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ckan2zenodo-library
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Basic mapping implementation

This commit is contained in:
Fabio Sinibaldi 2019-12-02 18:02:11 +01:00
parent c56d2d53a2
commit 7553dd1964
7 changed files with 342 additions and 14 deletions
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73
ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/Transformer.java
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@ -1,16 +1,81 @@
package org.gcube.data.publishing.ckan2zenodo;
import java.util.ArrayList;
import java.util.HashMap;
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.Contributor;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.RelatedIdentifier;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata.AccessRights;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class Transformer {
private HashMap<String,String> mappings=new HashMap<>();
public ZenodoDeposition transform(CkanItemDescriptor toTransform) {
ZenodoDeposition dep=new ZenodoDeposition();
public ZenodoDeposition transform(CkanItemDescriptor toTransform, ZenodoDeposition deposition) {
log.debug("Transforming "+toTransform+". Existing Deposition is : "+deposition);
// dep.set
throw new RuntimeException("Implment this");
if(deposition==null) deposition=new ZenodoDeposition();
// default mappings
DepositionMetadata meta=deposition.getMetadata();
if(meta==null)
meta=new DepositionMetadata();
meta.setTitle(toTransform.getTitle());
meta.setDescription(toTransform.getNotes());
// Access Right
if(toTransform.isOpen())
meta.setAccess_right(AccessRights.open);
else {
meta.setAccess_right(AccessRights.restricted);
meta.setAccess_conditions("Visit the VRE "+toTransform.getVRE()+" to access it.");
}
meta.setLicense(toTransform.getLicenseId());
meta.setKeywords(new ArrayList<String>(toTransform.getTags()));
//Related Identifiers
String itemUrl=toTransform.getItemUrl();
ArrayList<RelatedIdentifier> relatedIdentifiers=new ArrayList<>();
if(itemUrl!=null) relatedIdentifiers.add(new RelatedIdentifier(itemUrl,RelatedIdentifier.Relation.compiles));
//Contributors
ArrayList<Contributor> contributors=new ArrayList<>();
String authorName=toTransform.getAuthor();
if(authorName!=null) {
Contributor author=new Contributor(Contributor.Type.Producer);
author.setName(authorName);
contributors.add(author);
}
String maintainerName=toTransform.getAuthor();
if(maintainerName!=null) {
Contributor maintainer=new Contributor(Contributor.Type.DataCurator);
maintainer.setName(maintainerName);
contributors.add(maintainer);
}
meta.setContributors(contributors);
meta.setVersion(toTransform.getVersion());
// Dates
deposition.setMetadata(meta);
// profile specific mappings
return deposition;
}
}

2
ckan2zenodo-library/src/main/java/org/gcube/data/publishing/ckan2zenodo/model/zenodo/RelatedIdentifier.java
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@ -3,9 +3,11 @@ package org.gcube.data.publishing.ckan2zenodo.model.zenodo;
import lombok.Data;
import lombok.NoArgsConstructor;
import lombok.NonNull;
import lombok.RequiredArgsConstructor;
@Data
@NoArgsConstructor
@RequiredArgsConstructor
public class RelatedIdentifier {
public static enum Relation{

5
ckan2zenodo-library/src/test/java/org/gcube/tests/ParsingTests.java
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@ -8,16 +8,15 @@ import org.junit.BeforeClass;
import org.junit.Test;
import com.fasterxml.jackson.core.JsonParseException;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class ParsingTests {
static ObjectMapper mapper=new ObjectMapper();
static ObjectMapper mapper=null;
@BeforeClass
public static void init () {
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false);
mapper=TestCommons.getMapper();
}

41
ckan2zenodo-library/src/test/java/org/gcube/tests/TestCommons.java Normal file
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@ -0,0 +1,41 @@
package org.gcube.tests;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
import com.fasterxml.jackson.annotation.JsonInclude.Include;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
public class TestCommons {
static ZenodoCredentials loadCredentials() throws IOException {
String BASE_URL="https://sandbox.zenodo.org/api/";
String key=Files.readAllLines(Paths.get("/home/fabio/workspaces/zenodo.key")).get(0);
System.out.println("Using key : "+key);
return new ZenodoCredentials(key,BASE_URL);
}
static String convertStreamToString(java.io.InputStream is) {
java.util.Scanner s = new java.util.Scanner(is).useDelimiter("\\A");
return s.hasNext() ? s.next() : "";
}
static ObjectMapper getMapper() {
ObjectMapper mapper=new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false);
mapper.configure(SerializationFeature.WRITE_EMPTY_JSON_ARRAYS, false);
mapper.setSerializationInclusion(Include.NON_NULL);
return mapper;
}
}

