Date parsing

ckan2zenodo-library/pom.xml

@@ -50,6 +50,12 @@
 			<groupId>org.gcube.data-publishing</groupId>
 			<artifactId>gcat-client</artifactId>
 			<version>[1.2.0,2.0.0-SNAPSHOT)</version>
+			<exclusions>
+				<exclusion>
+					<groupId>com.fasterxml.jackson.core</groupId>
+					<artifactId>jackson-core</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 
 		<!-- EXTERNAL -->
@@ -60,12 +66,26 @@
 			<version>1.14.8</version>
 		</dependency>
 
+		<dependency>
+			<groupId>org.glassfish.jersey.media</groupId>
+			<artifactId>jersey-media-json-jackson</artifactId>			
+		</dependency>
+ 
 		<dependency>
 			<groupId>com.jayway.jsonpath</groupId>
 			<artifactId>json-path</artifactId>
 			<version>2.4.0</version>
 		</dependency>
 
+
+		<!-- Test log binding -->
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<version>1.0.13</version>
+			<scope>test</scope>
+		</dependency>
+		
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/Ckan2ZenodoImpl.java

@@ -5,7 +5,7 @@ import java.net.MalformedURLException;
 import org.gcube.data.publishing.ckan2zenodo.clients.GCat;
 import org.gcube.data.publishing.ckan2zenodo.clients.Zenodo;
 import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
-import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
+import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
 
 public class Ckan2ZenodoImpl {
 
@@ -25,7 +25,7 @@ public class Ckan2ZenodoImpl {
 		
 	}
 	
-	private static final String getZenodoToken() {
+	private static final ZenodoCredentials getZenodoToken() {
 		throw new RuntimeException();
 	}
 }

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/Fixer.java

@@ -0,0 +1,64 @@
+package org.gcube.data.publishing.ckan2zenodo;
+
+import com.jayway.jsonpath.DocumentContext;
+import com.jayway.jsonpath.JsonPath;
+import com.jayway.jsonpath.PathNotFoundException;
+
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class Fixer {
+	
+	
+	public static final String fixIncoming(String toFix) {
+		DocumentContext ctx=JsonPath.parse(toFix);
+
+
+		ctx=fixIncomingDate(ctx, "$.created");
+		ctx=fixIncomingDate(ctx, "$.modified");
+		
+		return ctx.jsonString();
+	}
+	
+	
+	public static String fixSending(String toFix) {
+		DocumentContext ctx=JsonPath.parse(toFix);
+		
+		fixOutgoingDate(ctx, "$.created");
+		fixOutgoingDate(ctx, "$.modified");
+
+		return ctx.jsonString();
+	}
+	
+	//*** INCOMINGs
+	private static final DocumentContext fixIncomingDate(DocumentContext ctx,String toFixPath) {
+		try {
+		StringBuilder toFix=new StringBuilder(ctx.read(toFixPath));
+		
+		
+		ctx.put(toFixPath.substring(0,toFixPath.lastIndexOf(".")), 
+				toFixPath.substring(toFixPath.lastIndexOf(".")+1), 
+				toFix.deleteCharAt(toFix.lastIndexOf(":")).toString());		
+		}catch(Throwable e) {
+			log.warn("Unable to fix "+toFixPath+". Cause : ",e);
+		}
+		return ctx;
+	}
+	
+	
+	//*** OUTGOINGs
+	
+	private static final DocumentContext fixOutgoingDate(DocumentContext ctx,String toFixPath) {
+		try{
+			String toFix=ctx.read(toFixPath);
+		
+			ctx.put(toFixPath.substring(0,toFixPath.lastIndexOf(".")), 
+					toFixPath.substring(toFixPath.lastIndexOf(".")+1), 
+					toFix.substring(0,toFix.length()-2)+":"+
+							toFix.substring(toFix.length()-2, toFix.length()));
+		}catch(Throwable t) {
+			log.debug("Unable to fix "+toFixPath+".Cause : ",t);			
+		}
+			return ctx;
+	}
+}

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/Transformer.java

@@ -0,0 +1,16 @@
+package org.gcube.data.publishing.ckan2zenodo;
+
+import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
+import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
+
+public class Transformer {
+
+	
+	public ZenodoDeposition transform(CkanItemDescriptor toTransform) {
+		ZenodoDeposition dep=new ZenodoDeposition();
+		
+//		dep.set
+		throw new RuntimeException("Implment this");
+	}
+	
+}

