Release 1.16.2 (#431)

* Release 1.16.2 Co-authored-by: Alex Cumarav <[email protected]> Co-authored-by: Vitaly Koulakov <[email protected]> Co-authored-by: Konstantin Iaroshovets <[email protected]> Co-authored-by: molodkov yaroslav <[email protected]> Co-authored-by: Anton Gackovka <[email protected]> Co-authored-by: anastasiia klochkova <[email protected]> Co-authored-by: OdysseusBot <[email protected]> Co-authored-by: mpozhidaeva <[email protected]> Co-authored-by: Pavel Grafkin <[email protected]> Co-authored-by: Alexandr Ryabokon <[email protected]> Co-authored-by: Anastasiia Klochkova <[email protected]> Co-authored-by: Maria Pozhidaeva <[email protected]> Co-authored-by: Sergey Suvorov <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: alexandr cumarav <https://localhost:8080/study-manager/studies/6>
OHDSI · Sep 11, 2020 · b314f92 · b314f92
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diff --git a/README.md b/README.md
@@ -1,6 +1,13 @@
 # ArachneNodeAPI
 Arachne Data Node is a component that facilitates connection and communication between local databases and Arachne Central
 
+## Instalation
+### Prerequisites
+For building and run the Data Node please install following applications:
+- [Apache Maven 3](https://maven.apache.org/download.cgi)
+- [JDK up to 8u241](https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html)
+- [Postgres DBMS 9.6+](https://www.postgresql.org/download/)
+
 ## Running with Authenticator in a standalone mode
 
 - Create database to store users (or use another authentication provided by Authenticator)

diff --git a/build.sh b/build.sh
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <artifactId>datanode</artifactId>
     <groupId>com.odysseusinc.arachne</groupId>
-    <version>1.16.0</version>
+    <version>1.16.2</version>
     <packaging>jar</packaging>
 
 
@@ -236,7 +236,7 @@
         <dependency>
             <groupId>org.ohdsi.sql</groupId>
             <artifactId>SqlRender</artifactId>
-            <version>1.6.3</version>
+            <version>1.6.5</version>
         </dependency>
         <dependency>
             <groupId>org.ohdsi</groupId>
@@ -309,7 +309,7 @@
         <dependency>
             <groupId>mysql</groupId>
             <artifactId>mysql-connector-java</artifactId>
-            <version>5.1.30</version>
+            <version>8.0.16</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/com.microsoft.sqlserver/sqljdbc4 -->
         <dependency>
@@ -334,7 +334,11 @@
             <artifactId>authenticator</artifactId>
             <version>0.0.3-QA</version>
         </dependency>
-
+        <dependency>
+            <groupId>com.google.auth</groupId>
+            <artifactId>google-auth-library-oauth2-http</artifactId>
+            <version>0.20.0</version>
+        </dependency>
     </dependencies>
 
     <build>
@@ -532,6 +536,10 @@
                 <directory>src/test/resources</directory>
                 <filtering>true</filtering>
             </testResource>
+            <testResource>
+                <directory>src/test/resources-binary</directory>
+                <filtering>false</filtering>
+            </testResource>
         </testResources>
         <finalName>datanode</finalName>
     </build>

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/Constants.java b/src/main/java/com/odysseusinc/arachne/datanode/Constants.java
@@ -31,6 +31,8 @@ public interface Constants {
     int PASSWORD_MIN_LENGTH = 6;
     int PASSWORD_MAX_LENGTH = 100;
     String DUMMY_PASSWORD = "password_was_set";
+    String DUMMY_KEYFILE = "Replace current keyfile";
+    String GOOGLE_AUTH_SCOPE = "https://www.googleapis.com/auth/userinfo.email";
 
     interface AppConf {
         String PROFILE_DEVELOPMENT = "dev";
@@ -65,9 +67,9 @@ interface User {
             String PROFESSIONAL_TYPES = "/api/v1/user-management/professional-types";
             String COUNTRIES = "/api/v1/user-management/countries/search";
             String STATES_PROVINCES = "/api/v1/user-management/state-province/search";
-            String REGISTER_USER = "/api/v1/auth/registration";
             String LOGOUT = "/api/v1/auth/logout";
             String REGISTRATION = "/api/v1/auth/registration";
+            String REMIND_PASSWORD = "/api/v1/auth/remind-password";
             String SUGGEST = "/api/v1/user-management/users/suggest";
             String GET_USER = "/api/v1/user-management/users/byusername/{id}";
             String LINK_TO_NODE = "/api/v1/user-management/datanodes/{datanodeId}/users";
@@ -159,6 +161,7 @@ interface AnalysisMessages {
     }
 
     interface Analysis {
+        String ERROR_REPORT_FILENAME = "errorReport.txt";
         String SUBMISSION_ARCHIVE_SUBDIR = "archive";
     }
 

