Revision 48294
Added by Argiro Kokogiannaki over 7 years ago
| modules/uoa-claims/trunk/src/test/java/eu/dnetlib/data/claims/migration/parser/ExternalParserTest.java | ||
|---|---|---|
| 256 | 256 |
Assert.assertNull(result.getEmbargoEndDate()); |
| 257 | 257 |
|
| 258 | 258 |
} |
| 259 |
@Test |
|
| 260 |
public void testMD5() throws Exception {
|
|
| 261 |
String id = "10.1016/j.engstruct.2013.03.014"; |
|
| 262 |
String createdId = ExternalRecordParser.createOpenaireId(id); |
|
| 263 |
String openaireId = "userclaim___::07ec9eb2278a11e352e3fa93a621411d"; |
|
| 264 |
Assert.assertEquals(createdId,openaireId); |
|
| 265 |
|
|
| 266 |
} |
|
| 259 | 267 |
} |
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claims/migration/Migration.java | ||
|---|---|---|
| 351 | 351 |
try {
|
| 352 | 352 |
migration.claimHandler.getQueryGenerator().setMigrationTable("claims_view");
|
| 353 | 353 |
List<Claim> claims = null; |
| 354 |
claims = migration.createContextRelationClaims(); |
|
| 355 |
// claims = migration.createRelationsClaims();
|
|
| 354 |
// claims = migration.createContextRelationClaims();
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|
| 355 |
claims = migration.createRelationsClaims(); |
|
| 356 | 356 |
|
| 357 | 357 |
migration.printStatistics(claims); |
| 358 | 358 |
migration.saveClaims(claims); |
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claims/migration/parser/ExternalRecordParser.java | ||
|---|---|---|
| 271 | 271 |
} |
| 272 | 272 |
return result; |
| 273 | 273 |
} |
| 274 |
private static String createOpenaireId(String id){
|
|
| 274 |
public static String createOpenaireId(String id){
|
|
| 275 | 275 |
System.out.println("createOpenaireId from id:" +id);
|
| 276 | 276 |
if(id==null){
|
| 277 | 277 |
return null; |
| ... | ... | |
| 282 | 282 |
m = MessageDigest.getInstance("MD5");
|
| 283 | 283 |
m.update(id.getBytes(),0,id.length()); |
| 284 | 284 |
openaireId = new BigInteger(1,m.digest()).toString(16); |
| 285 |
while(openaireId.length() < 32 ){
|
|
| 286 |
openaireId = "0"+openaireId; |
|
| 287 |
} |
|
| 285 | 288 |
} catch (NoSuchAlgorithmException e) {
|
| 286 | 289 |
logger.error("Couldn't instatiate md5 algorithm",e);
|
| 287 | 290 |
} |
| 288 |
openaireId ="user:claim__"+openaireId;
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|
| 291 |
openaireId ="userclaim___::"+openaireId;
|
|
| 289 | 292 |
return openaireId; |
| 290 | 293 |
} |
| 291 | 294 |
|
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claims/migration/handler/ContextRelationHandler.java | ||
|---|---|---|
| 21 | 21 |
|
| 22 | 22 |
public List<ContextRelation> fetchAllConceptRelations() throws Exception, SQLStoreException {
|
| 23 | 23 |
List<ContextRelation> relations = null; |
| 24 |
// ResultSet rs = sqlDAO.executePreparedQuery(queryGenerator.generateQueryForTesting(-1,"169112")); |
|
| 25 | 24 |
ResultSet rs = sqlDAO.executePreparedQuery(queryGenerator.generateSelectConceptClaimsEnrichedWithDMFClaimsQuery(-1)); |
| 26 | 25 |
// ResultSet rs = sqlDAO.executePreparedQuery(queryGenerator.generateSelectConceptClaimsForLattestClaimsQuery(-1)); |
| 27 | 26 |
|
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claims/migration/handler/ClaimHandler.java | ||
|---|---|---|
| 259 | 259 |
String sourceId =rs.getString(3); |
| 260 | 260 |
String targetType =rs.getString(4); |
| 261 | 261 |
String targetId =rs.getString(5); |
| 262 |
this.checkRecordFile(sourceType, sourceId); |
|
| 263 |
this.checkRecordFile(targetType, targetId); |
|
| 264 |
|
|
| 262 | 265 |
