Merge pull request #724 from OHDSI/rc-1.17.1

Arachne Rc 1.17.1

pom.xml

@@ -6,7 +6,7 @@
 
     <artifactId>portal</artifactId>
     <groupId>com.odysseusinc.arachne</groupId>
-    <version>1.17.0-QA</version>
+    <version>1.17.1-QA</version>
     <packaging>jar</packaging>
 
     <parent>
@@ -21,23 +21,26 @@
         <start-class>com.odysseusinc.arachne.portal.PortalStarter</start-class>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <java.version>1.8</java.version>
-        <jjwt.version>0.10.5</jjwt.version>
+        <jjwt.version>0.10.8</jjwt.version>
+        <activemq.version>5.15.14</activemq.version>
+        <assertj.version>3.13.2</assertj.version>
+        <build.id>${BUILD_TIMESTAMP}</build.id>
+        <build.number>${BUILD_NUMBER}</build.number>
+        <clamav.version>2.0.1</clamav.version>
+        <commons.fileupload.version>1.4</commons.fileupload.version>
+        <commons.io.version>2.8.0</commons.io.version>
+        <commons.lang3.version>3.11</commons.lang3.version>
+        <commonsCsv.version>1.7</commonsCsv.version>
+        <dockerImagePrefix>hub.odysseusinc.com</dockerImagePrefix>
         <ehcache.version>1.3.0</ehcache.version>
-        <postgresql.version>42.2.1</postgresql.version>
         <gson.version>2.7</gson.version>
-        <commons.lang3.version>3.8.1</commons.lang3.version>
+        <hibernate.version>5.2.12.Final</hibernate.version>
         <hikaricp.version>2.6.3</hikaricp.version>
-        <build.number>${BUILD_NUMBER}</build.number>
-        <build.id>${BUILD_TIMESTAMP}</build.id>
-        <dockerImagePrefix>hub.arachnenetwork.com</dockerImagePrefix>
+        <jackson.version>2.10.5.20201202</jackson.version>
         <jodConverter.version>4.2.0</jodConverter.version>
-        <hibernate.version>5.2.12.Final</hibernate.version>
-        <clamav.version>2.0.1</clamav.version>
+        <postgresql.version>42.2.15</postgresql.version>
         <springRetryVersion>1.2.4.RELEASE</springRetryVersion>
-        <assertj.version>3.13.2</assertj.version>
-        <commonsCsv.version>1.7</commonsCsv.version>
-        <commons.fileupload.version>1.4</commons.fileupload.version>
-        <commons.io.version>2.5</commons.io.version>
+        <bcprov-jdk15on.version>1.68</bcprov-jdk15on.version>
     </properties>
 
     <profiles>
@@ -107,7 +110,7 @@
             <dependency>
                 <artifactId>solr-solrj</artifactId>
                 <groupId>org.apache.solr</groupId>
-                <version>7.2.1</version>
+                <version>7.7.3</version>
             </dependency>
             <dependency>
                 <groupId>org.flywaydb</groupId>
@@ -139,6 +142,13 @@
             <artifactId>arachne-common-utils</artifactId>
             <version>${project.version}</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.bouncycastle</groupId>
+            <artifactId>bcprov-jdk15on</artifactId>
+            <version>${bcprov-jdk15on.version}</version>
+        </dependency>
+
         <dependency>
             <groupId>com.odysseusinc.arachne</groupId>
             <artifactId>arachne-no-handler-found-exception-util</artifactId>
@@ -263,7 +273,7 @@
         <dependency>
             <groupId>net.lingala.zip4j</groupId>
             <artifactId>zip4j</artifactId>
-            <version>2.1.1</version>
+            <version>2.6.4</version>
         </dependency>
         <dependency>
             <groupId>edu.vt.middleware</groupId>
@@ -489,8 +499,8 @@
                             <include>${project.build.finalName}-exec.${project.packaging}</include>
                         </resource>
                     </resources>
-                    <serverId>arachne-hub</serverId>
-                    <registryUrl>https://hub.arachnenetwork.com/v2/</registryUrl>
+                    <serverId>hub.odysseusinc.com</serverId>
+                    <registryUrl>https://hub.odysseusinc.com/v2/</registryUrl>
                 </configuration>
                 <executions>
                     <execution>

solr_config/conf/solrconfig.xml

@@ -35,7 +35,7 @@
        that you fully re-index after changing this setting as it can
        affect both how text is indexed and queried.
   -->
-  <luceneMatchVersion>7.2.1</luceneMatchVersion>
+  <luceneMatchVersion>7.7.1</luceneMatchVersion>
 
