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ckan2zenodo-library
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Updated Fixer.fixIncomingDateString. Updated the DepositionMetadata 

dates without Time
This commit is contained in:
Francesco Mangiacrapa 2023-12-20 11:56:51 +01:00
parent 37df6bae7d
commit 8e91e2e869
7 changed files with 227 additions and 33 deletions
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18
src/main/java/org/gcube/data/publishing/ckan2zenodo/Fixer.java
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@ -2,7 +2,6 @@ package org.gcube.data.publishing.ckan2zenodo;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.time.LocalTime;
import java.time.ZoneOffset;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
@ -52,6 +51,11 @@ public class Fixer {
}
/**
* It seems never used to me - by Francesco M.
* @param toFix
* @return
*/
public static String fixSending(String toFix) {
DocumentContext ctx=JsonPath.using(Parsing.JSON_PATH_ALWAYS_LIST_CONFIG).parse(toFix);
DocumentContext pathCtx=JsonPath.using(Parsing.JSON_PATH_PATHS_CONFIGURATION).parse(toFix);
@ -85,6 +89,12 @@ public class Fixer {
return valuesCtx;
}
/**
* Updated by Francesco M., see #26166
* @param toFix
* @return
* @throws Exception
*/
public static final String fixIncomingDateString(String toFix) throws Exception {
TemporalAccessor accessor=INCOMING_FORMATTER.parse(toFix);
@ -93,7 +103,11 @@ public class Fixer {
zTime = LocalDateTime.from(accessor).atZone(ZoneOffset.UTC);
else {
LocalDate date=LocalDate.from(accessor);
zTime=LocalDateTime.of(date, LocalTime.of(0, 0, 0, 0)).atZone(ZoneOffset.UTC);
//original code
//zTime=LocalDateTime.of(date, LocalTime.of(0, 0, 0, 0)).atZone(ZoneOffset.UTC);
//new code by Francesco M. returning a date without the Time
return date.toString();
}
return zTime.format(INTERNAL_FORMATTER);

27
src/main/java/org/gcube/data/publishing/ckan2zenodo/clients/Zenodo.java
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@ -59,7 +59,9 @@ public class Zenodo {
private static final String ACCESS_TOKEN="access_token";
private static ObjectMapper mapper = new ObjectMapper();
//private static ObjectMapper mapper = new ObjectMapper();
//Updated by Francesco M.
public static final ObjectMapper mapper = new ObjectMapper();
static {
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false);
@ -223,39 +225,20 @@ public class Zenodo {
}
private ZenodoDeposition updateMetadata(Integer depositionId,DepositionMetadata meta) throws ZenodoException {
/*
* Original
try{
String serialized="{\"metadata\":"+Fixer.fixIncoming(mapper.writeValueAsString(meta))+"}";
try {
Response resp = getWebClient().target(credentials.getBaseUrl()).
path(DEPOSITION_BASE_URL).path(depositionId+"").
queryParam(ACCESS_TOKEN, credentials.getKey()).request(CONTENT_TYPE)
.put(Entity.json(serialized));
return check(resp,ZenodoDeposition.class);
}catch(Throwable t) {
log.debug("Error while tryin to update "+serialized);
throw t;
}
}catch(JsonProcessingException e) {
log.debug("Error while parsing "+meta,e);
throw new ZenodoException("Internal error.",e);
}*/
//Added logs by Francesco M.
try{
String serialized="{\"metadata\":"+Fixer.fixIncoming(mapper.writeValueAsString(meta))+"}";
log.debug("updateMetadata - serialized: {}",serialized);
try {
Entity<String> jsonEnt = Entity.json(serialized);
log.debug("updateMetadata - jsonEntity serialized: {}",jsonEnt.getEntity());
Response resp = getWebClient().target(credentials.getBaseUrl()).
path(DEPOSITION_BASE_URL).path(depositionId+"").
queryParam(ACCESS_TOKEN, credentials.getKey()).request(CONTENT_TYPE)
.put(jsonEnt);
return check(resp,ZenodoDeposition.class);
}catch(Throwable t) {
log.debug("Error while tryin to update "+serialized);
log.debug("Error while trying to update "+serialized);
throw t;
}
}catch(JsonProcessingException e) {

8
src/main/java/org/gcube/data/publishing/ckan2zenodo/model/zenodo/Commons.java
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@ -2,7 +2,9 @@ package org.gcube.data.publishing.ckan2zenodo.model.zenodo;
public class Commons {
public static final String ISO_DATE_PATTERN="yyyy-MM-dd'T'HH:mm:ss.SSSSSSZ";
public static final String ISO_DATE_PATTERN = "yyyy-MM-dd'T'HH:mm:ss.SSSSSSZ";
// Added by Francesco M. #26166
public static final String ISO_DATE_PATTERN_WITHOUT_TIME = "yyyy-MM-dd";
}