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/config/WebSecurityConfig.java b/src/main/java/com/odysseusinc/arachne/datanode/config/WebSecurityConfig.java
@@ -119,6 +119,7 @@ protected void configure(HttpSecurity http) throws Exception {
                 .antMatchers("/api/v1/user-management/countries/**").permitAll()
                 .antMatchers("/api/v1/user-management/state-province/**").permitAll()
                 .antMatchers("/api/v1/auth/registration**").permitAll()
+                .antMatchers("/api/v1/auth/remind-password/**").permitAll()
                 .antMatchers("/configuration/**").permitAll()
                 .antMatchers("/api/v1/submissions/**").permitAll()
                 .antMatchers("/admin-settings/**").permitAll()

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/controller/AtlasController.java b/src/main/java/com/odysseusinc/arachne/datanode/controller/AtlasController.java
@@ -34,17 +34,23 @@
 import com.odysseusinc.arachne.datanode.service.DataNodeService;
 import com.odysseusinc.arachne.datanode.util.DataNodeUtils;
 import io.swagger.annotations.ApiOperation;
+import org.apache.commons.io.IOUtils;
 import org.springframework.core.convert.ConversionService;
 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.data.web.SortDefault;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.*;
+import org.springframework.web.multipart.MultipartFile;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.util.Objects;
 
 @RestController
 public class AtlasController {
@@ -86,26 +92,39 @@ public AtlasDetailedDTO get(@PathVariable("id") Long id) {
 
     @ApiOperation("Create new Atlas")
     @RequestMapping(value = "/api/v1/atlases", method = POST)
-    public AtlasDetailedDTO save(@RequestBody AtlasDetailedDTO atlasDetailedDTO) {
+    public AtlasDetailedDTO save(@RequestPart("atlas") AtlasDetailedDTO atlasDetailedDTO,
+                                 @RequestPart(name = "keyfile", required = false) MultipartFile keyfile) throws IOException {
 
         Atlas atlas = conversionService.convert(atlasDetailedDTO, Atlas.class);
+        initKeyfile(atlas, keyfile);
         atlas = atlasService.save(atlas);
         return conversionService.convert(atlas, AtlasDetailedDTO.class);
     }
 
     @ApiOperation("Update Atlas entity")
-    @RequestMapping(value = "/api/v1/atlases/{id}", method = PUT)
+    @RequestMapping(value = "/api/v1/atlases/{id}", consumes = MediaType.MULTIPART_FORM_DATA_VALUE,
+            method = PUT)
     public AtlasDetailedDTO update(
             @PathVariable("id") Long id,
-            @RequestBody AtlasDetailedDTO atlasDetailedDTO
-    ) {
+            @RequestPart(name = "atlas") AtlasDetailedDTO atlasDetailedDTO,
+            @RequestPart(name = "keyfile", required = false) MultipartFile keyfile
+    ) throws IOException {
 
         DataNodeUtils.requireNetworkMode(dataNodeService);
         Atlas atlas = conversionService.convert(atlasDetailedDTO, Atlas.class);
+        initKeyfile(atlas, keyfile);
         atlas = atlasService.update(id, atlas);
         return conversionService.convert(atlas, AtlasDetailedDTO.class);
     }
 
+    private void initKeyfile(Atlas atlas, MultipartFile keyfile) throws IOException {
+        if (Objects.nonNull(keyfile)) {
+            try (InputStream in = keyfile.getInputStream()) {
+                atlas.setKeyfile(IOUtils.toString(in, StandardCharsets.UTF_8));
+            }
+        }
+    }
+
     @ApiOperation("Delete Atlas entity")
     @RequestMapping(value = "/api/v1/atlases/{id}", method = DELETE)
     public void delete(

