From dbc47abe40ed576a30791e963e73a15b7ace9545 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 9 Jan 2023 09:32:20 -0800 Subject: [PATCH 01/20] Restrict manual tiers to tiers enabled in the settings --- .../ubc/pavlab/rdp/controllers/UserController.java | 8 ++++++-- .../ubc/pavlab/rdp/services/UserGeneServiceImpl.java | 8 ++++++-- .../java/ubc/pavlab/rdp/services/UserServiceImpl.java | 10 +++++++--- 3 files changed, 19 insertions(+), 7 deletions(-) diff --git a/src/main/java/ubc/pavlab/rdp/controllers/UserController.java b/src/main/java/ubc/pavlab/rdp/controllers/UserController.java index f6b42547..77cb787b 100644 --- a/src/main/java/ubc/pavlab/rdp/controllers/UserController.java +++ b/src/main/java/ubc/pavlab/rdp/controllers/UserController.java @@ -83,7 +83,7 @@ public ModelAndView model( @PathVariable Integer taxonId ) { } else { modelAndView.addObject( "viewOnly", null ); modelAndView.addObject( "user", user ); - modelAndView.addObject( "userGenes", user.getGenesByTaxonAndTier( taxon, TierType.MANUAL ) ); + modelAndView.addObject( "userGenes", user.getGenesByTaxonAndTier( taxon, getManualTiers() ) ); modelAndView.addObject( "taxon", taxon ); } return modelAndView; @@ -106,7 +106,7 @@ public ModelAndView getTermsGenesForTaxon( @PathVariable Integer taxonId, @PathV if ( term != null ) { Collection geneIds = goService.getGenesInTaxon( term, taxon ); modelAndView.addObject( "genes", - user.getGenesByTaxonAndTier( taxon, TierType.MANUAL ).stream() + user.getGenesByTaxonAndTier( taxon, getManualTiers() ).stream() .filter( ug -> geneIds.contains( ug.getGeneId() ) ) .collect( Collectors.toSet() ) ); } else { @@ -511,4 +511,8 @@ public Object getRecommendedTermsForTaxon( @PathVariable Integer taxonId, return userService.recommendTerms( userService.findCurrentUser(), genes, taxon ); } + + private Set getManualTiers() { + return applicationSettings.getEnabledTiers().stream().filter( TierType.MANUAL::contains ).collect( Collectors.toSet() ); + } } diff --git a/src/main/java/ubc/pavlab/rdp/services/UserGeneServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/UserGeneServiceImpl.java index 12b4301a..ae9e4229 100644 --- a/src/main/java/ubc/pavlab/rdp/services/UserGeneServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/UserGeneServiceImpl.java @@ -85,13 +85,13 @@ public Page findByUserEnabledTrueAndPrivacyLevelNoAuth( PrivacyLevelTy @Cacheable(cacheNames = "ubc.pavlab.rdp.stats", key = "#root.methodName") @Override public long countUniqueAssociations() { - return userGeneRepository.countDistinctGeneByUserEnabledTrueAndTierIn( TierType.MANUAL ); + return userGeneRepository.countDistinctGeneByUserEnabledTrueAndTierIn( getManualTiers() ); } @Cacheable(cacheNames = "ubc.pavlab.rdp.stats", key = "#root.methodName") @Override public long countAssociations() { - return userGeneRepository.countByUserEnabledTrueAndTierIn( TierType.MANUAL ); + return userGeneRepository.countByUserEnabledTrueAndTierIn( getManualTiers() ); } @Cacheable(cacheNames = "ubc.pavlab.rdp.stats", key = "#root.methodName") @@ -221,4 +221,8 @@ public void updateUserGenes() { } log.info( "Done updating user genes." ); } + + private Set getManualTiers() { + return applicationSettings.getEnabledTiers().stream().filter( TierType.MANUAL::contains ).collect( Collectors.toSet() ); + } } diff --git a/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java index 30a19790..dbea04a6 100644 --- a/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java @@ -549,7 +549,7 @@ public Collection convertTerms( User user, Taxon taxon, Collection recommendTerms( @NonNull User user, @NonNull Taxon taxon ) { - return recommendTerms( user, user.getGenesByTaxonAndTier( taxon, TierType.MANUAL ), taxon, 10, applicationSettings.getGoTermSizeLimit(), 2 ); + return recommendTerms( user, user.getGenesByTaxonAndTier( taxon, getManualTiers() ), taxon, 10, applicationSettings.getGoTermSizeLimit(), 2 ); } @Override @@ -564,7 +564,7 @@ public Collection recommendTerms( User user, Set genes */ @PostFilter("hasPermission(filterObject, 'read')") Collection recommendTerms( @NonNull User user, @NonNull Taxon taxon, long minSize, long maxSize, long minFrequency ) { - return recommendTerms( user, user.getGenesByTaxonAndTier( taxon, TierType.MANUAL ), taxon, minSize, maxSize, minFrequency ); + return recommendTerms( user, user.getGenesByTaxonAndTier( taxon, getManualTiers() ), taxon, minSize, maxSize, minFrequency ); } private Collection recommendTerms( @NonNull User user, Set genes, @NonNull Taxon taxon, long minSize, long maxSize, long minFrequency ) { @@ -677,7 +677,7 @@ public long computeTermOverlaps( UserTerm userTerm, Collection genes ) @Override public long computeTermFrequencyInTaxon( User user, GeneOntologyTerm term, Taxon taxon ) { Set geneIds = new HashSet<>( goService.getGenes( goService.getTerm( term.getGoId() ) ) ); - return user.getGenesByTaxonAndTier( taxon, TierType.MANUAL ).stream() + return user.getGenesByTaxonAndTier( taxon, getManualTiers() ).stream() .map( UserGene::getGeneId ) .filter( geneIds::contains ) .count(); @@ -930,4 +930,8 @@ private String createSecureRandomToken() { secureRandom.nextBytes( tokenBytes ); return Base64.getEncoder().encodeToString( tokenBytes ); } + + private Set getManualTiers() { + return applicationSettings.getEnabledTiers().stream().filter( TierType.MANUAL::contains ).collect( Collectors.toSet() ); + } } From 229b400ab394e7ad3e65750677c8ffe0a67bbf24 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 9 Jan 2023 09:44:38 -0800 Subject: [PATCH 02/20] Update versions for hotfix --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index cff18b30..a63590e7 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ ubc.pavlab rdp - 1.5.4 + 1.5.5 Registry for model organism researchers, developed for the Canadian Rare Disease Models & Mechanisms Network. From 29a6105324558d9330f305f4d3f2cc8ab2fe6826 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 9 Jan 2023 09:32:20 -0800 Subject: [PATCH 03/20] Restrict manual tiers to tiers enabled in the settings --- src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java