Release 1.14.0 (#602)

OHDSI · May 27, 2019 · 28791fe · 28791fe
1 parent 553d863
commit 28791fe
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Showing 25 changed files with 167 additions and 256 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <artifactId>portal</artifactId>
     <groupId>com.odysseusinc.arachne</groupId>
-    <version>1.13.0</version>
+    <version>1.14.0</version>
     <packaging>jar</packaging>
 
     <parent>
@@ -25,7 +25,6 @@
         <jjwt.version>0.6.0</jjwt.version>
         <ehcache.version>1.3.0</ehcache.version>
         <postgresql.version>42.2.1</postgresql.version>
-        <flyway.version>4.2.0</flyway.version>
         <gson.version>2.7</gson.version>
         <commons.lang3.version>3.5</commons.lang3.version>
         <hikaricp.version>2.6.3</hikaricp.version>
@@ -107,6 +106,11 @@
                 <groupId>org.apache.solr</groupId>
                 <version>7.2.1</version>
             </dependency>
+            <dependency>
+                <groupId>org.flywaydb</groupId>
+                <artifactId>flyway-core</artifactId>
+                <version>4.2.0</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 
@@ -195,11 +199,6 @@
             <artifactId>postgresql</artifactId>
             <version>${postgresql.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.flywaydb</groupId>
-            <artifactId>flyway-core</artifactId>
-            <version>${flyway.version}</version>
-        </dependency>
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
@@ -320,7 +319,7 @@
         <dependency>
             <groupId>org.ohdsi.sql</groupId>
             <artifactId>SqlRender</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
+            <version>1.6.1-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>com.cosium.spring.data</groupId>

diff --git a/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/AnalysisController.java b/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/AnalysisController.java
@@ -161,7 +161,7 @@ protected void attachIncidenceRatesFiles(List<MultipartFile> files) throws IOExc
 
 
     @Override
-    protected void attachCohortCharacterizationFiles(List<MultipartFile> files) throws IOException, URISyntaxException {
+    protected void attachCohortHeraclesFiles(List<MultipartFile> files) throws IOException, URISyntaxException {
 
         files.add(new MockMultipartFile(RUN_CC_REPORTS_FILE_NAME, RUN_CC_REPORTS_FILE_NAME, null,
                 readResource("r/" + RUN_CC_REPORTS_FILE_NAME)));

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
@@ -31,7 +31,6 @@
 import static org.springframework.web.bind.annotation.RequestMethod.POST;
 import static org.springframework.web.bind.annotation.RequestMethod.PUT;
 
-import com.google.common.collect.ImmutableMap;
 import com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType;
 import com.odysseusinc.arachne.commons.api.v1.dto.CommonEntityRequestDTO;
 import com.odysseusinc.arachne.commons.api.v1.dto.OptionDTO;
@@ -146,6 +145,7 @@ public abstract class BaseAnalysisController<T extends Analysis,
             = "'%s' with guid='%s' from DataNode with id='%d' is not available";
     private static final String DEFAULT_EXTENSION = ".txt";
     private static final String DEFAULT_MIMETYPE = "plain/text";
+    private static final String HYDRATED_ANALYSIS_RUNNER = "runAnalysis.R";
     protected final BaseDataSourceService dataSourceService;
     protected final BaseDataNodeService dataNodeService;
     protected final BaseAnalysisService<T> analysisService;
@@ -699,21 +699,24 @@ protected List<MultipartFile> getEntityFiles(DataReferenceDTO entityReference, D
         }
         List<MultipartFile> files = new LinkedList<>();
         final List<ImportedFile> importedFiles = (List<ImportedFile>) responseMessage.getObject();
-        if (entityType.equals(CommonAnalysisType.ESTIMATION)) {
+        boolean hasAnalysisRunner = hasAnalysisRunner(importedFiles);
+        if (entityType.equals(CommonAnalysisType.ESTIMATION) && !hasAnalysisRunner) {
             files.addAll(importService.processEstimation(importedFiles));
         } else {
             files = importedFiles.stream()
                     .map(file -> conversionService.convert(file, MockMultipartFile.class))
                     .collect(Collectors.toList());
         }
-        if (entityType.equals(CommonAnalysisType.PREDICTION)) {
-            attachPredictionFiles(files);
-        }
-        if (entityType.equals(CommonAnalysisType.COHORT_CHARACTERIZATION)) {
-            attachCohortCharacterizationFiles(files);
-        }
-        if (entityType.equals(CommonAnalysisType.INCIDENCE)) {
-            attachIncidenceRatesFiles(files);
+        if (!hasAnalysisRunner) {
+            if (entityType.equals(CommonAnalysisType.PREDICTION)) {
+                attachPredictionFiles(files);
+            }
+						if (entityType.equals(CommonAnalysisType.COHORT_HERACLES)) {
+							attachCohortHeraclesFiles(files);
+						}
+            if (entityType.equals(CommonAnalysisType.INCIDENCE)) {
+                attachIncidenceRatesFiles(files);
+            }
         }
         return files;
     }
@@ -732,8 +735,13 @@ protected void afterCreate(T analysis, A_C_DTO analysisDTO) {
 
