EVA-3999 - Add an ro-crate data catalog

eva-lib/src/main/java/uk/ac/ebi/eva/lib/metadata/eva/RoCrateMetadataAdaptor.java

@@ -13,7 +13,9 @@
 import uk.ac.ebi.eva.lib.entities.Submission;
 import uk.ac.ebi.eva.lib.entities.Taxonomy;
 import uk.ac.ebi.eva.lib.models.rocrate.CommentEntity;
-import uk.ac.ebi.eva.lib.models.rocrate.DatasetEntity;
+import uk.ac.ebi.eva.lib.models.rocrate.DataCatalogEntity;
+import uk.ac.ebi.eva.lib.models.rocrate.MinimalProjectDatasetEntity;
+import uk.ac.ebi.eva.lib.models.rocrate.ProjectDatasetEntity;
 import uk.ac.ebi.eva.lib.models.rocrate.FileEntity;
 import uk.ac.ebi.eva.lib.models.rocrate.LabProcessEntity;
 import uk.ac.ebi.eva.lib.models.rocrate.Reference;
@@ -86,7 +88,7 @@ public RoCrateMetadata getMetadataByProjectAccession(String accession) {
         List<RoCrateEntity> entities = new ArrayList<>();
         List<String> publications = getPublications(project);
         List<RoCrateEntity> additionalProjectProperties = getAdditionalProjectProperties(project);
-        entities.add(new DatasetEntity(project.getProjectAccession(), project.getTitle(), project.getDescription(),
+        entities.add(new ProjectDatasetEntity(project.getProjectAccession(), project.getTitle(), project.getDescription(),
                                        getFirstSubmissionDate(project), project.getCenterName(), publications,
                                        getReferences(analysisRoEntities), getReferences(allFiles),
                                        getReferences(additionalProjectProperties)));
@@ -100,6 +102,26 @@ public RoCrateMetadata getMetadataByProjectAccession(String accession) {
         return new RoCrateMetadata(entities);
     }
 
+    public RoCrateMetadata getAllProjects(){
+        List<Project> projects = projectRepository.findAll();
+        // Construct the project-related entities
+        List<RoCrateEntity> projectsRoEntities = new ArrayList<>();
+        List<RoCrateEntity> allAdditionalProjectProperties = new ArrayList<>();
+        for (Project project : projects) {
+            List<RoCrateEntity> additionalProjectProperties = getAdditionalProjectProperties(project);
+            allAdditionalProjectProperties.addAll(additionalProjectProperties);
+            projectsRoEntities.add(new MinimalProjectDatasetEntity(project.getProjectAccession(), project.getTitle(), project.getDescription(),
+                    getFirstSubmissionDate(project), getReferences(additionalProjectProperties)));
+        }
+
+        // Construct the DataCatalogEntity and add all entities to the RO-crate metadata
+        List<RoCrateEntity> entities = new ArrayList<>();
+        entities.add(new DataCatalogEntity(getReferences(projectsRoEntities), getMostRecentDatePublished(projectsRoEntities)));
+        entities.addAll(projectsRoEntities);
+        entities.addAll(allAdditionalProjectProperties);
+        return new RoCrateMetadata(entities);
+    }
+
     private List<String> getPublications(Project project) {
         return project.getDbXrefs()
                       .stream()
@@ -118,6 +140,14 @@ private LocalDate getFirstSubmissionDate(Project project) {
                       .map(Submission::getDate).orElse(null);
     }
 
+    private LocalDate getMostRecentDatePublished(List<RoCrateEntity> projectsRoEntities) {
+
+        return projectsRoEntities.stream()
+                .map(entity -> (MinimalProjectDatasetEntity) entity)
+                .max(Comparator.comparing(MinimalProjectDatasetEntity::getDatePublished))
+                .map(MinimalProjectDatasetEntity::getDatePublished).orElse(null);
+    }
+
     private List<RoCrateEntity> getAdditionalProjectProperties(Project project) {
         List<RoCrateEntity> additionalProperties = new ArrayList<>();
         Long taxonomyId = null;
@@ -133,11 +163,11 @@ private List<RoCrateEntity> getAdditionalProjectProperties(Project project) {
             scientificName = taxonomy.getScientificName();
         }
 