39
ckan2zenodo-library/src/test/java/org/gcube/tests/TransformationTests.java Normal file
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@ -0,0 +1,39 @@
package org.gcube.tests;
import org.gcube.data.publishing.ckan2zenodo.Fixer;
import org.gcube.data.publishing.ckan2zenodo.Transformer;
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
import org.junit.BeforeClass;
import org.junit.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class TransformationTests {
static ObjectMapper mapper=null;
@BeforeClass
public static void init () {
mapper=TestCommons.getMapper();
}
@Test
public void transform() throws JsonProcessingException {
String json=TestCommons.convertStreamToString(this.getClass().getResourceAsStream("/simpleItem.json"));
Transformer defaultTransformer=new Transformer();
CkanItemDescriptor desc=new CkanItemDescriptor("sampleontable_in_prevre", json);
System.out.println("Going to transform : "+desc.getContent());
System.out.println("Result : ");
ZenodoDeposition dep=defaultTransformer.transform(desc, null);
System.out.println(dep);
System.out.println("As JSON : ");
System.out.println(Fixer.fixSending(mapper.writeValueAsString(dep)));
}
}

23
ckan2zenodo-library/src/test/java/org/gcube/tests/ZenodoTests.java
View File

@ -6,7 +6,9 @@ import java.nio.file.Paths;
import java.util.Arrays;
import java.util.Date;
import org.gcube.data.publishing.ckan2zenodo.Transformer;
import org.gcube.data.publishing.ckan2zenodo.clients.Zenodo;
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
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.Creator;
@ -21,16 +23,12 @@ import com.fasterxml.jackson.core.JsonProcessingException;
public class ZenodoTests {
private static ZenodoCredentials credentials;
private static ZenodoCredentials credentials;
@BeforeClass
public static final void init() throws IOException {
String BASE_URL="https://sandbox.zenodo.org/api/";
String key=Files.readAllLines(Paths.get("/home/fabio/workspaces/zenodo.key")).get(0);
System.out.println("Using key : "+key);
credentials=new ZenodoCredentials(key,BASE_URL);
credentials=TestCommons.loadCredentials();
}
@ -61,4 +59,15 @@ public class ZenodoTests {
System.out.println(z.updateMetadata(dep.getId(),dep.getMetadata()));
}
// @Test
// public void createFromSimpleItem() throws JsonProcessingException, ZenodoException {
// Zenodo z=new Zenodo(credentials);
// String json=TestCommons.convertStreamToString(this.getClass().getResourceAsStream("/simpleItem.json"));
// Transformer defaultTransformer=new Transformer();
// CkanItemDescriptor desc=new CkanItemDescriptor("sampleontable_in_prevre", json);
// ZenodoDeposition dep=z.createNew();
// defaultTransformer.transform(desc, dep);
// System.out.println(z.updateMetadata(dep.getId(), dep.getMetadata()));
// }
}

