WIP: Feature/skfp 146 delete phantom sets

Dockerfile

@@ -1,7 +1,7 @@
 FROM openjdk:8u121-jdk-alpine
 
-ARG MAVEN_VERSION=3.5.3
-ARG SHA=b52956373fab1dd4277926507ab189fb797b3bc51a2a267a193c931fffad8408
+ARG MAVEN_VERSION=3.5.4
+ARG SHA=ce50b1c91364cb77efe3776f756a6d92b76d9038b0a0782f7d53acf1e997a14d
 ARG BASE_URL=https://apache.osuosl.org/maven/maven-3/${MAVEN_VERSION}/binaries
 
 RUN apk add --no-cache curl tar bash \

Jenkinsfile

@@ -1,2 +1,21 @@
-@Library(value="oicr", changelog=false) _
-riff_api{}
+@Library(value='kids-first/aws-infra-jenkins-shared-libraries', changelog=false) _
+ecs_service_type_1_standard {
+    projectName = "riff"
+    agentLabel = "terraform-testing"
+    environments = "dev,qa,prd"
+    docker_image_type = "alpine"
+    entrypoint_command = "/srv/riff/exec/run.sh"
+    quick_deploy = "true"
+    external_config_repo = "false"
+    internal_app         = "false"
+    container_port = "8081"
+    vcpu_container             = "1024"
+    memory_container           = "2048"
+    vcpu_task                  = "1024"
+    memory_task                = "2048"
+    health_check_path = "/swagger-ui.html"
+    dependencies = "ecr"
+    additional_ssl_cert_domain_name = "*.kidsfirstdrc.org"
+    publish_to_public_repo = "true"
+    create_additional_internal_alb = "1"
+}

pom.xml

@@ -22,7 +22,7 @@
 
     <groupId>bio.overture</groupId>
     <artifactId>riff</artifactId>
-    <version>1.1.2-SNAPSHOT</version>
+    <version>1.2.3-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <name>riff</name>

src/main/java/bio/overture/riff/controller/RiffController.java

@@ -97,4 +97,16 @@ public boolean deleteRiff(@RequestHeader(value = HttpHeaders.AUTHORIZATION, requ
     }
   }
 
+  @DeleteMapping("/delete-phantom-sets")
+  public int deletePhantomSets(@RequestHeader(value = HttpHeaders.AUTHORIZATION) final String accessToken) {
+    int result;
+    val user = jwtFacade.getUser();
+    if (user.isPresent()) {
+      result = service.deletePhantomSets(user.get());
+    } else {
+      throw new UnauthorizedUserException("No user");
+    }
+    return result;
+  }
+
 }

src/main/java/bio/overture/riff/model/Riff.java

@@ -35,16 +35,15 @@
 @AllArgsConstructor
 public class Riff {
 
-  @Id
-  @Column(nullable = false, name = "id", updatable = false)
-  @GeneratedValue(strategy = GenerationType.IDENTITY)
-  Long id;
-  String uid;
-  @Type(type = "bio.overture.riff.utils.CustomJsonType")
-  Map<String, Object> content;
-  String alias;
-  boolean sharedPublicly;
-  Date creationDate;
-  Date updatedDate;
-
+    @Id
+    @Column(nullable = false, name = "id", updatable = false)
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    Long id;
+    String uid;
+    @Type(type = "bio.overture.riff.utils.CustomJsonType")
+    Map<String, Object> content;
+    String alias;
+    boolean sharedPublicly;
+    Date creationDate;
+    Date updatedDate;
 }

src/main/java/bio/overture/riff/model/RiffResponse.java

@@ -20,7 +20,6 @@
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
-import lombok.RequiredArgsConstructor;
 
 import java.util.Date;
 import java.util.Map;

src/main/java/bio/overture/riff/model/ShortenRequest.java

@@ -18,14 +18,15 @@
 package bio.overture.riff.model;
 
 import lombok.Data;
-
+import java.util.Date;
 import java.util.Map;
 
 @Data
 public class ShortenRequest {
 
-  Map<String, Object> content;
-  String alias;
-  boolean sharedPublicly;
+    Map<String, Object> content;
+    String alias;
+    boolean sharedPublicly;
+    Date creationDate;
 
 }

src/main/java/bio/overture/riff/repository/RiffRepository.java

@@ -18,12 +18,22 @@
 package bio.overture.riff.repository;
 
 import bio.overture.riff.model.Riff;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
+import org.springframework.data.repository.query.Param;
 
+import javax.transaction.Transactional;
+import java.util.Date;
 import java.util.List;
 
 public interface RiffRepository extends CrudRepository<Riff, Long> {
 
-  List<Riff> findByUidAndSharedPublicly(String uid, Boolean shared);
+    List<Riff> findByUidAndSharedPublicly(String uid, Boolean shared);
+
+    @Modifying
+    @Transactional
+    @Query("DELETE FROM Riff r WHERE r.creationDate <= :creationDate AND r.alias = :alias")
+    int deleteByAliasAndCreationDateBefore(@Param("alias") String alias, @Param("creationDate") Date creationDate);
 