b/src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java index 56ea6d4f..1f011c44 100644 --- a/src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java +++ b/src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java @@ -164,6 +164,7 @@ public void setUp() { when( passwordResetTokenRepository.save( any( PasswordResetToken.class ) ) ).then( i -> i.getArgument( 0, PasswordResetToken.class ) ); when( tokenRepository.save( any( VerificationToken.class ) ) ).then( i -> i.getArgument( 0, VerificationToken.class ) ); + when( applicationSettings.getEnabledTiers() ).thenReturn( TierType.ANY ); when( applicationSettings.getGoTermSizeLimit() ).thenReturn( 100L ); when( applicationSettings.getOrgans() ).thenReturn( organSettings ); when( organSettings.isEnabled() ).thenReturn( true ); From 8c1071b8f167050683f4fe03d696cef63e48ac81 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 9 Jan 2023 10:25:20 -0800 Subject: [PATCH 04/20] Update frontend dependencies --- src/main/resources/package-lock.json | 1025 ++++++++++++++------------ src/main/resources/package.json | 10 +- 2 files changed, 555 insertions(+), 480 deletions(-) diff --git a/src/main/resources/package-lock.json b/src/main/resources/package-lock.json index a17d94bb..e4f80389 100644 --- a/src/main/resources/package-lock.json +++ b/src/main/resources/package-lock.json @@ -17,14 +17,14 @@ "popper.js": "~1.16.1" }, "devDependencies": { - 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"version": "4.0.0", - "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz", - "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==", + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", + "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", "dev": true }, "yaml": { diff --git a/src/main/resources/package.json b/src/main/resources/package.json index 086cf652..b54e138b 100644 --- a/src/main/resources/package.json +++ b/src/main/resources/package.json @@ -17,14 +17,14 @@ "popper.js": "~1.16.1" }, "devDependencies": { - "@babel/core": "^7.20.2", + "@babel/core": "^7.20.12", "@babel/preset-env": "^7.20.2", "babel-loader": "^8.3.0", - "css-loader": "^6.7.2", - "postcss": "^8.4.19", - "postcss-loader": "^7.0.1", + "css-loader": "^6.7.3", + "postcss": "^8.4.21", + "postcss-loader": "^7.0.2", "postcss-preset-env": "^7.8.3", - "sass": "^1.56.1", + "sass": "^1.57.1", "sass-loader": "^13.2.0", "source-map-loader": "^4.0.1", "style-loader": "^3.3.1", From 48d17b92a53100314fc3d591b4f55213cbe8e58c Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Mon, 9 Jan 2023 11:20:13 -0800 Subject: [PATCH 05/20] Update Maven wrapper distribution to 3.8.5 --- .mvn/wrapper/maven-wrapper.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.mvn/wrapper/maven-wrapper.properties b/.mvn/wrapper/maven-wrapper.properties index e83fa695..db95c131 100644 --- a/.mvn/wrapper/maven-wrapper.properties +++ b/.mvn/wrapper/maven-wrapper.properties @@ -14,5 +14,5 @@ # KIND, either express or implied. See the License for the # specific language governing permissions and limitations # under the License. -distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip +distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.8.5/apache-maven-3.8.5-bin.zip wrapperUrl=https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.0/maven-wrapper-3.1.0.jar From 700cc3fc1884e0ef12c208e9733c131652a08936 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 10 Jan 2023 10:44:00 -0800 Subject: [PATCH 06/20] Update Spring Boot to 2.6.14 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index a63590e7..78366584 100644 --- a/pom.xml +++ b/pom.xml @@ -28,7 +28,7 @@ org.springframework.boot spring-boot-starter-parent - 2.6.13 + 2.6.14 From 6207ce69c67f1e49a506721dae534250a412bb74 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 10 Jan 2023 11:43:20 -0800 Subject: [PATCH 07/20] Use Spring-managed AsyncTaskExecutt or for sending emails and importing Reactome --- src/main/java/ubc/pavlab/rdp/EmailConfig.java | 22 +++++++++++++++++++ .../java/ubc/pavlab/rdp/WebMvcConfig.java | 8 ++++++- .../rdp/controllers/AdminController.java | 16 +++++--------- .../pavlab/rdp/services/EmailServiceImpl.java | 7 +++++- .../rdp/controllers/AdminControllerTest.java | 8 ++++++- .../rdp/services/EmailServiceImplTest.java | 5 ++++- 6 files changed, 51 insertions(+), 15 deletions(-) create mode 100644 src/main/java/ubc/pavlab/rdp/EmailConfig.java diff --git a/src/main/java/ubc/pavlab/rdp/EmailConfig.java b/src/main/java/ubc/pavlab/rdp/EmailConfig.java new file mode 100644 index 00000000..4781c540 --- /dev/null +++ b/src/main/java/ubc/pavlab/rdp/EmailConfig.java @@ -0,0 +1,22 @@ +package ubc.pavlab.rdp; + +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; +import org.springframework.core.task.AsyncTaskExecutor; +import org.springframework.mail.javamail.JavaMailSender; +import org.springframework.mail.javamail.JavaMailSenderImpl; +import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor; + +@Configuration +public class EmailConfig { + + @Bean + public JavaMailSender emailSender() { + return new JavaMailSenderImpl(); + } + + @Bean + public AsyncTaskExecutor emailTaskExecutor() { + return new ThreadPoolTaskExecutor(); + } +} diff --git a/src/main/java/ubc/pavlab/rdp/WebMvcConfig.java b/src/main/java/ubc/pavlab/rdp/WebMvcConfig.java index 87b85dfa..d459bd09 100644 --- a/src/main/java/ubc/pavlab/rdp/WebMvcConfig.java +++ b/src/main/java/ubc/pavlab/rdp/WebMvcConfig.java @@ -7,6 +7,8 @@ import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.context.support.ReloadableResourceBundleMessageSource; +import org.springframework.core.task.AsyncTaskExecutor; +import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor; import org.springframework.security.crypto.bcrypt.BCryptPasswordEncoder; import org.springframework.web.servlet.config.annotation.CorsRegistry; import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; @@ -40,7 +42,6 @@ public HierarchicalMessageSource messageSourceWithoutOntology() { } @Bean - public MessageSource