Merge branch 'hotfix-1.4.4'

Author: arteymix

docs/installation.md

@@ -24,14 +24,14 @@ cache, and much more!
 Create the database and an associated user that the application will use to store and retrieve data.
 
 ```sql
-create database <database name> character set utf8mb4 collate utf8mb4_general_ci;
+create database '<database name>' character set utf8mb4;
 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 and `utf8_general_ci` collate. 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 `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).
 
 ## Setup application.properties
 

docs/release-notes.md

@@ -1,5 +1,15 @@
 # Release Notes
 
+## 1.4.4
+
+Use the build version for the OpenAPI specification so that it is always up-to-date.
+
+Fix calculation of human gene coverage, the orthologs were commented out and the SQL query has been added.
+
+Fix field length in the profile to use the value previously set in `profile.css`. The CSS code it contains as well as
+other files have been merged in `common.css`. A flexbox is used for the email since it needs to also account for the
+verify button.
+
 ## 1.4.3
 
 Fix `hideGenelist` accessor in the user profile template which resulted in an error. For now on, property names will be
@@ -17,12 +27,20 @@ where email in (select email
                 having count(email) > 1);
 ```
 
-You should then take action by removing or merging those users. We recommend removing those with the latest `id`
+You should then take action by removing or merging those users. We recommend removing those with the latest `user_id`
 fields, but this is ultimately at your discretion.
 
+Since these users are not valid, you will have to remove the verification token that was generated at registration
+before removing the user itself:
+
+```sql
+delete from verification_token where user_id = ?;
+delete from user where user_id = ?;
+```
+
 ## 1.4.2
 
-Restore rdp.site.shortname and `rdp.site.fullname` in `application.properties` since they're still being used in the
+Restore `rdp.site.shortname` and `rdp.site.fullname` in `application.properties` since they're still being used in the
 user FAQ.
 
 Fix missing TaskExecutor when using an HTTP proxy. It now uses native`-Dhttp.proxyHost` and `-Dhttp.proxyPort` JVM
@@ -34,7 +52,7 @@ Move all email text into messages.properties, so they can be adjusted and transl
 
 Fix missing flash messages after confirming registration and contact email.
 
-Fix /api/users API endpoint for registries that are not using gene-level privacy. In this case, the gene privacy level
+Fix `/api/users` API endpoint for registries that are not using gene-level privacy. In this case, the gene privacy level
 is always set to `null` and the value in the profile must be used instead as a fallback.
 
 Require MySQL 5.7+ and add instructions for using MySQL 5.6 and prior. This is due to a index size limit that is busted

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.4.3</version>
+    <version>1.4.4</version>
 
     <developers>
         <developer>
@@ -183,6 +183,14 @@
             <plugin>
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>build-info</id>
+                        <goals>
+                            <goal>build-info</goal>
+                        </goals>
+                    </execution>
+                </executions>
             </plugin>
             <plugin>
                 <groupId>com.amashchenko.maven.plugin</groupId>

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

@@ -5,6 +5,7 @@
 import io.swagger.v3.oas.models.info.Info;
 import io.swagger.v3.oas.models.servers.Server;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.info.BuildProperties;
 import org.springframework.context.MessageSource;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -24,6 +25,9 @@ public class ApiConfig {
     @Autowired
     private SiteSettings siteSettings;
 
+    @Autowired
+    private BuildProperties buildProperties;
+
     @Bean
     public OpenAPI openAPI( MessageSource messageSource ) {
         // FIXME: retrieve that from the request context
@@ -34,7 +38,7 @@ public OpenAPI openAPI( MessageSource messageSource ) {
                         .title( messageSource.getMessage( "ApiConfig.title", new String[]{ shortname }, locale ) )
                         .description( messageSource.getMessage( "ApiConfig.description", new String[]{ shortname }, locale ) )
                         .contact( new Contact().email( siteSettings.getContactEmail() ) )
-                        .version( ApiController.API_VERSION ) )
+                        .version( buildProperties.getVersion() ) )
                 .servers( Collections.singletonList( new Server().url( siteSettings.getHostUri().toString() ) ) );
 
     }

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

@@ -31,7 +31,7 @@
 import java.util.stream.Collectors;
 
 /**
- * This class provides API access for remote applications
+ * This class provides API accesses for remote applications
  * <p>
  * It's worth mentioning that the '/api' endpoint is delegated to springdoc OpenAPI JSON generator and welcome the
  * client with a specification of the endpoints of this API.
@@ -41,11 +41,6 @@
 @CommonsLog
 public class ApiController {
 
