Merge pull request #393 from BBMRI-ERIC/feat/submit_additional_inform…

…ation

feat: add functionality to submit additional information

.github/workflows/CI.yml

@@ -65,6 +65,11 @@ jobs:
 
 
     steps:
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'temurin'
 
       - name: Checkout Code
         uses: actions/checkout@v4

pom.xml

@@ -361,6 +361,11 @@
             <artifactId>spring-boot-devtools</artifactId>
             <version>3.3.2</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.8</version>
+        </dependency>
     </dependencies>
 
 </project>

src/main/java/eu/bbmri_eric/negotiator/api/controller/v3/InformationRequirementController.java

@@ -10,6 +10,7 @@
 import jakarta.validation.Valid;
 import org.springframework.hateoas.CollectionModel;
 import org.springframework.hateoas.EntityModel;
+import org.springframework.hateoas.MediaTypes;
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.DeleteMapping;
 import org.springframework.web.bind.annotation.GetMapping;
@@ -22,7 +23,9 @@
 import org.springframework.web.bind.annotation.RestController;
 
 @RestController
-@RequestMapping(InformationRequirementController.BASE_URL)
+@RequestMapping(
+    value = InformationRequirementController.BASE_URL,
+    produces = MediaTypes.HAL_JSON_VALUE)
 @Tag(
     name = "Information requirements",
     description = "Set requirements for Resource states in Negotiations.")

src/main/java/eu/bbmri_eric/negotiator/api/controller/v3/InformationSubmissionController.java

@@ -0,0 +1,81 @@
+package eu.bbmri_eric.negotiator.api.controller.v3;
+
+import eu.bbmri_eric.negotiator.dto.InformationSubmissionDTO;
+import eu.bbmri_eric.negotiator.dto.SubmittedInformationDTO;
+import eu.bbmri_eric.negotiator.service.InformationRequirementService;
+import eu.bbmri_eric.negotiator.service.InformationSubmissionService;
+import eu.bbmri_eric.negotiator.service.NegotiationService;
+import io.swagger.v3.oas.annotations.security.SecurityRequirement;
+import io.swagger.v3.oas.annotations.tags.Tag;
+import java.io.IOException;
+import org.springframework.hateoas.EntityModel;
+import org.springframework.hateoas.MediaTypes;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseStatus;
+import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.multipart.MultipartFile;
+import org.springframework.web.server.ServerErrorException;
+
+@RestController
+@RequestMapping(value = InformationSubmissionController.BASE_URL)
+@Tag(
+    name = "Submit required information",
+    description = "Submit required information on behalf of a resource in a Negotiation.")
+@SecurityRequirement(name = "security_auth")
+public class InformationSubmissionController {
+  private final InformationRequirementService requirementService;
+  private final NegotiationService negotiationService;
+  private final InformationSubmissionService submissionService;
+  public static final String BASE_URL = "/v3";
+
+  public InformationSubmissionController(
+      InformationRequirementService requirementService,
+      NegotiationService negotiationService,
+      InformationSubmissionService submissionService) {
+    this.requirementService = requirementService;
+    this.negotiationService = negotiationService;
+    this.submissionService = submissionService;
+  }
+
+  @ResponseStatus(HttpStatus.OK)
+  @GetMapping(
+      value = "/negotiations/{negotiationId}/info-requirements/{requirementId}",
+      produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
+  public ResponseEntity<byte[]> getSummaryInformation(
+      @PathVariable String negotiationId, @PathVariable Long requirementId) {
+    MultipartFile file = submissionService.createSummary(requirementId, negotiationId);
+    try {
+      return ResponseEntity.ok()
+          .header("Content-Disposition", "attachment; filename=\"%s\"".formatted(file.getName()))
+          .contentType(MediaType.valueOf("text/csv"))
+          .body(file.getBytes());
+    } catch (IOException e) {
+      throw new ServerErrorException("Failed to create summary information", e);
+    }
+  }
+
+  @ResponseStatus(HttpStatus.OK)
+  @PostMapping(
+      value = "/negotiations/{negotiationId}/info-requirements/{requirementId}",
+      consumes = MediaType.APPLICATION_JSON_VALUE,
+      produces = MediaTypes.HAL_JSON_VALUE)
+  public EntityModel<SubmittedInformationDTO> submitInformation(
+      @PathVariable String negotiationId,
+      @PathVariable Long requirementId,
+      @RequestBody InformationSubmissionDTO dto) {
+    return EntityModel.of(submissionService.submit(dto, requirementId, negotiationId));
+  }
+
+  @ResponseStatus(HttpStatus.OK)
+  @GetMapping(value = "/info-submissions/{id}", produces = MediaTypes.HAL_JSON_VALUE)
+  public EntityModel<SubmittedInformationDTO> getInfoSubmission(@PathVariable Long id) {
+    return EntityModel.of(submissionService.findById(id));
+  }
+}

src/main/java/eu/bbmri_eric/negotiator/api/controller/v3/NegotiationController.java