-        additionalProperties.add(new CommentEntity("taxonomyId", "" + taxonomyId));
-        additionalProperties.add(new CommentEntity("scientificName", scientificName));
-        additionalProperties.add(new CommentEntity("scope", project.getScope()));
-        additionalProperties.add(new CommentEntity("material", project.getMaterial()));
-        additionalProperties.add(new CommentEntity("sourceType", project.getSourceType()));
+        additionalProperties.add(new CommentEntity(project.getProjectAccession(), "taxonomyId", "" + taxonomyId));
+        additionalProperties.add(new CommentEntity(project.getProjectAccession(), "scientificName", scientificName));
+        additionalProperties.add(new CommentEntity(project.getProjectAccession(), "scope", project.getScope()));
+        additionalProperties.add(new CommentEntity(project.getProjectAccession(), "material", project.getMaterial()));
+        additionalProperties.add(new CommentEntity(project.getProjectAccession(), "sourceType", project.getSourceType()));
 
         return additionalProperties;
     }

eva-lib/src/main/java/uk/ac/ebi/eva/lib/models/rocrate/DataCatalogEntity.java

@@ -0,0 +1,59 @@
+package uk.ac.ebi.eva.lib.models.rocrate;
+
+import com.fasterxml.jackson.annotation.JsonFormat;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import com.fasterxml.jackson.datatype.jsr310.deser.LocalDateDeserializer;
+import com.fasterxml.jackson.datatype.jsr310.ser.LocalDateSerializer;
+
+import java.time.LocalDate;
+import java.util.List;
+
+public class DataCatalogEntity extends RoCrateEntity {
+
+    private static final String ID = "https://www.ebi.ac.uk/eva/";
+    private static final String TYPE = "DataCatalog";
+    private static final String IDENTIFIER = "EVA studies";
+    private static final String LICENSE = "https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website/";
+
+    @JsonDeserialize(using = LocalDateDeserializer.class)
+    @JsonSerialize(using = LocalDateSerializer.class)
+    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd")
+    private LocalDate datePublished;
+
+    private String license;
+
+    private String identifier;
+
+    @JsonProperty("dataset")
+    private List<Reference> projects;
+
+    public DataCatalogEntity() {
+    }
+
+    public DataCatalogEntity(List<Reference> projects, LocalDate datePublished) {
+        super(ID , TYPE);
+        this.license = LICENSE;
+        this.identifier = IDENTIFIER;
+        this.projects = projects;
+        this.datePublished = datePublished;
+    }
+
+    public String getIdentifier() {
+        return identifier;
+    }
+
+    public List<Reference> getProjects() {
+        return projects;
+    }
+
+    public LocalDate getDatePublished() {
+        return datePublished;
+    }
+
+    public String getLicense() {
+        return license;
+    }
+
+}

eva-lib/src/main/java/uk/ac/ebi/eva/lib/models/rocrate/DatasetEntity.java → eva-lib/src/main/java/uk/ac/ebi/eva/lib/models/rocrate/MinimalProjectDatasetEntity.java

@@ -10,54 +10,37 @@
 import java.time.LocalDate;
 import java.util.List;
 
-public class DatasetEntity extends RoCrateEntity {
+public class MinimalProjectDatasetEntity extends RoCrateEntity {
 
-    private String name;
+    protected String name;
 
-    private String description;
+    protected String description;
 
     @JsonDeserialize(using = LocalDateDeserializer.class)
     @JsonSerialize(using = LocalDateSerializer.class)
     @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = "yyyy-MM-dd")
-    private LocalDate datePublished;
+    protected LocalDate datePublished;
 
-    private String license;
-
-    @JsonProperty("creator")
-    private String centerName;
-
-    @JsonProperty("citation")
-    private List<String> publications;
+    protected String license;
 
     @JsonProperty("identifier")
-    private String projectAccession;
-
-    @JsonProperty("processSequence")
-    private List<Reference> analyses;
-
-    @JsonProperty("hasPart")
-    private List<Reference> files;
+    protected String projectAccession;
 
     @JsonProperty("comment")
     // Project-level properties that aren't in schema.org/Dataset are included as Comments
-    private List<Reference> additionalProperties;
+    protected List<Reference> additionalProperties;
 
