More Nullable checks and fixes

Use the Optional API for all repository methods that can return null.

Fix a pretty nasty bug where Spring Data would honor the non-null return
value for UserRepository.findByEmailIgnoreCase().

Remove unused imports.

src/main/java/ubc/pavlab/rdp/Application.java

@@ -4,7 +4,6 @@
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.cache.annotation.EnableCaching;
-import org.springframework.data.jpa.repository.config.EnableJpaAuditing;
 import org.springframework.scheduling.annotation.EnableScheduling;
 
 @SpringBootApplication

src/main/java/ubc/pavlab/rdp/ResourceLoaderConfig.java

@@ -1,12 +1,8 @@
 package ubc.pavlab.rdp;
 
 import lombok.extern.apachecommons.CommonsLog;
-import org.springframework.beans.BeansException;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
 import org.springframework.context.ResourceLoaderAware;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.support.GenericApplicationContext;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.ResourceLoader;
 import ubc.pavlab.rdp.util.PurlResolver;

src/main/java/ubc/pavlab/rdp/ValidationConfig.java

@@ -8,6 +8,7 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.core.io.Resource;
 import org.springframework.http.converter.FormHttpMessageConverter;
+import org.springframework.lang.Nullable;
 import org.springframework.web.client.RestTemplate;
 import ubc.pavlab.rdp.validation.*;
 
@@ -27,8 +28,8 @@ public class ValidationConfig {
 
     @Bean
     public EmailValidator emailValidator(
-            @Value("${rdp.settings.allowed-email-domains}") List<String> allowedEmailDomains,
-            @Value("${rdp.settings.allowed-email-domains-file}") Resource allowedEmailDomainsFile,
+            @Value("${rdp.settings.allowed-email-domains}") @Nullable List<String> allowedEmailDomains,
+            @Value("${rdp.settings.allowed-email-domains-file}") @Nullable Resource allowedEmailDomainsFile,
             @Value("${rdp.settings.allowed-email-domains-file-refresh-delay}") @DurationUnit(ChronoUnit.SECONDS) Duration refreshDelay,
             @Value("${rdp.settings.allow-internationalized-email-domains}") boolean allowIdn ) throws IOException {
         List<AllowedDomainStrategy> strategies = new ArrayList<>();

src/main/java/ubc/pavlab/rdp/WebSecurityConfig.java

@@ -25,7 +25,6 @@
 import ubc.pavlab.rdp.security.authentication.TokenBasedAuthenticationManager;
 import ubc.pavlab.rdp.services.UserService;
 import ubc.pavlab.rdp.settings.ApplicationSettings;
-import ubc.pavlab.rdp.settings.SiteSettings;
 
 import javax.servlet.*;
 import javax.servlet.http.HttpServletRequest;
@@ -63,9 +62,6 @@ public class WebSecurityConfig extends WebSecurityConfigurerAdapter {
     @Autowired
     private UserService userService;
 
-    @Autowired
-    private SiteSettings siteSettings;
-
     @Override
     protected void configure( AuthenticationManagerBuilder auth ) throws Exception {
         auth.userDetailsService( userDetailsService ).passwordEncoder( bCryptPasswordEncoder );

src/main/java/ubc/pavlab/rdp/controllers/AdminController.java

@@ -148,7 +148,7 @@ public Object createServiceAccount( @Validated(User.ValidationServiceAccount.cla
     }
 
