Release 2.5 (PR #435 from virtual-imaging-platform/develop)

virtual-imaging-platform · Jul 14, 2023 · b62c908 · b62c908
2 parents 820a51b + 0faf399
commit b62c908
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Showing 40 changed files with 576 additions and 99 deletions.
diff --git a/database_update.sql b/database_update.sql
@@ -35,4 +35,8 @@ alter table VIPAppVersions ADD useBoutiquesForm BOOLEAN;
 ALTER TABLE VIPUsers DROP COLUMN phone;
 
 -- v2.4
+DROP TABLE VIPAccountsGroups;
 DROP TABLE VIPAccounts;
+ALTER TABLE VIPExternalPlatforms ADD upload_url VARCHAR(255);
+ALTER TABLE VIPExternalPlatforms ADD keycloak_client_id VARCHAR(255);
+ALTER TABLE VIPExternalPlatforms ADD refresh_token_url VARCHAR(255);
diff --git a/pom.xml b/pom.xml
@@ -43,8 +43,8 @@ knowledge of the CeCILL-B license and that you accept its terms.
     <properties>
         <!-- project version. Only to change it here (and in CoreConstants.java
            Follow this practice : https://maven.apache.org/maven-ci-friendly.html-->
-        <revision>2.4.1</revision>
-        <changelist></changelist>
+        <revision>2.5</revision>
+        <changelist/>
         <sha1/>
 
         <!-- other maven config -->

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/ApiUserBusiness.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/ApiUserBusiness.java
@@ -11,7 +11,8 @@
 import org.springframework.core.env.Environment;
 import org.springframework.stereotype.Service;
 
-import java.util.List;
+import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * @author khalilkes service to signup a user in VIP
@@ -34,20 +35,25 @@ public ApiUserBusiness(Environment env, ConfigurationBusiness configurationBusin
      *
      * @param user
      * @param comments
-     * @param applicationName
+     * @param applicationNames
      * @throws ApiException
      */
-    public void signup(User user, String comments, String applicationName) throws ApiException {
+    public void signup(User user, String comments, List<String> applicationNames) throws ApiException {
         try {
-            List<Group> groups = applicationBusiness.getPublicGroupsForApplication(applicationName);
-            configurationBusiness
-                    .signup(user, comments, false, true, groups);
+            Set<Group> allGroups = new TreeSet<>(Comparator.comparing(Group::getName));
+            for (String applicationName : applicationNames) {
+                List<Group> appGroups = applicationBusiness.getPublicGroupsForApplication(applicationName);
+                allGroups.addAll(appGroups);
+            }
+            configurationBusiness.signup(user, comments, false, true, new ArrayList<>(allGroups));
             logger.info("Signing up with the " + user.getEmail());
         } catch (BusinessException e) {
             throw new ApiException("Signing up Error", e);
         }
     }
 
+
+
     public void sendResetCode(String email) throws ApiException {
         try {
             configurationBusiness.sendResetCode(email);

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/DataApiBusiness.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/DataApiBusiness.java
@@ -40,6 +40,7 @@
 import fr.insalyon.creatis.vip.core.client.bean.Group;
 import fr.insalyon.creatis.vip.core.client.bean.User;
 import fr.insalyon.creatis.vip.core.server.business.BusinessException;
+import fr.insalyon.creatis.vip.core.server.business.Server;
 import fr.insalyon.creatis.vip.datamanager.client.bean.Data;
 import fr.insalyon.creatis.vip.datamanager.client.bean.Data.Type;
 import fr.insalyon.creatis.vip.datamanager.client.bean.PoolOperation;
@@ -92,21 +93,24 @@ public class DataApiBusiness {
     private final LFCPermissionBusiness lfcPermissionBusiness;
     private final DataManagerBusiness dataManagerBusiness;
 
