Merge pull request #468 from OHDSI/release-1.17.1

Release 1.17.1

pom.xml

@@ -6,7 +6,7 @@
 
     <artifactId>datanode</artifactId>
     <groupId>com.odysseusinc.arachne</groupId>
-    <version>1.17.0</version>
+    <version>1.17.1</version>
     <packaging>jar</packaging>
 
 
@@ -25,15 +25,16 @@
         <start-class>com.odysseusinc.arachne.datanode.WebApplicationStarter</start-class>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <java.version>1.8</java.version>
-        <jjwt.version>0.10.5</jjwt.version>
-        <postgresql.version>42.2.1</postgresql.version>
+        <jjwt.version>0.10.8</jjwt.version>
+        <postgresql.version>42.2.15</postgresql.version>
         <flywayVersion>4.2.0</flywayVersion>
-        <javaDockerVersion>3.2.6</javaDockerVersion>
+        <javaDockerVersion>3.2.7</javaDockerVersion>
         <springRetryVersion>1.2.4.RELEASE</springRetryVersion>
         <hikaricp.version>2.6.3</hikaricp.version>
         <build.number>${BUILD_NUMBER}</build.number>
         <build.id>${BUILD_TIMESTAMP}</build.id>
-        <dockerImagePrefix>hub.arachnenetwork.com</dockerImagePrefix>
+        <dockerImagePrefix>hub.odysseusinc.com</dockerImagePrefix>
+        <jackson.version>2.10.5.20201202</jackson.version>
         <!-- Overrides SpringBoot defaults to conform Hydra -->
         <json.version>20170516</json.version>
         <feign.version>10.11</feign.version>
@@ -100,10 +101,6 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.springframework.boot</groupId>
-            <artifactId>spring-boot-starter-mail</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-test</artifactId>
@@ -159,11 +156,10 @@
             <artifactId>docker-java</artifactId>
             <version>${javaDockerVersion}</version>
         </dependency>
-
         <dependency>
-            <groupId>org.springframework.statemachine</groupId>
-            <artifactId>spring-statemachine-core</artifactId>
-            <version>1.1.1.RELEASE</version>
+            <groupId>com.github.docker-java</groupId>
+            <artifactId>docker-java-transport-httpclient5</artifactId>
+            <version>${javaDockerVersion}</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
@@ -465,8 +461,8 @@
                             <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>

src/main/docker/Dockerfile

@@ -1,5 +1,5 @@
-FROM hub.arachnenetwork.com/datanode_env:1.0.1
-MAINTAINER alexandr.ryabokon@odysseusinc.com
+FROM hub.odysseusinc.com/datanode_env:1.1.0
+MAINTAINER alexandr.cumarav@odysseusinc.com
 USER root
 VOLUME /tmp
 ADD datanode-exec.jar /datanode.jar

src/main/java/com/odysseusinc/arachne/datanode/config/DockerClientConfiguration.java → src/main/java/com/odysseusinc/arachne/datanode/config/DockerConfig.java

@@ -1,3 +1,5 @@
+package com.odysseusinc.arachne.datanode.config;
+
 /*
  *
  * Copyright 2018 Odysseus Data Services, inc.
@@ -20,11 +22,7 @@
  *
  */
 
-package com.odysseusinc.arachne.datanode.config;
-
-import com.github.dockerjava.api.DockerClient;
 import com.github.dockerjava.core.DefaultDockerClientConfig;
-import com.github.dockerjava.core.DockerClientBuilder;
 import com.github.dockerjava.core.DockerClientConfig;
 import com.odysseusinc.arachne.datanode.config.properties.DockerProperties;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
@@ -33,21 +31,17 @@
 
 @Configuration
 @EnableConfigurationProperties(DockerProperties.class)
-public class DockerClientConfiguration {
-
+public class DockerConfig {
     @Bean
-    public DockerClient dockerClient(DockerProperties properties) {
+    public DockerClientConfig dockerClient(DockerProperties properties) {
 
-        DockerClientConfig config = DefaultDockerClientConfig.createDefaultConfigBuilder()
+        return DefaultDockerClientConfig.createDefaultConfigBuilder()
                 .withDockerHost(properties.getHost())
                 .withDockerTlsVerify(properties.isTlsVerify())
                 .withDockerCertPath(properties.getCertPath())
                 .withRegistryUrl(properties.getRegistry().getHost())
                 .withRegistryUsername(properties.getRegistry().getUsername())
                 .withRegistryPassword(properties.getRegistry().getPassword())
                 .build();
-
-        return DockerClientBuilder.getInstance(config)
-                .build();
     }
-}
+}

src/main/java/com/odysseusinc/arachne/datanode/controller/AuthController.java

@@ -116,7 +116,7 @@ public class AuthController {
     @Deprecated
     public JsonResult<CommonAuthMethodDTO> authMethod() {
 