     @PostMapping(value = "/admin/users/{user}/roles")
-    public Object updateRoles( @PathVariable User user, @RequestParam(required = false) Set<Role> roles, RedirectAttributes redirectAttributes, Locale locale ) {
+    public Object updateRoles( @PathVariable User user, @RequestParam(required = false) @Nullable Set<Role> roles, RedirectAttributes redirectAttributes, Locale locale ) {
         if ( roles == null ) {
             roles = Collections.emptySet();
         }
@@ -176,7 +176,7 @@ public Object updateRoles( @PathVariable User user, @RequestParam(required = fal
      * Retrieve a user's details.
      */
     @GetMapping(value = "/admin/users/{user}")
-    public Object getUser( @PathVariable(required = false) User user, @SuppressWarnings("unused") ConfirmEmailForm confirmEmailForm, Locale locale ) {
+    public Object getUser( @PathVariable(required = false) @Nullable User user, @SuppressWarnings("unused") ConfirmEmailForm confirmEmailForm, Locale locale ) {
         if ( user == null ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.userNotFoundById", null, locale ) );
@@ -185,7 +185,7 @@ public Object getUser( @PathVariable(required = false) User user, @SuppressWarni
     }
 
     @PostMapping(value = "/admin/users/{user}/create-access-token")
-    public Object createAccessTokenForUser( @PathVariable(required = false) User user, RedirectAttributes redirectAttributes, Locale locale ) {
+    public Object createAccessTokenForUser( @PathVariable(required = false) @Nullable User user, RedirectAttributes redirectAttributes, Locale locale ) {
         if ( user == null ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.userNotFoundById", null, locale ) );
@@ -196,7 +196,7 @@ public Object createAccessTokenForUser( @PathVariable(required = false) User use
     }
 
     @PostMapping(value = "/admin/users/{user}/revoke-access-token/{accessToken}")
-    public Object revokeAccessTn( @PathVariable(required = false) User user, @PathVariable(required = false) AccessToken accessToken, RedirectAttributes redirectAttributes, Locale locale ) {
+    public Object revokeAccessTn( @PathVariable(required = false) @Nullable User user, @PathVariable(required = false) @Nullable AccessToken accessToken, RedirectAttributes redirectAttributes, Locale locale ) {
         if ( user == null ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.userNotFoundById", null, locale ) );
@@ -218,7 +218,7 @@ public static class ConfirmEmailForm {
      * Delete a given user.
      */
     @DeleteMapping(value = "/admin/users/{user}")
-    public Object deleteUser( @PathVariable(required = false) User user,
+    public Object deleteUser( @PathVariable(required = false) @Nullable User user,
                               @Valid ConfirmEmailForm confirmEmailForm, BindingResult bindingResult,
                               Locale locale ) {
         if ( user == null ) {
@@ -245,7 +245,7 @@ public ModelAndView getOntologies( @SuppressWarnings("unused") ImportOntologyFor
     }
 
     @GetMapping("/admin/ontologies/{ontology}")
-    public ModelAndView getOntology( @PathVariable(required = false) Ontology ontology, Locale locale ) {
+    public ModelAndView getOntology( @PathVariable(required = false) @Nullable Ontology ontology, Locale locale ) {
         if ( ontology == null ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
@@ -293,15 +293,17 @@ public static UpdateOntologyForm fromOntology( Ontology ontology ) {
         @Size(min = 1, max = Ontology.MAX_NAME_LENGTH)
         private String name;
 
+        @Nullable
         private String definition;
 
+        @Nullable
         private URL ontologyUrl;
 
         private boolean availableForGeneSearch;
     }
 
     @PostMapping("/admin/ontologies/{ontology}")
-    public ModelAndView updateOntology( @PathVariable(required = false) Ontology ontology,
+    public ModelAndView updateOntology( @PathVariable(required = false) @Nullable Ontology ontology,
                                         @Valid UpdateOntologyForm updateOntologyForm, BindingResult bindingResult,
                                         Locale locale ) {
         if ( ontology == null ) {
@@ -337,7 +339,7 @@ public ModelAndView updateOntology( @PathVariable(required = false) Ontology ont
     }
 