ArrayList<Object> params2 = new ArrayList<>(); |
| 263 | 266 |
String query2 = queryGenerator.generateDeleteFullClaimQuery(claimId,user,sourceType,sourceId,targetType,targetId, params2); |
| 264 | 267 |
sqlDAO.executeUpdateQuery(query2, params2); |
| ... | ... | |
| 268 | 271 |
rs.close(); |
| 269 | 272 |
} |
| 270 | 273 |
|
| 274 |
public void checkRecordFile(String type, String id) throws SQLStoreException, SQLException {
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|
| 275 |
if(type.equals("publication") || type.equals("dataset")){
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|
| 276 |
this.resultHandler.deleteRecordFile(type,id); |
|
| 277 |
} |
|
| 278 |
} |
|
| 271 | 279 |
public boolean deleteClaim(String claimId) throws Exception, SQLStoreException {
|
| 272 | 280 |
|
| 273 | 281 |
ArrayList<Object> params = new ArrayList<>(); |
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claims/migration/handler/ResultHandler.java | ||
|---|---|---|
| 3 | 3 |
import eu.dnetlib.data.claims.migration.entity.Result; |
| 4 | 4 |
import eu.dnetlib.data.claimsDemo.ClaimUtils; |
| 5 | 5 |
import eu.dnetlib.data.claimsDemo.QueryGenerator; |
| 6 |
import eu.dnetlib.data.claimsDemo.SQLStoreException; |
|
| 6 | 7 |
import eu.dnetlib.data.claimsDemo.SqlDAO; |
| 7 | 8 |
import org.apache.commons.io.FileUtils; |
| 8 | 9 |
import org.apache.log4j.Logger; |
| 9 | 10 |
|
| 10 | 11 |
import java.io.File; |
| 11 | 12 |
import java.io.IOException; |
| 13 |
import java.sql.ResultSet; |
|
| 14 |
import java.sql.SQLException; |
|
| 12 | 15 |
|
| 13 | 16 |
/** |
| 14 | 17 |
* Created by kiatrop on 5/2/2016. |
| ... | ... | |
| 55 | 58 |
return type+"/"+datasource+"/"+openaireId.replace("/","*");
|
| 56 | 59 |
|
| 57 | 60 |
} |
| 61 |
public void deleteRecordFile(String type, String id) throws SQLStoreException, SQLException {
|
|
| 62 |
ResultSet rs = sqlDAO.executePreparedQuery(queryGenerator.generateCountClaimsForResultQuery(id)); |
|
| 63 |
if(rs.next()){
|
|
| 64 |
Integer count = rs.getInt(1); |
|
| 65 |
log.debug("Count is:" + count );
|
|
| 66 |
|
|
| 67 |
if(count != null && count ==1){
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|
| 68 |
ResultSet rs1 = sqlDAO.executePreparedQuery(queryGenerator.generateSelectResultSource(id)); |
|
| 69 |
if(rs1.next()){
|
|
| 70 |
String source = rs1.getString(1); |
|
| 71 |
|
|
| 72 |
log.debug("source is:" + source );
|
|
| 73 |
String path=createExportPath(type, source, id); |
|
| 74 |
File file = new File(this.pathToSaveRecord+path); |
|
| 75 |
log.debug("path is:" + path );
|
|
| 76 |
|
|
| 77 |
|
|
| 78 |
if (file.delete()) {
|
|
| 79 |
log.info(file.getName() + " is deleted!"); |
|
| 80 |
} else {
|
|
| 81 |
log.warn("Delete operation is failed for file "+ this.pathToSaveRecord+path);
|
|
| 82 |
} |
|
| 83 |
}else{
|
|
| 84 |
log.error("Couldn't get result source for result with id : "+ id );
|
|
| 85 |
|
|
| 86 |
} |
|
| 87 |
|
|
| 88 |
}else{
|
|
| 89 |
log.info("This metadata file cannot be removed (count="+count+") for result with id : "+ id );
|
|
| 90 |
} |
|
| 91 |
}else{
|
|
| 92 |
log.error("Couldn't fetch claims count for result with id : "+ id );
|
|
| 93 |
} |
|
| 94 |
} |
|
| 95 |
|
|
| 58 | 96 |
public SqlDAO getSqlDAO() {
|
| 59 | 97 |
return sqlDAO; |
| 60 | 98 |
} |
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claimsDemo/TestClass.java | ||
|---|---|---|
| 18 | 18 |
import eu.dnetlib.data.claims.migration.entity.Result; |
| 19 | 19 |
import eu.dnetlib.data.claims.migration.handler.*; |
