Prefilling changes

This commit is contained in:
Efstratios Giannopoulos 2024-02-29 17:51:20 +02:00
parent 96696f1a14
commit 46862e06cc
14 changed files with 152 additions and 1089 deletions

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package eu.eudat.service.externalfetcher.config;
import eu.eudat.commons.enums.ExternalFetcherSourceType;
import eu.eudat.service.externalfetcher.config.entities.SourceBaseConfiguration;
public class UrlConfiguration implements SourceBaseConfiguration {
private String key;
private String label;
private Integer ordinal;
private ExternalFetcherSourceType type;
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
public Integer getOrdinal() {
return ordinal;
}
public void setOrdinal(Integer ordinal) {
this.ordinal = ordinal;
}
public ExternalFetcherSourceType getType() {
return type;
}
public void setType(ExternalFetcherSourceType type) {
this.type = type;
}
}

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package eu.eudat.service.externalfetcher.config.entities;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlRootElement;
@XmlRootElement(name = "mapping")
public class DefaultPrefillingMapping implements PrefillingMapping{
private String source;
private String target;
private String semanticTarget;
private String subSource;
private String trimRegex;
public String getSource() {
return source;
}
@XmlAttribute(name = "source")
public void setSource(String source) {
this.source = source;
}
public String getTarget() {
return target;
}
@XmlAttribute(name = "target")
public void setTarget(String target) {
this.target = target;
}
public String getSemanticTarget() {
return semanticTarget;
}
@XmlAttribute(name = "semanticTarget")
public void setSemanticTarget(String semanticTarget) {
this.semanticTarget = semanticTarget;
}
public String getSubSource() {
return subSource;
}
@XmlAttribute(name = "subSource")
public void setSubSource(String subSource) {
this.subSource = subSource;
}
public String getTrimRegex() {
return trimRegex;
}
@XmlAttribute(name = "trimRegex")
public void setTrimRegex(String trimRegex) {
this.trimRegex = trimRegex;
}
}

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package eu.eudat.service.externalfetcher.config.entities;
import java.util.List;
public abstract class GenericUrls {
public abstract List<SourceBaseConfiguration> getUrls();
}

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package eu.eudat.service.externalfetcher.config.entities;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlRootElement;
@XmlRootElement(name = "config")
public class PrefillingConfig {
private PrefillingSearch prefillingSearch;
private PrefillingGet prefillingGet;
private String type;
public PrefillingSearch getPrefillingSearch() {
return prefillingSearch;
}
@XmlElement(name = "prefillingSearch")
public void setPrefillingSearch(PrefillingSearch prefillingSearch) {
this.prefillingSearch = prefillingSearch;
}
public PrefillingGet getPrefillingGet() {
return prefillingGet;
}
@XmlElement(name = "prefillingGet")
public void setPrefillingGet(PrefillingGet prefillingGet) {
this.prefillingGet = prefillingGet;
}
@XmlAttribute(name = "type")
public void setType(String type) {
this.type = type;
}
public String getType(){
return type;
}
}

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package eu.eudat.service.externalfetcher.config.entities;
import jakarta.xml.bind.annotation.XmlAttribute;
import jakarta.xml.bind.annotation.XmlRootElement;
@XmlRootElement(name = "fixedMapping")
public class PrefillingFixedMapping implements PrefillingMapping{
private String target;
private String semanticTarget;
private String value;
public String getTarget() {
return target;
}
@XmlAttribute(name = "target")
public void setTarget(String target) {
this.target = target;
}
public String getSemanticTarget() {
return semanticTarget;
}
@XmlAttribute(name = "semanticTarget")
public void setSemanticTarget(String semanticTarget) {
this.semanticTarget = semanticTarget;
}
@Override
public String getSubSource() {
return "";
}
@Override
public String getTrimRegex() {
return "";
}
public String getValue() {
return value;
}
@XmlAttribute(name = "value")
public void setValue(String value) {
this.value = value;
}
}

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package eu.eudat.service.externalfetcher.config.entities;
import jakarta.xml.bind.annotation.XmlElement;
import jakarta.xml.bind.annotation.XmlElementWrapper;
import java.util.List;
public class PrefillingGet{
private String url;
private List<DefaultPrefillingMapping> mappings;
private List<PrefillingFixedMapping> fixedMappings;
public String getUrl() {
return url;
}
@XmlElement(name = "url")
public void setUrl(String url) {
this.url = url;
}
public List<DefaultPrefillingMapping> getMappings() {
return mappings;
}
@XmlElement(name = "mapping")
@XmlElementWrapper
public void setMappings(List<DefaultPrefillingMapping> mappings) {
this.mappings = mappings;
}
public List<PrefillingFixedMapping> getFixedMappings() {
return fixedMappings;
}
@XmlElement(name = "fixedMapping")
@XmlElementWrapper
public void setFixedMappings(List<PrefillingFixedMapping> fixedMappings) {
this.fixedMappings = fixedMappings;
}
}

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package eu.eudat.service.externalfetcher.config.entities;
public interface PrefillingMapping {
String getTarget();
void setTarget(String target);
String getSemanticTarget();
void setSemanticTarget(String semanticTarget);
String getSubSource();
String getTrimRegex();
}

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package eu.eudat.service.externalfetcher.config.entities;
import eu.eudat.service.externalfetcher.config.UrlConfiguration;
import jakarta.xml.bind.annotation.XmlElement;
import java.util.ArrayList;
import java.util.List;
public class PrefillingSearch extends GenericUrls {
private UrlConfiguration urlConfig;
public UrlConfiguration getUrlConfig() {
return urlConfig;
}
@XmlElement(name = "urlConfig")
public void setUrlConfig(UrlConfiguration urlConfig) {
this.urlConfig = urlConfig;
}
@Override
public List<SourceBaseConfiguration> getUrls() {
List<SourceBaseConfiguration> urls = new ArrayList<>();
urls.add(urlConfig);
return urls;
}
}

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package eu.eudat.service.externalfetcher.config.prefilling;
import eu.eudat.service.externalfetcher.config.entities.PrefillingConfig;
import org.w3c.dom.Element;
import jakarta.xml.bind.JAXBContext;
import jakarta.xml.bind.Unmarshaller;
import jakarta.xml.bind.annotation.adapters.XmlAdapter;
import java.util.HashMap;
import java.util.Map;
public class PrefillingConfigMapAdapter extends XmlAdapter<Object, Map<String, PrefillingConfig>> {
@Override
public Map<String, PrefillingConfig> unmarshal(Object v) throws Exception {
Map<String, PrefillingConfig> configMap = new HashMap<>();
Element element = (Element) v;
JAXBContext jaxbContext = JAXBContext.newInstance(PrefillingConfig.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
for (int i = 0; i < element.getChildNodes().getLength(); i++) {
if (element.getChildNodes().item(i).getAttributes() == null) {
continue;
}
String id = element.getChildNodes().item(i).getAttributes().getNamedItem("id").getNodeValue();
PrefillingConfig prefillingConfig = (PrefillingConfig) jaxbUnmarshaller.unmarshal(element.getChildNodes().item(i));
prefillingConfig = configMap.put(id, prefillingConfig);
System.out.println(prefillingConfig);
}
return configMap;
}
@Override
public Object marshal(Map<String, PrefillingConfig> v) throws Exception {
return null;
}
}

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package eu.eudat.service.externalfetcher.models;
public class ExternalAutocompleteFieldResult {
private String id;
private String label;
private String source;
private String uri;
public ExternalAutocompleteFieldResult(String id, String label, String source, String uri) {
this.id = id;
this.label = label;
this.source = source;
this.uri = uri;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public String getUri() {
return uri;
}
public void setUri(String uri) {
this.uri = uri;
}
}

