Merge branch 'Development'

This commit is contained in:
Diamantis Tziotzios 2024-02-22 11:09:31 +02:00
commit e8aef281d4
348 changed files with 15489 additions and 3497 deletions

1
.gitignore vendored
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@ -48,3 +48,4 @@ bin/
*.classpath
openDMP/dmp-backend/uploads/
openDMP/dmp-backend/tmp/
dmp-frontend/.angular/

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@ -0,0 +1,16 @@
package eu.eudat.data.dao.criteria;
import eu.eudat.data.entities.DMPProfile;
public class DataManagementPlanBlueprintCriteria extends Criteria<DMPProfile> {
private Integer status;
public Integer getStatus() {
return status;
}
public void setStatus(Integer status) {
this.status = status;
}
}

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@ -1,6 +1,7 @@
package eu.eudat.data.dao.criteria;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.DMPProfile;
import eu.eudat.data.entities.Grant;
import java.util.Date;
@ -10,6 +11,7 @@ import java.util.UUID;
public class DataManagementPlanCriteria extends Criteria<DMP> {
private Date periodStart;
private Date periodEnd;
private DMPProfile profile;
private List<eu.eudat.data.entities.Grant> grants;
private boolean allVersions;
private List<UUID> groupIds;
@ -37,6 +39,13 @@ public class DataManagementPlanCriteria extends Criteria<DMP> {
this.periodEnd = periodEnd;
}
public DMPProfile getProfile() {
return profile;
}
public void setProfile(DMPProfile profile) {
this.profile = profile;
}
public List<Grant> getGrants() {
return grants;
}

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@ -1,13 +1,13 @@
package eu.eudat.data.dao.criteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import java.util.Date;
import java.util.List;
import java.util.UUID;
public class DatasetProfileCriteria extends Criteria<DatasetProfile> {
public class DatasetProfileCriteria extends Criteria<DescriptionTemplate> {
public enum DatasetProfileFilter {
DMPs((short) 0), Datasets((short) 1);
@ -25,7 +25,7 @@ public class DatasetProfileCriteria extends Criteria<DatasetProfile> {
case 1:
return Datasets;
default:
throw new RuntimeException("Unsupported DatasetProfile filter");
throw new RuntimeException("Unsupported DescriptionTemplate filter");
}
}
}

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@ -1,11 +1,11 @@
package eu.eudat.data.dao.criteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import java.util.UUID;
public class DatasetProfileWizardCriteria extends Criteria<DatasetProfile> {
public class DatasetProfileWizardCriteria extends Criteria<DescriptionTemplate> {
private UUID id;
public UUID getId() {

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@ -42,6 +42,8 @@ public class DMPDaoImpl extends DatabaseAccess<DMP> implements DMPDao {
query.where((builder, root) -> builder.lessThan(root.get("created"), criteria.getPeriodEnd()));
if (criteria.getPeriodStart() != null)
query.where((builder, root) -> builder.greaterThan(root.get("created"), criteria.getPeriodStart()));
if (criteria.getProfile() != null)
query.where((builder, root) -> builder.equal(root.get("profile"), criteria.getProfile()));
if (criteria.getGrants() != null && !criteria.getGrants().isEmpty())
query.where(((builder, root) -> root.get("grant").in(criteria.getGrants())));
if (!criteria.getAllVersions())
@ -75,7 +77,7 @@ public class DMPDaoImpl extends DatabaseAccess<DMP> implements DMPDao {
query.where((builder, root) -> root.join("users", JoinType.LEFT).join("user", JoinType.LEFT).get("id").in(criteria.getCollaborators()));
}
if (criteria.getDatasetTemplates() != null && !criteria.getDatasetTemplates().isEmpty()) {
query.where((builder, root) -> root.join("associatedDmps", JoinType.LEFT).get("id").in(criteria.getDatasetTemplates()));
query.where((builder, root) -> root.join("associatedDmps", JoinType.LEFT).get("datasetprofile").get("id").in(criteria.getDatasetTemplates()));
}
if (criteria.getGrantStatus() != null) {
if (criteria.getGrantStatus().equals(GrantStateType.FINISHED.getValue().shortValue()))

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@ -1,6 +1,7 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.dao.criteria.DataManagementPlanBlueprintCriteria;
import eu.eudat.data.dao.criteria.DataManagementPlanProfileCriteria;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.DMPProfile;
@ -15,4 +16,6 @@ public interface DMPProfileDao extends DatabaseAccessLayer<DMPProfile, UUID> {
QueryableList<DMPProfile> getWithCriteria(DataManagementPlanProfileCriteria criteria);
QueryableList<DMPProfile> getWithCriteriaBlueprint(DataManagementPlanBlueprintCriteria criteria);
}

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@ -1,6 +1,7 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.criteria.DataManagementPlanBlueprintCriteria;
import eu.eudat.data.dao.criteria.DataManagementPlanProfileCriteria;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.DMPProfile;
@ -65,4 +66,20 @@ public class DMPProfileDaoImpl extends DatabaseAccess<DMPProfile> implements DMP
query.where(((builder, root) -> builder.notEqual(root.get("status"), DMPProfile.Status.DELETED.getValue())));
return query;
}
@Override
public QueryableList<DMPProfile> getWithCriteriaBlueprint(DataManagementPlanBlueprintCriteria criteria){
QueryableList<DMPProfile> query = getDatabaseService().getQueryable(DMPProfile.class);
if (criteria.getLike() != null && !criteria.getLike().isEmpty())
query.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + criteria.getLike().toUpperCase() + "%"));
if (criteria.getStatus() != null) {
if (criteria.getStatus() == DMPProfile.Status.FINALIZED.getValue()) {
query.where((builder, root) -> builder.equal(root.get("status"), DMPProfile.Status.FINALIZED.getValue()));
} else if (criteria.getStatus() == DMPProfile.Status.SAVED.getValue()) {
query.where((builder, root) -> builder.equal(root.get("status"), DMPProfile.Status.SAVED.getValue()));
}
}
query.where(((builder, root) -> builder.notEqual(root.get("status"), DMPProfile.Status.DELETED.getValue())));
return query;
}
}

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@ -3,7 +3,6 @@ package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.DatasetExternalDataset;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Async;

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@ -2,20 +2,23 @@ package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.dao.criteria.DatasetProfileCriteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.DescriptionTemplateType;
import eu.eudat.queryable.QueryableList;
import java.util.List;
import java.util.UUID;
public interface DatasetProfileDao extends DatabaseAccessLayer<DatasetProfile, UUID> {
public interface DatasetProfileDao extends DatabaseAccessLayer<DescriptionTemplate, UUID> {
QueryableList<DatasetProfile> getWithCriteria(DatasetProfileCriteria criteria);
QueryableList<DescriptionTemplate> getWithCriteria(DatasetProfileCriteria criteria);
QueryableList<DatasetProfile> getAll();
QueryableList<DescriptionTemplate> getAll();
QueryableList<DatasetProfile> getAuthenticated(QueryableList<DatasetProfile> query, UUID principal, List<Integer> roles);
QueryableList<DescriptionTemplate> getAuthenticated(QueryableList<DescriptionTemplate> query, UUID principal, List<Integer> roles);
List<DatasetProfile> getAllIds();
List<DescriptionTemplate> getAllIds();
Long countWithType(DescriptionTemplateType type);
}

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@ -3,8 +3,8 @@ package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.criteria.DatasetProfileCriteria;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.DescriptionTemplateType;
import eu.eudat.queryable.QueryableList;
import eu.eudat.queryable.types.FieldSelectionType;
import eu.eudat.queryable.types.SelectionField;
@ -21,16 +21,16 @@ import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@Component("datasetProfileDao")
public class DatasetProfileDaoImpl extends DatabaseAccess<DatasetProfile> implements DatasetProfileDao {
public class DatasetProfileDaoImpl extends DatabaseAccess<DescriptionTemplate> implements DatasetProfileDao {
@Autowired
public DatasetProfileDaoImpl(DatabaseService<DatasetProfile> databaseService) {
public DatasetProfileDaoImpl(DatabaseService<DescriptionTemplate> databaseService) {
super(databaseService);
}
@Override
public QueryableList<DatasetProfile> getWithCriteria(DatasetProfileCriteria criteria) {
QueryableList<DatasetProfile> query = getDatabaseService().getQueryable(DatasetProfile.class);
public QueryableList<DescriptionTemplate> getWithCriteria(DatasetProfileCriteria criteria) {
QueryableList<DescriptionTemplate> query = getDatabaseService().getQueryable(DescriptionTemplate.class);
if (criteria.getLike() != null && !criteria.getLike().isEmpty())
query.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + criteria.getLike().toUpperCase() + "%"));
if (!criteria.getAllVersions())
@ -63,9 +63,9 @@ public class DatasetProfileDaoImpl extends DatabaseAccess<DatasetProfile> implem
query.where(((builder, root) -> root.get("id").in(criteria.getIds())));
}
if (criteria.getFinalized()) {
query.where(((builder, root) -> builder.equal(root.get("status"), DatasetProfile.Status.FINALIZED.getValue())));
query.where(((builder, root) -> builder.equal(root.get("status"), DescriptionTemplate.Status.FINALIZED.getValue())));
} else {
query.where(((builder, root) -> builder.notEqual(root.get("status"), DatasetProfile.Status.DELETED.getValue())));
query.where(((builder, root) -> builder.notEqual(root.get("status"), DescriptionTemplate.Status.DELETED.getValue())));
}
if (criteria.getPeriodStart() != null)
query.where((builder, root) -> builder.greaterThanOrEqualTo(root.get("created"), criteria.getPeriodStart()));
@ -73,48 +73,48 @@ public class DatasetProfileDaoImpl extends DatabaseAccess<DatasetProfile> implem
}
@Override
public DatasetProfile createOrUpdate(DatasetProfile item) {
return this.getDatabaseService().createOrUpdate(item, DatasetProfile.class);
public DescriptionTemplate createOrUpdate(DescriptionTemplate item) {
return this.getDatabaseService().createOrUpdate(item, DescriptionTemplate.class);
}
@Override
public DatasetProfile find(UUID id) {
return getDatabaseService().getQueryable(DatasetProfile.class).where((builder, root) -> builder.equal(root.get("id"), id)).getSingle();
public DescriptionTemplate find(UUID id) {
return getDatabaseService().getQueryable(DescriptionTemplate.class).where((builder, root) -> builder.equal(root.get("id"), id)).getSingle();
}
@Override
public QueryableList<DatasetProfile> getAll() {
return getDatabaseService().getQueryable(DatasetProfile.class);
public QueryableList<DescriptionTemplate> getAll() {
return getDatabaseService().getQueryable(DescriptionTemplate.class);
}
@Override
public List<DatasetProfile> getAllIds(){
return getDatabaseService().getQueryable(DatasetProfile.class).withFields(Collections.singletonList("id")).toList();
public List<DescriptionTemplate> getAllIds(){
return getDatabaseService().getQueryable(DescriptionTemplate.class).withFields(Collections.singletonList("id")).toList();
}
@Override
public void delete(DatasetProfile item) {
public void delete(DescriptionTemplate item) {
this.getDatabaseService().delete(item);
}
@Override
public QueryableList<DatasetProfile> asQueryable() {
return this.getDatabaseService().getQueryable(DatasetProfile.class);
public QueryableList<DescriptionTemplate> asQueryable() {
return this.getDatabaseService().getQueryable(DescriptionTemplate.class);
}
@Async
@Override
public CompletableFuture<DatasetProfile> createOrUpdateAsync(DatasetProfile item) {
public CompletableFuture<DescriptionTemplate> createOrUpdateAsync(DescriptionTemplate item) {
return CompletableFuture.supplyAsync(() -> this.createOrUpdate(item));
}
@Override
public DatasetProfile find(UUID id, String hint) {
public DescriptionTemplate find(UUID id, String hint) {
throw new UnsupportedOperationException();
}
@Override
public QueryableList<DatasetProfile> getAuthenticated(QueryableList<DatasetProfile> query, UUID principal, List<Integer> roles) {
public QueryableList<DescriptionTemplate> getAuthenticated(QueryableList<DescriptionTemplate> query, UUID principal, List<Integer> roles) {
if (roles != null && !roles.isEmpty()) {
query.where((builder, root) -> {
Join userJoin = root.join("users", JoinType.LEFT);
@ -126,4 +126,9 @@ public class DatasetProfileDaoImpl extends DatabaseAccess<DatasetProfile> implem
return query;
}
@Override
public Long countWithType(DescriptionTemplateType type) {
return this.getDatabaseService().getQueryable(DescriptionTemplate.class).where((builder, root) -> builder.equal(root.get("type"), type)).count();
}
}

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@ -1,7 +1,6 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DatasetService;
import java.util.UUID;

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@ -2,8 +2,6 @@ package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.DatasetExternalDataset;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DatasetService;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;

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@ -0,0 +1,10 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.entities.DescriptionTemplateType;
import java.util.UUID;
public interface DescriptionTemplateTypeDao extends DatabaseAccessLayer<DescriptionTemplateType, UUID> {
DescriptionTemplateType findFromName(String name);
}

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@ -0,0 +1,65 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.DescriptionTemplateType;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Async;
import org.springframework.stereotype.Component;
import javax.transaction.Transactional;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@Component("descriptionTemplateTypeDao")
public class DescriptionTemplateTypeDaoImpl extends DatabaseAccess<DescriptionTemplateType> implements DescriptionTemplateTypeDao {
@Autowired
public DescriptionTemplateTypeDaoImpl(DatabaseService<DescriptionTemplateType> databaseService) {
super(databaseService);
}
@Override
public DescriptionTemplateType findFromName(String name){
try {
return this.getDatabaseService().getQueryable(DescriptionTemplateType.class).where((builder, root) -> builder.and(builder.equal(root.get("name"), name), builder.notEqual(root.get("status"), DescriptionTemplateType.Status.DELETED.getValue()))).getSingle();
}
catch(Exception e){
return null;
}
}
@Override
@Transactional
public DescriptionTemplateType createOrUpdate(DescriptionTemplateType item) {
return this.getDatabaseService().createOrUpdate(item, DescriptionTemplateType.class);
}
@Override
public DescriptionTemplateType find(UUID id) {
return getDatabaseService().getQueryable(DescriptionTemplateType.class).where((builder, root) -> builder.equal((root.get("id")), id)).getSingle();
}
@Override
public void delete(DescriptionTemplateType item) {
this.getDatabaseService().delete(item);
}
@Override
public QueryableList<DescriptionTemplateType> asQueryable() {
return this.getDatabaseService().getQueryable(DescriptionTemplateType.class).where((builder, root) -> builder.notEqual((root.get("status")), DescriptionTemplateType.Status.DELETED.getValue()));
}
@Async
@Override
public CompletableFuture<DescriptionTemplateType> createOrUpdateAsync(DescriptionTemplateType item) {
return CompletableFuture.supplyAsync(() -> this.createOrUpdate(item));
}
@Override
public DescriptionTemplateType find(UUID id, String hint) {
throw new UnsupportedOperationException();
}
}

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@ -0,0 +1,9 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.entities.DMPDatasetProfile;
import java.util.UUID;
public interface DmpDatasetProfileDao extends DatabaseAccessLayer<DMPDatasetProfile, UUID> {
}

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@ -0,0 +1,52 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.Content;
import eu.eudat.data.entities.DMPDatasetProfile;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Async;
import org.springframework.stereotype.Service;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@Service("dmpDatasetProfileDao")
public class DmpDatasetProfileDaoImpl extends DatabaseAccess<DMPDatasetProfile> implements DmpDatasetProfileDao {
@Autowired
public DmpDatasetProfileDaoImpl(DatabaseService<DMPDatasetProfile> databaseService) {
super(databaseService);
}
@Override
public DMPDatasetProfile createOrUpdate(DMPDatasetProfile item) {
return this.getDatabaseService().createOrUpdate(item, DMPDatasetProfile.class);
}
@Override
@Async
public CompletableFuture<DMPDatasetProfile> createOrUpdateAsync(DMPDatasetProfile item) {
return CompletableFuture.supplyAsync(() -> this.createOrUpdate(item));
}
@Override
public DMPDatasetProfile find(UUID id) {
return this.getDatabaseService().getQueryable(DMPDatasetProfile.class).where((builder, root) -> builder.equal(root.get("id"), id)).getSingle();
}
@Override
public DMPDatasetProfile find(UUID id, String hint) {
throw new UnsupportedOperationException();
}
@Override
public void delete(DMPDatasetProfile item) {
this.getDatabaseService().delete(item);
}
@Override
public QueryableList<DMPDatasetProfile> asQueryable() {
return this.getDatabaseService().getQueryable(DMPDatasetProfile.class);
}
}

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@ -112,12 +112,8 @@ public class DMP implements DataEntity<DMP, UUID> {
/*@Type(type = "eu.eudat.configurations.typedefinition.XMLType")
@Column(name = "\"AssociatedDmps\"", columnDefinition = "xml", nullable = true)
private String associatedDmps;*/
@OneToMany(fetch = FetchType.LAZY)
@JoinTable(name = "\"DMPDatasetProfile\"",
joinColumns = {@JoinColumn(name = "\"dmp\"", referencedColumnName = "\"ID\"")},
inverseJoinColumns = {@JoinColumn(name = "\"datasetprofile\"", referencedColumnName = "\"ID\"")}
)
private Set<DatasetProfile> associatedDmps;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "dmp")
private Set<DMPDatasetProfile> associatedDmps;
@ManyToOne(fetch = FetchType.LAZY)
@ -274,10 +270,10 @@ public class DMP implements DataEntity<DMP, UUID> {
this.grant = grant;
}
public Set<DatasetProfile> getAssociatedDmps() {
public Set<DMPDatasetProfile> getAssociatedDmps() {
return associatedDmps;
}
public void setAssociatedDmps(Set<DatasetProfile> associatedDmps) {
public void setAssociatedDmps(Set<DMPDatasetProfile> associatedDmps) {
this.associatedDmps = associatedDmps;
}

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@ -0,0 +1,76 @@
package eu.eudat.data.entities;
import eu.eudat.queryable.queryableentity.DataEntity;
import org.hibernate.annotations.GenericGenerator;
import javax.persistence.*;
import java.util.List;
import java.util.UUID;
@Entity
@Table(name = "\"DMPDatasetProfile\"")
public class DMPDatasetProfile implements DataEntity<DMPDatasetProfile, UUID> {
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;
@ManyToOne
@JoinColumn(name = "\"dmp\"")
private DMP dmp;
@ManyToOne
@JoinColumn(name = "\"datasetprofile\"")
private DescriptionTemplate datasetprofile;
@Column(name = "\"data\"")
private String data;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public DMP getDmp() {
return dmp;
}
public void setDmp(DMP dmp) {
this.dmp = dmp;
}
public DescriptionTemplate getDatasetprofile() {
return datasetprofile;
}
public void setDatasetprofile(DescriptionTemplate datasetprofile) {
this.datasetprofile = datasetprofile;
}
public String getData() {
return data;
}
public void setData(String data) {
this.data = data;
}
@Override
public void update(DMPDatasetProfile entity) {
this.dmp = entity.getDmp();
this.datasetprofile = entity.getDatasetprofile();
this.data = entity.getData();
}
@Override
public UUID getKeys() {
return this.id;
}
@Override
public DMPDatasetProfile buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
this.id = UUID.fromString((String) tuple.get(0).get(base.isEmpty() ? base + "." + "id" : "id"));
return this;
}
}

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@ -100,6 +100,9 @@ public class Dataset implements DataEntity<Dataset, UUID> {
@JoinColumn(name = "\"DMP\"", nullable = false)
private DMP dmp;
@Column(name = "\"DmpSectionIndex\"")
private Integer dmpSectionIndex;
@Column(name = "\"Uri\"")
private String uri;
@ -110,7 +113,7 @@ public class Dataset implements DataEntity<Dataset, UUID> {
@ManyToOne(fetch = FetchType.LAZY)
//@Cascade(value=org.hibernate.annotations.CascadeType.ALL)
@JoinColumn(name = "\"Profile\"")
private DatasetProfile profile;
private DescriptionTemplate profile;
@Type(type = "eu.eudat.configurations.typedefinition.XMLType")
@Column(name = "\"Reference\"", columnDefinition = "xml")
@ -232,6 +235,12 @@ public class Dataset implements DataEntity<Dataset, UUID> {
this.dmp = dmp;
}
public Integer getDmpSectionIndex() {
return dmpSectionIndex;
}
public void setDmpSectionIndex(Integer dmpSectionIndex) {
this.dmpSectionIndex = dmpSectionIndex;
}
public String getUri() {
return uri;
@ -249,10 +258,10 @@ public class Dataset implements DataEntity<Dataset, UUID> {
}
public DatasetProfile getProfile() {
public DescriptionTemplate getProfile() {
return profile;
}
public void setProfile(DatasetProfile profile) {
public void setProfile(DescriptionTemplate profile) {
this.profile = profile;
}
@ -328,6 +337,7 @@ public class Dataset implements DataEntity<Dataset, UUID> {
this.setRegistries(entity.getRegistries());
this.setDmp(entity.getDmp());
this.setDmpSectionIndex(entity.getDmpSectionIndex());
this.setStatus(entity.getStatus());
this.setProfile(entity.getProfile());
this.setModified(new Date());

View File

@ -14,8 +14,8 @@ import java.util.UUID;
@Entity
@Table(name = "\"DatasetProfile\"")
public class DatasetProfile implements DataEntity<DatasetProfile,UUID>{
@Table(name = "\"DescriptionTemplate\"")
public class DescriptionTemplate implements DataEntity<DescriptionTemplate,UUID>{
public enum Status {
SAVED((short) 0), FINALIZED((short) 1), DELETED((short) 99);
@ -79,19 +79,21 @@ public class DatasetProfile implements DataEntity<DatasetProfile,UUID>{
@Column(name = "\"Version\"", nullable = false)
private Short version;
@ManyToMany(fetch = FetchType.LAZY)
@JoinTable(name = "\"DMPDatasetProfile\"",
joinColumns = {@JoinColumn(name = "\"datasetprofile\"", referencedColumnName = "\"ID\"")},
inverseJoinColumns = {@JoinColumn(name = "\"dmp\"", referencedColumnName = "\"ID\"")}
)
private List<DMP> dmps;
@OneToMany(fetch = FetchType.LAZY)
private Set<DMP> dmps;
@Column(name = "\"Language\"", nullable = false)
private String language;
@OneToMany(mappedBy = "datasetProfile", fetch = FetchType.LAZY)
@OneToOne(fetch = FetchType.EAGER)
@JoinColumn(name = "\"Type\"", nullable = false)
private DescriptionTemplateType type;
@OneToMany(mappedBy = "descriptionTemplate", fetch = FetchType.LAZY)
private Set<UserDatasetProfile> users;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "datasetprofile")
private Set<DMPDatasetProfile> associatedDmps;
public String getDescription() {
return description;
@ -156,26 +158,31 @@ public class DatasetProfile implements DataEntity<DatasetProfile,UUID>{
public String getLanguage() {
return language;
}
public void setLanguage(String language) {
this.language = language;
}
public DescriptionTemplateType getType() {
return type;
}
public void setType(DescriptionTemplateType type) {
this.type = type;
}
public Set<UserDatasetProfile> getUsers() {
return users;
}
public void setUsers(Set<UserDatasetProfile> users) {
this.users = users;
}
@Override
public String toString() {
return "DatasetProfileListingModel [id=" + id + ", label=" + label + ", dataset=" + dataset + ", definition=" + definition + ", version=" + version + ", language=" + language + "]";
return "DatasetProfileListingModel [id=" + id + ", label=" + label + ", dataset=" + dataset + ", definition=" + definition + ", version=" + version + ", language=" + language + ", type=" + type +"]";
}
@Override
public void update(DatasetProfile entity) {
public void update(DescriptionTemplate entity) {
}
@Override
@ -184,7 +191,7 @@ public class DatasetProfile implements DataEntity<DatasetProfile,UUID>{
}
@Override
public DatasetProfile buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
public DescriptionTemplate buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
this.id = UUID.fromString((String) tuple.get(0).get(base.isEmpty() ? base + "." + "id" : "id"));
return this;
}

View File

@ -0,0 +1,89 @@
package eu.eudat.data.entities;
import eu.eudat.queryable.queryableentity.DataEntity;
import org.hibernate.annotations.GenericGenerator;
import javax.persistence.*;
import java.util.List;
import java.util.UUID;
@Entity
@Table(name = "\"DescriptionTemplateType\"")
public class DescriptionTemplateType implements DataEntity<DescriptionTemplateType, UUID> {
public enum Status {
SAVED((short) 0), FINALIZED((short) 1), DELETED((short) 99);
private short value;
private Status(short value) {
this.value = value;
}
public short getValue() {
return value;
}
public static Status fromInteger(int value) {
switch (value) {
case 0:
return SAVED;
case 1:
return FINALIZED;
case 99:
return DELETED;
default:
throw new RuntimeException("Unsupported Description Template Type Status");
}
}
}
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;
@Column(name = "\"Name\"", nullable = false)
private String name;
@Column(name = "\"Status\"", nullable = false)
private Short status;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public Short getStatus() {
return status;
}
public void setStatus(Short status) {
this.status = status;
}
@Override
public void update(DescriptionTemplateType entity) {
this.name = entity.name;
this.status = entity.status;
}
@Override
public UUID getKeys() {
return this.id;
}
@Override
public DescriptionTemplateType buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
this.id = UUID.fromString((String) tuple.get(0).get(!base.isEmpty() ? base + "." + "id" : "id"));
return this;
}
}

View File

@ -22,8 +22,8 @@ public class UserDatasetProfile implements DataEntity<UserDatasetProfile, UUID>
private UserInfo user;
@OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "\"datasetProfile\"")
private DatasetProfile datasetProfile;
@JoinColumn(name = "\"descriptionTemplate\"")
private DescriptionTemplate descriptionTemplate;
@Column(name = "role")
private Integer role;
@ -44,12 +44,12 @@ public class UserDatasetProfile implements DataEntity<UserDatasetProfile, UUID>
this.user = user;
}
public DatasetProfile getDatasetProfile() {
return datasetProfile;
public DescriptionTemplate getDatasetProfile() {
return descriptionTemplate;
}
public void setDatasetProfile(DatasetProfile datasetProfile) {
this.datasetProfile = datasetProfile;
public void setDatasetProfile(DescriptionTemplate descriptionTemplate) {
this.descriptionTemplate = descriptionTemplate;
}
public Integer getRole() {

View File

@ -0,0 +1,27 @@
package eu.eudat.data.query.items.dmpblueprint;
import eu.eudat.data.dao.criteria.DataManagementPlanBlueprintCriteria;
import eu.eudat.data.entities.DMPProfile;
import eu.eudat.data.query.PaginationService;
import eu.eudat.data.query.definition.TableQuery;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public class DataManagementPlanBlueprintTableRequest extends TableQuery<DataManagementPlanBlueprintCriteria, DMPProfile, UUID> {
@Override
public QueryableList<DMPProfile> applyCriteria() {
QueryableList<DMPProfile> query = this.getQuery();
if (this.getCriteria().getLike() != null && !this.getCriteria().getLike().isEmpty())
query.where((builder, root) -> builder.like(root.get("label"), "%" + this.getCriteria().getLike() + "%"));
if (this.getCriteria().getStatus() != null)
query.where((builder, root) -> builder.equal(root.get("status"), this.getCriteria().getStatus()));
return query;
}
@Override
public QueryableList<DMPProfile> applyPaging(QueryableList<DMPProfile> items) {
return PaginationService.applyPaging(items, this);
}
}

