Merge branch 'dmp-refactoring' of https://code-repo.d4science.org/MaDgiK-CITE/argos into dmp-refactoring
This commit is contained in:
commit
9e18aea655
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@ -56,7 +56,7 @@
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<dependency>
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<groupId>org.opencdmp</groupId>
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<artifactId>common-models</artifactId>
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<version>0.0.14</version>
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<version>0.0.15</version>
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</dependency>
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<dependency>
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<groupId>gr.cite</groupId>
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@ -6,6 +6,7 @@ import gr.cite.tools.exception.MyNotFoundException;
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import gr.cite.tools.exception.MyValidationException;
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import gr.cite.tools.fieldset.FieldSet;
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import jakarta.xml.bind.JAXBException;
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import org.opencdmp.commonmodels.models.description.DescriptionModel;
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import org.opencdmp.commons.types.description.importexport.DescriptionImportExport;
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import org.opencdmp.data.DmpDescriptionTemplateEntity;
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import org.opencdmp.data.StorageFileEntity;
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@ -54,4 +55,6 @@ public interface DescriptionService {
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Description importXml(DescriptionImportExport descriptionXml, UUID dmpId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, TransformerException, InvalidApplicationException, IOException, InstantiationException, IllegalAccessException, SAXException;
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Description importJson(DescriptionModel model, UUID dmpId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates, FieldSet fields) throws MyForbiddenException, MyNotFoundException, InvalidApplicationException, IOException ;
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}
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@ -18,6 +18,10 @@ import org.opencdmp.authorization.AffiliatedResource;
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import org.opencdmp.authorization.AuthorizationFlags;
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import org.opencdmp.authorization.Permission;
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import org.opencdmp.authorization.authorizationcontentresolver.AuthorizationContentResolver;
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import org.opencdmp.commonmodels.models.description.*;
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import org.opencdmp.commonmodels.models.descriptiotemplate.DescriptionTemplateModel;
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import org.opencdmp.commonmodels.models.descriptiotemplate.fielddata.ReferenceTypeDataModel;
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import org.opencdmp.commonmodels.models.reference.ReferenceModel;
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import org.opencdmp.commons.JsonHandlingService;
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import org.opencdmp.commons.XmlHandlingService;
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import org.opencdmp.commons.enums.*;
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@ -1267,7 +1271,7 @@ public class DescriptionServiceImpl implements DescriptionService {
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//endregion
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//region Import
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//region Import xml
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public Description importXml(DescriptionImportExport descriptionXml, UUID dmpId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, TransformerException, InvalidApplicationException, IOException, InstantiationException, IllegalAccessException, SAXException{
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@ -1427,4 +1431,170 @@ public class DescriptionServiceImpl implements DescriptionService {
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//endregion
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//region Import RDA Json
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public Description importJson(DescriptionModel model, UUID dmpId, List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates, FieldSet fields) throws MyForbiddenException, MyNotFoundException, InvalidApplicationException, IOException {
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if (model == null) throw new MyNotFoundException("Description common model not found");
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logger.debug(new MapLogEntry("import description").And("dmpId", dmpId).And("fields", fields));
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DescriptionPersist persist = new DescriptionPersist();
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persist.setLabel(model.getLabel());
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persist.setDescription(model.getDescription());
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persist.setStatus(DescriptionStatus.Draft);
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persist.setDmpId(dmpId);
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if (model.getDescriptionTemplate() != null) {
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persist.setDescriptionTemplateId(model.getDescriptionTemplate().getId());
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if (!this.conventionService.isListNullOrEmpty(dmpDescriptionTemplates) && model.getSectionId() != null && model.getDescriptionTemplate().getGroupId() != null){