-    /**
-     * API version
-     */
-    public static final String API_VERSION = "1.4.0";
-
     @Autowired
     private MessageSource messageSource;
     @Autowired
@@ -66,12 +61,12 @@ public class ApiController {
     private PermissionEvaluator permissionEvaluator;
 
     @ExceptionHandler({ AuthenticationException.class })
-    public ResponseEntity handleAuthenticationException() {
+    public ResponseEntity<?> handleAuthenticationException() {
         return ResponseEntity.status( HttpStatus.UNAUTHORIZED ).build();
     }
 
     @ExceptionHandler({ ApiException.class })
-    public ResponseEntity handleApiException( ApiException e ) {
+    public ResponseEntity<String> handleApiException( ApiException e ) {
         return ResponseEntity.status( e.getStatus() ).body( e.getMessage() );
     }
 
@@ -96,10 +91,6 @@ public Object getStats() {
      * Retrieve all users in a paginated format.
      * <p>
      * Results that cannot be displayed are anonymized.
-     *
-     * @param pageable
-     * @param locale
-     * @return
      */
     @GetMapping(value = "/api/users", produces = MediaType.APPLICATION_JSON_VALUE)
     public Object getUsers( @RequestHeader(value = HttpHeaders.AUTHORIZATION, required = false) String authorizationHeader,
@@ -122,10 +113,6 @@ public Object getUsers( @RequestHeader(value = HttpHeaders.AUTHORIZATION, requir
      * Retrieve all genes in a paginated format.
      * <p>
      * Results that cannot be displayed are anonymized.
-     *
-     * @param pageable
-     * @param locale
-     * @return
      */
     @GetMapping(value = "/api/genes", produces = MediaType.APPLICATION_JSON_VALUE)
     public Object getGenes( @RequestHeader(value = HttpHeaders.AUTHORIZATION, required = false) String authorizationHeader,

src/main/java/ubc/pavlab/rdp/repositories/UserGeneRepository.java

@@ -7,6 +7,7 @@
 import org.springframework.data.jpa.repository.QueryHints;
 import org.springframework.data.repository.query.Param;
 import org.springframework.stereotype.Repository;
+import ubc.pavlab.rdp.model.GeneInfo;
 import ubc.pavlab.rdp.model.Taxon;
 import ubc.pavlab.rdp.model.UserGene;
 import ubc.pavlab.rdp.model.UserOrgan;
@@ -82,6 +83,14 @@ public interface UserGeneRepository extends JpaRepository<UserGene, Integer> {
     @Query("select user_gene from UserGene user_gene where user_gene.geneId in (select ortholog.geneId from GeneInfo gene_info join gene_info.orthologs as ortholog where gene_info.geneId = :geneId and ortholog.taxon = :taxon)")
     Collection<UserGene> findOrthologsByGeneIdAndTaxon( @Param("geneId") Integer geneId, @Param("taxon") Taxon taxon );
 
+    /**
+     * @param taxonId a taxon identifier in which to perform orthology search from
+     * @return a collection of tuple whose first element is a {@link UserGene} and second element is the corresponding
+     * {@link GeneInfo} ortholog in the supplied taxon.
+     */
+    @Query(value = "select gi.gene_id from gene_info as gi join ortholog on gi.id = ortholog.source_gene  join gene_info as gi2 on gi2.id = ortholog.target_gene join gene ug on ug.gene_id = gi2.gene_id where gi.taxon_id = :taxonId", nativeQuery = true)
+    Collection<Integer> findOrthologGeneIdsByOrthologToTaxon( @Param("taxonId") Integer taxonId );
+
     // Return all human genes.
     @QueryHints(@QueryHint(name = "org.hibernate.cacheable", value = "true"))
     @Query("select geneId FROM UserGene where taxon = '9606'")

src/main/java/ubc/pavlab/rdp/services/UserGeneServiceImpl.java

@@ -113,20 +113,17 @@ public Integer countUniqueAssociationsAllTiers() {
         return userGeneRepository.countDistinctGeneByTierIn( tierService.getEnabledTiers() );
     }
 