messageSource( @Qualifier("ontologyMessageSource") MessageSource ontologyMessageSource ) { HierarchicalMessageSource messageSource = messageSourceWithoutOntology(); // if it cannot be resolved in messages.properties, then lookup some of our built-in resolution for @@ -49,6 +50,11 @@ public MessageSource messageSource( @Qualifier("ontologyMessageSource") MessageS return messageSource; } + @Bean + public AsyncTaskExecutor adminTaskExecutor() { + return new ThreadPoolTaskExecutor(); + } + /** * CORS configuration for the /stats endpoint so that statistics can be queried from the main website. */ diff --git a/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java b/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java index 908e81da..7c75e380 100644 --- a/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java +++ b/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java @@ -7,9 +7,11 @@ import lombok.extern.apachecommons.CommonsLog; import org.apache.commons.io.FilenameUtils; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.context.MessageSource; import org.springframework.context.support.ReloadableResourceBundleMessageSource; import org.springframework.core.io.Resource; +import org.springframework.core.task.AsyncTaskExecutor; import org.springframework.dao.DataIntegrityViolationException; import org.springframework.data.domain.Pageable; import org.springframework.data.web.PageableDefault; @@ -57,8 +59,6 @@ import java.time.Duration; import java.time.Instant; import java.util.*; -import java.util.concurrent.ExecutorService; -import java.util.concurrent.Executors; import java.util.concurrent.atomic.AtomicBoolean; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -94,15 +94,9 @@ public class AdminController { * Task executor used for background tasks. * TODO: make this a configurable bean */ - private final ExecutorService taskExecutor = Executors.newSingleThreadExecutor(); - - /** - * This is only meant for testing, please don't use. - */ - @Secured(value = {}) - ExecutorService getTaskExecutor() { - return taskExecutor; - } + @Autowired + @Qualifier("adminTaskExecutor") + private AsyncTaskExecutor taskExecutor; /** * List all users diff --git a/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java index d353f2ce..13776495 100644 --- a/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java +++ b/src/main/java/ubc/pavlab/rdp/services/EmailServiceImpl.java @@ -2,7 +2,10 @@ import lombok.extern.apachecommons.CommonsLog; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.context.MessageSource; +import org.springframework.core.task.AsyncTaskExecutor; +import org.springframework.core.task.TaskExecutor; import org.springframework.mail.SimpleMailMessage; import org.springframework.mail.javamail.JavaMailSender; import org.springframework.mail.javamail.MimeMessageHelper; @@ -46,7 +49,9 @@ public class EmailServiceImpl implements EmailService { @Autowired private MessageSource messageSource; - private final ExecutorService executorService = Executors.newSingleThreadExecutor(); + @Autowired + @Qualifier("emailTaskExecutor") + private AsyncTaskExecutor executorService; private Future sendSimpleMessage( String subject, String content, InternetAddress to, InternetAddress replyTo, InternetAddress cc ) throws AddressException { SimpleMailMessage email = new SimpleMailMessage(); diff --git a/src/test/java/ubc/pavlab/rdp/controllers/AdminControllerTest.java b/src/test/java/ubc/pavlab/rdp/controllers/AdminControllerTest.java index 651d136f..bca4cea6 100644 --- a/src/test/java/ubc/pavlab/rdp/controllers/AdminControllerTest.java +++ b/src/test/java/ubc/pavlab/rdp/controllers/AdminControllerTest.java @@ -5,6 +5,7 @@ import org.mockito.ArgumentCaptor; import org.mockito.internal.verification.VerificationModeFactory; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; import org.springframework.boot.test.mock.mockito.MockBean; import org.springframework.context.MessageSource; @@ -12,6 +13,7 @@ import org.springframework.core.convert.converter.Converter; import org.springframework.core.io.ClassPathResource; import org.springframework.core.io.ResourceLoader; +import org.springframework.core.task.AsyncTaskExecutor; import org.springframework.dao.DataIntegrityViolationException; import org.springframework.data.domain.PageImpl; import org.springframework.data.domain.PageRequest; @@ -111,6 +113,10 @@ public class AdminControllerTest { @Autowired private ResourceLoader resourceLoader; + @Autowired + @Qualifier("adminTaskExecutor") + private AsyncTaskExecutor adminTaskExecutor; + private class UserIdToUserConverter implements Converter { @Override @@ -809,7 +815,7 @@ public void importReactomePathways() throws Exception { verify( reactomeService ).importPathwaysOntology(); // the admin controller uses a single-threaded task executor, so if we queue and wait for a task to finish, it // will guarantee that the pathways summations update has been invoked - Future dummyTask = adminController.getTaskExecutor().submit( () -> { + Future dummyTask = adminTaskExecutor.submit( () -> { } ); assertThat( dummyTask ).succeedsWithin( 1, TimeUnit.SECONDS ); verify( reactomeService ).updatePathwaySummations( null ); diff --git a/src/test/java/ubc/pavlab/rdp/services/EmailServiceImplTest.java b/src/test/java/ubc/pavlab/rdp/services/EmailServiceImplTest.java index 9639ccf3..e4ab424c 100644 --- a/src/test/java/ubc/pavlab/rdp/services/EmailServiceImplTest.java +++ b/src/test/java/ubc/pavlab/rdp/services/EmailServiceImplTest.java @@ -10,9 +10,12 @@ import org.springframework.context.MessageSource; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Import; +import org.springframework.core.task.AsyncTaskExecutor; +import org.springframework.core.task.SimpleAsyncTaskExecutor; import org.springframework.mail.SimpleMailMessage; import org.springframework.mail.javamail.JavaMailSender; import org.springframework.test.context.junit4.SpringRunner; +import ubc.pavlab.rdp.EmailConfig; import ubc.pavlab.rdp.WebMvcConfig; import ubc.pavlab.rdp.model.PasswordResetToken; import ubc.pavlab.rdp.model.User; @@ -35,7 +38,7 @@ import static ubc.pavlab.rdp.util.TestUtils.