8
src/main/java/org/gcube/data/publishing/ckan2zenodo/model/zenodo/DateInterval.java
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@ -17,11 +17,13 @@ public class DateInterval {
public static enum Type{
Collected, Valid, Withdrawn
}
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN)
//Updated by Francesco M. #26166
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN_WITHOUT_TIME)
@JsonDeserialize(using = DateParser.class)
private Date start;
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN)
//Updated by Francesco M. #26166
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN_WITHOUT_TIME)
@JsonDeserialize(using = DateParser.class)
private Date end;
// @NonNull

6
src/main/java/org/gcube/data/publishing/ckan2zenodo/model/zenodo/DepositionMetadata.java
View File

@ -66,8 +66,8 @@ public class DepositionMetadata {
private UploadType upload_type;
private PublicationType publication_type;
private ImageType image_type;
// @NonNull
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN)
// @NonNull - Updated by Francesco M.
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN_WITHOUT_TIME)
private Date publication_date;
// @NonNull
private String title;
@ -78,7 +78,7 @@ public class DepositionMetadata {
// @NonNull
private AccessRights access_right;
private String license; // TODO ENUM https://licenses.opendefinition.org/licenses/groups/all.json
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN)
@JsonFormat(pattern = Commons.ISO_DATE_PATTERN_WITHOUT_TIME)
private Date embargo_date;
private String access_conditions; // TODO HTML
private String doi;

4
src/test/java/org/gcube/data/publishing/ckan2zenodo/TestCommons.java
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@ -4,12 +4,15 @@ import java.io.IOException;
import java.io.PrintStream;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.time.Instant;
import java.util.Date;
import java.util.HashMap;
import java.util.Map;
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
@ -74,4 +77,5 @@ public class TestCommons {
throw new Exception("Errors with json file "+jsonFile,t);
}
}
}