-        if (dataNodeService.getDataNodeMode() == FunctionalMode.NETWORK) {
+        if (dataNodeService.isNetworkMode()) {
             return integrationService.getAuthMethod();
         }
         throw new BadRequestException();

src/main/java/com/odysseusinc/arachne/datanode/controller/BaseDataSourceController.java

@@ -193,9 +193,8 @@ public JsonResult<List<DataSourceDTO>> list(
         List<DataSourceDTO> dtos = dataSourceService.findAllNotDeleted(sortBy, sortAsc).stream()
                 .map(dataSource -> conversionService.convert(dataSource, DataSourceDTO.class))
                 .collect(Collectors.toList());
-        FunctionalMode mode = dataNodeService.getDataNodeMode();
 
-        if (!CollectionUtils.isEmpty(dtos) && Objects.equals(mode, FunctionalMode.NETWORK)) {
+        if (!CollectionUtils.isEmpty(dtos) && dataNodeService.isNetworkMode()) {
             dtos = setFieldsFromCentral(getUser(principal), dtos);
         }
         result.setResult(dtos);
@@ -250,7 +249,7 @@ public JsonResult<DataSourceDTO> get(Principal principal, @PathVariable("id") Lo
         JsonResult<DataSourceDTO> result = new JsonResult<>(NO_ERROR);
         DataSource dataSource = dataSourceService.getById(id);
         DataSourceDTO resultDTO = conversionService.convert(dataSource, DataSourceDTO.class);
-        if (Objects.equals(dataNodeService.getDataNodeMode(), FunctionalMode.NETWORK)) {
+        if (dataNodeService.isNetworkMode()) {
             resultDTO = setFieldsFromCentral(getUser(principal), Collections.singletonList(resultDTO)).get(0);
         }
         result.setResult(resultDTO);

src/main/java/com/odysseusinc/arachne/datanode/controller/admin/BaseAdminController.java

@@ -23,7 +23,6 @@
 package com.odysseusinc.arachne.datanode.controller.admin;
 
 import com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult;
-import com.odysseusinc.arachne.commons.utils.UserIdUtils;
 import com.odysseusinc.arachne.datanode.Constants;
 import com.odysseusinc.arachne.datanode.controller.BaseController;
 import com.odysseusinc.arachne.datanode.dto.submission.SubmissionDTO;
@@ -33,34 +32,34 @@
 import com.odysseusinc.arachne.datanode.exception.PermissionDeniedException;
 import com.odysseusinc.arachne.datanode.model.analysis.Analysis;
 import com.odysseusinc.arachne.datanode.model.atlas.Atlas;
-import com.odysseusinc.arachne.datanode.model.datanode.FunctionalMode;
 import com.odysseusinc.arachne.datanode.model.user.User;
 import com.odysseusinc.arachne.datanode.repository.AnalysisRepository;
 import com.odysseusinc.arachne.datanode.service.AnalysisService;
 import com.odysseusinc.arachne.datanode.service.AtlasService;
 import com.odysseusinc.arachne.datanode.service.DataNodeService;
 import com.odysseusinc.arachne.datanode.service.UserService;
-import com.odysseusinc.arachne.datanode.service.events.user.UserDeletedEvent;
 import io.swagger.annotations.ApiOperation;
+
 import java.security.Principal;
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
-import java.util.Objects;
 import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.convert.support.GenericConversionService;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;
 import org.springframework.data.web.PageableDefault;
+import org.springframework.web.bind.annotation.DeleteMapping;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.RequestParam;
 
 public abstract class BaseAdminController extends BaseController {
@@ -94,7 +93,7 @@ public BaseAdminController(
     }
 
     @ApiOperation(value = "Get all admins", hidden = true)
-    @RequestMapping(value = "/api/v1/admin/admins", method = RequestMethod.GET)
+    @GetMapping("/api/v1/admin/admins")
     public JsonResult<List<UserDTO>> getAdmins(
             @RequestParam(name = "sortBy", required = false) String sortBy,
             @RequestParam(name = "sortAsc", required = false) Boolean sortAsc
@@ -111,7 +110,7 @@ public JsonResult<List<UserDTO>> getAdmins(
     }
 
     @ApiOperation("Suggests user according to query to add admin")
-    @RequestMapping(value = "/api/v1/admin/admins/suggest", method = RequestMethod.GET)
+    @GetMapping("/api/v1/admin/admins/suggest")
     public JsonResult<List<UserDTO>> suggestAdmins(
             Principal principal,
             @RequestParam("query") String query,
@@ -132,25 +131,25 @@ public JsonResult<List<UserDTO>> suggestAdmins(
     }
 
