Merge pull request #774 from OHDSI/1.19.0-QA-into-master

Merging the latest 'qa' into 'master'
OHDSI · Mar 14, 2022 · 5da00cf · 5da00cf
2 parents de63ba2 + 93f9d85
commit 5da00cf
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Showing 54 changed files with 1,137 additions and 340 deletions.
diff --git a/ARACHNE 2.0 User Guide 2021.pdf b/ARACHNE 2.0 User Guide 2021.pdf
diff --git a/pom.xml b/pom.xml
@@ -6,13 +6,13 @@
 
     <artifactId>portal</artifactId>
     <groupId>com.odysseusinc.arachne</groupId>
-    <version>1.18.0</version>
+    <version>1.19.0</version>
     <packaging>jar</packaging>
 
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.1.18.RELEASE</version>
+        <version>2.2.13.RELEASE</version>
         <relativePath/>
     </parent>
 
@@ -33,9 +33,12 @@
         <ehcache.version>1.3.0</ehcache.version>
         <gson.version>2.7</gson.version>
         <jodConverter.version>4.3.0</jodConverter.version>
-        <postgresql.version>42.2.19</postgresql.version>
+        <postgresql.version>42.2.25</postgresql.version>
         <springRetryVersion>1.2.4.RELEASE</springRetryVersion>
         <bcprov-jdk15on.version>1.68</bcprov-jdk15on.version>
+
+        <!-- Referencing https://github.com/OHDSI/ArachneUI -->
+        <portal-resources.version>1.19.1</portal-resources.version>        
     </properties>
 
     <profiles>
@@ -95,7 +98,7 @@
             <dependency>
                 <artifactId>solr-solrj</artifactId>
                 <groupId>org.apache.solr</groupId>
-                <version>7.7.3</version>
+                <version>8.2.0</version>
             </dependency>
             <dependency>
                 <groupId>org.ohdsi</groupId>
@@ -183,6 +186,10 @@
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-acl</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-oauth2-client</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-test</artifactId>
@@ -319,12 +326,17 @@
         <dependency>
             <groupId>org.ohdsi.sql</groupId>
             <artifactId>SqlRender</artifactId>
-            <version>1.6.5</version>
+            <version>1.9.0</version>
         </dependency>
         <dependency>
             <groupId>com.cosium.spring.data</groupId>
             <artifactId>spring-data-jpa-entity-graph</artifactId>
-            <version>2.1.0</version>
+            <version>2.2.8</version>
+        </dependency>
+        <!-- Ensure that spring-data-jpa version is taken from parent dependency management, not from spring-data-jpa-entity-graph -->
+        <dependency>
+            <groupId>org.springframework.data</groupId>
+            <artifactId>spring-data-jpa</artifactId>
         </dependency>
         <dependency>
             <groupId>org.jodconverter</groupId>
@@ -360,6 +372,30 @@
             <groupId>org.ohdsi</groupId>
             <artifactId>authenticator</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>testcontainers</artifactId>
+            <version>1.16.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>1.16.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>postgresql</artifactId>
+            <version>1.16.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>solr</artifactId>
+            <version>1.16.2</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
@@ -417,7 +453,7 @@
                                 <artifactItem>
                                     <groupId>com.odysseusinc.arachne</groupId>
                                     <artifactId>portal-resources</artifactId>
-                                    <version>${project.version}</version>
+                                    <version>${portal-resources.version}</version>
                                     <type>zip</type>
                                     <overWrite>false</overWrite>
                                     <outputDirectory>${project.basedir}/src/main/resources/public/</outputDirectory>

diff --git a/src/main/docker/Dockerfile b/src/main/docker/Dockerfile
@@ -1,9 +1,9 @@
-FROM hub.odysseusinc.com/portal_env:1.1.0
+FROM hub.odysseusinc.com/portal_env:1.1.1
 MAINTAINER [email protected]
 USER root
 VOLUME /tmp
 ADD portal-exec.jar /portal.jar
 ADD run.sh /bin/run.sh
 RUN chmod +x /bin/run.sh
-EXPOSE 8080 5434 8983
-CMD ["/bin/run.sh"]
+EXPOSE 8443 5434 8983
+CMD ["/bin/run.sh"]
diff --git a/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/AuthenticationController.java b/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/AuthenticationController.java
@@ -22,6 +22,7 @@
 
 package com.odysseusinc.arachne.portal.api.v1.controller;
 