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DmpDescriptionTemplateEntity dmpDescriptionTemplate = dmpDescriptionTemplates.stream().filter(x -> x.getDmpId().equals(dmpId) &&
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x.getDescriptionTemplateGroupId().equals(model.getDescriptionTemplate().getGroupId()) &&
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x.getSectionId().equals(model.getSectionId())).findFirst().orElse(null);
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if (dmpDescriptionTemplate != null) persist.setDmpDescriptionTemplateId(dmpDescriptionTemplate.getId());
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}
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}
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persist.setTags(model.getTags());
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persist.setProperties(this.commonPropertyDefinitionToPersist(model));
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this.validatorFactory.validator(DescriptionPersist.DescriptionPersistValidator.class).validateForce(persist);
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return this.persist(persist, fields);
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}
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private PropertyDefinitionPersist commonPropertyDefinitionToPersist(DescriptionModel model) {
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if (model == null)
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return null;
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PropertyDefinitionPersist persist = new PropertyDefinitionPersist();
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Map<String, PropertyDefinitionFieldSetPersist> fieldSetsMap = new HashMap<>();
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if (model.getDescriptionTemplate() != null && model.getDescriptionTemplate().getDefinition() != null && !this.conventionService.isListNullOrEmpty(model.getDescriptionTemplate().getDefinition().getPages())) {
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if (model.getProperties() != null && model.getProperties().getFieldSets() != null && !model.getProperties().getFieldSets().isEmpty()){
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for (String fieldSetId: model.getProperties().getFieldSets().keySet()){
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fieldSetsMap.put(fieldSetId, this.commonPropertyDefinitionFieldSetToPersist(model.getProperties().getFieldSets().get(fieldSetId), model.getDescriptionTemplate()));
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}
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}
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}
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persist.setFieldSets(fieldSetsMap);
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return persist;
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}
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private PropertyDefinitionFieldSetPersist commonPropertyDefinitionFieldSetToPersist(PropertyDefinitionFieldSetModel model, DescriptionTemplateModel descriptionTemplate) {
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if (model == null)
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return null;
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PropertyDefinitionFieldSetPersist persist = new PropertyDefinitionFieldSetPersist();
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if (!this.conventionService.isListNullOrEmpty(model.getItems())){
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List<PropertyDefinitionFieldSetItemPersist> items = new ArrayList<>();
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for (PropertyDefinitionFieldSetItemModel fieldSetItem: model.getItems()) {
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items.add(this.commonPropertyDefinitionFieldSetItemToPersist(fieldSetItem, descriptionTemplate));
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}
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persist.setItems(items);
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return persist;
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}
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return null;
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}
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private PropertyDefinitionFieldSetItemPersist commonPropertyDefinitionFieldSetItemToPersist(PropertyDefinitionFieldSetItemModel model, DescriptionTemplateModel descriptionTemplate) {
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if (model == null)
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return null;
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PropertyDefinitionFieldSetItemPersist persist = new PropertyDefinitionFieldSetItemPersist();
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persist.setComment(model.getComment());
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persist.setOrdinal(model.getOrdinal());
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Map<String, FieldPersist> fields = new HashMap<>();
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if (model.getFields() != null && !model.getFields().isEmpty()){
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for (String fieldId: model.getFields().keySet()) {
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fields.put(fieldId, this.commonFieldToPersist(model.getFields().get(fieldId), descriptionTemplate));
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}
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}
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persist.setFields(fields);
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return persist;
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}
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private FieldPersist commonFieldToPersist(FieldModel model, DescriptionTemplateModel descriptionTemplate) {
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if (model == null || descriptionTemplate == null)
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return null;
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org.opencdmp.commonmodels.models.descriptiotemplate.FieldModel descriptionTemplateField = descriptionTemplate.getDefinition().getFieldById(model.getId()).stream().findFirst().orElse(null);