173
ckan2zenodo-library/src/test/resources/simpleItem.json Normal file
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@ -0,0 +1,173 @@
{
"rating": 0.0,
"license_title": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0",
"maintainer": null,
"searchable": "true",
"relationships_as_object": [],
"private": true,
"maintainer_email": null,
"num_tags": 4,
"id": "a5a7db8c-9b11-4522-bf5c-17baf59f2e9d",
"metadata_created": "2019-06-05T16:08:38.579293",
"metadata_modified": "2019-07-01T13:25:49.169770",
"author": "fabio_sinibaldi",
"author_email": "fabio_sinibaldi@gcube.ckan.org",
"state": "active",
"version": null,
"creator_user_id": "7d9008ef-2328-4fd7-8995-2c697faa7201",
"type": "dataset",
"resources": [
{
"mimetype": null,
"cache_url": null,
"hash": "",
"description": "Link to the GUI designed to operate with DataMiner",
"name": "Gateway Link",
"format": "HTTP",
"url": "https://pre.d4science.org/group/prevre/dataminer-manager?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SAMPLEONTABLE",
"datastore_active": false,
"cache_last_updated": null,
"package_id": "a5a7db8c-9b11-4522-bf5c-17baf59f2e9d",
"created": "2019-07-01T13:25:48.958747",
"state": "active",
"mimetype_inner": null,
"last_modified": null,
"position": 0,
"revision_id": "6d36b2ae-aedc-4c3d-bb8a-a9afeea273df",
"url_type": null,
"id": "1a27d3d7-12e9-4367-b618-3f82dde5909e",
"resource_type": null,
"size": null
},
{
"mimetype": null,
"cache_url": null,
"hash": "",
"description": "WPS Link to the DataMiner Process",
"name": "WPS Link",
"format": "WPS",
"url": "https://dataminer1-pre.d4science.org/wps/WebProcessingService?Request=DescribeProcess&Version=1.0.0&Service=WPS&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SAMPLEONTABLE",
"datastore_active": false,
"cache_last_updated": null,
"package_id": "a5a7db8c-9b11-4522-bf5c-17baf59f2e9d",
"created": "2019-07-01T13:25:49.192891",
"state": "active",
"mimetype_inner": null,
"last_modified": null,
"position": 1,
"revision_id": "6d36b2ae-aedc-4c3d-bb8a-a9afeea273df",
"url_type": null,
"id": "d190c17e-0065-448f-af8d-b37ebe911c76",
"resource_type": null,
"size": null
}],
"num_resources": 2,
"tags": [
{
"vocabulary_id": null,
"state": "active",
"display_name": "Analytics",
"id": "b9408e0e-5a78-47b6-825f-fd6458af73d6",
"name": "Analytics"
},
{
"vocabulary_id": null,
"state": "active",
"display_name": "Databases",
"id": "6db27a4c-71ff-448d-ad8d-3e1ee35440dd",
"name": "Databases"
},
{
"vocabulary_id": null,
"state": "active",
"display_name": "WPS",
"id": "195bab7c-04c6-4892-b35f-1248b4414304",
"name": "WPS"
},
{
"vocabulary_id": null,
"state": "active",
"display_name": "preVRE",
"id": "22a50ee0-82e9-4092-a589-5f749d5edbb7",
"name": "preVRE"
}],
"groups": [],
"license_id": "CC-BY-NC-SA-4.0",
"relationships_as_subject": [],
"organization":
{
"description": "The preVRE organisation",
"created": "2019-05-02T12:41:26.149836",
"title": "preVRE",
"name": "prevre",
"is_organization": true,
"state": "active",
"image_url": "https://pre.d4science.org/image/layout_set_logo?img_id=12949941",
"revision_id": "a44aebb5-5f88-4d53-94d2-bfb17b8d340b",
"type": "organization",
"id": "46ce33da-dbc1-4116-b41d-eb961435a53d",
"approval_status": "approved"
},
"name": "sampleontable_in_prevre",
"isopen": false,
"url": null,
"notes": "Algorithm that allows to perform a sample operation on a table",
"owner_org": "46ce33da-dbc1-4116-b41d-eb961435a53d",
"extras": [
{
"key": "DataMiner Process:Input Parameter",
"value": "TableName [OBJECT] : The name of the table"
},
{
"key": "DataMiner Process:Input Parameter",
"value": "ResourceName [OBJECT] : The name of the resource"
},
{
"key": "DataMiner Process:Input Parameter",
"value": "SchemaName [OBJECT] : The name of the schema"
},
{
"key": "DataMiner Process:Input Parameter",
"value": "DatabaseName [OBJECT] : The name of the database"
},
{
"key": "DataMiner Process:Output Parameter",
"value": "non_deterministic_output [FILE] : NonDeterministicOutput"
},
{
"key": "DataMiner Process:Process Author",
"value": "Sinibaldi,Fabio"
},
{
"key": "DataMiner Process:Process Maintainer",
"value": "Sinibaldi,Fabio"
},
{
"key": "Input Parameter",
"value": ""
},
{
"key": "Item URL",
"value": "http://data-pre.d4science.org/ctlg/preVRE/sampleontable_in_prevre"
},
{
"key": "Output Parameter",
"value": ""
},
{
"key": "Process Author",
"value": ""
},
{
"key": "Process Maintainer",
"value": ""
},
{
"key": "system:type",
"value": "DataMiner Process"
}],
"license_url": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
"ratings_count": 0,
"title": "Sampleontable in preVRE",
"revision_id": "44b644e5-ebdd-485c-8271-50d81d0407aa"
}