     @ApiOperation("Remove admin")
-    @RequestMapping(value = "/api/v1/admin/admins/{username:.+}", method = RequestMethod.DELETE)
+    @DeleteMapping("/api/v1/admin/admins/{username:.+}")
     public JsonResult removeAdmin(@PathVariable String username) {
 
         userService.findByUsername(username).ifPresent(user -> userService.remove(user.getId()));
         return new JsonResult<>(JsonResult.ErrorCode.NO_ERROR);
     }
 
     @ApiOperation("Add admin from central")
-    @RequestMapping(value = "/api/v1/admin/admins/{username:.+}", method = RequestMethod.POST)
+    @PostMapping("/api/v1/admin/admins/{username:.+}")
     public JsonResult addAdminFromCentral(
             Principal principal,
             @PathVariable String username) {
 
         JsonResult<UserDTO> result = new JsonResult<>(JsonResult.ErrorCode.NO_ERROR);
-        if (Objects.equals(dataNodeService.getDataNodeMode(), FunctionalMode.NETWORK)) {
+        if (dataNodeService.isNetworkMode()) {
             userService
                     .findByUsername(principal.getName())
-                    .ifPresent(loginedUser -> {
-                        final User user = userService.addUserFromCentral(loginedUser, username);
+                    .ifPresent(currentUser -> {
+                        final User user = userService.addUserFromCentral(currentUser, username);
                         result.setResult(conversionService.convert(user, UserDTO.class));
                     });
         } else {
@@ -160,7 +159,7 @@ public JsonResult addAdminFromCentral(
     }
 
     @ApiOperation("Check Atlas Connection")
-    @RequestMapping(value = "/api/v1/admin/atlases/{id}/connection", method = RequestMethod.POST)
+    @PostMapping("/api/v1/admin/atlases/{id}/connection")
     public JsonResult checkAtlasConnection(@PathVariable("id") Long id) {
 
         JsonResult result = new JsonResult<>(JsonResult.ErrorCode.NO_ERROR);
@@ -171,7 +170,7 @@ public JsonResult checkAtlasConnection(@PathVariable("id") Long id) {
     }
 
     @ApiOperation(value = "Invalidate all unfinished analyses")
-    @RequestMapping(value = Constants.Api.Analysis.INVALIDATE_ALL_UNFINISHED, method = RequestMethod.POST)
+    @PostMapping(Constants.Api.Analysis.INVALIDATE_ALL_UNFINISHED)
     public Integer invalidateAllUnfinishedAnalyses(final Principal principal) throws PermissionDeniedException {
 
         if (principal == null) {
@@ -182,7 +181,7 @@ public Integer invalidateAllUnfinishedAnalyses(final Principal principal) throws
     }
 
     @ApiOperation(value = "list submissions")
-    @RequestMapping(value = "/api/v1/admin/submissions", method = RequestMethod.GET)
+    @GetMapping("/api/v1/admin/submissions")
     public Page<SubmissionDTO> list(@PageableDefault(value = DEFAULT_PAGE_SIZE, sort = "id",
             direction = Sort.Direction.DESC) Pageable pageable) {
 
@@ -195,7 +194,7 @@ public Page<SubmissionDTO> list(@PageableDefault(value = DEFAULT_PAGE_SIZE, sort
         Page<Analysis> analyses;
         if (isFinishedSort(pageable)) {
             analyses = analysisRepository.findAllPagedOrderByFinished(p);
-        } else  if (isSubmittedSort(pageable)) {
+        } else if (isSubmittedSort(pageable)) {
             analyses = analysisRepository.findAllPagedOrderBySubmitted(p);
         } else if (isStatusSort(pageable)) {
             analyses = analysisRepository.findAllPagedOrderByState(p);

src/main/java/com/odysseusinc/arachne/datanode/model/datanode/validation/DataNodeTokenValidator.java

@@ -23,7 +23,6 @@
 package com.odysseusinc.arachne.datanode.model.datanode.validation;
 
 import com.odysseusinc.arachne.datanode.model.datanode.DataNode;
-import com.odysseusinc.arachne.datanode.model.datanode.FunctionalMode;
 import com.odysseusinc.arachne.datanode.service.DataNodeService;
 import java.util.Objects;
 import javax.validation.ConstraintValidator;
@@ -43,7 +42,7 @@ public void initialize(NonEmptyToken nonEmptyToken) {
     @Override
     public boolean isValid(DataNode dataNode, ConstraintValidatorContext context) {
 
