added zenodo api

Former-commit-id: 4c0da8ac

fda-table-service/.env

+ZENODO_API_KEY=OjphEf9axmjOxPqe419sTkhlVKZKA335NH5OGw0g4DyRUSd0LMryNtjNWg7x
\ No newline at end of file

fda-table-service/.gitignore

@@ -4,6 +4,9 @@ target/
 !**/src/main/**/target/
 !**/src/test/**/target/
 
+### Environment ###
+.env
+
 ### Generated ###
 mapping.xml
 rest-service/src/main/java/at/tuwien/userdb/Table.java

fda-table-service/api/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>fda-table-service</artifactId>
+        <groupId>at.tuwien</groupId>
+        <version>0.0.1-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>api</artifactId>
+
+    <properties>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+
+</project>
\ No newline at end of file

fda-table-service/api/src/main/java/at/tuwien/api/zenodo/MetadataDto.java

+package at.tuwien.api.zenodo;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.*;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class MetadataDto {
+
+    @JsonProperty("prereserve_doi")
+    private PreserveDoiDto prereserveDoi;
+
+}

fda-table-service/api/src/main/java/at/tuwien/api/zenodo/PreserveDoiDto.java

+package at.tuwien.api.zenodo;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.*;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class PreserveDoiDto {
+
+    private String doi;
+
+    @JsonProperty("recid")
+    private Long recId;
+
+}

fda-table-service/api/src/main/java/at/tuwien/api/zenodo/deposit/DepositDto.java

+package at.tuwien.api.zenodo.deposit;
+
+import at.tuwien.api.zenodo.MetadataDto;
+import at.tuwien.api.zenodo.files.FileDto;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.*;
+
+import java.time.Instant;
+import java.util.List;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class DepositDto {
+
+    @JsonProperty("conceptrecid")
+    private Long conceptRecId;
+
+    private Instant created;
+
+    private List<FileDto> files;
+
+    private Long id;
+
+    private Instant modified;
+
+    private Long owner;
+
+    private MetadataDto metadata;
+
+    @JsonProperty("record_id")
+    private Long recordId;
+
+    private String state;
+
+    private Boolean submitted;
+
+    private String title;
+
+}

fda-table-service/api/src/main/java/at/tuwien/api/zenodo/deposit/DepositLinksDto.java

+package at.tuwien.api.zenodo.deposit;
+
+import lombok.*;
+
+@Setter
+@Getter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class DepositLinksDto {
+
+    private String bucket;
+
+    private String discard;
+
+    private String edit;
+
+    private String files;
+
+    private String html;
+
+    private String latest_draft;
+
+    private String latest_draft_html;
+
+    private String publish;
+
+    private String self;
+
+}

fda-table-service/api/src/main/java/at/tuwien/api/zenodo/files/FileDto.java

+package at.tuwien.api.zenodo.files;
+
+import lombok.*;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class FileDto {
+
+    private String checksum;
+
+    private String filename;
+
+    private Long filesize;
+
+    private String id;
+
+    private FileLinksDto links;
+
+}

fda-table-service/api/src/main/java/at/tuwien/api/zenodo/files/FileLinksDto.java

+package at.tuwien.api.zenodo.files;
+
+import lombok.*;
+
+@Getter
+@Setter
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class FileLinksDto {
+
+    private String download;
+
+    private String self;
+
+}

fda-table-service/gateways/pom.xml → fda-table-service/gateway/pom.xml

@@ -2,29 +2,26 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <modelVersion>4.0.0</modelVersion>
     <parent>
         <artifactId>fda-table-service</artifactId>
         <groupId>at.tuwien</groupId>
         <version>0.0.1-SNAPSHOT</version>
     </parent>
+    <modelVersion>4.0.0</modelVersion>
 
-    <artifactId>gateways</artifactId>
-    <version>0.0.1-SNAPSHOT</version>
-    <name>fda-table-service-gateways</name>
-
-    <properties>
-        <maven.compiler.source>11</maven.compiler.source>
-        <maven.compiler.target>11</maven.compiler.target>
-    </properties>
-
+    <artifactId>gateway</artifactId>
     <dependencies>
         <dependency>
             <groupId>at.tuwien</groupId>
             <artifactId>api</artifactId>
-            <version>${project.version}</version>
+            <version>0.0.1-SNAPSHOT</version>
+            <scope>compile</scope>
         </dependency>
     </dependencies>
 
