Release 1.0.6

.github/workflows/sanity.yml

@@ -0,0 +1,34 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will build a Java project with Gradle and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-gradle
+
+name: Java CI with Gradle
+
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          java-version: '11'
+          distribution: 'temurin'
+      - name: Build with Gradle
+        uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+        with:
+          arguments: test

build.gradle

@@ -10,7 +10,7 @@ plugins {
 }
 
 group = 'org.monarchinitiative.poet'
-version = '1.0.5'
+version = '1.0.6'
 sourceCompatibility = '11'
 
 configurations {
@@ -57,6 +57,7 @@ task genJaxb {
 repositories {
 	mavenCentral()
 }
+
 dependencies {
 	implementation 'org.springframework.boot:spring-boot-starter-actuator'
 	implementation 'org.springframework.boot:spring-boot-starter-data-jpa'
@@ -67,28 +68,30 @@ dependencies {
 	implementation 'org.springframework.security:spring-security-oauth2-jose'
 	implementation 'org.springframework.security:spring-security-config'
 	implementation 'org.springframework.boot:spring-boot-starter-security'
-	implementation group: 'org.monarchinitiative.phenol', name: 'phenol-core', version: '1.6.1'
+	implementation group: 'org.monarchinitiative.phenol', name: 'phenol-core', version: '2.0.0'
 	implementation 'org.mariadb.jdbc:mariadb-java-client:2.7.4'
-	implementation 'org.monarchinitiative.phenol:phenol-annotations:1.6.2'
-	implementation 'org.monarchinitiative.phenol:phenol-io:1.6.2'
+	implementation 'org.monarchinitiative.phenol:phenol-annotations:2.0.0'
+	implementation 'org.monarchinitiative.phenol:phenol-io:2.0.0'
 	implementation 'org.apache.commons:commons-csv:1.9.0'
 	implementation 'org.springframework.ws:spring-ws-core'
+	implementation 'org.apache.commons:commons-text:1.10.0'
 	// For Java 11:
 	implementation 'org.glassfish.jaxb:jaxb-runtime'
 	implementation(files(genJaxb.classesDir).builtBy(genJaxb))
-	implementation ('org.springframework.boot:spring-boot-starter-web-services') {
+	implementation('org.springframework.boot:spring-boot-starter-web-services') {
 		exclude group: 'org.springframework.boot', module: 'spring-boot-starter-tomcat'
 	}
 
 	jaxb "com.sun.xml.bind:jaxb-xjc:2.1.7"
 
-	runtimeOnly 'com.h2database:h2'
+	testRuntimeOnly 'com.h2database:h2'
 	providedRuntime 'org.springframework.boot:spring-boot-starter-tomcat'
 	testImplementation('org.springframework.boot:spring-boot-starter-test') {
 		exclude group: 'org.junit.vintage', module: 'junit-vintage-engine'
 	}
 	testImplementation group: 'org.spockframework', name: 'spock-core', version: '1.3-groovy-2.4'
 	testImplementation group: 'org.spockframework', name: 'spock-spring', version: '1.3-groovy-2.4'
+	testImplementation 'org.springframework.security:spring-security-test:4.2.3.RELEASE'
 }
 
 def profile = 'development'
@@ -128,8 +131,21 @@ test {
 	systemProperty 'spring.profiles.active', 'test'
 }
 
+jacocoTestReport {
+	afterEvaluate {
+		classDirectories.setFrom(files(classDirectories.files.collect {
+			fileTree(dir: it, exclude: [
+					"org/monarchinitiative/poet/service/InitDatabaseService.class",
+					"org/monarchinitiative/poet/views/*",
+					"org/monarchinitiative/poet/model/utility/HpoAnnotationLine.class",
+			])
+		}))
+	}
+}
+
 test.finalizedBy(jacocoTestReport)
 
+
 clean {
 	delete fileTree(dir: "src/main/resources/static")
 }
@@ -174,4 +190,4 @@ bootRun {
 		profile = "initialize"
 	}
 	systemProperty "spring.profiles.active", profile
-}
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.7-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/main/java/org/monarchinitiative/poet/controller/ExportController.java

@@ -1,8 +1,6 @@
 package org.monarchinitiative.poet.controller;
 
 import org.apache.commons.csv.CSVFormat;
-import org.monarchinitiative.poet.model.entities.Version;
-import org.monarchinitiative.poet.model.enumeration.AnnotationStatus;
 import org.monarchinitiative.poet.service.ExportService;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.http.HttpStatus;

src/main/java/org/monarchinitiative/poet/controller/StatisticsController.java

@@ -15,11 +15,7 @@
 import org.springframework.data.domain.Sort;
 import org.springframework.security.core.Authentication;
 import org.springframework.web.bind.annotation.*;
-
-import java.util.Comparator;
 import java.util.List;
-import java.util.Map;
-import java.util.stream.Collector;
 import java.util.stream.Collectors;
 
