Merge pull request #359 from wcmc-its/development

Release of 1.1
wcmc-its · Jun 12, 2019 · f9e2c33 · f9e2c33
2 parents ed91318 + 6a70dca
commit f9e2c33
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diff --git a/Procfile b/Procfile
@@ -1 +1 @@
-web: java -jar reciter-0.0.1-SNAPSHOT.jar
+web: java -jar reciter-1.1.jar
diff --git a/buildspec.yml b/buildspec.yml
@@ -2,21 +2,21 @@ version: 0.2
 # https://docs.aws.amazon.com/codebuild/latest/userguide/getting-started.html
 phases:
   install:
-    commands:
-      - echo Nothing to do in the install phase...
+    runtime-versions:
+      java: openjdk8
   pre_build:
     commands:
       - echo Nothing to do in the pre_build phase...
   build:
     commands:
       - echo Build started on `date`
       - mvn clean install -Dmaven.test.skip=true
-      - cp target/reciter-0.0.1-SNAPSHOT.jar .
+      - cp target/reciter-1.1.jar .
   post_build:
     commands:
       - echo Build completed on `date`
 artifacts:
   files:
-    - reciter-0.0.1-SNAPSHOT.jar 
+    - reciter-1.1.jar 
     - .ebextensions/**/* 
     - Procfile
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.cornell.weill.reciter</groupId>
     <artifactId>reciter</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
+    <version>1.1</version>
     <name>ReCiter</name>
     <description>ReCiter is a publication suggestions engine</description>
     <url>https://github.com/wcmc-its/ReCiter</url>
@@ -124,59 +124,28 @@
         </dependencies>
     </dependencyManagement>
     <dependencies>
+    	<dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
         </dependency>
-        <!--&lt;!&ndash; https://mvnrepository.com/artifact/org.springframework.security.oauth/spring-security-oauth2 &ndash;&gt;-->
-        <!--<dependency>-->
-        <!--<groupId>org.springframework.security.oauth</groupId>-->
-        <!--<artifactId>spring-security-oauth2</artifactId>-->
-        <!--<version>2.2.1.RELEASE</version>-->
-        <!--</dependency>-->
-        <!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-security -->
-        <!--<dependency>-->
-        <!--<groupId>org.springframework.boot</groupId>-->
-        <!--<artifactId>spring-boot-starter-security</artifactId>-->
-        <!--<version>1.5.10.RELEASE</version>-->
-        <!--</dependency>-->
-        <!-- https://mvnrepository.com/artifact/com.auth0/auth0-spring-security-api -->
-        <!--<dependency>-->
-        <!--<groupId>com.auth0</groupId>-->
-        <!--<artifactId>auth0-spring-security-api</artifactId>-->
-        <!--<version>1.0.0</version>-->
-        <!--</dependency>-->
-        <!--&lt;!&ndash; https://mvnrepository.com/artifact/com.auth0/auth0 &ndash;&gt;-->
-        <!--<dependency>-->
-        <!--<groupId>com.auth0</groupId>-->
-        <!--<artifactId>auth0</artifactId>-->
-        <!--<version>1.5.0</version>-->
-        <!--</dependency>-->
-        <!--&lt;!&ndash; https://mvnrepository.com/artifact/io.jsonwebtoken/jjwt &ndash;&gt;-->
-        <!--<dependency>-->
-        <!--<groupId>io.jsonwebtoken</groupId>-->
-        <!--<artifactId>jjwt</artifactId>-->
-        <!--<version>0.9.0</version>-->
-        <!--</dependency>-->
-        <!--https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-websocket-->
-
-        <!-- https://mvnrepository.com/artifact/org.springframework.security/spring-security-config -->
 		<dependency>
 		    <groupId>org.springframework.security</groupId>
 		    <artifactId>spring-security-config</artifactId>
-		    <version>5.1.4.RELEASE</version>
 		</dependency>
         <!-- https://mvnrepository.com/artifact/org.springframework.security/spring-security-web -->
 		<dependency>
 		    <groupId>org.springframework.security</groupId>
 		    <artifactId>spring-security-web</artifactId>
-		    <version>5.1.4.RELEASE</version>
 		</dependency>
         <!-- https://mvnrepository.com/artifact/org.springframework.security/spring-security-core -->
 		<dependency>
 		    <groupId>org.springframework.security</groupId>
 		    <artifactId>spring-security-core</artifactId>
-		    <version>5.1.4.RELEASE</version>
 		</dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -186,7 +155,6 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.5</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
 		<dependency>
@@ -202,7 +170,6 @@
         <dependency>
             <groupId>com.unboundid</groupId>
             <artifactId>unboundid-ldapsdk</artifactId>
-            <version>3.2.0</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/ch.mfrey.jackson/jackson-antpathfilter -->
         <dependency>
@@ -213,7 +180,6 @@
         <dependency>
             <groupId>org.projectlombok</groupId>
             <artifactId>lombok</artifactId>
-            <version>1.16.16</version>
             <scope>provided</scope>
         </dependency>
         <!-- https://mvnrepository.com/artifact/com.github.derjust/spring-data-dynamodb -->
@@ -261,7 +227,6 @@
 	    <dependency>
 	    	<groupId>com.amazonaws</groupId>
 	    	<artifactId>aws-java-sdk-sqs</artifactId>
-	    	<version>1.11.405</version>
 	    </dependency>
 	    <dependency>
 	    	<groupId>com.amazonaws</groupId>
@@ -293,17 +258,17 @@
 	    <dependency>
 	    	<groupId>edu.cornell.weill.reciter</groupId>
 	    	<artifactId>reciter-identity-model</artifactId>
-	    	<version>2.0.3</version>
+	    	<version>2.0.5</version>
 	    </dependency>
 	    <dependency>
 	    	<groupId>edu.cornell.weill.reciter</groupId>
 	    	<artifactId>reciter-article-model</artifactId>
-	    	<version>2.0.9</version>
+	    	<version>2.0.10</version>
 	    </dependency>
 	    <dependency>
 	    	<groupId>edu.cornell.weill.reciter</groupId>
 	    	<artifactId>reciter-dynamodb-model</artifactId>
-	    	<version>2.0.2</version>
+	    	<version>2.0.3</version>
 	    </dependency>
 	    <dependency>
 	    	<groupId>com.github.bohnman</groupId>
@@ -313,7 +278,6 @@
 	    <dependency>
 	    	<groupId>org.mockito</groupId>
 	    	<artifactId>mockito-core</artifactId>
-	    	<version>2.27.0</version>
 	    </dependency>
     </dependencies>
     <repositories>