*; @RunWith(SpringRunner.class) -@Import(WebMvcConfig.class) +@Import({ WebMvcConfig.class, EmailConfig.class }) public class EmailServiceImplTest { @TestConfiguration From a8e91b5eefcd7abd181d9a633dea79ce782a0532 Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 10 Jan 2023 11:44:04 -0800 Subject: [PATCH 08/20] Upate dependencies --- pom.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index 78366584..9a2a973b 100644 --- a/pom.xml +++ b/pom.xml @@ -113,7 +113,7 @@ org.springdoc springdoc-openapi-webmvc-core - 1.6.12 + 1.6.14 @@ -191,7 +191,7 @@ org.json json - 20220320 + 20220924 test @@ -268,7 +268,7 @@ com.amashchenko.maven.plugin gitflow-maven-plugin - 1.16.0 + 1.19.0 false From c424d230dfd010a7a4b8d2a4825713cbf8f90d7b Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 10 Jan 2023 12:48:29 -0800 Subject: [PATCH 09/20] Make forms model public --- .../rdp/controllers/AdminController.java | 22 +++++++++---------- .../rdp/controllers/SearchController.java | 2 +- .../rdp/controllers/UserController.java | 2 +- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java b/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java index 7c75e380..e311bd4b 100644 --- a/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java +++ b/src/main/java/ubc/pavlab/rdp/controllers/AdminController.java @@ -204,7 +204,7 @@ public Object revokeAccessTn( @PathVariable(required = false) User user, @PathVa } @Data - private static class ConfirmEmailForm { + public static class ConfirmEmailForm { private String email; } @@ -273,7 +273,7 @@ public ModelAndView getOntology( @PathVariable(required = false) Ontology ontolo } @Data - private static class UpdateOntologyForm { + public static class UpdateOntologyForm { public static UpdateOntologyForm fromOntology( Ontology ontology ) { UpdateOntologyForm form = new UpdateOntologyForm(); form.setName( ontology.getName() ); @@ -365,7 +365,7 @@ public Object deleteOntology( @PathVariable(required = false) Ontology ontology, } @Data - private static class DeleteOntologyForm { + public static class DeleteOntologyForm { @NotNull private String ontologyNameConfirmation; } @@ -414,7 +414,7 @@ public Object updateSimpleOntology( @PathVariable(required = false) Ontology ont } @Data - private static class SimpleOntologyForm { + public static class SimpleOntologyForm { public static final int DEFAULT_INITIAL_EMPTY_ROWS = 5; @@ -792,18 +792,18 @@ private static class ReactomePathwaySummationsUpdateProgress { } @Data - private static class ActivateOrDeactivateOntologyForm { + public static class ActivateOrDeactivateOntologyForm { private boolean includeTerms; } @Data @EqualsAndHashCode(callSuper = true) - private static class ActivateOntologyForm extends ActivateOrDeactivateOntologyForm { + public static class ActivateOntologyForm extends ActivateOrDeactivateOntologyForm { } @Data @EqualsAndHashCode(callSuper = true) - private static class DeactivateOntologyForm extends ActivateOrDeactivateOntologyForm { + public static class DeactivateOntologyForm extends ActivateOrDeactivateOntologyForm { } @PostMapping("/admin/ontologies/{ontology}/activate") @@ -831,7 +831,7 @@ public Object deactivateOntology( @PathVariable(required = false) Ontology ontol } @Data - private static class ActivateOrDeactivateTermForm { + public static class ActivateOrDeactivateTermForm { @NotEmpty private String ontologyTermInfoId; /** @@ -842,7 +842,7 @@ private static class ActivateOrDeactivateTermForm { @Data @EqualsAndHashCode(callSuper = true) - private static class ActivateTermForm extends ActivateOrDeactivateTermForm { + public static class ActivateTermForm extends ActivateOrDeactivateTermForm { /** * Include the ontology in the activation. */ @@ -851,7 +851,7 @@ private static class ActivateTermForm extends ActivateOrDeactivateTermForm { @Data @EqualsAndHashCode(callSuper = true) - private static class DeactivateTermForm extends ActivateOrDeactivateTermForm { + public static class DeactivateTermForm extends ActivateOrDeactivateTermForm { } @PostMapping("/admin/ontologies/{ontology}/activate-term") @@ -1002,7 +1002,7 @@ public Object move( @PathVariable(required = false) Ontology ontology, @RequestP } @Data - private static class ImportOntologyForm { + public static class ImportOntologyForm { private URL ontologyUrl; private MultipartFile ontologyFile; diff --git a/src/main/java/ubc/pavlab/rdp/controllers/SearchController.java b/src/main/java/ubc/pavlab/rdp/controllers/SearchController.java index 8d0b078d..7046518c 100644 --- a/src/main/java/ubc/pavlab/rdp/controllers/SearchController.java +++ b/src/main/java/ubc/pavlab/rdp/controllers/SearchController.java @@ -363,7 +363,7 @@ public String viewUser( @PathVariable Integer userId, } @Data - private static class RequestAccessForm { + public static class RequestAccessForm { @NotNull(message = "Reason cannot be blank.") @Size(min = 1, message = "Reason cannot be blank.") private String reason; diff --git a/src/main/java/ubc/pavlab/rdp/controllers/UserController.java b/src/main/java/ubc/pavlab/rdp/controllers/UserController.java index 77cb787b..57bd4f87 100644 --- a/src/main/java/ubc/pavlab/rdp/controllers/UserController.java +++ b/src/main/java/ubc/pavlab/rdp/controllers/UserController.java @@ -157,7 +157,7 @@ public ModelAndView support( SupportForm supportForm ) { } @Data - private static class SupportForm { + public static class SupportForm { @NotNull(message = "You must provide your name.") @Size(min = 1, message = "You must provide your name.") private String name; From 2b3d25c7f0d5c90970d7bd4f41383accf6b4641c Mon Sep 17 00:00:00 2001 From: Guillaume Poirier-Morency Date: Tue, 10 Jan 2023 12:05:40 -0800 Subject: [PATCH 10/20] Use more generic Model System term for Model Organism --- README.md | 2 +- docs/customization.md | 4 +- docs/deployment.md | 2 +- docs/index.md | 2 +- pom.xml | 2 +- src/main/resources/faq.properties | 56 +++++++++---------- src/main/resources/messages.properties | 14 ++--- .../resources/templates/fragments/stats.html | 2 +- .../templates/fragments/user-table.html | 2 +- .../resources/templates/layouts/common.html | 2 +- src/main/resources/templates/search.html | 8 +-- .../templates/user/documentation.html | 41 +++++++------- src/main/resources/templates/user/model.html | 10 ++-- .../resources/templates/user/profile.html | 6 +- 14 files changed, 77 insertions(+), 76 deletions(-) diff --git a/README.md b/README.md index 48c4d130..68618fa0 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # Rare Disease Project -Registry for model organism researchers, developed for the Canadian Rare +Registry for model organism/system researchers, developed for the Canadian Rare Disease Models & Mechanisms Network diff --git a/docs/customization.md b/docs/customization.md index 3af0c2de..70006baf 100644 --- a/docs/customization.md +++ b/docs/customization.md @@ -65,7 +65,7 @@ set active = 1 where taxon_id = 10090; ``` -Every time the new model organisms are added to the application, they will have to be activated in this manner. +Every time new model systems are added to the application, they will have to be activated in this manner. ## Ortholog mapping @@ -578,8 +578,6 @@ Here's the list of paths that can be adjusted using the above setting: ``` static/ images/ - model-organisms/ - .svg organs/ .svg researcher-categories/ diff --git a/docs/deployment.md b/docs/deployment.md index 34a6c7f3..e935e8cb 100644 --- a/docs/deployment.md +++ b/docs/deployment.md @@ -37,7 +37,7 @@ Likewise, you can set up a proxy for FTP connections with `-Dftp.proxyHost` and 4. Create `application.properties`, and optionally `faq.properties` and `messages.properties` if you want to [customize messages](customization.md#customizing-the-applications-messages). 5. Test your setup: `java -jar rdp-{{ config.extra.rdp_version }}.jar` -6. Log into the database and activate other organisms and organ systems (optional) +6. Log into the database and activate other model and organ systems (optional) 7. Deploy using [systemd](#integration-with-systemd) or a Docker container ## Integration with systemd diff --git a/docs/index.md b/docs/index.md index 569c3d57..74f82837 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,4 @@ # Rare Disease Project -Registry for model organism researchers, developed for the Canadian Rare Disease Models & Mechanisms Network +Registry for model organism/system researchers, developed for the Canadian Rare Disease Models & Mechanisms Network diff --git a/pom.xml b/pom.xml index 9a2a973b..7dbf9146 100644 --- a/pom.xml +++ b/pom.xml @@ -8,7 +8,7 @@ 1.5.5 - Registry for model organism researchers, developed for the Canadian Rare Disease Models & Mechanisms Network. + Registry for model organism/system researchers, developed for the Canadian Rare Disease Models & Mechanisms Network. diff --git a/src/main/resources/faq.properties b/src/main/resources/faq.properties index 494ea473..b2cdceb2 100644 --- a/src/main/resources/faq.properties +++ b/src/main/resources/faq.properties @@ -5,7 +5,7 @@ # Identify which entries appear in which order in the FAQ # If unset, the default is to arrange entries by alphabetic order of the key -rdp.faq.keys=what,purpose,who,privacy,privacy-settings,isearch,whatnow,process,organisms,genes,more,human,missing,ortholog,genome +rdp.faq.keys=what,purpose,who,privacy,privacy-settings,isearch,whatnow,process,systems,genes,more,human,missing,ortholog,genome rdp.faq.questions.what=What is the registry? rdp.faq.questions.purpose=What is the purpose of the registry? @@ -15,16 +15,16 @@ rdp.faq.questions.privacy-settings=What Data Privacy Settings should I choose? rdp.faq.questions.isearch=What does it mean to share data with partner registries? rdp.faq.questions.whatnow=What happens after I fill in my information? rdp.faq.questions.process=What is the process for making a catalyst grant award? -rdp.faq.questions.organisms=What model organisms are directly supported within the registry? +rdp.faq.questions.systems=What model systems are directly supported within the registry? rdp.faq.questions.genes=Which genes should I enter into the registry? -rdp.faq.questions.more=What if I study more than one model organism? +rdp.faq.questions.more=What if I study more than one model system? rdp.faq.questions.human=Are humans a "model" for the purposes of the registry? -rdp.faq.questions.missing=What if the organism I study is not listed? +rdp.faq.questions.missing=What if the system I study is not listed? rdp.faq.questions.ortholog=Should I fill in the human orthologs of genes I study? rdp.faq.questions.genome=I study the entire genome, or have the ability to assay the function of any gene. How do I select which genes I should list? rdp.faq.answers.what=The {0} registry is an online \ -registration tool and a database of Canadian model organism \ +registration tool and a database of Canadian model system \ researchers and the specific genes they study. The Scientific \ Advisory Committee uses the {0} registry to determine which \ scientists are doing work relevant to a newly identified human \ @@ -32,14 +32,14 @@ disease gene. Registrants who meet the criteria for a given \ gene will be invited to apply for a Catalyst Grant. rdp.faq.answers.purpose=The purpose of the {0} registry \ -is to collect information about model organism researchers, \ +is to collect information about model system researchers, \ focusing on genes they are studying. The registry is used by \ the Scientific Advisory Committee and the Bioinformatics Core \ to look for orthologs of a newly identified human disease \ -gene. Model organism researchers studying the identified genes \ +gene. Model system researchers studying the identified genes \ may be invited to apply for a Catalyst Grant. -rdp.faq.answers.who=All model organism researchers eligible for CIHR funds should register if they want to be \ +rdp.faq.answers.who=All model system researchers eligible for CIHR funds should register if they want to be \ considered for a Network Catalyst Grant. \ (Read more here) @@ -64,7 +64,7 @@ We have shared the registry software with these partner networks and implemented