 /**
@@ -79,9 +75,11 @@ public List<DiseaseCount> getDiseaseActivity(@RequestParam(value = "all", defaul
                 map(UserActivity::getAnnotation).map(Annotation::getAnnotationSource)
                 .collect(Collectors.groupingByConcurrent(AnnotationSource::getDisease, Collectors.counting()))
                 .entrySet().stream()
-                .map(entry ->
-                        new DiseaseCount(entry.getKey().getDiseaseId(), entry.getKey().getDiseaseName(),
-                                entry.getValue())).collect(Collectors.toList());
+                .map(entry -> {
+                    return new DiseaseCount(entry.getKey().getDiseaseId(), entry.getKey().getDiseaseName(),
+                            entry.getValue());
+
+                }).collect(Collectors.toList());
     }
 
     /**

src/main/java/org/monarchinitiative/poet/model/entities/Annotation.java

@@ -9,7 +9,9 @@
 
 import javax.persistence.*;
 import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.List;
+import java.util.Locale;
 import java.util.Objects;
 
 @Entity
@@ -47,6 +49,9 @@ public class Annotation {
     @JsonView({AnnotationViews.Simple.class, AnnotationViews.UserSpecific.class})
     private LocalDateTime lastUpdatedDate;
 
+    @Transient
+    private LocalDateTime createdDate;
+
     @OneToOne
     @JsonView({AnnotationViews.Simple.class, AnnotationViews.UserSpecific.class})
     private User owner;
@@ -102,10 +107,22 @@ public LocalDateTime getLastUpdatedDate() {
         return lastUpdatedDate;
     }
 
+    public String getExportLastUpdatedDate(){
+        return DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH).format(this.lastUpdatedDate);
+    }
+
     public void setLastUpdatedDate(LocalDateTime lastUpdatedDate) {
         this.lastUpdatedDate = lastUpdatedDate;
     }
 
+    public String getCreatedDate() {
+        return DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH).format(this.createdDate);
+    }
+
+    public void setCreatedDate(LocalDateTime createdDate) {
+        this.createdDate = createdDate;
+    }
+
     public void newMessage(Message message){
         this.reviewMessages.add(message);
     }

src/main/java/org/monarchinitiative/poet/model/entities/Disease.java

@@ -111,6 +111,10 @@ public void setTreatmentCount(int treatmentCount) {
         this.treatmentCount = treatmentCount;
     }
 
+    public String getExportDiseaseId(){
+        return this.equivalentId == null || this.equivalentId.isBlank() ? this.diseaseId : this.equivalentId;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;

src/main/java/org/monarchinitiative/poet/model/entities/TreatmentAnnotation.java

@@ -3,6 +3,7 @@
 
 import com.fasterxml.jackson.annotation.JsonView;
 import org.monarchinitiative.poet.model.enumeration.AnnotationStatus;
+import org.monarchinitiative.poet.model.enumeration.Relation;
 import org.monarchinitiative.poet.model.requests.TreatmentRequest;
 import org.monarchinitiative.poet.views.AnnotationViews;
 
@@ -30,7 +31,8 @@ public class TreatmentAnnotation extends Annotation {
     private String evidence;
     @JsonView(AnnotationViews.Simple.class)
     @NotNull
-    private String relation;
+    @Enumerated(EnumType.STRING)
+    private Relation relation;
     @JsonView(AnnotationViews.Simple.class)
     private String extensionId;
     @JsonView(AnnotationViews.Simple.class)
@@ -51,7 +53,7 @@ public TreatmentAnnotation(AnnotationSource annotationSource, AnnotationStatus s
         this.hpoId = hpoId;
         this.evidence = evidence;
         this.comment = comment;
-        this.relation = relation;
+        this.relation = Relation.valueOf(relation);
         this.extensionId = extensionId;
         this.extensionLabel = extensionLabel;
     }
@@ -64,7 +66,7 @@ public TreatmentAnnotation(String maxoId, String maxoName, String hpoName, Strin
         this.hpoId = hpoId;
         this.evidence = evidence;
         this.comment = comment;
-        this.relation = relation;
+        this.relation = Relation.valueOf(relation);
         this.extensionId = extensionId;
         this.extensionLabel = extensionLabel;
     }
@@ -79,7 +81,7 @@ public TreatmentAnnotation(TreatmentRequest treatmentRequest, AnnotationSource a
         this.hpoName = treatmentRequest.getHpoName();
         this.evidence = treatmentRequest.getEvidence();
         this.comment = treatmentRequest.getComment();
-        this.relation = treatmentRequest.getRelation();
+        this.relation = Relation.valueOf(treatmentRequest.getRelation());
         this.extensionId = treatmentRequest.getExtensionId();
         this.extensionLabel = treatmentRequest.getExtensionLabel();
     }
@@ -91,7 +93,7 @@ public void updateAnnotation(TreatmentRequest treatmentRequest, AnnotationSource
         this.hpoName = treatmentRequest.getHpoName();
         this.evidence = treatmentRequest.getEvidence();
         this.comment = treatmentRequest.getComment();
-        this.relation = treatmentRequest.getRelation();
+        this.relation = Relation.valueOf(treatmentRequest.getRelation());
         this.extensionId = treatmentRequest.getExtensionId();
         this.extensionLabel = treatmentRequest.getExtensionLabel();
         this.setAnnotationSource(annotationSource);
@@ -121,7 +123,7 @@ public String getComment() {
         return comment;
     }
 
