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Add extra sanity checks

This commit is contained in:
George Kalampokis 2021-10-13 17:47:50 +03:00
parent 045dd51014
commit 65644c3a35
7 changed files with 32 additions and 181 deletions
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3
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Dmp.java
View File

@ -287,6 +287,9 @@ public class Dmp implements ElasticEntity<Dmp> {
@Override @Override
public Dmp fromElasticEntity(Map<String, Object> fields) { public Dmp fromElasticEntity(Map<String, Object> fields) {
if (fields == null || fields.isEmpty()) {
return null;
}
this.id = UUID.fromString((String) fields.get(MapKey.ID.getName())); this.id = UUID.fromString((String) fields.get(MapKey.ID.getName()));
if (fields.size() > 1) { if (fields.size() > 1) {
this.label = (String) fields.get(MapKey.LABEL.getName()); this.label = (String) fields.get(MapKey.LABEL.getName());

30
dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/DatasetRepository.java
View File

@ -55,24 +55,26 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
if (this.getClient() != null) { if (this.getClient() != null) {
XContentBuilder builder = XContentFactory.jsonBuilder(); XContentBuilder builder = XContentFactory.jsonBuilder();
Dmp dmp = this.dmpRepository.findDocument(entity.getDmp().toString()); Dmp dmp = this.dmpRepository.findDocument(entity.getDmp().toString());
boolean found = false; if (dmp != null) {
if (dmp.getDatasets() != null && !dmp.getDatasets().isEmpty()) { boolean found = false;
for (int i = 0; i < dmp.getDatasets().size(); i++) { if (dmp.getDatasets() != null && !dmp.getDatasets().isEmpty()) {
if (dmp.getDatasets().get(i).getId().equals(entity.getId())) { for (int i = 0; i < dmp.getDatasets().size(); i++) {
dmp.getDatasets().set(i, entity); if (dmp.getDatasets().get(i).getId().equals(entity.getId())) {
found = true; dmp.getDatasets().set(i, entity);
break; found = true;
break;
}
} }
} }
} if (!found) {
if (!found) { if (dmp.getDatasets() == null) {
if (dmp.getDatasets() == null) { dmp.setDatasets(new ArrayList<>());
dmp.setDatasets(new ArrayList<>()); }
dmp.getDatasets().add(entity);
} }
dmp.getDatasets().add(entity); IndexRequest request = new IndexRequest(this.environment.getProperty("elasticsearch.index")).id(dmp.getId().toString()).source(dmp.toElasticEntity(builder));//new IndexRequest("datasets", "doc", entity.getId()).source(entity.toElasticEntity(builder));
this.getClient().index(request, RequestOptions.DEFAULT);
} }
IndexRequest request = new IndexRequest(this.environment.getProperty("elasticsearch.index")).id(dmp.getId().toString()).source(dmp.toElasticEntity(builder));//new IndexRequest("datasets", "doc", entity.getId()).source(entity.toElasticEntity(builder));
this.getClient().index(request, RequestOptions.DEFAULT);
return entity; return entity;
} }
return null; return null;

159
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DocumentManager.java
View File