+import com.odysseusinc.arachne.portal.config.PortalAuthMethodConfig;
 import com.odysseusinc.arachne.portal.security.passwordvalidator.ArachnePasswordValidator;
 import com.odysseusinc.arachne.portal.service.AuthenticationService;
 import com.odysseusinc.arachne.portal.service.LoginAttemptService;
@@ -30,6 +31,8 @@
 import com.odysseusinc.arachne.portal.service.AuthenticationHelperService;
 import com.odysseusinc.arachne.portal.service.UserService;
 import org.ohdsi.authenticator.service.authentication.Authenticator;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.autoconfigure.security.oauth2.client.OAuth2ClientProperties;
 import org.springframework.web.bind.annotation.RestController;
 
 @RestController
@@ -42,15 +45,18 @@ public AuthenticationController(Authenticator authenticator,
                                     ProfessionalTypeService professionalTypeService,
                                     LoginAttemptService loginAttemptService,
                                     AuthenticationService authenticationService,
-                                    AuthenticationHelperService authenticationHelperService) {
-
+                                    AuthenticationHelperService authenticationHelperService,
+                                    @Autowired(required = false) PortalAuthMethodConfig oAuth2ClientProperties
+    ) {
         super(  authenticator,
                 userService,
                 passwordResetService,
                 passwordValidator,
                 professionalTypeService,
                 loginAttemptService,
                 authenticationService,
-                authenticationHelperService);
+                authenticationHelperService,
+                oAuth2ClientProperties
+        );
     }
 }
diff --git a/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseAnalysisController.java b/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseAnalysisController.java
@@ -25,6 +25,7 @@
 import com.odysseusinc.arachne.commons.api.v1.dto.CommonEntityRequestDTO;
 import com.odysseusinc.arachne.commons.api.v1.dto.OptionDTO;
 import com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult;
+import com.odysseusinc.arachne.commons.conditions.modules.ModuleEnabled;
 import com.odysseusinc.arachne.commons.service.messaging.ProducerConsumerTemplate;
 import com.odysseusinc.arachne.commons.utils.CommonFilenameUtils;
 import com.odysseusinc.arachne.portal.api.v1.dto.AnalysisCreateDTO;
@@ -63,6 +64,7 @@
 import com.odysseusinc.arachne.portal.model.Submission;
 import com.odysseusinc.arachne.portal.model.SubmissionInsight;
 import com.odysseusinc.arachne.portal.model.search.SubmissionGroupSearch;
+import com.odysseusinc.arachne.portal.modules.ModuleHelper;
 import com.odysseusinc.arachne.portal.service.BaseDataNodeService;
 import com.odysseusinc.arachne.portal.service.DataReferenceService;
 import com.odysseusinc.arachne.portal.service.ImportService;
@@ -75,7 +77,9 @@
 import com.odysseusinc.arachne.portal.service.submission.BaseSubmissionService;
 import com.odysseusinc.arachne.portal.service.submission.SubmissionInsightService;
 import com.odysseusinc.arachne.portal.util.ImportedFile;
+import com.odysseusinc.arachne.portal.util.UserUtils;
 import io.swagger.annotations.ApiOperation;
+import java.util.Optional;
 import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -89,6 +93,7 @@
 import org.springframework.jms.support.destination.DestinationResolver;
 import org.springframework.messaging.simp.SimpMessagingTemplate;
 import org.springframework.mock.web.MockMultipartFile;
+import org.springframework.security.core.Authentication;
 import org.springframework.util.StringUtils;
 import org.springframework.validation.BindingResult;
 import org.springframework.validation.FieldError;
@@ -123,6 +128,7 @@
 import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.NO_ERROR;
 import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.PERMISSION_DENIED;
 import static com.odysseusinc.arachne.commons.api.v1.dto.util.JsonResult.ErrorCode.VALIDATION_ERROR;
+import static com.odysseusinc.arachne.commons.utils.CommonFilenameUtils.sanitizeFilename;
 import static com.odysseusinc.arachne.portal.util.CommentUtils.getRecentCommentables;
 import static com.odysseusinc.arachne.portal.util.HttpUtils.putFileContentToResponse;
 import static org.springframework.web.bind.annotation.RequestMethod.DELETE;
@@ -300,12 +306,12 @@ public JsonResult<Boolean> delete(
     @ApiOperation("List analyses.")
     @RequestMapping(value = "/api/v1/analysis-management/analyses", method = GET)
     public JsonResult<List<D>> list(
-            Principal principal,
+            Authentication principal,
             @RequestParam("study-id") Long studyId)
             throws PermissionDeniedException, NotExistException {
 