 }

src/main/java/bio/overture/riff/service/RiffService.java

@@ -24,87 +24,97 @@
 import bio.overture.riff.model.ShortenRequest;
 import bio.overture.riff.repository.RiffRepository;
 import lombok.SneakyThrows;
+import lombok.extern.slf4j.Slf4j;
 import lombok.val;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import java.util.Calendar;
 import java.util.Date;
 import java.util.List;
 import java.util.stream.Collectors;
 
+@Slf4j
 @Service
 public class RiffService {
 
-  private RiffRepository repository;
-
-  @Autowired
-  public RiffService(RiffRepository repository) {
-    this.repository = repository;
-  }
-
-  public List<RiffResponse> getUserRiffs(JWTUser user) {
-    return repository.findByUidAndSharedPublicly(user.getUid(), false)
-      .stream()
-      .map(RiffResponse::new)
-      .collect(Collectors.toList());
-  }
-
-  @SneakyThrows
-  public RiffResponse getRiff(String id) {
-    val opt = repository.findById(Long.valueOf(id, 36));
-    if (opt.isPresent()) {
-      return new RiffResponse(opt.get());
-    } else {
-      throw new RiffNotFoundException();
+    private RiffRepository repository;
+
+    @Autowired
+    public RiffService(RiffRepository repository) {
+        this.repository = repository;
+    }
+
+    public List<RiffResponse> getUserRiffs(JWTUser user) {
+        return repository.findByUidAndSharedPublicly(user.getUid(), false)
+                .stream()
+                .map(RiffResponse::new)
+                .collect(Collectors.toList());
+    }
+
+    @SneakyThrows
+    public RiffResponse getRiff(String id) {
+        val opt = repository.findById(Long.valueOf(id, 36));
+        return opt.map(RiffResponse::new).orElseThrow(RiffNotFoundException::new);
+    }
+
+    @SneakyThrows
+    public RiffResponse makeRiff(JWTUser user, ShortenRequest request) {
+        val riff = Riff.builder()
+                .content(request.getContent())
+                .uid(user.getUid())
+                .alias(request.getAlias())
+                .sharedPublicly(request.isSharedPublicly())
+                .creationDate(request.getCreationDate() == null? new Date() : request.getCreationDate())
+                .updatedDate(new Date())
+                .build();
+
+        val newRiff = repository.save(riff);
+        return new RiffResponse(newRiff);
     }
-  }
-
-  @SneakyThrows
-  public RiffResponse makeRiff(JWTUser user, ShortenRequest request) {
-    val riff = Riff.builder()
-      .content(request.getContent())
-      .uid(user.getUid())
-      .alias(request.getAlias())
-      .sharedPublicly(request.isSharedPublicly())
-      .creationDate(new Date())
-      .updatedDate(new Date())
-      .build();
-
-    val newRiff = repository.save(riff);
-    return new RiffResponse(newRiff);
-  }
-
-  public boolean deleteRiff(JWTUser user, String id) {
-    val optionalRiff = repository.findById(Long.valueOf(id, 36));
-    if (optionalRiff.isPresent()) {
-      val riff = optionalRiff.get();
-      if (user.getUid().equals(riff.getUid())) {
-        repository.delete(riff);
-        return true;
-      }
+
+    public boolean deleteRiff(JWTUser user, String id) {
+        val optionalRiff = repository.findById(Long.valueOf(id, 36));
+        return optionalRiff
+                .filter(r -> canAccessRiff(user, r))
+                .map(r -> {
+                    repository.delete(r);
+                    return true;
+                })
+                .orElse(false);
+    }
+
+    public int deletePhantomSets(JWTUser user) {
+        //TODO: add user verification
+        Calendar cal = Calendar.getInstance();
+        cal.add(Calendar.MONTH, -1);
+
+        return repository.deleteByAliasAndCreationDateBefore("", cal.getTime());
     }
-    return false;
-  }
-
-  @SneakyThrows
-  public RiffResponse updateRiff(JWTUser user, String id, ShortenRequest request) {
-    val storageId = Long.valueOf(id, 36);
-    val optionalRiff = repository.findById(storageId);
-    if (optionalRiff.isPresent()) {
-      val riff = Riff.builder()
-        .id(storageId)
-        .content(request.getContent())
-        .uid(user.getUid())
-        .alias(request.getAlias())
-        .sharedPublicly(request.isSharedPublicly())
-        .creationDate(optionalRiff.get().getCreationDate())
-        .updatedDate(new Date())
-        .build();
-      val updated = repository.save(riff);
-      return new RiffResponse(updated);
-    } else {
-     throw new RiffNotFoundException();
+
+    @SneakyThrows
+    public RiffResponse updateRiff(JWTUser user, String id, ShortenRequest request) {
+        val storageId = Long.valueOf(id, 36);
+        val optionalRiff = repository.findById(storageId);
+        val riff = optionalRiff
+                .filter(r -> canAccessRiff(user, r))
+                .map(r ->
+                        Riff.builder().id(storageId).content(request.getContent())
+                                .uid(user.getUid())
+                                .alias(request.getAlias())
+                                .sharedPublicly(request.isSharedPublicly())
+                                .creationDate(r.getCreationDate())
+                                .updatedDate(new Date())
+                                .build()
+                )
+                .orElseThrow(RiffNotFoundException::new);
+        val updated = repository.save(riff);
+        return new RiffResponse(updated);
+    }
+
+    private boolean canAccessRiff(JWTUser user, Riff r) {
+        return r.getUid().equals(user.getUid());
     }
-  }
+
 