-    public DatasetEntity() {
+    public MinimalProjectDatasetEntity() {
     }
 
-    public DatasetEntity(String accession, String name, String description, LocalDate datePublished, String centerName,
-                         List<String> publications, List<Reference> analyses, List<Reference> files,
-                         List<Reference> additionalProperties) {
+    public MinimalProjectDatasetEntity(String accession, String name, String description, LocalDate datePublished,
+                                       List<Reference> additionalProperties) {
         super("https://www.ebi.ac.uk/eva/?eva-study=" + accession, "Dataset");
         this.projectAccession = accession;
         this.name = name;
         this.description = description;
         this.datePublished = datePublished;
         this.license = "https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website/";
-        this.centerName = centerName;
-        this.publications = publications;
-        this.analyses = analyses;
-        this.files = files;
         this.additionalProperties = additionalProperties;
     }
 
@@ -77,26 +60,10 @@ public String getLicense() {
         return license;
     }
 
-    public String getCenterName() {
-        return centerName;
-    }
-
-    public List<String> getPublications() {
-        return publications;
-    }
-
     public String getProjectAccession() {
         return projectAccession;
     }
 
-    public List<Reference> getAnalyses() {
-        return analyses;
-    }
-
-    public List<Reference> getFiles() {
-        return files;
-    }
-
     public List<Reference> getAdditionalProperties() {
         return additionalProperties;
     }

eva-lib/src/main/java/uk/ac/ebi/eva/lib/models/rocrate/ProjectDatasetEntity.java

@@ -0,0 +1,52 @@
+package uk.ac.ebi.eva.lib.models.rocrate;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+
+import java.time.LocalDate;
+import java.util.List;
+
+public class ProjectDatasetEntity extends MinimalProjectDatasetEntity {
+
+    @JsonProperty("creator")
+    private String centerName;
+
+    @JsonProperty("citation")
+    private List<String> publications;
+
+    @JsonProperty("processSequence")
+    private List<Reference> analyses;
+
+    @JsonProperty("hasPart")
+    private List<Reference> files;
+
+    public ProjectDatasetEntity() {
+    }
+
+    public ProjectDatasetEntity(String accession, String name, String description, LocalDate datePublished, String centerName,
+                                List<String> publications, List<Reference> analyses, List<Reference> files,
+                                List<Reference> additionalProperties) {
+        super(accession, name, description, datePublished, additionalProperties);
+        this.centerName = centerName;
+        this.publications = publications;
+        this.analyses = analyses;
+        this.files = files;
+    }
+
+    public String getCenterName() {
+        return centerName;
+    }
+
+    public List<String> getPublications() {
+        return publications;
+    }
+
+    public List<Reference> getAnalyses() {
+        return analyses;
+    }
+
+    public List<Reference> getFiles() {
+        return files;
+    }
+
+}

eva-lib/src/main/java/uk/ac/ebi/eva/lib/models/rocrate/RoCrateEntity.java

@@ -13,7 +13,8 @@
 )
 @JsonSubTypes({
         @JsonSubTypes.Type(value = CommentEntity.class, name = "Comment"),
-        @JsonSubTypes.Type(value = DatasetEntity.class, name = "Dataset"),
+        @JsonSubTypes.Type(value = DataCatalogEntity.class, name = "DataCatalog"),
+        @JsonSubTypes.Type(value = ProjectDatasetEntity.class, name = "Dataset"),
         @JsonSubTypes.Type(value = FileEntity.class, name = "File"),
         @JsonSubTypes.Type(value = LabProcessEntity.class, name = "LabProcess"),
         @JsonSubTypes.Type(value = MetadataEntity.class, name = "CreativeWork"),

eva-lib/src/main/java/uk/ac/ebi/eva/lib/repositories/ProjectRepository.java

@@ -21,4 +21,5 @@
 public interface ProjectRepository extends JpaRepository<Project,String > {
 
