invenio-damap: enable connection from InvenioRDM

* Update re3data XML with root element * Update library usages due to library migration --------- Co-authored-by: Sotiris Tsepelakis <[email protected]> Co-authored-by: ValentinFutterer <[email protected]>
tuwien-csd · Sep 19, 2024 · ab4f13e · ab4f13e
1 parent f6500db
commit ab4f13e
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Showing 26 changed files with 806 additions and 74 deletions.
diff --git a/pom.xml b/pom.xml
@@ -94,6 +94,11 @@
       <artifactId>quarkus-junit5</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>io.quarkus</groupId>
+      <artifactId>quarkus-junit5-component</artifactId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>io.quarkus</groupId>
       <artifactId>quarkus-junit5-mockito</artifactId>
@@ -126,36 +131,32 @@
     <!-- Rest -->
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-resteasy-multipart</artifactId>
+      <artifactId>quarkus-rest</artifactId>
     </dependency>
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-resteasy</artifactId>
+      <artifactId>quarkus-rest-jackson</artifactId>
     </dependency>
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-resteasy-client</artifactId>
+      <artifactId>quarkus-rest-client</artifactId>
     </dependency>
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-resteasy-client-jaxb</artifactId>
+      <artifactId>quarkus-rest-client-jaxb</artifactId>
     </dependency>
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-resteasy-jaxb</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-resteasy-jackson</artifactId>
+      <artifactId>quarkus-rest-client-jackson</artifactId>
     </dependency>
+    <!-- Authentication -->
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-jaxb</artifactId>
+      <artifactId>quarkus-oidc</artifactId>
     </dependency>
-    <!-- Authentication -->
     <dependency>
       <groupId>io.quarkus</groupId>
-      <artifactId>quarkus-oidc</artifactId>
+      <artifactId>quarkus-smallrye-jwt</artifactId>
     </dependency>
     <!-- Database -->
     <dependency>
@@ -260,7 +261,7 @@
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>jaxb2-maven-plugin</artifactId>
-        <version>3.1.0</version>
+        <version>3.2.0</version>
         <executions>
           <execution>
             <id>xjc</id>

diff --git a/src/main/java/org/damap/base/enums/EDataAccessType.java b/src/main/java/org/damap/base/enums/EDataAccessType.java
@@ -46,4 +46,36 @@ public static EDataAccessType getByValue(String value) {
       MAP.put(type.getValue(), type);
     }
   }
+
+  /**
+   * Compares this {@code EDataAccessType} instance with another {@code EDataAccessType} to
+   * determine which is more restrictive. The order of restriction is defined as:
+   *
+   * <ul>
+   *   <li>{@code CLOSED} is the most restrictive.
+   *   <li>{@code RESTRICTED} is more restrictive than {@code OPEN} but less restrictive than {@code
+   *       CLOSED}.
+   *   <li>{@code OPEN} is the least restrictive.
+   * </ul>
+   *
+   * @param other the other {@code EDataAccessType} to compare to; can be {@code null}. If {@code
+   *     null}, this instance is considered more restrictive.
+   * @return {@code 1} if this instance is more restrictive than {@code other}, {@code -1} if this
+   *     instance is less restrictive than {@code other}, and {@code 0} if both instances are equal.
+   */
+  public int compare(EDataAccessType other) {
+    if (other == null) {
+      return 1;
+    }
+
+    if (this == other) {
+      return 0;
+    }
+
+    return switch (this) {
+      case CLOSED -> 1;
+      case RESTRICTED -> (other == CLOSED) ? -1 : 1;
+      case OPEN -> -1;
+    };
+  }
 }
diff --git a/src/main/java/org/damap/base/r3data/RepositoriesRemoteResource.java b/src/main/java/org/damap/base/r3data/RepositoriesRemoteResource.java
@@ -1,14 +1,13 @@
 package org.damap.base.r3data;
 
-import generated.Repository;
 import jakarta.ws.rs.GET;
 import jakarta.ws.rs.Path;
 import jakarta.ws.rs.Produces;
 import jakarta.ws.rs.core.MediaType;
 import java.util.List;
 import org.eclipse.microprofile.rest.client.inject.RegisterRestClient;
-import org.jboss.resteasy.annotations.jaxrs.PathParam;
-import org.jboss.resteasy.annotations.jaxrs.QueryParam;
+import org.jboss.resteasy.reactive.RestPath;
+import org.jboss.resteasy.reactive.RestQuery;
 import org.re3data.schema._2_2.Re3Data;
 
