WIP

Former-commit-id: c7a97b9f

fda-citation-service/api/src/main/java/at/tuwien/api/zenodo/deposit/DepositChangeResponseDto.java

 package at.tuwien.api.zenodo.deposit;
 
-import at.tuwien.api.zenodo.files.FileDto;
+import at.tuwien.api.zenodo.files.FileResponseDto;
 import com.fasterxml.jackson.annotation.JsonFormat;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import lombok.*;
@@ -40,7 +40,7 @@ public class DepositChangeResponseDto {
 
     private CreatorDto[] contributors;
 
-    private List<FileDto> files;
+    private List<FileResponseDto> files;
 
     private Long id;
 

fda-citation-service/api/src/main/java/at/tuwien/api/zenodo/deposit/DepositResponseDto.java

 package at.tuwien.api.zenodo.deposit;
 
-import at.tuwien.api.zenodo.files.FileDto;
+import at.tuwien.api.zenodo.files.FileResponseDto;
 import com.fasterxml.jackson.annotation.JsonFormat;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import lombok.*;
@@ -46,7 +46,7 @@ public class DepositResponseDto {
 
     private CreatorDto[] contributors;
 
-    private List<FileDto> files;
+    private List<FileResponseDto> files;
 
     private Long id;
 

fda-citation-service/api/src/main/java/at/tuwien/api/zenodo/deposit/FileBinaryRequestDto.java

+package at.tuwien.api.zenodo.deposit;
+
+import lombok.*;
+import org.springframework.core.io.ByteArrayResource;
+import org.springframework.http.HttpEntity;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class FileBinaryRequestDto {
+
+    private HttpEntity<ByteArrayResource> file;
+
+}

fda-citation-service/api/src/main/java/at/tuwien/api/zenodo/deposit/FileRequestDto.java

+package at.tuwien.api.zenodo.deposit;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import lombok.*;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class FileRequestDto {
+
+    private String name;
+
+}

fda-citation-service/api/src/main/java/at/tuwien/api/zenodo/files/FileDto.java → fda-citation-service/api/src/main/java/at/tuwien/api/zenodo/files/FileResponseDto.java

@@ -7,7 +7,7 @@ import lombok.*;
 @Builder
 @NoArgsConstructor
 @AllArgsConstructor
-public class FileDto {
+public class FileResponseDto {
 
     private String checksum;
 

fda-citation-service/rest-service/src/test/java/at/tuwien/BaseUnitTest.java

 package at.tuwien;
 
 import at.tuwien.api.zenodo.deposit.*;
-import at.tuwien.api.zenodo.files.FileDto;
+import at.tuwien.api.zenodo.files.FileResponseDto;
 import at.tuwien.api.zenodo.files.FileLinksDto;
 import org.apache.commons.lang.RandomStringUtils;
 import org.springframework.test.context.TestPropertySource;
@@ -37,6 +37,11 @@ public abstract class BaseUnitTest {
     public final static String CREATOR_2_AFFIL = "TU Graz";
     public final static String CREATOR_2_ORCID = "0000-0002-2606-4059";
 
+    public final static String FILE_1_ID = "deadbeef-deafdeed";
+    public final static String FILE_1_NAME = "testdata-othername.csv";
+    public final static String FILE_1_CHECKSUM = "d393c7fa1240c18473133793f7901aaa";
+    public final static Long FILE_1_SIZE = 34614L;
+
     public final static Long DEPOSIT_2_ID = 2L;
     public final static String DEPOSIT_2_TITLE = "Test Document " + RandomStringUtils.randomAlphanumeric(10);
     public final static String DEPOSIT_2_DESCRIPTION = "Test Description " + RandomStringUtils.randomAlphanumeric(100);
@@ -46,12 +51,6 @@ public abstract class BaseUnitTest {
     public final static String DEPOSIT_2_STATE = "draft";
     public final static Boolean DEPOSIT_2_SUBMITTED = false;
 
-
-    public final static String FILE_1_CHECKSUM = "deadbeef";
-    public final static String FILE_1_NAME = "data.csv";
-    public final static String FILE_1_ID = "73d5674b-2bda-400c-844e-4eef309afe5e";
-    public final static Long FILE_1_SIZE = 3943498L;
-
     public final static String FILE_1_LINKS_DOWNLOAD = "http://localhost:5500/file/" + FILE_1_ID + "/download";
     public final static String FILE_1_LINKS_SELF = "http://localhost:5500/file/" + FILE_1_ID;
 
