Merge branch 'release-1.1.1'

JacobsonMT · JacobsonMT · commit dd3734caa376 · 2018-03-02T14:41:00.000-08:00
diff --git a/README.md b/README.md
@@ -0,0 +1,173 @@
+# Rare Disease Project
+Registry for model organism researchers, developed for the Canadian Rare Disease Models &amp; Mechanisms Network
+
+## Setup Instructions
+
+### Requirements
+* Java 8+
+* MySQL 5.5+ or equivalent
+
+### Obtain Distribution
+Download the latest jar distribution [here](https://github.com/PavlidisLab/modinvreg/releases/latest).
+
+The jar contains the core application, including an embedded webserver (Tomcat 8.5.x). 
+
+### Set up database
+Create database and associated user that the application will use to connect.
+
+Ex.
+```SQL
+CREATE DATABASE afg CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci;
+CREATE USER  'rdpuser'@'%' identified by 'rdppassword';
+grant all on rdp.* to 'rdpuser'@'%';
+```
+
+### Customize Settings
+The only thing that's left is customization and connection with your database.
+This is done by creating the following properties files
+
+* application-prod.properties
+  - Location: Working directory of running jar
+  - Defaults: https://github.com/PavlidisLab/modinvreg/blob/master/src/main/resources/application.properties
+  - Contents: Majority of the properties related to the running of the application (including database connection information) and message customisation.
+  - Example:
+```Ini
+# ===============================
+# = DATA SOURCE
+# ===============================
+
+### Database Connection ###
+spring.datasource.url = jdbc:mysql://<Host Here>:3306/<Database Name Here>
+spring.datasource.username = DB_USER
+spring.datasource.password = DB_PASS
+
+# ==============================================================
+# = Spring Email
+# ==============================================================
+
+### Email Server Setup ##
+spring.mail.host=smtp.gmail.com
+spring.mail.username=example@gmail.com
+spring.mail.password=example_password
+spring.mail.port=587
+
+# ==============================================================
+# = Application Specific Defaults
+# ==============================================================
+
+# Default user will be ROLE_MANAGER instead of ROLE_USER
+# Set to true if you want the default newly created user
+# to be able to search and view other users' profile.
+rdp.settings.send-email-on-registration=true
+
+### Host of your production website (No Trailing Slash) ###
+rdp.site.host=http://register.rare-diseases-catalyst-network.ca
+
+## Context Root Path of production website (leave blank if none) ###
+rdp.site.context=
+
+### Emails (these can be the same) ###
+
+### Contact Email is the one displayed in the website ###
+rdp.site.contact-email=registry-help@example.ca
+
+### Admin Email is the one used by the system to send and receive email ###
+rdp.site.admin-email=registry-help@example.ca
+
+# ==============================================================
+# = Custom Messages
+# ==============================================================
+
+### Customisable HTML Embeddings ###
+rdp.site.fullname=Rare Diseases: Models & Mechanisms Network
+rdp.site.shortname=RDMMN
+
+rdp.site.logohtml=<h2 class="navbar-text m-0">${rdp.site.fullname}</h2>
+
+rdp.site.welcome=<p>The ${rdp.site.fullname} Registry collects information on model organism researchers \
+  and the specific genes they study. The Registry is the mechanism by which researchers can find potential \
+  matches of model organism researchers to human rare disease or cancer researchers.</p>
+
+rdp.site.email.registration-welcome=Thank you for registering with ${rdp.site.fullname}. (${rdp.site.host}${rdp.site.context}).
+
+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 If you have questions or difficulties with registration please \
+  feel free to contact us: ${rdp.site.contact-email}
+```
+* faq.properties
+  - Location: Specified using `-Dspring.config.location=file:<location>`
+  - Defaults: Empty
+  - Contents: All of the question and answer style items that will display in the frequently asked questions page. Each entry requires two parts: `rdp.faq.questions.<q_key>` and `rdp.faq.answers.<q_key>` which hold the question and the corresponding answer, respectively.
+  - Example: https://github.com/PavlidisLab/modinvreg/blob/master/faq.properties