@@ -241,6 +241,10 @@ private static void checkAuthorization(Long id) {
   public EntityModel<NegotiationDTO> retrieve(@Valid @PathVariable String id) {
     NegotiationDTO negotiationDTO = negotiationService.findById(id, true);
     if (isAuthorizedForNegotiation(negotiationDTO)) {
+      if (negotiationService.isNegotiationCreator(id)
+          || NegotiatorUserDetailsService.isCurrentlyAuthenticatedUserAdmin()) {
+        return assembler.toModelWithRequirementLink(negotiationDTO);
+      }
       return assembler.toModel(negotiationDTO);
     } else {
       throw new ResponseStatusException(HttpStatus.FORBIDDEN);

src/main/java/eu/bbmri_eric/negotiator/api/controller/v3/NetworkController.java

@@ -49,8 +49,7 @@ public class NetworkController {
   private final NegotiationService negotiationService;
   private final NetworkModelAssembler networkModelAssembler;
   private final ResourceModelAssembler resourceModelAssembler;
-  private final NegotiationModelAssembler negotiationModelAssembler =
-      new NegotiationModelAssembler();
+  private final NegotiationModelAssembler negotiationModelAssembler;
   private final UserModelAssembler userModelAssembler;
   private final NetworkRepository networkRepository;
 
@@ -61,6 +60,7 @@ public NetworkController(
       ResourceModelAssembler resourceModelAssembler,
       PersonService personService,
       NegotiationService negotiationService,
+      NegotiationModelAssembler negotiationModelAssembler,
       UserModelAssembler userModelAssembler,
       NetworkRepository networkRepository) {
     this.networkService = networkService;
@@ -69,6 +69,7 @@ public NetworkController(
     this.resourceModelAssembler = resourceModelAssembler;
     this.personService = personService;
     this.negotiationService = negotiationService;
+    this.negotiationModelAssembler = negotiationModelAssembler;
     this.userModelAssembler = userModelAssembler;
     this.networkRepository = networkRepository;
   }

src/main/java/eu/bbmri_eric/negotiator/configuration/security/OAuthSecurityConfig.java

@@ -179,6 +179,8 @@ public SecurityFilterChain filterChain(HttpSecurity http, MvcRequestMatcher.Buil
                     .hasRole("ADMIN")
                     .requestMatchers(mvc.pattern(HttpMethod.DELETE, "/v3/info-requirements/**"))
                     .hasRole("ADMIN")
+                    .requestMatchers(mvc.pattern("/v3/info-submissions/**"))
+                    .authenticated()
                     .requestMatchers(mvc.pattern("/actuator/prometheus"))
                     // Needs to be IPv6 address
                     .access(

src/main/java/eu/bbmri_eric/negotiator/database/model/InformationSubmission.java

@@ -0,0 +1,64 @@
+package eu.bbmri_eric.negotiator.database.model;
+
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.GenerationType;
+import jakarta.persistence.Id;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import lombok.Getter;
+import lombok.Setter;
+import org.hibernate.annotations.JdbcTypeCode;
+import org.hibernate.type.SqlTypes;
+
+/** Represents a submission of additional information by the resource representative. */
+@Setter
+@Getter
+@Entity
+public class InformationSubmission {
+
+  protected InformationSubmission() {}
+
+  protected InformationSubmission(
+      Long id,
+      InformationRequirement requirement,
+      Resource resource,
+      Negotiation negotiation,
+      String payload) {
+    this.id = id;
+    this.requirement = requirement;
+    this.resource = resource;
+    this.negotiation = negotiation;
+    this.payload = payload;
+  }
+
+  public InformationSubmission(
+      InformationRequirement requirement,
+      Resource resource,
+      Negotiation negotiation,
+      String payload) {
+    this.requirement = requirement;
+    this.resource = resource;
+    this.negotiation = negotiation;
+    this.payload = payload;
+  }
+
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  private Long id;
+
+  @ManyToOne
+  @JoinColumn(name = "requirement_id")
+  private InformationRequirement requirement;
+
+  @ManyToOne
+  @JoinColumn(name = "resource_id")
+  private Resource resource;
+
+  @ManyToOne
+  @JoinColumn(name = "negotiation_id")
+  private Negotiation negotiation;
+
+  @JdbcTypeCode(SqlTypes.JSON)
+  private String payload;
+}

src/main/java/eu/bbmri_eric/negotiator/database/repository/InformationSubmissionRepository.java

@@ -0,0 +1,19 @@
+package eu.bbmri_eric.negotiator.database.repository;
+
+import eu.bbmri_eric.negotiator.database.model.InformationSubmission;
+import java.util.List;
+import java.util.Set;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public interface InformationSubmissionRepository
+    extends JpaRepository<InformationSubmission, Long> {
+  boolean existsByResource_SourceIdAndNegotiation_Id(String sourceId, String negotiationId);
+
+  boolean existsByResource_SourceIdAndNegotiation_IdAndRequirement_Id(
+      String sourceId, String negotiationId, Long requirementId);
+
+  Set<InformationSubmission> findAllByNegotiation_Id(String negotiationId);
+
+  List<InformationSubmission> findAllByRequirement_IdAndNegotiation_Id(
+      Long requirementId, String negotiationId);
+}

src/main/java/eu/bbmri_eric/negotiator/database/repository/ResourceRepository.java