View File

@ -1,25 +1,24 @@
package eu.eudat.data.query.items.item.datasetprofile;
import eu.eudat.data.dao.criteria.DatasetProfileCriteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.query.PaginationService;
import eu.eudat.data.query.definition.Query;
import eu.eudat.data.query.definition.TableQuery;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public class DatasetProfileAutocompleteRequest extends TableQuery<DatasetProfileCriteria,DatasetProfile, UUID> {
public class DatasetProfileAutocompleteRequest extends TableQuery<DatasetProfileCriteria, DescriptionTemplate, UUID> {
@Override
public QueryableList<DatasetProfile> applyCriteria() {
QueryableList<DatasetProfile> query = this.getQuery();
public QueryableList<DescriptionTemplate> applyCriteria() {
QueryableList<DescriptionTemplate> query = this.getQuery();
if (this.getCriteria().getLike() != null && !this.getCriteria().getLike().isEmpty())
query.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + this.getCriteria().getLike().toUpperCase() + "%"));
return query;
}
@Override
public QueryableList<DatasetProfile> applyPaging(QueryableList<DatasetProfile> items) {
public QueryableList<DescriptionTemplate> applyPaging(QueryableList<DescriptionTemplate> items) {
return PaginationService.applyPaging(items, this);
}
}

View File

@ -1,15 +1,13 @@
package eu.eudat.data.query.items.item.datasetprofile;
import eu.eudat.data.dao.criteria.DatasetProfileWizardCriteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.query.definition.Query;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public class DatasetProfileWizardAutocompleteRequest extends Query<DatasetProfileWizardCriteria,DatasetProfile> {
public class DatasetProfileWizardAutocompleteRequest extends Query<DatasetProfileWizardCriteria, DescriptionTemplate> {
@Override
public QueryableList<DatasetProfile> applyCriteria() {
public QueryableList<DescriptionTemplate> applyCriteria() {
return null;
}
}

View File

@ -1,23 +1,23 @@
package eu.eudat.data.query.items.table.datasetprofile;
import eu.eudat.data.dao.criteria.DatasetProfileCriteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.query.definition.TableQuery;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public class DatasetProfileTableRequestItem extends TableQuery<DatasetProfileCriteria, DatasetProfile, UUID> {
public class DatasetProfileTableRequestItem extends TableQuery<DatasetProfileCriteria, DescriptionTemplate, UUID> {
@Override
public QueryableList<DatasetProfile> applyCriteria() {
QueryableList<DatasetProfile> query = this.getQuery();
public QueryableList<DescriptionTemplate> applyCriteria() {
QueryableList<DescriptionTemplate> query = this.getQuery();
if (this.getCriteria().getLike() != null && !this.getCriteria().getLike().isEmpty())
query.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + this.getCriteria().getLike().toUpperCase() + "%"));
return query;
}
@Override
public QueryableList<DatasetProfile> applyPaging(QueryableList<DatasetProfile> items) {
public QueryableList<DescriptionTemplate> applyPaging(QueryableList<DescriptionTemplate> items) {
return null;
}
}

View File

@ -231,7 +231,9 @@ public class Dataset implements ElasticEntity<Dataset> {
if (this.group != null) {
builder.field("group", this.group.toString());
}
if (this.grant != null) {
builder.field("grant", this.grant.toString());
}
if (collaborators != null) {
builder.startArray("collaborators");
this.collaborators.forEach(x -> {
@ -300,7 +302,9 @@ public class Dataset implements ElasticEntity<Dataset> {
this.status = Short.valueOf((String) fields.get("status"));
this.dmp = UUID.fromString((String) fields.get("dmp"));
this.group = UUID.fromString((String) fields.get("group"));
if (fields.get("grant") != null) {
this.grant = UUID.fromString((String) fields.get("grant"));
}
if (fields.get("created") != null)
this.created = Date.from(Instant.parse((String) fields.get("created")));
if (fields.get("modified") != null)

View File

@ -1,14 +1,18 @@
package eu.eudat.elastic.entities;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.elasticsearch.common.xcontent.XContentBuilder;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.UUID;
public class DatasetTempalate implements ElasticEntity<DatasetTempalate> {
private UUID id;
private String name;
private Map<String, Object> data;
public UUID getId() {
return id;
@ -26,11 +30,25 @@ public class DatasetTempalate implements ElasticEntity<DatasetTempalate> {
this.name = name;
}
public Map<String, Object> getData() {
return data;
}
public void setData(Map<String, Object> data) {
this.data = data;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
builder.field("id", this.id.toString());
builder.field("name", this.name);
if(this.data != null) {
builder.field("data", new ObjectMapper().writeValueAsString(this.data));
}
else{
builder.field("data", "");
}
builder.endObject();
return builder;
}
@ -39,6 +57,12 @@ public class DatasetTempalate implements ElasticEntity<DatasetTempalate> {
public DatasetTempalate fromElasticEntity(Map<String, Object> fields) {
this.id = UUID.fromString((String) fields.get("id"));
this.name = (String) fields.get("name");
try {
this.data = new ObjectMapper().readValue((String) fields.get("data"), new TypeReference<Map<String, Object>>() {});
}
catch (Exception e){
this.data = new HashMap<>();
}
return this;
}
}

View File

@ -323,7 +323,9 @@ public class Dmp implements ElasticEntity<Dmp> {
if (fields.get(MapKey.DATASETS.getName()) != null) {
this.datasets = ((List<HashMap<String, Object>>) fields.get(MapKey.DATASETS.getName())).stream().map(map -> new Dataset().fromElasticEntity(map)).collect(Collectors.toList());
}
if (fields.containsKey(MapKey.GRANT.getName()) && fields.get(MapKey.GRANT.getName()) != null) {
this.grant = UUID.fromString((String) fields.get(MapKey.GRANT.getName()));
}
if (fields.get(MapKey.GRANTSTATUS.getName()) != null) {
this.grantStatus = Short.valueOf(fields.get(MapKey.GRANTSTATUS.getName()).toString());
}

View File

@ -146,7 +146,7 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
}
NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery("datasets", boolQuery, ScoreMode.Avg).innerHit(new InnerHitBuilder().setFetchSourceContext(new FetchSourceContext(true, new String[]{"datasets.tags"}, null)));
NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery("datasets", boolQuery, ScoreMode.Avg).innerHit(new InnerHitBuilder().setFetchSourceContext(new FetchSourceContext(true, new String[]{"datasets.tags"}, null)).setSize(this.environment.getProperty("elasticsearch.innerHitsSize", Integer.class)));
searchSourceBuilder.query(nestedQueryBuilder)/*.from(criteria.getOffset())*/.fetchSource("datasets.tags", null);
/*if (criteria.getSize() > 0) {
searchSourceBuilder.size(criteria.getSize());
@ -206,7 +206,7 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
}
NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery("datasets", boolQuery, ScoreMode.None).innerHit(new InnerHitBuilder().setFetchSourceContext(new FetchSourceContext(true, new String[]{"datasets.id"}, null)));
NestedQueryBuilder nestedQueryBuilder = QueryBuilders.nestedQuery("datasets", boolQuery, ScoreMode.None).innerHit(new InnerHitBuilder().setFetchSourceContext(new FetchSourceContext(true, new String[]{"datasets.id"}, null)).setSize(this.environment.getProperty("elasticsearch.innerHitsSize", Integer.class)));
searchSourceBuilder.query(nestedQueryBuilder)/*.from(criteria.getOffset()).size(criteria.getSize())*/.fetchSource("datasets.id", null);
sortBuilders.forEach(searchSourceBuilder::sort);
searchRequest.source(searchSourceBuilder);
@ -261,6 +261,7 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
}
if (criteria.getDatasetTemplates() != null && criteria.getDatasetTemplates().size() > 0) {
criteria.setDatasetTemplates(criteria.getDatasetTemplates().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.template", criteria.getDatasetTemplates().stream().map(UUID::toString).collect(Collectors.toList())));
}
@ -269,14 +270,17 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
}
if (criteria.getDmps() != null && criteria.getDmps().size() > 0) {
criteria.setDmps(criteria.getDmps().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.dmp", criteria.getDmps().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGroupIds() != null && criteria.getGroupIds().size() > 0) {
criteria.setGroupIds(criteria.getGroupIds().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.group", criteria.getGroupIds().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGrants() != null && criteria.getGrants().size() > 0) {
criteria.setGrants(criteria.getGrants().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.grant", criteria.getGrants().stream().map(UUID::toString).collect(Collectors.toList())));
}
@ -285,6 +289,7 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
}
if (criteria.getCollaborators() != null && criteria.getCollaborators().size() > 0) {
criteria.setCollaborators(criteria.getCollaborators().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.collaborators.id.keyword", criteria.getCollaborators().stream().map(UUID::toString).collect(Collectors.toList())));
}
@ -295,10 +300,12 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
}
if (criteria.getOrganiztions() != null && criteria.getOrganiztions().size() > 0) {
criteria.setOrganiztions(criteria.getOrganiztions().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.organizations.id", criteria.getOrganiztions()));
}
if (criteria.getTags() != null && criteria.getTags().size() > 0) {
criteria.setTags(criteria.getTags().stream().filter(Objects::nonNull).collect(Collectors.toList()));
boolQuery = boolQuery.should(QueryBuilders.termsQuery("datasets.tags.name", criteria.getTags().stream().map(Tag::getName).collect(Collectors.toList())));
}

View File

@ -34,7 +34,7 @@
<dependency>
<groupId>gr.cite.opendmp</groupId>
<artifactId>repositorydepositbase</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
@ -46,6 +46,10 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-mail</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-webflux</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/com.googlecode.json-simple/json-simple -->
<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->

View File

@ -22,22 +22,15 @@ public class AboutController {
private Environment environment;
private MaterialManager materialManager;
private final MetricsManager metricsManager;
@Autowired
public AboutController(Environment environment, MaterialManager materialManager, MetricsManager metricsManager) {
this.environment = environment;
this.materialManager = materialManager;
this.metricsManager = metricsManager;
}
@RequestMapping(path = "{lang}", method = RequestMethod.GET )
public ResponseEntity<byte[]> getAbout(@PathVariable(name = "lang") String lang) throws IOException {
// long files = 0;
// try (Stream<Path> paths = Files.list(Paths.get(Objects.requireNonNull(this.environment.getProperty("about.path"))))) {
// files = paths.count();
// }
// metricsManager.calculateValue(MetricNames.LANGUAGES, (int) files, null);
try (Stream<Path> paths = Files.walk(Paths.get(Objects.requireNonNull(this.environment.getProperty("about.path"))))) {
return this.materialManager.getResponseEntity(lang, paths);
}

View File

@ -1,5 +1,6 @@
package eu.eudat.controllers;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.UserDatasetProfile;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
@ -16,7 +17,6 @@ import eu.eudat.models.data.admin.composite.DatasetProfile;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.listingmodels.UserInfoListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.types.ApiMessageCode;
@ -32,7 +32,6 @@ import javax.validation.Valid;
import java.io.IOException;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
import static eu.eudat.types.Authorities.ADMIN;
import static eu.eudat.types.Authorities.DATASET_PROFILE_MANAGER;
@ -58,41 +57,42 @@ public class Admin extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/addDmp"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<Object> addDmp(@Valid @RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN ,DATASET_PROFILE_MANAGER}) Principal principal) {
public ResponseEntity<Object> addDmp(@Valid @RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN ,DATASET_PROFILE_MANAGER}) Principal principal) throws Exception {
//this.getLoggerService().info(principal, "Admin Added Dataset Profile");
DatasetProfile shortenProfile = profile.toShort();
eu.eudat.data.entities.DatasetProfile modelDefinition = AdminManager.generateViewStyleDefinition(shortenProfile, getApiContext());
DescriptionTemplate modelDefinition = AdminManager.generateViewStyleDefinition(shortenProfile, getApiContext());
modelDefinition.setType(getApiContext().getOperationsContext().getDatabaseRepository().getDescriptionTemplateTypeDao().findFromName(profile.getType()));
modelDefinition.setGroupId(UUID.randomUUID());
modelDefinition.setVersion((short) 0);
eu.eudat.data.entities.DatasetProfile datasetProfile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
DescriptionTemplate descriptionTemplate = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
UserDatasetProfile userDatasetProfile = new UserDatasetProfile();
userDatasetProfile.setDatasetProfile(datasetProfile);
userDatasetProfile.setDatasetProfile(descriptionTemplate);
UserInfo userInfo = getApiContext().getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
userDatasetProfile.setUser(userInfo);
userDatasetProfile.setRole(0);
getApiContext().getOperationsContext().getDatabaseRepository().getUserDatasetProfileDao().createOrUpdate(userDatasetProfile);
datasetProfileManager.storeDatasetProfileUsers(datasetProfile, profile);
datasetProfileManager.storeDatasetProfileUsers(descriptionTemplate, profile);
metricsManager.increaseValue(MetricNames.DATASET_TEMPLATE, 1, MetricsManager.datasetTemplateStatus.get(datasetProfile.getStatus()) );
metricsManager.increaseValue(MetricNames.DATASET_TEMPLATE, 1, MetricsManager.datasetTemplateStatus.get(descriptionTemplate.getStatus()) );
return ResponseEntity.status(HttpStatus.OK).body(modelDefinition.getId());
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/addDmp/{id}"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<ResponseItem<UUID>> updateDmp(@PathVariable String id, @RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) {
public ResponseEntity<ResponseItem<UUID>> updateDmp(@PathVariable String id, @RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) throws Exception {
DatasetProfile shortenProfile = profile.toShort();
eu.eudat.data.entities.DatasetProfile modelDefinition = AdminManager.generateViewStyleDefinition(shortenProfile, getApiContext());
eu.eudat.data.entities.DatasetProfile datasetprofile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
DescriptionTemplate modelDefinition = AdminManager.generateViewStyleDefinition(shortenProfile, getApiContext());
DescriptionTemplate datasetprofile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
datasetprofile.setDefinition(modelDefinition.getDefinition());
Short oldStatus = datasetprofile.getStatus();
datasetprofile.setStatus(modelDefinition.getStatus());
datasetprofile.setLabel(modelDefinition.getLabel());
datasetprofile.setDescription(modelDefinition.getDescription());
datasetprofile.setLanguage(modelDefinition.getLanguage());
eu.eudat.data.entities.DatasetProfile datasetProfile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(datasetprofile);
datasetProfileManager.storeDatasetProfileUsers(datasetProfile, profile);
if (datasetProfile.getStatus() == 1 && oldStatus == 0) {
DescriptionTemplate descriptionTemplate = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(datasetprofile);
datasetProfileManager.storeDatasetProfileUsers(descriptionTemplate, profile);
if (descriptionTemplate.getStatus() == 1 && oldStatus == 0) {
metricsManager.increaseValue(MetricNames.DATASET_TEMPLATE, 1, MetricNames.ACTIVE);
}
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<UUID>().status(ApiMessageCode.NO_MESSAGE));
@ -102,7 +102,7 @@ public class Admin extends BaseController {
@RequestMapping(method = RequestMethod.POST, value = {"/newVersion/{id}"}, produces = "application/json")
public ResponseEntity newVersionDatasetProfile(@PathVariable String id, @RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) throws Exception {
try {
eu.eudat.data.entities.DatasetProfile modelDefinition = this.datasetProfileManager.createNewVersionDatasetProfile(id, profile);
DescriptionTemplate modelDefinition = this.datasetProfileManager.createNewVersionDatasetProfile(id, profile);
return ResponseEntity.status(HttpStatus.OK).body(modelDefinition.getId());
} catch (DatasetProfileNewVersionException exception) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<eu.eudat.models.data.admin.composite.DatasetProfile>().status(ApiMessageCode.ERROR_MESSAGE).message(exception.getMessage()));
@ -124,8 +124,8 @@ public class Admin extends BaseController {
}
@RequestMapping(method = RequestMethod.POST, value = {"/preview"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<ResponseItem<PagedDatasetProfile>> getPreview(@RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) {
eu.eudat.data.entities.DatasetProfile modelDefinition = AdminManager.generateViewStyleDefinition(profile, getApiContext());
public ResponseEntity<ResponseItem<PagedDatasetProfile>> getPreview(@RequestBody DatasetProfile profile, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) throws Exception {
DescriptionTemplate modelDefinition = AdminManager.generateViewStyleDefinition(profile, getApiContext());
eu.eudat.models.data.user.composite.DatasetProfile datasetProfile = userManager.generateDatasetProfileModel(modelDefinition);
PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
pagedDatasetProfile.buildPagedDatasetProfile(datasetProfile);
@ -145,7 +145,7 @@ public class Admin extends BaseController {
public @ResponseBody
ResponseEntity<ResponseItem<DatasetProfile>> inactivate(@PathVariable String id, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) {
try {
eu.eudat.data.entities.DatasetProfile ret = AdminManager.inactivate(this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao(), this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetDao(), id);
DescriptionTemplate ret = AdminManager.inactivate(this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao(), this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetDao(), id);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<eu.eudat.models.data.admin.composite.DatasetProfile>().status(ApiMessageCode.SUCCESS_MESSAGE));
} catch (DatasetProfileWithDatasetsExeption exception) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<eu.eudat.models.data.admin.composite.DatasetProfile>().status(ApiMessageCode.UNSUCCESS_DELETE).message(exception.getMessage()));
@ -156,11 +156,12 @@ public class Admin extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"/getXml/{id}"}, produces = "application/json")
public ResponseEntity getDatasetProfileXml(@PathVariable String id, @RequestHeader("Content-Type") String contentType, @ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) throws IllegalAccessException, IOException, InstantiationException {
if (contentType.equals("application/xml")) {
eu.eudat.data.entities.DatasetProfile profile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
DescriptionTemplate profile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
eu.eudat.models.data.user.composite.DatasetProfile datasetProfile = userManager.generateDatasetProfileModel(profile);
datasetProfile.setStatus(profile.getStatus());
datasetProfile.setDescription(profile.getDescription());
datasetProfile.setLanguage(profile.getLanguage());
datasetProfile.setType(profile.getType().getName());
return this.datasetProfileManager.getDocument(datasetProfile, profile.getLabel());
} else {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<eu.eudat.models.data.admin.composite.DatasetProfile>().status(ApiMessageCode.ERROR_MESSAGE).message("NOT AUTHORIZE"));
@ -173,12 +174,12 @@ public class Admin extends BaseController {
@ClaimedAuthorities(claims = {ADMIN, DATASET_PROFILE_MANAGER}) Principal principal) throws Exception {
eu.eudat.logic.utilities.documents.xml.datasetProfileXml.datasetProfileModel.DatasetProfile datasetProfileModel = this.datasetProfileManager.createDatasetProfileFromXml(file);
eu.eudat.models.data.admin.composite.DatasetProfile datasetProfileEntity = datasetProfileModel.toAdminCompositeModel(file.getOriginalFilename());
eu.eudat.data.entities.DatasetProfile modelDefinition;
DescriptionTemplate modelDefinition;
if (id == null) {
modelDefinition = AdminManager.generateViewStyleDefinition(datasetProfileEntity, getApiContext());
eu.eudat.data.entities.DatasetProfile datasetProfile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
DescriptionTemplate descriptionTemplate = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
UserDatasetProfile userDatasetProfile = new UserDatasetProfile();
userDatasetProfile.setDatasetProfile(datasetProfile);
userDatasetProfile.setDatasetProfile(descriptionTemplate);
UserInfo userInfo = getApiContext().getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
userDatasetProfile.setUser(userInfo);
userDatasetProfile.setRole(0);
@ -186,7 +187,7 @@ public class Admin extends BaseController {
} else {
modelDefinition = datasetProfileManager.createNewVersionDatasetProfile(id, datasetProfileEntity);
}
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<eu.eudat.data.entities.DatasetProfile>>()
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<DescriptionTemplate>>()
.status(ApiMessageCode.SUCCESS_MESSAGE).message(""));
}

View File

@ -2,7 +2,10 @@ package eu.eudat.controllers;
import eu.eudat.data.dao.criteria.RequestItem;
import eu.eudat.data.entities.DMPProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.query.items.dmpblueprint.DataManagementPlanBlueprintTableRequest;
import eu.eudat.data.query.items.table.dmpprofile.DataManagementPlanProfileTableRequest;
import eu.eudat.exceptions.dmpblueprint.DmpBlueprintUsedException;
import eu.eudat.logic.managers.DataManagementProfileManager;
import eu.eudat.logic.security.claims.ClaimedAuthorities;
import eu.eudat.logic.services.ApiContext;
@ -10,6 +13,7 @@ import eu.eudat.models.data.helpermodels.Tuple;
import eu.eudat.models.data.helpers.common.AutoCompleteLookupItem;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.listingmodels.DataManagementPlanBlueprintListingModel;
import eu.eudat.models.data.listingmodels.DataManagementPlanProfileListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
@ -26,6 +30,7 @@ import java.io.IOException;
import java.util.List;
import static eu.eudat.types.Authorities.ADMIN;
import static eu.eudat.types.Authorities.DATASET_PROFILE_MANAGER;
/**
* Created by ikalyvas on 3/21/2018.
@ -51,6 +56,14 @@ public class DMPProfileController extends BaseController {
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DMPProfile>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created"));
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/blueprint"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DMPProfile>> createOrUpdateBlueprint(@RequestBody DataManagementPlanBlueprintListingModel dataManagementPlan, @ClaimedAuthorities(claims = {ADMIN}) Principal principal) throws Exception {
this.dataManagementProfileManager.createOrUpdateBlueprint(dataManagementPlan, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DMPProfile>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created"));
}
@RequestMapping(method = RequestMethod.GET, value = {"/getSingle/{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataManagementPlanProfileListingModel>> getSingle(@PathVariable String id, Principal principal) throws IllegalAccessException, InstantiationException {
@ -58,6 +71,13 @@ public class DMPProfileController extends BaseController {
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataManagementPlanProfileListingModel>().status(ApiMessageCode.NO_MESSAGE).payload(dataManagementPlanProfileListingModel));
}
@RequestMapping(method = RequestMethod.GET, value = {"/getSingleBlueprint/{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataManagementPlanBlueprintListingModel>> getSingleBlueprint(@PathVariable String id, Principal principal) {
DataManagementPlanBlueprintListingModel dataManagementPlanBlueprintListingModel = this.dataManagementProfileManager.getSingleBlueprint(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataManagementPlanBlueprintListingModel>().status(ApiMessageCode.NO_MESSAGE).payload(dataManagementPlanBlueprintListingModel));
}
@RequestMapping(method = RequestMethod.POST, value = {"/getPaged"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataTableData<DataManagementPlanProfileListingModel>>> getPaged(@Valid @RequestBody DataManagementPlanProfileTableRequest dataManagementPlanProfileTableRequest, Principal principal) throws Exception {
@ -65,24 +85,51 @@ public class DMPProfileController extends BaseController {
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataTableData<DataManagementPlanProfileListingModel>>().status(ApiMessageCode.NO_MESSAGE).payload(dataTable));
}
@RequestMapping(method = RequestMethod.POST, value = {"/getPagedBlueprint"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataTableData<DataManagementPlanBlueprintListingModel>>> getPagedBlueprint(@Valid @RequestBody DataManagementPlanBlueprintTableRequest dataManagementPlanBlueprintTableRequest, Principal principal) throws Exception {
DataTableData<DataManagementPlanBlueprintListingModel> dataTable = this.dataManagementProfileManager.getPagedBlueprint(dataManagementPlanBlueprintTableRequest, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataTableData<DataManagementPlanBlueprintListingModel>>().status(ApiMessageCode.NO_MESSAGE).payload(dataTable));
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/clone/{id}"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<ResponseItem<DataManagementPlanBlueprintListingModel>> clone(@PathVariable String id, @ClaimedAuthorities(claims = {ADMIN}) Principal principal) {
DataManagementPlanBlueprintListingModel dmpBlueprint = this.dataManagementProfileManager.getSingleBlueprint(id, principal);
dmpBlueprint.setLabel(dmpBlueprint.getLabel() + " new ");
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataManagementPlanBlueprintListingModel>().payload(dmpBlueprint));
}
@Transactional
@RequestMapping(method = RequestMethod.DELETE, value = {"{id}"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<Void>> inactivate(@PathVariable String id, @ClaimedAuthorities(claims = {ADMIN}) Principal principal) {
try {
this.dataManagementProfileManager.inactivate(id);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Void>().status(ApiMessageCode.SUCCESS_MESSAGE));
} catch (DmpBlueprintUsedException exception) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<Void>().status(ApiMessageCode.UNSUCCESS_DELETE).message(exception.getMessage()));
}
}
@RequestMapping(method = RequestMethod.GET, value = {"/getXml/{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity getXml( @RequestHeader("Content-Type") String contentType, @PathVariable String id, Principal principal) throws IllegalAccessException, InstantiationException, IOException {
ResponseEntity getXml( @RequestHeader("Content-Type") String contentType, @PathVariable String id, Principal principal) throws IOException {
if (contentType.equals("application/xml")) {
DataManagementPlanProfileListingModel dataManagementPlanProfileListingModel = this.dataManagementProfileManager.getSingle(id, principal);
return this.dataManagementProfileManager.getDocument(dataManagementPlanProfileListingModel,dataManagementPlanProfileListingModel.getLabel());
DataManagementPlanBlueprintListingModel dataManagementPlanBlueprintListingModel = this.dataManagementProfileManager.getSingleBlueprint(id, principal);
return this.dataManagementProfileManager.getDocument(dataManagementPlanBlueprintListingModel);
}else {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<DataManagementPlanProfileListingModel>().status(ApiMessageCode.ERROR_MESSAGE).message("NOT AUTHORIZE"));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<DataManagementPlanBlueprintListingModel>().status(ApiMessageCode.ERROR_MESSAGE).message("NOT AUTHORIZE"));
}
}
@RequestMapping(method = RequestMethod.POST, value = {"/upload"})
public ResponseEntity<Object> setDatasetProfileXml(@RequestParam("file") MultipartFile file,
@ClaimedAuthorities(claims = {ADMIN}) Principal principal) throws IllegalAccessException,IOException,Exception{
eu.eudat.logic.utilities.documents.xml.dmpXml.dmpProfileModel.DmpProfile dmpProfileModel = this.dataManagementProfileManager.createDmpProfileFromXml(file);
DataManagementPlanProfileListingModel dataManagementPlan = dmpProfileModel.toDmpProfileCompositeModel(file.getOriginalFilename());
this.dataManagementProfileManager.createOrUpdate(dataManagementPlan, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<eu.eudat.data.entities.DatasetProfile>>()
@ClaimedAuthorities(claims = {ADMIN}) Principal principal) throws Exception {
eu.eudat.logic.utilities.documents.xml.dmpXml.dmpBlueprintModel.DmpBlueprint dmpBlueprintModel = this.dataManagementProfileManager.createDmpProfileFromXml(file);
DataManagementPlanBlueprintListingModel dmpBlueprint = dmpBlueprintModel.toDmpProfileCompositeModel(file.getOriginalFilename());
this.dataManagementProfileManager.createOrUpdateBlueprint(dmpBlueprint, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<DescriptionTemplate>>()
.status(ApiMessageCode.SUCCESS_MESSAGE).message(""));
}

View File

@ -260,7 +260,7 @@ public class DMPs extends BaseController {
@RequestMapping(method = RequestMethod.POST, value = {"/clone/{id}"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<UUID>> clone(@PathVariable UUID id, @RequestBody eu.eudat.models.data.dmp.DataManagementPlanNewVersionModel dataManagementPlan, Principal principal) throws Exception {
UUID cloneId = this.dataManagementPlanManager.clone(dataManagementPlan, principal);
UUID cloneId = this.dataManagementPlanManager.clone(id, dataManagementPlan, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<UUID>().status(ApiMessageCode.SUCCESS_MESSAGE).payload(cloneId));
}

