Merge branch 'hotfix-1.5.4'

.gitattributes

@@ -19,3 +19,4 @@ src/test/resources/cache/reactome_stable_ids.txt filter=lfs diff=lfs merge=lfs -
 src/test/resources/cache/nbo-base.obo filter=lfs diff=lfs merge=lfs -text
 src/main/resources/cache/DIOPT_filtered_data_Sept2022.gz filter=lfs diff=lfs merge=lfs -text
 src/main/resources/cache/DIOPT_filtered_data_May2021.gz filter=lfs diff=lfs merge=lfs -text
+src/test/resources/cache/mondo2.obo filter=lfs diff=lfs merge=lfs -text

docker-compose.yml

@@ -1,11 +1,36 @@
+mysql56:
+  image: mysql:5.6
+  ports:
+    - "3306:3306"
+  environment:
+    - MYSQL_USER=springuser
+    - MYSQL_PASSWORD=ThePassword
+    - MYSQL_DATABASE=db_example
+    - MYSQL_RANDOM_ROOT_PASSWORD=true
+mysql57:
+  image: mysql:5.7
+  ports:
+    - "3306:3306"
+  environment:
+    - MYSQL_USER=springuser
+    - MYSQL_PASSWORD=ThePassword
+    - MYSQL_DATABASE=db_example
+    - MYSQL_RANDOM_ROOT_PASSWORD=true
 mysql:
-  image: mysql
+  image: mysql:8.0
   ports:
     - "3306:3306"
   environment:
     - MYSQL_USER=springuser
     - MYSQL_PASSWORD=ThePassword
     - MYSQL_DATABASE=db_example
     - MYSQL_RANDOM_ROOT_PASSWORD=true
-  volumes:
-    - "./conf.d:/etc/mysql/conf.d:ro"
+mariadb:
+  image: mariadb:10.6
+  ports:
+    - "3306:3306"
+  environment:
+    - MARIADB_USER=springuser
+    - MARIADB_PASSWORD=ThePassword
+    - MARIADB_DATABASE=db_example
+    - MARIADB_RANDOM_ROOT_PASSWORD=true

docs/customization.md

@@ -318,10 +318,10 @@ The content of `messages.properties` has precedence over the values stored in th
 categories and terms. This allows you to override values that are imported from an OBO source as you see fit.
 
 ```properties
-rdp.ontologies.{ontologyName}.title
-rdp.ontologies.{ontologyName}.definition
-rdp.ontologies.{ontologyName}.terms.{termName}.title
-rdp.ontologies.{ontologyName}.terms.{termName}.definition
+rdp.ontologies.{ontologyName}.title=
+rdp.ontologies.{ontologyName}.definition=
+rdp.ontologies.{ontologyName}.terms.{termName}.title=
+rdp.ontologies.{ontologyName}.terms.{termName}.definition=
 ```
 
 If your ontology/category is based on a [PURL](https://obofoundry.org/principles/fp-003-uris.html) source, its name will
@@ -520,13 +520,30 @@ In the file, each entry requires two parts: `rdp.faq.questions.<q_key>` and `rdp
 question and the corresponding answer, respectively.
 
 ```properties
+rdp.faq.keys=<q_key>
 rdp.faq.questions.<q_key>=A relevant question.
 rdp.faq.answers.<q_key>=A plausible answer.
 ```
 
-The provided default file can be found
-in [faq.properties](https://github.com/PavlidisLab/rdp/tree/{{ config.extra.git_ref
-}}/src/main/resources/faq.properties).
+The provided default file can be found in [faq.properties](https://github.com/PavlidisLab/rdp/tree/{{ config.extra.git_ref }}/src/main/resources/faq.properties).
+
+### Ordering FAQ entries
+
+!!! note
+
+    New in 1.5.4
+
+he `rdp.faq.keys` FAQ setting can be used to customize the ordering and appearance of FAQ entries. If the setting is
+left unset, the default will be to arrange FAQ questions in alphabetic order of their keys.
+
+### Translating FAQ entries
+
+!!! note
+
+    New in 1.5.4
+
+The FAQ messages can now be translated by reusing the `rdp.faq.questions.<q_key>` and `rdp.faq.answers.<q_key>` as codes
+for the `messages.properties` file.
 
 ## Terms of service and privacy policy
 

docs/installation.md

@@ -10,7 +10,7 @@ This section describes the essential steps to deploy an RDP registry.
 