-    // 2 threads are needed for every download
-    private ScheduledExecutorService scheduler = Executors.newScheduledThreadPool(2 * 5);
+    private final ScheduledExecutorService scheduler;
 
     @Autowired
     public DataApiBusiness(
             Environment env, Supplier<User> currentUserProvider,
             LFCBusiness lfcBusiness, TransferPoolBusiness transferPoolBusiness,
             LFCPermissionBusiness lfcPermissionBusiness,
-            DataManagerBusiness dataManagerBusiness) {
+            DataManagerBusiness dataManagerBusiness, Server server) {
         this.env = env;
         this.currentUserProvider = currentUserProvider;
         this.lfcBusiness = lfcBusiness;
         this.transferPoolBusiness = transferPoolBusiness;
         this.lfcPermissionBusiness = lfcPermissionBusiness;
         this.dataManagerBusiness = dataManagerBusiness;
+        int parallelDownloadsNb = server.getApiParallelDownloadNb();
+        logger.info("Starting threads for {} parallel downloads", parallelDownloadsNb);
+        // 2 threads are needed for every download
+        this.scheduler = Executors.newScheduledThreadPool(2 * parallelDownloadsNb);
     }
 
     @PreDestroy

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/ExecutionBusiness.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/ExecutionBusiness.java
@@ -123,7 +123,8 @@ public Execution getExecution(String executionId, boolean summarize)
 
             // Return null if execution doesn't exist or is cleaned (cleaned status is not supported in Carmin)
             if (s == null || s.getStatus() == SimulationStatus.Cleaned) {
-                return null;
+                logger.error("Error accessing invalid execution {}. (is cleaned : {})", executionId, s != null);
+                throw new ApiException(ApiException.ApiError.INVALID_EXECUTION_ID, executionId);
             }
 
             // Build Carmin's execution object
@@ -258,6 +259,7 @@ public String initExecution(Execution execution)
             inputMap.put(CoreConstants.RESULTS_DIRECTORY_PARAM_NAME,
                          resultsLocation);
         }
+
         checkInputExecNameIsValid(execution.getName());
         return initExecution(
             execution.getPipelineIdentifier(), inputMap, execution.getTimeout(),

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/PipelineBusiness.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/PipelineBusiness.java
@@ -112,6 +112,9 @@ public Pipeline getPipelineWithResultsDirectory(String pipelineId)
 
             for (Source s : d.getSources()) {
                 ParameterType sourceType = ParameterType.fromVipType(s.getType());
+                if ("flag".equalsIgnoreCase(s.getVipTypeRestriction())) {
+                    sourceType = ParameterType.Boolean;
+                }
                 PipelineParameter pp = new PipelineParameter(s.getName(),
                                                              sourceType,
                                                              s.isOptional(),

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/controller/RegisterUserController.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/controller/RegisterUserController.java
@@ -55,9 +55,8 @@ public ResponseEntity<?> signup(
                 );
         user.setRegistration(new Date());
         user.setLastLogin(new Date());
-        this.apiUserBusiness.signup(user, signUpUser.getComments(), signUpUser.getApplication());
+        this.apiUserBusiness.signup(user, signUpUser.getComments(), signUpUser.getApplications());
         return new ResponseEntity(HttpStatus.CREATED);
     }
 
-
 }
diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/exception/ApiException.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/exception/ApiException.java
@@ -57,7 +57,8 @@ public enum ApiError implements VipError{
         WRONG_STAT_SERVICE(8011),
         COUNTRY_UNKNOWN(8012),
         UNAUTHORIZED_DATA_ACCESS(8013),
-        WRONG_OIDC_LOGIN(8014);
+        WRONG_OIDC_LOGIN(8014),
+        INVALID_EXECUTION_ID(8015);
 