   <!-- <lib/> directives can be used to instruct Solr to load any Jars
        identified and use them to resolve any "plugins" specified in

src/main/docker/Dockerfile

@@ -1,5 +1,5 @@
-FROM hub.arachnenetwork.com/portal_env:1.0.13
-MAINTAINER alexandr.ryabokon@odysseusinc.com
+FROM hub.odysseusinc.com/portal_env:1.1.0
+MAINTAINER alexandr.cumarav@odysseusinc.com
 USER root
 VOLUME /tmp
 ADD portal-exec.jar /portal.jar

src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseAuthenticationController.java

@@ -164,12 +164,14 @@ private void checkIfUserBlocked(String username) throws PermissionDeniedExceptio
 
     protected void checkIfUserHasTenant(String username) throws AuthenticationException {
 
-        IUser user = userService.getByUsernameInAnyTenant(username);
-        if (user == null) {
-            throw new BadCredentialsException(ErrorMessages.BAD_CREDENTIALS.getMessage());
-        }
-        if (user.getTenants() == null || user.getTenants().isEmpty()) {
-            throw new NoDefaultTenantException("Request admin to add you into a tenant.");
+        if (authenticationHelperService.isNative()) {
+            IUser user = userService.getByUsernameInAnyTenant(username);
+            if (user == null) {
+                throw new BadCredentialsException(ErrorMessages.BAD_CREDENTIALS.getMessage());
+            }
+            if (user.getTenants() == null || user.getTenants().isEmpty()) {
+                throw new NoDefaultTenantException("Request admin to add you into a tenant.");
+            }
         }
     }
 

src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseExpertFinderController.java

@@ -89,12 +89,12 @@ public JsonResult<UserProfileDTO> viewProfile(
             Principal principal,
             @PathVariable("userId") String userId) {
 
-        IUser logginedUser = userService.getByUsername(principal.getName());
+        IUser loggedInUser = userService.getByUsername(principal.getName());
         JsonResult<UserProfileDTO> result;
         IUser user = userService.getByUuidAndInitializeCollections(userId);
 
         UserProfileDTO userProfileDTO = conversionService.convert(user, UserProfileDTO.class);
-        userProfileDTO.setIsEditable(logginedUser.getUuid().equals(userId));
+        userProfileDTO.setIsEditable(loggedInUser.getUuid().equals(userId));
         result = new JsonResult<>(JsonResult.ErrorCode.NO_ERROR);
         result.setResult(userProfileDTO);
         return result;

src/main/java/com/odysseusinc/arachne/portal/component/ldap/ImportResult.java

@@ -0,0 +1,79 @@
+/*
+ *
+ * Copyright 2021 Odysseus Data Services, inc.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Company: Odysseus Data Services, Inc.
+ * Product Owner/Architecture: Gregory Klebanov
+ * Authors: Yaroslav Molodkov, Alexandr Cumarav, Vitaliy Kulakov
+ * Created: March 17, 2021
+ *
+ */
+
+package com.odysseusinc.arachne.portal.component.ldap;
+
+public class ImportResult {
+
+    public enum ImportResultState {
+        CREATED,
+        UPDATED,
+        ERROR
+    }
+
+    private String id;
+    private ImportResultState state;
+    private String message;
+
+    public ImportResult(String id, ImportResultState state) {
+
+        this.id = id;
+        this.state = state;
+    }
+
+    public ImportResult(String id, ImportResultState state, String message) {
+
+        this.id = id;
+        this.state = state;
+        this.message = message;
+    }
+
+    public String getId() {
+
+        return id;
+    }
+
+    public void setId(String id) {
+
+        this.id = id;
+    }
+
+    public ImportResultState getState() {
+
+        return state;
+    }
+
+    public void setState(ImportResultState state) {
+
+        this.state = state;
+    }
+
+    public String getMessage() {
+
+        return message;
+    }
+
+    public void setMessage(String message) {
+
+        this.message = message;
+    }
+}