\ Partner registry sharing section on your Profile page gives you the option to set your preference for sharing your data with the {0} Network's \ partner registries for the purposes of establishing connections between clinician sciences who are submitting their rare \ - disease genes to partner registries and Canadian model organism researchers. \ + disease genes to partner registries and Canadian model system researchers. \ The shared data will only be visible to the administrators of the partner registries. \ If your data privacy level is set to "public", partner registries will gain access automatically.

@@ -79,30 +79,30 @@ your information. rdp.faq.answers.process=Briefly, the Scientific Advisory \ Committee (SAC) will attempt to match a new disease gene to as \ -many model organism researchers as possible, based on the \ -genes that model organism researchers have self-declared. The \ -SAC will then invite the model organism researcher to submit a \ +many model system researchers as possible, based on the \ +genes that model system researchers have self-declared. The \ +SAC will then invite the model system researcher to submit a \ 2-page application (receipt deadline within a week or two). \ The SAC will review the applications (within a week), and for \ those accepted, will invite the clinician scientist to \ -establish a connection with the corresponding model organism \ +establish a connection with the corresponding model system \ researcher. Following a successful connection, the model \ -organism lab will be connected to the clinician scientist and \ +system lab will be connected to the clinician scientist and \ receive $25,000 to seed immediate collaborative experiments. -rdp.faq.answers.organisms=The model organisms that are \ +rdp.faq.answers.systems=The model systems that are \ supported within the registry (by maintaining their most \ current gene annotation) are human (Homo sapiens), mouse (Mus musculus), \ rat (Rattus norvegicus), zebrafish (Danio rerio), frog (Xenopus tropicalis), \ roundworm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), \ budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and E. coli. \ -We indirectly support other organisms through Human/Other option, see \ -What if the organism I study is not listed?. +We indirectly support other systems through Human/Other option, see \ +What if the system I study is not listed?. rdp.faq.answers.genes=