 }

src/main/resources/application.yml

@@ -3,7 +3,7 @@ server:
 
 auth:
   jwt:
-   publicKeyUrl: "https://demo.ego.kfdrc.org/oauth/token/public_key"
+   publicKeyUrl: "https://kf-strides-ego-qa.kidsfirstdrc.org/oauth/token/public_key"
 
 spring:
   jpa:

src/main/resources/flyway/sql/V3__rename_studies_with_KF_prefix.sql

@@ -0,0 +1,39 @@
+/**
+ * Database migration script for Riff's PostgreSQL database.
+ *
+ * This script renames the study names stored in the queries for the cohort builder and the file repository.
+ * This is done so that the former queries remain valid once the studies have been renamed in the release coordinator.
+ * 
+ * @date 2019-06-28
+ */
+
+/*
+ * The search queries in the cohort builder are stored as JSON.
+ * The elements in this list are alphatically sorted.
+ * We include the initial double quote, to reduce risks of false positives.
+ */
+UPDATE riff SET content = REPLACE(content::TEXT, '"Adolescent Idiopathic Scoliosis', '"Kids First: Adolescent Idiopathic Scoliosis')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Congenital Diaphragmatic Hernia', '"Kids First: Congenital Diaphragmatic Hernia')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Congenital Hearth Defects', '"Kids First: Congenital Hearth Defects')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Disorder of Sex Development', '"Kids First: Disorder of Sex Development')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Ewing Sarcoma: Genetic Risk', '"Kids First: Ewing Sarcoma - Genetic Risk')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Orofacial Cleft: European Ancestry', '"Kids First: Orofacial Cleft - European Ancestry')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Orofacial Cleft: Latin American', '"Kids First: Orofacial Cleft - Latin American')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Pediatric Brain Tumors: CBTTC', '"Consortium: Pediatric Brain Tumors - CBTTC')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '"Syndromic Cranial Dysinnervation', '"Kids First: Syndromic Cranial Dysinnervation')::JSON;
+
+/*
+ * The search queries in the file repository are stored as their full URL. The SQON is therefore URL-encoded:
+ * The elements in this list are alphatically sorted.
+ * We include the initial double quote, to reduce risks of false positives.
+ */
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Adolescent%20Idiopathic%20Scoliosis', '%22Kids%20First%3A%20Adolescent%20Idiopathic%20Scoliosis')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Congenital%20Diaphragmatic%20Hernia', '%22Kids%20First%3A%20Congenital%20Diaphragmatic%20Hernia')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Congenital%20Hearth%20Defects', '%22Kids%20First%3A%20Congenital%20Hearth%20Defects')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Disorder%20of%20Sex%20Development', '%22Kids%20First%3A%20Disorder%20of%20Sex%20Development')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Ewing%20Sarcoma%3A%20Genetic%20Risk', '%22Kids%20First%3A%20Ewing%20Sarcoma%20-%20Genetic%20Risk')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Orofacial%20Cleft:%20European%20Ancestry', '%22Kids%20First%3A%20Orofacial%20Cleft%20-%20European%20Ancestry')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Orofacial%20Cleft:%20Latin%20American', '%22Kids%20First%3A%20Orofacial%20Cleft%20-%20Latin%20American')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Pediatric%20Brain%20Tumors%3A%20CBTTC', '%22Consortium3A%20Pediatric%20Brain%20Tumors%20-%20CBTTC')::JSON;
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Syndromic%20Cranial%20Dysinnervation', '%22Kids%20First%3A%20Syndromic%20Cranial%20Dysinnervation')::JSON;
+

src/main/resources/flyway/sql/V4__rename_study_cbttc_atlas.sql

@@ -0,0 +1,21 @@
+/**
+ * Database migration script for Riff's PostgreSQL database.
+ *
+ * This script renames the study names stored in the queries for the cohort builder and the file repository.
+ * This is done so that the former queries remain valid once the studies have been renamed in the release coordinator.
+ * 
+ * @date 2019-08-07
+ */
+
+/*
+ * The search queries in the cohort builder are stored as JSON.
+ * We include the initial double quote, to reduce risks of false positives.
+ */
+UPDATE riff SET content = REPLACE(content::TEXT, '"Consortium: Pediatric Brain Tumors - CBTTC', '"Pediatric Brain Tumor Atlas: CBTTC')::JSON;
+
+/*
+ * The search queries in the file repository are stored as their full URL. The SQON is therefore URL-encoded:
+ * We include the initial double quote, to reduce risks of false positives.
+ */
+UPDATE riff SET content = REPLACE(content::TEXT, '%22Consortium3A%20Pediatric%20Brain%20Tumors%20-%20CBTTC', '%22Pediatric%20Brain%20Tumors%20Atlas%3A%20CBTTC')::JSON;
+