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if (descriptionTemplateField == null){
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return null;
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}
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FieldPersist persist = new FieldPersist();
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if (descriptionTemplateField.getData().getFieldType().equals(FieldType.REFERENCE_TYPES)){
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ReferenceTypeDataModel referenceTypeDataModel = (ReferenceTypeDataModel) descriptionTemplateField.getData();
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if (referenceTypeDataModel != null){
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if (!this.conventionService.isListNullOrEmpty(model.getReferences()))
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if (referenceTypeDataModel.getMultipleSelect()){
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List<ReferencePersist> referencePersists = new ArrayList<>();
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for (ReferenceModel referenceModel: model.getReferences()) {
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referencePersists.add(this.commonReferenceToPersist(referenceModel));
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}
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persist.setReferences(referencePersists);
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}else {
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persist.setReference(this.commonReferenceToPersist(model.getReferences().stream().findFirst().orElse(null)));
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}
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}
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} else {
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persist.setBooleanValue(model.getBooleanValue());
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persist.setDateValue(model.getDateValue());
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persist.setTextValue(model.getTextValue());
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persist.setTextListValue(model.getTextListValue());
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if (model.getExternalIdentifier() != null){
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persist.setExternalIdentifier(this.commonExternalIdentifierToPersist(model.getExternalIdentifier()));
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}
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}
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return persist;
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}
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private ReferencePersist commonReferenceToPersist(ReferenceModel model) {
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if (model == null)
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return null;
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ReferencePersist persist = new ReferencePersist();
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persist.setId(model.getId());
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persist.setLabel(model.getLabel());
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persist.setDescription(model.getDescription());
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persist.setReference(model.getReference());
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persist.setAbbreviation(model.getAbbreviation());
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persist.setSource(model.getSource());
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switch (model.getSourceType()){
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case Internal -> persist.setSourceType(ReferenceSourceType.Internal);
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case External -> persist.setSourceType(ReferenceSourceType.External);
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default -> throw new MyApplicationException("Unrecognized Type " + model.getSourceType().getValue());
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}
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return persist;
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}
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private ExternalIdentifierPersist commonExternalIdentifierToPersist(ExternalIdentifierModel model) {
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if (model == null)
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return null;
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ExternalIdentifierPersist persist = new ExternalIdentifierPersist();
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persist.setType(model.getType());
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persist.setIdentifier(model.getIdentifier());
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return persist;
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}
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//endregion
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}
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@ -12,6 +12,7 @@ import gr.cite.tools.exception.MyValidationException;
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import gr.cite.tools.fieldset.FieldSet;
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import jakarta.xml.bind.JAXBException;
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import org.springframework.http.ResponseEntity;
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import org.springframework.web.multipart.MultipartFile;
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import org.xml.sax.SAXException;
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import javax.crypto.BadPaddingException;
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@ -58,4 +59,5 @@ public interface DmpService {
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Dmp importXml(byte[] bytes, String label, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, TransformerException, InvalidApplicationException, IOException, InstantiationException, IllegalAccessException, SAXException;