+* login.properties
+  - Location: Working directory of running jar
+  - Defaults: https://github.com/PavlidisLab/modinvreg/blob/master/src/main/resources/application.properties
+  - Contents: Create this file if you would like to customise spring specific messages such as incorrect username/password.
+
+### Running Application
+To start the application the simplest command is: java -jar rdp-x.x.x.jar
+
+That being said, there a few options you will likely want to specify
+
+* `-Dserver.port=<port>`: Port for the webserver to listen on.
+* `-Dspring.config.location=file:<faq location>`: Location to find the FAQ question & answers
+* `-Djava.security.egd=file:/dev/./urandom`:  Specify this if you receive logs such as: _"Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [235,853] milliseconds."_ The secure random calls may be blocking as there is not enough entropy to feed them in /dev/random.
+
+The webserver will start initialising, create any missing required tables in the connected database and shortly be serving content at the provided port.
+
+#### Notes
+* The organisms table is prepopulated on creation however all but human are turned off. Set the active column to 1 in the database to turn on an organism (Example (this will activate mouse): `update taxon set active=1 where taxon_id=10090`)
+* If a required table is not found in the database upon application startup it will create it, it will NOT delete existing data.
+
+## Building From Source
+
+* Clone the repo or download the source distribution.
+  - `git clone https://github.com/PavlidisLab/modinvreg.git`
+* Package
+  - `cd modinvreg/`
+  - `./mvnw package`
+
+The jar will be create in the target directory.
+
+For custom deployments see: https://docs.spring.io/spring-boot/docs/current/reference/html/cloud-deployment.html
+To install as a system service see: https://docs.spring.io/spring-boot/docs/current/reference/html/deployment-install.html
+
+## Example Setup for Centos 7 With Mysql 5.5+ & Apache
+
+### Database
+* mysql -uroot -p
+* CREATE DATABASE rdp CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci;
+* CREATE USER  'rdpuser'@'%' identified by 'rdppassword';
+* grant all on rdp.* to 'rdpuser'@'%';
+
+### Application
+* `cd /project/directory`
+* `wget https://github.com/PavlidisLab/modinvreg/releases/download/vx.x/rdp-x.x.x.jar`
+* create application-prod.properties, faq.properties and optionally login.properties
+* test run the jar: java -Dserver.port=8080 -Dspring.config.location=file:faq.properties -Djava.security.egd=file:/dev/./urandom -jar rdp-x.x.x.jar
+* (Optional) Log into the database and activate other organisms.
+* Set up jar as systemd service:
+  - create file /etc/systemd/system/rdp.service containing similar to the following:
+  
+```Ini
+[Unit]
+Description=rdp
+After=syslog.target
+
+[Service]
+User=tomcat
+Group=tomcat
+WorkingDirectory=/project/directory
+ExecStart=/bin/java -Dserver.port=8083 -Dspring.config.location=file:faq.properties -Djava.security.egd=file:/dev/./urandom -jar rdp-x.x.x.jar
+SuccessExitStatus=143
+
+[Install]
+WantedBy=multi-user.target
+```
+* Start service: `systemctl start rdp.service`
+* View logs: `journalctl -f -u rdp.service`
+
+### Apache
+* Create a standard virtualhost with the following proxies:
+  - `ProxyPass / http://localhost:<port>/`
+  - `ProxyPassReverse / http://localhost:<port>/`
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>ubc.pavlab</groupId>
     <artifactId>rdp</artifactId>
-    <version>1.1.0</version>
+    <version>1.1.1</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>
diff --git a/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java b/src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java
@@ -297,7 +297,7 @@ public void updateTermsAndGenesInTaxon( User user, Taxon taxon, Map<Gene, TierTy
         Map<String, Integer> goIdToHibernateId = user.getUserTerms().stream()
                 .filter( t -> t.getTaxon().equals( taxon ) )
                 .collect( Collectors.toMap( GeneOntologyTerm::getGoId, UserTerm::getId ) );
-        Collection<UserTerm> updatedTerms = convertTerms( user, taxon, goTerms );
+        Collection<UserTerm> updatedTerms = convertTermTypes( goTerms, taxon, genesToTierMap.keySet() );
         updatedTerms.forEach( t -> t.setId( goIdToHibernateId.get( t.getGoId() ) ) );
 