Key to the success of the Network is our ability to \ -match human disease genes to model organism researchers who \ +match human disease genes to model system researchers who \ can study those genes. We recognize that for any given human \ -gene, there is a limited chance that a model organism \ +gene, there is a limited chance that a model system \ researcher in Canada is actively studying that specific gene. \ Therefore we need to be able to cast a wider net. On the \ other hand, we must strike a balance between restricting the \ @@ -111,7 +111,7 @@ gene.

\

To reach this balance, genes are divided into Tiers:

\
    \
  • Tier 1 or Primary genes are those you \ -currently work on in a model organism. You must be able to \ +currently work on in a model system. You must be able to \ immediately, specifically and rapidly study them in your \ laboratory. Genes you have recently published on are \ especially good Primary genes. We expect this to typically \ @@ -147,7 +147,7 @@ Catalyst Grant, you will have to provide evidence of your \ readiness to study that gene. Keep that in mind as you select \ your genes. -rdp.faq.answers.more=In the registry you can enter information for each model organism separately. +rdp.faq.answers.more=In the registry you can enter information for each model system separately. rdp.faq.answers.human=Yes, if you have an appropriate \ @@ -157,25 +157,25 @@ disease genes. This might include biochemical assays or assays \ based on cell lines. New research on human subjects is not \ considered to be within the scope of {0} Catalyst Grant projects. \ Do not register human genes merely because they are orthologs \ -of the genes you study in one of the supported model organism.\ -For organisms that are not currently supported in the registry see What if the organism I study is not listed?. +of the genes you study in one of the supported model system.\ +For systems that are not currently supported in the registry see What if the system I study is not listed?. rdp.faq.answers.missing=The registry was constructed \ assuming that the vast majority of registrants work on one or \ -more of the most popular model organisms, but we recognize \ -this does not cover all researchers. If your organism is not \ +more of the most popular model systems, but we recognize \ +this does not cover all researchers. If your system is not \ listed, we recommend that you select Human/Other option in the Model \ Organism drop-down menu, enter the human orthologs \ of your genes of interest, and indicate clearly in \ -your "Research Focus" section what is the model organisam you actually work with. \ +your "Research Focus" section what is the model system you actually work with. \ Remember that the match will always be to a human gene, \ so as long as we can identify you through a search of the \ registry via an ortholog, you will be considered as a \ potential Catalyst Grant applicant. -rdp.faq.answers.ortholog=Generally, no. Only register genes from the model organisms you currently work on. \ +rdp.faq.answers.ortholog=Generally, no. Only register genes from the model systems you currently work on. \ You should register human genes if you either work on them or you are registering human orthologs of genes \ -from an organisam that is not supported by the registry. See also What if the organism I study is not listed? \ +from an organisam that is not supported by the registry. See also What if the system I study is not listed? \ and Which genes should I enter into the \ registry? and Are humans a "model". diff --git a/src/main/resources/messages.properties b/src/main/resources/messages.properties index 11984fe4..7dfea2e4 100644 --- a/src/main/resources/messages.properties +++ b/src/main/resources/messages.properties @@ -112,7 +112,7 @@ rdp.site.anonymized-user-name={0} User # {0} contains the site URL # {1} contains the site full name -rdp.site.email.registration-welcome=Thank you for registering for the {1} as a model organism researcher. ({0}). +rdp.site.email.registration-welcome=Thank you for registering for the {1} as a model organism/system researcher. ({0}). # {0} contains the contact email rdp.site.email.registration-ending=You will then be able to log in using the password you provided, and start filling in your profile.\r\n\r\n\ @@ -167,9 +167,9 @@ rdp.site.logohtml=
    \ # {0} contains the site shortname rdp.site.welcome-public=The {0} registry \ -collects information on model organism researchers and the specific \ +collects information on model organism/system researchers and the specific \ genes they study. The registry is the mechanism by which the {0} will \ -find potential matches of model organism researchers to human rare \ +find potential matches of model organism/system researchers to human rare \ disease researchers. Registered users have the option to share their \ data publicly and these data are accessible through the search interface \ below. @@ -179,13 +179,13 @@ below. # {2} contains the FAQ URL # {3} contains the documentation URL # {4} contains the contact us URL -rdp.site.welcome=

    The {0} registry collects information on model organism researchers and the specific genes they \ -study. The registry is the mechanism by which the {0} will find potential matches of model organism researchers to human \ +rdp.site.welcome=

    The {0} registry collects information on model organism/system researchers and the specific genes they \ +study. The registry is the mechanism by which the {0} will find potential matches of model organism/system researchers to human \ rare disease researchers.

    \

    The Registry collects two types of information. First, you will enter your basic contact information and some general \ information about your research (under "Profile"). Second, you will enter information about genes you \ -study, for one or more Model Organisms. Obtaining a correct and comprehensive list of genes is of key interest. \ -In order to assist registrants in this regard we devised a three-tier gene model described. Please read carefully \ +study, for one or more Model System. Obtaining a correct and comprehensive list of genes is of key interest. \ +In order to assist registrants in this regard we devised a three-tier gene model. Please read carefully \ before you start adding genes to your profile.