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Dmp importJson(MultipartFile file, String label, String repositoryId, String format, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, InvalidApplicationException, IOException, InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException;
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}
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@ -21,6 +21,18 @@ import org.jetbrains.annotations.NotNull;
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import org.opencdmp.authorization.AuthorizationFlags;
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import org.opencdmp.authorization.Permission;
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import org.opencdmp.authorization.authorizationcontentresolver.AuthorizationContentResolver;
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import org.opencdmp.commonmodels.models.DmpUserModel;
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import org.opencdmp.commonmodels.models.UserModel;
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import org.opencdmp.commonmodels.models.description.DescriptionModel;
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import org.opencdmp.commonmodels.models.dmp.DmpBlueprintValueModel;
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import org.opencdmp.commonmodels.models.dmp.DmpContactModel;
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import org.opencdmp.commonmodels.models.dmp.DmpModel;
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import org.opencdmp.commonmodels.models.dmpblueprint.FieldModel;
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import org.opencdmp.commonmodels.models.dmpblueprint.ReferenceTypeFieldModel;
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import org.opencdmp.commonmodels.models.dmpblueprint.SectionModel;
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import org.opencdmp.commonmodels.models.dmpdescriptiontemplate.DmpDescriptionTemplateModel;
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import org.opencdmp.commonmodels.models.dmpreference.DmpReferenceModel;
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import org.opencdmp.commonmodels.models.reference.ReferenceModel;
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import org.opencdmp.commons.JsonHandlingService;
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import org.opencdmp.commons.XmlHandlingService;
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import org.opencdmp.commons.enums.*;
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@ -87,6 +99,7 @@ import org.springframework.http.HttpStatus;
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import org.springframework.http.MediaType;
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import org.springframework.http.ResponseEntity;
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import org.springframework.stereotype.Service;
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import org.springframework.web.multipart.MultipartFile;
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import org.xml.sax.SAXException;
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import javax.crypto.BadPaddingException;
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@ -1626,12 +1639,12 @@ public class DmpServiceImpl implements DmpService {
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//endregion
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//region Import
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//region Import Xml
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public Dmp importXml(byte[] bytes, String label, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, ParserConfigurationException, TransformerException, InvalidApplicationException, IOException, InstantiationException, IllegalAccessException, SAXException {
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logger.debug(new MapLogEntry("import data").And("bytes", bytes).And("label", label).And("fields", fields));
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// this.authorizationService.authorizeForce(Permission.ImportDmpBlueprint);
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this.authorizationService.authorizeForce(Permission.NewDmp);
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DmpPersist persist = new DmpPersist();
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@ -1828,4 +1841,224 @@ public class DmpServiceImpl implements DmpService {
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||||
//endregion
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||||
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||||
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||||
//region Import RDA JSON
|
||||
|
||||
public Dmp importJson(MultipartFile file, String label, String repositoryId, String format, FieldSet fields) throws MyForbiddenException, MyNotFoundException, JAXBException, InvalidApplicationException, IOException, InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException {
|
||||
DmpModel model = this.fileTransformerService.importDmp(file, repositoryId, format);
|
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if (model == null) throw new MyNotFoundException("Plan Import Error");
|
||||
|
||||
logger.debug(new MapLogEntry("import data").And("bytes", file.getBytes()).And("label", label).And("fields", fields));
|
||||
|
||||
DmpPersist persist = new DmpPersist();
|
||||
|
||||
persist.setLabel(label);
|
||||
persist.setStatus(DmpStatus.Draft);
|
||||
persist.setDescription(model.getDescription());
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switch (model.getAccessType()) {
|
||||
case Public -> persist.setAccessType(DmpAccessType.Public);
|
||||
case Restricted -> persist.setAccessType(DmpAccessType.Restricted);
|
||||
default -> throw new MyApplicationException("Unrecognized Type " + model.getAccessType().getValue());
|
||||
}
|
||||
|
||||
persist.setLanguage(model.getLanguage());
|
||||
persist.setProperties(this.commonDmpPropertiesToPersist(model));
|
||||
|
||||