     @DeleteMapping("/admin/ontologies/{ontology}")
-    public Object deleteOntology( @PathVariable(required = false) Ontology ontology,
+    public Object deleteOntology( @PathVariable(required = false) @Nullable Ontology ontology,
                                   @Valid DeleteOntologyForm deleteOntologyForm, BindingResult bindingResult,
                                   RedirectAttributes redirectAttributes,
                                   Locale locale ) {
@@ -395,7 +397,7 @@ public Object createSimpleOntology( @SuppressWarnings("unused") ImportOntologyFo
     }
 
     @PostMapping("/admin/ontologies/{ontology}/update-simple-ontology")
-    public Object updateSimpleOntology( @PathVariable(required = false) Ontology ontology,
+    public Object updateSimpleOntology( @PathVariable(required = false) @Nullable Ontology ontology,
                                         @Valid SimpleOntologyForm simpleOntologyForm, BindingResult bindingResult,
                                         RedirectAttributes redirectAttributes, Locale locale ) {
         if ( ontology == null ) {
@@ -483,6 +485,7 @@ public static SimpleOntologyTermForm emptyRow() {
         /**
          * Auto-generated if null or empty, which is why we allow zero as a size.
          */
+        @Nullable
         @Size(max = OntologyTermInfo.MAX_TERM_ID_LENGTH, groups = RowNotEmpty.class)
         private String termId;
         @NotNull(groups = RowNotEmpty.class)
@@ -631,7 +634,7 @@ public void initBinding2( WebDataBinder webDataBinder ) {
     }
 
     @PostMapping("/admin/ontologies/{ontology}/update")
-    public Object updateOntology( @PathVariable(required = false) Ontology ontology,
+    public Object updateOntology( @PathVariable(required = false) @Nullable Ontology ontology,
                                   RedirectAttributes redirectAttributes,
                                   Locale locale ) {
         if ( ontology == null ) {
@@ -716,7 +719,12 @@ public Object importReactomePathways( RedirectAttributes redirectAttributes ) {
     @PostMapping("/admin/ontologies/{ontology}/update-reactome-pathways")
     public Object updateReactomePathways( @PathVariable(required = false) @Nullable Ontology ontology, RedirectAttributes redirectAttributes, Locale locale ) {
         // null-check is not necessary, but can save a database call
-        if ( ontology == null || !ontology.equals( reactomeService.findPathwaysOntology() ) ) {
+        if ( ontology == null ) {
+            return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
+                    .addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
+        }
+        Ontology reactome = reactomeService.findPathwaysOntology();
+        if ( reactome == null || !reactome.equals( ontology ) ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
         }
@@ -821,7 +829,7 @@ public static class DeactivateOntologyForm extends ActivateOrDeactivateOntologyF
     }
 
     @PostMapping("/admin/ontologies/{ontology}/activate")
-    public Object activateOntology( @PathVariable(required = false) Ontology ontology, ActivateOntologyForm activateOntologyForm, RedirectAttributes redirectAttributes, Locale locale ) {
+    public Object activateOntology( @PathVariable(required = false) @Nullable Ontology ontology, ActivateOntologyForm activateOntologyForm, RedirectAttributes redirectAttributes, Locale locale ) {
         if ( ontology == null ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
@@ -833,7 +841,7 @@ public Object activateOntology( @PathVariable(required = false) Ontology ontolog
     }
 
     @PostMapping("/admin/ontologies/{ontology}/deactivate")
-    public Object deactivateOntology( @PathVariable(required = false) Ontology ontology, DeactivateOntologyForm deactivateOntologyForm, RedirectAttributes redirectAttributes, Locale locale ) {
+    public Object deactivateOntology( @PathVariable(required = false) @Nullable Ontology ontology, DeactivateOntologyForm deactivateOntologyForm, RedirectAttributes redirectAttributes, Locale locale ) {
         if ( ontology == null ) {
             return new ModelAndView( "error/404", HttpStatus.NOT_FOUND )
                     .addObject( "message", messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
@@ -890,7 +898,7 @@ public Object deactivateTerm( @PathVariable(required = false) Ontology ontology,
         return activateOrDeactivateTerm( ontology, deactivateTermForm, bindingResult, redirectAttributes, locale );
     }
 