 /** RepositoriesRemoteResource interface. */
@@ -23,7 +22,7 @@ public interface RepositoriesRemoteResource {
    */
   @GET
   @Path("/v1/repositories")
-  List<Repository> getAll();
+  generated.List getAll();
 
   /**
    * getById.
@@ -33,7 +32,7 @@ public interface RepositoriesRemoteResource {
    */
   @GET
   @Path("/v1/repository/{id}")
-  Re3Data getById(@PathParam String id);
+  Re3Data getById(@RestPath String id);
 
   /**
    * search.
@@ -56,19 +55,19 @@ public interface RepositoriesRemoteResource {
    */
   @GET
   @Path("/beta/repositories")
-  List<Repository> search(
-      @QueryParam("subjects[]") List<String> subjects,
-      @QueryParam("contentTypes[]") List<String> contentTypes,
-      @QueryParam("countries[]") List<String> countries,
-      @QueryParam("certificates[]") List<String> certificates,
-      @QueryParam("pidSystems[]") List<String> pidSystems,
-      @QueryParam("aidSystems[]") List<String> aidSystems,
-      @QueryParam("repositoryAccess[]") List<String> repositoryAccess,
-      @QueryParam("dataAccess[]") List<String> dataAccess,
-      @QueryParam("dataUpload[]") List<String> dataUpload,
-      @QueryParam("dataLicenses[]") List<String> dataLicenses,
-      @QueryParam("repositoryTypes[]") List<String> repositoryTypes,
-      @QueryParam("institutionTypes[]") List<String> institutionTypes,
-      @QueryParam("versioning[]") List<String> versioning,
-      @QueryParam("metadataStandards[]") List<String> metadataStandards);
+  generated.List search(
+      @RestQuery("subjects[]") List<String> subjects,
+      @RestQuery("contentTypes[]") List<String> contentTypes,
+      @RestQuery("countries[]") List<String> countries,
+      @RestQuery("certificates[]") List<String> certificates,
+      @RestQuery("pidSystems[]") List<String> pidSystems,
+      @RestQuery("aidSystems[]") List<String> aidSystems,
+      @RestQuery("repositoryAccess[]") List<String> repositoryAccess,
+      @RestQuery("dataAccess[]") List<String> dataAccess,
+      @RestQuery("dataUpload[]") List<String> dataUpload,
+      @RestQuery("dataLicenses[]") List<String> dataLicenses,
+      @RestQuery("repositoryTypes[]") List<String> repositoryTypes,
+      @RestQuery("institutionTypes[]") List<String> institutionTypes,
+      @RestQuery("versioning[]") List<String> versioning,
+      @RestQuery("metadataStandards[]") List<String> metadataStandards);
 }
diff --git a/src/main/java/org/damap/base/r3data/RepositoriesResource.java b/src/main/java/org/damap/base/r3data/RepositoriesResource.java
@@ -1,6 +1,6 @@
 package org.damap.base.r3data;
 
-import generated.Repository;
+import generated.List.Repository;
 import io.quarkus.security.Authenticated;
 import jakarta.inject.Inject;
 import jakarta.ws.rs.GET;
@@ -14,7 +14,7 @@
 import lombok.extern.jbosslog.JBossLog;
 import org.damap.base.r3data.dto.RepositoryDetails;
 import org.damap.base.r3data.mapper.RepositoryMapper;
-import org.jboss.resteasy.annotations.jaxrs.PathParam;
+import org.jboss.resteasy.reactive.RestPath;
 
 /** RepositoriesResource class. */
 @Path("/api/repositories")
@@ -33,7 +33,7 @@ public class RepositoriesResource {
   @GET
   public List<Repository> getAll() {
     log.info("Get all repositories");
-    return repositoriesService.getAll();
+    return repositoriesService.getAll().getRepository();
   }
 
   /**
@@ -56,7 +56,7 @@ public List<RepositoryDetails> getRecommended() {
    */
   @GET
   @Path("/{id}")
-  public RepositoryDetails getById(@PathParam String id) {
+  public RepositoryDetails getById(@RestPath String id) {
     log.info("Get repository with id: " + id);
     return RepositoryMapper.mapToRepositoryDetails(repositoriesService.getById(id), id);
   }
@@ -72,6 +72,6 @@ public RepositoryDetails getById(@PathParam String id) {
   public List<Repository> search(@Context UriInfo uriInfo) {
     log.info("Search repositories: " + uriInfo.getQueryParameters());
     MultivaluedMap<String, String> params = uriInfo.getQueryParameters();
-    return repositoriesService.search(params);
+    return repositoriesService.search(params).getRepository();
   }
 }
diff --git a/src/main/java/org/damap/base/r3data/RepositoriesService.java b/src/main/java/org/damap/base/r3data/RepositoriesService.java
@@ -1,6 +1,5 @@
 package org.damap.base.r3data;
 