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/TransformerManager.java

@@ -2,6 +2,8 @@ package org.gcube.data.publishing.ckan2zenodo;
 
 public class TransformerManager {
 
-	
+	public Transformer getByProfile(String profile) {
+		throw new RuntimeException("Implement this");
+	}
 	
 }

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/clients/Zenodo.java

@@ -1,65 +1,103 @@
 package org.gcube.data.publishing.ckan2zenodo.clients;
 
+import java.io.IOException;
+
 import javax.ws.rs.client.Client;
 import javax.ws.rs.client.ClientBuilder;
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 
+import org.gcube.data.publishing.ckan2zenodo.Fixer;
+import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
 import org.gcube.data.publishing.ckan2zenodo.model.faults.ZenodoException;
+import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata;
 import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
 import org.glassfish.jersey.client.ClientProperties;
 
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
 import lombok.NonNull;
 import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
 
 @RequiredArgsConstructor
+@Slf4j
 public class Zenodo {
 
-	private static final String BASE_URL="https://zenodo.org/api/";
-	
 	private static final String CONTENT_TYPE="application/json";
-	
+
 	private static final String DEPOSITION_BASE_URL="deposit/depositions";
-	
+
-	private static final String AUTH="Authorization";
+
-	private static final String BEARER="Bearer ";
+	private static final String ACCESS_TOKEN="access_token";
-	
+
+	private static ObjectMapper mapper = new ObjectMapper();
+
+	static {
+		mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false);
+		//		mapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+	}
+
+
 	@NonNull
-	private String tokenValue;
+	private ZenodoCredentials credentials;
-	
+
-	
 	Client client;
-	
+
 	private synchronized Client getWebClient() {
 		if(client==null)
-		client = ClientBuilder.newClient(
+			client = ClientBuilder.newClient()
-//				new ClientConfig().register(new HTTPBasicProvider(username, password))
+			.property(ClientProperties.SUPPRESS_HTTP_COMPLIANCE_VALIDATION, true);
-				)
-				.property(ClientProperties.SUPPRESS_HTTP_COMPLIANCE_VALIDATION, true);
 		return client;
 	}
-	
+
 	public ZenodoDeposition readDeposition(String id) throws ZenodoException {
-		
+		Response resp= getWebClient().target(credentials.getBaseUrl()).
-//		String respString=null;
+				path(DEPOSITION_BASE_URL).path(id).
-		return getWebClient().target(BASE_URL).
+				queryParam(ACCESS_TOKEN, credentials.getKey()).request(CONTENT_TYPE)
-				path(DEPOSITION_BASE_URL).path(id).request(CONTENT_TYPE)
+				.get();
-	    		.header(AUTH, BEARER+tokenValue)
+		return check(resp,ZenodoDeposition.class);		
-	    		.get(ZenodoDeposition.class);
-//		respString=check(resp);
-		
 	}
-	
+
-	
+
-	
+	private static <T> T check(Response resp, Class<T> clazz) throws ZenodoException{
-	
-	private static String check(Response resp) throws ZenodoException {
 		if(resp.getStatus()<200||resp.getStatus()>=300) {			
 			throw new ZenodoException("RESP STATUS IS "+resp.getStatus()+". Message : "+resp.readEntity(String.class));
-		}else 
+		}else {
-			return resp.readEntity(String.class);			
+			String respString=resp.readEntity(String.class);
+			try {
+				return mapper.readValue(Fixer.fixIncoming(respString), clazz);
+			} catch (IOException e) {
+				throw new ZenodoException("Unable to parse response from Zenodo. Content was : \n "+respString,e);
+			}	
+		}
 	}
-	
+
-	public ZenodoDeposition publishOrUpdate(ZenodoDeposition d) {
+	public ZenodoDeposition Update(ZenodoDeposition d) {
 		throw new RuntimeException("Implement This");
 	}
+
+	public ZenodoDeposition create(DepositionMetadata meta) throws ZenodoException, JsonParseException, JsonMappingException, IOException {
+		ZenodoDeposition toSend=new ZenodoDeposition();
+		toSend.setMetadata(meta);
+		String serialized=Fixer.fixSending(mapper.writeValueAsString(toSend));
+		try{
+			Response resp = getWebClient().target(credentials.getBaseUrl()).
+				path(DEPOSITION_BASE_URL).
+				queryParam(ACCESS_TOKEN, credentials.getKey()).request(CONTENT_TYPE)
+				.post(Entity.json(serialized));
+		return check(resp,ZenodoDeposition.class);				
+		}catch(Throwable t) {
+			log.debug("Exception while sending : "+serialized);
+			throw t;
+		}
+	}
+
+
+
+	
 }