@@ -82,7 +81,7 @@ public abstract class BaseUnitTest {
             .self(FILE_1_LINKS_SELF)
             .build();
 
-    public final static FileDto FILE_1 = FileDto.builder()
+    public final static FileResponseDto FILE_1 = FileResponseDto.builder()
             .checksum(FILE_1_CHECKSUM)
             .filename(FILE_1_NAME)
             .id(FILE_1_ID)

fda-citation-service/rest-service/src/test/java/at/tuwien/service/FileServiceIntegrationTest.java

+package at.tuwien.service;
+
+import at.tuwien.BaseUnitTest;
+import at.tuwien.api.zenodo.deposit.DepositChangeRequestDto;
+import at.tuwien.api.zenodo.deposit.DepositChangeResponseDto;
+import at.tuwien.api.zenodo.deposit.FileRequestDto;
+import at.tuwien.api.zenodo.files.FileResponseDto;
+import at.tuwien.config.ReadyConfig;
+import at.tuwien.exception.ZenodoApiException;
+import at.tuwien.exception.ZenodoAuthenticationException;
+import at.tuwien.exception.ZenodoNotFoundException;
+import org.apache.commons.io.FileUtils;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+import org.springframework.util.ResourceUtils;
+import org.springframework.web.client.RestTemplate;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.ArgumentMatchers.*;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.when;
+
+@SpringBootTest
+@ExtendWith(SpringExtension.class)
+public class FileServiceIntegrationTest extends BaseUnitTest {
+
+    @MockBean
+    private ReadyConfig readyConfig;
+
+    @Autowired
+    private ZenodoFileService fileService;
+
+    @Autowired
+    private ZenodoMetadataService metadataService;
+
+    @Test
+    public void createResource_succeeds() throws IOException, ZenodoApiException, ZenodoNotFoundException, ZenodoAuthenticationException {
+//        final DepositChangeResponseDto deposit = metadataService.storeCitation();
+        final byte[] file = FileUtils.readFileToByteArray(ResourceUtils.getFile("classpath:testdata.csv"));
+
+        /* test */
+        final FileResponseDto response = fileService.createResource(1L, FILE_1_NAME, file);
+        assertEquals(FILE_1_NAME, response.getFilename());
+        assertEquals(FILE_1_CHECKSUM, response.getChecksum());
+        assertEquals(FILE_1_SIZE, response.getFilesize());
+    }
+
+}
\ No newline at end of file

fda-citation-service/rest-service/src/test/java/at/tuwien/service/FileServiceUnitTest.java

+package at.tuwien.service;
+
+import at.tuwien.BaseUnitTest;
+import at.tuwien.api.zenodo.deposit.*;
+import at.tuwien.api.zenodo.files.FileResponseDto;
+import at.tuwien.config.ReadyConfig;
+import at.tuwien.exception.ZenodoApiException;
+import at.tuwien.exception.ZenodoAuthenticationException;
+import at.tuwien.exception.ZenodoNotFoundException;
+import org.apache.commons.io.FileUtils;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+import org.springframework.util.ResourceUtils;
+import org.springframework.web.client.RestTemplate;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.anyLong;
+import static org.mockito.Mockito.when;
+
+@SpringBootTest
+@ExtendWith(SpringExtension.class)
+public class FileServiceUnitTest extends BaseUnitTest {
+
+    @MockBean
+    private ReadyConfig readyConfig;
+
+    @Autowired
+    private ZenodoFileService fileService;
+
+    @MockBean
+    private RestTemplate zenodoTemplate;
+
+    @Test
+    public void createResource_succeeds() throws IOException, ZenodoApiException, ZenodoNotFoundException,
+            ZenodoAuthenticationException {
+        final byte[] file = FileUtils.readFileToByteArray(ResourceUtils.getFile("classpath:testdata.csv"));
+        when(zenodoTemplate.exchange(anyString(), eq(HttpMethod.POST), Mockito.any(),
+                eq(FileResponseDto.class), anyLong(), anyString()))
+                .thenReturn(ResponseEntity.status(HttpStatus.OK)
+                        .body(FILE_1));
+
+        /* test */
+        final FileResponseDto response = fileService.createResource(DEPOSIT_1_ID, FILE_1_NAME, file);
+        assertEquals(FILE_1_NAME, response.getFilename());
+        assertEquals(FILE_1_CHECKSUM, response.getChecksum());
+        assertEquals(FILE_1_SIZE, response.getFilesize());
+    }
+
+    @Test
+    public void createResource_notExists_fails() throws IOException {
+        final byte[] file = FileUtils.readFileToByteArray(ResourceUtils.getFile("classpath:testdata.csv"));
+        when(zenodoTemplate.exchange(anyString(), eq(HttpMethod.POST), Mockito.any(),
+                eq(FileResponseDto.class), anyLong(), anyString()))
+                .thenReturn(ResponseEntity.status(HttpStatus.BAD_REQUEST)
+                        .build());
+
+        /* test */
+        assertThrows(ZenodoNotFoundException.class, () -> {
+            fileService.createResource(DEPOSIT_1_ID, FILE_1_NAME, file);
+        });
+    }
+
+}
\ No newline at end of file