| 20 | 20 |
import eu.dnetlib.data.claims.migration.parser.DMFParser; |
| 21 |
import eu.dnetlib.data.claims.migration.parser.ExternalRecordParser; |
|
| 21 | 22 |
import org.apache.log4j.BasicConfigurator; |
| 22 | 23 |
import org.apache.log4j.Logger; |
| 23 | 24 |
import org.junit.Before; |
| ... | ... | |
| 35 | 36 |
import javax.xml.parsers.ParserConfigurationException; |
| 36 | 37 |
import javax.xml.transform.TransformerException; |
| 37 | 38 |
import javax.xml.xpath.XPathExpressionException; |
| 39 |
import java.io.File; |
|
| 38 | 40 |
import java.io.IOException; |
| 39 | 41 |
import java.math.BigInteger; |
| 40 | 42 |
import java.security.MessageDigest; |
| ... | ... | |
| 194 | 196 |
// String id=claimHandler.buildAndInsertClaim("argirok@di.uoa.gr", "project", "corda_______::2c37878a0cede85dbbd1081bb9b4a2f8", "openaire", "OPEN", null,"dataset", "10.5281/ZENODO.154647", "datacite", "EMBARGO","2017-05-01");
|
| 195 | 197 |
|
| 196 | 198 |
|
| 197 |
String id=claimHandler.buildAndInsertClaim("argirok@di.uoa.gr", "context", "egi::country::gr",
|
|
| 198 |
"openaire", null, null,"dataset", "10.4225/41/55A111BDE741C", "datacite", "OPEN","2017-05-01"); |
|
| 199 |
// String id=claimHandler.buildAndInsertClaim("argirok@di.uoa.gr", "context", "egi::country::gr",
|
|
| 200 |
// "openaire", null, null,"dataset", "10.4225/41/55A111BDE741C", "datacite", "OPEN","2017-05-01");
|
|
| 199 | 201 |
} |
| 200 | 202 |
@Test |
| 201 |
public void testDelete() throws Exception {
|
|
| 203 |
public void testDelete() throws Exception, SQLStoreException {
|
|
| 202 | 204 |
|
| 203 |
// claimHandler.deleteClaim("argirok@di.uoa.gr","94");
|
|
| 205 |
// claimHandler.deleteClaim("argirok@di.uoa.gr","2876");
|
|
| 204 | 206 |
// claimHandler.deleteClaim("argirok@di.uoa.gr","3101");
|
| 205 | 207 |
} |
| 206 | 208 |
|
| ... | ... | |
| 393 | 395 |
List<String> mails = new ArrayList<String>(); |
| 394 | 396 |
mails.add("test11111@mail.com");
|
| 395 | 397 |
mails.add("test122222@mail.com");
|
| 396 |
// this.projectHandler.updateContactEmailsByProjectId("123",mails);
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| 398 |
this.projectHandler.updateContactEmailsByProjectId("123",mails);
|
|
| 397 | 399 |
// System.out.println("\n"+this.projectHandler.fetchContactEmailsByProjectId("123")+"\n");
|
| 398 | 400 |
// String token = UUID.randomUUID().toString(); |
| 399 | 401 |
// this.projectHandler.updateTokenByProjectId("123",token);
|
| ... | ... | |
| 403 | 405 |
} |
| 404 | 406 |
@Test |
| 405 | 407 |
public void testMD5() throws Exception {
|
| 406 |
String id = "10.1371/journal.pone.0130756"; |
|
| 407 |
MessageDigest m = MessageDigest.getInstance("MD5");
|
|
| 408 |
m.update(id.getBytes(), 0, id.length()); |
|
| 409 |
id = new BigInteger(1, m.digest()).toString(16); |
|
| 410 |
System.out.println(id); |
|
| 411 |
System.out.println(this.resultHandler.getPathToSaveRecord()); |
|
| 408 |
String id = "10.1016/j.engstruct.2013.03.014"; |
|
| 409 |
String createdId = ExternalRecordParser.createOpenaireId(id); |
|
| 410 |
String openaireId = "userclaim___::07ec9eb2278a11e352e3fa93a621411d"; |
|
| 411 |
System.out.println(createdId ); |
|
| 412 | 412 |
|
| 413 | 413 |
} |
| 414 | 414 |
@Test |
| 415 | 415 |
public void testCuration() throws Exception, SQLStoreException {
|
| 416 |
boolean updated = claimHandler.updateClaimCurationInfo("argiro@gmail.com","1",true);
|
|
| 417 |
System.out.println(updated); |
|
| 416 |
// boolean updated = claimHandler.updateClaimCurationInfo("argiro@gmail.com","1",true);