         private Integer code;
         ApiError(Integer code) { this.code = code; }
@@ -79,6 +80,7 @@ public enum ApiError implements VipError{
             addMessage(ApiError.COUNTRY_UNKNOWN, "Country unknown : {}", 1);
             addMessage(ApiError.UNAUTHORIZED_DATA_ACCESS, "Unauthorized data access to : {}", 1);
             addMessage(ApiError.WRONG_OIDC_LOGIN, "The login process encountered an error", 0);
+            addMessage(ApiError.INVALID_EXECUTION_ID, "No execution available with this id : {}", 1);
         }
 
         public Optional<String> getMessage() {

diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/model/SignUpUserDTO.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/model/SignUpUserDTO.java
@@ -3,6 +3,8 @@
 import fr.insalyon.creatis.vip.core.client.view.user.UserLevel;
 import fr.insalyon.creatis.vip.core.client.view.util.CountryCode;
 
+import java.util.List;
+
 /**
  * @author KhalilKes
  *
@@ -18,12 +20,12 @@ public class SignUpUserDTO {
     private UserLevel level;
     private CountryCode countryCode;
     private String comments;
-    private String application;
+    private List<String> applications;
 
     public SignUpUserDTO(){
 
     }
-    public SignUpUserDTO(String firstName, String lastName, String email, String institution, String password, UserLevel level, CountryCode countryCode, String comments, String application) {
+    public SignUpUserDTO(String firstName, String lastName, String email, String institution, String password, UserLevel level, CountryCode countryCode, String comments, List<String> applications) {
         this.firstName = firstName;
         this.lastName = lastName;
         this.email = email;
@@ -32,9 +34,10 @@ public SignUpUserDTO(String firstName, String lastName, String email, String ins
         this.level = level;
         this.countryCode = countryCode;
         this.comments = comments;
-        this.application = application;
+        this.applications = applications;
     }
 
+
     public String getFirstName() {
         return firstName;
     }
@@ -99,8 +102,6 @@ public void setComments(String comments) {
         this.comments = comments;
     }
 
-    public String getApplication() { return application; }
-
-    public void setApplication(String application) { this.application = application;}
+    public List<String> getApplications() { return applications; }
 
 }
diff --git a/vip-api/src/main/java/fr/insalyon/creatis/vip/api/security/egi/EgiSecurityClientConfig.java b/vip-api/src/main/java/fr/insalyon/creatis/vip/api/security/egi/EgiSecurityClientConfig.java
@@ -4,6 +4,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.DependsOn;
 import org.springframework.core.env.Environment;
 import org.springframework.security.oauth2.client.registration.ClientRegistration;
 import org.springframework.security.oauth2.client.registration.ClientRegistrationRepository;
@@ -22,7 +23,13 @@ public EgiSecurityClientConfig(Environment env) {
         this.env = env;
     }
 
+    /*
+        This needs the properties that could be in vip-api.conf (especially in the test)
+        For vip-api.conf properties to be loaded, the ApiPropertyInitializer must be run before
+        Spring is not aware of that, so we must tell him explicitly with @DependsOn
+     */
     @Bean
+    @DependsOn("apiPropertiesInitializer")
     public ClientRegistrationRepository clientRegistrationRepository() {
         return new InMemoryClientRegistrationRepository(this.egiClientRegistration());
     }

diff --git a/vip-api/src/test/java/fr/insalyon/creatis/vip/api/business/ExecutionBusinessTest.java b/vip-api/src/test/java/fr/insalyon/creatis/vip/api/business/ExecutionBusinessTest.java
@@ -32,13 +32,16 @@
 package fr.insalyon.creatis.vip.api.business;
 
 import fr.insalyon.creatis.vip.api.exception.ApiException;
+import fr.insalyon.creatis.vip.api.model.Execution;
 import fr.insalyon.creatis.vip.application.client.bean.Simulation;
 import fr.insalyon.creatis.vip.application.client.view.monitor.SimulationStatus;
 import fr.insalyon.creatis.vip.application.server.business.WorkflowBusiness;
 import fr.insalyon.creatis.vip.core.client.bean.User;
 import fr.insalyon.creatis.vip.core.client.view.user.UserLevel;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.mockito.Mockito;
+import org.springframework.util.Assert;
 
 import java.util.function.Supplier;
 