         removeTermsFromUserByTaxon( user, taxon );
diff --git a/src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java b/src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java
@@ -2,10 +2,12 @@
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.assertj.core.util.Maps;
 import org.junit.Before;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mockito.Mockito;
+import org.mockito.internal.util.collections.Sets;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.TestConfiguration;
 import org.springframework.boot.test.mock.mockito.MockBean;
@@ -160,7 +162,7 @@ private void setUpRecomendTermsMocks() {
 
         expected.forEach( ( key, value ) -> key.getSizesByTaxon().put( taxon, value + 10 ) );
 
-        Mockito.when( goService.termFrequencyMap( Mockito.anyCollectionOf(Gene.class) ) ).thenReturn( expected );
+        Mockito.when( goService.termFrequencyMap( Mockito.anyCollectionOf( Gene.class ) ) ).thenReturn( expected );
     }
 
 
@@ -701,7 +703,7 @@ public void updateTermsAndGenesInTaxon_whenUserHasNoGeneOrTerms() {
         Collection<Gene> calculatedGenes = IntStream.range( 101, 110 ).boxed().map(
                 nbr -> createGene( nbr, taxon )
         ).collect( Collectors.toList() );
-        Mockito.when( goService.getGenes( Mockito.anyCollectionOf(GeneOntologyTerm.class), Mockito.any() ) ).thenReturn( calculatedGenes );
+        Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.any() ) ).thenReturn( calculatedGenes );
 
         Collection<GeneOntologyTerm> terms = IntStream.range( 1, 10 ).boxed().map(
                 nbr -> createTermWithGene( toGOId( nbr ), createGene( nbr, taxon ) )
@@ -743,7 +745,7 @@ public void updateTermsAndGenesInTaxon_whenUserHasGenesAndTerms() {
         Collection<Gene> calculatedGenes = IntStream.range( 101, 110 ).boxed().map(
                 nbr -> createGene( nbr, taxon )
         ).collect( Collectors.toList() );
-        Mockito.when( goService.getGenes( Mockito.anyCollectionOf(GeneOntologyTerm.class), Mockito.any() ) ).thenReturn( calculatedGenes );
+        Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.any() ) ).thenReturn( calculatedGenes );
 
         Collection<GeneOntologyTerm> terms = IntStream.range( 1, 10 ).boxed().map(
                 nbr -> createTermWithGene( toGOId( nbr ), createGene( nbr, taxon ) )
@@ -774,7 +776,7 @@ public void updateTermsAndGenesInTaxon_whenManualAndCalculatedGenesOverlap_thenK
         Collection<Gene> calculatedGenes = IntStream.range( 5, 14 ).boxed().map(
                 nbr -> createGene( nbr, taxon )
         ).collect( Collectors.toList() );
-        Mockito.when( goService.getGenes( Mockito.anyCollectionOf(GeneOntologyTerm.class), Mockito.any() ) ).thenReturn( calculatedGenes );
+        Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.any() ) ).thenReturn( calculatedGenes );
 
         Collection<GeneOntologyTerm> terms = IntStream.range( 1, 10 ).boxed().map(
                 nbr -> createTermWithGene( toGOId( nbr ), createGene( nbr, taxon ) )
@@ -814,7 +816,7 @@ public void updateTermsAndGenesInTaxon_whenOldAndNewOverlap_thenRetainIds() {
 
         // Mock goService.getRelatedGenes
         Collection<Gene> calculatedGenes = Collections.singleton( createGene( 105, taxon ) );
-        Mockito.when( goService.getGenes( Mockito.anyCollectionOf(GeneOntologyTerm.class), Mockito.any() ) ).thenReturn( calculatedGenes );
+        Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.any() ) ).thenReturn( calculatedGenes );
 
         Collection<GeneOntologyTerm> terms = Collections.singleton( createTermWithGene( toGOId( 5 ), createGene( 5, taxon ) ) );
 
@@ -837,13 +839,47 @@ public void updateTermsAndGenesInTaxon_whenOldAndNewOverlap_thenRetainIds() {
         assertThat( user.getUserGenes().values().iterator().next().getId() ).isEqualTo( 1 );
     }
 