if (!this.conventionService.isListNullOrEmpty(model.getUsers())) {
|
||||
List<UserEntity> users = this.queryFactory.query(UserQuery.class).disableTracking().ids(model.getUsers().stream().map(x -> x.getUser()).collect(Collectors.toList()).stream().map(UserModel::getId).filter(Objects::nonNull).distinct().toList()).isActive(IsActive.Active).collect();
|
||||
List<UUID> userIds = users == null ? new ArrayList<>() : users.stream().map(x -> x.getId()).collect(Collectors.toList());
|
||||
|
||||
List<DmpUserPersist> dmpUsers = new ArrayList<>();
|
||||
for (DmpUserModel user : model.getUsers()) {
|
||||
dmpUsers.add(this.commonDmpUserToPersist(user, userIds));
|
||||
}
|
||||
persist.setUsers(dmpUsers);
|
||||
}
|
||||
|
||||
if (model.getDmpBlueprint() != null) persist.setBlueprint(model.getDmpBlueprint().getId());
|
||||
|
||||
if (!this.conventionService.isListNullOrEmpty(model.getDescriptionTemplates())) {
|
||||
List<DmpDescriptionTemplatePersist> descriptionTemplates = new ArrayList<>();
|
||||
for (DmpDescriptionTemplateModel descriptionTemplate : model.getDescriptionTemplates()) {
|
||||
descriptionTemplates.add(this.commonDmpDescriptionTemplateToPersist(descriptionTemplate));
|
||||
}
|
||||
persist.setDescriptionTemplates(descriptionTemplates);
|
||||
}
|
||||
|
||||
this.validatorFactory.validator(DmpPersist.DmpPersistValidator.class).validateForce(persist);
|
||||
|
||||
Dmp dmp = this.persist(persist, fields);
|
||||
|
||||
if (!this.conventionService.isListNullOrEmpty(model.getDescriptions())) {
|
||||
if (dmp == null || dmp.getId() == null) throw new MyApplicationException("Error creating dmp");
|
||||
|
||||
List<DmpDescriptionTemplateEntity> dmpDescriptionTemplates = this.queryFactory.query(DmpDescriptionTemplateQuery.class).disableTracking()
|
||||
.isActive(IsActive.Active)
|
||||
.dmpIds(dmp.getId())
|
||||
.collect();
|
||||
|
||||
for (DescriptionModel description: model.getDescriptions()){
|
||||
this.descriptionService.importJson(description, dmp.getId(), dmpDescriptionTemplates, fields != null ? fields.extractPrefixed(this.conventionService.asPrefix(Dmp._description)) : null);
|
||||
}
|
||||
}
|
||||
|
||||
return dmp;
|
||||
}
|
||||
|
||||
private DmpPropertiesPersist commonDmpPropertiesToPersist(DmpModel model) {
|
||||
if (model == null)
|
||||
return null;
|
||||
|
||||
DmpPropertiesPersist persist = new DmpPropertiesPersist();
|
||||
|
||||
List<DmpContactPersist> contacts = new ArrayList<>();
|
||||
if (model.getProperties() != null && !this.conventionService.isListNullOrEmpty(model.getProperties().getContacts())) {
|
||||
List<UserEntity> users = this.queryFactory.query(UserQuery.class).disableTracking().ids(model.getProperties().getContacts().stream().map(x -> x.getUser()).collect(Collectors.toList()).stream().map(UserModel::getId).filter(Objects::nonNull).distinct().toList()).isActive(IsActive.Active).collect();
|
||||
List<UUID> usersIds = users == null ? new ArrayList<>() : users.stream().map(x -> x.getId()).collect(Collectors.toList());
|
||||
for (DmpContactModel contact : model.getProperties().getContacts()) {
|
||||
contacts.add(this.commonDmpContactToPersist(contact, usersIds));
|
||||
}
|
||||
}
|
||||
|
||||
Map<UUID, DmpBlueprintValuePersist> dmpBlueprintValues = new HashMap<>();
|
||||
|
||||
if (model.getDmpBlueprint() != null && model.getDmpBlueprint().getDefinition() != null && !this.conventionService.isListNullOrEmpty(model.getDmpBlueprint().getDefinition().getSections())) {
|
||||
List<SectionModel> sections = model.getDmpBlueprint().getDefinition().getSections();
|
||||
if (!this.conventionService.isListNullOrEmpty(sections)){
|
||||
for (SectionModel section : model.getDmpBlueprint().getDefinition().getSections()) {
|
||||
if (!this.conventionService.isListNullOrEmpty(section.getFields()) && !this.conventionService.isListNullOrEmpty(model.getReferences())){
|
||||
for (FieldModel field : section.getFields()) {
|
||||
// reference
|
||||
if (field.getCategory().equals(DmpBlueprintFieldCategory.ReferenceType)){
|
||||
ReferenceTypeFieldModel referenceField = (ReferenceTypeFieldModel) field;
|
||||
List<DmpReferenceModel> dmpReferencesByField = model.getReferences().stream().filter(x -> x.getData() != null && x.getData().getBlueprintFieldId().equals(referenceField.getId())).collect(Collectors.toList());
|
||||
if (!this.conventionService.isListNullOrEmpty(dmpReferencesByField)){
|
||||
dmpBlueprintValues.put(referenceField.getId(), this.commonDmpReferenceFieldToDmpBlueprintValuePersist(referenceField, dmpReferencesByField));
|
||||
}
|
||||
} else {
|
||||
// custom fields
|
||||
if (model.getProperties() != null && this.conventionService.isListNullOrEmpty(model.getProperties().getDmpBlueprintValues())){
|
||||
DmpBlueprintValueModel dmpBlueprintValueModel = model.getProperties().getDmpBlueprintValues().stream().filter(x -> x.getFieldId().equals(field.getId())).findFirst().orElse(null);
|
||||
if (dmpBlueprintValueModel != null) dmpBlueprintValues.put(dmpBlueprintValueModel.getFieldId(), this.commonDmpBlueprintValueToPersist(dmpBlueprintValueModel));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
persist.setContacts(contacts);
|
||||
persist.setDmpBlueprintValues(dmpBlueprintValues);
|
||||
|
||||
return persist;
|
||||
}
|
||||
|
||||
private DmpBlueprintValuePersist commonDmpReferenceFieldToDmpBlueprintValuePersist(ReferenceTypeFieldModel model, List<DmpReferenceModel> dmpReferences) {
|
||||
if (model == null || this.conventionService.isListNullOrEmpty(dmpReferences))
|
||||
return null;
|
||||
|
||||
DmpBlueprintValuePersist persist = new DmpBlueprintValuePersist();
|
||||
|
||||
persist.setFieldId(model.getId());
|
||||
if (model.getMultipleSelect()){
|
||||
List<ReferencePersist> references = new ArrayList<>();
|
||||
for (DmpReferenceModel dmpReference : dmpReferences) {
|
||||
references.add(this.commonDmpReferenceToReferencePersist(dmpReference.getReference()));
|
||||
}
|
||||
persist.setReferences(references);
|
||||
} else {
|
||||
persist.setReference(this.commonDmpReferenceToReferencePersist(dmpReferences.get(0).getReference()));
|
||||
}
|
||||
|
||||
return persist;
|
||||
}
|
||||
|
||||
private ReferencePersist commonDmpReferenceToReferencePersist(ReferenceModel model) {
|
||||