 ## Obtain a distribution of RDP
 
-Download the [latest JAR distribution](https://github.com/PavlidisLab/rdp/releases/latest) from GitHub.
+Download the [JAR distribution from GitHub](https://github.com/PavlidisLab/rdp/releases/v{{ config.extra.rdp_version }}).
 
 ```bash
 wget https://github.com/PavlidisLab/rdp/releases/download/v{{ config.extra.rdp_version }}/rdp-{{ config.extra.rdp_version }}.jar
@@ -29,9 +29,21 @@ create user  '<database username>'@'%' identified by '<database password>';
 grant all on rdp.* to '<database username>'@'%';
 ```
 
-If you're using MySQL 5.6 or prior, use the `utf8` character set. It is a 3 bytes subset of the typical 4-bytes UTF-8
-character encoding. Otherwise, you will face issues with the index size limit of 767 bytes due to some of our indexed
-columns containing 255 characters (4 * 255 = 1020 > 767, but 3 * 255 = 765).
+If you're using MySQL 5.6 or prior, use the `utf8mb3` character set. It is a 3 bytes subset of the typical 4-bytes 
+UTF-8 character encoding. Otherwise, you will face issues with the index size limit of 767 bytes due to some of our
+indexed columns containing 255 characters (4 * 255 = 1020 > 767, but 3 * 255 = 765).
+
+You should also adjust Hibernate dialect by adding the following to your `application.properties`:
+
+```properties
+spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL55Dialect
+```
+
+Likewise, if you are using MariaDB, for which we recommend the current 10.6 LTS, use the following dialect:
+
+```properties
+spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MariaDB106Dialect
+```
 
 ## Setup application.properties
 

mkdocs.yml

@@ -14,5 +14,5 @@ plugins:
 markdown_extensions:
   - admonition
 extra:
-  rdp_version: 1.5.3
+  rdp_version: 1.5.4
   git_ref: master

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.5.3</version>
+    <version>1.5.4</version>
 
     <description>
         Registry for model organism researchers, developed for the Canadian Rare Disease Models &amp; Mechanisms Network.
@@ -28,7 +28,7 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.6.12</version>
+        <version>2.6.13</version>
     </parent>
 
     <dependencies>
@@ -113,7 +113,7 @@
         <dependency>
             <groupId>org.springdoc</groupId>
             <artifactId>springdoc-openapi-webmvc-core</artifactId>
-            <version>1.6.11</version>
+            <version>1.6.12</version>
         </dependency>
 
         <!-- Database Migration -->
@@ -198,7 +198,7 @@
 
     <properties>
         <java.version>1.8</java.version>
-        <flyway.version>7.15.0</flyway.version>
+        <flyway.version>5.2.4</flyway.version>
         <skipWebpack>false</skipWebpack>
     </properties>
 

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

@@ -1,12 +1,14 @@
 package ubc.pavlab.rdp;
 
+import org.springframework.context.annotation.Configuration;
 import org.springframework.data.jpa.repository.config.EnableJpaAuditing;
 
 /**
  * Configuration for auditing entities creation and modification with Spring Data JPA.
  *
  * @author poirigui
  */
+@Configuration
 @EnableJpaAuditing
 public class JpaAuditingConfig {
 }

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

@@ -6,10 +6,10 @@
 import org.springframework.boot.autoconfigure.flyway.FlywayMigrationStrategy;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.jdbc.core.ConnectionCallback;
+import org.springframework.jdbc.core.JdbcTemplate;
 
-import java.sql.Connection;
 import java.sql.ResultSet;
-import java.sql.SQLException;
 import java.util.Arrays;
 
 /**
@@ -21,26 +21,43 @@
 @CommonsLog
 public class MigrationConfig {
 
+    @RequiredArgsConstructor
+    private enum NewChecksumReason {
+        /**
+         * A migration applied with Flyway 3.
+         * <p>
+         * The checksum algorithm has changed.
+         */
+        FLYWAY_3( "has been performed with Flyway 3.2.1" ),
+        /**
+         * A migration that introduced a regression with MySQL 5.7.
+         */
+        MYSQL_5_7_REGRESSION( "introduced a regression with MySQL 5.7" );
+        final String reason;
+    }
+
     /**
      * Expected migration information that are used to determine if a repair is necessary.
      */
     @RequiredArgsConstructor
     private static class ExpectedMigrationInfo {
         private final String version;
-        private final int pre15Checksum;
-        private final int post15Checksum;
+        private final int preRepairChecksum;
+        private final int postRepairChecksum;
+        private final NewChecksumReason newChecksumReason;
     }
 