View File

@ -1,6 +1,7 @@
package eu.eudat.controllers;
import eu.eudat.data.dao.criteria.RequestItem;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.logic.managers.AdminManager;
import eu.eudat.logic.managers.DatasetProfileManager;
import eu.eudat.logic.security.claims.ClaimedAuthorities;
@ -8,6 +9,7 @@ import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.components.commons.datafield.AutoCompleteData;
import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
import eu.eudat.models.data.helpers.common.AutoCompleteLookupItem;
import eu.eudat.models.data.helpers.common.AutoCompleteOptionsLookupItem;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.properties.PropertiesModel;
import eu.eudat.models.data.security.Principal;
@ -55,7 +57,7 @@ public class DatasetProfileController extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/datasetprofile/clone/{id}"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<ResponseItem<eu.eudat.models.data.admin.composite.DatasetProfile>> clone(@PathVariable String id, @ClaimedAuthorities(claims = {ADMIN})Principal principal) {
eu.eudat.data.entities.DatasetProfile profile = this.datasetProfileManager.clone(id);
DescriptionTemplate profile = this.datasetProfileManager.clone(id);
eu.eudat.models.data.admin.composite.DatasetProfile datasetprofile = AdminManager.generateDatasetProfileModel(profile);
datasetprofile.setLabel(profile.getLabel() + " new ");
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<eu.eudat.models.data.admin.composite.DatasetProfile>().payload(datasetprofile));
@ -63,11 +65,19 @@ public class DatasetProfileController extends BaseController {
@RequestMapping(method = RequestMethod.POST, value = {"/search/autocomplete"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<Object> getDataForAutocomplete(@RequestBody RequestItem<AutoCompleteLookupItem> lookupItem) throws XPathExpressionException {
eu.eudat.data.entities.DatasetProfile datasetProfile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(lookupItem.getCriteria().getProfileID()));
eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Field modelfield = this.datasetProfileManager.queryForField(datasetProfile.getDefinition(), lookupItem.getCriteria().getFieldID());
DescriptionTemplate descriptionTemplate = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(lookupItem.getCriteria().getProfileID()));
eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Field modelfield = this.datasetProfileManager.queryForField(descriptionTemplate.getDefinition(), lookupItem.getCriteria().getFieldID());
AutoCompleteData data = (AutoCompleteData) modelfield.getData();
List<ExternalAutocompleteFieldModel> items = this.datasetProfileManager.getAutocomplete(data, lookupItem.getCriteria().getLike());
return ResponseEntity.status(HttpStatus.OK).body(items);
}
@RequestMapping(method = RequestMethod.POST, value = {"/search/autocompleteOptions"}, consumes = "application/json", produces = "application/json")
public ResponseEntity<Object> getDataForAutocompleteOptions(@RequestBody RequestItem<AutoCompleteOptionsLookupItem> lookupItem) {
AutoCompleteData data = new AutoCompleteData();
data.setAutoCompleteSingleDataList(lookupItem.getCriteria().getAutoCompleteSingleDataList());
List<ExternalAutocompleteFieldModel> items = this.datasetProfileManager.getAutocomplete(data, lookupItem.getCriteria().getLike());
return ResponseEntity.status(HttpStatus.OK).body(items);
}
}

View File

@ -6,6 +6,7 @@ import eu.eudat.logic.managers.DatasetProfileManager;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.datasetprofile.DatasetProfileAutocompleteItem;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.datasetprofile.DatasetProfileWithPrefillingPropertyModel;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.types.ApiMessageCode;
import org.springframework.beans.factory.annotation.Autowired;
@ -42,5 +43,12 @@ public class DatasetProfiles extends BaseController {
List<DatasetProfileListingModel> datasetProfileTableData = this.datasetProfileManager.getAll(tableRequestItem);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<DatasetProfileListingModel>>().status(ApiMessageCode.NO_MESSAGE).payload(datasetProfileTableData));
}
@RequestMapping(method = RequestMethod.POST, value = {"/datasetprofiles/getAllWithPrefilling"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<List<DatasetProfileWithPrefillingPropertyModel>>> getAllWithPrefilling(@RequestBody DatasetProfileTableRequestItem tableRequestItem) {
List<DatasetProfileWithPrefillingPropertyModel> datasetProfileTableData = this.datasetProfileManager.getAllWithPrefilling(tableRequestItem);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<DatasetProfileWithPrefillingPropertyModel>>().status(ApiMessageCode.NO_MESSAGE).payload(datasetProfileTableData));
}
}

View File

@ -1,6 +1,7 @@
package eu.eudat.controllers;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.query.items.item.dataset.DatasetWizardAutocompleteRequest;
import eu.eudat.data.query.items.item.datasetprofile.DatasetProfileWizardAutocompleteRequest;
import eu.eudat.data.query.items.table.dataset.DatasetPublicTableRequest;
@ -202,7 +203,7 @@ public class Datasets extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"/get/{id}"}, produces = "application/json")
public ResponseEntity<ResponseItem<PagedDatasetProfile>> getSingle(@PathVariable String id) {
eu.eudat.data.entities.DatasetProfile profile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
DescriptionTemplate profile = this.getApiContext().getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
eu.eudat.models.data.user.composite.DatasetProfile datasetprofile = userManager.generateDatasetProfileModel(profile);
PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
pagedDatasetProfile.buildPagedDatasetProfile(datasetprofile);
@ -256,6 +257,7 @@ public class Datasets extends BaseController {
public @ResponseBody
ResponseEntity<ResponseItem<DatasetWizardModel>> createOrUpdate(@RequestBody DatasetWizardModel profile, Principal principal) throws Exception {
DatasetWizardModel dataset = new DatasetWizardModel().fromDataModel(this.datasetManager.createOrUpdate(profile, principal));
dataset.setTags(profile.getTags());
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DatasetWizardModel>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created").payload(dataset));
}

View File

@ -0,0 +1,94 @@
package eu.eudat.controllers;
import eu.eudat.exceptions.descriptiontemplate.DescriptionTemplatesWithTypeException;
import eu.eudat.logic.managers.DescriptionTemplateTypeManager;
import eu.eudat.logic.security.claims.ClaimedAuthorities;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.descriptiontemplatetype.DescriptionTemplateTypeModel;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
import eu.eudat.types.Authorities;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import javax.transaction.Transactional;
import java.util.UUID;
import static eu.eudat.types.Authorities.ADMIN;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/descriptionTemplateType/"})
public class DescriptionTemplateTypeController extends BaseController {
private DescriptionTemplateTypeManager descriptionTemplateTypeManager;
@Autowired
public DescriptionTemplateTypeController(ApiContext apiContext, DescriptionTemplateTypeManager descriptionTemplateTypeManager){
super(apiContext);
this.descriptionTemplateTypeManager = descriptionTemplateTypeManager;
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"create"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DescriptionTemplateTypeModel>> create(@RequestBody DescriptionTemplateTypeModel type, @ClaimedAuthorities(claims = {ADMIN}) Principal principal) throws Exception {
try {
this.descriptionTemplateTypeManager.create(type);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created"));
}
catch(DescriptionTemplatesWithTypeException e){
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.ERROR_MESSAGE).message(e.getMessage()));
}
}
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"update"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DescriptionTemplateTypeModel>> update(@RequestBody DescriptionTemplateTypeModel type, @ClaimedAuthorities(claims = {ADMIN}) Principal principal) throws Exception {
try {
this.descriptionTemplateTypeManager.update(type);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Updated"));
}
catch(DescriptionTemplatesWithTypeException e){
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.ERROR_MESSAGE).message(e.getMessage()));
}
}
@RequestMapping(method = RequestMethod.GET, value = {"get"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataTableData<DescriptionTemplateTypeModel>>> get(@ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) throws Exception {
DataTableData<DescriptionTemplateTypeModel> dataTable = this.descriptionTemplateTypeManager.get();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataTableData<DescriptionTemplateTypeModel>>().status(ApiMessageCode.NO_MESSAGE).payload(dataTable));
}
@RequestMapping(method = RequestMethod.GET, value = {"get/{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DescriptionTemplateTypeModel>> getSingle(@PathVariable(value = "id") UUID id, @ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) throws Exception {
try {
DescriptionTemplateTypeModel typeModel = this.descriptionTemplateTypeManager.getSingle(id);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.NO_MESSAGE).payload(typeModel));
}
catch(DescriptionTemplatesWithTypeException e){
return ResponseEntity.status(HttpStatus.NOT_FOUND).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.ERROR_MESSAGE).message(e.getMessage()));
}
}
@Transactional
@RequestMapping(method = RequestMethod.DELETE, value = {"/delete/{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DescriptionTemplateTypeModel>> delete(@PathVariable(value = "id") UUID id, @ClaimedAuthorities(claims = {ADMIN}) Principal principal) throws Exception {
try{
this.descriptionTemplateTypeManager.delete(id);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Deleted"));
}
catch(DescriptionTemplatesWithTypeException e){
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<DescriptionTemplateTypeModel>().status(ApiMessageCode.UNSUCCESS_DELETE).message(e.getMessage()));
}
}
}

View File

@ -32,16 +32,16 @@ public class EmailMergeConfirmation {
@Transactional
@RequestMapping(method = RequestMethod.GET, value = {"/{emailToken}"})
public @ResponseBody
ResponseEntity<ResponseItem> emailConfirmation(@PathVariable(value = "emailToken") String token) {
ResponseEntity<ResponseItem<String>> emailConfirmation(@PathVariable(value = "emailToken") String token) {
try {
this.emailConfirmationManager.confirmEmail(token);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem().status(ApiMessageCode.SUCCESS_MESSAGE));
String emailToBeMerged = this.emailConfirmationManager.confirmEmail(token);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().payload(emailToBeMerged).status(ApiMessageCode.SUCCESS_MESSAGE));
} catch
(HasConfirmedEmailException | TokenExpiredException ex) {
if (ex instanceof TokenExpiredException) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.NO_MESSAGE));
} else {
return ResponseEntity.status(HttpStatus.FOUND).body(new ResponseItem().status(ApiMessageCode.WARN_MESSAGE));
return ResponseEntity.status(HttpStatus.FOUND).body(new ResponseItem<String>().status(ApiMessageCode.WARN_MESSAGE));
}
}
}

View File

@ -21,22 +21,15 @@ public class FaqController {
private Environment environment;
private MaterialManager materialManager;
private final MetricsManager metricsManager;
@Autowired
public FaqController(Environment environment, MaterialManager materialManager, MetricsManager metricsManager) {
this.environment = environment;
this.materialManager = materialManager;
this.metricsManager = metricsManager;
}
@RequestMapping(path = "{lang}", method = RequestMethod.GET )
public ResponseEntity<byte[]> getFaq(@PathVariable(name = "lang") String lang) throws IOException {
// long files = 0;
// try (Stream<Path> paths = Files.list(Paths.get(Objects.requireNonNull(this.environment.getProperty("faq.path"))))) {
// files = paths.count();
// }
// metricsManager.calculateValue(MetricNames.LANGUAGES, (int) files, null);
try (Stream<Path> paths = Files.walk(Paths.get(Objects.requireNonNull(this.environment.getProperty("faq.path"))))) {
return this.materialManager.getResponseEntity(lang, paths);
}

View File

@ -21,22 +21,15 @@ public class GlossaryController {
private Environment environment;
private MaterialManager materialManager;
private final MetricsManager metricsManager;
@Autowired
public GlossaryController(Environment environment, MaterialManager materialManager, MetricsManager metricsManager) {
this.environment = environment;
this.materialManager = materialManager;
this.metricsManager = metricsManager;
}
@RequestMapping(path = "{lang}", method = RequestMethod.GET )
public ResponseEntity<byte[]> getGlossary(@PathVariable(name = "lang") String lang) throws IOException {
// long files = 0;
// try (Stream<Path> paths = Files.list(Paths.get(Objects.requireNonNull(this.environment.getProperty("glossary.path"))))) {
// files = paths.count();
// }
// metricsManager.calculateValue(MetricNames.LANGUAGES, (int) files, null);
try (Stream<Path> paths = Files.walk(Paths.get(Objects.requireNonNull(this.environment.getProperty("glossary.path"))))) {
return this.materialManager.getResponseEntity(lang, paths);
}

View File

@ -11,6 +11,7 @@ import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import java.util.List;
import java.util.Map;
import java.util.UUID;
@RestController
@ -26,8 +27,8 @@ public class Prefillings {
}
@RequestMapping(method = RequestMethod.GET, value = {"/prefilling/list"}, produces = "application/json")
public ResponseEntity<ResponseItem<List<Prefilling>>> getPrefillingList(@RequestParam String like, @RequestParam String configId) {
List<Prefilling> prefillingList = prefillingManager.getPrefillings(like, configId);
public ResponseEntity<ResponseItem<List<Prefilling>>> getPrefillingList(@RequestParam String like) {
List<Prefilling> prefillingList = prefillingManager.getPrefillings(like);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Prefilling>>().payload(prefillingList).status(ApiMessageCode.NO_MESSAGE));
}
@ -36,4 +37,10 @@ public class Prefillings {
DatasetWizardModel datasetWizardModel = prefillingManager.getPrefilledDataset(id, configId, profileId);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DatasetWizardModel>().payload(datasetWizardModel).status(ApiMessageCode.NO_MESSAGE));
}
@RequestMapping(method = RequestMethod.POST, value = {"/prefilling/generateUsingData"}, produces = "application/json")
public ResponseEntity<ResponseItem<DatasetWizardModel>> getPrefillingDataset(@RequestBody Map<String, Object> data, @RequestParam String configId, @RequestParam UUID profileId) throws Exception {
DatasetWizardModel datasetWizardModel = prefillingManager.getPrefilledDatasetUsingData(data, configId, profileId);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DatasetWizardModel>().payload(datasetWizardModel).status(ApiMessageCode.NO_MESSAGE));
}
}

View File

@ -1,8 +1,7 @@
package eu.eudat.controllers;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.Funder;
import eu.eudat.data.entities.Project;
import eu.eudat.logic.managers.DatasetManager;
@ -23,7 +22,6 @@ import org.springframework.web.bind.annotation.*;
import javax.transaction.Transactional;
import javax.validation.Valid;
import java.util.UUID;
@RestController
@CrossOrigin
@ -48,9 +46,9 @@ public class QuickWizardController extends BaseController {
Funder funderEntity;
//Create Funder
if (quickWizard.getFunder() == null) {
throw new Exception("Funder is a mandatory entity");
funderEntity = null;
} else if (quickWizard.getFunder().getExistFunder() == null && quickWizard.getFunder().getLabel() == null) {
throw new Exception("Funder is a mandatory entity");
funderEntity = null;
} else if (quickWizard.getFunder().getExistFunder() == null && quickWizard.getFunder().getLabel() != null) {
funderEntity = this.quickWizardManager.createOrUpdate(quickWizard.getFunder().toDataFunder(), principal);
} else {
@ -60,9 +58,9 @@ public class QuickWizardController extends BaseController {
eu.eudat.data.entities.Grant grantEntity;
//Create Grant
if (quickWizard.getGrant() == null) {
throw new Exception("Grant is a mandatory entity");
grantEntity = null;
} else if (quickWizard.getGrant().getExistGrant() == null && quickWizard.getGrant().getLabel() == null) {
throw new Exception("Grant is a mandatory entity");
grantEntity = null;
} else if (quickWizard.getGrant().getExistGrant() == null) {
grantEntity = this.quickWizardManager.createOrUpdate(quickWizard.getGrant().toDataGrant(), principal);
} else {
@ -88,7 +86,7 @@ public class QuickWizardController extends BaseController {
quickWizard.getDmp().setId(dmpEntity.getId());
for (DatasetDescriptionQuickWizardModel dataset : quickWizard.getDatasets().getDatasetsList()) {
DataManagementPlan dmp = quickWizard.getDmp().toDataDmp(grantEntity, projectEntity, principal);
DatasetProfile profile = quickWizard.getDmp().getDatasetProfile();
DescriptionTemplate profile = quickWizard.getDmp().getDatasetProfile();
DatasetWizardModel datasetWizardModel = dataset.toDataModel(dmp, profile);
this.datasetManager.createOrUpdate(datasetWizardModel, principal);
}
@ -100,7 +98,7 @@ public class QuickWizardController extends BaseController {
public @ResponseBody
ResponseEntity<ResponseItem<DatasetCreateWizardModel>> addDatasetWizard(@RequestBody DatasetCreateWizardModel datasetCreateWizardModel, Principal principal) throws Exception{
for(DatasetDescriptionQuickWizardModel dataset : datasetCreateWizardModel.getDatasets().getDatasetsList()){
DatasetProfile profile = new DatasetProfile();
DescriptionTemplate profile = new DescriptionTemplate();
profile.setId(datasetCreateWizardModel.getDmpMeta().getDatasetProfile().getId());
profile.setLabel(datasetCreateWizardModel.getDmpMeta().getDatasetProfile().getLabel());
this.datasetManager.createOrUpdate(dataset.toDataModel(datasetCreateWizardModel.getDmpMeta().getDmp(), profile), principal);

View File

@ -5,6 +5,7 @@ import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.sam
import eu.eudat.logic.security.validators.configurableProvider.Saml2SSOUtils;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.saml2.AuthnRequestModel;
import eu.eudat.types.ApiMessageCode;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
@ -56,14 +57,14 @@ public class Saml2MetadataController extends BaseController {
}
@RequestMapping(method = RequestMethod.GET, value = {"authnRequest/{configurableProviderId}"})
public @ResponseBody
ResponseEntity<ResponseItem<String>> getAuthnRequest(@PathVariable String configurableProviderId) {
ResponseEntity getAuthnRequest(@PathVariable String configurableProviderId) {
Saml2ConfigurableProvider saml2ConfigurableProvider = (Saml2ConfigurableProvider) this.configLoader.getConfigurableProviders().getProviders().stream()
.filter(prov -> prov.getConfigurableLoginId().equals(configurableProviderId))
.findFirst().orElse(null);
if (saml2ConfigurableProvider != null) {
try {
String authnRequestXml = Saml2SSOUtils.getAuthnRequest(saml2ConfigurableProvider);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created").payload(authnRequestXml));
AuthnRequestModel authnRequest = Saml2SSOUtils.getAuthnRequest(saml2ConfigurableProvider);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<AuthnRequestModel>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created").payload(authnRequest));
}
catch (Exception e) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create authentication request."));

View File

@ -21,22 +21,15 @@ public class TermsOfServiceController {
private Environment environment;
private MaterialManager materialManager;
private final MetricsManager metricsManager;
@Autowired
public TermsOfServiceController(Environment environment, MaterialManager materialManager, MetricsManager metricsManager) {
this.environment = environment;
this.materialManager = materialManager;
this.metricsManager = metricsManager;
}
@RequestMapping(path = "{lang}", method = RequestMethod.GET )
public ResponseEntity<byte[]> getTermsOfService(@PathVariable(name = "lang") String lang) throws IOException {
// long files = 0;
// try (Stream<Path> paths = Files.list(Paths.get(Objects.requireNonNull(this.environment.getProperty("termsofservice.path"))))) {
// files = paths.count();
// }
// metricsManager.calculateValue(MetricNames.LANGUAGES, (int) files, null);
try (Stream<Path> paths = Files.walk(Paths.get(Objects.requireNonNull(this.environment.getProperty("termsofservice.path"))))) {
return this.materialManager.getResponseEntity(lang, paths);
}

View File

@ -34,22 +34,15 @@ public class UserGuideController {
private Environment environment;
private MaterialManager materialManager;
private final MetricsManager metricsManager;
@Autowired
public UserGuideController(Environment environment, MaterialManager materialManager, MetricsManager metricsManager) {
this.environment = environment;
this.materialManager = materialManager;
this.metricsManager = metricsManager;
}
@RequestMapping(path = "{lang}", method = RequestMethod.GET )
public ResponseEntity<byte[]> getUserGuide(@PathVariable(name = "lang") String lang) throws IOException {
long files = 0;
try (Stream<Path> paths = Files.list(Paths.get(Objects.requireNonNull(this.environment.getProperty("userguide.path"))))) {
files = paths.count();
}
metricsManager.calculateValue(MetricNames.LANGUAGES, (int) files, null);
try (Stream<Path> paths = Files.walk(Paths.get(Objects.requireNonNull(this.environment.getProperty("userguide.path"))))) {
return this.materialManager.getResponseEntity(lang, paths);
}

View File

@ -3,6 +3,7 @@ package eu.eudat.criteria;
public class RecentActivityCriteria {
private String like;
private String order;
private Integer status;
public String getLike() {
return like;
@ -19,4 +20,12 @@ public class RecentActivityCriteria {
public void setOrder(String order) {
this.order = order;
}
public Integer getStatus() {
return status;
}
public void setStatus(Integer status) {
this.status = status;
}
}

View File

@ -0,0 +1,9 @@
package eu.eudat.exceptions.descriptiontemplate;
public class DescriptionTemplatesWithTypeException extends RuntimeException {
public DescriptionTemplatesWithTypeException(String message) {
super(message);
}
}

View File

@ -0,0 +1,18 @@
package eu.eudat.exceptions.dmpblueprint;
public class DmpBlueprintUsedException extends RuntimeException {
public DmpBlueprintUsedException() {
}
public DmpBlueprintUsedException(String message) {
super(message);
}
public DmpBlueprintUsedException(String message, Throwable cause) {
super(message, cause);
}
public DmpBlueprintUsedException(Throwable cause) {
super(cause);
}
}

View File

@ -1,8 +1,9 @@
package eu.eudat.logic.builders.entity;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.DescriptionTemplateType;
import eu.eudat.logic.builders.Builder;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.DatasetProfile;
import java.util.Date;
import java.util.Set;
@ -11,12 +12,14 @@ import java.util.UUID;
/**
* Created by ikalyvas on 2/15/2018.
*/
public class DatasetProfileBuilder extends Builder<DatasetProfile> {
public class DatasetProfileBuilder extends Builder<DescriptionTemplate> {
private UUID id;
private String label;
private DescriptionTemplateType type;
private Set<Dataset> dataset;
private String definition;
@ -41,6 +44,11 @@ public class DatasetProfileBuilder extends Builder<DatasetProfile> {
return this;
}
public DatasetProfileBuilder type(DescriptionTemplateType type) {
this.type = type;
return this;
}
public DatasetProfileBuilder dataset(Set<Dataset> dataset) {
this.dataset = dataset;
return this;
@ -77,17 +85,18 @@ public class DatasetProfileBuilder extends Builder<DatasetProfile> {
}
@Override
public DatasetProfile build() {
DatasetProfile datasetProfile = new DatasetProfile();
datasetProfile.setCreated(created);
datasetProfile.setStatus(status);
datasetProfile.setId(id);
datasetProfile.setDataset(dataset);
datasetProfile.setDefinition(definition);
datasetProfile.setDescription(description);
datasetProfile.setModified(modified);
datasetProfile.setLabel(label);
datasetProfile.setLanguage(language);
return datasetProfile;
public DescriptionTemplate build() {
DescriptionTemplate descriptionTemplate = new DescriptionTemplate();
descriptionTemplate.setCreated(created);
descriptionTemplate.setStatus(status);
descriptionTemplate.setId(id);
descriptionTemplate.setDataset(dataset);
descriptionTemplate.setDefinition(definition);
descriptionTemplate.setDescription(description);
descriptionTemplate.setModified(modified);
descriptionTemplate.setLabel(label);
descriptionTemplate.setLanguage(language);
descriptionTemplate.setType(type);
return descriptionTemplate;
}
}

View File

@ -2,6 +2,8 @@ package eu.eudat.logic.managers;
import eu.eudat.data.dao.entities.DatasetDao;
import eu.eudat.data.dao.entities.DatasetProfileDao;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.DescriptionTemplateType;
import eu.eudat.exceptions.datasetprofile.DatasetProfileWithDatasetsExeption;
import eu.eudat.logic.builders.entity.DatasetProfileBuilder;
import eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.ViewStyleModel;
@ -17,8 +19,9 @@ import java.util.UUID;
public class AdminManager {
public static eu.eudat.data.entities.DatasetProfile generateViewStyleDefinition(DatasetProfile profile, ApiContext apiContext) {
public static DescriptionTemplate generateViewStyleDefinition(DatasetProfile profile, ApiContext apiContext) throws Exception {
ViewStyleModel viewStyleModel = new ViewStyleModel();
viewStyleModel.setEnablePrefilling(profile.isEnablePrefilling());
viewStyleModel.setSections(new ModelBuilder().toViewStyleDefinition(profile.getSections(), eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Section.class));
viewStyleModel.setPages(new ModelBuilder().toViewStyleDefinition(profile.getPages(), eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Page.class));
Document viewStyleDoc = XmlBuilder.getDocument();
@ -34,22 +37,31 @@ public class AdminManager {
profile.setLanguage("en");
}
eu.eudat.data.entities.DatasetProfile datasetProfile = apiContext.getOperationsContext().getBuilderFactory().getBuilder(DatasetProfileBuilder.class).definition(xml).label(profile.getLabel())
DescriptionTemplateType type;
try {
type = apiContext.getOperationsContext().getDatabaseRepository().getDescriptionTemplateTypeDao().findFromName(profile.getType());
}
catch (Exception e) {
throw new Exception("Description template type '" + profile.getType() + "' could not be found.");
}
DescriptionTemplate descriptionTemplate = apiContext.getOperationsContext().getBuilderFactory().getBuilder(DatasetProfileBuilder.class).definition(xml).label(profile.getLabel())
.status(profile.getStatus()).created(new Date()).description(profile.getDescription()).language(profile.getLanguage())
.type(type)
.build();
if (datasetProfile.getGroupId() == null) {
datasetProfile.setGroupId(UUID.randomUUID());
if (descriptionTemplate.getGroupId() == null) {
descriptionTemplate.setGroupId(UUID.randomUUID());
}
if (datasetProfile.getVersion() == null) {
datasetProfile.setVersion((short)1);
if (descriptionTemplate.getVersion() == null) {
descriptionTemplate.setVersion((short)1);
}
return datasetProfile;
return descriptionTemplate;
}
public static eu.eudat.models.data.admin.composite.DatasetProfile generateDatasetProfileModel(eu.eudat.data.entities.DatasetProfile profile) {
public static eu.eudat.models.data.admin.composite.DatasetProfile generateDatasetProfileModel(DescriptionTemplate profile) {
Document viewStyleDoc = XmlBuilder.fromXml(profile.getDefinition());
Element root = viewStyleDoc.getDocumentElement();
eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.ViewStyleModel viewstyle = new eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.ViewStyleModel().fromXml(root);
@ -60,12 +72,12 @@ public class AdminManager {
}
public static eu.eudat.data.entities.DatasetProfile inactivate(DatasetProfileDao datasetProfileRepository, DatasetDao datasetDao, String id) {
public static DescriptionTemplate inactivate(DatasetProfileDao datasetProfileRepository, DatasetDao datasetDao, String id) {
eu.eudat.data.dao.criteria.DatasetCriteria datasetsForThatDatasetProfile = new eu.eudat.data.dao.criteria.DatasetCriteria();
datasetsForThatDatasetProfile.setProfileDatasetId(UUID.fromString(id));
if (datasetDao.getWithCriteria(datasetsForThatDatasetProfile).count() == 0) {
eu.eudat.data.entities.DatasetProfile detasetProfile = datasetProfileRepository.find(UUID.fromString(id));
detasetProfile.setStatus(eu.eudat.data.entities.DatasetProfile.Status.DELETED.getValue());
DescriptionTemplate detasetProfile = datasetProfileRepository.find(UUID.fromString(id));
detasetProfile.setStatus(DescriptionTemplate.Status.DELETED.getValue());
detasetProfile = datasetProfileRepository.createOrUpdate(detasetProfile);
return detasetProfile;
} else {