if (model == null)
|
||||
return null;
|
||||
|
||||
ReferencePersist persist = new ReferencePersist();
|
||||
|
||||
persist.setId(model.getId());
|
||||
persist.setLabel(model.getLabel());
|
||||
persist.setDescription(model.getDescription());
|
||||
persist.setReference(model.getReference());
|
||||
persist.setAbbreviation(model.getAbbreviation());
|
||||
persist.setSource(model.getSource());
|
||||
switch (model.getSourceType()){
|
||||
case Internal -> persist.setSourceType(ReferenceSourceType.Internal);
|
||||
case External -> persist.setSourceType(ReferenceSourceType.External);
|
||||
default -> throw new MyApplicationException("Unrecognized Type " + model.getSourceType().getValue());
|
||||
}
|
||||
|
||||
return persist;
|
||||
}
|
||||
|
||||
private DmpBlueprintValuePersist commonDmpBlueprintValueToPersist(DmpBlueprintValueModel model) {
|
||||
if (model == null)
|
||||
return null;
|
||||
|
||||
DmpBlueprintValuePersist persist = new DmpBlueprintValuePersist();
|
||||
|
||||
persist.setFieldId(model.getFieldId());
|
||||
persist.setFieldValue(model.getValue());
|
||||
|
||||
return persist;
|
||||
}
|
||||
|
||||
private DmpDescriptionTemplatePersist commonDmpDescriptionTemplateToPersist(DmpDescriptionTemplateModel model) {
|
||||
if (model == null)
|
||||
return null;
|
||||
|
||||
DmpDescriptionTemplatePersist persist = new DmpDescriptionTemplatePersist();
|
||||
|
||||
persist.setDescriptionTemplateGroupId(model.getDescriptionTemplateGroupId());
|
||||
persist.setSectionId(model.getSectionId());
|
||||
|
||||
return persist;
|
||||
}
|
||||
|
||||
private DmpUserPersist commonDmpUserToPersist(DmpUserModel model, List<UUID> userIds) {
|
||||
if (model == null)
|
||||
return null;
|
||||
|
||||
if (model.getUser() != null && model.getUser().getId() != null && !userIds.isEmpty() && userIds.contains(model.getUser().getId())) {
|
||||
DmpUserPersist persist = new DmpUserPersist();
|
||||
|
||||
persist.setUser(model.getUser().getId());
|
||||
|
||||
switch (model.getRole()){
|
||||
case Owner -> persist.setRole(DmpUserRole.Owner);
|
||||
case User -> persist.setRole(DmpUserRole.User);
|
||||
case DescriptionContributor -> persist.setRole(DmpUserRole.DescriptionContributor);
|
||||
case Reviewer -> persist.setRole(DmpUserRole.Reviewer);
|
||||
default -> throw new MyApplicationException("Unrecognized Type " + model.getRole().getValue());
|
||||
}
|
||||
persist.setSectionId(model.getSectionId());
|
||||
return persist;
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
private DmpContactPersist commonDmpContactToPersist(DmpContactModel model, List<UUID> userIds) {
|
||||
if (model == null)
|
||||
return null;
|
||||
|
||||
DmpContactPersist persist = new DmpContactPersist();
|
||||
|
||||
if (model.getUser() != null && model.getUser().getId() != null && !userIds.isEmpty() && userIds.contains(model.getUser().getId())){
|
||||
persist.setUserId(model.getUser().getId());
|
||||
} else {
|
||||
persist.setEmail(model.getEmail());
|
||||
persist.setFirstName(model.getEmail());
|
||||
persist.setLastName(model.getLastName());
|
||||
}
|
||||
|
||||
return persist;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,11 +1,15 @@
|
|||
package org.opencdmp.service.filetransformer;
|
||||
|
||||
import jakarta.xml.bind.JAXBException;
|
||||
import org.opencdmp.commonmodels.models.dmp.DmpModel;
|
||||
import org.opencdmp.model.file.RepositoryFileFormat;
|
||||
import org.springframework.web.multipart.MultipartFile;
|
||||
|
||||
import javax.crypto.BadPaddingException;
|
||||
import javax.crypto.IllegalBlockSizeException;
|
||||
import javax.crypto.NoSuchPaddingException;
|
||||
import javax.management.InvalidApplicationException;
|
||||
import java.io.IOException;
|
||||
import java.security.InvalidAlgorithmParameterException;
|
||||
import java.security.InvalidKeyException;
|
||||
import java.security.NoSuchAlgorithmException;
|
||||
|
|
@ -18,4 +22,7 @@ public interface FileTransformerService {
|
|||
org.opencdmp.model.file.FileEnvelope exportDmp(UUID dmpId, String repositoryId, String format) throws InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, InvalidApplicationException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException;
|
||||
|
||||
org.opencdmp.model.file.FileEnvelope exportDescription(UUID descriptionId, String repositoryId, String format) throws InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, InvalidApplicationException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException;
|
||||
|
||||
DmpModel importDmp(MultipartFile file, String repositoryId, String format) throws InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, InvalidApplicationException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException, IOException, JAXBException;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -10,27 +10,30 @@ 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 jakarta.xml.bind.JAXBException;
|
||||
import org.apache.commons.io.FilenameUtils;
|
||||
import org.opencdmp.authorization.AuthorizationFlags;
|
||||
import org.opencdmp.authorization.Permission;
|
||||
import org.opencdmp.commonmodels.models.FileEnvelopeModel;
|
||||
import org.opencdmp.commonmodels.models.description.DescriptionModel;
|
||||
import org.opencdmp.commonmodels.models.dmp.DmpModel;
|
||||
import org.opencdmp.commons.JsonHandlingService;
|
||||
import org.opencdmp.commons.enums.IsActive;
|
||||
import org.opencdmp.commons.enums.StorageType;
|
||||
import org.opencdmp.commons.enums.TenantConfigurationType;
|
||||
import org.opencdmp.commons.enums.*;
|
||||
import org.opencdmp.commons.scope.tenant.TenantScope;
|
||||
import org.opencdmp.commons.scope.user.UserScope;
|
||||
import org.opencdmp.commons.types.filetransformer.FileTransformerSourceEntity;
|
||||
import org.opencdmp.commons.types.tenantconfiguration.FileTransformerTenantConfigurationEntity;
|
||||
import org.opencdmp.convention.ConventionService;
|
||||
import org.opencdmp.data.TenantConfigurationEntity;
|
||||
import org.opencdmp.event.TenantConfigurationTouchedEvent;
|
||||
import org.opencdmp.filetransformerbase.interfaces.FileTransformerConfiguration;
|
||||
import org.opencdmp.model.StorageFile;
|
||||