+    <properties>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
 
 </project>
\ No newline at end of file

fda-table-service/gateway/src/main/java/at/tuwien/config/ZenodoConfig.java

+package at.tuwien.config;
+
+import lombok.Getter;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.web.client.RestTemplateBuilder;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.web.client.RestTemplate;
+import org.springframework.web.util.DefaultUriTemplateHandler;
+
+@Configuration
+public class ZenodoConfig {
+
+    @Getter
+    @Value("${zenodo.endpoint}")
+    private String zenodoEndpoint;
+
+    @Getter
+    @Value("${zenodo.api_key}")
+    private String zenodoApiKey;
+
+    @Bean
+    public RestTemplate zenodo() {
+        DefaultUriTemplateHandler defaultUriTemplateHandler = new DefaultUriTemplateHandler();
+        defaultUriTemplateHandler.setBaseUrl(zenodoEndpoint);
+        return new RestTemplateBuilder()
+                .uriTemplateHandler(defaultUriTemplateHandler)
+                .build();
+    }
+
+}

fda-table-service/gateway/src/main/java/at/tuwien/exception/ZenodoApiException.java

+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.FORBIDDEN)
+public class ZenodoApiException extends Exception {
+
+    public ZenodoApiException(String msg) {
+        super(msg);
+    }
+
+    public ZenodoApiException(String msg, Throwable thr) {
+        super(msg, thr);
+    }
+
+    public ZenodoApiException(Throwable thr) {
+        super(thr);
+    }
+
+}

fda-table-service/gateway/src/main/java/at/tuwien/exception/ZenodoAuthenticationException.java

+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.FORBIDDEN)
+public class ZenodoAuthenticationException extends Exception {
+
+    public ZenodoAuthenticationException(String msg) {
+        super(msg);
+    }
+
+    public ZenodoAuthenticationException(String msg, Throwable thr) {
+        super(msg, thr);
+    }
+
+    public ZenodoAuthenticationException(Throwable thr) {
+        super(thr);
+    }
+
+}

fda-table-service/gateway/src/main/java/at/tuwien/gateway/ZenodoGateway.java

+package at.tuwien.gateway;
+
+import at.tuwien.api.zenodo.deposit.DepositDto;
+import at.tuwien.config.ZenodoConfig;
+import at.tuwien.exception.ZenodoApiException;
+import at.tuwien.exception.ZenodoAuthenticationException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Component;
+import org.springframework.web.client.RestTemplate;
+
+import java.util.Arrays;
+import java.util.List;
+
+@Component
+public class ZenodoGateway {
+
+    private final RestTemplate zenodoRestTemplate;
+    private final ZenodoConfig zenodoConfig;
+
+    @Autowired
+    public ZenodoGateway(RestTemplate zenodoRestTemplate, ZenodoConfig zenodoConfig) {
+        this.zenodoRestTemplate = zenodoRestTemplate;
+        this.zenodoConfig = zenodoConfig;
+    }
+
+    public List<DepositDto> listDeposits() throws ZenodoAuthenticationException, ZenodoApiException {
+        final ResponseEntity<DepositDto[]> response = zenodoRestTemplate.exchange("/api/deposit/depositions?access_token={token}",
+                HttpMethod.GET, null, DepositDto[].class, zenodoConfig.getZenodoApiKey());
+        if (response.getStatusCode().is4xxClientError()) {
+            throw new ZenodoAuthenticationException("Token is missing or invalid.");
+        }
+        if (response.getBody() == null) {
+            throw new ZenodoApiException("Endpoint returned null body");
+        }
+        if (response.getBody().length == 0) {
+            throw new ZenodoApiException("Endpoint returned empty body");
+        }
+        return Arrays.asList(response.getBody());
+    }
+}

fda-table-service/gateways/src/main/java/at/tuwien/client/FdaQueryServiceClient.java

