Merge pull request #124 from TheJacksonLaboratory/develop

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;
- }
 }