View File

@ -91,8 +91,10 @@ public class DashBoardManager {
for (DMP dmp : dmps) {
numberOfDatasets = numberOfDatasets + dmp.getDataset().stream()
.filter(item -> item.getStatus() == Dataset.Status.FINALISED.getValue()).count();
if (dmp.getGrant() != null) {
grants.add(dmp.getGrant());
}
}
statistics.setTotalDataManagementPlanCount((long) dmps.size());
statistics.setTotalDataSetCount(numberOfDatasets);
@ -221,11 +223,17 @@ public class DashBoardManager {
}
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setLike(tableRequest.getCriteria().getLike());
if(tableRequest.getCriteria().getStatus() != null) {
datasetCriteria.setStatus(tableRequest.getCriteria().getStatus());
}
datasetCriteria.setAllVersions(false);
datasetCriteria.setIsPublic(!isAuthenticated);
DataManagementPlanCriteria dataManagementPlanCriteria = new DataManagementPlanCriteria();
dataManagementPlanCriteria.setAllVersions(false);
dataManagementPlanCriteria.setLike(tableRequest.getCriteria().getLike());
if(tableRequest.getCriteria().getStatus() != null) {
dataManagementPlanCriteria.setStatus(tableRequest.getCriteria().getStatus());
}
dataManagementPlanCriteria.setIsPublic(!isAuthenticated);
dataManagementPlanCriteria.setOnlyPublic(!isAuthenticated);

View File

@ -2,21 +2,29 @@ package eu.eudat.logic.managers;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.eudat.data.dao.criteria.DataManagementPlanCriteria;
import eu.eudat.data.dao.criteria.RequestItem;
import eu.eudat.data.dao.entities.DMPProfileDao;
import eu.eudat.data.dao.entities.DatasetDao;
import eu.eudat.data.dao.entities.DatasetProfileDao;
import eu.eudat.data.entities.DMPProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.query.items.dmpblueprint.DataManagementPlanBlueprintTableRequest;
import eu.eudat.data.query.items.item.dmpprofile.DataManagementPlanProfileCriteriaRequest;
import eu.eudat.data.query.items.table.dmpprofile.DataManagementPlanProfileTableRequest;
import eu.eudat.exceptions.datasetprofile.DatasetProfileWithDatasetsExeption;
import eu.eudat.exceptions.dmpblueprint.DmpBlueprintUsedException;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.logic.utilities.builders.XmlBuilder;
import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
import eu.eudat.logic.utilities.documents.xml.dmpXml.ExportXmlBuilderDmpProfile;
import eu.eudat.logic.utilities.documents.xml.dmpXml.ImportXmlBuilderDmpProfile;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DmpProfileExternalAutoComplete;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.Field;
import eu.eudat.logic.utilities.documents.xml.dmpXml.ExportXmlBuilderDmpBlueprint;
import eu.eudat.logic.utilities.documents.xml.dmpXml.ImportXmlBuilderDmpBlueprint;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.*;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.types.FieldCategory;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.types.SystemFieldType;
import eu.eudat.models.data.helpermodels.Tuple;
import eu.eudat.models.data.helpers.common.AutoCompleteLookupItem;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.listingmodels.DataManagementPlanBlueprintListingModel;
import eu.eudat.models.data.listingmodels.DataManagementPlanProfileListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.queryable.QueryableList;
@ -78,6 +86,20 @@ public class DataManagementProfileManager {
return dataTable;
}
public DataTableData<DataManagementPlanBlueprintListingModel> getPagedBlueprint(DataManagementPlanBlueprintTableRequest dataManagementPlanBlueprintTableRequest, Principal principal) throws Exception {
QueryableList<DMPProfile> items = apiContext.getOperationsContext().getDatabaseRepository().getDmpProfileDao().getWithCriteriaBlueprint(dataManagementPlanBlueprintTableRequest.getCriteria());
QueryableList<DMPProfile> pagedItems = PaginationManager.applyPaging(items, dataManagementPlanBlueprintTableRequest);
DataTableData<DataManagementPlanBlueprintListingModel> dataTable = new DataTableData<>();
CompletableFuture itemsFuture = pagedItems
.selectAsync(item -> new DataManagementPlanBlueprintListingModel().fromDataModel(item)).whenComplete((resultList, throwable) -> dataTable.setData(resultList));
CompletableFuture countFuture = items.countAsync().whenComplete((count, throwable) -> dataTable.setTotalCount(count));
CompletableFuture.allOf(itemsFuture, countFuture).join();
return dataTable;
}
public DataManagementPlanProfileListingModel getSingle(String id, Principal principal) throws InstantiationException, IllegalAccessException {
DMPProfile dmpProfile = databaseRepository.getDmpProfileDao().find(UUID.fromString(id));
DataManagementPlanProfileListingModel dataManagementPlanProfileListingModel = new DataManagementPlanProfileListingModel();
@ -85,6 +107,45 @@ public class DataManagementProfileManager {
return dataManagementPlanProfileListingModel;
}
public DataManagementPlanBlueprintListingModel getSingleBlueprint(String id, Principal principal) {
DMPProfile dmpProfile = databaseRepository.getDmpProfileDao().find(UUID.fromString(id));
DataManagementPlanBlueprintListingModel dataManagementPlanBlueprintListingModel = new DataManagementPlanBlueprintListingModel();
dataManagementPlanBlueprintListingModel.fromDataModel(dmpProfile);
return dataManagementPlanBlueprintListingModel;
}
public boolean fieldInBlueprint(String id, SystemFieldType type, Principal principal) {
DMPProfile dmpProfile = databaseRepository.getDmpProfileDao().find(UUID.fromString(id));
return this.fieldInBlueprint(dmpProfile, type, principal);
}
public boolean fieldInBlueprint(DMPProfile dmpProfile, SystemFieldType type, Principal principal) {
DataManagementPlanBlueprintListingModel dmpBlueprint = new DataManagementPlanBlueprintListingModel();
dmpBlueprint.fromDataModel(dmpProfile);
for(Section section: dmpBlueprint.getDefinition().getSections()){
for(FieldModel field: section.getFields()){
if(field.getCategory().equals(FieldCategory.SYSTEM)){
SystemField systemField = field.toSystemField();
if(systemField.getType().equals(type)){
return true;
}
}
}
}
return false;
}
public List<Integer> sectionIndexesForDescriptionTemplate(DMPProfile dmpProfile, UUID descriptionTemplateId) {
DataManagementPlanBlueprintListingModel dmpBlueprint = new DataManagementPlanBlueprintListingModel();
dmpBlueprint.fromDataModel(dmpProfile);
List<Integer> sectionIndexes = new ArrayList<>();
for(int i = 0; i < dmpBlueprint.getDefinition().getSections().size(); i++) {
Section section = dmpBlueprint.getDefinition().getSections().get(i);
if(section.getHasTemplates() && section.getDescriptionTemplates().stream().anyMatch(x -> x.getDescriptionTemplateId().equals(descriptionTemplateId))) sectionIndexes.add(i);
}
return sectionIndexes;
}
public List<DataManagementPlanProfileListingModel> getWithCriteria(DataManagementPlanProfileCriteriaRequest dataManagementPlanProfileCriteriaRequest) throws IllegalAccessException, InstantiationException {
QueryableList<DMPProfile> items = databaseRepository.getDmpProfileDao().getWithCriteria(dataManagementPlanProfileCriteriaRequest.getCriteria());
List<DataManagementPlanProfileListingModel> datamanagementPlans = items.select(item -> new DataManagementPlanProfileListingModel().fromDataModel(item));
@ -96,8 +157,25 @@ public class DataManagementProfileManager {
apiContext.getOperationsContext().getDatabaseRepository().getDmpProfileDao().createOrUpdate(dmpProfile);
}
public ResponseEntity<byte[]> getDocument(DataManagementPlanProfileListingModel dmpProfile, String label) throws IllegalAccessException, IOException, InstantiationException {
FileEnvelope envelope = getXmlDocument(dmpProfile, label);
public void createOrUpdateBlueprint(DataManagementPlanBlueprintListingModel dataManagementPlanBlueprintListingModel, Principal principal) throws Exception {
DMPProfile dmpProfile = dataManagementPlanBlueprintListingModel.toDataModel();
apiContext.getOperationsContext().getDatabaseRepository().getDmpProfileDao().createOrUpdate(dmpProfile);
}
public void inactivate(String id) {
DMPProfile dmpProfile = databaseRepository.getDmpProfileDao().find(UUID.fromString(id));
DataManagementPlanCriteria dataManagementPlanCriteria = new DataManagementPlanCriteria();
dataManagementPlanCriteria.setProfile(dmpProfile);
if (dmpProfile.getStatus() == DMPProfile.Status.SAVED.getValue() || databaseRepository.getDmpDao().getWithCriteria(dataManagementPlanCriteria).count() == 0) {
dmpProfile.setStatus(DMPProfile.Status.DELETED.getValue());
databaseRepository.getDmpProfileDao().createOrUpdate(dmpProfile);
} else {
throw new DmpBlueprintUsedException("This blueprint can not deleted, because DMPs are associated with it");
}
}
public ResponseEntity<byte[]> getDocument(DataManagementPlanBlueprintListingModel dmpProfile) throws IOException {
FileEnvelope envelope = getXmlDocument(dmpProfile);
InputStream resource = new FileInputStream(envelope.getFile());
logger.info("Mime Type of " + envelope.getFilename() + " is " +
new MimetypesFileTypeMap().getContentType(envelope.getFile()));
@ -116,18 +194,18 @@ public class DataManagementProfileManager {
HttpStatus.OK);
}
public FileEnvelope getXmlDocument(DataManagementPlanProfileListingModel dmpProfile, String label) throws InstantiationException, IllegalAccessException, IOException {
ExportXmlBuilderDmpProfile xmlBuilder = new ExportXmlBuilderDmpProfile();
public FileEnvelope getXmlDocument(DataManagementPlanBlueprintListingModel dmpProfile) throws IOException {
ExportXmlBuilderDmpBlueprint xmlBuilder = new ExportXmlBuilderDmpBlueprint();
File file = xmlBuilder.build(dmpProfile, environment);
FileEnvelope fileEnvelope = new FileEnvelope();
fileEnvelope.setFile(file);
fileEnvelope.setFilename(label);
fileEnvelope.setFilename(dmpProfile.getLabel());
return fileEnvelope;
}
public eu.eudat.logic.utilities.documents.xml.dmpXml.dmpProfileModel.DmpProfile createDmpProfileFromXml(MultipartFile multiPartFile) {
ImportXmlBuilderDmpProfile xmlBuilder = new ImportXmlBuilderDmpProfile();
public eu.eudat.logic.utilities.documents.xml.dmpXml.dmpBlueprintModel.DmpBlueprint createDmpProfileFromXml(MultipartFile multiPartFile) {
ImportXmlBuilderDmpBlueprint xmlBuilder = new ImportXmlBuilderDmpBlueprint();
try {
return xmlBuilder.build(convert(multiPartFile));
} catch (IOException e) {

View File

@ -289,6 +289,45 @@ public class DatasetManager {
.stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
.collect(Collectors.toList()).size() == 0 && !datasetEntity.getDmp().isPublic())
throw new UnauthorisedException();
dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
dataset.fromDataModel(datasetEntity);
// Creates the Criteria to get all version of DescriptionTemplate in question.
DatasetProfileCriteria profileCriteria = new DatasetProfileCriteria();
UUID profileId = datasetEntity.getProfile().getGroupId();
List<UUID> uuidList = new LinkedList<>();
uuidList.add(profileId);
profileCriteria.setGroupIds(uuidList);
profileCriteria.setAllVersions(true);
List<DescriptionTemplate> profileVersions = databaseRepository.getDatasetProfileDao().getWithCriteria(profileCriteria)
.orderBy(((builder, root) -> builder.desc(root.get("version"))))
.toList();
List<DescriptionTemplate> profileVersionsIncluded = new LinkedList<>();
// Iterate through the versions and remove those that are not included in the DMP of the dataset in question.
for (DescriptionTemplate version : profileVersions) {
for (AssociatedProfile p : dataset.getDmp().getProfiles()) {
if (version.getId().toString().equals(p.getDescriptionTemplateId().toString())) {
profileVersionsIncluded.add(version);
}
}
}
// Sort the list with the included Versions.
Stream<DescriptionTemplate> sorted = profileVersionsIncluded.stream().sorted(Comparator.comparing(DescriptionTemplate::getVersion).reversed());
// Make the Stream into List and get the first item.
List<DescriptionTemplate> profiles = sorted.collect(Collectors.toList());
if (profiles.isEmpty())
throw new NoSuchElementException("No profiles found for the specific Dataset");
DescriptionTemplate profile = profiles.get(0);
// Check if the dataset is on the latest Version.
boolean latestVersion = profile.getVersion().toString().equals(datasetEntity.getProfile().getVersion().toString());
dataset.setIsProfileLatestVersion(latestVersion);
eu.eudat.elastic.entities.Dataset datasetElastic;
try {
datasetElastic = datasetRepository.exists() ?
@ -297,45 +336,6 @@ public class DatasetManager {
logger.warn(ex.getMessage());
datasetElastic = null;
}
dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
dataset.fromDataModel(datasetEntity);
// Creates the Criteria to get all version of DatasetProfile in question.
DatasetProfileCriteria profileCriteria = new DatasetProfileCriteria();
UUID profileId = datasetEntity.getProfile().getGroupId();
List<UUID> uuidList = new LinkedList<>();
uuidList.add(profileId);
profileCriteria.setGroupIds(uuidList);
profileCriteria.setAllVersions(true);
List<eu.eudat.data.entities.DatasetProfile> profileVersions = databaseRepository.getDatasetProfileDao().getWithCriteria(profileCriteria)
.orderBy(((builder, root) -> builder.desc(root.get("version"))))
.toList();
List<DatasetProfile> profileVersionsIncluded = new LinkedList<>();
// Iterate through the versions and remove those that are not included in the DMP of the dataset in question.
for (DatasetProfile version : profileVersions) {
for (AssociatedProfile p : dataset.getDmp().getProfiles()) {
if (version.getId().toString().equals(p.getId().toString())) {
profileVersionsIncluded.add(version);
}
}
}
// Sort the list with the included Versions.
Stream<DatasetProfile> sorted = profileVersionsIncluded.stream().sorted(Comparator.comparing(DatasetProfile::getVersion).reversed());
// Make the Stream into List and get the first item.
List<DatasetProfile> profiles = sorted.collect(Collectors.toList());
if (profiles.isEmpty())
throw new NoSuchElementException("No profiles found for the specific Dataset");
DatasetProfile profile = profiles.get(0);
// Check if the dataset is on the latest Version.
boolean latestVersion = profile.getVersion().toString().equals(datasetEntity.getProfile().getVersion().toString());
dataset.setIsProfileLatestVersion(latestVersion);
if (datasetElastic != null && datasetElastic.getTags() != null && !datasetElastic.getTags().isEmpty()) {
dataset.setTags(datasetElastic.getTags());
}
@ -397,7 +397,7 @@ public class DatasetManager {
}
private XWPFDocument getWordDocument(ConfigLoader configLoader, eu.eudat.data.entities.Dataset datasetEntity, VisibilityRuleService visibilityRuleService, Principal principal) throws IOException {
WordBuilder wordBuilder = new WordBuilder(this.environment);
WordBuilder wordBuilder = new WordBuilder(this.environment, configLoader);
DatasetWizardModel dataset = new DatasetWizardModel();
XWPFDocument document = configLoader.getDatasetDocument();
@ -509,7 +509,7 @@ public class DatasetManager {
}
private XWPFDocument getLightWordDocument(ConfigLoader configLoader, DatasetWizardModel dataset, VisibilityRuleService visibilityRuleService) throws IOException {
WordBuilder wordBuilder = new WordBuilder(this.environment);
WordBuilder wordBuilder = new WordBuilder(this.environment, configLoader);
XWPFDocument document = configLoader.getDocument();
// Space below Dataset title.
@ -717,7 +717,7 @@ public class DatasetManager {
public String checkDatasetValidation(Dataset dataset) throws Exception {
List<String> datasetProfileValidators = new LinkedList<>();
DatasetProfile profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(dataset.getProfile().getId());
DescriptionTemplate profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(dataset.getProfile().getId());
DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = builderFactory.newDocumentBuilder();
Document xmlDocument = builder.parse(new ByteArrayInputStream(profile.getDefinition().getBytes()));
@ -975,9 +975,9 @@ public class DatasetManager {
// Checks if XML datasetProfileId GroupId matches the one selected.
try {
eu.eudat.data.entities.DatasetProfile importDatasetProfile = databaseRepository.getDatasetProfileDao().find(UUID.fromString(importModel.getDatasetProfileId()));
eu.eudat.data.entities.DatasetProfile latestVersionDatasetProfile = databaseRepository.getDatasetProfileDao().find(UUID.fromString(datasetProfileId));
if (latestVersionDatasetProfile.getGroupId() != importDatasetProfile.getGroupId()) {
DescriptionTemplate importDescriptionTemplate = databaseRepository.getDatasetProfileDao().find(UUID.fromString(importModel.getDatasetProfileId()));
DescriptionTemplate latestVersionDescriptionTemplate = databaseRepository.getDatasetProfileDao().find(UUID.fromString(datasetProfileId));
if (latestVersionDescriptionTemplate.getGroupId() != importDescriptionTemplate.getGroupId()) {
throw new Exception();
}
} catch (Exception e) {
@ -1010,7 +1010,7 @@ public class DatasetManager {
entity.setStatus((short) 0);
entity.setCreated(new Date());
entity.setModified(new Date());
DatasetProfile profile = new DatasetProfile();
DescriptionTemplate profile = new DescriptionTemplate();
profile.setId(UUID.fromString(datasetProfileId));
entity.setProfile(profile);
@ -1034,18 +1034,10 @@ public class DatasetManager {
public DatasetWizardModel datasetUpdateProfile(String id) {
DatasetWizardModel dataset = new DatasetWizardModel();
eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
eu.eudat.elastic.entities.Dataset datasetElastic;
try {
datasetElastic = datasetRepository.exists() ?
datasetRepository.findDocument(id) : new eu.eudat.elastic.entities.Dataset();
} catch (Exception ex) {
logger.warn(ex.getMessage());
datasetElastic = null;
}
dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
dataset.fromDataModel(datasetEntity);
// Creates the Criteria to get all version of DatasetProfile in question.
// Creates the Criteria to get all version of DescriptionTemplate in question.
DatasetProfileCriteria profileCriteria = new DatasetProfileCriteria();
UUID profileId = datasetEntity.getProfile().getGroupId();
List<UUID> uuidList = new LinkedList<>();
@ -1053,7 +1045,7 @@ public class DatasetManager {
profileCriteria.setGroupIds(uuidList);
// Gets the latest version of the datasetProfile.
eu.eudat.data.entities.DatasetProfile item = databaseRepository.getDatasetProfileDao().getWithCriteria(profileCriteria).getSingle();
DescriptionTemplate item = databaseRepository.getDatasetProfileDao().getWithCriteria(profileCriteria).getSingle();
// Sets the latest version of dataet Profile to the Dataset in question.
dataset.setDatasetProfileDefinition(getLatestDatasetProfile(datasetEntity, item));
@ -1062,6 +1054,14 @@ public class DatasetManager {
// Now at latest version.
dataset.setIsProfileLatestVersion(true);
eu.eudat.elastic.entities.Dataset datasetElastic;
try {
datasetElastic = datasetRepository.exists() ?
datasetRepository.findDocument(id) : new eu.eudat.elastic.entities.Dataset();
} catch (Exception ex) {
logger.warn(ex.getMessage());
datasetElastic = null;
}
if (datasetElastic != null && datasetElastic.getTags() != null && !datasetElastic.getTags().isEmpty()) {
dataset.setTags(datasetElastic.getTags());
}
@ -1071,7 +1071,7 @@ public class DatasetManager {
return dataset;
}
public PagedDatasetProfile getLatestDatasetProfile(Dataset datasetEntity, DatasetProfile profile) {
public PagedDatasetProfile getLatestDatasetProfile(Dataset datasetEntity, DescriptionTemplate profile) {
eu.eudat.models.data.user.composite.DatasetProfile datasetprofile = userManager.generateDatasetProfileModel(profile);
datasetprofile.setStatus(datasetEntity.getStatus());
if (datasetEntity.getProperties() != null) {
@ -1088,7 +1088,7 @@ public class DatasetManager {
datasetProfileTableRequestItem.getCriteria().setFilter(DatasetProfileCriteria.DatasetProfileFilter.Datasets.getValue());
datasetProfileTableRequestItem.getCriteria().setUserId(principal.getId());
QueryableList<DatasetProfile> items = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(datasetProfileTableRequestItem.getCriteria());
QueryableList<DescriptionTemplate> items = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(datasetProfileTableRequestItem.getCriteria());
List<DatasetProfileListingModel> listingModels = items.select(item -> new DatasetProfileListingModel().fromDataModel(item));
DataTableData<DatasetProfileListingModel> data = new DataTableData<>();
@ -1143,7 +1143,8 @@ public class DatasetManager {
if (!tagNodes.isEmpty()) {
tagNodes.forEach(node -> {
JsonNode value = node.get("value");
if (!value.toString().equals("\"\"") && !value.toString().equals("null") && value.toString().startsWith("[")) {
if (!value.toString().equals("\"\"") && !value.toString().equals("null")) {
if (value.toString().startsWith("[")) {
String stringValue = value.toString().replaceAll("=", ":");
JSONArray values = new JSONArray(stringValue);
values.iterator().forEachRemaining(element -> {
@ -1157,6 +1158,7 @@ public class DatasetManager {
this.addTag(tags, wizardModel.getTags(), tag.getId(), tag.getName());
});
}
}
});
}
}
@ -1181,10 +1183,10 @@ public class DatasetManager {
DatasetListingModel listingModel = new DatasetListingModel().fromDataModel(item);
/*DatasetProfileCriteria criteria = new DatasetProfileCriteria();
criteria.setGroupIds(Collections.singletonList(item.getProfile().getGroupId()));
List<DatasetProfile> profiles = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(criteria).toList();
List<DescriptionTemplate> profiles = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(criteria).toList();
boolean islast = false;
if (!profiles.isEmpty()) {
profiles = profiles.stream().sorted(Comparator.comparing(DatasetProfile::getVersion)).collect(Collectors.toList());
profiles = profiles.stream().sorted(Comparator.comparing(DescriptionTemplate::getVersion)).collect(Collectors.toList());
islast = profiles.get(0).getId().equals(item.getProfile().getId());
}
listingModel.setProfileLatestVersion(islast);*/