-package at.tuwien.client;
-
-import at.tuwien.dto.CreateTableViaCsvDTO;
-import at.tuwien.mapper.ContainerIdAndQueryToExecuteInternalQueryMapper;
-import at.tuwien.mapper.CreateTableViaCsvToExecuteStatementMapper;
-import at.tuwien.model.CreateCSVTableWithDataset;
-import at.tuwien.model.ExecuteInternalQueryDTO;
-import at.tuwien.model.ExecuteStatementDTO;
-import at.tuwien.model.QueryResult;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.stereotype.Component;
-import org.springframework.web.reactive.function.client.ClientResponse;
-import org.springframework.web.reactive.function.client.WebClient;
-import reactor.core.publisher.Mono;
-
-@Component
-public class FdaQueryServiceClient {
-    private static final Logger LOGGER = LoggerFactory.getLogger(FdaQueryServiceClient.class);
-
-
-    private WebClient.Builder webClientBuilder;
-    private CreateTableViaCsvToExecuteStatementMapper mapper;
-
-    @Autowired
-    public FdaQueryServiceClient(WebClient.Builder webClientBuilder, CreateTableViaCsvToExecuteStatementMapper mapper) {
-        this.webClientBuilder = webClientBuilder;
-        this.mapper = mapper;
-    }
-
-    /**
-     * @deprecated use Spring RestTempaltes in future releases
-     */
-    public boolean executeStatement(CreateTableViaCsvDTO dto, String statement) {
-        LOGGER.debug("request fda-query-service for executing statement");
-        ExecuteStatementDTO statementDTO = mapper.map(dto, statement);
-        ClientResponse response = webClientBuilder
-                .build()
-                .post()
-                .uri("http://fda-query-service/query/executeStatement")
-                .contentType(MediaType.APPLICATION_JSON)
-                .body(Mono.just(statementDTO), ExecuteStatementDTO.class)
-                .exchange()
-                .block();
-
-        return true;
-    }
-
-    /**
-     * @deprecated use Spring RestTempaltes in future releases
-     */
-    public QueryResult executeQuery(String containerID, String query) {
-        ContainerIdAndQueryToExecuteInternalQueryMapper mapper = new ContainerIdAndQueryToExecuteInternalQueryMapper();
-        ExecuteInternalQueryDTO execInternalQueryDTO = mapper.map(containerID, query);
-        QueryResult queryResult = webClientBuilder
-                .build()
-                .post()
-                .uri("http://fda-query-service/query/executeQuery")
-                .contentType(MediaType.APPLICATION_JSON)
-                .body(Mono.just(execInternalQueryDTO), ExecuteInternalQueryDTO.class)
-                .retrieve()
-                .bodyToMono(QueryResult.class)
-                .block();
-
-        return queryResult;
-
-    }
-
-    /**
-     * @deprecated use Spring RestTempaltes in future releases
-     */
-    public boolean copyCSVIntoTable(CreateCSVTableWithDataset tableWithDataset) {
-        ClientResponse response = webClientBuilder
-                .build()
-                .post()
-                .uri("http://fda-query-service/query/copyCSVIntoTable")
-                .contentType(MediaType.APPLICATION_JSON)
-                .body(Mono.just(tableWithDataset), CreateCSVTableWithDataset.class)
-                .exchange()
-                .block();
-
-        if(response.statusCode().is2xxSuccessful()){
-            return true;
-        }
-        return false;
-    }
-}

fda-table-service/gateways/src/main/java/at/tuwien/mapper/CreateTableViaCsvToExecuteStatementMapper.java

-package at.tuwien.mapper;
-
-import at.tuwien.dto.CreateTableViaCsvDTO;
-import at.tuwien.model.ExecuteStatementDTO;
-import org.springframework.stereotype.Component;
-
-@Component
-public class CreateTableViaCsvToExecuteStatementMapper {
-
-    public ExecuteStatementDTO map(CreateTableViaCsvDTO dto, String statement){
-        ExecuteStatementDTO statementDTO = new ExecuteStatementDTO();
-        statementDTO.setContainerID(dto.getContainerId());
-        statementDTO.setStatement(statement);
-        return statementDTO;
-    }
-}

fda-table-service/pom.xml

@@ -19,6 +19,8 @@
         <module>rest-service</module>
         <module>services</module>
         <module>report</module>
+        <module>gateway</module>
+        <module>api</module>
     </modules>
 
     <properties>

fda-table-service/rest-service/pom.xml

@@ -19,6 +19,12 @@
             <artifactId>services</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>at.tuwien</groupId>
+            <artifactId>gateway</artifactId>
+            <version>0.0.1-SNAPSHOT</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>

fda-table-service/rest-service/src/main/resources/application-docker.yml

@@ -31,3 +31,6 @@ eureka:
 fda:
   mapping.path: /root
   table.path: /root
+zenodo:
+  endpoint: https://sandbox.zenodo.org/
+  api_key: "${ZENODO_API_KEY}"
\ No newline at end of file

fda-table-service/rest-service/src/main/resources/application.yml

@@ -32,3 +32,6 @@ eureka:
 fda:
   mapping.path: rest-service/src/main/resources
   table.path: rest-service/src/main/java/at/tuwien/userdb
+zenodo:
+  endpoint: https://sandbox.zenodo.org/
+  api_key: "${ZENODO_API_KEY}"
\ No newline at end of file