanuop

* adapt to new openbis instance and model

* remove workarounds, fix issues

* fix small issues

* rename experiment

* remove unused impot

* use autoclosable sessions

* address review

* remove todo

Author: wow-such-code

project-management-infrastructure/pom.xml

@@ -35,13 +35,8 @@
     <dependency>
       <groupId>life.qbic</groupId>
       <artifactId>openbis-api</artifactId>
-      <version>19.06.5</version>
-      <scope>compile</scope>
-    </dependency>
-    <dependency>
-      <groupId>life.qbic</groupId>
-      <artifactId>openbis-client-lib</artifactId>
-      <version>1.6.0</version>
+      <version>20.10.7.3</version>
+      <classifier>r1700646105</classifier>
       <scope>compile</scope>
     </dependency>
     <dependency>

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/QbicSampleDataRepo.java

@@ -35,7 +35,7 @@ public interface QbicSampleDataRepo {
    */
   void deleteAll(ProjectCode projectCode, Collection<SampleCode> samples);
 
-  void updateAll(Collection<Sample> samples);
+  void updateAll(Project project, Collection<Sample> samples);
 
   boolean canDeleteSample(ProjectCode projectCode, SampleCode sampleCode);
 }

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/SampleRepositoryImpl.java

@@ -131,7 +131,7 @@ public List<Sample> findSamplesByBatchId(
   public void updateAll(Project project,
       Collection<Sample> updatedSamples) {
     qbicSampleRepository.saveAll(updatedSamples);
-    sampleDataRepo.updateAll(updatedSamples);
+    sampleDataRepo.updateAll(project, updatedSamples);
   }
 
   @Override

project-management-infrastructure/src/main/java/life/qbic/projectmanagement/infrastructure/sample/openbis/AnalyteTermMapper.java

@@ -0,0 +1,162 @@
+package life.qbic.projectmanagement.infrastructure.sample.openbis;
+
+import static java.util.Objects.requireNonNull;
+import static org.slf4j.LoggerFactory.getLogger;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import org.slf4j.Logger;
+
+/**
+ *
+ * <b>Handles openBIS login and session</b>
+ *
+ * @since 1.0.0
+ */
+public class OpenbisSessionFactory {
+
+  private final String applicationServerUrl;
+  private final String userName;
+  private final String password;
+
+  public OpenbisSessionFactory(String applicationServerUrl, String userName, String password) {
+    this.applicationServerUrl = applicationServerUrl;
+    this.userName = userName;
+    this.password = password;
+  }
+
+  public OpenBisSession getSession() {
+    return new AutoCloseableOpenBisSession(userName, password, applicationServerUrl);
+  }
+  public OpenBisSession getSession(String token) {
+    return new TokenBaseOpenBisSession(token, applicationServerUrl);
+  }
+
+  public static class OpenBisSessionException extends RuntimeException {
+
+    public OpenBisSessionException() {
+    }
+
+    public OpenBisSessionException(String message) {
+      super(message);
+    }
+
+    public OpenBisSessionException(String message, Throwable cause) {
+      super(message, cause);
+    }
+
+    public OpenBisSessionException(Throwable cause) {
+      super(cause);
+    }
+
+    public OpenBisSessionException(String message, Throwable cause, boolean enableSuppression,
+        boolean writableStackTrace) {
+      super(message, cause, enableSuppression, writableStackTrace);
+    }
+  }
+
+  private static final class TokenBaseOpenBisSession implements OpenBisSession {
+
+    private final String token;
+    private final IApplicationServerApi applicationServer;
+
+
+    private TokenBaseOpenBisSession(String token, String applicationServerUrl) {
+      applicationServer = ApiV3.applicationServer(applicationServerUrl);
+      try {
+        if (!applicationServer.isSessionActive(token)) {
+          throw new IllegalArgumentException("Session no longer active.");
+        }
+      } catch (UserFailureException userFailureException) {
+        throw new IllegalArgumentException(userFailureException.getMessage());
+      }
+      this.token = token;
+    }
+
+    @Override
+    public String getToken() {
+      return token;
+    }
+
+    @Override
+    public void close() {
+      applicationServer.logout(token);
+    }
+  }
+
+  private static final class AutoCloseableOpenBisSession implements OpenBisSession, Refreshable {
+
+    private static final Logger log = getLogger(AutoCloseableOpenBisSession.class);
+
+    private String token;
+    private final IApplicationServerApi apiV3;
+    private final String userName;
+    private final String password;
+
+    private AutoCloseableOpenBisSession(String userName, String password, String applicationServerApiUrl) {
+      requireNonNull(applicationServerApiUrl, "applicationServerApiUrl must not be null");
+      apiV3 = ApiV3.applicationServer(applicationServerApiUrl);
+      this.password = password;
+      this.userName = userName;
+      login();
+    }
+
+
+    @Override
+    public void refresh() {
+      logout();
+      login();
+    }
+
+    private void login() throws OpenBisSessionException {
+      String sessionToken = apiV3.login(userName, password);
+      if (sessionToken == null) {
+        throw new OpenBisSessionException("No session token generated.");
+      }
+      token = sessionToken;
+      log.debug("Successfully logged in");
+    }
+
+    private void logout() {
+      apiV3.logout(token);
+      token = null;
+      log.debug("Successfully logged out");
+    }
+
+    public String getToken() {
+      return token;
+    }
+
+    @Override
+    public void close() {
+      logout();
+    }
+  }
+
+  public interface OpenBisSession extends AutoCloseable {
+
+    String getToken();
+
+    @Override
+    void close();
+  }
+
+  public interface Refreshable {
+    void refresh();
+  }
+  public class ApiV3 {
+
+    private ApiV3() {
+    }
+
+    public static IApplicationServerApi applicationServer(String url) {
+      return HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, url, 100_000L);
+    }
+    public static IDataStoreServerApi dataStoreServer(String url) {
+      return HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class, url, 100_000L);
+    }
+
+  }
+}