+    /**
+     * Count the number of unique associations to human genes that are either direct or indirect via orthology among all
+     * tiers.
+     * <p>
+     * This is also known as the "human gene coverage".
+     */
     @Cacheable(cacheNames = "stats", key = "#root.methodName")
     @Override
     public Integer countUniqueAssociationsToHumanAllTiers() {
-        /* This is also called the "human gene coverage" */
         Collection<Integer> humanGenes = new HashSet<>( userGeneRepository.findAllHumanGenes() );
-
-        // Add orthologs mapped to humans
-        // TODO
-        // humanGenes.addAll( userGeneRepository.findHumanGenesForTarget(
-        //         userGeneRepository.findDistinctGeneByTierIn( TierType.ANY )
-        // ));
-
-        // Add directly entered human genes
-
+        humanGenes.addAll( userGeneRepository.findOrthologGeneIdsByOrthologToTaxon( 9606 ) );
         return humanGenes.size();
     }
 

src/main/resources/ehcache.xml

@@ -27,7 +27,7 @@
            eternal="true"/>
 
     <cache name="ubc.pavlab.rdp.model.UserGene"
-           maxElementsInMemory="1000"
+           maxElementsInMemory="10000"
            timeToLiveSeconds="600"/>
 
     <cache name="ubc.pavlab.rdp.model.UserTerm"

src/main/resources/static/css/common.css

@@ -181,17 +181,18 @@ table.table-fixed tr {
 }
 
 table.table-fixed {
-    height:220px;
+    height: 220px;
     display: -moz-groupbox;
 }
-table.table-fixed tbody{
+
+table.table-fixed tbody {
     overflow-y: scroll;
     height: 200px;
     /*width: 100%;*/
     position: absolute;
 }
 
-.tip{
+.tip {
     font-size: x-small !important;
     background: cornflowerblue;
     color: whitesmoke;
@@ -202,4 +203,132 @@ table.table-fixed tbody{
     text-align: center;
     vertical-align: middle;
     line-height: 1.5em;
-}
+}
+
+.section {
+    width: 600px;
+    margin-bottom: 15px;
+}
+
+.pubmed-error:before {
+    content: "Issue obtaining metadata.";
+    color: red;
+}
+
+input.data-edit {
+    width: 90%;
+    -ms-text-overflow: ellipsis;
+    text-overflow: ellipsis;
+}
+
+#privacy-levels .radio {
+    margin: 12px 0 0 12px;
+}
+
+#privacy-levels .radio input {
+    margin-right: 3px;
+}
+
+.margin-chbox div {
+    margin: 0 12px 12px 14px;
+}
+
+hr {
+    margin: 0 0 10px;
+}
+
+.tip {
+    margin-top: -4px;
+}
+
+.input-group {
+    width: 99%;
+}
+
+.isearch-settings, .form-group.row {
+    margin-left: 0 !important;
+    padding-left: 12px;
+    padding-right: 12px;
+}
+
+.isearch-settings * {
+    font-size: 1rem;
+    font-weight: 400;
+    line-height: 1.5;
+    vertical-align: center;
+
+    margin: 0 0 7px;
+    padding: 0;
+}
+
+.isearch-settings .label-text {
+    position: relative;
+    bottom: 1px;
+}
+
+.isearch-settings #isearch-checkbox {
+    transform: scale(1.2);
+    padding: 0;
+}
+
+.text-right {
+    text-align: right;
+}
+
+.tab-content {
+    /*
+    padding-top: 21px;
+    margin-top: -1px;
+    border: lightgray 1px solid;
+    border-bottom-right-radius: 3px;
+    border-bottom-left-radius: 3px;
+    border-top: none;
+    */
+}
+
+/*
+#gene-search-btn{
+    margin-left: 4px;
+    margin-right: -4px;
+}
+
+#ortholog-box{
+    margin-top: -17px;
+}
+
+.ortholog-select{
+    margin-left: -2px;
+}
+*/
+
+#alpha-grp button:active, #alpha-grp button.active, .input-group-prepend button[type='submit'] {
+    background-color: dodgerblue;
+    border-color: dodgerblue;
+    color: whitesmoke;
+}
+
+/*
+.tab-content h5{
+    margin-left: 12px;
+}
+*/
+
+.hide {
+    height: 0 !important;
+    display: none;
+}
+
+.ortholog-search-text {
+    font-style: italic;
+    color: steelblue;
+}
+
+.gene-error:before {
+    content: "Could Not Find Gene.";
+    color: red;
+}
+
+.term-error:before {
+    content: "Could Not Find Term.";
+    color: red;
+}