-    public String getRelation() {
+    public Relation getRelation() {
         return relation;
     }
 

src/main/java/org/monarchinitiative/poet/model/entities/User.java

@@ -7,6 +7,9 @@
 import org.monarchinitiative.poet.views.UserViews;
 
 import javax.persistence.*;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
+import java.util.Locale;
 import java.util.Objects;
 
 @Entity
@@ -62,10 +65,10 @@ public String getOrcid(){
     }
 
     public String getExportName(){
-        if (orcid != null) {
-            return String.format("%s[%s]", nickname, orcid);
+        if (orcid != null && !orcid.isBlank()) {
+            return String.format("ORCID:%s",orcid);
         } else {
-            return String.format("%s[]", nickname);
+            return email;
         }
     }
 

src/main/java/org/monarchinitiative/poet/model/entities/UserActivity.java

@@ -91,4 +91,8 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(id, owner, annotation, dateTime, curationAction);
     }
+
+    public Annotation getOldAnnotation() {
+        return oldAnnotation;
+    }
 }

src/main/java/org/monarchinitiative/poet/model/enumeration/Category.java

@@ -1,5 +1,6 @@
 package org.monarchinitiative.poet.model.enumeration;
 
 public enum Category {
-    PHENOTYPE, TREATMENT
+    PHENOTYPE, TREATMENT, UNKNOWN
 }
+

src/main/java/org/monarchinitiative/poet/model/enumeration/Relation.java

@@ -0,0 +1,8 @@
+package org.monarchinitiative.poet.model.enumeration;
+
+/**
+ * The relation of the MAXO term to the HPO term.
+ */
+public enum Relation {
+	TREATS, PREVENTS, INVESTIGATES, CONTRAINDICATED, NO_OBSERVED_BENEFIT
+}

src/main/java/org/monarchinitiative/poet/model/requests/DiseaseRequest.java

@@ -1,24 +1,18 @@
 package org.monarchinitiative.poet.model.requests;
 
 public class DiseaseRequest {
-    private final String id;
     private final String diseaseId;
     private final String diseaseName;
     private final String description;
     private final String equivalentId;
 
-    public DiseaseRequest(String id, String diseaseId, String diseaseName, String description, String equivalentId) {
-        this.id = id;
+    public DiseaseRequest(String diseaseId, String diseaseName, String description, String equivalentId) {
         this.diseaseId = diseaseId;
         this.diseaseName = diseaseName;
         this.description = description;
         this.equivalentId = equivalentId;
     }
 
-    public String getId() {
-        return id;
-    }
-
     public String getDiseaseId() {
         return diseaseId;
     }

src/main/java/org/monarchinitiative/poet/model/responses/Contribution.java

@@ -1,25 +1,20 @@
 package org.monarchinitiative.poet.model.responses;
 
 public class Contribution {
-    Integer treatment;
-    Integer phenotype;
-    Integer phenopackets;
+    private final int treatment;
+    private final int phenotype;
 
-    public Contribution(Integer treatment, Integer phenotype, Integer phenopackets) {
-        this.treatment = treatment == null ? 0 : treatment;
-        this.phenotype = phenotype == null ? 0 : phenotype;
-        this.phenopackets = phenopackets == null ? 0 : phenopackets;
+    public Contribution(int treatment, int phenotype) {
+        this.treatment = Math.max(treatment, 0);
+        this.phenotype = Math.max(phenotype, 0);
     }
 
-    public Integer getTreatment() {
+    public int getTreatment() {
         return treatment;
     }
 
-    public Integer getPhenotype() {
+    public int getPhenotype() {
         return phenotype;
     }
 
-    public Integer getPhenopackets() {
-        return phenopackets;
-    }
 }