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package eu.eudat.service.prefilling;
import eu.eudat.model.Description;
import eu.eudat.model.Prefilling;
import eu.eudat.model.PrefillingLookup;
import eu.eudat.model.persist.DescriptionProfilingRequest;
import eu.eudat.model.persist.DescriptionProfilingWithDataRequest;
import jakarta.xml.bind.JAXBException;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import java.util.UUID;
public interface PrefillingService {
List<Prefilling> getPrefillings(PrefillingLookup like);
Description getPrefilledDescription(DescriptionProfilingRequest model) throws JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException;
Description getPrefilledDescriptionUsingData(DescriptionProfilingWithDataRequest model) throws JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException;
}

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package eu.eudat.service.prefilling;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.types.descriptiontemplate.FieldEntity;
import eu.eudat.commons.types.descriptiontemplate.FieldSetEntity;
import eu.eudat.commons.types.prefillingsource.PrefillingEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.DescriptionTemplateEntity;
import eu.eudat.model.*;
import eu.eudat.model.builder.DescriptionTemplateBuilder;
import eu.eudat.model.builder.PrefillingBuilder;
import eu.eudat.model.descriptionproperties.Field;
import eu.eudat.model.descriptionproperties.PropertyDefinition;
import eu.eudat.model.descriptionproperties.PropertyDefinitionFieldSet;
import eu.eudat.model.descriptionproperties.PropertyDefinitionFieldSetItem;
import eu.eudat.model.persist.DescriptionProfilingRequest;
import eu.eudat.model.persist.DescriptionProfilingWithDataRequest;
import eu.eudat.service.externalfetcher.config.entities.*;
import eu.eudat.service.externalfetcher.criteria.ExternalReferenceCriteria;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.exception.MyNotFoundException;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.logging.LoggerService;
import gr.cite.tools.logging.MapLogEntry;
import gr.cite.tools.validation.ValidatorFactory;
import jakarta.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.MessageSource;
import org.springframework.context.i18n.LocaleContextHolder;
import org.springframework.http.HttpEntity;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpMethod;
import org.springframework.http.MediaType;
import org.springframework.stereotype.Service;
import org.springframework.web.client.RestTemplate;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.time.LocalDate;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.stream.Collectors;
@Service
public class PrefillingServiceImpl implements PrefillingService {
private final static String Zenodo = "zenodo";
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(PrefillingServiceImpl.class));
private final EntityManager entityManager;
private final BuilderFactory builderFactory;
private final ConventionService conventionService;
private final MessageSource messageSource;
private final XmlHandlingService xmlHandlingService;
private final ValidatorFactory validatorFactory;
@Autowired
public PrefillingServiceImpl(
EntityManager entityManager,
BuilderFactory builderFactory,
ConventionService conventionService,
MessageSource messageSource,
XmlHandlingService xmlHandlingService,
ValidatorFactory validatorFactory) {
this.entityManager = entityManager;
this.builderFactory = builderFactory;
this.conventionService = conventionService;
this.messageSource = messageSource;
this.xmlHandlingService = xmlHandlingService;
this.validatorFactory = validatorFactory;
}
@Override
public List<Prefilling> getPrefillings(PrefillingLookup lookup) {
logger.debug(new MapLogEntry("persisting data").And("lookup", lookup));
ExternalReferenceCriteria externalReferenceCriteria = new ExternalReferenceCriteria();
externalReferenceCriteria.setLike(lookup.getLike());
List<PrefillingEntity> prefillings = new ArrayList<>();
List<Map<String, String>> map;
// for (PrefillingConfig prefillingConfig: prefillingConfigs.values()) {//TODO new reference logic
// map = remoteFetcherService.getExternalData(prefillingConfig.getPrefillingSearch().getUrls(), externalReferenceCriteria, prefillingConfig.getPrefillingSearch().getFetchMode());
// prefillings.addAll(map.stream().map(submap -> PrefillingEntity.build(submap, this.jsonHandlingService)).toList());
// if (prefillingConfig.getPrefillingSearch().getUrlConfig().isDataInListing()) {
// List<Map<String, Object>> mapData = remoteFetcherService.getExternalGenericWithData(externalReferenceCriteria, prefillingConfig.getPrefillingSearch());
// for (int i = 0; i < mapData.size(); i++) {
// prefillings.get(i).setData(mapData.get(i));
// }
// prefillings = prefillings.stream().filter(prefilling -> prefilling.getData() != null).collect(Collectors.toList());
// }
// }
return this.builderFactory.builder(PrefillingBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(BaseFieldSet.build(lookup.getProject(), Prefilling._pid), prefillings);
}
@Override
public Description getPrefilledDescription(DescriptionProfilingRequest model) throws JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException {
PrefillingConfig prefillingConfig = null;
PrefillingGet prefillingGet = prefillingConfig.getPrefillingGet();
Map<String, Object> prefillingEntity = getSinglePrefillingData(prefillingGet.getUrl(), model.getPrefillId());
DescriptionProfilingWithDataRequest descriptionProfilingWithDataRequest = new DescriptionProfilingWithDataRequest();
descriptionProfilingWithDataRequest.setConfigId(model.getConfigId());
descriptionProfilingWithDataRequest.setProject(model.getProject());
descriptionProfilingWithDataRequest.setDescriptionTemplateId(model.getDescriptionTemplateId());
descriptionProfilingWithDataRequest.setData(prefillingEntity);
validatorFactory.validator(DescriptionProfilingWithDataRequest.DescriptionProfilingWithDataRequestValidator.ValidatorName).validateForce(descriptionProfilingWithDataRequest);
return this.getPrefilledDescriptionUsingData(descriptionProfilingWithDataRequest);
}
private Map<String, Object> getSinglePrefillingData(String url, String id) {
RestTemplate restTemplate = new RestTemplate();
String parsedUrl = url.replace("{id}", id);
HttpHeaders headers = new HttpHeaders();
headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
HttpEntity<String> entity = new HttpEntity("", headers);
return restTemplate.exchange(parsedUrl, HttpMethod.GET, entity, LinkedHashMap.class).getBody();
}
@Override
public Description getPrefilledDescriptionUsingData(DescriptionProfilingWithDataRequest model) throws JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException {
PrefillingConfig prefillingConfig = null;
PrefillingGet prefillingGet = prefillingConfig.getPrefillingGet();
DescriptionTemplateEntity descriptionTemplateEntity = this.entityManager.find(DescriptionTemplateEntity.class, model.getDescriptionTemplateId());
if (descriptionTemplateEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getDescriptionTemplateId(), DescriptionTemplate.class.getSimpleName()}, LocaleContextHolder.getLocale()));
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinition = this.xmlHandlingService.fromXml(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition());
Description description = new Description();
description.setDescriptionTemplate(this.builderFactory.builder(DescriptionTemplateBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(model.getProject(), descriptionTemplateEntity));
return mapPrefilledEntityToDescription(description, model.getData(), prefillingGet, prefillingConfig.getType(), descriptionTemplateDefinition);
}
//region Description Mapping
private Object getValueFromPath(Map<String, Object> data, String path){
if (path == null || this.conventionService.isNullOrEmpty(path) || data == null) return null;
if (path.contains(".")){
String[] paths = path.split("\\.");
if (paths.length == 0) return null;
else {
Object value = data.getOrDefault(paths[0], null);
if (value instanceof Map) return this.getValueFromPath((Map) value, path.substring(paths[0].length() + 1));