-import generated.Repository;
 import io.quarkus.cache.CacheResult;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
@@ -32,7 +31,7 @@ public class RepositoriesService {
    * @return a {@link java.util.List} object
    */
   @CacheResult(cacheName = "repositories")
-  public List<Repository> getAll() {
+  public generated.List getAll() {
     return repositoriesRemoteResource.getAll();
   }
 
@@ -78,7 +77,7 @@ public Re3Data getById(String id) {
    * @param params a {@link jakarta.ws.rs.core.MultivaluedMap} object
    * @return a {@link java.util.List} object
    */
-  public List<Repository> search(MultivaluedMap<String, String> params) {
+  public generated.List search(MultivaluedMap<String, String> params) {
     List<String> subjects = params.get("subjects");
     List<String> contentTypes = params.get("contentTypes");
     List<String> certificates = params.get("certificates");

diff --git a/src/main/java/org/damap/base/rest/AccessResource.java b/src/main/java/org/damap/base/rest/AccessResource.java
@@ -11,7 +11,6 @@
 import org.damap.base.rest.access.service.AccessService;
 import org.damap.base.rest.dmp.domain.ContributorDO;
 import org.damap.base.validation.AccessValidator;
-import org.jboss.resteasy.annotations.jaxrs.PathParam;
 
 /** AccessResource class. */
 @Path("/api/access")

diff --git a/src/main/java/org/damap/base/rest/DataManagementPlanResource.java b/src/main/java/org/damap/base/rest/DataManagementPlanResource.java
@@ -15,7 +15,7 @@
 import org.damap.base.rest.dmp.service.DmpService;
 import org.damap.base.security.SecurityService;
 import org.damap.base.validation.AccessValidator;
-import org.jboss.resteasy.annotations.jaxrs.PathParam;
+import org.jboss.resteasy.reactive.RestPath;
 
 /** DataManagementPlanResource class. */
 @Path("/api/dmps")
@@ -52,7 +52,7 @@ public List<DmpListItemDO> getAll() {
   /*@GET
   @Path("/person/{personId}")
   @RolesAllowed("Damap Admin")
-  public List<DmpListItemDO> getDmpListByPerson(@PathParam String personId) {
+  public List<DmpListItemDO> getDmpListByPerson(@RestPath String personId) {
       log.info("Return dmp for person id: " + personId);
       return dmpService.getDmpListByPersonId(personId);
   }*/
@@ -92,7 +92,7 @@ public List<DmpListItemDO> getDmpsSubordinates() {
    */
   @GET
   @Path("/{id}")
-  public DmpDO getDmpById(@PathParam String id) {
+  public DmpDO getDmpById(@RestPath String id) {
     log.info("Return dmp with id: " + id);
     String personId = this.getPersonId();
     long dmpId = Long.parseLong(id);
@@ -126,7 +126,7 @@ public DmpDO saveDmp(@Valid DmpDO dmpDO) {
   @PUT
   @Path("/{id}")
   @Consumes(MediaType.APPLICATION_JSON)
-  public DmpDO updateDmp(@PathParam String id, @Valid DmpDO dmpDO) {
+  public DmpDO updateDmp(@RestPath String id, @Valid DmpDO dmpDO) {
     log.info("Update dmp with id: " + id);
     String personId = this.getPersonId();
     long dmpId = Long.parseLong(id);
@@ -143,7 +143,7 @@ public DmpDO updateDmp(@PathParam String id, @Valid DmpDO dmpDO) {
    */
   @DELETE
   @Path("/{id}")
-  public void deleteDmp(@PathParam String id) {
+  public void deleteDmp(@RestPath String id) {
     log.info("Delete dmp with id: " + id);
     String personId = this.getPersonId();
     long dmpId = Long.parseLong(id);
@@ -169,7 +169,7 @@ private String getPersonId() {
    */
   @GET
   @Path("/{id}/{revision}")
-  public DmpDO getDmpByIdAndRevision(@PathParam String id, @PathParam long revision) {
+  public DmpDO getDmpByIdAndRevision(@RestPath String id, @RestPath long revision) {
     log.info("Return dmp with id: " + id + " and revision number: " + revision);
     String personId = this.getPersonId();
     long dmpId = Long.parseLong(id);

diff --git a/src/main/java/org/damap/base/rest/FitsResource.java b/src/main/java/org/damap/base/rest/FitsResource.java
@@ -9,7 +9,6 @@
 import org.damap.base.rest.dmp.domain.MultipartBodyDO;
 import org.damap.base.rest.dmp.mapper.DatasetDOMapper;
 import org.damap.base.rest.fits.service.FitsService;
-import org.jboss.resteasy.annotations.providers.multipart.MultipartForm;
 