fda-citation-service/rest-service/src/test/resources/application.properties

@@ -17,4 +17,4 @@ spring.jpa.show-sql=false
 fda.mapping.path: /tmp
 fda.table.path: /tmp
 
-zenodo.endpoint: https://sandbox.zenodo.org/
+zenodo.endpoint: http://sandbox.zenodo.org/
\ No newline at end of file

fda-citation-service/rest-service/src/test/resources/intercept.py

-#!/usr/bin/env python3
-import socket
-
-HOST = ''                 # Symbolic name meaning all available interfaces
-PORT = 50000              # Arbitrary non-privileged port
-s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-s.bind((HOST, PORT))
-s.listen(1)
-
-conn, addr = s.accept()
-print ('Connected by' + str(addr))
-while 1:
-  data = conn.recv(1024)
-  if not data: break
-  print("===> recv " + str(data))
-conn.close()
\ No newline at end of file

fda-citation-service/services/src/main/java/at/tuwien/config/ZenodoConfig.java

 package at.tuwien.config;
 
 import at.tuwien.exception.ZenodoAuthenticationException;
-import at.tuwien.utils.ZenodoTemplateInterceptor;
-import com.fasterxml.jackson.databind.DeserializationFeature;
+import at.tuwien.utils.ApiTemplateInterceptor;
+import at.tuwien.utils.UploadTemplateInterceptor;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import lombok.Getter;
@@ -49,13 +48,23 @@ public class ZenodoConfig {
                 .registerModule(new Jdk8Module());
     }
 
-    @Bean
-    public RestTemplate zenodo() {
+    @Bean("apiTemplate")
+    public RestTemplate apiTemplate() {
+        final UriBuilderFactory factory = new DefaultUriBuilderFactory(zenodoEndpoint);
+        final RestTemplate template = new RestTemplateBuilder()
+                .uriTemplateHandler(factory)
+                .build();
+        template.setInterceptors(List.of(new ApiTemplateInterceptor()));
+        return template;
+    }
+
+    @Bean("uploadTemplate")
+    public RestTemplate uploadTemplate() {
         final UriBuilderFactory factory = new DefaultUriBuilderFactory(zenodoEndpoint);
         final RestTemplate template = new RestTemplateBuilder()
                 .uriTemplateHandler(factory)
                 .build();
-        template.setInterceptors(List.of(new ZenodoTemplateInterceptor()));
+        template.setInterceptors(List.of(new UploadTemplateInterceptor()));
         return template;
     }
 

fda-citation-service/services/src/main/java/at/tuwien/mapper/ZenodoMapper.java

+package at.tuwien.mapper;
+
+import at.tuwien.api.zenodo.deposit.FileBinaryRequestDto;
+import at.tuwien.api.zenodo.deposit.FileRequestDto;
+import org.mapstruct.Mapper;
+import org.springframework.core.io.ByteArrayResource;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
+
+import java.util.List;
+import java.util.Map;
+
+@Mapper(componentModel = "spring")
+public interface ZenodoMapper {
+
+    default HttpEntity<MultiValueMap<String, Object>> resourceToHttpEntity(String name, byte[] resource) {
+        final HttpHeaders headers = new HttpHeaders();
+        headers.setAccept(List.of(MediaType.APPLICATION_JSON));
+        headers.setContentType(MediaType.MULTIPART_FORM_DATA);
+        final HttpHeaders parts = new HttpHeaders();
+        parts.setContentType(MediaType.TEXT_PLAIN);
+        final ByteArrayResource byteArrayResource = new ByteArrayResource(resource) {
+            @Override
+            public String getFilename() {
+                return name;
+            }
+        };
+        MultiValueMap<String, Object> body = new LinkedMultiValueMap<>();
+        body.add("file", new HttpEntity<>(byteArrayResource, parts));
+        body.add("data", new HttpEntity<>(name, parts));
+        return new HttpEntity<>(body, headers);
+    }
+
+}

fda-citation-service/services/src/main/java/at/tuwien/service/FileService.java

 package at.tuwien.service;
 