@ -1,159 +0,0 @@
package eu.eudat.logic.managers;
import eu.eudat.data.dao.entities.DatasetDao;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.forms.VisibilityRuleService;
import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
import eu.eudat.logic.utilities.documents.word.WordBuilder;
import eu.eudat.logic.utilities.documents.xml.ExportXmlBuilder;
import eu.eudat.models.HintedModelFactory;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import org.apache.commons.io.IOUtils;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
import org.springframework.http.*;
import org.springframework.http.converter.ByteArrayHttpMessageConverter;
import org.springframework.stereotype.Service;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.web.client.RestTemplate;
import java.io.*;
import java.net.URL;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.UUID;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
/**
* Created by ikalyvas on 10/16/2018.
*/
@Service
public class DocumentManager {
private static final Logger logger = LoggerFactory.getLogger(DocumentManager.class);
private ApiContext context;
private DatasetManager datasetManager;
private ConfigLoader configLoader;
private Environment environment;
public DocumentManager(ApiContext context, DatasetManager datasetManager, ConfigLoader configLoader, Environment environment) {
this.context = context;
this.datasetManager = datasetManager;
this.configLoader = configLoader;
this.environment = environment;
}
public File getWordDocument(ConfigLoader configLoader, DatasetDao datatasetRepository, String id, VisibilityRuleService visibilityRuleService) throws InstantiationException, IllegalAccessException, IOException {
WordBuilder wordBuilder = new WordBuilder();
DatasetWizardModel dataset = new DatasetWizardModel();
XWPFDocument document = configLoader.getDocument();
eu.eudat.data.entities.Dataset datasetEntity = datatasetRepository.find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
Map<String, Object> properties = new HashMap<>();
if (datasetEntity.getProperties() != null) {
JSONObject jobject = new JSONObject(datasetEntity.getProperties());
properties = jobject.toMap();
}
PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
wordBuilder.build(document, pagedDatasetProfile, visibilityRuleService);
File exportFile = new File(dataset.getLabel() + ".docx");
FileOutputStream out = new FileOutputStream(exportFile);
document.write(out);
out.close();
return exportFile;
}
public FileEnvelope getXmlDocument(eu.eudat.data.entities.Dataset datasetEntity, String id, VisibilityRuleService visibilityRuleService) throws InstantiationException, IllegalAccessException, IOException {
ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
DatasetWizardModel dataset = new DatasetWizardModel();
Map<String, Object> properties = new HashMap<>();
if (datasetEntity.getProperties() != null) {
JSONObject jobject = new JSONObject(datasetEntity.getProperties());
properties = jobject.toMap();
}
PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
File file = xmlBuilder.build(pagedDatasetProfile, UUID.fromString(id), visibilityRuleService, environment);
FileEnvelope fileEnvelope = new FileEnvelope();
fileEnvelope.setFile(file);
fileEnvelope.setFilename(datasetEntity.getLabel());
return fileEnvelope;
}
public File convertToPDF(File file, Environment environment, String label) throws IOException, InterruptedException {
LinkedMultiValueMap<String, Object> map = new LinkedMultiValueMap<>();
map.add("file", new FileSystemResource(file));
HttpHeaders headers = new HttpHeaders();
headers.setContentType(MediaType.MULTIPART_FORM_DATA);
headers.add("Content-disposition", "attachment; filename=" + label + ".docx");
headers.add("Content-type", "application/vnd.openxmlformats-officedocument.wordprocessingml.document");
HttpEntity<LinkedMultiValueMap<String, Object>> requestEntity = new HttpEntity<LinkedMultiValueMap<String, Object>>(
map, headers);
Map queueResult = new RestTemplate().postForObject(
environment.getProperty("pdf.converter.url") +
"api/v1/", requestEntity, Map.class);
Map mediaResult = new RestTemplate().getForObject(environment.getProperty("pdf.converter.url") +
"/api/v1/" + queueResult.get("id"), Map.class);
logger.info("Status: " + mediaResult.get("status"));
while (!mediaResult.get("status").equals("finished")) {
Thread.sleep(500);
mediaResult = new RestTemplate().getForObject(environment.getProperty("pdf.converter.url") +
"api/v1/" + queueResult.get("id"), Map.class);
logger.info("Polling");
}
RestTemplate restTemplate = new RestTemplate();
restTemplate.getMessageConverters().add(new ByteArrayHttpMessageConverter());
HttpHeaders headers2 = new HttpHeaders();
headers.setAccept(Arrays.asList(MediaType.APPLICATION_OCTET_STREAM));
HttpEntity<String> entity = new HttpEntity<String>(headers2);
ResponseEntity<byte[]> response = restTemplate.exchange(environment.getProperty("pdf.converter.url") +
mediaResult.get("result_url"), HttpMethod.GET, entity, byte[].class, "1");
UUID uuid = UUID.randomUUID();
File zip = new File(uuid + ".zip");
if (response.getStatusCode().equals(HttpStatus.OK)) {
FileOutputStream output = new FileOutputStream(zip);
IOUtils.write(response.getBody(), output);
}
return extractFromZip(zip, label + ".pdf");
}
private File extractFromZip(File file, String filename) throws IOException {
byte[] buffer = new byte[1024];
File newFile = new File(filename);
ZipInputStream zis = new ZipInputStream(new FileInputStream(file));
ZipEntry zipEntry = zis.getNextEntry();
while (zipEntry != null) {
String zippedFileName = zipEntry.getName();
if (zippedFileName.equals("pdf")) {
FileOutputStream fos = new FileOutputStream(newFile);
int len;
while ((len = zis.read(buffer)) > 0) {
fos.write(buffer, 0, len);
}
fos.close();
zipEntry = zis.getNextEntry();
}
}
zis.closeEntry();
zis.close();
return newFile;
}
}