@@ -65,7 +68,7 @@ public void checkIfAdminCanAccessAnyExecution() throws Exception {
     @Test
     public void checkIfBasicUserCannotAccessAnyExecution() throws Exception {
         Supplier<User> userSupplier = () -> prepareTestUser(0, false);
-        Simulation simulation = prepareSimulation(EXEC_ID, 1); // choose a different user
+        Simulation simulation = prepareRunningSimulation(EXEC_ID, 1); // choose a different user
         WorkflowBusiness mockedWb = prepareMockedWorkflowBusiness(EXEC_ID, simulation);
         ExecutionBusiness sut = new ExecutionBusiness(userSupplier, null, mockedWb, null, null, null, null);
         ApiException apiException = assertThrows(ApiException.class,
@@ -77,23 +80,39 @@ public void checkIfBasicUserCannotAccessAnyExecution() throws Exception {
     @Test
     public void checkIfBasicUserCanAccessItsExecution() throws Exception {
         Supplier<User> userSupplier = () -> prepareTestUser(0, false);
-        Simulation simulation = prepareSimulation(EXEC_ID, 0); // the creator of the execution is the same user
+        Simulation simulation = prepareRunningSimulation(EXEC_ID, 0); // the creator of the execution is the same user
         WorkflowBusiness mockedWb = prepareMockedWorkflowBusiness(EXEC_ID, simulation);
         ExecutionBusiness sut = new ExecutionBusiness(userSupplier, null, mockedWb, null, null, null, null);
         sut.checkIfUserCanAccessExecution(EXEC_ID);
     }
 
+    @Test
+    public void checkErrorWhenAccessingACleanedExecution() throws Exception {
+        Supplier<User> userSupplier = () -> prepareTestUser(0, false);
+        Simulation simulation = prepareSimulation(EXEC_ID, SimulationStatus.Cleaned, 0); // the creator of the execution is the same user
+        WorkflowBusiness mockedWb = prepareMockedWorkflowBusiness(EXEC_ID, simulation);
+        ExecutionBusiness sut = new ExecutionBusiness(userSupplier, null, mockedWb, null, null, null, null);
+        ApiException ex = Assertions.assertThrows(ApiException.class, () -> sut.getExecution(EXEC_ID, false));
+        Assertions.assertTrue(ex.getVipErrorCode().isPresent());
+        Assertions.assertEquals(ApiException.ApiError.INVALID_EXECUTION_ID.getCode(), ex.getVipErrorCode().get());
+    }
+
+
     // UTILS to be externalized later
 
     private User prepareTestUser(int userIndex, boolean isAdmin) {
         return new User(USER_FIRST_NAME[userIndex], USER_LAST_NAME[userIndex], USER_MAIL[userIndex], null,
                 isAdmin ? UserLevel.Administrator : UserLevel.Beginner, null);
     }
 
-    private Simulation prepareSimulation(String exedId, int userIndex) {
+    private Simulation prepareRunningSimulation(String exedId, int userIndex) {
+        return prepareSimulation(exedId, SimulationStatus.Running, userIndex);
+    }
+
+    private Simulation prepareSimulation(String exedId, SimulationStatus status, int userIndex) {
         User creator = prepareTestUser(userIndex, false);
         return new Simulation(null, null, null, exedId, creator.getFullName(), null, null,
-                SimulationStatus.Running.name(), null);
+                status.name(), null);
     }
 
     private WorkflowBusiness prepareMockedWorkflowBusiness(String execId, Simulation simu) throws Exception {