else return null;
}
}else {
return data.getOrDefault(path, null);
}
}
private Description mapPrefilledEntityToDescription(Description description, Map<String, Object> prefilledData, PrefillingGet prefillingGet, String type, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinition){
for (DefaultPrefillingMapping prefillingMapping: prefillingGet.getMappings()) {
Object sourceValue = this.getValueFromPath(prefilledData, prefillingMapping.getSource());
try {
setValueToDescription(description, prefillingMapping, sourceValue, descriptionTemplateDefinition, type);
}
catch (Exception e) {
logger.warn("Couldn't map " + (this.conventionService.isNullOrEmpty(prefillingMapping.getSemanticTarget()) ? prefillingMapping.getTarget() : prefillingMapping.getSemanticTarget()));
}
}
for (PrefillingFixedMapping fixedMapping: prefillingGet.getFixedMappings()) {
try {
setValueToDescription(description, fixedMapping, fixedMapping.getValue(), descriptionTemplateDefinition, type);
}
catch (Exception e) {
logger.warn("Couldn't map " + (this.conventionService.isNullOrEmpty(fixedMapping.getSemanticTarget()) ? fixedMapping.getTarget() : fixedMapping.getSemanticTarget()));
}
}
return description;
}
private void setValueToDescription(Description description, PrefillingMapping prefillingMapping, Object value, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity definition, String type) {
JsonNode valueNode = new ObjectMapper().valueToTree(value);
String parsedValue = this.getValueAsString(prefillingMapping, valueNode);
List<String> parsedValues = this.getValueAsStringArray(prefillingMapping, valueNode);
if (prefillingMapping.getTarget() != null) {
this.applyValueToDescriptionObject(description, prefillingMapping, parsedValue, parsedValues);
} else {
// zenodo prefilling customizations
if(type.equals(PrefillingServiceImpl.Zenodo)){
if(prefillingMapping.getSemanticTarget().equals("rda.dataset.distribution.data_access")){
if(parsedValue != null && parsedValue.equals("open")){
List<FieldEntity> issuedFieldEntities = definition.getAllField().stream().filter(x-> x.getSchematics() != null && x.getSchematics().contains("rda.dataset.issued")).toList();
if(this.conventionService.isListNullOrEmpty(issuedFieldEntities)){
String issuedIdNode = issuedFieldEntities.getFirst().getId();
String issuedValue = description.getProperties().getFieldSets().values().stream().map(PropertyDefinitionFieldSet::getItems).flatMap(List::stream)
.filter(x-> x.getFields() != null && x.getFields().containsKey(issuedIdNode)).map(x-> x.getFields().get(issuedIdNode).getTextValue()).findFirst().orElse(null); //TODO Update with the new logic of property definition
List<FieldSetEntity> licStartFieldSetsEntities = definition.getAllFieldSets().stream().filter(x-> x.getAllField() != null && x.getAllField().stream().anyMatch(y-> y.getSchematics() != null && y.getSchematics().contains("rda.dataset.distribution.license.start_date"))).toList();
for (FieldSetEntity licStartFieldSetEntity: licStartFieldSetsEntities) {
List<FieldEntity> licStartEntities = licStartFieldSetEntity.getAllField().stream().filter(x -> x.getSchematics() != null && x.getSchematics().contains("rda.dataset.distribution.license.start_date")).toList();
if (!this.conventionService.isListNullOrEmpty(licStartEntities)) {
this.ensureFieldSetEntity(description, licStartFieldSetEntity);
for (FieldEntity licStartDateNode : licStartEntities) {
description.getProperties().getFieldSets().get(licStartFieldSetEntity.getId()).getItems().add(buildPropertyDefinitionFieldSetItemValue(licStartDateNode, issuedValue, parsedValues, type));
}
}
}
}
}
}
if (prefillingMapping.getSemanticTarget().equals("rda.dataset.distribution.available_until") && parsedValue != null && !parsedValue.equals("null")) {
DateTimeFormatter formatter = DateTimeFormatter.ofPattern("uuuu-MM-dd");
LocalDate date = LocalDate.parse(parsedValue, formatter);
date = date.plusYears(20);
parsedValue = date.toString();
}
}
List<FieldSetEntity> fieldSetsEntities = definition.getAllFieldSets().stream().filter(x-> x.getAllField() != null && x.getAllField().stream().anyMatch(y-> y.getSchematics() != null && y.getSchematics().contains(prefillingMapping.getSemanticTarget()))).toList();
for (FieldSetEntity fieldSetEntity: fieldSetsEntities) {
List<FieldEntity> fieldEntities = fieldSetEntity.getAllField().stream().filter(x-> x.getSchematics() != null && x.getSchematics().contains(prefillingMapping.getSemanticTarget())).toList();
if (!this.conventionService.isListNullOrEmpty(fieldEntities)) {
this.ensureFieldSetEntity(description, fieldSetEntity);
for (FieldEntity fieldEntity : fieldEntities){
description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().add(buildPropertyDefinitionFieldSetItemValue(fieldEntity, parsedValue, parsedValues, type));
}
}
}
}
}
private void ensureFieldSetEntity(Description description, FieldSetEntity fieldSetEntity){
if (description.getProperties() == null) description.setProperties(new PropertyDefinition());
if (description.getProperties().getFieldSets() == null) description.getProperties().setFieldSets(new HashMap<>());
if (!description.getProperties().getFieldSets().containsKey(fieldSetEntity.getId())) description.getProperties().getFieldSets().put(fieldSetEntity.getId(), new PropertyDefinitionFieldSet());
if (description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems() == null) description.getProperties().getFieldSets().get(fieldSetEntity.getId()).setItems(new ArrayList<>());
}
private void applyValueToDescriptionObject(Description description, PrefillingMapping prefillingMapping, String parsedValue, List<String> parsedValues){
switch (prefillingMapping.getTarget()){
case Description._description:{
description.setDescription(parsedValue);
}
case Description._label:{
description.setLabel(parsedValue);
}
case Description._descriptionTags:{
if (!parsedValues.isEmpty()){
for (String tagString : parsedValues){
if (description.getDescriptionTags() == null) description.setDescriptionTags(new ArrayList<>());
if(description.getDescriptionTags().stream().anyMatch(x-> x.getTag() !=null && x.getTag().getLabel().equals(tagString))) continue;
DescriptionTag descriptionTag = new DescriptionTag();
Tag tag = new Tag();
tag.setLabel(tagString.trim());
descriptionTag.setTag(tag);
description.getDescriptionTags().add(descriptionTag);
}
}
}
}
}
private PropertyDefinitionFieldSetItem buildPropertyDefinitionFieldSetItemValue(FieldEntity fieldEntity, String parsedValue, List<String> parsedValues, String type){
String id = fieldEntity.getId();
PropertyDefinitionFieldSetItem fieldSetItem = new PropertyDefinitionFieldSetItem();
fieldSetItem.setFields(new HashMap<>());
Field field = new Field();
//TODO Update with the new logic of property definition
// switch (fieldEntity.getData().getFieldType()) {
// case EXTERNAL_SELECT:
// case SELECT: {
// if (!parsedValues.stream().allMatch(Objects::isNull)) {
// field.setValue(this.jsonHandlingService.toJsonSafe(parseComboBoxValues(fieldEntity, parsedValues)));
// }
// break;
// }
// case TAGS: {
// if (!parsedValues.isEmpty()) {
// field.setValue(jsonHandlingService.toJsonSafe(parseTags(String.join(", ", parsedValues))));
// }
// break;
// }
// case DATASET_IDENTIFIER: {
// JSONObject datasetID = new JSONObject();
// datasetID.put("identifier", parsedValue);
// if (type.equals(PrefillingServiceImpl.Zenodo)) {
// datasetID.put("type", "doi");
// }
// field.setValue(datasetID.toString());
// break;
// }
// case LICENSES: {
// List<ReferenceEntity> licenses = this.queryFactory.query(ReferenceQuery.class).references(parsedValues).collect();
// LabelAndMultiplicityDataEntity licenseDataEntity = (LabelAndMultiplicityDataEntity) fieldEntity.getData();
// if (licenses != null && !licenses.isEmpty() && licenseDataEntity != null) {
// boolean isMultiAutocomplete = licenseDataEntity.getMultipleSelect();
// List<Reference> licenseModels = this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(new BaseFieldSet(), licenses);
// if (isMultiAutocomplete) {
// field.setValue(jsonHandlingService.toJsonSafe(licenseModels));
// } else {
// field.setValue(jsonHandlingService.toJsonSafe(licenseModels.getFirst()));