-    private Object activateOrDeactivateTerm( Ontology ontology,
+    private Object activateOrDeactivateTerm( @Nullable Ontology ontology,
                                              ActivateOrDeactivateTermForm activateOrDeactivateTermForm, BindingResult bindingResult,
                                              RedirectAttributes redirectAttributes,
                                              Locale locale ) {
@@ -901,7 +909,7 @@ private Object activateOrDeactivateTerm( Ontology ontology,
         OntologyTermInfo ontologyTermInfo = null;
 
         if ( !bindingResult.hasFieldErrors( "ontologyTermInfoId" ) ) {
-            ontologyTermInfo = ontologyService.findTermByTermIdAndOntology( activateOrDeactivateTermForm.ontologyTermInfoId, ontology );
+            ontologyTermInfo = ontologyService.findTermByTermIdAndOntology( activateOrDeactivateTermForm.ontologyTermInfoId, ontology ).orElse( null );
             if ( ontologyTermInfo == null ) {
                 bindingResult.rejectValue( "ontologyTermInfoId", "AdminController.ActivateOrDeactivateTermForm.unknownTermInOntology",
                         new String[]{ activateOrDeactivateTermForm.getOntologyTermInfoId(), messageSource.getMessage( ontology.getResolvableTitle(), locale ) }, null );
@@ -953,7 +961,7 @@ private Object activateOrDeactivateTerm( Ontology ontology,
      * Provides the ontology in OBO format.
      */
     @GetMapping(value = "/admin/ontologies/{ontology}/download", produces = "text/plain")
-    public ResponseEntity<StreamingResponseBody> downloadOntology( @PathVariable(required = false) Ontology ontology, TimeZone timeZone ) {
+    public ResponseEntity<StreamingResponseBody> downloadOntology( @PathVariable(required = false) @Nullable Ontology ontology, TimeZone timeZone ) {
         if ( ontology == null ) {
             return ResponseEntity.notFound().build();
         }
@@ -969,7 +977,7 @@ public ResponseEntity<StreamingResponseBody> downloadOntology( @PathVariable(req
 
     @ResponseBody
     @GetMapping("/admin/ontologies/{ontology}/autocomplete-terms")
-    public Object autocompleteOntologyTerms( @PathVariable(required = false) Ontology ontology, @RequestParam String query, Locale locale ) {
+    public Object autocompleteOntologyTerms( @PathVariable(required = false) @Nullable Ontology ontology, @RequestParam String query, Locale locale ) {
         if ( ontology == null ) {
             return ResponseEntity.status( HttpStatus.NOT_FOUND )
                     .body( messageSource.getMessage( "AdminController.ontologyNotFoundById", null, locale ) );
@@ -993,7 +1001,7 @@ public ResponseEntity<String> refreshMessages() {
     }
 
     @PostMapping("/admin/ontologies/{ontology}/move")
-    public Object move( @PathVariable(required = false) Ontology ontology, @RequestParam String direction,
+    public Object move( @PathVariable(required = false) @Nullable Ontology ontology, @RequestParam String direction,
                         @SuppressWarnings("unused") ImportOntologyForm importOntologyForm,
                         Locale locale ) {
         if ( ontology == null ) {

src/main/java/ubc/pavlab/rdp/controllers/LoginController.java

@@ -26,6 +26,7 @@
 import ubc.pavlab.rdp.validation.Recaptcha;
 import ubc.pavlab.rdp.validation.RecaptchaValidator;
 
