Merge tag 'v1.5.10' into development

Tag hotfix

pom.xml

@@ -140,13 +140,13 @@
  <dependency>
  <groupId>commons-io</groupId>
  <artifactId>commons-io</artifactId>
- <version>2.16.1</version>
+ <version>2.17.0</version>
  </dependency>
 
  <dependency>
  <groupId>org.apache.commons</groupId>
  <artifactId>commons-csv</artifactId>
- <version>1.11.0</version>
+ <version>1.12.0</version>
  </dependency>
 
  <dependency>
@@ -159,7 +159,7 @@
  <dependency>
  <groupId>nl.basjes.parse.useragent</groupId>
  <artifactId>yauaa</artifactId>
- <version>7.26.1</version>
+ <version>7.28.1</version>
  </dependency>
 
  <!-- Testing Support -->
@@ -229,7 +229,7 @@
  <plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-enforcer-plugin</artifactId>
- <version>1.4.1</version>
+ <version>3.5.0</version>
  <executions>
  <execution>
  <id>enforce-maven</id>
@@ -239,7 +239,7 @@
  <configuration>
  <rules>
  <requireMavenVersion>
- <version>[3.0.5,)</version>
+ <version>[3.6.3,)</version>
  </requireMavenVersion>
  </rules>
  </configuration>
@@ -249,7 +249,7 @@
  <plugin>
  <groupId>org.codehaus.mojo</groupId>
  <artifactId>exec-maven-plugin</artifactId>
- <version>3.0.0</version>
+ <version>3.4.1</version>
  <executions>
  <execution>
  <id>npm-install-dependencies</id>
@@ -302,7 +302,7 @@
  <plugin>
  <groupId>com.amashchenko.maven.plugin</groupId>
  <artifactId>gitflow-maven-plugin</artifactId>
- <version>1.19.0</version>
+ <version>1.21.0</version>
  <configuration>
  <!-- Do not push to remote -->
  <pushRemote>false</pushRemote>
@@ -321,6 +321,15 @@
  </gitFlowConfig>
  </configuration>
  </plugin>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>versions-maven-plugin</artifactId>
+ <version>2.17.1</version>
+ <configuration>
+ <allowMajorUpdates>false</allowMajorUpdates>
+ <processDependencyManagement>false</processDependencyManagement>
+ </configuration>
+ </plugin>
  </plugins>
  </build>
 

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 ) {