import org.opencdmp.model.builder.commonmodels.description.DescriptionCommonModelBuilder;
|
||||
import org.opencdmp.model.builder.commonmodels.dmp.DmpCommonModelBuilder;
|
||||
import org.opencdmp.model.description.Description;
|
||||
import org.opencdmp.model.dmp.Dmp;
|
||||
import org.opencdmp.model.file.RepositoryFileFormat;
|
||||
import org.opencdmp.model.persist.*;
|
||||
import org.opencdmp.model.tenantconfiguration.TenantConfiguration;
|
||||
import org.opencdmp.query.DescriptionQuery;
|
||||
import org.opencdmp.query.DmpQuery;
|
||||
|
|
@ -44,6 +47,7 @@ import org.springframework.context.MessageSource;
|
|||
import org.springframework.context.event.EventListener;
|
||||
import org.springframework.context.i18n.LocaleContextHolder;
|
||||
import org.springframework.stereotype.Service;
|
||||
import org.springframework.web.multipart.MultipartFile;
|
||||
import org.springframework.web.reactive.function.client.ExchangeFilterFunction;
|
||||
import org.springframework.web.reactive.function.client.WebClient;
|
||||
import reactor.core.publisher.Mono;
|
||||
|
|
@ -52,6 +56,8 @@ import javax.crypto.BadPaddingException;
|
|||
import javax.crypto.IllegalBlockSizeException;
|
||||
import javax.crypto.NoSuchPaddingException;
|
||||
import javax.management.InvalidApplicationException;
|
||||
import java.io.IOException;
|
||||
import java.net.URLConnection;
|
||||
import java.security.InvalidAlgorithmParameterException;
|
||||
import java.security.InvalidKeyException;
|
||||
import java.security.NoSuchAlgorithmException;
|
||||
|
|
@ -74,11 +80,12 @@ public class FileTransformerServiceImpl implements FileTransformerService {
|
|||
private final EncryptionService encryptionService;
|
||||
private final TenantProperties tenantProperties;
|
||||
private final JsonHandlingService jsonHandlingService;
|
||||
private final FileTransformerSourcesCacheService fileTransformerSourcesCacheService;
|
||||
private final FileTransformerSourcesCacheService fileTransformerSourcesCacheService;
|
||||
private final UserScope userScope;
|
||||
|
||||
@Autowired
|
||||
public FileTransformerServiceImpl(FileTransformerProperties fileTransformerProperties, TokenExchangeCacheService tokenExchangeCacheService, FileTransformerConfigurationCacheService fileTransformerConfigurationCacheService, AuthorizationService authorizationService,
|
||||
QueryFactory queryFactory, BuilderFactory builderFactory, StorageFileService storageFileService, MessageSource messageSource, ConventionService conventionService, TenantScope tenantScope, EncryptionService encryptionService, TenantProperties tenantProperties, JsonHandlingService jsonHandlingService, FileTransformerSourcesCacheService fileTransformerSourcesCacheService) {
|
||||
QueryFactory queryFactory, BuilderFactory builderFactory, StorageFileService storageFileService, MessageSource messageSource, ConventionService conventionService, TenantScope tenantScope, EncryptionService encryptionService, TenantProperties tenantProperties, JsonHandlingService jsonHandlingService, FileTransformerSourcesCacheService fileTransformerSourcesCacheService, UserScope userScope) {
|
||||
this.fileTransformerProperties = fileTransformerProperties;
|
||||
this.tokenExchangeCacheService = tokenExchangeCacheService;
|
||||
this.fileTransformerConfigurationCacheService = fileTransformerConfigurationCacheService;
|
||||
|
|
@ -93,7 +100,8 @@ public class FileTransformerServiceImpl implements FileTransformerService {
|
|||
this.tenantProperties = tenantProperties;
|
||||
this.jsonHandlingService = jsonHandlingService;
|
||||
this.fileTransformerSourcesCacheService = fileTransformerSourcesCacheService;
|
||||
this.clients = new HashMap<>();
|
||||
this.userScope = userScope;
|
||||
this.clients = new HashMap<>();
|
||||
}
|
||||
|
||||
private FileTransformerRepository getRepository(String repoId) throws InvalidApplicationException, InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException {
|
||||
|
|
@ -283,4 +291,39 @@ public class FileTransformerServiceImpl implements FileTransformerService {
|
|||
|
||||
});
|
||||
}
|
||||
|
||||
@Override
|
||||
public DmpModel importDmp(MultipartFile file, String repositoryId, String format) throws InvalidAlgorithmParameterException, NoSuchPaddingException, IllegalBlockSizeException, InvalidApplicationException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException, IOException, JAXBException {
|
||||
this.authorizationService.authorize(Permission.NewDmp);
|
||||
|
||||
if (file == null) return null;
|
||||
|
||||
//GK: First get the right client
|
||||
FileTransformerRepository repository = this.getRepository(repositoryId);
|
||||
if (repository == null) throw new MyNotFoundException(this.messageSource.getMessage("General_ItemNotFound", new Object[]{format, FileTransformerRepository.class.getSimpleName()}, LocaleContextHolder.getLocale()));
|
||||
|
||||
String name = FilenameUtils.removeExtension(file.getOriginalFilename());
|
||||
String extension = FilenameUtils.getExtension(file.getOriginalFilename());
|
||||
String mimeType = URLConnection.guessContentTypeFromName(file.getOriginalFilename());
|
||||
|
||||
FileEnvelopeModel fileEnvelope = new FileEnvelopeModel();
|
||||
fileEnvelope.setFile(file.getBytes());
|
||||
fileEnvelope.setMimeType(mimeType);
|
||||
fileEnvelope.setFilename(name + (extension.startsWith(".") ? "" : ".") + extension);
|
||||
|
||||
if (repository.getConfiguration() != null && repository.getConfiguration().isUseSharedStorage()){
|
||||
StorageFilePersist storageFilePersist = new StorageFilePersist();
|
||||
storageFilePersist.setName(name);
|
||||
storageFilePersist.setExtension(extension);
|
||||
storageFilePersist.setMimeType(mimeType);
|
||||
storageFilePersist.setOwnerId(this.userScope.getUserIdSafe());
|
||||
storageFilePersist.setStorageType(StorageType.Transformer);
|
||||
|
||||
StorageFile storageFile = this.storageFileService.persistBytes(storageFilePersist, file.getBytes(), new BaseFieldSet(StorageFile._id, StorageFile._fileRef, StorageFile._mimeType, StorageFile._extension, StorageFile._name));
|
||||
fileEnvelope.setFileRef(storageFile.getFileRef());
|
||||
}
|
||||
|
||||
return repository.importDmp(fileEnvelope);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,7 +26,6 @@ import org.opencdmp.model.builder.dmp.DmpBuilder;