diff --git a/src/main/java/reciter/Application.java b/src/main/java/reciter/Application.java
@@ -52,17 +52,20 @@
 import com.google.common.collect.Iterables;
 
 import lombok.extern.slf4j.Slf4j;
+import reciter.database.dyanmodb.files.GenderFileImport;
 import reciter.database.dyanmodb.files.IdentityFileImport;
 import reciter.database.dyanmodb.files.InstitutionAfidFileImport;
 import reciter.database.dyanmodb.files.MeshTermFileImport;
 import reciter.database.dyanmodb.files.ScienceMetrixDepartmentCategoryFileImport;
 import reciter.database.dyanmodb.files.ScienceMetrixFileImport;
+import reciter.database.dynamodb.model.Gender;
 import reciter.database.dynamodb.model.InstitutionAfid;
 import reciter.database.dynamodb.model.MeshTerm;
 import reciter.database.dynamodb.model.ScienceMetrix;
 import reciter.database.dynamodb.model.ScienceMetrixDepartmentCategory;
 import reciter.engine.EngineParameters;
 import reciter.security.APIKey;
+import reciter.service.GenderService;
 import reciter.service.ScienceMetrixDepartmentCategoryService;
 import reciter.service.ScienceMetrixService;
 import reciter.service.dynamo.DynamoDbInstitutionAfidService;
@@ -98,6 +101,9 @@ public class Application {
     @Autowired
     private DynamoDbInstitutionAfidService dynamoDbInstitutionAfidService;
 
+    @Autowired
+    private GenderService genderService;
+
     @Value("${use.scopus.articles}")
     private boolean useScopusArticles;
 