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/controller/AuthController.java b/src/main/java/com/odysseusinc/arachne/datanode/controller/AuthController.java
@@ -22,6 +22,7 @@
 
 package com.odysseusinc.arachne.datanode.controller;
 
+import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.NO_ERROR;
 import static com.odysseusinc.arachne.datanode.util.RestUtils.requireNetworkMode;
 import static org.springframework.web.bind.annotation.RequestMethod.GET;
 
@@ -36,6 +37,7 @@
 import com.odysseusinc.arachne.commons.api.v1.dto.CommonUserDTO;
 import com.odysseusinc.arachne.commons.api.v1.dto.CommonUserRegistrationDTO;
 import com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult;
+import com.odysseusinc.arachne.datanode.dto.user.RemindPasswordDTO;
 import com.odysseusinc.arachne.datanode.dto.user.UserInfoDTO;
 import com.odysseusinc.arachne.datanode.exception.AuthException;
 import com.odysseusinc.arachne.datanode.exception.BadRequestException;
@@ -63,6 +65,7 @@
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.convert.ConversionService;
 import org.springframework.security.authentication.AuthenticationServiceException;
+import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
@@ -250,4 +253,13 @@ public ArachnePasswordInfoDTO getPasswordPolicies() throws URISyntaxException {
         requireNetworkMode(dataNodeService.getDataNodeMode());
         return integrationService.getPasswordInfo();
     }
+
+    @ApiOperation("Remind Password")
+    @PostMapping(value = "/api/v1/auth/remind-password")
+    public JsonResult remindPassword(@Valid @RequestBody RemindPasswordDTO remindPasswordDTO) {
+
+        requireNetworkMode(dataNodeService.getDataNodeMode());
+        integrationService.remindPassword(remindPasswordDTO);
+        return new JsonResult(NO_ERROR);
+    }
 }
diff --git a/src/main/java/com/odysseusinc/arachne/datanode/controller/ExceptionHandlingAdvice.java b/src/main/java/com/odysseusinc/arachne/datanode/controller/ExceptionHandlingAdvice.java
@@ -25,8 +25,6 @@
 import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.SYSTEM_ERROR;
 import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.UNAUTHORIZED;
 import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.VALIDATION_ERROR;
-import static com.odysseusinc.arachne.commons.utils.ErrorMessages.BAD_CREDENTIALS;
-import static com.odysseusinc.arachne.commons.utils.ErrorMessages.USER_NOT_REGISTERED;
 import static java.util.Arrays.asList;
 
 import com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult;
@@ -45,6 +43,8 @@
 import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
+import org.ohdsi.authenticator.exception.AuthenticationException;
+import org.ohdsi.authenticator.exception.BadCredentialsAuthenticationException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
@@ -118,13 +118,36 @@ public ResponseEntity<JsonResult> exceptionHandler(IOException ex) {
     @ExceptionHandler(AuthException.class)
     public ResponseEntity<JsonResult> exceptionHandler(AuthException ex) {
 
+        return authExceptionHandler(ex);
+    }
+
+    @ExceptionHandler(org.springframework.security.core.AuthenticationException.class)
+    public ResponseEntity<JsonResult> exceptionHandler(org.springframework.security.core.AuthenticationException ex) {
+
+        return authExceptionHandler(ex);
+    }
+
+    @ExceptionHandler(BadCredentialsAuthenticationException.class)
+    public ResponseEntity<JsonResult> exceptionHandler(BadCredentialsAuthenticationException ex) {
+        return getErrorResponse(UNAUTHORIZED, ex);
+    }
+
+    @ExceptionHandler(AuthenticationException.class)
+    public ResponseEntity<JsonResult> exceptionHandler(AuthenticationException ex) {
+
+        return authExceptionHandler(ex);
+    }
+
+    public ResponseEntity<JsonResult> authExceptionHandler(Exception ex) {
+
         JsonResult result = new JsonResult(UNAUTHORIZED);
         result.setErrorMessage(ex.getMessage());
         return ResponseEntity.status(HttpStatus.UNAUTHORIZED)
                 .contentType(MediaType.APPLICATION_JSON_UTF8)
                 .body(result);
     }
 
+
     private ResponseEntity<JsonResult> getErrorResponse(JsonResult.ErrorCode errorCode, Exception ex) {
 