+import at.tuwien.api.zenodo.files.FileResponseDto;
+import at.tuwien.exception.ZenodoApiException;
+import at.tuwien.exception.ZenodoAuthenticationException;
+import at.tuwien.exception.ZenodoNotFoundException;
 import org.springframework.stereotype.Service;
 
 @Service
 public interface FileService {
 
+    FileResponseDto createResource(Long id, String name, byte[] resource)
+            throws ZenodoAuthenticationException, ZenodoApiException, ZenodoNotFoundException;
 }

fda-citation-service/services/src/main/java/at/tuwien/service/ZenodoFileService.java

 package at.tuwien.service;
 
+import at.tuwien.api.zenodo.files.FileResponseDto;
+import at.tuwien.config.ZenodoConfig;
+import at.tuwien.exception.ZenodoApiException;
+import at.tuwien.exception.ZenodoAuthenticationException;
+import at.tuwien.exception.ZenodoNotFoundException;
+import at.tuwien.mapper.ZenodoMapper;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.*;
 import org.springframework.stereotype.Service;
+import org.springframework.web.client.RestTemplate;
 
 @Service
 public class ZenodoFileService implements FileService {
 
+    private final RestTemplate apiTemplate;
+    private final RestTemplate uploadTemplate;
+    private final ZenodoConfig zenodoConfig;
+    private final ZenodoMapper zenodoMapper;
+
+    @Autowired
+    public ZenodoFileService(RestTemplate apiTemplate, RestTemplate uploadTemplate, ZenodoConfig zenodoConfig,
+                             ZenodoMapper zenodoMapper) {
+        this.apiTemplate = apiTemplate;
+        this.uploadTemplate = uploadTemplate;
+        this.zenodoConfig = zenodoConfig;
+        this.zenodoMapper = zenodoMapper;
+    }
+
+    @Override
+    public FileResponseDto createResource(Long id, String name, byte[] resource)
+            throws ZenodoAuthenticationException, ZenodoApiException, ZenodoNotFoundException {
+        final ResponseEntity<FileResponseDto> response = uploadTemplate.exchange("/api/deposit/depositions/{deposit_id}/files?access_token={token}",
+                HttpMethod.POST, zenodoMapper.resourceToHttpEntity(name, resource), FileResponseDto.class, id,
+                zenodoConfig.getApiKey());
+        if (response.getStatusCode().equals(HttpStatus.UNAUTHORIZED)) {
+            throw new ZenodoAuthenticationException("Token is missing or invalid.");
+        }
+        if (response.getStatusCode().equals(HttpStatus.BAD_REQUEST)) {
+            throw new ZenodoNotFoundException("Did not find the deposit with this id");
+        }
+        if (response.getBody() == null) {
+            throw new ZenodoApiException("Endpoint returned null body");
+        }
+        return response.getBody();
+    }
 
 }

fda-citation-service/services/src/main/java/at/tuwien/service/ZenodoMetadataService.java

@@ -16,18 +16,18 @@ import java.util.List;
 @Service
 public class ZenodoMetadataService implements MetadataService {
 
-    private final RestTemplate zenodoRestTemplate;
+    private final RestTemplate apiTemplate;
     private final ZenodoConfig zenodoConfig;
 
     @Autowired
-    public ZenodoMetadataService(RestTemplate zenodoRestTemplate, ZenodoConfig zenodoConfig) {
-        this.zenodoRestTemplate = zenodoRestTemplate;
+    public ZenodoMetadataService(RestTemplate apiTemplate, ZenodoConfig zenodoConfig) {
+        this.apiTemplate = apiTemplate;
         this.zenodoConfig = zenodoConfig;
     }
 