@@ -232,6 +238,9 @@ public void loadDynamoDbTablesAfterStartUp() {
 			IdentityFileImport identityFileImport = ApplicationContextHolder.getContext().getBean(IdentityFileImport.class);
 			identityFileImport.importIdentity();
 
+			GenderFileImport genderFileImport = ApplicationContextHolder.getContext().getBean(GenderFileImport.class);
+			genderFileImport.importGender();
+
 			if(useScopusArticles) {
 				InstitutionAfidFileImport institutionAfidFileImport = ApplicationContextHolder.getContext().getBean(InstitutionAfidFileImport.class);
 				institutionAfidFileImport.importInstitutionAfids();
@@ -263,6 +272,12 @@ public void populateStaticEngineParameters() {
             }
             EngineParameters.setMeshCountMap(meshCountMap);
         }
+        log.info("Loading GenderProbability to Engine Parameters");
+        List<Gender> genders = genderService.findAll();
+        if(genders != null && !genders.isEmpty()) {
+        	EngineParameters.setGenders(genders);
+        }
+
         if(useScopusArticles) {
 	        log.info("Loading ScopusInstitutionalAfids to Engine Parameters");
 	        List<InstitutionAfid> instAfids = dynamoDbInstitutionAfidService.findAll();
@@ -271,6 +286,8 @@ public void populateStaticEngineParameters() {
 		        	EngineParameters.setAfiliationNameToAfidMap(institutionAfids);
 	        }
         }
+
+        log.info("ReCiter is up and ready to use. Please make sure its other components such as Pubmed-Retrieval-Tool is also setup if you wish to do retrieval.");
 	}
 
 

diff --git a/src/main/java/reciter/algorithm/cluster/article/scorer/ReCiterArticleScorer.java b/src/main/java/reciter/algorithm/cluster/article/scorer/ReCiterArticleScorer.java
@@ -35,6 +35,8 @@
 import reciter.algorithm.evidence.targetauthor.department.strategy.DepartmentStringMatchStrategy;
 import reciter.algorithm.evidence.targetauthor.email.EmailStrategyContext;
 import reciter.algorithm.evidence.targetauthor.email.strategy.EmailStringMatchStrategy;
+import reciter.algorithm.evidence.targetauthor.gender.GenderStrategyContext;
+import reciter.algorithm.evidence.targetauthor.gender.strategy.GenderStrategy;
 import reciter.algorithm.evidence.targetauthor.grant.GrantStrategyContext;
 import reciter.algorithm.evidence.targetauthor.grant.strategy.GrantStrategy;
 import reciter.algorithm.evidence.targetauthor.journalcategory.JournalCategoryStrategyContext;
@@ -150,9 +152,14 @@ public class ReCiterArticleScorer extends AbstractArticleScorer {
 	private StrategyContext personTypeStrategyContext;
 
 	/**
-	 * Accpeted Rejected .
+	 * Accepted Rejected .
 	 */
 	private StrategyContext acceptedRejectedStrategyContext;
+
+	/**
+	 * Gender Strategy
+	 */
+	private GenderStrategyContext genderStrategyContext;
 
 	/**
 	 * Remove clusters based on cluster information.
@@ -186,6 +193,7 @@ public ReCiterArticleScorer(Map<Long, ReCiterCluster> clusters, Identity identit
 		this.journalCategoryStrategyContext = new JournalCategoryStrategyContext(new JournalCategoryStrategy());
 		this.knownRelationshipsStrategyContext = new KnownRelationshipStrategyContext(new KnownRelationshipStrategy());
 		this.affiliationStrategyContext = new AffiliationStrategyContext(new CommonAffiliationStrategy());
+		this.genderStrategyContext = new GenderStrategyContext(new GenderStrategy());
 
 		// Using the following strategy contexts in sequence to reassign individual articles
 		// to selected clusters.
@@ -238,6 +246,10 @@ public ReCiterArticleScorer(Map<Long, ReCiterCluster> clusters, Identity identit
 		if(strategyParameters.isAverageClustering()) {
 			this.strategyContexts.add(this.averageClusteringStrategyContext);
 		}
+
+		if(strategyParameters.isGender()) {
+			this.strategyContexts.add(this.genderStrategyContext);
+		}
 	}
 