     }
 
+    protected boolean hasAnalysisRunner(List<ImportedFile> files) {
+
+    	return files.stream().anyMatch(file -> file.getOriginalFilename().equalsIgnoreCase(HYDRATED_ANALYSIS_RUNNER));
+		}
+
     protected abstract void attachPredictionFiles(List<MultipartFile> files) throws IOException;
 
-    protected abstract void attachCohortCharacterizationFiles(List<MultipartFile> files) throws IOException, URISyntaxException;
+    protected abstract void attachCohortHeraclesFiles(List<MultipartFile> files) throws IOException, URISyntaxException;
 
 }
diff --git a/...om/odysseusinc/arachne/portal/api/v1/controller/BaseDataNodeCommonAnalysisController.java b/...om/odysseusinc/arachne/portal/api/v1/controller/BaseDataNodeCommonAnalysisController.java
@@ -53,6 +53,7 @@ public BaseDataNodeCommonAnalysisController(BaseDataNodeService<DN> baseDataNode
         analysisTypeMap.put("estimations", CommonAnalysisType.ESTIMATION);
         analysisTypeMap.put("predictions", CommonAnalysisType.PREDICTION);
         analysisTypeMap.put("incidence-rates", CommonAnalysisType.INCIDENCE);
+        analysisTypeMap.put("cohort-characterizations", CommonAnalysisType.COHORT_CHARACTERIZATION);
     }
 
     /**

diff --git a/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseUserController.java b/src/main/java/com/odysseusinc/arachne/portal/api/v1/controller/BaseUserController.java
@@ -713,6 +713,17 @@ public JsonResult<List<StateProvinceDTO>> suggestStateProvince(
         return result;
     }
 
+    @ApiOperation("List DataNode users")
+    @RequestMapping(value = "/api/v1/user-management/datanodes/{dataNodeId}/users", method = GET)
+    public List<CommonUserDTO> listDataNodeUsers(@PathVariable("dataNodeId") Long dataNodeId) {
+
+        final DN dataNode = baseDataNodeService.getById(dataNodeId);
+        List<DataNodeUser> users = baseDataNodeService.listOwners(dataNode);
+        return users.stream()
+                .map(user -> conversionService.convert(user.getUser(), CommonUserDTO.class))
+                .collect(Collectors.toList());
+    }
+
     @ApiOperation("Link U to DataNode")
     @RequestMapping(value = "/api/v1/user-management/datanodes/{datanodeSid}/users", method = POST)
     public JsonResult linkUserToDataNode(@PathVariable("datanodeSid") Long datanodeId,