src/main/java/com/odysseusinc/arachne/portal/repository/BaseRawUserRepository.java

@@ -44,19 +44,17 @@ public interface BaseRawUserRepository<U extends IUser> extends EntityGraphJpaRe
 
     U findByIdAndEnabledTrue(Long id);
 
-    U findByOriginAndUsername(String userOrigin, String username);
+    U findByOriginAndUsernameIgnoreCase(String userOrigin, String username);
 
     U findByRegistrationCode(String activateCode);
 
-    U findByEmail(String email, EntityGraph entityGraph);
-
     U findByEmailIgnoreCase(String email, EntityGraph entityGraph);
 
     U findByEmail(String email);
 
     U findByEmailAndEnabledTrue(String email);
 
-    U findByOriginAndUsernameAndEnabledTrue(String userOrigin, String username);
+    U findByOriginAndUsernameIgnoreCaseAndEnabledTrue(String userOrigin, String username);
 
     @Query(nativeQuery = true, value = "SELECT * FROM users_data "
             + " WHERE "

src/main/java/com/odysseusinc/arachne/portal/repository/BaseUserRepository.java

@@ -40,12 +40,8 @@ public interface BaseUserRepository<U extends IUser> extends EntityGraphJpaRepos
 
     List<U> findByIdIn(List<Long> idList);
 
-    U findByEmail(String email);
-
     U findByEmailAndEnabledTrue(String email);
 
-    U findByEmailAndEmailConfirmedFalse(String email);
-
     U findByOriginAndUsername(String userOrigin, String username);
 
     U findByOriginAndUsernameAndEnabledTrue(String userOrigin, String username);
@@ -87,8 +83,6 @@ List<U> suggestToPaper(@Param("suggestRequest") String suggestRequest,
     @Query(nativeQuery = true, value = "SELECT * FROM users_data u WHERE enabled = TRUE")
     List<U> findAllEnabledFromAllTenants();
 
-    Page<U> findAllBy(Pageable pageable);
-
     List<U> findAllByUsernameInAndEnabledTrue(List<String> userNames);
 
     @Query(nativeQuery = true, value = "SELECT DISTINCT u.* FROM users u "

src/main/java/com/odysseusinc/arachne/portal/repository/CommentRepository.java

@@ -26,10 +26,10 @@
 import com.odysseusinc.arachne.portal.model.CommentTopic;
 import java.util.List;
 import java.util.Set;
-import javax.transaction.Transactional;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.repository.PagingAndSortingRepository;
+import org.springframework.transaction.annotation.Transactional;
 
 public interface CommentRepository extends PagingAndSortingRepository<Comment, Long> {
 

src/main/java/com/odysseusinc/arachne/portal/service/impl/AchillesImportServiceImpl.java

@@ -47,22 +47,22 @@
 import java.util.zip.ZipFile;
 import javax.persistence.EntityManager;
 import javax.persistence.FlushModeType;
-import javax.transaction.Transactional;
 import org.apache.commons.io.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
 
 @Service
 public class AchillesImportServiceImpl implements AchillesImportService {
 
     private static final String IMPORT_ACHILLES_RESULT_LOG =
             "{} import Achilles result for Data Source with id='{}', name='{}', Data Node with id='{}' name='{}'";
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(AchillesImportService.class);
+    private static final Logger LOGGER = LoggerFactory.getLogger(AchillesImportServiceImpl.class);
 
     @Value("${spring.jpa.properties.hibernate.jdbc.batch_size}")
     private int batchSize = 1000;