     Project getProjectByProjectAccession(String accession);
+
 }

eva-server/src/main/java/uk/ac/ebi/eva/server/ws/StudyWSServer.java

@@ -125,4 +125,14 @@ public ResponseEntity<RoCrateMetadata> getStudyRoCrate(@PathVariable("study") St
         }
         return ResponseEntity.ok(roCrateMetadata);
     }
+
+    @RequestMapping(value = "/ro-crate", method = RequestMethod.GET)
+    public ResponseEntity<RoCrateMetadata> getAllRoCrates() {
+        RoCrateMetadata roCrateMetadata = roCrateMetadataAdaptor.getAllProjects();
+        if (roCrateMetadata == null) {
+            return new ResponseEntity<>(HttpStatus.NOT_FOUND);
+        }
+        ResponseEntity<RoCrateMetadata> response = ResponseEntity.ok(roCrateMetadata);
+        return response;
+    }
 }

eva-server/src/test/java/uk/ac/ebi/eva/server/ws/StudyWSServerTest.java

@@ -24,7 +24,9 @@
 import uk.ac.ebi.eva.lib.entities.Submission;
 import uk.ac.ebi.eva.lib.entities.Taxonomy;
 import uk.ac.ebi.eva.lib.models.rocrate.CommentEntity;
-import uk.ac.ebi.eva.lib.models.rocrate.DatasetEntity;
+import uk.ac.ebi.eva.lib.models.rocrate.DataCatalogEntity;
+import uk.ac.ebi.eva.lib.models.rocrate.MinimalProjectDatasetEntity;
+import uk.ac.ebi.eva.lib.models.rocrate.ProjectDatasetEntity;
 import uk.ac.ebi.eva.lib.models.rocrate.FileEntity;
 import uk.ac.ebi.eva.lib.models.rocrate.LabProcessEntity;
 import uk.ac.ebi.eva.lib.models.rocrate.MetadataEntity;
@@ -175,15 +177,15 @@ public void testGetRoCrate() {
         assertEquals("ro-crate-metadata.json", metadata.getId());
 
         // Second entity is the dataset, corresponding to the project
-        DatasetEntity dataset = (DatasetEntity) roCrateMetadata.getGraph().get(1);
+        ProjectDatasetEntity dataset = (ProjectDatasetEntity) roCrateMetadata.getGraph().get(1);
         assertEquals("PRJEB0001", dataset.getProjectAccession());
         assertEquals("project title", dataset.getName());
         assertEquals(LocalDate.of(2025, 1, 1), dataset.getDatePublished());
 
         // Additional properties of project are separate entities
         List<Reference> taxonomyRefs = dataset.getAdditionalProperties()
                                               .stream()
-                                              .filter(ref -> ref.getId().equalsIgnoreCase("#taxonomyId"))
+                                              .filter(ref -> ref.getId().equalsIgnoreCase("#PRJEB0001-taxonomyId"))
                                               .collect(Collectors.toList());
         List<RoCrateEntity> taxonomyEntities = roCrateMetadata.getEntities(taxonomyRefs);
         assertEquals(1, taxonomyEntities.size());
@@ -218,6 +220,31 @@ public void testGetRoCrate() {
                      sampleEntities.stream().map(SampleEntity::getName).collect(Collectors.toSet()));
     }
 
+    @Test
+    public void testGetRoCrateCatalog() {
+        String url = "/v1/studies/ro-crate";
+        ResponseEntity<RoCrateMetadata> response = restTemplate.exchange(url, HttpMethod.GET, null,
+                RoCrateMetadata.class);
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+
+        RoCrateMetadata roCrateMetadata = response.getBody();
+
+        // First entity describes the metadata document itself
+        MetadataEntity metadata = (MetadataEntity) roCrateMetadata.getGraph().get(0);
+        assertEquals("ro-crate-metadata.json", metadata.getId());
+
+        // Second entity is the dataCatalog for all of EVA's projects
+        DataCatalogEntity dataCatalog = (DataCatalogEntity) roCrateMetadata.getGraph().get(1);
+        assertEquals("EVA studies", dataCatalog.getIdentifier());
+        assertEquals(LocalDate.of(2025, 1, 1), dataCatalog.getDatePublished());
+
+        // Check project entities (dataset)
+        List<RoCrateEntity> projects = roCrateMetadata.getEntitiesOfType("Dataset");
+        assertEquals(1, projects.size());
+        MinimalProjectDatasetEntity project = (MinimalProjectDatasetEntity) projects.stream().sorted().findFirst().get();
+        assertEquals("PRJEB0001", project.getProjectAccession());
+    }
+
     @Test
     public void testGetRoCrateNotFound() {
         String url = "/v1/studies/ro-crate/PRJEB999";