diff --git a/...in/java/com/odysseusinc/arachne/portal/api/v1/controller/ExceptionHandlingController.java b/...in/java/com/odysseusinc/arachne/portal/api/v1/controller/ExceptionHandlingController.java
@@ -47,15 +47,19 @@
 import com.odysseusinc.arachne.portal.exception.WrongFileFormatException;
 import com.odysseusinc.arachne.portal.security.LoginRequestContext;
 import java.io.IOException;
+import java.lang.reflect.Method;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Objects;
 import java.util.function.Consumer;
-import javax.servlet.http.Cookie;
-import java.util.Collection;
 import java.util.stream.Collectors;
+import javax.annotation.PostConstruct;
+import javax.servlet.http.Cookie;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.validation.ConstraintViolationException;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.dao.DataAccessException;
@@ -78,6 +82,8 @@ public class ExceptionHandlingController extends BaseController {
 
     private static final String ERROR_MESSAGE = "An error has occurred. Please contact system administrator";
 
+    private final Map<Class<? extends Throwable>, Method> exceptionHandlersMap = new HashMap<>();
+
     private static final Consumer<HttpServletResponse> ADD_COOKIE_FUNCTION = response -> {
 
         if (Objects.nonNull(LoginRequestContext.getUserName())) {
@@ -94,6 +100,19 @@ public ExceptionHandlingController(NoHandlerFoundExceptionUtils noHandlerFoundEx
         this.noHandlerFoundExceptionUtils = noHandlerFoundExceptionUtils;
     }
 
+    @PostConstruct
+    public void mapExceptionHandlers() {
+
+        Method[] methods = ExceptionHandlingController.class.getDeclaredMethods();
+        for(Method method : methods) {
+            if (method.isAnnotationPresent(ExceptionHandler.class)) {
+                ExceptionHandler annotation = method.getAnnotation(ExceptionHandler.class);
+                Arrays.stream(annotation.value())
+                        .forEach(clz -> exceptionHandlersMap.put(clz, method));
+            }
+        }
+    }
+
     @ExceptionHandler(Exception.class)
     public ResponseEntity<JsonResult> exceptionHandler(Exception ex) {
 
@@ -103,6 +122,21 @@ public ResponseEntity<JsonResult> exceptionHandler(Exception ex) {
         return new ResponseEntity<>(result, HttpStatus.OK);
     }
 
+    @ExceptionHandler(RuntimeException.class)
+    public ResponseEntity<JsonResult> exceptionHandler(HttpServletRequest req, HttpServletResponse res, RuntimeException ex) throws Exception {
+
+        if (Objects.isNull(ex.getCause())) {
+            handleNotFoundError(req, res);
+            return null;
+        }
+        Method method = exceptionHandlersMap.get(ex.getCause().getClass());
+        if (Objects.nonNull(method)) {
+            return (ResponseEntity<JsonResult>) method.invoke(this, ex.getCause());
+        } else {
+            return exceptionHandler((Exception) ex.getCause());
+        }
+    }
+
     @ExceptionHandler(ValidationException.class)
     public ResponseEntity<JsonResult> exceptionHandler(ValidationException ex) {
 

diff --git a/.../odysseusinc/arachne/portal/api/v1/dto/converters/study/BaseStudyToStudyDTOConverter.java b/.../odysseusinc/arachne/portal/api/v1/dto/converters/study/BaseStudyToStudyDTOConverter.java
@@ -23,7 +23,6 @@
 package com.odysseusinc.arachne.portal.api.v1.dto.converters.study;
 
 import com.odysseusinc.arachne.portal.api.v1.dto.ParticipantDTO;
-import com.odysseusinc.arachne.portal.api.v1.dto.PermissionsDTO;
 import com.odysseusinc.arachne.portal.api.v1.dto.StudyDTO;
 import com.odysseusinc.arachne.portal.api.v1.dto.dictionary.StudyStatusDTO;
 import com.odysseusinc.arachne.portal.api.v1.dto.dictionary.StudyTypeDTO;
@@ -33,6 +32,10 @@
 import com.odysseusinc.arachne.portal.service.BaseStudyService;
 import com.odysseusinc.arachne.portal.service.analysis.AnalysisService;
 import com.odysseusinc.arachne.portal.util.ArachneConverterUtils;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 
 public abstract class BaseStudyToStudyDTOConverter<S extends Study, DTO extends StudyDTO> extends BaseStudyToCommonStudyDTOConverter<S, DTO> {
@@ -48,7 +51,11 @@ public DTO convert(final S source) {
 