// }
// }
//
// break;
// }
// default:
// field.setValue(parsedValue);
// break;
// }
fieldSetItem.getFields().put(fieldEntity.getId(), field);
return fieldSetItem;
}
private List<String> getValueAsStringArray(PrefillingMapping prefillingMapping, Object value){
String trimRegex = !this.conventionService.isNullOrEmpty(prefillingMapping.getTrimRegex()) ? prefillingMapping.getTrimRegex() : "";
List<String> parsedValues = new ArrayList<>();
if (value instanceof String){
parsedValues.add(((String) value).replace(trimRegex, ""));
} else if (value.getClass().isArray()){
if (value instanceof String[]){
List<String> values = new LinkedList<>();
for (String val : (String[]) value) {
parsedValues.add(val.replace(trimRegex, ""));
}
} else {
if (prefillingMapping.getSubSource() == null || prefillingMapping.getSubSource().isEmpty()) {
throw new MyApplicationException("Source value is an array but no subSource field have been set");
}
for (Object obj : (Object[]) value) {
if (obj instanceof Map) {
Object property = ((Map)obj).getOrDefault(prefillingMapping.getSubSource(), null);
if (property instanceof String) {
parsedValues.add(((String) property).replaceAll(trimRegex, ""));
}
}
}
}
}
parsedValues = parsedValues.stream().distinct().collect(Collectors.toList());
return parsedValues;
}
private String getValueAsString(PrefillingMapping prefillingMapping, Object value){
List<String> parsedValues = this.getValueAsStringArray(prefillingMapping, value);
return parsedValues.isEmpty() ? null : String.join(", ", parsedValues);
}
// private Object parseComboBoxValues(FieldEntity fieldEntity, List<String> parsedValues) {
// List<String> normalizedValues = new ArrayList<>();
// boolean isMultiSelect;
// if(fieldEntity.getData().getFieldType().equals(FieldType.EXTERNAL_SELECT)) {
// ExternalSelectDataEntity autoCompleteData = (ExternalSelectDataEntity)fieldEntity.getData();
// isMultiSelect = autoCompleteData.getMultipleSelect();
// for (String format : parsedValues) {
// List<ExternalAutocompleteFieldResult> result = new ArrayList<>();
// try {
// result = this.getAutocomplete(autoCompleteData, format);
// }
// catch (Exception e) {
// logger.error(e.getMessage(), e);
// }
// result = result.stream().filter(StreamDistinctBy.distinctByKey(ExternalAutocompleteFieldResult::getId)).collect(Collectors.toList());
// if(!result.isEmpty()){
// List<String> tempValues = new LinkedList<>();
// for (ExternalAutocompleteFieldResult f : result) {
// if (format.equals(f.getId()) || f.getLabel().toUpperCase(Locale.ROOT).contains(format.toUpperCase(Locale.ROOT)))
// tempValues.add(this.jsonHandlingService.toJsonSafe(f));
// }
// if (isMultiSelect)
// normalizedValues.addAll(tempValues);
// else if (!tempValues.isEmpty())
// normalizedValues.add(tempValues.get(0));
// }
// }
// return !normalizedValues.isEmpty() ? (isMultiSelect ? normalizedValues : normalizedValues.getFirst()) : null;
// } else {
// SelectDataEntity selectDataEntity = (SelectDataEntity)fieldEntity.getData();
// isMultiSelect = selectDataEntity.getMultipleSelect();
// if (selectDataEntity.getOptions() != null) {
// for (SelectDataEntity.OptionEntity option : selectDataEntity.getOptions()) {
// if (parsedValues.contains(option.getValue())) {
// normalizedValues.add(option.getValue());
// }
// }
// }
// List<String> normalizedStringValues = normalizedValues.stream().map(Object::toString).collect(Collectors.toList());
//
// return !normalizedValues.isEmpty() ? (isMultiSelect ? String.join(", ", normalizedStringValues) : normalizedValues.getFirst()) : null;
// }
// }
private static List<Tag> parseTags(String value) {
if (value == null || value.isEmpty())
return new LinkedList<>();
String[] rawTags = value.split(",");
List<Tag> parsedTags = new LinkedList<>();
for (String rawTag : rawTags) {
Tag tag = new Tag();
tag.setLabel(rawTag.trim());
parsedTags.add(tag);
}
return parsedTags;
}
// public List<ExternalAutocompleteFieldResult> getAutocomplete(ExternalSelectDataEntity data, String like) throws URISyntaxException {
//
// List<ExternalAutocompleteFieldResult> result = new LinkedList<>();
// ExternalReferenceCriteria urlCriteria = new ExternalReferenceCriteria();
// GeneralUrls genericUrls = new GeneralUrls();
// int ordinal = 1;
// List<Map<String, String>> rawResults = new ArrayList<>();
// genericUrls.setFetchMode(FetchStrategy.FIRST);
// urlCriteria.setLike(like);
// for (ExternalSelectDataEntity.ExternalSelectSourceEntity singleData : data.getSources()) {
// UrlConfiguration urlConfiguration = new UrlConfiguration();
// try {
// URI uri;
// if (singleData.getUrl().contains("?")) {
// uri = new URI(singleData.getUrl().substring(0, singleData.getUrl().lastIndexOf("?")));
// } else {
// uri = new URI(singleData.getUrl());
// }
// String source = singleData.getSourceBinding().getSource();
// source = source != null && !source.isEmpty() ? source : uri.getHost();
//// String uriString = singleData.getSourceBinding().getUrl();
//// uriString = uriString != null && !uriString.isEmpty() ? uriString : "uri";
// String uriString = "uri";
// String parsedUrl = singleData.getUrl();
// parsedUrl = parsedUrl.replace("%20", " ");
// parsedUrl = parsedUrl.replace("%22", "\"");
// while (parsedUrl.contains("&amp;")) {
// parsedUrl = parsedUrl.replace("&amp;", "&");
// }
// urlConfiguration.setUrl(parsedUrl);
// urlConfiguration.setOrdinal(ordinal);
// urlConfiguration.setType("External");
// urlConfiguration.setContentType(MediaType.APPLICATION_JSON_VALUE);
// urlConfiguration.setFirstpage("1");
// urlConfiguration.setRequestType(singleData.getMethod() != null ? singleData.getMethod() : "GET");
// DataUrlConfiguration dataUrlConfiguration = new DataUrlConfiguration();
// dataUrlConfiguration.setPath(singleData.getOptionsRoot());
// DataFieldsUrlConfiguration fieldsUrlConfiguration = new DataFieldsUrlConfiguration();
// fieldsUrlConfiguration.setId(singleData.getSourceBinding().getValue());
// fieldsUrlConfiguration.setName(singleData.getSourceBinding().getLabel());
// fieldsUrlConfiguration.setSource(singleData.getSourceBinding().getSource().isEmpty()? null : singleData.getSourceBinding().getSource());
// fieldsUrlConfiguration.setUri(uriString);
// dataUrlConfiguration.setFieldsUrlConfiguration(fieldsUrlConfiguration);
// urlConfiguration.setKey(source);
// urlConfiguration.setLabel(source);
// urlConfiguration.setData(dataUrlConfiguration);
// if (singleData.getHasAuth()) {
// AuthenticationConfiguration authenticationConfiguration = new AuthenticationConfiguration();
// authenticationConfiguration.setAuthUrl(singleData.getAuth().getUrl());
// authenticationConfiguration.setAuthMethod(singleData.getAuth().getMethod());
// authenticationConfiguration.setAuthTokenPath(singleData.getAuth().getPath());
// authenticationConfiguration.setAuthRequestBody(singleData.getAuth().getBody());
// authenticationConfiguration.setType(singleData.getAuth().getType());
// urlConfiguration.setAuth(authenticationConfiguration);
// }
// genericUrls.getUrls().add(urlConfiguration);
// List<Map<String, String>> singleResults = this.remoteFetcherService.getExternalGeneric(urlCriteria, genericUrls);
// if (!singleResults.isEmpty() && !singleResults.get(0).containsKey("source") && !singleData.getSourceBinding().getSource().isEmpty()) {
// singleResults.forEach(singleResult -> singleResult.put("source", singleData.getSourceBinding().getSource()));
// }
// rawResults.addAll(singleResults);
// genericUrls.getUrls().clear();
// } catch (URISyntaxException e) {
// logger.error(e.getMessage(), e);
// }
// }
// rawResults.forEach(item -> result.add(new ExternalAutocompleteFieldResult(parseItem(item.get("pid")), parseItem(item.get("name")), parseItem(item.get("source")), parseItem(item.get("uri")))));
// return result;
// }
private static String parseItem(Object item) {
if (item instanceof String) {
return (String) item;
}
if (item instanceof List) {
List listedItems = (List) item;
return parseItem(listedItems.get(0));
}
if (item instanceof Map) {
return String.valueOf(((Map)item).get("$"));
}
return item != null ? item.toString() : null;
}
//endregion Description Mapping
}