     private static final ExpectedMigrationInfo[] MIGRATION_META = {
-            new ExpectedMigrationInfo( "1.0.0", -330642568, 1889522940 ),
-            new ExpectedMigrationInfo( "1.3.2", 1109324745, 1109324745 ),
-            new ExpectedMigrationInfo( "1.4.0", 310023814, 1017485172 ),
-            new ExpectedMigrationInfo( "1.4.1", -1543189200, 1330781885 ),
-            new ExpectedMigrationInfo( "1.4.2", 1706447069, 253128706 ),
-            new ExpectedMigrationInfo( "1.4.3", 571489108, 571489108 ),
-            new ExpectedMigrationInfo( "1.4.6", 399726006, 504755998 ),
-            new ExpectedMigrationInfo( "1.4.11", 1536441374, 709491229 ),
-            new ExpectedMigrationInfo( "1.4.11.1", -1312864724, -907949910 )
+            new ExpectedMigrationInfo( "1.0.0", -330642568, 1889522940, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.3.2", 1109324745, 1109324745, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.0", 310023814, 1017485172, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.1", -1543189200, 1330781885, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.2", 1706447069, 253128706, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.3", 571489108, 571489108, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.6", 399726006, 504755998, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.11", 1536441374, 709491229, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.4.11.1", -1312864724, -907949910, NewChecksumReason.FLYWAY_3 ),
+            new ExpectedMigrationInfo( "1.5.0.4", 625408518, -1065145387, NewChecksumReason.MYSQL_5_7_REGRESSION )
     };
 
     /**
@@ -50,20 +67,17 @@ private static class ExpectedMigrationInfo {
     @Bean
     public FlywayMigrationStrategy flywayMigrationStrategy() {
         return flyway -> {
-            try {
-                // drop version_rank column
-                Connection connection = flyway.getConfiguration().getDataSource().getConnection();
-                // lookup the schema_version table and version_rank column
-                boolean hasVersionRankColumn;
-                try ( ResultSet resultSet = connection.getMetaData().getColumns( null, null, "schema_version", "version_rank" ) ) {
-                    hasVersionRankColumn = resultSet.next();
-                }
-                if ( hasVersionRankColumn ) {
-                    log.warn( "The 'schema_version' table is still using the 'version_rank' column from Flyway 3.2.1; will proceed to remove it..." );
-                    connection.createStatement().execute( "alter table schema_version drop column version_rank" );
+            // drop version_rank column
+            JdbcTemplate jdbcTemplate = new JdbcTemplate( flyway.getConfiguration().getDataSource() );
+            // lookup the schema_version table and version_rank column
+            Boolean hasVersionRankColumn = jdbcTemplate.execute( (ConnectionCallback<Boolean>) con -> {
+                try ( ResultSet resultSet = con.getMetaData().getColumns( null, null, "schema_version", "version_rank" ) ) {
+                    return resultSet.next();
                 }
-            } catch ( SQLException e ) {
-                throw new RuntimeException( e );
+            } );
+            if ( hasVersionRankColumn != null && hasVersionRankColumn ) {
+                log.warn( "The 'schema_version' table is still using the 'version_rank' column from Flyway 3.2.1; will proceed to remove it..." );
+                jdbcTemplate.execute( "alter table schema_version drop column version_rank" );
             }
             MigrationInfo[] appliedMigrations = flyway.info().applied();
             boolean repairNeeded = false;
@@ -74,15 +88,16 @@ public FlywayMigrationStrategy flywayMigrationStrategy() {
                         .orElse( null );
                 if ( expectedMigration != null &&
                         appliedMigration.getChecksum() != null &&
-                        appliedMigration.getChecksum().equals( expectedMigration.pre15Checksum ) &&
-                        !appliedMigration.getChecksum().equals( expectedMigration.post15Checksum ) ) {
-                    log.warn( String.format( "Flyway migration %s has been performed with Flyway 3.2.1, checksum will be bumped from %s to %s after repair.",
-                            appliedMigration.getVersion(), appliedMigration.getChecksum(), expectedMigration.post15Checksum ) );
+                        appliedMigration.getChecksum().equals( expectedMigration.preRepairChecksum ) &&
+                        !appliedMigration.getChecksum().equals( expectedMigration.postRepairChecksum ) ) {
                     repairNeeded = true;
+                    log.warn( String.format( "Flyway migration %s %s, checksum will be bumped from %s to %s after repair.",
+                            appliedMigration.getVersion(), expectedMigration.newChecksumReason.reason,
+                            appliedMigration.getChecksum(), expectedMigration.postRepairChecksum ) );
                 }
             }
             if ( repairNeeded ) {
-                log.warn( "Flyway 3.2.1 migrations detected, Flyway repair will be performed." );
+                log.warn( "Flyway repair will now be performed." );
                 flyway.repair();
             }
             flyway.migrate();