 /** FitsResource class. */
 @Path("/api/fits")
@@ -29,7 +28,7 @@ public class FitsResource {
    */
   @POST
   @Path("/examine")
-  public DatasetDO examine(@MultipartForm MultipartBodyDO data) {
+  public DatasetDO examine(MultipartBodyDO data) {
     log.info("Analyse file");
     return DatasetDOMapper.mapEntityToDO(fitsService.analyseFile(data), new DatasetDO());
   }

diff --git a/src/main/java/org/damap/base/rest/InternalStorageResource.java b/src/main/java/org/damap/base/rest/InternalStorageResource.java
@@ -10,7 +10,7 @@
 import lombok.extern.jbosslog.JBossLog;
 import org.damap.base.rest.storage.InternalStorageDO;
 import org.damap.base.rest.storage.InternalStorageService;
-import org.jboss.resteasy.annotations.jaxrs.PathParam;
+import org.jboss.resteasy.reactive.RestPath;
 
 /** InternalStorageResource class. */
 @Path("/api/storages")
@@ -29,7 +29,7 @@ public class InternalStorageResource {
    */
   @GET
   @Path("/{languageCode}")
-  public List<InternalStorageDO> getAllByLanguage(@PathParam String languageCode) {
+  public List<InternalStorageDO> getAllByLanguage(@RestPath String languageCode) {
     log.debug("Return all internal storage options for language " + languageCode);
     return internalStorageService.getAllByLanguage(languageCode);
   }

diff --git a/src/main/java/org/damap/base/rest/OpenAireResource.java b/src/main/java/org/damap/base/rest/OpenAireResource.java
@@ -10,7 +10,7 @@
 import org.damap.base.rest.dmp.domain.DatasetDO;
 import org.damap.base.rest.openaire.mapper.OpenAireMapper;
 import org.damap.base.rest.openaire.service.OpenAireService;
-import org.jboss.resteasy.annotations.jaxrs.QueryParam;
+import org.jboss.resteasy.reactive.RestQuery;
 
 /** OpenAireResource class. */
 @Path("/api/openaire")
@@ -28,7 +28,7 @@ public class OpenAireResource {
    * @return a {@link org.damap.base.rest.dmp.domain.DatasetDO} object
    */
   @GET
-  public DatasetDO search(@QueryParam String doi) {
+  public DatasetDO search(@RestQuery String doi) {
     log.info("Search for dataset with DOI: " + doi);
     return OpenAireMapper.mapAtoB(doi, openAireService.search(doi), new DatasetDO());
   }

diff --git a/src/main/java/org/damap/base/rest/VersionResource.java b/src/main/java/org/damap/base/rest/VersionResource.java
@@ -12,7 +12,7 @@
 import org.damap.base.rest.version.VersionService;
 import org.damap.base.security.SecurityService;
 import org.damap.base.validation.AccessValidator;
-import org.jboss.resteasy.annotations.jaxrs.PathParam;
+import org.jboss.resteasy.reactive.RestPath;
 
 /** VersionResource class. */
 @Path("/api/versions")
@@ -35,7 +35,7 @@ public class VersionResource {
    */
   @GET
   @Path("/list/{id}")
-  public List<VersionDO> getDmpVersions(@PathParam String id) {
+  public List<VersionDO> getDmpVersions(@RestPath String id) {
     log.debug("Return dmp versions for dmp with id: " + id);
     String personId = this.getPersonId();
     long dmpId = Long.parseLong(id);

diff --git a/src/main/java/org/damap/base/rest/dmp/domain/MultipartBodyDO.java b/src/main/java/org/damap/base/rest/dmp/domain/MultipartBodyDO.java
@@ -2,13 +2,13 @@
 
 import jakarta.ws.rs.FormParam;
 import jakarta.ws.rs.core.MediaType;
-import java.io.InputStream;
-import org.jboss.resteasy.annotations.providers.multipart.PartType;
+import java.io.File;
+import org.jboss.resteasy.reactive.PartType;
 
 /** MultipartBodyDO class. */
 public class MultipartBodyDO {
 
   @FormParam("file")
   @PartType(MediaType.APPLICATION_OCTET_STREAM)
-  public InputStream file;
+  public File file;
 }