View File

@ -1,26 +1,28 @@
package eu.eudat.logic.managers;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.eudat.data.dao.criteria.DatasetProfileCriteria;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.UserDatasetProfile;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.query.items.item.datasetprofile.DatasetProfileAutocompleteRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.exceptions.datasetprofile.DatasetProfileNewVersionException;
import eu.eudat.logic.builders.model.models.DataTableDataBuilder;
import eu.eudat.logic.proxy.config.Semantic;
import eu.eudat.logic.proxy.config.*;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.proxy.config.entities.GeneralUrls;
import eu.eudat.logic.proxy.fetching.RemoteFetcher;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.logic.utilities.builders.XmlBuilder;
import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
import eu.eudat.logic.utilities.documents.xml.datasetProfileXml.ExportXmlBuilderDatasetProfile;
import eu.eudat.logic.utilities.documents.xml.datasetProfileXml.ImportXmlBuilderDatasetProfile;
import eu.eudat.models.data.admin.composite.DatasetProfile;
import eu.eudat.models.data.components.commons.datafield.AutoCompleteData;
import eu.eudat.models.data.datasetprofile.DatasetProfileAutocompleteItem;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.datasetprofile.DatasetProfileWithPrefillingPropertyModel;
import eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Field;
import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
import eu.eudat.models.data.helpers.common.DataTableData;
@ -34,10 +36,11 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.*;
import org.springframework.http.client.SimpleClientHttpRequestFactory;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Component;
import org.springframework.web.client.RestTemplate;
import org.springframework.web.multipart.MultipartFile;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -54,6 +57,8 @@ import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.xpath.*;
import java.io.*;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.util.*;
import java.util.stream.Collectors;
@ -64,29 +69,30 @@ public class DatasetProfileManager {
private static final Logger logger = LoggerFactory.getLogger(DatasetProfileManager.class);
private static final List<String> cache = new ArrayList<>();
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
private Environment environment;
private ConfigLoader configLoader;
private final ApiContext apiContext;
private final DatabaseRepository databaseRepository;
private final Environment environment;
private final ConfigLoader configLoader;
private final MetricsManager metricsManager;
private final RemoteFetcher remoteFetcher;
@Autowired
public DatasetProfileManager(ApiContext apiContext, Environment environment, ConfigLoader configLoader, MetricsManager metricsManager) {
public DatasetProfileManager(ApiContext apiContext, Environment environment, ConfigLoader configLoader, MetricsManager metricsManager, RemoteFetcher remoteFetcher) {
this.apiContext = apiContext;
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.environment = environment;
this.configLoader = configLoader;
this.metricsManager = metricsManager;
this.remoteFetcher = remoteFetcher;
}
@Transactional
public eu.eudat.models.data.admin.composite.DatasetProfile getDatasetProfile(String id) {
eu.eudat.data.entities.DatasetProfile profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
DescriptionTemplate profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
eu.eudat.models.data.admin.composite.DatasetProfile datasetprofile = AdminManager.generateDatasetProfileModel(profile);
datasetprofile.setLabel(profile.getLabel());
datasetprofile.setStatus(profile.getStatus());
datasetprofile.setDescription(profile.getDescription());
datasetprofile.setType(profile.getType().getName());
datasetprofile.setLanguage(profile.getLanguage());
datasetprofile.setUsers(new ArrayList<>());
retrieveUsers(profile, datasetprofile);
@ -94,40 +100,55 @@ public class DatasetProfileManager {
}
public List<DatasetProfileAutocompleteItem> getWithCriteria(DatasetProfileAutocompleteRequest datasetProfileAutocompleteRequest) throws IllegalAccessException, InstantiationException {
QueryableList<DatasetProfile> items = databaseRepository.getDatasetProfileDao().getWithCriteria(datasetProfileAutocompleteRequest.getCriteria());
QueryableList<DatasetProfile> pagedItems = datasetProfileAutocompleteRequest.applyPaging(items);
QueryableList<DescriptionTemplate> items = databaseRepository.getDatasetProfileDao().getWithCriteria(datasetProfileAutocompleteRequest.getCriteria());
QueryableList<DescriptionTemplate> pagedItems = datasetProfileAutocompleteRequest.applyPaging(items);
List<DatasetProfileAutocompleteItem> datasetProfiles = pagedItems.select(item -> new DatasetProfileAutocompleteItem().fromDataModel(item));
return datasetProfiles;
}
public DatasetProfile clone(String id) {
DatasetProfile profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
public DescriptionTemplate clone(String id) {
DescriptionTemplate profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
apiContext.getOperationsContext().getDatabaseRepository().detachEntity(profile);
profile.setId(null);
return profile;
}
public DataTableData<DatasetProfileListingModel> getPaged(DatasetProfileTableRequestItem datasetProfileTableRequestItem, Principal principal) throws Exception {
QueryableList<DatasetProfile> items = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(datasetProfileTableRequestItem.getCriteria());
QueryableList<DatasetProfile> authItems = null;
QueryableList<DescriptionTemplate> items = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(datasetProfileTableRequestItem.getCriteria());
QueryableList<DescriptionTemplate> authItems = null;
if (principal.getAuthz().contains(Authorities.ADMIN)) {
authItems = items;
} else if (principal.getAuthz().contains(Authorities.DATASET_PROFILE_MANAGER)) {
List<Integer> roles = Arrays.asList(0, 1);
authItems = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getAuthenticated(items, principal.getId(), roles);
}
QueryableList<DatasetProfile> pagedItems = PaginationManager.applyPaging(authItems, datasetProfileTableRequestItem);
QueryableList<DescriptionTemplate> pagedItems = PaginationManager.applyPaging(authItems, datasetProfileTableRequestItem);
List<DatasetProfileListingModel> datasetProfiles = pagedItems.select(item -> new DatasetProfileListingModel().fromDataModel(item));
return apiContext.getOperationsContext().getBuilderFactory().getBuilder(DataTableDataBuilder.class).data(datasetProfiles).totalCount(items.count()).build();
}
public List<DatasetProfileListingModel> getAll(DatasetProfileTableRequestItem tableRequestItem) throws IllegalAccessException, InstantiationException {
QueryableList<DatasetProfile> items = databaseRepository.getDatasetProfileDao().getWithCriteria(tableRequestItem.getCriteria());
QueryableList<DescriptionTemplate> items = databaseRepository.getDatasetProfileDao().getWithCriteria(tableRequestItem.getCriteria());
List<DatasetProfileListingModel> datasetProfiles = items.select(item -> new DatasetProfileListingModel().fromDataModel(item));
return datasetProfiles;
}
public List<DatasetProfileWithPrefillingPropertyModel> getAllWithPrefilling(DatasetProfileTableRequestItem tableRequestItem) {
List<DatasetProfileWithPrefillingPropertyModel> datasetProfiles = new ArrayList<>();
if (!tableRequestItem.getCriteria().getIds().isEmpty()) {
tableRequestItem.getCriteria().getIds().forEach(id -> {
DatasetProfile datasetProfile = this.getDatasetProfile(id.toString());
DatasetProfileWithPrefillingPropertyModel profileModel = new DatasetProfileWithPrefillingPropertyModel();
profileModel.setId(id);
profileModel.setLabel(datasetProfile.getLabel());
profileModel.setEnablePrefilling(datasetProfile.isEnablePrefilling());
datasetProfiles.add(profileModel);
});
}
return datasetProfiles;
}
public eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Field queryForField(String xml, String fieldId) throws XPathExpressionException {
eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.Field field = new Field();
Document document = XmlBuilder.fromXml(xml);
@ -140,8 +161,8 @@ public class DatasetProfileManager {
return field;
}
public static List<ExternalAutocompleteFieldModel> getAutocomplete(AutoCompleteData data, String like) {
List<ExternalAutocompleteFieldModel> result = new LinkedList<>();
public List<ExternalAutocompleteFieldModel> getAutocomplete(AutoCompleteData data, String like) {
/*List<ExternalAutocompleteFieldModel> result = new LinkedList<>();
SimpleClientHttpRequestFactory simpleFactory = new SimpleClientHttpRequestFactory();
RestTemplate restTemplate = new RestTemplate(simpleFactory);
@ -204,8 +225,72 @@ public class DatasetProfileManager {
}
return result.stream().sorted(Comparator.comparing(ExternalAutocompleteFieldModel::getLabel)).collect(Collectors.toList());
//return result;
*/
List<ExternalAutocompleteFieldModel> result = new LinkedList<>();
ExternalUrlCriteria urlCriteria = new ExternalUrlCriteria();
GeneralUrls genericUrls = new GeneralUrls();
int ordinal = 1;
List<Map<String, String>> rawResults = new ArrayList<>();
genericUrls.setFetchMode(FetchStrategy.FIRST);
urlCriteria.setLike(like);
for (AutoCompleteData.AutoCompleteSingleData singleData : data.getAutoCompleteSingleDataList()) {
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.getAutoCompleteOptions().getSource();
source = source != null && !source.isEmpty() ? source : uri.getHost();
String uriString = singleData.getAutoCompleteOptions().getUri();
uriString = uriString != null && !uriString.isEmpty() ? 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.getAutoCompleteOptions().getValue());
fieldsUrlConfiguration.setName(singleData.getAutoCompleteOptions().getLabel());
fieldsUrlConfiguration.setSource(singleData.getAutoCompleteOptions().getSource().isEmpty()? null : singleData.getAutoCompleteOptions().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.remoteFetcher.getExternalGeneric(urlCriteria, genericUrls);
if (!singleResults.isEmpty() && !singleResults.get(0).containsKey("source") && !singleData.getAutoCompleteOptions().getSource().isEmpty()) {
singleResults.forEach(singleResult -> singleResult.put("source", singleData.getAutoCompleteOptions().getSource()));
}
rawResults.addAll(singleResults);
genericUrls.getUrls().clear();
} catch (URISyntaxException e) {
logger.error(e.getMessage(), e);
}
}
rawResults.forEach(item -> result.add(new ExternalAutocompleteFieldModel(parseItem(item.get("pid")), parseItem(item.get("name")), parseItem(item.get("source")), parseItem(item.get("uri")))));
return result;
}
private static String parseItem(Object item) {
@ -276,36 +361,36 @@ public class DatasetProfileManager {
return convFile;
}
public eu.eudat.data.entities.DatasetProfile createNewVersionDatasetProfile(String id, eu.eudat.models.data.admin.composite.DatasetProfile profile) throws Exception {
// Getting the DatasetProfile which we will create its new version.
eu.eudat.data.entities.DatasetProfile oldDatasetProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
public DescriptionTemplate createNewVersionDatasetProfile(String id, eu.eudat.models.data.admin.composite.DatasetProfile profile) throws Exception {
// Getting the DescriptionTemplate which we will create its new version.
DescriptionTemplate oldDescriptionTemplate = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(UUID.fromString(id));
// Getting the DatasetProfile with the latest Version.
// Getting the DescriptionTemplate with the latest Version.
DatasetProfileCriteria criteria = new DatasetProfileCriteria();
LinkedList<UUID> list = new LinkedList<>();
list.push(oldDatasetProfile.getGroupId());
list.push(oldDescriptionTemplate.getGroupId());
criteria.setGroupIds(list);
criteria.setAllVersions(false);
QueryableList<DatasetProfile> datasetProfileQueryableList = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(criteria);
eu.eudat.data.entities.DatasetProfile latestVersionDatasetProfile = datasetProfileQueryableList.getSingle();
QueryableList<DescriptionTemplate> datasetProfileQueryableList = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(criteria);
DescriptionTemplate latestVersionDescriptionTemplate = datasetProfileQueryableList.getSingle();
if (latestVersionDatasetProfile.getVersion().equals(oldDatasetProfile.getVersion())){
if (latestVersionDescriptionTemplate.getVersion().equals(oldDescriptionTemplate.getVersion())){
eu.eudat.models.data.admin.composite.DatasetProfile sortedProfile = profile.toShort();
eu.eudat.data.entities.DatasetProfile modelDefinition = AdminManager.generateViewStyleDefinition(sortedProfile, apiContext);
// modelDefinition.setLabel(oldDatasetProfile.getLabel());
modelDefinition.setVersion((short) (oldDatasetProfile.getVersion() + 1));
modelDefinition.setGroupId(oldDatasetProfile.getGroupId());
// modelDefinition.setLanguage(oldDatasetProfile.getLanguage());
DescriptionTemplate modelDefinition = AdminManager.generateViewStyleDefinition(sortedProfile, apiContext);
// modelDefinition.setLabel(oldDescriptionTemplate.getLabel());
modelDefinition.setVersion((short) (oldDescriptionTemplate.getVersion() + 1));
modelDefinition.setGroupId(oldDescriptionTemplate.getGroupId());
// modelDefinition.setLanguage(oldDescriptionTemplate.getLanguage());
apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
eu.eudat.data.entities.DatasetProfile datasetProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
this.storeDatasetProfileUsers(datasetProfile, profile);
DescriptionTemplate descriptionTemplate = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().createOrUpdate(modelDefinition);
this.storeDatasetProfileUsers(descriptionTemplate, profile);
return modelDefinition;
} else {
throw new DatasetProfileNewVersionException("Version to update not the latest.");
}
}
public void storeDatasetProfileUsers(DatasetProfile entity, eu.eudat.models.data.admin.composite.DatasetProfile model) {
public void storeDatasetProfileUsers(DescriptionTemplate entity, eu.eudat.models.data.admin.composite.DatasetProfile model) {
if (model.getUsers() != null && !model.getUsers().isEmpty()) {
if (entity.getUsers() == null) {
entity.setUsers(new HashSet<>());
@ -340,7 +425,7 @@ public class DatasetProfileManager {
}
@Transactional
public void retrieveUsers(DatasetProfile entity, eu.eudat.models.data.admin.composite.DatasetProfile model) {
public void retrieveUsers(DescriptionTemplate entity, eu.eudat.models.data.admin.composite.DatasetProfile model) {
if (entity.getUsers() != null && !entity.getUsers().isEmpty()) {
model.setUsers(entity.getUsers().stream().filter(userDatasetProfile -> userDatasetProfile.getRole() < 2).map(userDatasetProfile -> {
UserInfoListingModel userInfoListingModel = new UserInfoListingModel();
@ -381,10 +466,10 @@ public class DatasetProfileManager {
}
public void addSemanticsInDatasetProfiles() throws XPathExpressionException {
List<DatasetProfile> ids = this.databaseRepository.getDatasetProfileDao().getAllIds();
for(DatasetProfile dp: ids){
DatasetProfile datasetProfile = this.databaseRepository.getDatasetProfileDao().find(dp.getId());
Document document = XmlBuilder.fromXml(datasetProfile.getDefinition());
List<DescriptionTemplate> ids = this.databaseRepository.getDatasetProfileDao().getAllIds();
for(DescriptionTemplate dp: ids){
DescriptionTemplate descriptionTemplate = this.databaseRepository.getDatasetProfileDao().find(dp.getId());
Document document = XmlBuilder.fromXml(descriptionTemplate.getDefinition());
XPathFactory xpathFactory = XPathFactory.newInstance();
XPath xpath = xpathFactory.newXPath();
XPathExpression expr = xpath.compile("//rdaCommonStandard");
@ -402,15 +487,15 @@ public class DatasetProfileManager {
fieldParent.insertBefore(schematics, rdaPropertyNode);
fieldParent.removeChild(rdaPropertyNode);
}
this.updateDatasetProfileXml(document, datasetProfile);
this.updateDatasetProfileXml(document, descriptionTemplate);
}
}
public void addRdaInSemanticsInDatasetProfiles() throws XPathExpressionException {
List<DatasetProfile> ids = this.databaseRepository.getDatasetProfileDao().getAllIds();
for(DatasetProfile dp: ids){
DatasetProfile datasetProfile = this.databaseRepository.getDatasetProfileDao().find(dp.getId());
Document document = XmlBuilder.fromXml(datasetProfile.getDefinition());
List<DescriptionTemplate> ids = this.databaseRepository.getDatasetProfileDao().getAllIds();
for(DescriptionTemplate dp: ids){
DescriptionTemplate descriptionTemplate = this.databaseRepository.getDatasetProfileDao().find(dp.getId());
Document document = XmlBuilder.fromXml(descriptionTemplate.getDefinition());
XPathFactory xpathFactory = XPathFactory.newInstance();
XPath xpath = xpathFactory.newXPath();
XPathExpression expr = xpath.compile("//schematic");
@ -422,11 +507,11 @@ public class DatasetProfileManager {
schematicNode.setTextContent("rda." + schematicRda);
}
}
this.updateDatasetProfileXml(document, datasetProfile);
this.updateDatasetProfileXml(document, descriptionTemplate);
}
}
private void updateDatasetProfileXml(Document document, DatasetProfile datasetProfile) {
private void updateDatasetProfileXml(Document document, DescriptionTemplate descriptionTemplate) {
try {
DOMSource domSource = new DOMSource(document);
StringWriter writer = new StringWriter();
@ -437,8 +522,8 @@ public class DatasetProfileManager {
transformer.transform(domSource, result);
String newDefinition = writer.toString();
if(newDefinition != null){
datasetProfile.setDefinition(newDefinition);
this.databaseRepository.getDatasetProfileDao().createOrUpdate(datasetProfile);
descriptionTemplate.setDefinition(newDefinition);
this.databaseRepository.getDatasetProfileDao().createOrUpdate(descriptionTemplate);
}
}
catch(TransformerException ex) {

View File

@ -5,7 +5,7 @@ import eu.eudat.data.dao.entities.DMPDao;
import eu.eudat.data.dao.entities.DatasetProfileDao;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.query.items.item.dataset.DatasetWizardAutocompleteRequest;
import eu.eudat.data.query.items.item.datasetprofile.DatasetProfileWizardAutocompleteRequest;
@ -40,12 +40,12 @@ public class DatasetWizardManager {
return new LinkedList<>();
}
DatasetProfileCriteria criteria = new DatasetProfileCriteria();
criteria.setIds(dataManagementPlan.getProfiles().stream().map(AssociatedProfile::getId).collect(Collectors.toList()));
List<DatasetProfile> datasetProfiles = profileDao.getWithCriteria(criteria).toList();
criteria.setIds(dataManagementPlan.getProfiles().stream().map(AssociatedProfile::getDescriptionTemplateId).collect(Collectors.toList()));
List<DescriptionTemplate> descriptionTemplates = profileDao.getWithCriteria(criteria).toList();
criteria.setIds(null);
criteria.setGroupIds(datasetProfiles.stream().map(DatasetProfile::getGroupId).collect(Collectors.toList()));
datasetProfiles = profileDao.getWithCriteria(criteria).toList();
List<AssociatedProfile> profiles = datasetProfiles.stream().map(profile -> new AssociatedProfile().fromData(profile)).collect(Collectors.toList());
criteria.setGroupIds(descriptionTemplates.stream().map(DescriptionTemplate::getGroupId).collect(Collectors.toList()));
descriptionTemplates = profileDao.getWithCriteria(criteria).toList();
List<AssociatedProfile> profiles = descriptionTemplates.stream().map(profile -> new AssociatedProfile().fromData(profile)).collect(Collectors.toList());
return profiles;
}

View File

@ -31,18 +31,24 @@ public class DepositManager {
public List<RepositoryConfig> getAvailableRepos() {
List<RepositoryConfig> reposConfigModel = new ArrayList<>();
for (RepositoryDeposit r: this.repositories) {
RepositoryConfig repoModel = new RepositoryConfig();
RepositoryDepositConfiguration repoConf = r.getConfiguration();
List<RepositoryDepositConfiguration> repoConf = r.getConfiguration();
if(repoConf != null) {
reposConfigModel.add(repoModel.toModel(repoConf));
for(RepositoryDepositConfiguration cf: repoConf){
RepositoryConfig repoModel = new RepositoryConfig();
reposConfigModel.add(repoModel.toModel(cf));
}
}
}
return reposConfigModel;
}
public String authenticate(String id, String code) {
Optional<RepositoryDeposit> repo = repositories.stream().filter(x -> x.getConfiguration().getRepositoryId().equals(id)).findFirst();
return repo.map(repositoryDeposit -> repositoryDeposit.authenticate(code)).orElse(null);
for(RepositoryDeposit r: this.repositories){
if(r.getConfiguration().stream().anyMatch(x -> x.getRepositoryId().equals(id))){
return r.authenticate(id, code);
}
}
return null;
}
public Doi deposit(DepositRequest depositRequest, Principal principal) throws Exception {
@ -50,9 +56,12 @@ public class DepositManager {
}
public String getRepositoryLogo(String repositoryId){
Optional<RepositoryDeposit> repo = repositories.stream().filter(x -> x.getConfiguration().getRepositoryId().equals(repositoryId)).findFirst();
return repo.map(repositoryDeposit ->
(repositoryDeposit.getConfiguration().isHasLogo()) ? repositoryDeposit.getLogo() : null
).orElse(null);
for(RepositoryDeposit r: this.repositories){
Optional<RepositoryDepositConfiguration> cf = r.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst();
if(cf.isPresent()){
return cf.get().isHasLogo() ? r.getLogo(repositoryId) : null;
}
}
return null;
}
}

View File

@ -0,0 +1,84 @@
package eu.eudat.logic.managers;
import eu.eudat.data.entities.DescriptionTemplateType;
import eu.eudat.exceptions.descriptiontemplate.DescriptionTemplatesWithTypeException;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.models.data.descriptiontemplatetype.DescriptionTemplateTypeModel;
import eu.eudat.models.data.helpers.common.DataTableData;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import java.util.List;
import java.util.UUID;
import java.util.stream.Collectors;
@Component
public class DescriptionTemplateTypeManager {
private static final Logger logger = LoggerFactory.getLogger(DescriptionTemplateTypeManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
@Autowired
public DescriptionTemplateTypeManager(ApiContext apiContext, DatabaseRepository databaseRepository) {
this.apiContext = apiContext;
this.databaseRepository = databaseRepository;
}
public DataTableData<DescriptionTemplateTypeModel> get() {
List<DescriptionTemplateType> types = this.databaseRepository.getDescriptionTemplateTypeDao().asQueryable().toList();
List<DescriptionTemplateTypeModel> typesModelList = types.stream().map(type -> new DescriptionTemplateTypeModel().fromDataModel(type)).collect(Collectors.toList());
DataTableData<DescriptionTemplateTypeModel> dataTableData = new DataTableData<>();
dataTableData.setData(typesModelList);
dataTableData.setTotalCount((long) typesModelList.size());
return dataTableData;
}
public DescriptionTemplateTypeModel getSingle(UUID id) throws Exception {
DescriptionTemplateType type = this.databaseRepository.getDescriptionTemplateTypeDao().find(id);
if (type != null) {
return new DescriptionTemplateTypeModel().fromDataModel(type);
}
else {
throw new DescriptionTemplatesWithTypeException("No description template type found with this id");
}
}
public void create(DescriptionTemplateTypeModel type) throws Exception {
DescriptionTemplateType existed = this.databaseRepository.getDescriptionTemplateTypeDao().findFromName(type.getName());
if (existed == null) {
this.databaseRepository.getDescriptionTemplateTypeDao().createOrUpdate(type.toDataModel());
}
else {
throw new DescriptionTemplatesWithTypeException("There is already a description template type with that name.");
}
}
public void update(DescriptionTemplateTypeModel type) throws Exception {
DescriptionTemplateType existed = this.databaseRepository.getDescriptionTemplateTypeDao().findFromName(type.getName());
if (existed != null) {
this.databaseRepository.getDescriptionTemplateTypeDao().createOrUpdate(type.toDataModel());
}
else {
throw new DescriptionTemplatesWithTypeException("No description template type found.");
}
}
public void delete(UUID id) throws DescriptionTemplatesWithTypeException {
DescriptionTemplateType type = this.databaseRepository.getDescriptionTemplateTypeDao().find(id);
if (type != null) {
Long descriptionsWithType = this.databaseRepository.getDatasetProfileDao().countWithType(type);
if(descriptionsWithType == 0) {
type.setStatus(DescriptionTemplateType.Status.DELETED.getValue());
this.databaseRepository.getDescriptionTemplateTypeDao().createOrUpdate(type);
}
else{
throw new DescriptionTemplatesWithTypeException("This type can not deleted, because Descriptions are associated with it");
}
}
}
}

View File

@ -48,6 +48,9 @@ public class EmailConfirmationManager {
// Checks if mail is used by another user. If it is, merges the new the old.
Long existingUsers = databaseRepository.getUserInfoDao().asQueryable().where((builder, root) -> builder.equal(root.get("email"), loginConfirmationEmail.getEmail())).count();
if (existingUsers > 0) {
Credential credential = databaseRepository.getCredentialDao().asQueryable().where((builder, root) -> builder.equal(root.get("userInfo"), user)).getSingle();
credential.setEmail(loginConfirmationEmail.getEmail());
databaseRepository.getCredentialDao().createOrUpdate(credential);
UserInfo oldUser = databaseRepository.getUserInfoDao().asQueryable().where((builder, root) -> builder.equal(root.get("email"), loginConfirmationEmail.getEmail())).getSingle();
mergeNewUserToOld(user, oldUser);
expireUserToken(user);
@ -57,6 +60,12 @@ public class EmailConfirmationManager {
user.setEmail(loginConfirmationEmail.getEmail());
databaseRepository.getUserInfoDao().createOrUpdate(user);
Credential credential = databaseRepository.getCredentialDao().asQueryable()
.where((builder, root) -> builder.equal(root.get("userInfo"), user)).getSingle();
if(credential.getEmail() == null){
credential.setEmail(user.getEmail());
databaseRepository.getCredentialDao().createOrUpdate(credential);
}
databaseRepository.getLoginConfirmationEmailDao().createOrUpdate(loginConfirmationEmail);
}

View File

@ -140,6 +140,7 @@ public class GrantManager {
grants.add(grant);
}
grants = grants.stream().filter(grant -> grant.getLabel() != null).collect(Collectors.toList());
grants.sort(Comparator.comparing(Grant::getLabel));
grants = grants.stream().filter(listHelper.distinctByKey(Grant::getLabel)).collect(Collectors.toList());
return grants;

View File

@ -5,6 +5,10 @@ import eu.eudat.data.entities.EmailConfirmation;
import eu.eudat.data.entities.UserDMP;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.entities.UserToken;
import eu.eudat.elastic.criteria.DmpCriteria;
import eu.eudat.elastic.entities.Collaborator;
import eu.eudat.elastic.entities.Dmp;
import eu.eudat.elastic.repository.DmpRepository;
import eu.eudat.exceptions.emailconfirmation.HasConfirmedEmailException;
import eu.eudat.exceptions.emailconfirmation.TokenExpiredException;
import eu.eudat.logic.services.ApiContext;
@ -25,21 +29,25 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import javax.transaction.Transactional;
import java.io.IOException;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@Component
public class MergeEmailConfirmationManager {
private static Logger logger = LoggerFactory.getLogger(MergeEmailConfirmationManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
private DmpRepository dmpRepository;
@Autowired
public MergeEmailConfirmationManager(ApiContext apiContext) {
this.apiContext = apiContext;
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.dmpRepository = apiContext.getOperationsContext().getElasticRepository().getDmpRepository();
}
@Transactional
public void confirmEmail(String token) throws TokenExpiredException, HasConfirmedEmailException {
public String confirmEmail(String token) throws TokenExpiredException, HasConfirmedEmailException {
EmailConfirmation loginConfirmationEmail = apiContext.getOperationsContext()
.getDatabaseRepository().getLoginConfirmationEmailDao().asQueryable()
.where((builder, root) -> builder.equal(root.get("token"), UUID.fromString(token))).getSingle();
@ -49,7 +57,7 @@ public class MergeEmailConfirmationManager {
UserInfo userToBeMerged = databaseRepository.getUserInfoDao().asQueryable()
.where((builder, root) -> builder.equal(root.get("id"), loginConfirmationEmail.getUserId())).getSingle();
String userToBeMergedEmail = userToBeMerged.getEmail();
try {
Map<String, Object> map = new ObjectMapper().readValue(loginConfirmationEmail.getData(), HashMap.class);
UUID otherUserId = UUID.fromString((String) map.get("userId"));
@ -64,6 +72,8 @@ public class MergeEmailConfirmationManager {
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
return userToBeMergedEmail;
}
public void sendConfirmationEmail(String email, Principal principal, UUID userId, Integer provider) throws HasConfirmedEmailException {
@ -91,6 +101,38 @@ public class MergeEmailConfirmationManager {
userDmp.setUser(newUser);
databaseRepository.getUserDmpDao().createOrUpdate(userDmp);
});
try {
DmpCriteria dmpCriteria = new DmpCriteria();
dmpCriteria.setCollaborators(Collections.singletonList(oldUser.getId()));
List<Dmp> elasticDmpsIds = dmpRepository.query(dmpCriteria);
for(Dmp dmpId: elasticDmpsIds){
Dmp dmp = dmpRepository.findDocument(dmpId.getId().toString());
if(dmp.getDatasets() != null) {
dmp.getDatasets().forEach(dataset -> {
if(dataset.getCollaborators() != null) {
for (Collaborator collaborator : dataset.getCollaborators()) {
if (collaborator.getId().equals(oldUser.getId().toString())) {
collaborator.setId(newUser.getId().toString());
collaborator.setName(newUser.getName());
}
}
}
});
}
if(dmp.getCollaborators() != null) {
for (Collaborator collaborator : dmp.getCollaborators()) {
if (collaborator.getId().equals(oldUser.getId().toString())) {
collaborator.setId(newUser.getId().toString());
collaborator.setName(newUser.getName());
}
}
}
dmpRepository.createOrUpdate(dmp);
}
}
catch (IOException e){
logger.warn("Warning: Could not fetch dmps from elastic.", e);
}
oldUser.setUserStatus((short)1);
oldUser.setEmail(null);
List<Credential> credentials = databaseRepository.getCredentialDao().asQueryable().where((builder, root) -> builder.equal(root.get("userInfo"), oldUser)).toList();

View File

@ -1,7 +1,7 @@
package eu.eudat.logic.managers;
import eu.eudat.data.dao.criteria.*;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.types.MetricNames;
import io.micrometer.prometheus.PrometheusMeterRegistry;
@ -33,8 +33,8 @@ public class MetricsManager {
private final Map<String, Gauge> gauges;
public static final Map<Short, String> datasetTemplateStatus = Stream.of(new Object[][] {
{ DatasetProfile.Status.SAVED.getValue(), MetricNames.DRAFT },
{ DatasetProfile.Status.FINALIZED.getValue(), MetricNames.ACTIVE },
{ DescriptionTemplate.Status.SAVED.getValue(), MetricNames.DRAFT },
{ DescriptionTemplate.Status.FINALIZED.getValue(), MetricNames.ACTIVE },
}).collect(Collectors.toMap(data -> (Short) data[0], data -> (String) data[1]));
public void increaseValue(String name, int amount, String label) {
@ -180,6 +180,8 @@ public class MetricsManager {
try (Stream<Path> paths = Files.list(Paths.get(Objects.requireNonNull(this.environment.getProperty("userguide.path"))))) {
long files = paths.count();
calculateValue(MetricNames.LANGUAGES, (int) files, null);
} catch (Exception e) {
logger.error("Could not calculate languages.");
}
calculateValue(MetricNames.INSTALLATIONS, 1, null);
@ -404,9 +406,9 @@ public class MetricsManager {
criteria.setStatus(1);
criteria.setAllVersions(false);
if (countNexus) criteria.setPeriodStart(getNexusDate());
List<DatasetProfile> datasetProfiles = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(criteria).withFields(Collections.singletonList("id")).toList();
List<DescriptionTemplate> descriptionTemplates = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().getWithCriteria(criteria).withFields(Collections.singletonList("id")).toList();
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setDatasetTemplates(datasetProfiles.stream().map(DatasetProfile::getId).collect(Collectors.toList()));
datasetCriteria.setDatasetTemplates(descriptionTemplates.stream().map(DescriptionTemplate::getId).collect(Collectors.toList()));
return apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().getWithCriteria(datasetCriteria).select(root -> root.getProfile().getId()).stream().distinct().count();
}

View File

@ -60,20 +60,20 @@ public class NotificationManager {
case DMP_MODIFIED:
case DATASET_MODIFIED:
subjectTemplate = this.environment.getProperty("notification.modified.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/modifiedNotification.html");
contentTemplate = mailService.getMailTemplateContent(this.environment.getProperty("notification.modified.template"));
break;
case DMP_PUBLISH:
subjectTemplate = this.environment.getProperty("notification.publish.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/publishNotification.html");
contentTemplate = mailService.getMailTemplateContent(this.environment.getProperty("notification.publish.template"));
break;
case DMP_FINALISED:
subjectTemplate = this.environment.getProperty("notification.finalised.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/finalisedNotification.html");
contentTemplate = mailService.getMailTemplateContent(this.environment.getProperty("notification.finalised.template"));
break;
case DMP_MODIFIED_FINALISED:
case DATASET_MODIFIED_FINALISED:
subjectTemplate = this.environment.getProperty("notification.modifiedFinalised.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/modifiedFinalisedNotification.html");
contentTemplate = mailService.getMailTemplateContent(this.environment.getProperty("notification.modified_finalised.template"));
break;
}