         JsonResult<List<D>> result;
-        IUser user = userService.getByUsername(principal.getName());
+        IUser user = userService.getById(UserUtils.getCurrentUser(principal).getId());
         if (user == null) {
             result = new JsonResult<>(PERMISSION_DENIED);
             return result;
@@ -445,6 +451,7 @@ public JsonResult<Boolean> updateFile(
 
     @ApiOperation("Get submission insight")
     @RequestMapping(value = "/api/v1/analysis-management/submissions/{submissionId}/insight", method = GET)
+    @ModuleEnabled(ModuleHelper.INSIGHT)
     public JsonResult<SubmissionInsightDTO> getSubmissionInsight(
             @PathVariable("submissionId") Long submissionId,
             @RequestParam(value = "size", required = false) Integer size,
@@ -469,6 +476,7 @@ public JsonResult<SubmissionInsightDTO> getSubmissionInsight(
 
     @ApiOperation("Create submission insight")
     @RequestMapping(value = "/api/v1/analysis-management/submissions/{submissionId}/insight", method = POST)
+    @ModuleEnabled(ModuleHelper.INSIGHT)
     public JsonResult<SubmissionInsightDTO> addSubmissionInsight(
             @PathVariable("submissionId") Long submissionId,
             @RequestBody @Valid SubmissionInsightDTO insightDTO
@@ -485,6 +493,7 @@ public JsonResult<SubmissionInsightDTO> addSubmissionInsight(
 
     @ApiOperation("Update submission insight")
     @RequestMapping(value = "/api/v1/analysis-management/submissions/{submissionId}/insight", method = PUT)
+    @ModuleEnabled(ModuleHelper.INSIGHT)
     public JsonResult<SubmissionInsightDTO> updateSubmissionInsight(
             @PathVariable("submissionId") Long submissionId,
             @RequestBody SubmissionInsightUpdateDTO insightDTO
@@ -614,14 +623,7 @@ public void getAllAnalysisFiles(
 
         final Analysis analysis = analysisService.getById(analysisId);
 
-        final String archiveName;
-        if (analysis.getStudy() != null) {
-            archiveName = String.format("%s_%s_code.zip",
-                    CommonFilenameUtils.sanitizeFilename(analysis.getStudy().getTitle()),
-                    CommonFilenameUtils.sanitizeFilename(analysis.getTitle()));
-        } else {
-            archiveName = CommonFilenameUtils.sanitizeFilename(analysis.getTitle()) + "_code.zip";
-        }
+        String archiveName = formatStudyName(analysis);
 
         String contentType = "application/zip, application/octet-stream";
         response.setContentType(contentType);
@@ -632,6 +634,16 @@ public void getAllAnalysisFiles(
         response.flushBuffer();
     }
 
+    public static String formatStudyName(Analysis analysis) {
+        String code = analysis.getType().getCode();
+        String title = sanitizeFilename(analysis.getTitle()).replaceAll("-", "_");
+        return Optional.ofNullable(analysis.getStudy()).map(study ->
+                String.format("%s-%s-%s-code.zip", code, sanitizeFilename(study.getTitle()).replaceAll("-", "_"), title)
+        ).orElseGet(() ->
+                String.format("%s-%s-code.zip", code, title)
+        );
+    }
+
     @ApiOperation("Update code file.")
     @PutMapping("/api/v1/analysis-management/analyses/{analysisId}/code-files/{fileUuid}")
     public JsonResult<Boolean> putFileContent(