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/model/ZenodoCredentials.java

@@ -0,0 +1,15 @@
+package org.gcube.data.publishing.ckan2zenodo.model;
+
+import lombok.Getter;
+import lombok.NonNull;
+import lombok.RequiredArgsConstructor;
+
+@Getter
+@RequiredArgsConstructor
+public class ZenodoCredentials {
+
+	@NonNull
+	private String key;
+	@NonNull
+	private String baseUrl;
+}

ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/model/zenodo/ZenodoDeposition.java

@@ -4,20 +4,20 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.Date;
 
-import lombok.Getter;
+import com.fasterxml.jackson.annotation.JsonFormat;
-import lombok.Setter;
-import lombok.ToString;
 
-@Getter
+import lombok.Data;
-@Setter
+
-@ToString
+@Data
 public class ZenodoDeposition {
 
+	@JsonFormat(pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSZ")
 	private Date created; 
 	private String doi;
 	private ArrayList<FileDeposition> files;
 	private Integer id;
 	private DepositionMetadata metadata;
+	@JsonFormat(pattern = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSZ")
 	private Date modified;
 	private Integer owner;
 	private Integer record_id;

ckan2zenodo-library/src/test/java/org/gcube/tests/ParsingTests.java

@@ -0,0 +1,36 @@
+package org.gcube.tests;
+
+import java.io.IOException;
+import java.util.Date;
+
+import org.gcube.data.publishing.ckan2zenodo.Fixer;
+import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class ParsingTests {
+
+	static ObjectMapper mapper=new ObjectMapper();
+	@BeforeClass
+	public static void init () {
+		mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false);
+	}
+	
+	
+	@Test
+	public void DateTest() throws IOException {
+		ZenodoDeposition z=new ZenodoDeposition();
+		z.setCreated(new Date(System.currentTimeMillis()));
+		System.out.println("Write : ");		
+		System.out.println(Fixer.fixSending(mapper.writeValueAsString(z)));
+		String s="{\"conceptrecid\":\"422982\",\"created\":\"2019-11-26T15:43:49.879+00:00\",\"files\":[],\"id\":422983,\"links\":{\"bucket\":\"https://sandbox.zenodo.org/api/files/a6b09898-1807-4f03-a7ac-ed06b2d3ba2b\",\"discard\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983/actions/discard\",\"edit\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983/actions/edit\",\"files\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983/files\",\"html\":\"https://sandbox.zenodo.org/deposit/422983\",\"latest_draft\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983\",\"latest_draft_html\":\"https://sandbox.zenodo.org/deposit/422983\",\"newversion\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983/actions/newversion\",\"publish\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983/actions/publish\",\"registerconceptdoi\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983/actions/registerconceptdoi\",\"self\":\"https://sandbox.zenodo.org/api/deposit/depositions/422983\"},\"metadata\":{\"prereserve_doi\":{\"doi\":\"10.5072/zenodo.422983\",\"recid\":422983}},\"modified\":\"2019-11-26T15:43:49.876858+00:00\",\"owner\":31041,\"record_id\":422983,\"state\":\"unsubmitted\",\"submitted\":false,\"title\":\"\"}";
+		
+		System.out.println("READ : ");
+		
+		System.out.println(mapper.readValue(Fixer.fixIncoming(s), ZenodoDeposition.class));
+	}
+	
+}

ckan2zenodo-library/src/test/java/org/gcube/tests/ZenodoTests.java

@@ -5,16 +5,27 @@ import java.nio.file.Files;
 import java.nio.file.Paths;
 
 import org.gcube.data.publishing.ckan2zenodo.clients.Zenodo;
+import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
 import org.gcube.data.publishing.ckan2zenodo.model.faults.ZenodoException;
+import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata;
 import org.junit.Test;
 
 public class ZenodoTests {
 	
 	@Test
 	public void readFromZenodo() throws IOException, ZenodoException {
+		
+//		private static final String BASE_URL="https://zenodo.org/api/";
+		String BASE_URL="https://sandbox.zenodo.org/api/";
+		
 		String key=Files.readAllLines(Paths.get("/home/fabio/workspaces/zenodo.key")).get(0);
 		
-		System.out.println(new Zenodo(key).readDeposition("10"));
+		System.out.println("Using key : "+key);
+		Zenodo z=new Zenodo(new ZenodoCredentials(key,BASE_URL));
+		
+		System.out.println(z.readDeposition("422983"));
+		
+		System.out.println(z.create(new DepositionMetadata()));
 	}
 
 }