View File

@ -1,7 +1,8 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.logic.mapper.prefilling.PrefillingMapper;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
@ -11,10 +12,7 @@ import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.prefilling.Prefilling;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpEntity;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpMethod;
import org.springframework.http.MediaType;
import org.springframework.http.*;
import org.springframework.stereotype.Service;
import org.springframework.web.client.RestTemplate;
@ -29,30 +27,51 @@ public class PrefillingManager {
private final ObjectMapper objectMapper;
private final DatasetManager datasetManager;
private final LicenseManager licenseManager;
private final PrefillingMapper prefillingMapper;
@Autowired
public PrefillingManager(ApiContext apiContext, ConfigLoader configLoader, DatasetManager datasetManager, LicenseManager licenseManager) {
public PrefillingManager(ApiContext apiContext, ConfigLoader configLoader, DatasetManager datasetManager, LicenseManager licenseManager, PrefillingMapper prefillingMapper) {
this.apiContext = apiContext;
this.configLoader = configLoader;
this.objectMapper = new ObjectMapper();
this.prefillingMapper = prefillingMapper;
this.objectMapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
this.datasetManager = datasetManager;
this.licenseManager = licenseManager;
}
public List<Prefilling> getPrefillings(String like, String configId) {
PrefillingConfig prefillingConfig = configLoader.getExternalUrls().getPrefillings().get(configId);
public List<Prefilling> getPrefillings(String like) {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria();
externalUrlCriteria.setLike(like);
List<Map<String, String>> map = apiContext.getOperationsContext().getRemoteFetcher().getExternalGeneric(externalUrlCriteria, prefillingConfig.getPrefillingSearch());
return map.stream().map(submap -> objectMapper.convertValue(submap, Prefilling.class)).collect(Collectors.toList());
List<Prefilling> prefillings = new ArrayList<>();
List<Map<String, String>> map;
Map<String, PrefillingConfig> prefillingConfigs = configLoader.getExternalUrls().getPrefillings();
for (PrefillingConfig prefillingConfig: prefillingConfigs.values()) {
map = apiContext.getOperationsContext().getRemoteFetcher().getExternalGeneric(externalUrlCriteria, prefillingConfig.getPrefillingSearch());
prefillings.addAll(map.stream().map(submap -> objectMapper.convertValue(submap, Prefilling.class)).collect(Collectors.toList()));
if (prefillingConfig.getPrefillingSearch().getUrlConfig().isDataInListing()) {
List<Map<String, Object>> mapData = apiContext.getOperationsContext().getRemoteFetcher().getExternalGenericWithData(externalUrlCriteria, 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 prefillings;
}
public DatasetWizardModel getPrefilledDataset(String prefillId, String configId, UUID profileId) throws Exception {
PrefillingConfig prefillingConfig = configLoader.getExternalUrls().getPrefillings().get(configId);
PrefillingGet prefillingGet = prefillingConfig.getPrefillingGet();
Map<String, Object> prefillingEntity = getSingle(prefillingGet.getUrl(), prefillId);
DatasetProfile datasetProfile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(profileId);
return PrefillingMapper.mapPrefilledEntityToDatasetWizard(prefillingEntity, prefillingGet, prefillingConfig.getType(), datasetProfile, datasetManager, licenseManager);
DescriptionTemplate descriptionTemplate = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(profileId);
return prefillingMapper.mapPrefilledEntityToDatasetWizard(prefillingEntity, prefillingGet, prefillingConfig.getType(), descriptionTemplate, datasetManager, licenseManager);
}
public DatasetWizardModel getPrefilledDatasetUsingData(Map<String, Object> data, String configId, UUID profileId) throws Exception {
PrefillingConfig prefillingConfig = configLoader.getExternalUrls().getPrefillings().get(configId);
PrefillingGet prefillingGet = prefillingConfig.getPrefillingGet();
DescriptionTemplate descriptionTemplate = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(profileId);
return prefillingMapper.mapPrefilledEntityToDatasetWizard(data, prefillingGet, prefillingConfig.getType(), descriptionTemplate, datasetManager, licenseManager);
}
private Map<String, Object> getSingle(String url, String id) {

View File

@ -72,20 +72,7 @@ public class UnlinkEmailConfirmationManager {
Credential credential = databaseRepository.getCredentialDao().asQueryable()
.where((builder, root) -> builder.and(builder.equal(root.get("email"), emailTobeUnlinked), builder.equal(root.get("provider"), provider))).getSingle();
if(credential != null) {
UserInfo userTobeUnlinked = databaseRepository.getUserInfoDao().asQueryable()
.where((builder, root) -> builder.and(builder.equal(root.get("userStatus"), 1), builder.equal(root.get("name"), credential.getPublicValue()))).getSingle();
userTobeUnlinked.setEmail(emailTobeUnlinked);
userTobeUnlinked.setUserStatus((short) 0);
databaseRepository.getUserInfoDao().createOrUpdate(userTobeUnlinked);
credential.setUserInfo(userTobeUnlinked);
databaseRepository.getCredentialDao().createOrUpdate(credential);
UserToken userToken = this.apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserTokenBuilder.class)
.token(UUID.randomUUID()).user(userTobeUnlinked)
.expiresAt(Timestamp.valueOf(LocalDateTime.now().plusDays(10))).issuedAt(new Date())
.build();
apiContext.getOperationsContext().getDatabaseRepository().getUserTokenDao().createOrUpdate(userToken);
databaseRepository.getCredentialDao().delete(credential);
}
}

View File

@ -3,13 +3,8 @@ package eu.eudat.logic.managers;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.dao.criteria.DataManagementPlanCriteria;
import eu.eudat.data.dao.entities.UserInfoDao;
import eu.eudat.data.entities.Credential;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.entities.UserRole;
import eu.eudat.data.entities.*;
import eu.eudat.data.query.items.table.userinfo.UserInfoTableRequestItem;
import eu.eudat.exceptions.security.ExpiredTokenException;
import eu.eudat.exceptions.security.NonValidTokenException;
import eu.eudat.exceptions.security.NullEmailException;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.builders.entity.UserRoleBuilder;
@ -72,7 +67,7 @@ public class UserManager {
this.environment = environment;
}
public eu.eudat.models.data.user.composite.DatasetProfile generateDatasetProfileModel(eu.eudat.data.entities.DatasetProfile profile) {
public eu.eudat.models.data.user.composite.DatasetProfile generateDatasetProfileModel(DescriptionTemplate profile) {
Document viewStyleDoc = XmlBuilder.fromXml(profile.getDefinition());
Element root = (Element) viewStyleDoc.getDocumentElement();
eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.ViewStyleModel viewstyle = new eu.eudat.models.data.entities.xmlmodels.datasetprofiledefinition.ViewStyleModel().fromXml(root);

View File

@ -50,7 +50,9 @@ public class DatasetMapper {
elastic.setStatus(dataset.getStatus());
elastic.setDmp(dataset.getDmp().getId());
elastic.setGroup(dataset.getDmp().getGroupId());
if (dataset.getDmp().getGrant() != null) {
elastic.setGrant(dataset.getDmp().getGrant().getId());
}
elastic.setCreated(dataset.getCreated());
elastic.setModified(dataset.getModified());
elastic.setFinalizedAt(dataset.getFinalizedAt());
@ -74,7 +76,9 @@ public class DatasetMapper {
elastic.setOrganizations(dataset.getDmp().getOrganisations().stream().map(OrganizationMapper::toElastic).collect(Collectors.toList()));
}
elastic.setPublic(dataset.getDmp().isPublic());
if (dataset.getDmp().getGrant() != null) {
elastic.setGrantStatus(dataset.getDmp().getGrant().getStatus());
}
elastic.setFormData(datasetManager.getWordDocumentText(dataset));
return elastic;

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@ -1,14 +1,26 @@
package eu.eudat.logic.mapper.elastic;
import eu.eudat.data.entities.DatasetProfile;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.entities.DMPDatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.elastic.entities.DatasetTempalate;
import java.util.HashMap;
import java.util.Map;
public class DatasetTemplateMapper {
public static DatasetTempalate toElastic(DatasetProfile profile) {
public static DatasetTempalate toElastic(DMPDatasetProfile profile) {
DatasetTempalate elastic = new DatasetTempalate();
elastic.setId(profile.getId());
elastic.setName(profile.getLabel());
elastic.setId(profile.getDatasetprofile().getId());
elastic.setName(profile.getDatasetprofile().getLabel());
try {
elastic.setData(new ObjectMapper().readValue(profile.getData(), new TypeReference<Map<String, Object>>() {}));
}
catch (Exception e){
elastic.setData(new HashMap<>());
}
return elastic;
}
}

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@ -37,7 +37,9 @@ public class DmpMapper {
elastic.setCollaborators(dmp.getUsers().stream().map(user -> CollaboratorMapper.toElastic(user.getUser(), user.getRole())).collect(Collectors.toList()));
}
elastic.setDescription(dmp.getDescription());
if (dmp.getGrant() != null) {
elastic.setGrant(dmp.getGrant().getId());
}
elastic.setLabel(dmp.getLabel());
elastic.setPublic(dmp.isPublic());
elastic.setStatus(dmp.getStatus());

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@ -5,7 +5,7 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.DatasetProfile;
import eu.eudat.data.entities.DescriptionTemplate;
import eu.eudat.elastic.entities.Tag;
import eu.eudat.logic.managers.DatasetManager;
import eu.eudat.logic.managers.DatasetProfileManager;
@ -25,6 +25,10 @@ import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
import eu.eudat.models.data.license.LicenseModel;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
@ -33,11 +37,19 @@ import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.stream.Collectors;
@Component
public class PrefillingMapper {
private static final Logger logger = LoggerFactory.getLogger(PrefillingMapper.class);
private static final ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
private final DatasetProfileManager datasetProfileManager;
public static DatasetWizardModel mapPrefilledEntityToDatasetWizard(Map<String, Object> prefilledEntity, PrefillingGet prefillingGet, String type,
DatasetProfile profile, DatasetManager datasetManager, LicenseManager licenseManager) throws Exception {
@Autowired
public PrefillingMapper(DatasetProfileManager datasetProfileManager) {
this.datasetProfileManager = datasetProfileManager;
}
public DatasetWizardModel mapPrefilledEntityToDatasetWizard(Map<String, Object> prefilledEntity, PrefillingGet prefillingGet, String type,
DescriptionTemplate profile, DatasetManager datasetManager, LicenseManager licenseManager) throws Exception {
DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
datasetWizardModel.setProfile(new DatasetProfileOverviewModel().fromDataModel(profile));
Dataset dataset = new Dataset();
@ -54,8 +66,18 @@ public class PrefillingMapper {
sourceValue = ((Map)sourceValue).get(sourceKey);
}
}
try {
setValue(prefillingMapping, mapper.writeValueAsString(sourceValue), datasetWizardModel, parentNode, properties, type, licenseManager);
}
catch (Exception e) {
if (prefillingMapping.getSemanticTarget() != null && !prefillingMapping.getSemanticTarget().isEmpty()) {
logger.warn("Couldn't map " + prefillingMapping.getSemanticTarget());
}
else if (prefillingMapping.getTarget() != null && !prefillingMapping.getTarget().isEmpty()) {
logger.warn("Couldn't map " + prefillingMapping.getTarget());
}
}
}
for (PrefillingFixedMapping fixedMapping: prefillingGet.getFixedMappings()) {
setValue(fixedMapping, fixedMapping.getValue(), datasetWizardModel, parentNode, properties, type, licenseManager);
}
@ -64,7 +86,7 @@ public class PrefillingMapper {
return datasetWizardModel;
}
private static void setValue(PrefillingMapping prefillingMapping, String value, DatasetWizardModel datasetWizardModel, JsonNode parentNode, Map<String, Object> properties, String type, LicenseManager licenseManager) throws InvocationTargetException, IllegalAccessException, JsonProcessingException {
private void setValue(PrefillingMapping prefillingMapping, String value, DatasetWizardModel datasetWizardModel, JsonNode parentNode, Map<String, Object> properties, String type, LicenseManager licenseManager) throws InvocationTargetException, IllegalAccessException, JsonProcessingException {
String trimRegex = prefillingMapping.getTrimRegex() != null ? prefillingMapping.getTrimRegex() : "";
if (!value.startsWith("\"") && !value.startsWith("[") && !value.equals("null")) {
value = "\"" + value + "\"";
@ -104,7 +126,11 @@ public class PrefillingMapper {
//GK: Tags Special logic
if (parsedValue != null && !parsedValue.equals("null") && prefillingMapping.getTarget().equals("tags")) {
parsedValue = mapper.valueToTree(parseTags(parsedValue)).toString();
} else {
}
else if(!parsedValues.isEmpty() && prefillingMapping.getTarget().equals("tags")) {
parsedValue = mapper.valueToTree(parseTags(String.join(", ", parsedValues))).toString();
}
else {
parsedValue = mapper.valueToTree(parsedValue).toString();
}
setterMethod.invoke(datasetWizardModel, mapper.readValue(parsedValue, params[0]));
@ -112,11 +138,11 @@ public class PrefillingMapper {
throw e;
}
} else {
List<JsonNode> nodes = JsonSearcher.findNodes(parentNode, "schematics", "rda." + prefillingMapping.getMaDmpTarget());
List<JsonNode> nodes = JsonSearcher.findNodes(parentNode, "schematics", prefillingMapping.getSemanticTarget());
// zenodo prefilling customizations
if(type.equals("zenodo")){
if(prefillingMapping.getMaDmpTarget().equals("dataset.distribution.data_access")){
if(prefillingMapping.getSemanticTarget().equals("rda.dataset.distribution.data_access")){
if(parsedValue != null && parsedValue.equals("open")){
List<JsonNode> issuedNodes = JsonSearcher.findNodes(parentNode, "schematics", "rda.dataset.issued");
if(!issuedNodes.isEmpty()){
@ -131,7 +157,7 @@ public class PrefillingMapper {
}
}
if (prefillingMapping.getMaDmpTarget().equals("dataset.distribution.available_until") && parsedValue != null && !parsedValue.equals("null")) {
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);
@ -152,7 +178,12 @@ public class PrefillingMapper {
}
break;
case TAGS:
if(parsedValues.isEmpty()) {
properties.put(id, mapper.valueToTree(parseTags(parsedValue)).toString());
}
else {
properties.put(id, mapper.valueToTree(parseTags(String.join(", ", parsedValues))).toString());
}
break;
case DATASET_IDENTIFIER:
JSONObject datasetID = new JSONObject();
@ -194,7 +225,7 @@ public class PrefillingMapper {
}
}
private static Object parseComboBoxValues(JsonNode node, List<String> parsedValues) throws JsonProcessingException {
private Object parseComboBoxValues(JsonNode node, List<String> parsedValues) throws JsonProcessingException {
List<Object> normalizedValues = new ArrayList<>();
boolean isMultiSelect;
String type = node.isArray() ? node.get(0).get("data").get("type").asText() : node.get("data").get("type").asText();
@ -203,7 +234,13 @@ public class PrefillingMapper {
AutoCompleteData autoCompleteData = mapper.treeToValue(dataNode, AutoCompleteData.class);
isMultiSelect = autoCompleteData.getMultiAutoComplete();
for (String format : parsedValues) {
List<ExternalAutocompleteFieldModel> result = DatasetProfileManager.getAutocomplete(autoCompleteData, format);
List<ExternalAutocompleteFieldModel> result = new ArrayList<>();
try {
result = datasetProfileManager.getAutocomplete(autoCompleteData, format);
}
catch (Exception e) {
logger.error(e.getMessage(), e);
}
result = result.stream().filter(StreamDistinctBy.distinctByKey(ExternalAutocompleteFieldModel::getId)).collect(Collectors.toList());
if(!result.isEmpty()){
List<String> tempValues = new LinkedList<>();

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@ -0,0 +1,23 @@
package eu.eudat.logic.proxy.config;
public enum AuthType {
;
private final String name;
AuthType(String name) {
this.name = name;
}
public String getName() {
return name;
}
public static AuthType fromName(String name) {
for (AuthType authType : AuthType.values()) {
if (authType.getName().equals(name)) {
return authType;
}
}
throw new IllegalArgumentException("AuthType [" + name + "] is not supported");
}
}

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@ -0,0 +1,57 @@
package eu.eudat.logic.proxy.config;
import javax.xml.bind.annotation.XmlElement;
public class AuthenticationConfiguration {
private String authUrl;
private String authMethod = "GET";
private String authTokenPath;
private String authRequestBody;
private String type;
public String getAuthUrl() {
return authUrl;
}
@XmlElement(name = "authUrl")
public void setAuthUrl(String authUrl) {
this.authUrl = authUrl;
}
public String getAuthMethod() {
return authMethod;
}
@XmlElement(name = "authUrlMethod")
public void setAuthMethod(String authMethod) {
this.authMethod = authMethod;
}
public String getAuthTokenPath() {
return authTokenPath;
}
@XmlElement(name = "authTokenJpath")
public void setAuthTokenPath(String authTokenPath) {
this.authTokenPath = authTokenPath;
}
public String getAuthRequestBody() {
return authRequestBody;
}
@XmlElement(name = "authUrlBody")
public void setAuthRequestBody(String authRequestBody) {
this.authRequestBody = authRequestBody;
}
public String getType() {
return type;
}
@XmlElement(name = "authType")
public void setType(String type) {
this.type = type;
}
}

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@ -11,6 +11,7 @@ public class UrlConfiguration {
private String label;
private Integer ordinal;
private String url;
private boolean dataInListing;
private DataUrlConfiguration data;
private String type;
private String paginationPath;
@ -20,6 +21,7 @@ public class UrlConfiguration {
private String requestType = "GET";
private String requestBody = "";
private String filterType = "remote";
private AuthenticationConfiguration auth;
private List<QueryConfig> queries;
@ -47,6 +49,14 @@ public class UrlConfiguration {
this.url = url;
}
public boolean isDataInListing() {
return dataInListing;
}
@XmlElement(name = "dataInListing")
public void setDataInListing(boolean dataInListing) {
this.dataInListing = dataInListing;
}
public Integer getOrdinal() {
return ordinal;
}
@ -134,4 +144,13 @@ public class UrlConfiguration {
public void setQueries(List<QueryConfig> queries) {
this.queries = queries;
}
public AuthenticationConfiguration getAuth() {
return auth;
}
@XmlElement(name="authentication")
public void setAuth(AuthenticationConfiguration auth) {
this.auth = auth;
}
}

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@ -3,6 +3,7 @@ package eu.eudat.logic.proxy.config.configloaders;
import eu.eudat.logic.proxy.config.ExternalUrls;
import eu.eudat.logic.proxy.config.Semantic;
import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
import eu.eudat.models.data.pid.PidLinks;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import java.util.List;
@ -14,5 +15,6 @@ public interface ConfigLoader {
XWPFDocument getDocument();
XWPFDocument getDatasetDocument();
ConfigurableProviders getConfigurableProviders();
PidLinks getPidLinks();
Map<String, String> getKeyToSourceMap();
}

View File

@ -6,6 +6,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.logic.proxy.config.ExternalUrls;
import eu.eudat.logic.proxy.config.Semantic;
import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
import eu.eudat.models.data.pid.PidLinks;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -41,6 +42,7 @@ public class DefaultConfigLoader implements ConfigLoader {
private XWPFDocument document;
private XWPFDocument datasetDocument;
private ConfigurableProviders configurableProviders;
private PidLinks pidLinks;
private Map<String, String> keyToSourceMap;
@Autowired
@ -134,6 +136,25 @@ public class DefaultConfigLoader implements ConfigLoader {
}
}
private void setPidLinks() {
String filePath = environment.getProperty("configuration.pid_links");
logger.info("Loaded also config file: " + filePath);
InputStream is = null;
try {
is = getStreamFromPath(filePath);
ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
this.pidLinks = mapper.readValue(is, PidLinks.class);
} catch (IOException | NullPointerException e) {
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
}
private void setKeyToSourceMap() {
String filePath = this.environment.getProperty("configuration.externalUrls");
logger.info("Loaded also config file: " + filePath);
@ -192,6 +213,14 @@ public class DefaultConfigLoader implements ConfigLoader {
return configurableProviders;
}
public PidLinks getPidLinks() {
if (pidLinks == null) {
pidLinks = new PidLinks();
this.setPidLinks();
}
return pidLinks;
}
public Map<String, String> getKeyToSourceMap() {
if (keyToSourceMap == null) {
keyToSourceMap = new HashMap<>();

View File

@ -7,7 +7,7 @@ import javax.xml.bind.annotation.XmlRootElement;
public class DefaultPrefillingMapping implements PrefillingMapping{
private String source;
private String target;
private String maDmpTarget;
private String semanticTarget;
private String subSource;
private String trimRegex;
@ -29,13 +29,13 @@ public class DefaultPrefillingMapping implements PrefillingMapping{
this.target = target;
}
public String getMaDmpTarget() {
return maDmpTarget;
public String getSemanticTarget() {
return semanticTarget;
}
@XmlAttribute(name = "maDmpTarget")
public void setMaDmpTarget(String maDmpTarget) {
this.maDmpTarget = maDmpTarget;
@XmlAttribute(name = "semanticTarget")
public void setSemanticTarget(String semanticTarget) {
this.semanticTarget = semanticTarget;
}
public String getSubSource() {

View File

@ -0,0 +1,31 @@
package eu.eudat.logic.proxy.config.entities;
import eu.eudat.logic.proxy.config.FetchStrategy;
import eu.eudat.logic.proxy.config.UrlConfiguration;
import java.util.ArrayList;
import java.util.List;
public class GeneralUrls extends GenericUrls{
List<UrlConfiguration> urls;
FetchStrategy fetchMode;
public GeneralUrls() {
this.urls = new ArrayList<>();
}
@Override
public List<UrlConfiguration> getUrls() {
return urls;
}
@Override
public FetchStrategy getFetchMode() {
return fetchMode;
}
public void setFetchMode(FetchStrategy fetchMode) {
this.fetchMode = fetchMode;
}
}

View File

@ -6,7 +6,7 @@ import javax.xml.bind.annotation.XmlRootElement;
@XmlRootElement(name = "fixedMapping")
public class PrefillingFixedMapping implements PrefillingMapping{
private String target;
private String maDmpTarget;
private String semanticTarget;
private String value;
public String getTarget() {
@ -18,13 +18,13 @@ public class PrefillingFixedMapping implements PrefillingMapping{
this.target = target;
}
public String getMaDmpTarget() {
return maDmpTarget;
public String getSemanticTarget() {
return semanticTarget;
}
@XmlAttribute(name = "maDmpTarget")
public void setMaDmpTarget(String maDmpTarget) {
this.maDmpTarget = maDmpTarget;
@XmlAttribute(name = "semanticTarget")
public void setSemanticTarget(String semanticTarget) {
this.semanticTarget = semanticTarget;
}
@Override

View File

@ -7,9 +7,9 @@ public interface PrefillingMapping {
void setTarget(String target);
String getMaDmpTarget();
String getSemanticTarget();
void setMaDmpTarget(String maDmpTarget);
void setSemanticTarget(String semanticTarget);
String getSubSource();

