Refactor BioDataCatalyst to ProjectMetaData

This server two purposes. More accurate naming and to fix json parsing.

Author: Gcolon021

pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/FenceMapping.java

@@ -1,16 +1,19 @@
 package edu.harvard.hms.dbmi.avillach.auth.model;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
+
 import java.util.ArrayList;
 
 public class FenceMapping {
 
-    private ArrayList<BioDataCatalyst> projectMetaData;
+    @JsonProperty("bio_data_catalyst")
+    private ArrayList<ProjectMetaData> bio_data_catalyst;
 
-    public ArrayList<BioDataCatalyst> getProjectMetaData() {
-        return projectMetaData;
+    public ArrayList<ProjectMetaData> getBio_data_catalyst() {
+        return bio_data_catalyst;
     }
 
-    public void setProjectMetaData(ArrayList<BioDataCatalyst> projectMetaData) {
-        this.projectMetaData = projectMetaData;
+    public void setBio_data_catalyst(ArrayList<ProjectMetaData> bio_data_catalyst) {
+        this.bio_data_catalyst = bio_data_catalyst;
     }
 }

pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/BioDataCatalyst.java pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/model/ProjectMetaData.java

@@ -1,6 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.auth.model;
 
-public class BioDataCatalyst {
+public class ProjectMetaData {
     private int raw_clinical_variable_count;
     private int raw_clinical_sample_size;
     private String study_identifier;

pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/StudyAccessService.java

@@ -1,8 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.auth.rest;
 
-import edu.harvard.hms.dbmi.avillach.auth.data.entity.Role;
-import edu.harvard.hms.dbmi.avillach.auth.data.repository.RoleRepository;
-import edu.harvard.hms.dbmi.avillach.auth.model.BioDataCatalyst;
+import edu.harvard.hms.dbmi.avillach.auth.model.ProjectMetaData;
 import edu.harvard.hms.dbmi.avillach.auth.service.auth.FENCEAuthenticationService;
 import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility;
 import io.swagger.annotations.Api;
@@ -55,9 +53,9 @@ public Response addStudyAccess(@ApiParam(value="The Study Identifier of the new
             return Response.status(Response.Status.BAD_REQUEST).entity("Study identifier cannot be blank").build();
         }
 
-        BioDataCatalyst fenceMappingForStudy;
+        ProjectMetaData fenceMappingForStudy;
         try {
-            Map<String, BioDataCatalyst> fenceMapping = fenceMappingUtility.getFENCEMapping();
+            Map<String, ProjectMetaData> fenceMapping = fenceMappingUtility.getFENCEMapping();
             if (fenceMapping == null) {
                 throw new Exception("Fence mapping is null");
             }

pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/auth/FENCEAuthenticationService.java

@@ -6,7 +6,6 @@
 import static edu.harvard.hms.dbmi.avillach.auth.JAXRSConfiguration.fence_standard_access_rules;
 import static edu.harvard.hms.dbmi.avillach.auth.JAXRSConfiguration.fence_topmed_consent_group_concept_path;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.*;
 import java.util.regex.Matcher;
@@ -20,7 +19,7 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.node.ObjectNode;
-import edu.harvard.hms.dbmi.avillach.auth.model.BioDataCatalyst;
+import edu.harvard.hms.dbmi.avillach.auth.model.ProjectMetaData;
 import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.Header;
@@ -247,7 +246,7 @@ public Response getFENCEProfile(String callback_url, Map<String, String> authReq
 
     private void createAndUpsertRole(String access_role_name, User current_user) {
         logger.debug("createAndUpsertRole() starting...");
-        BioDataCatalyst projectMetadata = fenceMappingUtility.getFenceMappingByAuthZ().get(access_role_name);
+        ProjectMetaData projectMetadata = fenceMappingUtility.getFenceMappingByAuthZ().get(access_role_name);
 
         if (projectMetadata == null) {
             logger.error("getFENCEProfile() -> createAndUpsertRole could not find study in FENCE mapping SKIPPING: {}", access_role_name);

pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/FenceMappingUtility.java

@@ -1,7 +1,7 @@
 package edu.harvard.hms.dbmi.avillach.auth.utils;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import edu.harvard.hms.dbmi.avillach.auth.model.BioDataCatalyst;
+import edu.harvard.hms.dbmi.avillach.auth.model.ProjectMetaData;
 import edu.harvard.hms.dbmi.avillach.auth.model.FenceMapping;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -21,8 +21,8 @@
 public class FenceMappingUtility {
 
     private final Logger logger = LoggerFactory.getLogger(this.getClass());
-    private Map<String, BioDataCatalyst> _projectMap;
-    private Map<String, BioDataCatalyst> fenceMappingByAuthZ;
+    private Map<String, ProjectMetaData> _projectMap;
+    private Map<String, ProjectMetaData> fenceMappingByAuthZ;
     private static String templatePath;
     private ObjectMapper objectMapper;
 
@@ -43,9 +43,9 @@ public void init() {
     }
 
     private void initializeFENCEMapping() throws IOException {
-        ArrayList<BioDataCatalyst> projects = loadBioDataCatalystFenceMappingData();
+        ArrayList<ProjectMetaData> projects = loadBioDataCatalystFenceMappingData();
         _projectMap = new HashMap<>(projects.size());
-        for (BioDataCatalyst project : projects) {
+        for (ProjectMetaData project : projects) {
             String consentVal = (project.getConsent_group_code() != null && !project.getConsent_group_code().isEmpty()) ?
                     project.getStudy_identifier() + "." + project.getConsent_group_code() :
                     project.getStudy_identifier();
@@ -54,24 +54,24 @@ private void initializeFENCEMapping() throws IOException {
     }
 
     private void initializeFenceMappingByAuthZ() throws IOException {
-        ArrayList<BioDataCatalyst> projects = loadBioDataCatalystFenceMappingData();
+        ArrayList<ProjectMetaData> projects = loadBioDataCatalystFenceMappingData();
         fenceMappingByAuthZ = new HashMap<>(projects.size());
-        for (BioDataCatalyst project : projects) {
+        for (ProjectMetaData project : projects) {
             fenceMappingByAuthZ.put(project.getAuthZ().replace("\\/", "/"), project);
         }
     }
 
-    public Map<String, BioDataCatalyst> getFENCEMapping() {
+    public Map<String, ProjectMetaData> getFENCEMapping() {
         return _projectMap;
     }
 
-    public Map<String, BioDataCatalyst> getFenceMappingByAuthZ() {
+    public Map<String, ProjectMetaData> getFenceMappingByAuthZ() {
         return fenceMappingByAuthZ;
     }
 
-    private ArrayList<BioDataCatalyst> loadBioDataCatalystFenceMappingData() {
+    private ArrayList<ProjectMetaData> loadBioDataCatalystFenceMappingData() {
         FenceMapping fenceMapping;
-        ArrayList<BioDataCatalyst> projects;
+        ArrayList<ProjectMetaData> projects;
         try {
             logger.debug("getFENCEMapping: loading FENCE mapping from {}", templatePath);
             fenceMapping = objectMapper.readValue(

pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/StudyAccessServiceTest.java

@@ -1,19 +1,16 @@
 package edu.harvard.hms.dbmi.avillach;
 
-import edu.harvard.hms.dbmi.avillach.auth.data.repository.RoleRepository;
-import edu.harvard.hms.dbmi.avillach.auth.model.BioDataCatalyst;
+import edu.harvard.hms.dbmi.avillach.auth.model.ProjectMetaData;
 import edu.harvard.hms.dbmi.avillach.auth.rest.StudyAccessService;
 import edu.harvard.hms.dbmi.avillach.auth.service.auth.FENCEAuthenticationService;
 import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility;
 import org.junit.Before;
 import org.junit.Test;
 import org.mockito.InjectMocks;
 import org.mockito.Mock;
-import org.mockito.Mockito;
 import org.mockito.MockitoAnnotations;
 
 import javax.ws.rs.core.Response;
-import java.util.HashMap;
 import java.util.Map;
 
 import static org.junit.Assert.assertEquals;
@@ -47,7 +44,7 @@ public void testAddStudyAccessWithBlankIdentifier() {
     @Test
     public void testAddStudyAccess() {
         String studyIdentifier = "testStudy";
-        BioDataCatalyst bioDataCatalyst = new BioDataCatalyst();
+        ProjectMetaData bioDataCatalyst = new ProjectMetaData();
         bioDataCatalyst.setStudy_identifier("testStudy");
         bioDataCatalyst.setConsent_group_code("");
         when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, bioDataCatalyst));
@@ -61,7 +58,7 @@ public void testAddStudyAccess() {
     @Test
     public void testAddStudyAccessWithConsent() {
         String studyIdentifier = "testStudy2.c2";
-        BioDataCatalyst bioDataCatalyst = new BioDataCatalyst();
+        ProjectMetaData bioDataCatalyst = new ProjectMetaData();
         bioDataCatalyst.setStudy_identifier("testStudy2");
         bioDataCatalyst.setConsent_group_code("c2");