 
@@ -293,6 +305,10 @@ public void runArticleScorer(Map<Long, ReCiterCluster> clusters, Identity identi
 				((ReCiterArticleStrategyContext) acceptedRejectedStrategyContext).executeStrategy(reCiterArticles);
 			}
 
+			if(strategyParameters.isGender()) {
+				((TargetAuthorStrategyContext) genderStrategyContext).executeStrategy(reCiterArticles, identity);
+			}
+
 			if (strategyParameters.isAverageClustering()) {
 				((ClusterStrategyContext) averageClusteringStrategyContext).executeStrategy(entry.getValue());
 			}

diff --git a/...iter/algorithm/evidence/cluster/averageclustering/strategy/AverageClusteringStrategy.java b/...iter/algorithm/evidence/cluster/averageclustering/strategy/AverageClusteringStrategy.java
@@ -36,8 +36,9 @@ public double executeStrategy(ReCiterCluster reCiterCluster) {
 				if(ReCiterArticleScorer.strategyParameters.isUseGoldStandardEvidence()) {
 					double totalArticleScoreWithoutClustering =  ((reCiterArticle.getAuthorNameEvidence() != null)?(reCiterArticle.getAuthorNameEvidence().getNameScoreTotal()):0) +
 							((reCiterArticle.getEmailEvidence() != null)?reCiterArticle.getEmailEvidence().getEmailMatchScore():0) +
+							((reCiterArticle.getGenderEvidence() != null && reCiterArticle.getGenderEvidence().getGenderScoreIdentityArticleDiscrepancy() != null)?reCiterArticle.getGenderEvidence().getGenderScoreIdentityArticleDiscrepancy():0) +
 							reCiterArticle.getGrantEvidenceTotalScore() +
-							reCiterArticle.getRelationshipEvidencesTotalScore() +
+							((reCiterArticle.getRelationshipEvidence() != null)?reCiterArticle.getRelationshipEvidence().getRelationshipEvidenceTotalScore():0) +
 							((reCiterArticle.getEducationYearEvidence() != null)?reCiterArticle.getEducationYearEvidence().getDiscrepancyDegreeYearBachelorScore():0) +
 							((reCiterArticle.getEducationYearEvidence() != null)?reCiterArticle.getEducationYearEvidence().getDiscrepancyDegreeYearDoctoralScore():0) +
 							reCiterArticle.getOrganizationalEvidencesTotalScore() +
@@ -53,8 +54,9 @@ public double executeStrategy(ReCiterCluster reCiterCluster) {
 				} else {
 					double totalArticleScoreWithoutClustering = ((reCiterArticle.getAuthorNameEvidence() != null)?(reCiterArticle.getAuthorNameEvidence().getNameScoreTotal()):0) + 
 							((reCiterArticle.getEmailEvidence() != null)?reCiterArticle.getEmailEvidence().getEmailMatchScore():0) + 
+							((reCiterArticle.getGenderEvidence() != null && reCiterArticle.getGenderEvidence().getGenderScoreIdentityArticleDiscrepancy() != null)?reCiterArticle.getGenderEvidence().getGenderScoreIdentityArticleDiscrepancy():0) +
 							reCiterArticle.getGrantEvidenceTotalScore() +
-							reCiterArticle.getRelationshipEvidencesTotalScore() +
+							((reCiterArticle.getRelationshipEvidence() != null)?reCiterArticle.getRelationshipEvidence().getRelationshipEvidenceTotalScore():0) +
 							((reCiterArticle.getEducationYearEvidence() != null)?reCiterArticle.getEducationYearEvidence().getDiscrepancyDegreeYearBachelorScore():0) +
 							((reCiterArticle.getEducationYearEvidence() != null)?reCiterArticle.getEducationYearEvidence().getDiscrepancyDegreeYearDoctoralScore():0) +
 							reCiterArticle.getOrganizationalEvidencesTotalScore() +
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		web: java -jar reciter-0.0.1-SNAPSHOT.jar
		web: java -jar reciter-1.1.jar