|
|||
import org.opencdmp.model.censorship.PublicDmpCensor;
|
||||
import org.opencdmp.model.censorship.dmp.DmpCensor;
|
||||
import org.opencdmp.model.dmp.Dmp;
|
||||
import org.opencdmp.model.dmpblueprint.DmpBlueprint;
|
||||
import org.opencdmp.model.persist.*;
|
||||
import org.opencdmp.model.result.QueryResult;
|
||||
import org.opencdmp.query.DmpQuery;
|
||||
|
|
@ -364,4 +363,20 @@ public class DmpController {
|
|||
return model;
|
||||
}
|
||||
|
||||
@PostMapping("json/import")
|
||||
@Transactional
|
||||
public Dmp importJson(@RequestParam("file") MultipartFile file, @RequestParam("label") String label, @RequestParam("repositoryId") String repositoryId, @RequestParam("format") String format, FieldSet fields) throws InvalidAlgorithmParameterException, JAXBException, NoSuchPaddingException, IllegalBlockSizeException, InvalidApplicationException, IOException, NoSuchAlgorithmException, BadPaddingException, InvalidKeyException {
|
||||
logger.debug(new MapLogEntry("import json" + Dmp.class.getSimpleName()).And("transformerId", repositoryId).And("file", file).And("label", label));
|
||||
|
||||
Dmp model = this.dmpService.importJson(file, label, repositoryId, format, fields);
|
||||
|
||||
this.auditService.track(AuditableAction.Dmp_Import, Map.ofEntries(
|
||||
new AbstractMap.SimpleEntry<String, Object>("transformerId", repositoryId),
|
||||
new AbstractMap.SimpleEntry<String, Object>("file", file),
|
||||
new AbstractMap.SimpleEntry<String, Object>("fields", fields)
|
||||
));
|
||||
|
||||
return model;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ web:
|
|||
security:
|
||||
enabled: true
|
||||
authorized-endpoints: [ api ]
|
||||
allowed-endpoints: [ api/public, api/dmp/public, api/description/public, /api/supportive-material/public, api/language/public, api/contact-support/public, api/dashboard/public, prometheus, health, metrics ]
|
||||
allowed-endpoints: [ api/public, api/dmp/public, api/description/public, /api/supportive-material/public, api/language/public, api/contact-support/public, api/dashboard/public, prometheus, health, metrics, swagger-ui, v3/api-docs ]
|
||||
idp:
|
||||
api-key:
|
||||
enabled: false
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
springdoc:
|
||||
packagesToScan: org.opencdmp.publicapi.controllers
|
||||
packagesToScan: org.opencdmp.controllers.publicapi
|
||||
pathsToScan: "/api/public/(dmps|datasets)/?.*"
|
||||
swagger-ui:
|
||||
enabled: true
|
||||
useRootPath: true
|
||||
docExpansion: none
|
||||
|
|
@ -207,6 +207,28 @@ export class DmpService {
|
|||
catchError((error: any) => throwError(error)));;
|
||||
}
|
||||
|
||||
uploadJson(file: File, label: string, repositoryId: string, format: string, reqFields: string[] = []): Observable<Dmp> {
|
||||
const url = `${this.apiBase}/json/import`;
|
||||
const params = new BaseHttpParams();
|
||||
|
||||
params.interceptorContext = {
|
||||
excludedInterceptors: [InterceptorType.JSONContentType]
|
||||
};
|
||||
const formData = new FormData();
|
||||
formData.append('file', file);
|
||||
formData.append('label', label);
|
||||
formData.append('repositoryId', repositoryId);
|
||||
formData.append('format', format);
|
||||
|
||||
if (reqFields.length > 0){
|
||||
for (var i = 0; i < reqFields.length; i++) {
|
||||
formData.append('field[]', reqFields[i]);
|
||||
}
|
||||
}
|
||||
|
||||
return this.http.post<Dmp>(url, formData, { params: params }).pipe(catchError((error: any) => throwError(error)));
|
||||
}
|
||||
|
||||
//
|
||||
// Autocomplete Commons
|
||||
//
|
||||
|
|
|
|||
|
|
@ -66,15 +66,28 @@ export class StartNewDmpDialogComponent extends BaseComponent {
|
|||
});
|
||||
dialogRef.afterClosed().pipe(takeUntil(this._destroyed)).subscribe(result => {
|
||||
if (result && result.success) {
|
||||
this.dmpService.uploadXml(result.fileList[0], result.dmpTitle)
|
||||
.pipe(takeUntil(this._destroyed))
|
||||
.subscribe(
|
||||
(complete) => {
|
||||
this.onCallbackImportComplete();
|
||||
this.dialog.closeAll();
|
||||
},
|
||||
(error) => this.onCallbackImportFail(error.error)
|
||||
);
|
||||
const file = result.fileList[0] as File;
|
||||
if (file?.type.includes('/xml')){
|
||||
this.dmpService.uploadXml(result.fileList[0], result.dmpTitle)
|
||||
.pipe(takeUntil(this._destroyed))
|
||||
.subscribe(
|
||||
(complete) => {
|
||||
this.onCallbackImportComplete();
|
||||
this.dialog.closeAll();
|
||||
},
|
||||
(error) => this.onCallbackImportFail(error.error)
|
||||
);
|
||||
} else if (file?.type.includes('/json')){
|
||||
this.dmpService.uploadJson(result.fileList[0], result.dmpTitle, 'rda-file-transformer', 'json')
|
||||
.pipe(takeUntil(this._destroyed))
|
||||
.subscribe(
|
||||
(complete) => {
|
||||
this.onCallbackImportComplete();
|
||||
this.dialog.closeAll();
|
||||
},
|
||||
(error) => this.onCallbackImportFail(error.error)
|
||||
);
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
|
|
|
|||
|
|
@ -133,5 +133,6 @@ These are the semantics suggestions.
|
|||
- `zenodo.related_identifiers.isRequiredBy`
|
||||
- `zenodo.related_identifiers.isObsoletedBy`
|
||||
- `zenodo.related_identifiers.obsoletes`
|
||||
- `zenodo.publication_date`
|
||||
</TabItem>
|
||||
</Tabs>
|
||||
|
|
@ -3,4 +3,29 @@ sidebar_position: 1
|
|||
description: A brief guide on the API documentation tool this platform uses
|
||||
---
|
||||
|
||||
# Swagger
|
||||
import Tabs from '@theme/Tabs';
|
||||
import TabItem from '@theme/TabItem';
|
||||
import Admonition from '@theme/Admonition';
|
||||
|
||||
# Swagger
|
||||
|
||||
The swagger UI is available at the `/swagger-ui/index.html` url. It contains documentation for the following API endpoints.
|
||||
|
||||
<Tabs>
|
||||
<TabItem value="public" label="Public API">
|
||||
|
||||
- **/api/public/dmps/\*\***
|
||||
- **/api/public/descriptions/\*\***
|
||||
|
||||
</TabItem>
|
||||
<TabItem value="internal" label="Internal API">
|
||||
|
||||
- **/api/dmp/\*\***
|
||||
- **/api/description/\*\***
|
||||
|
||||
<Admonition type="info">
|
||||
<p>These endpoints require authentication.</p>
|
||||
</Admonition>
|
||||
|
||||
</TabItem>
|
||||
</Tabs>
|
||||
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Reference in New Issue