+    @Test
+    public void updateTermsAndGenesInTaxon_whenUserHasGenesAndTerms_thenUpdateFrequency() {
+        User user = createUser( 1 );
+        Taxon taxon = createTaxon( 1 );
+
+        Gene geneWillBeRemoved = createGene( 999, taxon );
+        GeneOntologyTerm termWillBeRemoved = createTermWithGene( toGOId( geneWillBeRemoved.getGeneId() ), geneWillBeRemoved );
+        user.getUserTerms().add( createUserTerm( 1, termWillBeRemoved, taxon ) );
+        user.getUserGenes().put( geneWillBeRemoved.getGeneId(), createUserGene( 1, geneWillBeRemoved, user, TierType.TIER1 ) );
+
+        Gene geneWillChangeTier = createGene( 5, taxon );
+        user.getUserGenes().put( geneWillChangeTier.getGeneId(), createUserGene( 2, geneWillChangeTier, user, TierType.TIER2 ) );
+
+        UserTerm termWillUpdateFrequency = createUserTerm( 3,
+                createTermWithGene( toGOId( geneWillChangeTier.getGeneId() ), geneWillBeRemoved, geneWillChangeTier ),
+                taxon );
+        // Should have frequency of 2
+        termWillUpdateFrequency.setFrequency( 2 );
+        user.getUserTerms().add( termWillUpdateFrequency );
+
+        becomeUser( user );
+
+        Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.any() ) ).thenReturn( Collections.emptySet() );
+
+        Map<Gene, TierType> geneTierMap = Maps.newHashMap( geneWillChangeTier, TierType.TIER1 );
+
+        userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, Sets.newSet( termWillUpdateFrequency) );
+
+        assertThat( user.getUserTerms() ).hasSize( 1 );
+        assertThat( user.getUserTerms().iterator().next() ).isEqualTo( termWillUpdateFrequency );
+        assertThat( user.getUserTerms().iterator().next().getFrequency() ).isEqualTo( 1 );
+
+    }
+
     private void assertThatUserTermsAreEqualTo( User user, Collection<GeneOntologyTerm> terms ) {
         assertThat( user.getUserTerms() ).hasSize( terms.size() );
         assertThat( user.getUserTerms().stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toSet() ) )
                 .isEqualTo( terms.stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toSet() ) );
     }
 
-    private void assertThatUserGenesAreEqualTo( User user,  Map<Gene, TierType> expectedGenes ) {
+    private void assertThatUserGenesAreEqualTo( User user, Map<Gene, TierType> expectedGenes ) {
         assertThat( user.getUserGenes().keySet() )
                 .containsExactlyElementsOf( expectedGenes.keySet().stream().map( Gene::getGeneId )
                         .collect( Collectors.toSet() ) );
@@ -893,7 +929,7 @@ public void recommendTerms_whenFrequencyLimited_thenReturnBestLimitedResultsOnly
 
         User user = createUser( 1 );
         Taxon taxon = createTaxon( 1 );
-        Collection<UserTerm> found = userService.recommendTerms( user, taxon, -1, -1, 3);
+        Collection<UserTerm> found = userService.recommendTerms( user, taxon, -1, -1, 3 );
         assertThat( found.stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toList() ) ).containsExactlyInAnyOrder( toGOId( 1 ), toGOId( 7 ), toGOId( 8 ) );
 
         found = userService.recommendTerms( user, taxon, -1, -1, 4 );
@@ -906,7 +942,7 @@ public void recommendTerms_whenFrequencyLimitedAndSizeLimited_thenReturnBestLimi
 
         User user = createUser( 1 );
         Taxon taxon = createTaxon( 1 );
-        Collection<UserTerm> found = userService.recommendTerms( user, taxon, 11, 12, 2);
+        Collection<UserTerm> found = userService.recommendTerms( user, taxon, 11, 12, 2 );
         assertThat( found.stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toList() ) ).containsExactlyInAnyOrder( toGOId( 0 ), toGOId( 4 ), toGOId( 6 ) );
 
         found = userService.recommendTerms( user, taxon, 1, 11, 2 );
@@ -919,7 +955,7 @@ public void recommendTerms_whenRedundantTerms_thenReturnOnlyMostSpecific() {
 