View File

@ -1,14 +1,15 @@
package eu.eudat.service.prefillingsource;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.types.description.ExternalIdentifierEntity;
import eu.eudat.commons.types.descriptiontemplate.DefinitionEntity;
import eu.eudat.commons.types.descriptiontemplate.FieldEntity;
import eu.eudat.commons.types.descriptiontemplate.FieldSetEntity;
import eu.eudat.commons.types.descriptiontemplate.fielddata.SelectDataEntity;
import eu.eudat.commons.types.externalfetcher.*;
import eu.eudat.commons.types.prefillingsource.PrefillingSourceDefinitionEntity;
import eu.eudat.commons.types.prefillingsource.PrefillingSourceDefinitionFieldEntity;
@ -21,18 +22,16 @@ import eu.eudat.model.*;
import eu.eudat.model.builder.DescriptionTemplateBuilder;
import eu.eudat.model.builder.PrefillingSourceBuilder;
import eu.eudat.model.deleter.PrefillingSourceDeleter;
import eu.eudat.model.descriptionproperties.Field;
import eu.eudat.model.descriptionproperties.PropertyDefinition;
import eu.eudat.model.descriptionproperties.PropertyDefinitionFieldSet;
import eu.eudat.model.descriptionproperties.PropertyDefinitionFieldSetItem;
import eu.eudat.model.externalfetcher.ExternalFetcherApiSourceConfiguration;
import eu.eudat.model.descriptionproperties.*;
import eu.eudat.model.persist.DescriptionProfilingRequest;
import eu.eudat.model.persist.DescriptionProfilingWithDataRequest;
import eu.eudat.model.persist.PrefillingSourcePersist;
import eu.eudat.model.persist.dmpblueprintdefinition.FieldPersist;
import eu.eudat.model.persist.externalfetcher.*;
import eu.eudat.model.persist.prefillingsourcedefinition.PrefillingSourceDefinitionFieldPersist;
import eu.eudat.model.persist.prefillingsourcedefinition.PrefillingSourceDefinitionFixedValueFieldPersist;
import eu.eudat.model.persist.prefillingsourcedefinition.PrefillingSourceDefinitionPersist;
import eu.eudat.model.prefillingsourcedefinition.PrefillingSourceDefinition;
import eu.eudat.query.PrefillingSourceQuery;
import eu.eudat.service.externalfetcher.ExternalFetcherService;
import eu.eudat.service.externalfetcher.models.ExternalDataResult;
@ -51,6 +50,8 @@ import gr.cite.tools.logging.MapLogEntry;
import gr.cite.tools.validation.ValidatorFactory;
import jakarta.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringEscapeUtils;
import org.jetbrains.annotations.NotNull;
import org.slf4j.LoggerFactory;
import org.springframework.context.MessageSource;
@ -63,7 +64,9 @@ import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.time.Instant;
import java.time.LocalDate;
import java.time.ZoneOffset;
import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeParseException;
import java.util.*;
@Service
@ -81,12 +84,14 @@ public class PrefillingSourceServiceImpl implements PrefillingSourceService {
private final ExternalFetcherService externalFetcherService;
private final ErrorThesaurusProperties errors;
private final ValidatorFactory validatorFactory;
private final JsonHandlingService jsonHandlingService;
private static final String Zenodo = "zenodo";
public PrefillingSourceServiceImpl(
EntityManager entityManager, AuthorizationService authorizationService, DeleterFactory deleterFactory, BuilderFactory builderFactory,
QueryFactory queryFactory, ConventionService conventionService, MessageSource messageSource,
XmlHandlingService xmlHandlingService, ExternalFetcherService externalFetcherService, ErrorThesaurusProperties errors, ValidatorFactory validatorFactory) {
EntityManager entityManager, AuthorizationService authorizationService, DeleterFactory deleterFactory, BuilderFactory builderFactory,
QueryFactory queryFactory, ConventionService conventionService, MessageSource messageSource,
XmlHandlingService xmlHandlingService, ExternalFetcherService externalFetcherService, ErrorThesaurusProperties errors, ValidatorFactory validatorFactory, JsonHandlingService jsonHandlingService) {
this.entityManager = entityManager;
this.authorizationService = authorizationService;
this.deleterFactory = deleterFactory;
@ -98,6 +103,7 @@ public class PrefillingSourceServiceImpl implements PrefillingSourceService {
this.externalFetcherService = externalFetcherService;
this.errors = errors;
this.validatorFactory = validatorFactory;
this.jsonHandlingService = jsonHandlingService;
}
@ -297,16 +303,13 @@ public class PrefillingSourceServiceImpl implements PrefillingSourceService {
}
public Description getPrefilledDescription(DescriptionProfilingRequest model) throws JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException {
PrefillingSourceEntity prefillingSourceEntity = this.queryFactory.query(PrefillingSourceQuery.class).ids(UUID.fromString(model.getPrefillId())).first();
if (prefillingSourceEntity == null){
return null;
}
PrefillingSourceEntity prefillingSourceEntity = this.queryFactory.query(PrefillingSourceQuery.class).ids(UUID.fromString(model.getPrefillId())).isActive(IsActive.Active).first();
if (prefillingSourceEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getPrefillId(), PrefillingSource.class.getSimpleName()}, LocaleContextHolder.getLocale()));
DescriptionProfilingWithDataRequest descriptionProfilingWithDataRequest = new DescriptionProfilingWithDataRequest();
descriptionProfilingWithDataRequest.setConfigId(model.getConfigId());
descriptionProfilingWithDataRequest.setProject(model.getProject());
descriptionProfilingWithDataRequest.setDescriptionTemplateId(model.getDescriptionTemplateId());
// descriptionProfilingWithDataRequest.setData(prefillingEntity);
validatorFactory.validator(DescriptionProfilingWithDataRequest.DescriptionProfilingWithDataRequestValidator.ValidatorName).validateForce(descriptionProfilingWithDataRequest);
return this.getPrefilledDescriptionUsingData(descriptionProfilingWithDataRequest);
}
@ -314,98 +317,75 @@ public class PrefillingSourceServiceImpl implements PrefillingSourceService {
public Description getPrefilledDescriptionUsingData(DescriptionProfilingWithDataRequest model) throws JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException {
PrefillingSourceEntity prefillingSourceEntity = this.queryFactory.query(PrefillingSourceQuery.class).ids(UUID.fromString(model.getConfigId())).first();
if (prefillingSourceEntity == null){
return null;
}
if (prefillingSourceEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getConfigId(), PrefillingSource.class.getSimpleName()}, LocaleContextHolder.getLocale()));
PrefillingSourceDefinitionEntity prefillingSourceDefinition = this.xmlHandlingService.fromXmlSafe(PrefillingSourceDefinitionEntity.class, prefillingSourceEntity.getDefinition());
ExternalDataResult data = this.externalFetcherService.getExternalData(List.of(prefillingSourceDefinition.getGetConfiguration()), null, null);
if (data == null || data.getResults() == null){
if (prefillingSourceDefinition == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getConfigId(), PrefillingSourceDefinition.class.getSimpleName()}, LocaleContextHolder.getLocale()));
ExternalDataResult externalData = this.externalFetcherService.getExternalData(List.of(prefillingSourceDefinition.getGetConfiguration()), null, null);
if (externalData == null || externalData.getResults() == null) {
return null;
}
DescriptionTemplateEntity descriptionTemplateEntity = this.entityManager.find(DescriptionTemplateEntity.class, model.getDescriptionTemplateId());
if (descriptionTemplateEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getDescriptionTemplateId(), DescriptionTemplate.class.getSimpleName()}, LocaleContextHolder.getLocale()));
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinition = this.xmlHandlingService.fromXml(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition());
Description description = new Description();
description.setDescriptionTemplate(this.builderFactory.builder(DescriptionTemplateBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(model.getProject(), descriptionTemplateEntity));