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@ -15,9 +15,14 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.core.ParameterizedTypeReference;
import org.springframework.http.*;
import org.springframework.http.client.reactive.ReactorClientHttpConnector;
import org.springframework.http.codec.json.Jackson2JsonDecoder;
import org.springframework.stereotype.Service;
import org.springframework.web.client.RestTemplate;
import org.springframework.web.reactive.function.client.WebClient;
import reactor.netty.http.client.HttpClient;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
@ -33,10 +38,16 @@ public class RemoteFetcher {
private static final Logger logger = LoggerFactory.getLogger(RemoteFetcher.class);
private ConfigLoader configLoader;
private final WebClient client;
@Autowired
public RemoteFetcher(ConfigLoader configLoader) {
this.configLoader = configLoader;
this.client = WebClient.builder().codecs(clientCodecConfigurer -> {
clientCodecConfigurer.defaultCodecs().jackson2JsonDecoder(new Jackson2JsonDecoder(new ObjectMapper(), MediaType.APPLICATION_JSON));
clientCodecConfigurer.defaultCodecs().maxInMemorySize(2 * ((int) Math.pow(1024, 3))); //GK: Why here???
}
).clientConnector(new ReactorClientHttpConnector(HttpClient.create().followRedirect(true))).build();
}
@Cacheable(value = "repositories", keyGenerator = "externalUrlsKeyGenerator")
@ -179,6 +190,10 @@ public class RemoteFetcher {
return getAll(urlConfigurations, fetchStrategy, externalUrlCriteria);
}
public List<Map<String, Object>> getExternalGenericWithData(ExternalUrlCriteria externalUrlCriteria, GenericUrls genericUrls) {
List<UrlConfiguration> urlConfigurations = genericUrls.getUrls();
return getAllWithData(urlConfigurations, externalUrlCriteria);
}
private List<Map<String, String>> getAll(List<UrlConfiguration> urlConfigs, FetchStrategy fetchStrategy, ExternalUrlCriteria externalUrlCriteria) {
@ -194,7 +209,11 @@ public class RemoteFetcher {
ifFunderQueryExist(urlConfiguration, externalUrlCriteria);
if (urlConfiguration.getType() == null || urlConfiguration.getType().equals("External")) {
try {
results.addAll(getAllResultsFromUrl(urlConfiguration.getUrl(), fetchStrategy, urlConfiguration.getData(), urlConfiguration.getPaginationPath(), externalUrlCriteria, urlConfiguration.getLabel(), urlConfiguration.getKey(), urlConfiguration.getContentType(), urlConfiguration.getFirstpage(), urlConfiguration.getRequestBody(), urlConfiguration.getRequestType(), urlConfiguration.getFilterType(), urlConfiguration.getQueries()));
String auth = null;
if (urlConfiguration.getAuth() != null) {
auth = this.getAuthentication(urlConfiguration.getAuth());
}
results.addAll(getAllResultsFromUrl(urlConfiguration.getUrl(), fetchStrategy, urlConfiguration.getData(), urlConfiguration.getPaginationPath(), externalUrlCriteria, urlConfiguration.getLabel(), urlConfiguration.getKey(), urlConfiguration.getContentType(), urlConfiguration.getFirstpage(), urlConfiguration.getRequestBody(), urlConfiguration.getRequestType(), urlConfiguration.getFilterType(), urlConfiguration.getQueries(), auth));
} catch (Exception e) {
logger.error(e.getLocalizedMessage(), e);
}
@ -213,6 +232,42 @@ public class RemoteFetcher {
return results;
}
private String getAuthentication(AuthenticationConfiguration authenticationConfiguration) {
HttpMethod method = HttpMethod.valueOf(authenticationConfiguration.getAuthMethod());
Map<String, Object> reponse = this.client.method(method).uri(authenticationConfiguration.getAuthUrl())
.contentType(MediaType.APPLICATION_JSON)
.bodyValue(this.parseBodyString(authenticationConfiguration.getAuthRequestBody()))
.exchangeToMono(mono -> mono.bodyToMono(new ParameterizedTypeReference<Map<String, Object>>() {
})).block();
return authenticationConfiguration.getType() + " " + reponse.get(authenticationConfiguration.getAuthTokenPath());
}
private List<Map<String, Object>> getAllWithData(List<UrlConfiguration> urlConfigs, ExternalUrlCriteria externalUrlCriteria) {
List<Map<String, Object>> results = new LinkedList<>();
if (urlConfigs == null || urlConfigs.isEmpty()) {
return results;
}
urlConfigs.sort(Comparator.comparing(UrlConfiguration::getOrdinal));
urlConfigs.forEach(urlConfiguration -> {
ifFunderQueryExist(urlConfiguration, externalUrlCriteria);
if (urlConfiguration.getType() == null || urlConfiguration.getType().equals("External")) {
try {
results.addAll(getAllResultsFromUrlWithData(urlConfiguration.getUrl(), urlConfiguration.getData(), externalUrlCriteria, urlConfiguration.getContentType(), urlConfiguration.getFirstpage(), urlConfiguration.getRequestBody(), urlConfiguration.getRequestType(), urlConfiguration.getQueries()));
} catch (Exception e) {
logger.error(e.getLocalizedMessage(), e);
}
}
});
return results;
}
private void ifFunderQueryExist(UrlConfiguration urlConfiguration, ExternalUrlCriteria externalUrlCriteria) {
if (urlConfiguration.getFunderQuery() != null) {
if (externalUrlCriteria.getFunderId() != null && !urlConfiguration.getFunderQuery().startsWith("dmp:")) {
@ -246,7 +301,7 @@ public class RemoteFetcher {
protected String replaceCriteriaOnUrl(String path, ExternalUrlCriteria externalUrlCriteria, String firstPage, List<QueryConfig> queries) {
String completedPath = path;
if (externalUrlCriteria.getLike() != null) {
if ((path.contains("openaire") || path.contains("orcid") || path.contains("ror")) && externalUrlCriteria.getLike().equals("")) {
if ((path.contains("openaire") || path.contains("orcid") || path.contains("ror") || path.contains("fairsharing")) && externalUrlCriteria.getLike().equals("")) {
completedPath = completedPath.replaceAll("\\{like}", "*");
completedPath = completedPath.replaceAll("\\{query}", "*");
} else {
@ -271,6 +326,10 @@ public class RemoteFetcher {
*/
completedPath = completedPath.replace("{funderId}", funderId);
}
else if(completedPath.contains("{funderId}")){
logger.warn("FunderId is null.");
completedPath = completedPath.replace("{funderId}", " ");
}
if (externalUrlCriteria.getPage() != null) {
completedPath = completedPath.replace("{page}", externalUrlCriteria.getPage());
} else {
@ -298,31 +357,32 @@ public class RemoteFetcher {
return completedPath;
}
private List<Map<String, String>> getAllResultsFromUrl(String path, FetchStrategy fetchStrategy, final DataUrlConfiguration jsonDataPath, final String jsonPaginationPath, ExternalUrlCriteria externalUrlCriteria, String tag, String key, String contentType, String firstPage, String requestBody, String requestType, String filterType, List<QueryConfig> queries) throws Exception {
private List<Map<String, String>> getAllResultsFromUrl(String path, FetchStrategy fetchStrategy, final DataUrlConfiguration jsonDataPath, final String jsonPaginationPath, ExternalUrlCriteria externalUrlCriteria, String tag, String key, String contentType, String firstPage, String requestBody, String requestType, String filterType, List<QueryConfig> queries, String auth) throws Exception {
Set<Integer> pages = new HashSet<>();
String replacedPath = replaceCriteriaOnUrl(path, externalUrlCriteria, firstPage, queries);
String replacedBody = replaceCriteriaOnUrl(requestBody, externalUrlCriteria, firstPage, queries);
Results results = getResultsFromUrl(replacedPath, jsonDataPath, jsonPaginationPath, contentType, replacedBody, requestType);
Results results = getResultsFromUrl(replacedPath, jsonDataPath, jsonPaginationPath, contentType, replacedBody, requestType, auth);
if(results != null) {
if (filterType != null && filterType.equals("local") && (externalUrlCriteria.getLike() != null && !externalUrlCriteria.getLike().isEmpty())) {
results.setResults(results.getResults().stream()
.filter(r -> r.get("name").toLowerCase().contains(externalUrlCriteria.getLike().toLowerCase()))
.collect(Collectors.toList()));
}
if (fetchStrategy == FetchStrategy.FIRST)
return results == null ? new LinkedList<>() : results.getResults().stream().peek(x -> x.put("tag", tag)).peek(x -> x.put("key", key)).collect(Collectors.toList());
return results.getResults().stream().peek(x -> x.put("tag", tag)).peek(x -> x.put("key", key)).collect(Collectors.toList());
if (results != null && results.getPagination() != null && results.getPagination().get("pages") != null) //if has more pages, add them to the pages set
if (results.getPagination() != null && results.getPagination().get("pages") != null) //if has more pages, add them to the pages set
for (int i = 2; i <= results.getPagination().get("pages"); i++)
pages.add(i);
Long maxResults = configLoader.getExternalUrls().getMaxresults();
if ((maxResults > 0 && results != null) && (results.getPagination().get("count") > maxResults))
if ((maxResults > 0) && (results.getPagination().get("count") > maxResults))
throw new HugeResultSet("The submitted search query " + externalUrlCriteria.getLike() + " is about to return " + results.getPagination().get("count") + " results... Please submit a more detailed search query");
Optional<Results> optionalResults = pages.parallelStream()
.map(page -> getResultsFromUrl(path + "&page=" + page, jsonDataPath, jsonPaginationPath, contentType, replacedBody, requestType))
.map(page -> getResultsFromUrl(path + "&page=" + page, jsonDataPath, jsonPaginationPath, contentType, replacedBody, requestType, auth))
.filter(Objects::nonNull)
.reduce((result1, result2) -> {
result1.getResults().addAll(result2.getResults());
@ -331,16 +391,52 @@ public class RemoteFetcher {
Results remainingResults = optionalResults.orElseGet(Results::new);
remainingResults.getResults().addAll(results.getResults());
return remainingResults.getResults().stream().peek(x -> x.put("tag", tag)).collect(Collectors.toList());
return remainingResults.getResults().stream().peek(x -> x.put("tag", tag)).peek(x -> x.put("key", key)).collect(Collectors.toList());
}
else {
return new LinkedList<>();
}
}
private List<Map<String, Object>> getAllResultsFromUrlWithData(String path, final DataUrlConfiguration jsonDataPath, ExternalUrlCriteria externalUrlCriteria, String contentType, String firstPage, String requestBody, String requestType, List<QueryConfig> queries) {
protected Results getResultsFromUrl(String urlString, DataUrlConfiguration jsonDataPath, String jsonPaginationPath, String contentType, String requestBody, String requestType) {
String replacedPath = replaceCriteriaOnUrl(path, externalUrlCriteria, firstPage, queries);
String replacedBody = replaceCriteriaOnUrl(requestBody, externalUrlCriteria, firstPage, queries);
try {
RestTemplate restTemplate = new RestTemplate();
HttpHeaders headers = new HttpHeaders();
HttpEntity<JsonNode> entity;
ResponseEntity<String> response;
if (contentType != null && !contentType.isEmpty()) {
headers.setAccept(Collections.singletonList(MediaType.valueOf(contentType)));
headers.setContentType(MediaType.valueOf(contentType));
}
JsonNode jsonBody = new ObjectMapper().readTree(replacedBody);
entity = new HttpEntity<>(jsonBody, headers);
response = restTemplate.exchange(replacedPath, HttpMethod.valueOf(requestType), entity, String.class);
if (response.getStatusCode() == HttpStatus.OK) {
if (response.getHeaders().get("Content-Type").get(0).contains("json")) {
DocumentContext jsonContext = JsonPath.parse(response.getBody());
return jsonContext.read(jsonDataPath.getPath());
}
}
}
catch (Exception exception) {
logger.error(exception.getMessage(), exception);
}
return new LinkedList<>();
}
protected Results getResultsFromUrl(String urlString, DataUrlConfiguration jsonDataPath, String jsonPaginationPath, String contentType, String requestBody, String requestType, String auth) {
try {
//RestTemplate restTemplate = new RestTemplate(new SimpleClientHttpRequestFactory());
//HttpHeaders headers = new HttpHeaders();
//HttpEntity<JsonNode> entity;
ResponseEntity<String> response;
/*
* URL url = new URL(urlString.replaceAll(" ", "%20"));
@ -348,14 +444,27 @@ public class RemoteFetcher {
* HttpURLConnection con = (HttpURLConnection) url.openConnection();
* con.setRequestMethod("GET");
*/
if (contentType != null && !contentType.isEmpty()) {
/* if (contentType != null && !contentType.isEmpty()) {
headers.setAccept(Collections.singletonList(MediaType.valueOf(contentType)));
headers.setContentType(MediaType.valueOf(contentType));
}
if (auth != null) {
headers.set("Authorization", auth);
}*/
JsonNode jsonBody = new ObjectMapper().readTree(requestBody);
entity = new HttpEntity<>(jsonBody, headers);
// entity = new HttpEntity<>(jsonBody, headers);
response = restTemplate.exchange(urlString, HttpMethod.resolve(requestType), entity, String.class);
response = this.client.method(HttpMethod.valueOf(requestType)).uri(urlString).headers(httpHeaders -> {
if (contentType != null && !contentType.isEmpty()) {
httpHeaders.setAccept(Collections.singletonList(MediaType.valueOf(contentType)));
httpHeaders.setContentType(MediaType.valueOf(contentType));
}
if (auth != null) {
httpHeaders.set("Authorization", auth);
}
}).bodyValue(jsonBody).retrieve().toEntity(String.class).block();
//response = restTemplate.exchange(urlString, HttpMethod.resolve(requestType), entity, String.class);
if (response.getStatusCode() == HttpStatus.OK) { // success
//do here all the parsing
Results results = new Results();
@ -363,7 +472,7 @@ public class RemoteFetcher {
DocumentContext jsonContext = JsonPath.parse(response.getBody());
if (jsonDataPath.getFieldsUrlConfiguration().getPath() != null) {
results = RemoteFetcherUtils.getFromJsonWithRecursiveFetching(jsonContext, jsonDataPath, this, requestBody, requestType);
results = RemoteFetcherUtils.getFromJsonWithRecursiveFetching(jsonContext, jsonDataPath, this, requestBody, requestType, auth);
} else if (jsonDataPath.getFieldsUrlConfiguration().getFirstName() != null) {
results = RemoteFetcherUtils.getFromJsonWithFirstAndLastName(jsonContext, jsonDataPath);
} else {
@ -485,8 +594,18 @@ public class RemoteFetcher {
return null;
}
private String parseBodyString(String bodyString) {
String finalBodyString = bodyString;
if (bodyString.contains("{env:")) {
int index = bodyString.indexOf("{env: ");
while (index >= 0) {
int endIndex = bodyString.indexOf("}", index + 6);
String envName = bodyString.substring(index + 6, endIndex);
finalBodyString = finalBodyString.replace("{env: " + envName + "}", System.getenv(envName));
index = bodyString.indexOf("{env: ", index + 6);
}
}
return finalBodyString;
}
}

View File

@ -28,7 +28,7 @@ public class RemoteFetcherUtils {
new HashMap<>(1, 1));
}
public static Results getFromJsonWithRecursiveFetching(DocumentContext jsonContext, DataUrlConfiguration jsonDataPath, RemoteFetcher remoteFetcher, String requestBody, String requestType) {
public static Results getFromJsonWithRecursiveFetching(DocumentContext jsonContext, DataUrlConfiguration jsonDataPath, RemoteFetcher remoteFetcher, String requestBody, String requestType, String auth) {
Results results = new Results(parseData(jsonContext, jsonDataPath),
new HashMap<>(1, 1));
@ -37,7 +37,7 @@ public class RemoteFetcherUtils {
externalUrlCriteria.setPath(result.get("path"));
externalUrlCriteria.setHost(result.get("host"));
String replacedPath = remoteFetcher.replaceCriteriaOnUrl(jsonDataPath.getUrlConfiguration().getUrl(), externalUrlCriteria, jsonDataPath.getUrlConfiguration().getFirstpage(), jsonDataPath.getUrlConfiguration().getQueries());
return remoteFetcher.getResultsFromUrl(replacedPath, jsonDataPath.getUrlConfiguration().getData(), jsonDataPath.getUrlConfiguration().getData().getPath(), jsonDataPath.getUrlConfiguration().getContentType(), requestBody, requestType);
return remoteFetcher.getResultsFromUrl(replacedPath, jsonDataPath.getUrlConfiguration().getData(), jsonDataPath.getUrlConfiguration().getData().getPath(), jsonDataPath.getUrlConfiguration().getContentType(), requestBody, requestType, auth);
}).filter(Objects::nonNull).map(results1 -> results1.getResults().get(0)).collect(Collectors.toList());
return new Results(multiResults, new HashMap<>(1, 1));
}
@ -70,7 +70,13 @@ public class RemoteFetcherUtils {
Object pidObj = stringObjectMap.get(value.split("\\.")[0]);
if(pidObj != null){
if(pidObj instanceof Map){
pid = ((Map<String, String>) pidObj).get(value.split("\\.")[1]);
Object o = ((Map<String, Object>) pidObj).get(value.split("\\.")[1]);
if(o instanceof String){
pid = (String)o;
}
else if(o instanceof Integer){
pid = String.valueOf(o);
}
}
else if(pidObj instanceof List){
Object o = ((List<Map<String,?>>) pidObj).get(0).get(value.split("\\.")[1]);
@ -92,11 +98,25 @@ public class RemoteFetcherUtils {
}
} else {
value = value.replace("'", "");
if (value.contains(".")) {
String[] parts = value.split("\\.");
Map<String, Object> tempMap = stringObjectMap;
for (int i = 0; i < parts.length; i++) {
if (tempMap.containsKey(parts[i])) {
if (i + 1 < parts.length) {
tempMap = (Map<String, Object>) tempMap.get(parts[i]);
} else {
parsedData.get(parsedData.size() - 1).put(field.getName().equals("types") ? "tags" : value, normalizeValue(tempMap.get(parts[i]), (field.getName().equals("types") || field.getName().equals("uri"))));
}
}
}
} else {
if (stringObjectMap.containsKey(value)) {
parsedData.get(parsedData.size() - 1).put(field.getName().equals("types") ? "tags" : value, normalizeValue(stringObjectMap.get(value), (field.getName().equals("types") || field.getName().equals("uri"))));
}
}
}
}
} catch (IllegalAccessException | InvocationTargetException e) {
logger.error(e.getLocalizedMessage(), e);
}
@ -129,7 +149,8 @@ public class RemoteFetcherUtils {
}
}
} else if (value instanceof Map) {
return ((Map<String, String>)value).get("content");
String key = ((Map<String, String>)value).containsKey("$") ? "$" : "content";
return ((Map<String, String>)value).get(key);
}
return value != null ? value.toString() : null;
}

View File

@ -37,7 +37,9 @@ public class DMPToDepositMapper {
deposit.setUsers(entity.getUsers().stream().map(DMPToDepositMapper::fromUserDMP).collect(Collectors.toSet()));
deposit.setOrganisations(entity.getOrganisations().stream().map(DMPToDepositMapper::fromOrganisation).collect(Collectors.toSet()));
deposit.setResearchers(entity.getResearchers().stream().map(DMPToDepositMapper::fromResearcher).collect(Collectors.toSet()));
if (entity.getGrant() != null) {
deposit.setGrant(fromGrant(entity.getGrant()));
}
deposit.setPdfFile(pdfFile);
deposit.setRdaJsonFile(jsonFile);

View File

@ -3,6 +3,7 @@ package eu.eudat.logic.security.validators.configurableProvider;
import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.saml2.CertificateInfo;
import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.saml2.Saml2ConfigurableProvider;
import eu.eudat.logic.utilities.builders.XmlBuilder;
import eu.eudat.models.data.saml2.AuthnRequestModel;
import jakarta.xml.soap.*;
import net.shibboleth.utilities.java.support.component.ComponentInitializationException;
import net.shibboleth.utilities.java.support.resolver.CriteriaSet;
@ -34,7 +35,6 @@ import org.opensaml.core.xml.config.XMLObjectProviderRegistry;
import org.opensaml.core.xml.io.*;
import org.opensaml.core.xml.schema.*;
import org.opensaml.saml.common.SAMLObject;
import org.opensaml.saml.common.SAMLObjectContentReference;
import org.opensaml.saml.common.SAMLVersion;
import org.opensaml.saml.common.xml.SAMLConstants;
import org.opensaml.saml.criterion.EntityRoleCriterion;
@ -64,8 +64,6 @@ import org.opensaml.xmlsec.keyinfo.impl.X509KeyInfoGeneratorFactory;
import org.opensaml.xmlsec.signature.KeyInfo;
import org.opensaml.xmlsec.signature.Signature;
import org.opensaml.xmlsec.signature.X509Data;
import org.opensaml.xmlsec.signature.impl.SignatureBuilder;
import org.opensaml.xmlsec.signature.support.SignatureConstants;
import org.opensaml.xmlsec.signature.support.SignatureValidator;
import org.opensaml.xmlsec.signature.support.Signer;
import org.slf4j.Logger;
@ -88,6 +86,7 @@ import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import java.io.*;
import java.net.URLEncoder;
import java.net.UnknownHostException;
import java.nio.charset.StandardCharsets;
import java.security.*;
@ -794,47 +793,68 @@ public class Saml2SSOUtils {
}
public static String getAuthnRequest(Saml2ConfigurableProvider provider) throws Exception {
public static AuthnRequestModel getAuthnRequest(Saml2ConfigurableProvider provider) throws Exception {
AuthnRequest authnRequest = buildAuthnRequest(provider);
String relayState = "spId=" + provider.getSpEntityId() + "&configurableLoginId=" + provider.getConfigurableLoginId();
String authnRequestXml = null;
DocumentBuilder builder;
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
String signatureBase64 = null;
try {
Signature signature = (Signature) buildXMLObject(Signature.DEFAULT_ELEMENT_NAME);
if(provider.isAuthnRequestsSigned()){
Credential credential = getCredential(provider.getSigningCert());
signature.setSigningCredential(credential);
signature.setSignatureAlgorithm(SignatureConstants.ALGO_ID_SIGNATURE_RSA_SHA256);
signature.setCanonicalizationAlgorithm(SignatureConstants.ALGO_ID_C14N_EXCL_OMIT_COMMENTS);
X509KeyInfoGeneratorFactory keyInfoGeneratorFactory = new X509KeyInfoGeneratorFactory();
keyInfoGeneratorFactory.setEmitEntityCertificate(true);
KeyInfoGenerator keyInfoGenerator = keyInfoGeneratorFactory.newInstance();
signature.setKeyInfo(keyInfoGenerator.generate(getCredential(provider.getSigningCert())));
authnRequest.setSignature(signature);
}
builder = factory.newDocumentBuilder();
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.newDocument();
Marshaller out = registry.getMarshallerFactory().getMarshaller(authnRequest);
out.marshall(authnRequest, document);
if(provider.isAuthnRequestsSigned()) {
Signer.signObject(signature);
}
authnRequestXml = XmlBuilder.generateXml(document);
if(provider.isAuthnRequestsSigned()) {
signatureBase64 = buildSignature(authnRequestXml, relayState, provider.getSigningCert());
}
}
catch (MarshallingException | ParserConfigurationException e) {
logger.error(e.getMessage(), e);
}
return authnRequestXml;
AuthnRequestModel authnRequestModel = new AuthnRequestModel();
authnRequestModel.setAuthnRequestXml(authnRequestXml);
authnRequestModel.setRelayState(relayState);
authnRequestModel.setAlgorithm("http://www.w3.org/2000/09/xmldsig#rsa-sha1");
authnRequestModel.setSignature(signatureBase64);
return authnRequestModel;
}
private static String buildSignature(String authnRequest, String relayState, CertificateInfo signingCertInfo) throws Exception{
KeyStore ks = (signingCertInfo.getKeyFormat().getType().equals("JKS")) ? KeyStore.getInstance("JKS") : KeyStore.getInstance("PKCS12");
String archivePassword = signingCertInfo.getKeystorePassword();
char[] pwdArray = (archivePassword != null) ? archivePassword.toCharArray() : "changeit".toCharArray();
ks.load(new FileInputStream(signingCertInfo.getKeystorePath()), pwdArray);
PrivateKey pk = (PrivateKey) ks.getKey(signingCertInfo.getAlias(), signingCertInfo.getPassword().toCharArray());
String signAlgorithm = "http://www.w3.org/2000/09/xmldsig#rsa-sha1";
String message = "SAMLRequest=" + URLEncoder.encode(authnRequest, "UTF-8")
+ "&RelayState=" + URLEncoder.encode(relayState, "UTF-8")
+ "&SigAlg=" + URLEncoder.encode(signAlgorithm, "UTF-8");
String signature = null;
try{
signature = new String(org.apache.commons.codec.binary.Base64.encodeBase64(sign(message, pk)), StandardCharsets.UTF_8);
}
catch(InvalidKeyException | SignatureException | NoSuchAlgorithmException e){
logger.error(e.getMessage(), e);
}
return signature;
}
private static byte[] sign(String message, PrivateKey key) throws InvalidKeyException, SignatureException, NoSuchAlgorithmException {
java.security.Signature instance = java.security.Signature.getInstance("SHA1withRSA");
instance.initSign(key);
instance.update(message.getBytes());
return instance.sign();
}
private static AuthnRequest buildAuthnRequest(Saml2ConfigurableProvider provider) throws Exception {

View File

@ -14,6 +14,8 @@ public interface DatabaseRepository {
DMPDao getDmpDao();
DmpDatasetProfileDao getDmpDatasetProfileDao();
OrganisationDao getOrganisationDao();
GrantDao getGrantDao();
@ -62,5 +64,7 @@ public interface DatabaseRepository {
EntityDoiDao getEntityDoiDao();
DescriptionTemplateTypeDao getDescriptionTemplateTypeDao();
<T> void detachEntity(T entity);
}

View File

@ -16,6 +16,7 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
private DatasetDao datasetDao;
private DatasetProfileDao datasetProfileDao;
private DMPDao dmpDao;
private DmpDatasetProfileDao dmpDatasetProfileDao;
private OrganisationDao organisationDao;
private GrantDao GrantDao;
private RegistryDao registryDao;
@ -40,6 +41,7 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
private NotificationDao notificationDao;
private FileUploadDao fileUploadDao;
private EntityDoiDao entityDoiDao;
private DescriptionTemplateTypeDao descriptionTemplateTypeDao;
private EntityManager entityManager;
@ -63,6 +65,11 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
this.dmpDao = dmpDao;
}
@Autowired
private void setDmpDatasetProfileDao(DmpDatasetProfileDao dmpDatasetProfileDao) {
this.dmpDatasetProfileDao = dmpDatasetProfileDao;
}
@Autowired
private void setOrganisationDao(OrganisationDao organisationDao) {
this.organisationDao = organisationDao;
@ -113,6 +120,11 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
return dmpDao;
}
@Override
public DmpDatasetProfileDao getDmpDatasetProfileDao() {
return dmpDatasetProfileDao;
}
@Override
public OrganisationDao getOrganisationDao() {
return organisationDao;
@ -328,6 +340,16 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
this.entityDoiDao = entityDoiDao;
}
@Override
public DescriptionTemplateTypeDao getDescriptionTemplateTypeDao() {
return descriptionTemplateTypeDao;
}
@Autowired
public void setDescriptionTemplateTypeDao(DescriptionTemplateTypeDao descriptionTemplateTypeDao) {
this.descriptionTemplateTypeDao = descriptionTemplateTypeDao;
}
public <T> void detachEntity(T entity) {
this.entityManager.detach(entity);
}

View File

@ -8,12 +8,14 @@ import eu.eudat.exceptions.security.NullEmailException;
import eu.eudat.logic.builders.entity.CredentialBuilder;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.builders.entity.UserTokenBuilder;
import eu.eudat.logic.managers.MetricsManager;
import eu.eudat.logic.security.validators.TokenValidatorFactoryImpl;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.login.Credentials;
import eu.eudat.models.data.loginprovider.LoginProviderUser;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.Authorities;
import eu.eudat.types.MetricNames;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -30,10 +32,12 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
protected ApiContext apiContext;
protected Environment environment;
protected MetricsManager metricsManager;
public AbstractAuthenticationService(ApiContext apiContext, Environment environment) {
public AbstractAuthenticationService(ApiContext apiContext, Environment environment, MetricsManager metricsManager) {
this.apiContext = apiContext;
this.environment = environment;
this.metricsManager = metricsManager;
}
protected Date addADay(Date date) {
@ -91,6 +95,7 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
if (credential == null && credentials.getUsername().equals(environment.getProperty("autouser.root.username"))) {
try {
credential = this.autoCreateUser(credentials.getUsername(), credentials.getSecret());
metricsManager.increaseValue(MetricNames.USERS, 1, MetricNames.TOTAL);
} catch (Exception e) {
logger.error(e.getMessage(), e);
return null;
@ -162,7 +167,7 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
role.setRole(Authorities.USER.getValue());
role.setUserInfo(userInfo);
apiContext.getOperationsContext().getDatabaseRepository().getUserRoleDao().createOrUpdate(role);
metricsManager.increaseValue(MetricNames.USERS, 1, MetricNames.TOTAL);
} else {
Map<String, Object> additionalInfo = userInfo.getAdditionalinfo() != null ?
new JSONObject(userInfo.getAdditionalinfo()).toMap() : new HashMap<>();

View File

@ -5,6 +5,7 @@ import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.entities.UserRole;
import eu.eudat.data.entities.UserToken;
import eu.eudat.logic.builders.model.models.PrincipalBuilder;
import eu.eudat.logic.managers.MetricsManager;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.Authorities;
@ -19,8 +20,8 @@ import java.util.List;
@Service("nonVerifiedUserAuthenticationService")
public class NonVerifiedUserEmailAuthenticationService extends AbstractAuthenticationService {
public NonVerifiedUserEmailAuthenticationService(ApiContext apiContext, Environment environment) {
super(apiContext, environment);
public NonVerifiedUserEmailAuthenticationService(ApiContext apiContext, Environment environment, MetricsManager metricsManager) {
super(apiContext, environment, metricsManager);
}
public Principal Touch(UserToken token) {

View File

@ -10,6 +10,7 @@ import eu.eudat.logic.builders.entity.CredentialBuilder;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.builders.entity.UserTokenBuilder;
import eu.eudat.logic.builders.model.models.PrincipalBuilder;
import eu.eudat.logic.managers.MetricsManager;
import eu.eudat.logic.security.validators.TokenValidatorFactoryImpl;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.login.Credentials;
@ -27,8 +28,8 @@ import java.util.*;
@Service("verifiedUserAuthenticationService")
public class VerifiedUserAuthenticationService extends AbstractAuthenticationService {
public VerifiedUserAuthenticationService(ApiContext apiContext, Environment environment) {
super(apiContext, environment);
public VerifiedUserAuthenticationService(ApiContext apiContext, Environment environment, MetricsManager metricsManager) {
super(apiContext, environment, metricsManager);
}
public Principal Touch(UserToken token) {

View File

@ -108,7 +108,10 @@ public class MailServiceImpl implements MailService {
lastIndex = content.indexOf("img src=\"", lastIndex);
if (lastIndex != -1) {
imagePaths.add(content.substring(lastIndex + 9, content.indexOf("\"", lastIndex + 9)));
String imagePath = content.substring(lastIndex + 9, content.indexOf("\"", lastIndex + 9));
if (!imagePath.contains("data:image/png;base64")) {
imagePaths.add(imagePath);
}
lastIndex++;
}
}