3
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/HtmlToWorldBuilder.java
View File

@ -63,7 +63,7 @@ public class HtmlToWorldBuilder implements NodeVisitor {
this.dumpRun = false; this.dumpRun = false;
} }
parseProperties(); parseProperties();
properties.clear();
} }
private void parseProperties() { private void parseProperties() {
@ -105,5 +105,6 @@ public class HtmlToWorldBuilder implements NodeVisitor {
String name = node.nodeName(); String name = node.nodeName();
properties.put(name, false); properties.put(name, false);
parseProperties(); parseProperties();
properties.clear();
} }
} }

2
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/ExportXmlBuilder.java
View File

@ -124,7 +124,7 @@ public class ExportXmlBuilder {
} catch (IOException ex) { } catch (IOException ex) {
try { try {
Map<String, Object> jsonElement = mapper.readValue(field.getValue().toString(), Map.class); Map<String, Object> jsonElement = mapper.readValue(field.getValue().toString(), Map.class);
valueField.setTextContent((jsonElement.get("label") != null ? jsonElement.get("label").toString() : jsonElement.get("name").toString())); valueField.setTextContent((jsonElement.get("label") != null ? jsonElement.get("label").toString() : jsonElement.get("name") != null ? jsonElement.get("name").toString() : ""));
} catch (IOException e) { } catch (IOException e) {
valueField.setTextContent(field.getValue().toString()); valueField.setTextContent(field.getValue().toString());
} }

8
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/DmpRDAMapper.java
View File

@ -127,9 +127,11 @@ public class DmpRDAMapper {
entity.setDescription(rda.getDescription()); entity.setDescription(rda.getDescription());
DatasetProfile defaultProfile = ((DatasetProfile)entity.getAssociatedDmps().toArray()[0]); DatasetProfile defaultProfile = ((DatasetProfile)entity.getAssociatedDmps().toArray()[0]);
entity.setDataset(rda.getDataset().stream().map(rda1 -> datasetRDAMapper.toEntity(rda1, defaultProfile)).collect(Collectors.toSet())); entity.setDataset(rda.getDataset().stream().map(rda1 -> datasetRDAMapper.toEntity(rda1, defaultProfile)).collect(Collectors.toSet()));
Map<String, Object> result = ProjectRDAMapper.toEntity(rda.getProject().get(0), apiContext); if (rda.getProject().size() > 0) {
entity.setProject((Project) result.get("project")); Map<String, Object> result = ProjectRDAMapper.toEntity(rda.getProject().get(0), apiContext);
result.entrySet().stream().filter(entry -> entry.getKey().startsWith("grant")).forEach(entry -> entity.setGrant((Grant) entry.getValue())); entity.setProject((Project) result.get("project"));
result.entrySet().stream().filter(entry -> entry.getKey().startsWith("grant")).forEach(entry -> entity.setGrant((Grant) entry.getValue()));
}
Map<String, Object> extraProperties = new HashMap<>(); Map<String, Object> extraProperties = new HashMap<>();
extraProperties.put("language", LanguageRDAMapper.mapRDAIsoToLanguageIso(rda.getLanguage())); extraProperties.put("language", LanguageRDAMapper.mapRDAIsoToLanguageIso(rda.getLanguage()));

8
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/KeywordRDAMapper.java
View File

@ -17,9 +17,11 @@ public class KeywordRDAMapper {
ObjectMapper mapper = new ObjectMapper(); ObjectMapper mapper = new ObjectMapper();
try { try {
value = JavaToJson.objectStringToJson(value); value = JavaToJson.objectStringToJson(value);
List<Tag> tags = Arrays.asList(mapper.readValue(value, Tag[].class)); if (!value.isEmpty()) {
List<String> keywordNames = tags.stream().map(Tag::getName).collect(Collectors.toList()); List<Tag> tags = Arrays.asList(mapper.readValue(value, Tag[].class));
return keywordNames; List<String> keywordNames = tags.stream().map(Tag::getName).collect(Collectors.toList());
return keywordNames;
}
} catch (IOException e) { } catch (IOException e) {
logger.error(e.getMessage(), e); logger.error(e.getMessage(), e);
} }