return mapPrefilledEntityToDescription(description, descriptionTemplateDefinition, prefillingSourceDefinition, prefillingSourceEntity.getLabel(), data.getResults());
return mapPrefilledEntityToDescription(description, descriptionTemplateDefinition, prefillingSourceDefinition, prefillingSourceEntity.getLabel(), externalData.getResults().getFirst());
}
private Description mapPrefilledEntityToDescription(Description description, DefinitionEntity descriptionTemplateDefinition, PrefillingSourceDefinitionEntity prefillingSourceDefinition, String type, List<Map<String, String>> data){
//TODO
private Description mapPrefilledEntityToDescription(Description description, DefinitionEntity descriptionTemplateDefinition, PrefillingSourceDefinitionEntity prefillingSourceDefinition, String type, Map<String, String> externalData){
for (PrefillingSourceDefinitionFieldEntity field: prefillingSourceDefinition.getFields()) {
String sourceValue = data.get(0).get(field.getCode());
try {
this.setValueToDescription(description, field, sourceValue, descriptionTemplateDefinition, type);
}
catch (Exception e) {
logger.warn("Couldn't map " + (this.conventionService.isNullOrEmpty(field.getSemanticTarget()) ? field.getSystemFieldTarget() : field.getSemanticTarget()));
}
String sourceValue = externalData.get(field.getCode());
this.prefillSystemValueToDescription(description, field.getSystemFieldTarget(), sourceValue);
this.prefillSemanticValueToDescription(description, field.getSemanticTarget(), sourceValue, descriptionTemplateDefinition, type);
}
for (PrefillingSourceDefinitionFixedValueFieldEntity field: prefillingSourceDefinition.getFixedValueFields()) {
try {
// this.setValueToDescription(description, field, field.getFixedValue(), descriptionTemplateDefinition, type);
}
catch (Exception e) {
logger.warn("Couldn't map " + (this.conventionService.isNullOrEmpty(field.getSemanticTarget()) ? field.getSystemFieldTarget() : field.getSemanticTarget()));
}
this.prefillSystemValueToDescription(description, field.getSystemFieldTarget(), field.getFixedValue());
this.prefillSemanticValueToDescription(description, field.getSemanticTarget(), field.getFixedValue(), descriptionTemplateDefinition, type);
}
for (PrefillingSourceDefinitionFieldEntity field: prefillingSourceDefinition.getFields()) {
String sourceValue = externalData.get(field.getCode());
this.ensureZenodoFields(description, field.getSemanticTarget(), sourceValue, descriptionTemplateDefinition, type);
}
for (PrefillingSourceDefinitionFixedValueFieldEntity field: prefillingSourceDefinition.getFixedValueFields()) {
this.ensureZenodoFields(description, field.getSemanticTarget(), field.getFixedValue(), descriptionTemplateDefinition, type);
}
return description;
}
private void ensureZenodoFields(Description description, String semanticTarget, String value, DefinitionEntity definition, String type) {
if (!this.conventionService.isNullOrEmpty(type) && !this.conventionService.isNullOrEmpty(semanticTarget) && !this.conventionService.isNullOrEmpty(value) && type.equals(Zenodo)) {
if (semanticTarget.equals("rda.dataset.distribution.data_access")) {
if (value.equals("open")) {
List<FieldEntity> issuedFieldEntities = definition.getAllField().stream().filter(x -> x.getSchematics() != null && x.getSchematics().contains("rda.dataset.issued")).toList();
if (this.conventionService.isListNullOrEmpty(issuedFieldEntities)) {
String issuedIdNode = issuedFieldEntities.getFirst().getId();
String issuedValue = this.conventionService.isNullOrEmpty(issuedIdNode) ? null : description.getProperties().getFieldSets().values().stream().map(PropertyDefinitionFieldSet::getItems).flatMap(List::stream)
.filter(x -> x.getFields() != null && x.getFields().containsKey(issuedIdNode)).map(x -> x.getFields().get(issuedIdNode).getTextValue()).findFirst().orElse(null);
private void setValueToDescription(Description description, PrefillingSourceDefinitionFieldEntity field, String value, DefinitionEntity definition, String type) {
// JsonNode valueNode = new ObjectMapper().valueToTree(value);
// String parsedValue = this.getValueAsString(prefillingMapping, valueNode);
// List<String> parsedValues = this.getValueAsStringArray(prefillingMapping, valueNode);
if (field.getSemanticTarget() != null) {
this.applyValueToDescriptionObject(description, field, value, null);
} else {
// zenodo prefilling customizations
if(type.equals("Zenodo")){
if(field.getSemanticTarget().equals("rda.dataset.distribution.data_access")){
if(value != null && value.equals("open")){
List<FieldEntity> issuedFieldEntities = definition.getAllField().stream().filter(x-> x.getSchematics() != null && x.getSchematics().contains("rda.dataset.issued")).toList();
if(this.conventionService.isListNullOrEmpty(issuedFieldEntities)){
String issuedIdNode = issuedFieldEntities.getFirst().getId();
String issuedValue = description.getProperties().getFieldSets().values().stream().map(PropertyDefinitionFieldSet::getItems).flatMap(List::stream)
.filter(x-> x.getFields() != null && x.getFields().containsKey(issuedIdNode)).map(x-> x.getFields().get(issuedIdNode).getTextValue()).findFirst().orElse(null); //TODO Update with the new logic of property definition
List<FieldSetEntity> licStartFieldSetsEntities = definition.getAllFieldSets().stream().filter(x-> x.getAllField() != null && x.getAllField().stream().anyMatch(y-> y.getSchematics() != null && y.getSchematics().contains("rda.dataset.distribution.license.start_date"))).toList();
for (FieldSetEntity licStartFieldSetEntity: licStartFieldSetsEntities) {
if (!this.conventionService.isNullOrEmpty(issuedValue)) {
List<FieldSetEntity> licStartFieldSetsEntities = definition.getAllFieldSets().stream().filter(x -> x.getAllField() != null && x.getAllField().stream().anyMatch(y -> y.getSchematics() != null && y.getSchematics().contains("rda.dataset.distribution.license.start_date"))).toList();
for (FieldSetEntity licStartFieldSetEntity : licStartFieldSetsEntities) {
List<FieldEntity> licStartEntities = licStartFieldSetEntity.getAllField().stream().filter(x -> x.getSchematics() != null && x.getSchematics().contains("rda.dataset.distribution.license.start_date")).toList();
if (!this.conventionService.isListNullOrEmpty(licStartEntities)) {
this.ensureFieldSetEntity(description, licStartFieldSetEntity);
for (FieldEntity licStartDateNode : licStartEntities) {
description.getProperties().getFieldSets().get(licStartFieldSetEntity.getId()).getItems().add(buildPropertyDefinitionFieldSetItemValue(licStartDateNode, issuedValue, null, type));
description.getProperties().getFieldSets().get(licStartFieldSetEntity.getId()).getItems().getFirst().getFields().put(licStartDateNode.getId(), buildPropertyDefinitionFieldItemValue(licStartDateNode, semanticTarget, issuedValue, type));
}
}
}
}
}
}
if (field.getSemanticTarget().equals("rda.dataset.distribution.available_until") && value != null && !value.equals("null")) {
DateTimeFormatter formatter = DateTimeFormatter.ofPattern("uuuu-MM-dd");
LocalDate date = LocalDate.parse(value, formatter);
date = date.plusYears(20);
value = date.toString();
}
}
List<FieldSetEntity> fieldSetsEntities = definition.getAllFieldSets().stream().filter(x-> x.getAllField() != null && x.getAllField().stream().anyMatch(y-> y.getSchematics() != null && y.getSchematics().contains(field.getSemanticTarget()))).toList();
for (FieldSetEntity fieldSetEntity: fieldSetsEntities) {
List<FieldEntity> fieldEntities = fieldSetEntity.getAllField().stream().filter(x-> x.getSchematics() != null && x.getSchematics().contains(field.getSemanticTarget())).toList();
if (!this.conventionService.isListNullOrEmpty(fieldEntities)) {
this.ensureFieldSetEntity(description, fieldSetEntity);
for (FieldEntity fieldEntity : fieldEntities){
description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().add(buildPropertyDefinitionFieldSetItemValue(fieldEntity, value, null, type));
}
}
}
}
}
@ -415,42 +395,111 @@ public class PrefillingSourceServiceImpl implements PrefillingSourceService {