View File

@ -7,11 +7,14 @@ import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.Organisation;
import eu.eudat.data.entities.Researcher;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.services.forms.VisibilityRuleService;
import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
import eu.eudat.logic.utilities.interfaces.ApplierWithValue;
import eu.eudat.logic.utilities.json.JavaToJson;
import eu.eudat.models.data.components.commons.datafield.*;
import eu.eudat.models.data.pid.PidLink;
import eu.eudat.models.data.pid.PidLinks;
import eu.eudat.models.data.user.components.datasetprofile.Field;
import eu.eudat.models.data.user.components.datasetprofile.FieldSet;
import eu.eudat.models.data.user.components.datasetprofile.Section;
@ -21,6 +24,7 @@ import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.apache.poi.util.Units;
import org.apache.poi.xwpf.usermodel.*;
import org.apache.xmlbeans.XmlCursor;
import org.apache.xmlbeans.XmlObject;
import org.json.JSONArray;
import org.json.JSONException;
import org.jsoup.Jsoup;
@ -71,8 +75,9 @@ public class WordBuilder {
private Integer indent;
private final ObjectMapper mapper;
private Integer imageCount;
private ConfigLoader configLoader;
public WordBuilder(Environment environment) {
public WordBuilder(Environment environment, ConfigLoader configLoader) {
this.cTAbstractNum = CTAbstractNum.Factory.newInstance();
this.cTAbstractNum.setAbstractNumId(BigInteger.valueOf(1));
this.indent = 0;
@ -80,6 +85,7 @@ public class WordBuilder {
this.mapper = new ObjectMapper();
this.buildOptions(environment);
this.buildOptionsInTable(environment);
this.configLoader = configLoader;
}
private void buildOptionsInTable(Environment environment) {
@ -568,6 +574,37 @@ public class WordBuilder {
return hasValue;
}
private void createHypeLink(XWPFDocument mainDocumentPart, String format, String pidType, String pid, boolean hasMultiplicityItems, boolean isMultiAutoComplete){
PidLink pidLink = this.configLoader.getPidLinks().getPidLinks().stream().filter(pl -> pl.getPid().equals(pidType)).findFirst().orElse(null);
if (pidLink != null) {
if (!hasMultiplicityItems) {
XWPFParagraph paragraph = mainDocumentPart.createParagraph();
paragraph.setIndentFromLeft(400 * indent);
if (numId != null) {
paragraph.setNumID(numId);
}
}
if (isMultiAutoComplete) {
XWPFRun r = mainDocumentPart.getLastParagraph().createRun();
r.setText("");
}
XWPFHyperlinkRun run = mainDocumentPart.getLastParagraph().createHyperlinkRun(pidLink.getLink().replace("{pid}", pid));
run.setText(format);
run.setUnderline(UnderlinePatterns.SINGLE);
run.setColor("0000FF");
run.setFontSize(11);
}
else {
String newFormat = (isMultiAutoComplete) ? "" + format : format;
if (hasMultiplicityItems) {
mainDocumentPart.getLastParagraph().createRun().setText(newFormat);
}
else {
addParagraphContent(newFormat, mainDocumentPart, ParagraphStyle.TEXT, numId, indent);
}
}
}
private Boolean createFields(List<Field> fields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService, boolean hasMultiplicityItems) {
if (createListing) this.addListing(mainDocumentPart, indent, false, false);
boolean hasValue = false;
@ -607,6 +644,59 @@ public class WordBuilder {
} else if (field.getViewStyle().getRenderStyle().equals("combobox") && field.getData() instanceof AutoCompleteData) {
format = getCommaSeparatedFormatsFromJson(format, "label");
}
switch (field.getViewStyle().getRenderStyle()) {
case "organizations":
case "externalDatasets":
case "publications":
if(format != null && !format.isEmpty()){
Object hasMultiAutoComplete = mapper.convertValue(field.getData(), Map.class).get("multiAutoComplete");
boolean isMultiAutoComplete = hasMultiAutoComplete != null && (boolean)hasMultiAutoComplete;
if(!isMultiAutoComplete){
Map<String, String> value = mapper.readValue((String)field.getValue(), Map.class);
if(hasMultiplicityItems){
createHypeLink(mainDocumentPart, format, value.get("pidTypeField"), value.get("pid"), true, false);
hasMultiplicityItems = false;
}
else{
createHypeLink(mainDocumentPart, format, value.get("pidTypeField"), value.get("pid"), false, false);
}
}
else{
mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
List<Map<String, Object>> values = new ArrayList<>();
try {
values = Arrays.asList(mapper.readValue(field.getValue().toString(), HashMap[].class));
}
catch (Exception e) {
Map <String, Object> map = new HashMap<>();
map.put("label", field.getValue());
values.add(map);
}
if (values.size() > 1) {
for (Map<String, Object> value : values) {
if(hasMultiplicityItems){
createHypeLink(mainDocumentPart, (String) value.get("name"), (String) value.get("pidTypeField"), (String) value.get("pid"), true, true);
hasMultiplicityItems = false;
}
else{
createHypeLink(mainDocumentPart, (String) value.get("name"), (String) value.get("pidTypeField"), (String) value.get("pid"), false, true);
}
}
}
else if(values.size() == 1){
if(hasMultiplicityItems){
createHypeLink(mainDocumentPart, format, (String) values.get(0).get("pidTypeField"), (String) values.get(0).get("pid"), true, false);
hasMultiplicityItems = false;
}
else{
createHypeLink(mainDocumentPart, format, (String) values.get(0).get("pidTypeField"), (String) values.get(0).get("pid"), false, false);
}
}
}
hasValue = true;
}
break;
default:
boolean isResearcher = field.getViewStyle().getRenderStyle().equals("researchers");
if(format != null && !format.isEmpty()){
Object hasMultiAutoComplete = mapper.convertValue(field.getData(), Map.class).get("multiAutoComplete");
@ -659,7 +749,8 @@ public class WordBuilder {
}
}
}
if(hasMultiplicityItems && format != null){
if (format != null) {
if (hasMultiplicityItems) {
mainDocumentPart.getLastParagraph().createRun().setText(format);
hasMultiplicityItems = false;
hasValue = true;
@ -673,6 +764,8 @@ public class WordBuilder {
}
}
}
}
}
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
@ -881,7 +974,7 @@ public class WordBuilder {
// logger.info("Reverting to custom parsing");
identifierData = customParse(field.getValue().toString());
}
return "id: " + identifierData.get("identifier") + ", Validation Type: " + identifierData.get("type");
return "id: " + identifierData.get("identifier") + ", Type: " + identifierData.get("type");
}
return "";
}
@ -927,32 +1020,15 @@ public class WordBuilder {
int descrParPos = -1;
XWPFParagraph descrPar = null;
for(XWPFParagraph p: document.getParagraphs()){
List<XWPFRun> runs = p.getRuns();
if(runs != null){
for(XWPFRun r : runs){
String text = r.getText(0);
if(text != null){
if(text.contains("{ARGOS.DMP.TITLE}")) {
text = text.replace("{ARGOS.DMP.TITLE}", dmpEntity.getLabel());
r.setText(text, 0);
} else if(text.contains("{ARGOS.DMP.VERSION}")) {
text = text.replace("{ARGOS.DMP.VERSION}", "Version " + dmpEntity.getVersion());
r.setText(text, 0);
} else if(datasetEntity != null && text.contains("{ARGOS.DATASET.TITLE}")) {
text = text.replace("{ARGOS.DATASET.TITLE}", datasetEntity.getLabel());
r.setText(text, 0);
// } else if(text.equals("Description") && ((!isDataset && (dmpEntity == null || dmpEntity.getDescription() != null)) || (isDataset && (datasetEntity == null || datasetEntity.getDescription() == null)))) {
// r.setText("", 0);
} else if((dmpEntity != null && text.contains("{ARGOS.DMP.DESCRIPTION}") && !isDataset) || (datasetEntity != null && text.contains("{ARGOS.DATASET.DESCRIPTION}") && isDataset)) {
descrParPos = parPos;
descrPar = p;
if(dmpEntity != null && !isDataset) {
text = text.replace("{ARGOS.DMP.DESCRIPTION}", "");
} else if(datasetEntity != null && isDataset) {
text = text.replace("{ARGOS.DATASET.DESCRIPTION}", "");
if( dmpEntity != null) {
this.replaceTextSegment(p, "'{ARGOS.DMP.TITLE}'", dmpEntity.getLabel());
this.replaceTextSegment(p, "'{ARGOS.DMP.VERSION}'", "Version " + dmpEntity.getVersion());
}
r.setText(text, 0);
} else if(text.equals("{ARGOS.DMP.RESEARCHERS}")) {
if( datasetEntity != null) {
this.replaceTextSegment(p, "'{ARGOS.DATASET.TITLE}'", datasetEntity.getLabel());
}
String researchersNames = "";
Set<Researcher> researchers = dmpEntity.getResearchers();
int i = 0;
@ -960,27 +1036,28 @@ public class WordBuilder {
i++;
researchersNames += researcher.getLabel() + (i < researchers.size() ? ", " : "");
}
text = text.replace("{ARGOS.DMP.RESEARCHERS}", researchersNames);
r.setText(text, 0);
r.setFontSize(17);
} else if(text.equals("{ARGOS.DMP.ORGANIZATIONS}")) {
this.replaceTextSegment(p, "'{ARGOS.DMP.RESEARCHERS}'", researchersNames, 15);
String organisationsNames = "";
Set<Organisation> organisations = dmpEntity.getOrganisations();
int i = 0;
i = 0;
for(Organisation organisation : organisations){
i++;
organisationsNames += organisation.getLabel() + (i < organisations.size() ? ", " : "");
}
text = text.replace("{ARGOS.DMP.ORGANIZATIONS}", organisationsNames);
r.setText(text, 0);
r.setFontSize(17);
}
}
}
}
parPos++;
}
this.replaceTextSegment(p, "'{ARGOS.DMP.ORGANIZATIONS}'", organisationsNames, 15);
if(this.textSegmentExists(p,"'{ARGOS.DMP.DESCRIPTION}'")) {
descrParPos = parPos;
descrPar = p;
this.replaceTextSegment(p, "'{ARGOS.DMP.DESCRIPTION}'", "");
}
if(this.textSegmentExists(p,"'{ARGOS.DATASET.DESCRIPTION}'")) {
descrParPos = parPos;
descrPar = p;
this.replaceTextSegment(p, "'{ARGOS.DATASET.DESCRIPTION}'", "");
}
}
if((descrParPos != -1) && (dmpEntity!=null) && (dmpEntity.getDescription() != null) && !isDataset) {
XmlCursor cursor = descrPar.getCTP().newCursor();
cursor.toNextSibling();
@ -1000,16 +1077,16 @@ public class WordBuilder {
XWPFTable tbl = document.getTables().get(0);
Iterator<XWPFTableRow> it = tbl.getRows().iterator();
it.next(); // skip first row
if(it.hasNext()){
if(it.hasNext() && dmpEntity.getGrant() != null){
XWPFParagraph p = it.next().getCell(0).getParagraphs().get(0);
XWPFRun run = p.createRun();
run.setText(dmpEntity.getGrant().getFunder().getLabel());
run.setFontSize(17);
run.setFontSize(15);
p.setAlignment(ParagraphAlignment.CENTER);
}
it = tbl.getRows().iterator();
it.next();
if(it.hasNext()){
if(it.hasNext() && dmpEntity.getGrant() != null){
XWPFParagraph p = it.next().getCell(1).getParagraphs().get(0);
XWPFRun run = p.createRun();
String text = dmpEntity.getGrant().getLabel();
@ -1019,7 +1096,7 @@ public class WordBuilder {
text += parts.length > 1 ? "/ No "+parts[parts.length - 1] : "";
}
run.setText(text);
run.setFontSize(17);
run.setFontSize(15);
p.setAlignment(ParagraphAlignment.CENTER);
}
}
@ -1027,43 +1104,165 @@ public class WordBuilder {
public void fillFooter(DMP dmpEntity, Dataset datasetEntity, XWPFDocument document, boolean isDataset) {
document.getFooterList().forEach(xwpfFooter -> {
List<XWPFRun> runs = xwpfFooter.getParagraphs().get(0).getRuns();
if(runs != null){
for(XWPFRun r : runs){
String text = r.getText(0);
if(text != null){
if(text.contains("{ARGOS.DMP.TITLE}")){
text = text.replace("{ARGOS.DMP.TITLE}", dmpEntity.getLabel());
r.setText(text, 0);
for(XWPFParagraph p : xwpfFooter.getParagraphs()){
if(p != null){
if( dmpEntity != null) {
this.replaceTextSegment(p, "'{ARGOS.DMP.TITLE}'", dmpEntity.getLabel());
}
if(text.contains("{ARGOS.DATASET.TITLE}") && datasetEntity != null){
text = text.replace("{ARGOS.DATASET.TITLE}", datasetEntity.getLabel());
r.setText(text, 0);
if( datasetEntity != null) {
this.replaceTextSegment(p, "'{ARGOS.DATASET.TITLE}'", datasetEntity.getLabel());
}
if(text.contains("{ARGOS.DMP.LICENSE}")){
Map<String, String> license = null;
try {
Map<String, String> license = ((Map<String, String>) mapper.readValue(dmpEntity.getExtraProperties(), Map.class).get("license"));
text = text.replace("{ARGOS.DMP.LICENSE}", license.get("pid"));
license = ((Map<String, String>) mapper.readValue(dmpEntity.getExtraProperties(), Map.class).get("license"));
if (license != null && license.get("pid") != null) {
this.replaceTextSegment(p, "'{ARGOS.DMP.LICENSE}'", license.get("pid"));
} else {
this.replaceTextSegment(p, "'{ARGOS.DMP.LICENSE}'", "License: -");
}
catch (JsonProcessingException | NullPointerException e){
text = text.replace("{ARGOS.DMP.LICENSE}", "License: -");
} catch (JsonProcessingException e) {
this.replaceTextSegment(p, "'{ARGOS.DMP.LICENSE}'", "License: -");
}
r.setText(text, 0);
if(dmpEntity.getDois() != null && !dmpEntity.getDois().isEmpty()) {
this.replaceTextSegment(p, "'{ARGOS.DMP.DOI}'", dmpEntity.getDois().iterator().next().getDoi());
} else {
this.replaceTextSegment(p, "'{ARGOS.DMP.DOI}'", "-");
}
if(text.contains("{ARGOS.DMP.DOI}")){
if(dmpEntity.getDois() != null && !dmpEntity.getDois().isEmpty())
text = text.replace("{ARGOS.DMP.DOI}", dmpEntity.getDois().iterator().next().getDoi());
else
text = text.replace("{ARGOS.DMP.DOI}", "-");
r.setText(text, 0);
}
if(text.contains("{ARGOS.DMP.LAST_MODIFIED}")){
DateFormat formatter = new SimpleDateFormat("dd/MM/yyyy");
text = text.replace("{ARGOS.DMP.LAST_MODIFIED}", formatter.format(dmpEntity.getModified()));
r.setText(text, 0);
}
}
this.replaceTextSegment(p, "'{ARGOS.DMP.LAST_MODIFIED}'", formatter.format(dmpEntity.getModified()));
}
}
});
}
private boolean textSegmentExists(XWPFParagraph paragraph, String textToFind) {
TextSegment foundTextSegment = null;
PositionInParagraph startPos = new PositionInParagraph(0, 0, 0);
while((foundTextSegment = this.searchText(paragraph, textToFind, startPos)) != null) {
return true;
}
return false;
}
private void replaceTextSegment(XWPFParagraph paragraph, String textToFind, String replacement) {
this.replaceTextSegment(paragraph, textToFind, replacement, null);
}
private void replaceTextSegment(XWPFParagraph paragraph, String textToFind, String replacement, Integer fontSize) {
TextSegment foundTextSegment = null;
PositionInParagraph startPos = new PositionInParagraph(0, 0, 0);
while((foundTextSegment = this.searchText(paragraph, textToFind, startPos)) != null) { // search all text segments having text to find
System.out.println(foundTextSegment.getBeginRun()+":"+foundTextSegment.getBeginText()+":"+foundTextSegment.getBeginChar());
System.out.println(foundTextSegment.getEndRun()+":"+foundTextSegment.getEndText()+":"+foundTextSegment.getEndChar());
// maybe there is text before textToFind in begin run
XWPFRun beginRun = paragraph.getRuns().get(foundTextSegment.getBeginRun());
String textInBeginRun = beginRun.getText(foundTextSegment.getBeginText());
String textBefore = textInBeginRun.substring(0, foundTextSegment.getBeginChar()); // we only need the text before
// maybe there is text after textToFind in end run
XWPFRun endRun = paragraph.getRuns().get(foundTextSegment.getEndRun());
String textInEndRun = endRun.getText(foundTextSegment.getEndText());
String textAfter = textInEndRun.substring(foundTextSegment.getEndChar() + 1); // we only need the text after
if (foundTextSegment.getEndRun() == foundTextSegment.getBeginRun()) {
textInBeginRun = textBefore + replacement + textAfter; // if we have only one run, we need the text before, then the replacement, then the text after in that run
} else {
textInBeginRun = textBefore + replacement; // else we need the text before followed by the replacement in begin run
endRun.setText(textAfter, foundTextSegment.getEndText()); // and the text after in end run
}
beginRun.setText(textInBeginRun, foundTextSegment.getBeginText());
if (fontSize != null) {
beginRun.setFontSize(fontSize);
}
// runs between begin run and end run needs to be removed
for (int runBetween = foundTextSegment.getEndRun() - 1; runBetween > foundTextSegment.getBeginRun(); runBetween--) {
paragraph.removeRun(runBetween); // remove not needed runs
}
}
}
/**
* this methods parse the paragraph and search for the string searched.
* If it finds the string, it will return true and the position of the String
* will be saved in the parameter startPos.
*
* @param searched
* @param startPos
*/
private TextSegment searchText(XWPFParagraph paragraph, String searched, PositionInParagraph startPos) {
int startRun = startPos.getRun(),
startText = startPos.getText(),
startChar = startPos.getChar();
int beginRunPos = 0, candCharPos = 0;
boolean newList = false;
//CTR[] rArray = paragraph.getRArray(); //This does not contain all runs. It lacks hyperlink runs for ex.
java.util.List<XWPFRun> runs = paragraph.getRuns();
int beginTextPos = 0, beginCharPos = 0; //must be outside the for loop
//for (int runPos = startRun; runPos < rArray.length; runPos++) {
for (int runPos = startRun; runPos < runs.size(); runPos++) {
//int beginTextPos = 0, beginCharPos = 0, textPos = 0, charPos; //int beginTextPos = 0, beginCharPos = 0 must be outside the for loop
int textPos = 0, charPos;
//CTR ctRun = rArray[runPos];
CTR ctRun = runs.get(runPos).getCTR();
XmlCursor c = ctRun.newCursor();
c.selectPath("./*");
try {
while (c.toNextSelection()) {
XmlObject o = c.getObject();
if (o instanceof CTText) {
if (textPos >= startText) {
String candidate = ((CTText) o).getStringValue();
if (runPos == startRun) {
charPos = startChar;
} else {
charPos = 0;
}
for (; charPos < candidate.length(); charPos++) {
if ((candidate.charAt(charPos) == searched.charAt(0)) && (candCharPos == 0)) {
beginTextPos = textPos;
beginCharPos = charPos;
beginRunPos = runPos;
newList = true;
}
if (candidate.charAt(charPos) == searched.charAt(candCharPos)) {
if (candCharPos + 1 < searched.length()) {
candCharPos++;
} else if (newList) {
TextSegment segment = new TextSegment();
segment.setBeginRun(beginRunPos);
segment.setBeginText(beginTextPos);
segment.setBeginChar(beginCharPos);
segment.setEndRun(runPos);
segment.setEndText(textPos);
segment.setEndChar(charPos);
return segment;
}
} else {
candCharPos = 0;
}
}
}
textPos++;
} else if (o instanceof CTProofErr) {
c.removeXml();
} else if (o instanceof CTRPr) {
//do nothing
} else {
candCharPos = 0;
}
}
} finally {
c.dispose();
}
}
return null;
}
}

View File

@ -36,6 +36,8 @@ public class ExportXmlBuilderDatasetProfile {
Element pages = (Element)xmlDoc.getFirstChild();
pages.setAttribute("description", datasetProfile.getDescription());
pages.setAttribute("language", datasetProfile.getLanguage());
pages.setAttribute("type", datasetProfile.getType());
pages.setAttribute("enablePrefilling", String.valueOf(datasetProfile.isEnablePrefilling()));
String xml = XmlBuilder.generateXml(xmlDoc);
writer.write(xml);
writer.close();

View File

@ -1,6 +1,8 @@
package eu.eudat.logic.utilities.documents.xml.datasetProfileXml.datasetProfileModel;
import eu.eudat.data.entities.DescriptionTemplate;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
@ -12,6 +14,8 @@ public class DatasetProfile {
private String description;
private String language;
private String type;
private boolean enablePrefilling;
private List<Page> page;
@ -42,12 +46,32 @@ public class DatasetProfile {
this.language = language;
}
@XmlAttribute(name = "type")
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
@XmlAttribute(name = "enablePrefilling")
public boolean isEnablePrefilling() {
return enablePrefilling;
}
public void setEnablePrefilling(boolean enablePrefilling) {
this.enablePrefilling = enablePrefilling;
}
public eu.eudat.models.data.admin.composite.DatasetProfile toAdminCompositeModel(String label){
eu.eudat.models.data.admin.composite.DatasetProfile newDatasetEntityProfile = new eu.eudat.models.data.admin.composite.DatasetProfile();
newDatasetEntityProfile.setLabel(label);
newDatasetEntityProfile.setStatus(eu.eudat.data.entities.DatasetProfile.Status.SAVED.getValue());
newDatasetEntityProfile.setStatus(DescriptionTemplate.Status.SAVED.getValue());
newDatasetEntityProfile.setDescription(description);
newDatasetEntityProfile.setLanguage(language);
newDatasetEntityProfile.setType(type);
newDatasetEntityProfile.setEnablePrefilling(enablePrefilling);
List<eu.eudat.models.data.admin.components.datasetprofile.Page> pagesDatasetEntity = new LinkedList<>();
List<eu.eudat.models.data.admin.components.datasetprofile.Section> sectionDatasetEntity = new LinkedList<>();
for (Page xmlPage: page) {

View File

@ -0,0 +1,46 @@
package eu.eudat.logic.utilities.documents.xml.dmpXml;
import eu.eudat.logic.utilities.builders.XmlBuilder;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DataManagementPlanBlueprint;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.Section;
import eu.eudat.models.data.listingmodels.DataManagementPlanBlueprintListingModel;
import org.springframework.core.env.Environment;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.UUID;
public class ExportXmlBuilderDmpBlueprint {
public File build(DataManagementPlanBlueprintListingModel dmpProfile, Environment environment) throws IOException {
File xmlFile = new File(environment.getProperty("temp.temp") + UUID.randomUUID() + ".xml");
BufferedWriter writer = new BufferedWriter(new FileWriter(xmlFile, true));
Document xmlDoc = XmlBuilder.getDocument();
Element root = xmlDoc.createElement("root");
Element definition = xmlDoc.createElement("definition");
// Element root = xmlDoc.createElement(dmpProfile.getLabel());
definition.appendChild(createDefinition(dmpProfile.getDefinition(), xmlDoc));
root.appendChild(definition);
xmlDoc.appendChild(root);
String xml = XmlBuilder.generateXml(xmlDoc);
writer.write(xml);
writer.close();
return xmlFile;
}
public Element createDefinition(DataManagementPlanBlueprint dmpDefinition, Document doc) {
Element sections = doc.createElement("sections");
for (Section section : dmpDefinition.getSections()) {
sections.appendChild(section.toXml(doc));
}
return sections;
}
}

View File

@ -1,56 +0,0 @@
package eu.eudat.logic.utilities.documents.xml.dmpXml;
import eu.eudat.logic.utilities.builders.XmlBuilder;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DataManagementPlanProfile;
import eu.eudat.models.data.listingmodels.DataManagementPlanProfileListingModel;
import org.springframework.core.env.Environment;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.UUID;
public class ExportXmlBuilderDmpProfile {
public File build(DataManagementPlanProfileListingModel dmpProfile, Environment environment) throws IOException {
File xmlFile = new File(environment.getProperty("temp.temp") + UUID.randomUUID() + ".xml");
BufferedWriter writer = new BufferedWriter(new FileWriter(xmlFile, true));
Document xmlDoc = XmlBuilder.getDocument();
Element root = xmlDoc.createElement("root");
Element definition = xmlDoc.createElement("definition");
// Element root = xmlDoc.createElement(dmpProfile.getLabel());
definition.appendChild(createDefinition(dmpProfile.getDefinition(), xmlDoc));
root.appendChild(definition);
xmlDoc.appendChild(root);
String xml = XmlBuilder.generateXml(xmlDoc);
writer.write(xml);
writer.close();
return xmlFile;
}
public Element createDefinition(DataManagementPlanProfile dmpDefinition, Document element) {
Element fields = element.createElement("fieldSets");
dmpDefinition.getFields().forEach(item -> {
Element field = element.createElement("field");
field.setAttribute("id", "" + item.getId());
field.setAttribute("type", "" + item.getType());
field.setAttribute("dataType", "" + item.getDataType());
field.setAttribute("required", "" + item.getRequired());
field.setAttribute("label", "" + item.getLabel());
if(item.getValue()!=null) {
Element value = element.createElement("value");
value.setAttribute("value", ""+item.getValue());
field.appendChild(value);
}
fields.appendChild(field);
});
return fields;
}
}

View File

@ -1,6 +1,6 @@
package eu.eudat.logic.utilities.documents.xml.dmpXml;
import eu.eudat.logic.utilities.documents.xml.dmpXml.dmpProfileModel.DmpProfile;
import eu.eudat.logic.utilities.documents.xml.dmpXml.dmpBlueprintModel.DmpBlueprint;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -10,16 +10,16 @@ import javax.xml.bind.Unmarshaller;
import java.io.File;
import java.io.IOException;
public class ImportXmlBuilderDmpProfile {
private static final Logger logger = LoggerFactory.getLogger(ImportXmlBuilderDmpProfile.class);
public class ImportXmlBuilderDmpBlueprint {
private static final Logger logger = LoggerFactory.getLogger(ImportXmlBuilderDmpBlueprint.class);
public DmpProfile build(File xmlFile) throws IOException {
DmpProfile dmpProfile = new DmpProfile();
public DmpBlueprint build(File xmlFile) throws IOException {
DmpBlueprint dmpProfile = new DmpBlueprint();
JAXBContext jaxbContext = null;
try {
jaxbContext = JAXBContext.newInstance(DmpProfile.class);
jaxbContext = JAXBContext.newInstance(DmpBlueprint.class);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
dmpProfile = (DmpProfile) unmarshaller.unmarshal(xmlFile);
dmpProfile = (DmpBlueprint) unmarshaller.unmarshal(xmlFile);
} catch (JAXBException e) {
logger.error(e.getMessage(), e);
}

View File

@ -0,0 +1,73 @@
package eu.eudat.logic.utilities.documents.xml.dmpXml.dmpBlueprintModel;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.types.FieldCategory;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlRootElement;
import java.util.UUID;
@XmlRootElement(name = "descriptionTemplate")
public class DescriptionTemplate {
private String id;
private String descriptionTemplateId;
private String label;
private Integer minMultiplicity;
private Integer maxMultiplicity;
@XmlAttribute(name = "id")
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
@XmlAttribute(name = "descriptionTemplateId")
public String getDescriptionTemplateId() {
return descriptionTemplateId;
}
public void setDescriptionTemplateId(String descriptionTemplateId) {
this.descriptionTemplateId = descriptionTemplateId;
}
@XmlAttribute(name = "label")
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
@XmlAttribute(name = "minMultiplicity")
public Integer getMinMultiplicity() {
return minMultiplicity;
}
public void setMinMultiplicity(Integer minMultiplicity) {
this.minMultiplicity = minMultiplicity;
}
@XmlAttribute(name = "maxMultiplicity")
public Integer getMaxMultiplicity() {
return maxMultiplicity;
}
public void setMaxMultiplicity(Integer maxMultiplicity) {
this.maxMultiplicity = maxMultiplicity;
}
public eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DescriptionTemplate toDmpBlueprintCompositeModel() {
eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DescriptionTemplate descriptionTemplate = new eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DescriptionTemplate();
descriptionTemplate.setId(UUID.fromString(this.id));
descriptionTemplate.setDescriptionTemplateId(UUID.fromString(this.descriptionTemplateId));
descriptionTemplate.setLabel(this.label);
descriptionTemplate.setMinMultiplicity(this.minMultiplicity);
descriptionTemplate.setMaxMultiplicity(this.maxMultiplicity);
return descriptionTemplate;
}
}

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@ -0,0 +1,20 @@
package eu.eudat.logic.utilities.documents.xml.dmpXml.dmpBlueprintModel;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import java.util.List;
@XmlRootElement(name = "descriptionTemplates")
public class DescriptionTemplates {
private List<DescriptionTemplate> descriptionTemplates;
@XmlElement(name = "descriptionTemplate")
public List<DescriptionTemplate> getDescriptionTemplates() {
return descriptionTemplates;
}
public void setDescriptionTemplates(List<DescriptionTemplate> descriptionTemplates) {
this.descriptionTemplates = descriptionTemplates;
}
}

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