         User user = createUser( 1 );
         Taxon taxon = createTaxon( 1 );
-        Collection<UserTerm> found = userService.recommendTerms( user, taxon, 11, 11, 1);
+        Collection<UserTerm> found = userService.recommendTerms( user, taxon, 11, 11, 1 );
         assertThat( found.stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toList() ) ).containsExactlyInAnyOrder( toGOId( 2 ), toGOId( 3 ), toGOId( 5 ), toGOId( 99 ) );
 
         found = userService.recommendTerms( user, taxon, 1, 11, 2 );
@@ -929,11 +965,11 @@ public void recommendTerms_whenRedundantTerms_thenReturnOnlyMostSpecific() {
     @Test
     public void recommendTerms_whenUserHasNoGenes_thenReturnEmpty() {
         Map<GeneOntologyTerm, Long> empyFMap = new HashMap<>();
-        Mockito.when( goService.termFrequencyMap( Mockito.anyCollectionOf(Gene.class) ) ).thenReturn( empyFMap );
+        Mockito.when( goService.termFrequencyMap( Mockito.anyCollectionOf( Gene.class ) ) ).thenReturn( empyFMap );
 
         User user = createUser( 1 );
         Taxon taxon = createTaxon( 1 );
-        Collection<UserTerm> found = userService.recommendTerms( user, taxon, -1, -1, -1);
+        Collection<UserTerm> found = userService.recommendTerms( user, taxon, -1, -1, -1 );
         assertThat( found ).isEmpty();
     }
 
@@ -942,7 +978,7 @@ public void recommendTerms_whenUserNull_thenReturnNull() {
         setUpRecomendTermsMocks();
 
         Taxon taxon = createTaxon( 1 );
-        Collection<UserTerm> found = userService.recommendTerms( null, taxon, -1, -1, -1);
+        Collection<UserTerm> found = userService.recommendTerms( null, taxon, -1, -1, -1 );
         assertThat( found ).isNull();
     }
 
@@ -951,7 +987,7 @@ public void recommendTerms_whenTaxonNull_thenReturnNull() {
         setUpRecomendTermsMocks();
 
         User user = createUser( 1 );
-        Collection<UserTerm> found = userService.recommendTerms( user, null, -1, -1, -1);
+        Collection<UserTerm> found = userService.recommendTerms( user, null, -1, -1, -1 );
         assertThat( found ).isNull();
     }
 
diff --git a/src/test/java/ubc/pavlab/rdp/util/BaseTest.java b/src/test/java/ubc/pavlab/rdp/util/BaseTest.java
@@ -7,6 +7,7 @@
 import ubc.pavlab.rdp.model.enums.TierType;
 
 import java.util.Arrays;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import static org.mockito.Mockito.mock;
@@ -92,13 +93,15 @@ protected GeneOntologyTerm createTerm( String id ) {
         return term;
     }
 
-    protected GeneOntologyTerm createTermWithGene( String id, Gene gene ) {
+    protected GeneOntologyTerm createTermWithGene( String id, Gene... genes ) {
         GeneOntologyTerm term = new GeneOntologyTerm();
         term.setGoId( id );
         term.setObsolete( false );
 
-        term.getDirectGenes().add( gene );
-        gene.getTerms().add( term );
+        Arrays.stream(genes).forEach( g -> {
+            term.getDirectGenes().add( g );
+            g.getTerms().add( term );
+        } );
 
         return term;
     }
@@ -117,6 +120,12 @@ protected UserTerm createUserTerm( int id, GeneOntologyTerm term, Taxon taxon )
         return ut;
     }
 
+    protected UserTerm createUserTerm( int id, GeneOntologyTerm term, Taxon taxon, Set<Gene> genes ) {
+        UserTerm ut = new UserTerm(term, taxon, genes );
+        ut.setId( id );
+        return ut;
+    }
+
     protected UserGene createUserGene( int id, Gene gene, User user, TierType tier ) {
         UserGene ug = new UserGene( gene, user, tier );
         ug.setId( id );