    \

    The default data privacy setting in the registry is "private" and, unless different data sharing preference is selected \ (under Profile), the information you enter is confidential and will only be \ diff --git a/src/main/resources/templates/fragments/stats.html b/src/main/resources/templates/fragments/stats.html index 301903c9..a2f2add8 100644 --- a/src/main/resources/templates/fragments/stats.html +++ b/src/main/resources/templates/fragments/stats.html @@ -4,7 +4,7 @@

    •  genes researched by
      • -
    •  researchers on following organisms:
      • +
    •  researchers on following systems:
      • ( researchers)
        • diff --git a/src/main/resources/templates/fragments/user-table.html b/src/main/resources/templates/fragments/user-table.html index cc3111d5..d4b8fa8c 100644 --- a/src/main/resources/templates/fragments/user-table.html +++ b/src/main/resources/templates/fragments/user-table.html @@ -73,7 +73,7 @@ title="Tier indicates the degree of involvement of a researcher with a gene."> Tier - Organism + Systems diff --git a/src/main/resources/templates/layouts/common.html b/src/main/resources/templates/layouts/common.html index 3f8f96f1..0823c1fc 100644 --- a/src/main/resources/templates/layouts/common.html +++ b/src/main/resources/templates/layouts/common.html @@ -45,7 +45,7 @@ + data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Model Systems
        diff --git a/src/main/resources/templates/search.html b/src/main/resources/templates/search.html index 3e0f7abd..fe4b2b4c 100644 --- a/src/main/resources/templates/search.html +++ b/src/main/resources/templates/search.html @@ -48,9 +48,9 @@
        - +
        @@ -124,7 +124,7 @@
        diff --git a/src/main/resources/templates/user/documentation.html b/src/main/resources/templates/user/documentation.html index 120eacb4..70e53adb 100644 --- a/src/main/resources/templates/user/documentation.html +++ b/src/main/resources/templates/user/documentation.html @@ -24,7 +24,7 @@
      • Model Organisms + aria-selected="true">Model Systems
      • Privacy Settings for sharing your data with the network’s partner registries for the purposes of establishing connections between clinician sciences who are submitting their rare disease genes to partner registries and Canadian - model organism researchers. The data shared with partner registries will + model organism/system researchers. The data shared with partner registries will only be visible to the administrators of those registries. If your data privacy level is set to "public", partner registries will gain access automatically. @@ -217,7 +217,7 @@
        • @@ -226,8 +226,8 @@
        data-parent="#model-accordion">

        - After selecting a model organism in the drop-down menu, you can optionally - enter a description of your research on this organism (Organism Research + After selecting a model system in the drop-down menu, you can optionally + enter a description of your research on this system (System Research Focus), if you feel it is different from the description you may have provided in your Profile (About My Research). @@ -266,7 +266,7 @@

        • Primary genes (Tier 1) are those you currently work on in a model - organism. You must be able to immediately, specifically and rapidly + system. You must be able to immediately, specifically and rapidly study them in your laboratory. Genes you have recently published on are especially good Primary genes. We expect this to typically be between 1-10 genes. @@ -364,11 +364,12 @@
          rel="noopener">geneontology.org.

          -

          To enter GO terms for an organism, click on the "Terms" tab on the Model - Organism Manager page. From here you can let us suggest some terms based on - the genes - you already entered by clicking on the "Recommend Terms" button or - input terms manually using the input box below the table.

          +

          + To enter GO terms for an system, click on the "Terms" tab on the Model + System Manager page. From here you can let us suggest some terms based on + the genes you already entered by clicking on the "Recommend Terms" button or + input terms manually using the input box below the table. +

          Note: You need to have at least two genes in order for us to @@ -395,7 +396,7 @@

        • Term Size, which indicates how many genes in the currently chosen model - organism are annotated with that term and will be added as Tier 3 genes + system are annotated with that term and will be added as Tier 3 genes if the term is selected (excluding the genes that are already added as Tier 1 or 2)
          • @@ -505,21 +506,21 @@
          Searches on the "Gene" tab

          The Gene tab allows you to search for registered users based on genes they study. Gene symbols are - organism-specific and will be matched against the list of known gene - symbols for the selected organism (selection made in a dropdown menu). + system-specific and will be matched against the list of known gene + symbols for the selected system (selection made in a dropdown menu). If you want to search for a match using a human gene, but consider - orthologs in other model organisms, you would use the secondary - dropdown menu to indicate the preferred organism. + orthologs in other model systems, you would use the secondary + dropdown menu to indicate the preferred system.

          The "Gene" tab allows you to search for registered users based on genes - they study. Gene symbols are organism-specific and will be matched - against the list of known gene symbols for the selected organism + they study. Gene symbols are system-specific and will be matched + against the list of known gene symbols for the selected system (selection made in a dropdown menu). If you want to search for a match - using a human gene, but consider orthologs in other model organisms, you + using a human gene, but consider orthologs in other model systems, you would use the secondary dropdown menu to indicate the preferred - organism. + system.

          You can filter the results of your search using any of the categories diff --git a/src/main/resources/templates/user/model.html b/src/main/resources/templates/user/model.html index a6858af8..ad4f6973 100644 --- a/src/main/resources/templates/user/model.html +++ b/src/main/resources/templates/user/model.html @@ -13,7 +13,7 @@

          -
          +
          ...
          @@ -29,13 +29,15 @@
          diff --git a/src/main/resources/templates/user/profile.html b/src/main/resources/templates/user/profile.html index 375d5dec..4396e7bf 100644 --- a/src/main/resources/templates/user/profile.html +++ b/src/main/resources/templates/user/profile.html @@ -46,7 +46,7 @@

          There are no genes associated with your profile. Get started by choosing a - Model Organism + Model System

          @@ -295,7 +295,7 @@

          Genes

          To add genes to your profile, start by choosing a - Model Organism + Model System
          @@ -453,7 +453,7 @@
          Content displayed on my profile
          -
          +