189
src/test/java/org/gcube/data/publishing/ckan2zenodo/Test_BugFix_26166.java Normal file
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@ -0,0 +1,189 @@
package org.gcube.data.publishing.ckan2zenodo;
import java.io.IOException;
import java.time.Instant;
import java.util.Date;
import javax.ws.rs.client.Entity;
import org.gcube.data.publishing.ckan2zenodo.clients.Zenodo;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
import org.junit.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import lombok.extern.slf4j.Slf4j;
/**
* The Class Test_BugFix_26166.
*
* @author Francesco Mangiacrapa at ISTI-CNR francesco.mangiacrapa@isti.cnr.it
*
* Dec 20, 2023
*/
@Slf4j
public class Test_BugFix_26166 {
@Test
public void testDate(){
ZenodoDeposition zenodo = new ZenodoDeposition();
zenodo.setCreated(Date.from(Instant.now()));
zenodo.setModified(Date.from(Instant.now()));
DepositionMetadata metadata = new DepositionMetadata();
metadata.setPublication_date(Date.from(Instant.now()));
metadata.setEmbargo_date(Date.from(Instant.now()));
zenodo.setMetadata(metadata);
ObjectMapper mapper = Zenodo.mapper;
try {
String serialized = "{\"metadata\":" + Fixer.fixIncoming(mapper.writeValueAsString(zenodo)) + "}";
log.debug("updateMetadata - serialized: {}", serialized);
try {
Entity<String> jsonEnt = Entity.json(serialized);
log.debug("updateMetadata - jsonEntity serialized: {}", jsonEnt.getEntity());
} catch (Throwable t) {
log.debug("Error while tryin to update " + serialized);
throw t;
}
} catch (JsonProcessingException e) {
log.debug("Error while parsing " + metadata, e);
e.printStackTrace();
}
}
@Test
public void testReadDepositionFromZenodo(){
String depoisitionString = " {\n"
+ " \"created\": \"2023-12-14T11:33:09.650134+00:00\",\n"
+ " \"modified\": \"2023-12-14T11:33:09.700320+00:00\",\n"
+ " \"id\": 10377042,\n"
+ " \"conceptrecid\": \"10377041\",\n"
+ " \"metadata\": {\n"
+ " \"title\": \"Blue-Cloud 2026 - D4.2 VLabs Implementation Guidelines\",\n"
+ " \"publication_date\": \"2023-12-14\",\n"
+ " \"description\": \"This deliverable provides guidelines on how to implement the Virtual \\nLaboratories (VLabs) in the Blue-Cloud Virtual Research Environment (VRE). \\nFirst a summary of the activities of WP4 is presented, followed by an \\noverview of the VRE services, that offer a comprehensive array of features, \\nfostering collaboration, facilitating data analytics, enabling result \\ndissemination, and ensuring seamless integration with external systems. In \\nfact, the VRE caters to the entirety of the research lifecycle.\",\n"
+ " \"access_right\": \"open\",\n"
+ " \"creators\": [\n"
+ " {\n"
+ " \"name\": \"Assante, Massimiliano\",\n"
+ " \"affiliation\": \"National Research Council of Italy - Institute of Information Science and Technologies\",\n"
+ " \"orcid\": \"0000-0002-3761-1492\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Martin-Cabrera\",\n"
+ " \"affiliation\": \"Flanders Marine Institute (VLIZ)\",\n"
+ " \"orcid\": \"0000-0003-3293-5612\"\n"
+ " }\n"
+ " ],\n"
+ " \"contributors\": [\n"
+ " {\n"
+ " \"name\": \"Vitorino, Joao\",\n"
+ " \"affiliation\": null,\n"
+ " \"type\": \"Other\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Troupin, Charles, ctroupin@uliege.be, orcid.org/\",\n"
+ " \"affiliation\": \"Université de Liège\",\n"
+ " \"type\": \"Other\",\n"
+ " \"orcid\": \"0000-0002-0265-1021\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Pint, Steven\",\n"
+ " \"affiliation\": \"Flanders Marine Institute (VLIZ)\",\n"
+ " \"type\": \"Other\",\n"
+ " \"orcid\": \"0000-0001-5530-6785\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Palermo, Francesco\",\n"
+ " \"affiliation\": \"Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC)\",\n"
+ " \"type\": \"Other\",\n"
+ " \"orcid\": \"0000-0002-0463-4655\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Grasset, Bastien\",\n"
+ " \"affiliation\": \"French National Research Institute for Sustainable Development (IRD)\",\n"
+ " \"type\": \"Other\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Barth, Alexander\",\n"
+ " \"affiliation\": \"Université de Liège\",\n"
+ " \"type\": \"Other\",\n"
+ " \"orcid\": \"0000-0003-2952-5997\"\n"
+ " },\n"
+ " {\n"
+ " \"name\": \"Barde, Julien\",\n"
+ " \"affiliation\": \"French National Research Institute for Sustainable Development (IRD)\",\n"
+ " \"type\": \"Other\",\n"
+ " \"orcid\": \"0000-0002-3519-6141\"\n"
+ " }\n"
+ " ],\n"
+ " \"keywords\": [\n"
+ " \"VLabs\",\n"
+ " \"VRE\"\n"
+ " ],\n"
+ " \"related_identifiers\": [\n"
+ " {\n"
+ " \"identifier\": \"https://data.d4science.org/ctlg/Blue-Cloud2026Project/d4_2_vlabs_implementation_guidelines\",\n"
+ " \"relation\": \"isCompiledBy\",\n"
+ " \"scheme\": \"url\"\n"
+ " }\n"
+ " ],\n"
+ " \"version\": \"1\",\n"
+ " \"grants\": [\n"
+ " {\n"
+ " \"id\": \"10.13039/501100000780::101094227\"\n"
+ " }\n"
+ " ],\n"
+ " \"license\": \"cc-by-4.0\",\n"
+ " \"imprint_publisher\": \"Zenodo\",\n"
+ " \"communities\": [\n"
+ " {\n"
+ " \"identifier\": \"bluecloud\"\n"
+ " }\n"
+ " ],\n"
+ " \"upload_type\": \"publication\",\n"
+ " \"publication_type\": \"deliverable\",\n"
+ " \"prereserve_doi\": {\n"
+ " \"doi\": \"10.5281/zenodo.10377042\",\n"
+ " \"recid\": 10377042\n"
+ " }\n"
+ " },\n"
+ " \"title\": \"Blue-Cloud 2026 - D4.2 VLabs Implementation Guidelines\",\n"
+ " \"links\": {\n"
+ " \"self\": \"https://zenodo.org/api/records/10377042\",\n"
+ " \"html\": \"https://zenodo.org/records/10377042\",\n"
+ " \"badge\": \"https://zenodo.org/badge/doi/.svg\",\n"
+ " \"files\": \"https://zenodo.org/api/records/10377042/files\",\n"
+ " \"latest_draft\": \"https://zenodo.org/api/deposit/depositions/10377042\",\n"
+ " \"latest_draft_html\": \"https://zenodo.org/deposit/10377042\",\n"
+ " \"publish\": \"https://zenodo.org/api/deposit/depositions/10377042/actions/publish\",\n"
+ " \"edit\": \"https://zenodo.org/api/deposit/depositions/10377042/actions/edit\",\n"
+ " \"discard\": \"https://zenodo.org/api/deposit/depositions/10377042/actions/discard\",\n"
+ " \"newversion\": \"https://zenodo.org/api/deposit/depositions/10377042/actions/newversion\",\n"
+ " \"registerconceptdoi\": \"https://zenodo.org/api/deposit/depositions/10377042/actions/registerconceptdoi\"\n"
+ " },\n"
+ " \"record_id\": 10377042,\n"
+ " \"owner\": 82231,\n"
+ " \"files\": [],\n"
+ " \"state\": \"unsubmitted\",\n"
+ " \"submitted\": false\n"
+ " }";
try {
ObjectMapper mapper = Zenodo.mapper;
ZenodoDeposition dep = mapper.readValue(Fixer.fixIncoming(depoisitionString), ZenodoDeposition.class);
System.out.println("The deposition: "+dep);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}