|
|
| 417 |
// System.out.println(updated);
|
|
| 418 | 418 |
} |
| 419 | 419 |
|
| 420 | 420 |
@Test |
| ... | ... | |
| 426 | 426 |
@Test |
| 427 | 427 |
public void directIndexClaim() throws Exception {
|
| 428 | 428 |
System.out.println(this.claimValidation.getPathToSaveReport()); |
| 429 |
String json = "{\"originalId\":\"user:claim__d1e668dc81fa714aa98a558d9ce515fa\",\"title\":\"Expression of Ik6 and Ik8 Isoforms and Their Association with Relapse and Death in Mexican Children with Acute Lymphoblastic Leukemia\",\"authors\":[\"Reyes-León Adriana\",\"Juárez-Velázquez Rocío\",\"Medrano-Hernández Alma\",\"Cuenca-Roldán Teresa\",\"Salas-Labadía Consuelo\",\"del Pilar Navarrete-Meneses María\",\"Rivera-Luna Roberto\",\"López-Hernández Gerardo\",\"Paredes-Aguilera Rogelio\",\"Pérez-Vera Patricia\"],\"publisher\":\"Public Library of Science (PLoS)\",\"type\":\"publication\",\"pids\":[{\"type\":\"doi\",\"value\":\"10.1371/journal.pone.0130756\"}],\"licenseCode\":\"OPEN\",\"resourceType\":\"0001\",\"url\":\"http://dx.doi.org/10.1371/journal.pone.0130756\",\"hostedById\":\"openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18\",\"collectedFromId\":\"openaire____::crossref\",\"contexts\":[\"egi::country::gr\"]}";
|
|
| 429 |
String json = "{\"originalId\":\"userclaim____::d1e668dc81fa714aa98a558d9ce515fa\",\"title\":\"Expression of Ik6 and Ik8 Isoforms and Their Association with Relapse and Death in Mexican Children with Acute Lymphoblastic Leukemia\",\"authors\":[\"Reyes-León Adriana\",\"Juárez-Velázquez Rocío\",\"Medrano-Hernández Alma\",\"Cuenca-Roldán Teresa\",\"Salas-Labadía Consuelo\",\"del Pilar Navarrete-Meneses María\",\"Rivera-Luna Roberto\",\"López-Hernández Gerardo\",\"Paredes-Aguilera Rogelio\",\"Pérez-Vera Patricia\"],\"publisher\":\"Public Library of Science (PLoS)\",\"type\":\"publication\",\"pids\":[{\"type\":\"doi\",\"value\":\"10.1371/journal.pone.0130756\"}],\"licenseCode\":\"OPEN\",\"resourceType\":\"0001\",\"url\":\"http://dx.doi.org/10.1371/journal.pone.0130756\",\"hostedById\":\"openaire____::1256f046-bf1f-4afc-8b47-d0b147148b18\",\"collectedFromId\":\"openaire____::crossref\",\"contexts\":[\"egi::country::gr\"]}";
|
|
| 430 | 430 |
// System.out.println("\n\nFeed Response is: "+directIndexHandler.insertRecord(json));
|
| 431 | 431 |
|
| 432 |
// System.out.println("\n\nDelete Response is: "+directIndexHandler.deleteRecord("user:claim__d1e668dc81fa714aa98a558d9ce515fa","openaire____::crossref"));
|
|
| 432 |
// System.out.println("\n\nDelete Response is: "+directIndexHandler.deleteRecord("userclaim___::d1e668dc81fa714aa98a558d9ce515fa","openaire____::crossref"));
|
|
| 433 | 433 |
} |
| 434 | 434 |
|
| 435 | 435 |
} |
| modules/uoa-claims/trunk/src/main/java/eu/dnetlib/data/claimsDemo/QueryGenerator.java | ||
|---|---|---|
| 318 | 318 |
*/ |
| 319 | 319 |
private String createSemanticsType(String sourceType,String targetType){
|
| 320 | 320 |
String semantics=null; |
| 321 |
if((targetType.equals(ClaimUtils.PUBLICATION)||targetType.equals(ClaimUtils.DATASET))&&(sourceType.equals(ClaimUtils.PUBLICATION)||sourceType.equals(ClaimUtils.DATASET))){
|
|
| 322 |
semantics="resultResult_"+targetType+sourceType+"_isRelatedTo";
|
|
| 321 |
if((targetType.equals(ClaimUtils.PUBLICATION))&&(sourceType.equals(ClaimUtils.DATASET))){
|
|
| 322 |
semantics="resultResult_publicationDataset_isRelatedTo";
|
|
| 323 | 323 |
} |
| 324 |
else if(targetType.equals(ClaimUtils.DATASET)&&sourceType.equals(ClaimUtils.PUBLICATION)){
|
|
| 325 |