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

@@ -17,7 +17,7 @@ public AsyncRestTemplate remoteResourceRestTemplate( ApplicationSettings applica
         SimpleClientHttpRequestFactory httpRequestFactory = new SimpleClientHttpRequestFactory();
         httpRequestFactory.setTaskExecutor( new SimpleAsyncTaskExecutor() );
         if ( applicationSettings.getIsearch().getRequestTimeout() != null ) {
-            log.warn( "The 'rdp.settings.isearch.request-timeout' configuration is deprecated." );
+            log.warn( "The 'rdp.settings.isearch.request-timeout' configuration is deprecated, use 'rdp.settings.isearch.connect-timeout' and 'rdp.settings.isearch.read-timeout' instead." );
             httpRequestFactory.setConnectTimeout( 1000 );
             httpRequestFactory.setReadTimeout( (int) applicationSettings.getIsearch().getRequestTimeout().toMillis() );
         } else {

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

@@ -53,7 +53,6 @@
 import javax.validation.constraints.Size;
 import java.io.*;
 import java.net.URL;
-import java.sql.Timestamp;
 import java.text.MessageFormat;
 import java.time.Duration;
 import java.time.Instant;
@@ -134,7 +133,7 @@ public Object createServiceAccount( @Validated(User.ValidationServiceAccount.cla
 
         user.setEmail( serviceEmail );
         user.setEnabled( true );
-        user.setEnabledAt( Timestamp.from( Instant.now() ) );
+        user.setEnabledAt( Instant.now() );
 
         Profile profile = user.getProfile();
         profile.setPrivacyLevel( PrivacyLevelType.PRIVATE );

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

@@ -29,6 +29,7 @@
 import ubc.pavlab.rdp.services.*;
 import ubc.pavlab.rdp.settings.ApplicationSettings;
 import ubc.pavlab.rdp.settings.SiteSettings;
+import ubc.pavlab.rdp.util.Messages;
 
 import java.net.URI;
 import java.util.*;
@@ -426,7 +427,7 @@ private void initUserTerm( UserOntologyTerm term, Locale locale ) {
 
     @SneakyThrows
     private <T extends RemoteResource> T initRemoteResource( T remoteResource, Locale locale ) {
-        remoteResource.setOrigin( messageSource.getMessage( "rdp.site.shortname", null, locale ) );
+        remoteResource.setOrigin( messageSource.getMessage( Messages.SHORTNAME, locale ) );
         // Ensure that the path of the URL is effectively stripped from any trailing slashes and that its string
         // representation is free of query parameters, fragments, etc.
         // The main reason we do this is to avoid double slashes when generating URLs to profiles on partner sites

src/main/java/ubc/pavlab/rdp/model/AccessToken.java

@@ -7,10 +7,8 @@
 import ubc.pavlab.rdp.model.enums.PrivacyLevelType;
 
 import javax.persistence.*;
-import java.sql.Timestamp;
 import java.time.Duration;
-import java.time.Period;
-import java.time.temporal.ChronoUnit;
+import java.time.Instant;
 import java.time.temporal.TemporalAmount;
 import java.util.Optional;
 
@@ -31,7 +29,7 @@ public class AccessToken extends Token implements UserContent {
     private User user;
 
     @CreatedDate
-    private Timestamp createdAt;
+    private Instant createdAt;
 
     @Override
     protected TemporalAmount getDuration() {

src/main/java/ubc/pavlab/rdp/model/Gene.java

@@ -9,7 +9,7 @@
 
 import javax.persistence.*;
 import java.io.Serializable;
-import java.util.Date;
+import java.time.LocalDate;
 
 /**
  * Created by mjacobson on 17/01/18.
@@ -41,7 +41,6 @@ public abstract class Gene implements Serializable {
     private String aliases;
 
     @JsonIgnore
-    @Temporal(TemporalType.DATE)
     @Column(name = "modification_date")
-    private Date modificationDate;
+    private LocalDate modificationDate;
 }