     @Override
     public List<DepositResponseDto> listCitations() throws ZenodoAuthenticationException, ZenodoApiException {
-        final ResponseEntity<DepositResponseDto[]> response = zenodoRestTemplate.exchange("/api/deposit/depositions?access_token={token}",
+        final ResponseEntity<DepositResponseDto[]> response = apiTemplate.exchange("/api/deposit/depositions?access_token={token}",
                 HttpMethod.GET, null, DepositResponseDto[].class, zenodoConfig.getApiKey());
         if (response.getStatusCode().equals(HttpStatus.UNAUTHORIZED)) {
             throw new ZenodoAuthenticationException("Token is missing or invalid.");
@@ -40,7 +40,7 @@ public class ZenodoMetadataService implements MetadataService {
 
     @Override
     public DepositChangeResponseDto storeCitation() throws ZenodoAuthenticationException, ZenodoApiException {
-        final ResponseEntity<DepositChangeResponseDto> response = zenodoRestTemplate.exchange("/api/deposit/depositions?access_token={token}",
+        final ResponseEntity<DepositChangeResponseDto> response = apiTemplate.exchange("/api/deposit/depositions?access_token={token}",
                 HttpMethod.POST, new HttpEntity<>("{}"), DepositChangeResponseDto.class, zenodoConfig.getApiKey());
         if (response.getStatusCode().equals(HttpStatus.UNAUTHORIZED)) {
             throw new ZenodoAuthenticationException("Token is missing or invalid.");
@@ -57,7 +57,7 @@ public class ZenodoMetadataService implements MetadataService {
     @Override
     public DepositChangeResponseDto updateCitation(Long id, DepositChangeRequestDto data) throws ZenodoAuthenticationException,
             ZenodoApiException, ZenodoNotFoundException {
-        final ResponseEntity<DepositChangeResponseDto> response = zenodoRestTemplate.exchange("/api/deposit/depositions/{deposit_id}?access_token={token}",
+        final ResponseEntity<DepositChangeResponseDto> response = apiTemplate.exchange("/api/deposit/depositions/{deposit_id}?access_token={token}",
                 HttpMethod.PUT, new HttpEntity<>(data), DepositChangeResponseDto.class, id, zenodoConfig.getApiKey());
         if (response.getStatusCode().equals(HttpStatus.UNAUTHORIZED)) {
             throw new ZenodoAuthenticationException("Token is missing or invalid.");
@@ -76,7 +76,7 @@ public class ZenodoMetadataService implements MetadataService {
 
     @Override
     public void deleteCitation(Long id) throws ZenodoAuthenticationException, ZenodoApiException {
-        final ResponseEntity<String> response = zenodoRestTemplate.exchange("/api/deposit/depositions/{deposit_id}?access_token={token}",
+        final ResponseEntity<String> response = apiTemplate.exchange("/api/deposit/depositions/{deposit_id}?access_token={token}",
                 HttpMethod.DELETE, null, String.class, id, zenodoConfig.getApiKey());
         if (response.getStatusCode().equals(HttpStatus.UNAUTHORIZED)) {
             throw new ZenodoAuthenticationException("Token is missing or invalid.");

fda-citation-service/services/src/main/java/at/tuwien/utils/ZenodoTemplateInterceptor.java → fda-citation-service/services/src/main/java/at/tuwien/utils/ApiTemplateInterceptor.java

@@ -9,7 +9,7 @@ import org.springframework.stereotype.Service;
 import java.io.IOException;
 
 @Service
-public class ZenodoTemplateInterceptor implements ClientHttpRequestInterceptor {
+public class ApiTemplateInterceptor implements ClientHttpRequestInterceptor {
 
     @Override
     public ClientHttpResponse intercept(HttpRequest request, byte[] body, ClientHttpRequestExecution execution)

fda-citation-service/services/src/main/java/at/tuwien/utils/UploadTemplateInterceptor.java

+package at.tuwien.utils;
+
+import org.springframework.http.HttpRequest;
+import org.springframework.http.client.ClientHttpRequestExecution;
+import org.springframework.http.client.ClientHttpRequestInterceptor;
+import org.springframework.http.client.ClientHttpResponse;
+import org.springframework.stereotype.Service;
+
+import java.io.IOException;
+
+@Service
+public class UploadTemplateInterceptor implements ClientHttpRequestInterceptor {
+
+    @Override
+    public ClientHttpResponse intercept(HttpRequest request, byte[] body, ClientHttpRequestExecution execution)
+            throws IOException {
+        request.getHeaders().set("Content-Type", "multipart/form-data");
+        request.getHeaders().set("Accept", "application/json");
+        return execution.execute(request, body);
+    }
+}