semantics="resultResult_publicationDataset_isRelatedTo"; |
|
| 326 |
} |
|
| 327 |
else if((targetType.equals(ClaimUtils.PUBLICATION))&&(sourceType.equals(ClaimUtils.PUBLICATION))){
|
|
| 328 |
semantics="resultResult_supplement_isSupplementedBy"; |
|
| 329 |
} |
|
| 330 |
else if(targetType.equals(ClaimUtils.DATASET)&&sourceType.equals(ClaimUtils.DATASET)){
|
|
| 331 |
semantics="resultResult_supplement_isSupplementTo"; |
|
| 332 |
} |
|
| 324 | 333 |
else if((targetType.equals(ClaimUtils.PUBLICATION)||targetType.equals(ClaimUtils.DATASET))&&(sourceType.equals(ClaimUtils.PROJECT))){
|
| 325 | 334 |
semantics= "resultProject_outcome_produces"; //"resultProject_outcome_isProducedBy"; |
| 326 | 335 |
} |
| ... | ... | |
| 446 | 455 |
" curated_by text,\n" + |
| 447 | 456 |
" approved boolean DEFAULT TRUE,\n" + |
| 448 | 457 |
" claim_status varchar(30),\n" + |
| 449 |
" semantics varchar(60)\n" + |
|
| 458 |
" semantics varchar(60) NOT NULL\n" +
|
|
| 450 | 459 |
");\n" + |
| 451 | 460 |
"\n" + |
| 452 | 461 |
"CREATE TABLE has_source_context(\n" + |
| ... | ... | |
| 939 | 948 |
return query; |
| 940 | 949 |
} |
| 941 | 950 |
|
| 951 |
public String generateCountClaimsForResultQuery(String resultId){
|
|
| 952 |
return " Select count(*) from claim where source_id = '"+ resultId +"' or target_id = '"+resultId+"' "; |
|
| 953 |
} |
|
| 954 |
public String generateSelectResultSource(String resultId){
|
|
| 955 |
return " Select collected_from from result where openaire_id = '"+ resultId +"' "; |
|
| 956 |
} |
|
| 957 |
|
|
| 942 | 958 |
/** |
| 943 | 959 |
* Select form a has_source_* or has_target_* table |
| 944 | 960 |
* ... |
| ... | ... | |
| 985 | 1001 |
String query =" "; |
| 986 | 1002 |
return " Select id, source_type, source_id, target_type, target_id from claim where id = ?::int and claimedBy = ? "; |
| 987 | 1003 |
} |
| 1004 |
|
|
| 988 | 1005 |
public String generateSelectClaimQuery(String id, ArrayList<Object> params){
|
| 989 | 1006 |
|
| 990 | 1007 |
params.add(id); |
| modules/uoa-claims/trunk/src/main/resources/eu/dnetlib/data/claims/migration/springContext-claimsDemo.properties | ||
|---|---|---|
| 1 | 1 |
|
| 2 | 2 |
services.claimsDemo.db.driverClassName = org.postgresql.Driver |
| 3 |
services.claimsDemo.db.url = jdbc:postgresql://scoobydoo.di.uoa.gr:5432/claimsnewschema
|
|
| 4 |
services.claimsDemo.db.username = invalid_username
|
|
| 5 |
services.claimsDemo.db.password = invalid_password
|
|
| 3 |
services.claimsDemo.db.url = jdbc:postgresql://scoobydoo.di.uoa.gr:5432/claims_beta_last
|
|
| 4 |
services.claimsDemo.db.username = postgres
|
|
| 5 |
services.claimsDemo.db.password = snowflakes
|
|
| 6 | 6 |
services.claimsDemo.directClaim.APIURL = http://beta.services.openaire.eu:8280/is/mvc/api/publications |
| 7 | 7 |
|
| 8 | 8 |
#email properties |
| ... | ... | |
| 14 | 14 |
services.claims.mail.angularUrl = http://duffy.di.uoa.gr:3000/claims-project-manager?token= |
| 15 | 15 |
services.claims.mail.specialRecipients = invalid_recipient@email.com |
| 16 | 16 |
|
| 17 |
services.claimsDemo.results.pathToSaveRecord = /home/argirok/claims/records/ |
|
| 18 |
services.claimsDemo.reports.pathToSaveReport = /home/argirok/claims/reports/ |
|
| 17 |
services.claimsDemo.results.pathToSaveRecord = /home/argirok/claims_beta/records/ |
|
| 18 |
services.claimsDemo.reports.pathToSaveReport = /home/argirok/claims_beta/reports/ |
|
Also available in: Unified diff
Delete file when claim is deleted and result has no other links| change semantics | change the openaireId generation