diff --git a/vip-api/src/test/java/fr/insalyon/creatis/vip/api/business/LFCPermissionBusinessTest.java b/vip-api/src/test/java/fr/insalyon/creatis/vip/api/business/LFCPermissionBusinessTest.java
@@ -0,0 +1,41 @@
+package fr.insalyon.creatis.vip.api.business;
+
+import fr.insalyon.creatis.vip.api.data.UserTestUtils;
+import fr.insalyon.creatis.vip.core.client.bean.Group;
+import fr.insalyon.creatis.vip.core.client.view.CoreConstants;
+import fr.insalyon.creatis.vip.core.server.business.BusinessException;
+import fr.insalyon.creatis.vip.datamanager.server.business.LFCPermissionBusiness;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class LFCPermissionBusinessTest {
+
+    @AfterEach
+    protected void tearDown() {
+        // to reset user groups
+        UserTestUtils.reset();
+    }
+
+    @Test
+    public void testGroupAccess() throws BusinessException {
+        String groupName="EGI tutorial";
+        String path = "/vip/EGI tutorial (group)/inputs";
+        Map<Group, CoreConstants.GROUP_ROLE> groups = new HashMap<>();
+        UserTestUtils.baseUser1.setGroups(groups);
+        UserTestUtils.baseUser2.setGroups(groups);
+        LFCPermissionBusiness sut = new LFCPermissionBusiness(null, null);
+
+        // First, test users does not belong to the group
+        Assertions.assertFalse(sut.isLFCPathAllowed(UserTestUtils.baseUser1, path, LFCPermissionBusiness.LFCAccessType.UPLOAD, false));
+        Assertions.assertFalse(sut.isLFCPathAllowed(UserTestUtils.baseUser2, path, LFCPermissionBusiness.LFCAccessType.UPLOAD, false));
+
+        // Then, they belong to the group, but baseUser1 is beginner although baseUser2 is advanced
+        groups.put(new Group(groupName, true, true, true), CoreConstants.GROUP_ROLE.User);
+        Assertions.assertFalse(sut.isLFCPathAllowed(UserTestUtils.baseUser1, path, LFCPermissionBusiness.LFCAccessType.UPLOAD, false));
+        Assertions.assertTrue(sut.isLFCPathAllowed(UserTestUtils.baseUser2, path, LFCPermissionBusiness.LFCAccessType.UPLOAD, false));
+    }
+}
diff --git a/vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/UserTestUtils.java b/vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/UserTestUtils.java
@@ -38,6 +38,8 @@
 import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors;
 import org.springframework.test.web.servlet.request.RequestPostProcessor;
 
+import java.util.Collections;
+
 /**
  * Created by abonnet on 7/26/16.
  */
@@ -53,6 +55,10 @@ public class UserTestUtils {
 
 
     static {
+        reset();
+    }
+
+    static public void reset() {
         baseUser1 = new User("base1", "User1", "[email protected]", null,
                 UserLevel.Beginner, null);
         baseUser1.setFolder("user1");
@@ -61,7 +67,7 @@ public class UserTestUtils {
         baseUser2.setFolder("user2");
 
         restUser1 = new SignUpUserDTO("base3", "User3", "[email protected]", "test", baseUser2Password,
-                UserLevel.Advanced, null, "test comment", "test applications");
+                UserLevel.Advanced, null, "test comment", Collections.singletonList("test applications"));
     }
 
     public static RequestPostProcessor baseUser1() {

diff --git a/.../main/java/fr/insalyon/creatis/vip/applicationimporter/server/business/VelocityUtils.java b/.../main/java/fr/insalyon/creatis/vip/applicationimporter/server/business/VelocityUtils.java
@@ -51,7 +51,7 @@ public class VelocityUtils {
 
     private VelocityEngine velocityEngine;
 
-    private VelocityUtils() {
+    public VelocityUtils() {
         velocityEngine = new VelocityEngine();
         velocityEngine.setProperty("resource.loader", "class");
         velocityEngine.setProperty("class.resource.loader.class", "org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader");