Patches and Enhancements

pom.xml

@@ -6,7 +6,7 @@
 
   <groupId>org.tdl</groupId>
   <artifactId>vireo</artifactId>
-  <version>4.2.7</version>
+  <version>4.2.8</version>
 
   <name>Vireo</name>
   <description>Vireo Thesis and Dissertation Submission System</description>

src/main/java/org/tdl/vireo/auth/service/VireoUserCredentialsService.java

@@ -3,7 +3,9 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 import org.tdl.vireo.config.constant.ConfigurationName;
 import org.tdl.vireo.model.Role;
@@ -17,80 +19,134 @@
 @Service
 public class VireoUserCredentialsService extends UserCredentialsService<User, UserRepo> {
 
+    private static final String NETID = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_NETID;
+    private static final String EMAIL = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_EMAIL;
+    private static final String BIRTH_YEAR = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_BIRTH_YEAR;
+    private static final String FIRST_NAME = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_FIRST_NAME;
+    private static final String MIDDLE_NAME = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_MIDDLE_NAME;
+    private static final String LAST_NAME = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_LAST_NAME;
+    private static final String ORCID = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_ORCID;
+    private static final String INSTITUTIONAL_IDENTIFIER = ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_INSTITUTIONAL_IDENTIFIER;
+
+    private static final String SHIBBOLETH = "shibboleth";
+
+    private static final Map<String, String> shibSettings = new HashMap<>();
+
+    static {
+        shibSettings.put(NETID, "netid");
+        shibSettings.put(EMAIL, "email");
+        shibSettings.put(BIRTH_YEAR, "birthYear");
+        shibSettings.put(FIRST_NAME, "firstName");
+        shibSettings.put(MIDDLE_NAME, "middleName");
+        shibSettings.put(LAST_NAME, "lastName");
+        shibSettings.put(ORCID, "orcid");
+        shibSettings.put(INSTITUTIONAL_IDENTIFIER, "uin");
+    }
+
     @Autowired
     private ConfigurationRepo configurationRepo;
 
+    @Value("${app.useNetidAsIdentifier:false}")
+    private boolean useNetidAsIdentifier;
+
     @Override
     public synchronized User updateUserByCredentials(Credentials credentials) {
-        User user = userRepo.findByEmail(credentials.getEmail());
+        Map<String, String> shibValues = new HashMap<>();
 
-        Map<String, String> shibSettings = new HashMap<String, String>();
-        Map<String, String> shibValues = new HashMap<String, String>();
+        shibSettings.forEach((k, v) ->
+            shibValues.put(k, configurationRepo.getValueByNameAndType(k, SHIBBOLETH) != null ? configurationRepo.getValueByNameAndType(k, SHIBBOLETH) : v)
+        );
 
-        shibSettings.put(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_NETID, "netid");
-        shibSettings.put(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_BIRTH_YEAR, "birthYear");
-        shibSettings.put(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_MIDDLE_NAME, "middleName");
-        shibSettings.put(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_ORCID, "orcid");
-        shibSettings.put(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_INSTITUTIONAL_IDENTIFIER, "uin");
+        String shibNetid = credentials.getAllCredentials().get(shibValues.get(NETID));
+        String shibEmail = credentials.getAllCredentials().get(shibValues.get(EMAIL));
+        String shibFirstName = credentials.getAllCredentials().get(shibValues.get(FIRST_NAME));
+        String shibMiddleName = credentials.getAllCredentials().get(shibValues.get(MIDDLE_NAME));
+        String shibLastName = credentials.getAllCredentials().get(shibValues.get(LAST_NAME));
+        String shibOrcid = credentials.getAllCredentials().get(shibValues.get(ORCID));
 
-        shibSettings.forEach((k, v) -> {
-            shibValues.put(k, configurationRepo.getValueByNameAndType(k, "shibboleth") != null ? configurationRepo.getValueByNameAndType(k, "shibboleth") : v);
-        });
+        User user = useNetidAsIdentifier
+            ? userRepo.findByNetid(shibNetid)
+            : userRepo.findByEmail(shibEmail);
 
-        String uin = credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_INSTITUTIONAL_IDENTIFIER));
-        if (uin == null) {
-            uin = credentials.getEmail();
-        }
-
-        // TODO: check to see if credentials is from basic login or shibboleth
-        // do not create new user from basic login credentials that have no user!
         if (user == null) {
-
             Role role = Role.ROLE_STUDENT;
 
-            if (credentials.getRole() == null) {
-                credentials.setRole(role.toString());
-            }
-
-            String shibEmail = credentials.getEmail();
-
             for (String email : admins) {
                 if (email.equals(shibEmail)) {
                     role = Role.ROLE_ADMIN;
-                    credentials.setRole(role.toString());
                 }
             }
 
-            user = userRepo.create(credentials.getEmail(), credentials.getFirstName(), credentials.getLastName(), role);
+            user = userRepo.create(shibEmail, shibFirstName, shibLastName, role);
 
-            user.setNetid(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_NETID)));
-            if (credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_BIRTH_YEAR)) != null) {
-                user.setBirthYear(Integer.parseInt(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_BIRTH_YEAR))));
+            user.setNetid(shibNetid);
+            user.setMiddleName(shibMiddleName);
+            user.setOrcid(shibOrcid);
+
+            if (credentials.getAllCredentials().containsKey(shibValues.get(BIRTH_YEAR))) {
+                String shibBirthYearValue = credentials.getAllCredentials().get(shibValues.get(BIRTH_YEAR));
+                if (StringUtils.isNotEmpty(shibBirthYearValue)) {
+                    user.setBirthYear(Integer.parseInt(shibBirthYearValue));
+                }
             }
-            user.setMiddleName(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_MIDDLE_NAME)));
-            user.setOrcid(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_ORCID)));
-            user.setUsername(credentials.getEmail());
 
             user = userRepo.save(user);
         } else {
+            boolean isUserUpdated = false;
 
-            // TODO: update only if user properties does not match current credentials
+            if (StringUtils.isNotEmpty(shibNetid) && !user.getNetid().equals(shibNetid)) {
+                user.setNetid(shibNetid);
+                isUserUpdated = true;
+            }
+
+            if (credentials.getAllCredentials().containsKey(shibValues.get(BIRTH_YEAR))) {
+                String shibBirthYearValue = credentials.getAllCredentials().get(shibValues.get(BIRTH_YEAR));
 
-//DONT OVERWRITE WITH NULL VALUE
-//MORE WORK NEEDED
-            //user.setNetid(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_INSTITUTIONAL_IDENTIFIER)));
-            if (credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_BIRTH_YEAR)) != null) {
-                user.setBirthYear(Integer.parseInt(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_BIRTH_YEAR))));
+                if (StringUtils.isNotEmpty(shibBirthYearValue)) {
+                    int shibBirthYear = Integer.parseInt(shibBirthYearValue);
+                    if (shibBirthYear != user.getBirthYear()) {
+                        user.setBirthYear(shibBirthYear);
+                        isUserUpdated = true;
+                    }
+                }
             }
-            user.setMiddleName(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_MIDDLE_NAME)));
-            user.setOrcid(credentials.getAllCredentials().get(shibValues.get(ConfigurationName.APPLICATION_AUTH_SHIB_ATTRIBUTE_ORCID)));
-            user.setUsername(credentials.getEmail());
 
-            user = userRepo.save(user);
+            if (StringUtils.isNotEmpty(shibFirstName) && !user.getFirstName().equals(shibFirstName)) {
+                user.setFirstName(shibFirstName);
+                isUserUpdated = true;
+            }
+
+            if (StringUtils.isNotEmpty(shibMiddleName) && !user.getMiddleName().equals(shibMiddleName)) {
+                user.setMiddleName(shibMiddleName);
+                isUserUpdated = true;
+            }
+
+            if (StringUtils.isNotEmpty(shibLastName) && !user.getLastName().equals(shibLastName)) {
+                user.setLastName(shibLastName);
+                isUserUpdated = true;
+            }
+
+            if (StringUtils.isNotEmpty(shibOrcid) && !user.getOrcid().equals(shibOrcid)) {
+                user.setOrcid(shibOrcid);
+                isUserUpdated = true;
+            }
+
+            if (StringUtils.isNotEmpty(shibEmail) && !user.getUsername().equals(shibEmail)) {
+                user.setEmail(shibEmail);
+                user.setUsername(shibEmail);
+                isUserUpdated = true;
+            }
+
+            if (isUserUpdated) {
+                user = userRepo.save(user);
+            }
         }
 
         credentials.setRole(user.getRole().toString());
-        credentials.setUin(user.getUsername());
+
+        credentials.setNetid(user.getNetid());
+        credentials.setFirstName(user.getFirstName());
+        credentials.setLastName(user.getLastName());
 
         return user;
     }

src/main/java/org/tdl/vireo/controller/FieldValueController.java

@@ -34,7 +34,7 @@ public class FieldValueController {
     @GetMapping("/predicate/{value}")
     @PreAuthorize("hasRole('STUDENT')")
     public ApiResponse getFieldValuesByPredicateValue(@PathVariable String value) {
-        return new ApiResponse(SUCCESS, fieldValueRepo.getAllValuesByFieldPredicateValue("submission_type"));
+        return new ApiResponse(SUCCESS, fieldValueRepo.getAllValuesByFieldPredicateValue(value));
     }
 
 }

src/main/java/org/tdl/vireo/controller/SubmissionListController.java

@@ -4,12 +4,11 @@
 import static edu.tamu.weaver.response.ApiStatus.SUCCESS;
 import static org.springframework.web.bind.annotation.RequestMethod.POST;
 
-import edu.tamu.weaver.auth.annotation.WeaverUser;
-import edu.tamu.weaver.response.ApiResponse;
-import edu.tamu.weaver.validation.aspect.annotation.WeaverValidatedModel;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -36,6 +35,10 @@
 import org.tdl.vireo.model.repo.UserRepo;
 import org.tdl.vireo.service.DefaultSubmissionListColumnService;
 
+import edu.tamu.weaver.auth.annotation.WeaverUser;
+import edu.tamu.weaver.response.ApiResponse;
+import edu.tamu.weaver.validation.aspect.annotation.WeaverValidatedModel;
+
 @RestController
 @RequestMapping("/submission-list")
 public class SubmissionListController {
@@ -228,7 +231,19 @@ public ApiResponse addFilterCriterion(@WeaverUser User user, @RequestBody Map<St
         }
 
         if (namedSearchFilter == null) {
-            namedSearchFilter = namedSearchFilterRepo.create(submissionListColumnRepo.findByTitle(criterionName));
+            SubmissionListColumn column = submissionListColumnRepo.findByTitle(criterionName);
+            for (NamedSearchFilter existingFilter : activeFilter.getNamedSearchFilters()) {
+                if (existingFilter.getSubmissionListColumn() != null &&
+                    existingFilter.getSubmissionListColumn().getPredicate().equals(column.getPredicate()) &&
+                    existingFilter.getSubmissionListColumn().getValuePath().equals(column.getValuePath())) {
+                    namedSearchFilter = existingFilter;
+                    break;
+                }
+            }
+
+            if (namedSearchFilter == null) {
+                namedSearchFilter = namedSearchFilterRepo.create(column);
+            }
         }
 
         namedSearchFilter.addFilter(filterCriterionRepo.create(filterValue, filterGloss));

src/main/java/org/tdl/vireo/controller/advice/CustomResponseEntityExceptionHandler.java

@@ -5,6 +5,8 @@
 
 import javax.persistence.EntityNotFoundException;
 
+import java.nio.file.NoSuchFileException;
+
 import org.hibernate.exception.ConstraintViolationException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -72,6 +74,15 @@ public ApiResponse handleEntityNotFoundException(EntityNotFoundException excepti
         return new ApiResponse(ERROR, exception.getMessage());
     }
 
+    @ExceptionHandler(NoSuchFileException.class)
+    @ResponseStatus(value = HttpStatus.NOT_FOUND)
+    @ResponseBody
+    public ApiResponse handleNoSuchFileExceptionn(NoSuchFileException exception) {
+        logger.error(exception.getMessage());
+        logger.debug(exception.getMessage(), exception);
+        return new ApiResponse(ERROR, exception.getMessage());
+    }
+
     @ExceptionHandler(MultipartException.class)
     @ResponseStatus(value = HttpStatus.PAYLOAD_TOO_LARGE)
     @ResponseBody

src/main/java/org/tdl/vireo/model/ActionLog.java

@@ -30,12 +30,12 @@ public class ActionLog extends ValidatingBaseEntity {
     @ManyToOne(optional = true)
     private User user;
 
-    @JsonView(Views.SubmissionIndividual.class)
+    @JsonView(Views.SubmissionList.class)
     @Column(nullable = true)
     @Temporal(TemporalType.TIMESTAMP)
     private Calendar actionDate;
 
-    @JsonView(Views.SubmissionIndividual.class)
+    @JsonView(Views.SubmissionList.class)
     @Column(nullable = false, columnDefinition = "text")
     private String entry;
 

src/main/java/org/tdl/vireo/model/ContactInfo.java

@@ -10,11 +10,13 @@
 import javax.persistence.Entity;
 import javax.persistence.OneToOne;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import org.tdl.vireo.model.validation.ContactInfoValidator;
 
 import edu.tamu.weaver.validation.model.ValidatingBaseEntity;
 
 @Entity
+@JsonIgnoreProperties({ "hibernateLazyInitializer", "handler" })
 public class ContactInfo extends ValidatingBaseEntity {
 
     @OneToOne(cascade = { DETACH, MERGE, REFRESH, REMOVE }, fetch = EAGER, optional = true, orphanRemoval = true)