if (description.getProperties().getFieldSets() == null) description.getProperties().setFieldSets(new HashMap<>());
if (!description.getProperties().getFieldSets().containsKey(fieldSetEntity.getId())) description.getProperties().getFieldSets().put(fieldSetEntity.getId(), new PropertyDefinitionFieldSet());
if (description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems() == null) description.getProperties().getFieldSets().get(fieldSetEntity.getId()).setItems(new ArrayList<>());
if (this.conventionService.isListNullOrEmpty(description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems())) description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().add(new PropertyDefinitionFieldSetItem());
if (description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().getFirst().getFields() == null) description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().getFirst().setFields(new HashMap<>());
if (description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().getFirst().getOrdinal() == null) description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().getFirst().setOrdinal(0);
}
private void applyValueToDescriptionObject(Description description, PrefillingSourceDefinitionFieldEntity field, String parsedValue, List<String> parsedValues) {
switch (field.getSemanticTarget()) {
case Description._description: {
description.setDescription(parsedValue);
}
case Description._label: {
description.setLabel(parsedValue);
}
case Description._descriptionTags: {
if (!parsedValues.isEmpty()) {
for (String tagString : parsedValues) {
if (description.getDescriptionTags() == null) description.setDescriptionTags(new ArrayList<>());
if (description.getDescriptionTags().stream().anyMatch(x -> x.getTag() != null && x.getTag().getLabel().equals(tagString)))
continue;
DescriptionTag descriptionTag = new DescriptionTag();
Tag tag = new Tag();
tag.setLabel(tagString.trim());
descriptionTag.setTag(tag);
description.getDescriptionTags().add(descriptionTag);
}
private void prefillSemanticValueToDescription(Description description, String semanticTarget, String parsedValue, DefinitionEntity definition, String type) {
if (this.conventionService.isNullOrEmpty(semanticTarget) || this.conventionService.isNullOrEmpty(parsedValue)) return;
List<FieldSetEntity> fieldSetsEntities = definition.getAllFieldSets().stream().filter(x-> x.getAllField() != null && x.getAllField().stream().anyMatch(y-> !this.conventionService.isListNullOrEmpty(y.getSchematics()) && y.getSchematics().contains(semanticTarget))).toList();
for (FieldSetEntity fieldSetEntity: fieldSetsEntities) {
List<FieldEntity> fieldEntities = fieldSetEntity.getAllField().stream().filter(x-> !this.conventionService.isListNullOrEmpty(x.getSchematics()) && x.getSchematics().contains(semanticTarget)).toList();
if (!this.conventionService.isListNullOrEmpty(fieldEntities)) {
this.ensureFieldSetEntity(description, fieldSetEntity);
for (FieldEntity fieldEntity : fieldEntities){
description.getProperties().getFieldSets().get(fieldSetEntity.getId()).getItems().getFirst().getFields().put(fieldEntity.getId() , buildPropertyDefinitionFieldItemValue(fieldEntity, semanticTarget, parsedValue, type));
}
}
}
}
private PropertyDefinitionFieldSetItem buildPropertyDefinitionFieldSetItemValue(FieldEntity fieldEntity, String value, List<String> parsedValues, String type) {
String id = fieldEntity.getId();
PropertyDefinitionFieldSetItem fieldSetItem = new PropertyDefinitionFieldSetItem();
fieldSetItem.setFields(new HashMap<>());
Field field = new Field();
private void prefillSystemValueToDescription(Description description, String systemFieldTarget, String parsedValue) {
if (this.conventionService.isNullOrEmpty(systemFieldTarget) || this.conventionService.isNullOrEmpty(parsedValue)) return;
switch (systemFieldTarget) {
case Description._description -> description.setDescription(parsedValue);
case Description._label -> description.setLabel(parsedValue);
case Description._descriptionTags -> {
String[] valuesParsed = this.tryParseJsonAsObjectString(String[].class, parsedValue);
List<String> finalValue = valuesParsed == null ? List.of(parsedValue) : Arrays.stream(valuesParsed).toList();
for (String tagString : finalValue) {
if (description.getDescriptionTags() == null) description.setDescriptionTags(new ArrayList<>());
if (description.getDescriptionTags().stream().anyMatch(x -> x.getTag() != null && x.getTag().getLabel().equals(tagString))) continue;
fieldSetItem.getFields().put(fieldEntity.getId(), field);
return fieldSetItem;
DescriptionTag descriptionTag = new DescriptionTag();
Tag tag = new Tag();
tag.setLabel(tagString.trim());
descriptionTag.setTag(tag);
description.getDescriptionTags().add(descriptionTag);
}
}
}
}
private Field buildPropertyDefinitionFieldItemValue(FieldEntity fieldEntity, String semanticTarget, String value, String type) {
Field field = new Field();
if (fieldEntity == null || fieldEntity.getData() == null || fieldEntity.getData().getFieldType() == null || this.conventionService.isNullOrEmpty(value)) return field;
try{
switch (fieldEntity.getData().getFieldType()){
case FREE_TEXT, TEXT_AREA, RICH_TEXT_AREA, RADIO_BOX -> field.setTextValue(value.toLowerCase(Locale.ROOT));
case CHECK_BOX, BOOLEAN_DECISION -> field.setTextValue(value.trim().toLowerCase(Locale.ROOT));
case DATE_PICKER ->{
Instant instant = null;
try {
if (!this.conventionService.isNullOrEmpty(type) && type.equals(Zenodo) && semanticTarget.equals("rda.dataset.distribution.available_until") ) {
DateTimeFormatter formatter = DateTimeFormatter.ofPattern("uuuu-MM-dd");
LocalDate date = LocalDate.parse(value, formatter);
date = date.plusYears(20);
instant = date.atStartOfDay().toInstant(ZoneOffset.UTC);
} else {
instant = Instant.parse(value);
}
} catch (DateTimeParseException ex) {
instant = LocalDate.parse(value).atStartOfDay().toInstant(ZoneOffset.UTC);
}
field.setDateValue(instant);
}
case DATASET_IDENTIFIER -> {
ExternalIdentifier externalIdentifier = new ExternalIdentifier();
externalIdentifier.setIdentifier(value);
if(!this.conventionService.isNullOrEmpty(type) && type.equals(Zenodo)) externalIdentifier.setType("doi");
field.setExternalIdentifier(externalIdentifier);
}
case SELECT -> {
String[] valuesParsed = this.tryParseJsonAsObjectString(String[].class, value);
List<String> finalValue = valuesParsed == null ? List.of(value) : Arrays.stream(valuesParsed).toList();
SelectDataEntity selectDataEntity = (SelectDataEntity) fieldEntity.getData();
if (selectDataEntity == null || selectDataEntity.getOptions() == null) throw new MyApplicationException("Can not cast fieldEntity data");
field.setTextListValue(new ArrayList<>());
for (SelectDataEntity.OptionEntity entity : selectDataEntity.getOptions()){
if (finalValue.contains(entity.getValue()) || finalValue.contains(entity.getLabel())){
field.getTextListValue().add(entity.getValue());
}
}
}
case TAGS, CURRENCY -> {
String[] valuesParsed = this.tryParseJsonAsObjectString(String[].class, value);
field.setTextListValue(valuesParsed == null ? List.of(value) : Arrays.stream(valuesParsed).toList()); //TODO Tags, Currency is ids
}
case REFERENCE_TYPES -> {
throw new NotImplementedException("");
}
case VALIDATION, UPLOAD, INTERNAL_ENTRIES_DMPS, INTERNAL_ENTRIES_DESCRIPTIONS -> throw new MyApplicationException("invalid type " + fieldEntity.getData().getFieldType());
default -> throw new MyApplicationException("invalid type " + fieldEntity.getData().getFieldType());
}
} catch (Exception e){
logger.error("Could not parse value " + value + " of field " + fieldEntity.getId() + " with type " + fieldEntity.getData().getFieldType(), e);
}
return field;
}
private <T> T tryParseJsonAsObjectString(Class<T> type, String value){
T item = this.jsonHandlingService.fromJsonSafe(type, value);
if (item == null) item = this.jsonHandlingService.fromJsonSafe(type, StringEscapeUtils.unescapeJava(value));
if (item == null) item = this.jsonHandlingService.fromJsonSafe(type, StringEscapeUtils.unescapeJson(value));
return item;
}
}