-        if (FunctionalMode.NETWORK == dataNodeService.getDataNodeMode()) {
+        if (dataNodeService.isNetworkMode()) {
             boolean valid = Objects.nonNull(dataNode) && StringUtils.isNotBlank(dataNode.getToken());
             if (!valid) {
                 context.disableDefaultConstraintViolation();

src/main/java/com/odysseusinc/arachne/datanode/repository/UserRepository.java

@@ -23,18 +23,19 @@
 package com.odysseusinc.arachne.datanode.repository;
 
 import com.odysseusinc.arachne.datanode.model.user.User;
-import java.util.List;
-import java.util.Optional;
 import org.springframework.data.domain.Sort;
 import org.springframework.data.jpa.repository.JpaRepository;
 
+import java.util.List;
+import java.util.Optional;
+
 public interface UserRepository extends JpaRepository<User, Long> {
 
-    Optional<User> findOneByUsernameAndEnabled(String username, boolean enabled);
+    Optional<User> findOneByUsernameIgnoreCaseAndEnabled(String username, boolean enabled);
 
     List<User> findAll(Sort sort);
 
-    Optional<User> findOneByUsername(String username);
+    Optional<User> findOneByUsernameIgnoreCase(String username);
 
-    List<User> findBySync(boolean isSync);
+    List<User> findBySyncAndEnabledIsTrue(boolean isSync);
 }

src/main/java/com/odysseusinc/arachne/datanode/scheduler/CentralScheduler.java

@@ -24,7 +24,7 @@
 
 import com.odysseusinc.arachne.datanode.model.datanode.DataNode;
 import com.odysseusinc.arachne.datanode.model.datasource.DataSource;
-import com.odysseusinc.arachne.datanode.model.user.User;
+import com.odysseusinc.arachne.datanode.service.CentralIntegrationService;
 import com.odysseusinc.arachne.datanode.service.DataNodeService;
 import com.odysseusinc.arachne.datanode.service.DataSourceService;
 import com.odysseusinc.arachne.datanode.service.UserRegistrationStrategy;
@@ -51,14 +51,17 @@ public class CentralScheduler {
     private final DataSourceService dataSourceService;
     @Value("${authenticator.user.registrationStrategy}")
     private String userRegistrationStrategy;
+    private final CentralIntegrationService centralIntegrationService;
 
     public CentralScheduler(DataNodeService dataNodeService,
                             UserService userService,
-                            DataSourceService dataSourceService) {
+                            DataSourceService dataSourceService,
+                            CentralIntegrationService centralIntegrationService) {
 
         this.dataNodeService = dataNodeService;
         this.userService = userService;
         this.dataSourceService = dataSourceService;
+        this.centralIntegrationService = centralIntegrationService;
     }
 
     @PostConstruct
@@ -74,20 +77,18 @@ public void checkRunMode() {
 
     private void checkModeSwitching() {
 
-        List<User> users = userService.findStandaloneUsers();
-        if (users.size() > 0) {
-            throw new BeanInitializationException("Cannot switch mode from Standalone to Network - there are some users not linked to the Central.");
+        DataNode currentDataNode = dataNodeService.findCurrentDataNode().orElse(null);
+        if (currentDataNode != null  && !userService.findStandaloneUsers().isEmpty()) {
+            centralIntegrationService.relinkUsersToDataNodeOnCentral(currentDataNode, userService.findStandaloneUsers());
         }
         List<DataSource> dataSources = dataSourceService.findStandaloneSources();
         if (dataSources.size() > 0) {
             throw new BeanInitializationException("Cannot switch mode from Standalone to Network - there are some data sources not linked to the Central.");
         }
 
-        DataNode currentDataNode = dataNodeService.findCurrentDataNode().orElse(null);
         if (currentDataNode != null && StringUtils.isEmpty(currentDataNode.getToken())) {
             throw new BeanInitializationException("Cannot switch mode from Standalone to Network - Data node is not linked to the Central.");
         }
-
     }
 
     private void warnUserRegistration() {

src/main/java/com/odysseusinc/arachne/datanode/service/BaseCentralIntegrationService.java

@@ -74,7 +74,7 @@ DTO sendDataSourceUpdateRequest(
 
     void unlinkUserToDataNodeOnCentral(DataNode dataNode, User user);
 
-    List<User> relinkAllUsersToDataNodeOnCentral(DataNode dataNode, List<User> users);
+    void relinkUsersToDataNodeOnCentral(DataNode dataNode, List<User> users);
 
     JsonResult<List<CommonStateProvinceDTO>> getStateProvinces(String countryId, String query, Integer limit, String includeId);