         JsonResult result = new JsonResult<>(errorCode);
@@ -138,10 +161,8 @@ private ResponseEntity<JsonResult> getErrorResponse(final JsonResult result, fin
 
         if (errorsTokenEnabled) {
             final String errorToken = generateErrorToken();
-            LOGGER.error(message + " token: " + errorToken, ex);
             result.setErrorMessage(String.format(ERROR_MESSAGE_WITH_TOKEN, errorToken));
-        } else if (asList(BAD_CREDENTIALS.getMessage().toLowerCase(), USER_NOT_REGISTERED.getMessage().toLowerCase()).contains(message.toLowerCase())) {
-            LOGGER.error(message);
+            LOGGER.error("{}. error-token: {}", message, errorToken, ex);
         } else {
             LOGGER.error(message, ex);
         }

diff --git a/...java/com/odysseusinc/arachne/datanode/controller/analysis/AnalysisCallbackController.java b/...java/com/odysseusinc/arachne/datanode/controller/analysis/AnalysisCallbackController.java
@@ -22,6 +22,7 @@
 
 package com.odysseusinc.arachne.datanode.controller.analysis;
 
+import com.odysseusinc.arachne.datanode.service.AnalysisResultsService;
 import com.odysseusinc.arachne.datanode.service.AnalysisService;
 import org.springframework.core.convert.support.GenericConversionService;
 import org.springframework.web.bind.annotation.RestController;
@@ -30,8 +31,9 @@
 public class AnalysisCallbackController extends BaseCallbackAnalysisController {
 
     public AnalysisCallbackController(GenericConversionService conversionService,
-                                      AnalysisService analysisService) {
+                                      AnalysisService analysisService,
+                                      AnalysisResultsService analysisResultsService) {
 
-        super(conversionService, analysisService);
+        super(conversionService, analysisService, analysisResultsService);
     }
 }
diff --git a/src/main/java/com/odysseusinc/arachne/datanode/controller/analysis/AnalysisController.java b/src/main/java/com/odysseusinc/arachne/datanode/controller/analysis/AnalysisController.java
@@ -34,6 +34,7 @@
 import com.odysseusinc.arachne.datanode.model.analysis.AnalysisFile;
 import com.odysseusinc.arachne.datanode.model.analysis.AnalysisOrigin;
 import com.odysseusinc.arachne.datanode.model.user.User;
+import com.odysseusinc.arachne.datanode.service.AnalysisResultsService;
 import com.odysseusinc.arachne.datanode.service.AnalysisService;
 import com.odysseusinc.arachne.datanode.service.UserService;
 import java.io.FileInputStream;
@@ -51,6 +52,7 @@
 import java.util.stream.Stream;
 import javax.servlet.http.HttpServletResponse;
 import javax.validation.Valid;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
@@ -72,15 +74,18 @@ public class AnalysisController {
     private static final Logger logger = LoggerFactory.getLogger(AnalysisController.class);
     private static final String ERROR_MESSAGE = "Failed to save analysis files";
     private final AnalysisService analysisService;
+    private final AnalysisResultsService analysisResultsService;
     private final UserService userService;
 
     private final GenericConversionService conversionService;
 
 	public AnalysisController(AnalysisService analysisService,
+                              AnalysisResultsService analysisResultsService,
                               UserService userService,
                               GenericConversionService conversionService) {
 
 		this.analysisService = analysisService;
+		this.analysisResultsService = analysisResultsService;
         this.userService = userService;
         this.conversionService = conversionService;
     }
@@ -121,7 +126,7 @@ public void downloadResults(@PathVariable("id") Long analysisId, HttpServletResp
 
 	    Analysis analysis = analysisService.findAnalysis(analysisId)
                 .orElseThrow(() -> new NotExistException(Analysis.class));
-	    List<AnalysisFile> resultFiles = analysisService.getAnalysisResults(analysis);
+	    List<AnalysisFile> resultFiles = analysisResultsService.getAnalysisResults(analysis);
 	    Path stdoutDir = Files.createTempDirectory("node_analysis");
 	    Path stdoutFile = stdoutDir.resolve("stdout.txt");
 	    try(Writer writer = new FileWriter(stdoutFile.toFile())) {