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@ -1,105 +0,0 @@
package eu.eudat.controllers;
import eu.eudat.audit.AuditableAction;
import gr.cite.tools.validation.ValidationFilterAnnotation;
import eu.eudat.model.Description;
import eu.eudat.model.Prefilling;
import eu.eudat.model.PrefillingLookup;
import eu.eudat.model.censorship.DescriptionCensor;
import eu.eudat.model.censorship.PrefillingCensor;
import eu.eudat.model.persist.DescriptionProfilingRequest;
import eu.eudat.model.persist.DescriptionProfilingWithDataRequest;
import eu.eudat.service.prefilling.PrefillingService;
import gr.cite.tools.auditing.AuditService;
import gr.cite.tools.data.censor.CensorFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.exception.MyForbiddenException;
import gr.cite.tools.exception.MyNotFoundException;
import gr.cite.tools.logging.LoggerService;
import gr.cite.tools.logging.MapLogEntry;
import jakarta.xml.bind.JAXBException;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.util.AbstractMap;
import java.util.List;
import java.util.Map;
@RestController
@RequestMapping(path = "api/prefilling")
public class PrefillingController {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(PrefillingController.class));
@Autowired
private final AuditService auditService;
private final PrefillingService prefillingService;
private final CensorFactory censorFactory;
public PrefillingController(
AuditService auditService,
PrefillingService prefillingService,
CensorFactory censorFactory) {
this.auditService = auditService;
this.prefillingService = prefillingService;
this.censorFactory = censorFactory;
}
@PostMapping("query")
public List<Prefilling> query(@RequestBody PrefillingLookup model) throws MyApplicationException, MyForbiddenException, MyNotFoundException {
this.censorFactory.censor(PrefillingCensor.class).censor(model.getProject(), null);
logger.debug(new MapLogEntry("persisting" + Prefilling.class.getSimpleName()).And("model", model));
List<Prefilling> items = this.prefillingService.getPrefillings(model);
this.auditService.track(AuditableAction.Prefilling_Query, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("model", model)
));
return items;
}
@PostMapping("generate")
@ValidationFilterAnnotation(validator = DescriptionProfilingRequest.DescriptionProfilingRequestValidator.ValidatorName, argumentName = "model")
public Description generate(@RequestBody DescriptionProfilingRequest model) throws MyApplicationException, MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException {
logger.debug(new MapLogEntry("persisting" + Prefilling.class.getSimpleName()).And("model", model));
this.censorFactory.censor(DescriptionCensor.class).censor(model.getProject(), null);
Description item = this.prefillingService.getPrefilledDescription(model);
this.auditService.track(AuditableAction.Prefilling_Generate, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("model", model)
));
return item;
}
@PostMapping("generate-with-data")
@ValidationFilterAnnotation(validator = DescriptionProfilingWithDataRequest.DescriptionProfilingWithDataRequestValidator.ValidatorName, argumentName = "model")
public Description generateWithData(@RequestBody DescriptionProfilingWithDataRequest model) throws MyApplicationException, MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, IOException, InstantiationException, IllegalAccessException, SAXException {
logger.debug(new MapLogEntry("persisting" + Prefilling.class.getSimpleName()).And("model", model));
this.censorFactory.censor(DescriptionCensor.class).censor(model.getProject(), null);
Description item = this.prefillingService.getPrefilledDescriptionUsingData(model);
this.auditService.track(AuditableAction.Prefilling_GenerateWithData, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("model", model)
));
return item;
}
}