         final DTO studyDTO = super.convert(source);
         final Tenant studyTenant = source.getTenant();
-        for (final UserStudyExtended studyUserLink : source.getParticipants()) {
+        List<UserStudyExtended> sourceParticipants = new ArrayList<>(source.getParticipants());
+        Comparator<UserStudyExtended> comparator = Comparator.comparing(p -> p.getStatus().ordinal());
+        sourceParticipants.sort(comparator.thenComparing((p1, p2) -> StringUtils.compare(p1.getUser().getFullName(), p2.getUser().getFullName())));
+
+        for (final UserStudyExtended studyUserLink : sourceParticipants) {
             final ParticipantDTO participantDTO = conversionService.convert(studyUserLink, ParticipantDTO.class);
             if (!studyUserLink.getUser().getTenants().contains(studyTenant)) {
                 participantDTO.setCanBeRecreated(Boolean.FALSE);

diff --git a/src/main/java/com/odysseusinc/arachne/portal/config/FlywayConfig.java b/src/main/java/com/odysseusinc/arachne/portal/config/FlywayConfig.java
@@ -22,7 +22,7 @@
 
 package com.odysseusinc.arachne.portal.config;
 
-import com.odysseusinc.arachne.portal.config.flyway.ApplicationContextAwareSpringJdbcMigrationResolver;
+import com.odysseusinc.arachne.commons.config.flyway.ApplicationContextAwareSpringJdbcMigrationResolver;
 import org.flywaydb.core.Flyway;
 import org.springframework.boot.autoconfigure.flyway.FlywayMigrationInitializer;
 import org.springframework.context.annotation.Bean;

diff --git a/src/main/java/com/odysseusinc/arachne/portal/config/WebSecurityConfig.java b/src/main/java/com/odysseusinc/arachne/portal/config/WebSecurityConfig.java
@@ -59,7 +59,6 @@
 import org.springframework.http.HttpMethod;
 import org.springframework.security.authentication.AuthenticationManager;
 import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
-import org.springframework.security.config.annotation.method.configuration.EnableGlobalMethodSecurity;
 import org.springframework.security.config.annotation.web.builders.HttpSecurity;
 import org.springframework.security.config.annotation.web.configuration.EnableWebSecurity;
 import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
@@ -73,7 +72,6 @@
 
 @Configuration
 @EnableWebSecurity
-@EnableGlobalMethodSecurity(prePostEnabled = true)
 public class WebSecurityConfig extends WebSecurityConfigurerAdapter {
 
     private static final Logger log = LoggerFactory.getLogger(WebSecurityConfig.class);
@@ -273,7 +271,6 @@ protected void configure(HttpSecurity http) throws Exception {
                 .antMatchers("/api/v1/auth/method**").permitAll()
                 .antMatchers("/api/v1/user-management/activation/**").permitAll()
                 .antMatchers("/api/v1/data-sources/dbms-types").permitAll()
-                .antMatchers("/api/v1/user-management/datanodes/**").hasRole(Roles.ROLE_DATA_NODE)
                 .antMatchers("/api/v1/user-management/professional-types**").permitAll()
                 .antMatchers("/api/v1/user-management/countries/**").permitAll()
                 .antMatchers("/api/v1/user-management/state-province/**").permitAll()

diff --git a/...sinc/arachne/portal/config/flyway/ApplicationContextAwareSpringJdbcMigrationExecutor.java b/...sinc/arachne/portal/config/flyway/ApplicationContextAwareSpringJdbcMigrationExecutor.java