+import javax.annotation.Nullable;
 import javax.servlet.http.HttpServletRequest;
 import java.util.List;
 import java.util.Locale;
@@ -110,8 +111,8 @@ public ModelAndView registration() {
     @PostMapping("/registration")
     public ModelAndView createNewUser( @Validated(User.ValidationUserAccount.class) User user,
                                        BindingResult bindingResult,
-                                       @RequestParam(name = "g-recaptcha-response", required = false) String recaptchaResponse,
-                                       @RequestHeader(name = "X-Forwarded-For", required = false) List<String> clientIp,
+                                       @RequestParam(name = "g-recaptcha-response", required = false) @Nullable String recaptchaResponse,
+                                       @RequestHeader(name = "X-Forwarded-For", required = false) @Nullable List<String> clientIp,
                                        RedirectAttributes redirectAttributes,
                                        Locale locale ) {
         ModelAndView modelAndView = new ModelAndView( "registration" );
@@ -129,19 +130,10 @@ public ModelAndView createNewUser( @Validated(User.ValidationUserAccount.class)
         }
 
         User existingUser = userService.findUserByEmailNoAuth( user.getEmail() );
-
-        // profile can be missing of no profile.* fields have been set
-        if ( user.getProfile() == null ) {
-            user.setProfile( new Profile() );
-        }
-
         user.setEnabled( false );
 
         // initialize a basic user profile
         Profile userProfile = user.getProfile();
-        if ( userProfile == null ) {
-            userProfile = new Profile();
-        }
         userProfile.setPrivacyLevel( privacyService.getDefaultPrivacyLevel() );
         userProfile.setShared( applicationSettings.getPrivacy().isDefaultSharing() );
         userProfile.setHideGenelist( false );

src/main/java/ubc/pavlab/rdp/controllers/PasswordController.java

@@ -22,6 +22,8 @@
 import javax.validation.Valid;
 import java.util.Locale;
 
+import static java.util.Objects.requireNonNull;
+
 /**
  * Created by mjacobson on 23/01/18.
  */
@@ -103,7 +105,7 @@ public ModelAndView showChangePasswordPage( @RequestParam("id") int id, @Request
         }
 
         // Log in
-        User user = userService.findUserByIdNoAuth( id );
+        User user = requireNonNull( userService.findUserByIdNoAuth( id ) );
         UserPrinciple principle = new UserPrinciple( user );
         Authentication auth = new UsernamePasswordAuthenticationToken( principle, null, principle.getAuthorities() );
         SecurityContextHolder.getContext().setAuthentication( auth );

src/main/java/ubc/pavlab/rdp/controllers/SearchViewController.java

@@ -264,8 +264,8 @@ public ModelAndView searchUsersByGeneView( @RequestParam String symbol,
     @GetMapping(value = "/search/view/orthologs")
     public ModelAndView searchOrthologsForGene( @RequestParam String symbol,
                                                 @RequestParam Integer taxonId,
-                                                @RequestParam(required = false) Set<TierType> tiers,
-                                                @RequestParam(required = false) Integer orthologTaxonId,
+                                                @RequestParam(required = false) @Nullable Set<TierType> tiers,
+                                                @RequestParam(required = false) @Nullable Integer orthologTaxonId,
                                                 Locale locale ) {
         // Only look for orthologs when taxon is human
         if ( taxonId != 9606 ) {
@@ -324,7 +324,7 @@ public ModelAndView searchOrthologsForGene( @RequestParam String symbol,
      */
     @PreAuthorize("hasPermission(null, 'international-search')")
     @GetMapping("/search/view/international/available-terms-by-partner")
-    public ModelAndView getAvailableTermsByPartner( @RequestParam(required = false) List<Integer> ontologyTermIds ) {
+    public ModelAndView getAvailableTermsByPartner( @RequestParam(required = false) @Nullable List<Integer> ontologyTermIds ) {
         if ( ontologyTermIds == null || ontologyTermIds.isEmpty() ) {
             return new ModelAndView( "fragments/error::message", HttpStatus.BAD_REQUEST )
                     .addObject( "errorMessage", "There must be at least one specified ontology term ID via 'ontologyTermIds'." );