@@ -17,10 +17,22 @@ public interface ResourceRepository extends JpaRepository<Resource, Long> {
 
   @Query(
       value =
-          "SELECT rs.id as id, rspn.negotiation_id as negotiationId, rs.name as name, rs.source_id as sourceId, rspn.current_state as currentState, o.name as organizationName, o.external_id as organizationExternalId, o.id as organizationId "
-              + "FROM resource rs join resource_state_per_negotiation rspn on rs.source_id = rspn.resource_id "
-              + "join organization o on o.id = rs.organization_id "
-              + "where rspn.negotiation_id = :negotiationId",
+          """
+select rs.id              as id,
+       r.negotiation_id   as negotiationId,
+       rs.name            as name,
+       rs.source_id       as sourceId,
+       rspn.current_state as currentState,
+       o.name             as organizationName,
+       o.external_id      as organizationExternalId,
+       o.id               as organizationId
+from resource rs
+         join public.request_resources_link rrl on rs.id = rrl.resource_id
+         join public.organization o on o.id = rs.organization_id
+        join public.request r on r.id = rrl.request_id
+         left join public.resource_state_per_negotiation rspn on rs.source_id = rspn.resource_id and r.negotiation_id = rspn.negotiation_id
+          where r.negotiation_id = :negotiationId;
+""",
       nativeQuery = true)
   List<ResourceViewDTO> findByNegotiation(String negotiationId);
 

src/main/java/eu/bbmri_eric/negotiator/dto/InformationSubmissionDTO.java

@@ -0,0 +1,19 @@
+package eu.bbmri_eric.negotiator.dto;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.JsonNode;
+import jakarta.validation.constraints.NotNull;
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@JsonInclude(value = JsonInclude.Include.NON_NULL)
+public class InformationSubmissionDTO {
+  @NotNull private Long resourceId;
+  @NotNull private JsonNode payload;
+}

src/main/java/eu/bbmri_eric/negotiator/dto/SubmittedInformationDTO.java

@@ -0,0 +1,21 @@
+package eu.bbmri_eric.negotiator.dto;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.databind.JsonNode;
+import jakarta.validation.constraints.NotNull;
+import lombok.AllArgsConstructor;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@JsonInclude(value = JsonInclude.Include.NON_NULL)
+public class SubmittedInformationDTO {
+  @NotNull private Long id;
+  @NotNull private Long resourceId;
+  private Long requirementId;
+  @NotNull private JsonNode payload;
+}

src/main/java/eu/bbmri_eric/negotiator/dto/resource/ResourceWithStatusDTO.java

@@ -32,5 +32,5 @@ public class ResourceWithStatusDTO {
 
   @Nullable private OrganizationDTO organization;
 
-  private NegotiationResourceState status;
+  private NegotiationResourceState currentState;
 }

src/main/java/eu/bbmri_eric/negotiator/events/InformationSubmissionEvent.java

@@ -0,0 +1,14 @@
+package eu.bbmri_eric.negotiator.events;
+
+import lombok.Getter;
+import org.springframework.context.ApplicationEvent;
+
+@Getter
+public class InformationSubmissionEvent extends ApplicationEvent {
+  private final String negotiationId;
+
+  public InformationSubmissionEvent(Object source, String negotiationId) {
+    super(source);
+    this.negotiationId = negotiationId;
+  }
+}

src/main/java/eu/bbmri_eric/negotiator/mappers/InformationSubmissionMapper.java

@@ -0,0 +1,48 @@
+package eu.bbmri_eric.negotiator.mappers;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.bbmri_eric.negotiator.database.model.InformationSubmission;
+import eu.bbmri_eric.negotiator.dto.SubmittedInformationDTO;
+import jakarta.annotation.PostConstruct;
+import org.modelmapper.Converter;
+import org.modelmapper.ModelMapper;
+import org.modelmapper.TypeMap;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class InformationSubmissionMapper {
+  ModelMapper modelMapper;
+
+  public InformationSubmissionMapper(ModelMapper modelMapper) {
+    this.modelMapper = modelMapper;
+  }
+
+  @PostConstruct
+  public void addMappings() {
+    TypeMap<InformationSubmission, SubmittedInformationDTO> typeMap =
+        modelMapper.createTypeMap(InformationSubmission.class, SubmittedInformationDTO.class);
+    Converter<String, JsonNode> payloadConverter =
+        p -> {
+          try {
+            return payloadConverter(p.getSource());
+          } catch (JsonProcessingException e) {
+            throw new RuntimeException(e); // TODO: raise the correct exception
+          }
+        };
+    typeMap.addMappings(
+        mapper ->
+            mapper
+                .using(payloadConverter)
+                .map(InformationSubmission::getPayload, SubmittedInformationDTO::setPayload));
+  }
+
+  private JsonNode payloadConverter(String jsonPayload) throws JsonProcessingException {
+    ObjectMapper mapper = new ObjectMapper();
+    if (jsonPayload == null) {
+      jsonPayload = "{}";
+    }
+    return mapper.readTree(jsonPayload);
+  }
+}