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geoportal-logic
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1.0.3

This commit is contained in:
Fabio Sinibaldi 2020-11-10 14:45:16 +01:00
parent 9a42faef00
commit ad7f439605
13 changed files with 200 additions and 24 deletions
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1
CHANGELOG.md
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@ -6,6 +6,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
Implemented list, list by type
Fixed : commit transaction when safelyCommit project
Fixed : exception encapsulation in DB initialization
## [v1.0.2] - 2020-11-4

3
src/main/java/org/gcube/application/geoportal/Uploader.java
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@ -17,6 +17,7 @@ import org.apache.commons.csv.CSVRecord;
import org.gcube.application.geoportal.model.Configuration;
import org.gcube.application.geoportal.model.db.DBConstants;
import org.gcube.application.geoportal.model.db.PostgisTable;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.model.fault.InvalidRecordException;
import org.gcube.application.geoportal.storage.PostgisDBManager;
import org.gcube.application.geoportal.storage.PostgisDBManagerI;
@ -65,7 +66,7 @@ public class Uploader {
// Expectcs CSV nome,anno,regione,xcentroid,ycentroid,csv,shp,nome_csv,poligono,punti,linee
// I.E {nome=Acquacadda Nuxis, anno=2019, regione=Sardegna, xcentroid=8.751, ycentroid=39.179, csv=TRUE, shp=TRUE, nome_csv=AcquacaddaNuxis_poligoni, poligono=TRUE, punti=FALSE, linee=FALSE}
public void insertConcessioni(File CSVFile,Boolean centroidsOnly) throws FileNotFoundException, IOException, SQLException {
public void insertConcessioni(File CSVFile,Boolean centroidsOnly) throws FileNotFoundException, IOException, SQLException, ConfigurationException {
log.info("Connecting to postgresDB.. ");
log.info("Parsing file "+CSVFile.getAbsolutePath());
File exportedFolder=new File(CSVFile.getParent()+File.separator+"esportazioni");

7
src/main/java/org/gcube/application/geoportal/managers/AbstractRecordManager.java
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@ -12,7 +12,6 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
import javax.persistence.DiscriminatorValue;
import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.EntityTransaction;
@ -29,6 +28,7 @@ import org.gcube.application.geoportal.model.db.DatabaseConnection;
import org.gcube.application.geoportal.model.db.PostgisTable;
import org.gcube.application.geoportal.model.db.PostgisTable.Field;
import org.gcube.application.geoportal.model.db.PostgisTable.FieldType;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.model.fault.PersistenceException;
import org.gcube.application.geoportal.model.fault.PublishException;
import org.gcube.application.geoportal.model.fault.SDIInteractionException;
@ -91,7 +91,7 @@ public abstract class AbstractRecordManager<T extends Record> {
}catch(Throwable t) {
if(defaultProvider==null)
throw new RuntimeException("NO INTERNAL DADATABASE. Please contact VRE Manager (Required SE [platform : postgresq, 'GNA-DB' flag : internal-db])");
throw new RuntimeException("NO INTERNAL DADATABASE. Please contact VRE Manager (Required SE [platform : postgresq, 'GNA-DB' flag : internal-db])",t);
else {
log.warn("Found default provider. This should happen only in test phase.");
emf=defaultProvider.getFactory();
@ -327,6 +327,9 @@ public abstract class AbstractRecordManager<T extends Record> {
}catch(SDIInteractionException e) {
log.warn("Unable to publish Centroid Layer for record type "+getRecord().getRecordType(),e);
throw new PublishException("Unable to publish centroid.",e, null);
} catch (ConfigurationException e) {
log.warn("Unable to contact centroids db "+getRecord().getRecordType(),e);
throw new PublishException("Unable to publish centroid.",e, null);
}
}

3
src/main/java/org/gcube/application/geoportal/model/db/DatabaseConnection.java
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@ -1,5 +1,6 @@
package org.gcube.application.geoportal.model.db;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.utils.ISUtils;
import lombok.Getter;
@ -19,7 +20,7 @@ public class DatabaseConnection {
Concessioni,Mosi,Mopr
}
public static DatabaseConnection get(TYPE type) {
public static DatabaseConnection get(TYPE type) throws ConfigurationException {
return ISUtils.queryForDB("postgis", type.toString());
}

38
src/main/java/org/gcube/application/geoportal/model/fault/ConfigurationException.java Normal file
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@ -0,0 +1,38 @@
package org.gcube.application.geoportal.model.fault;
public class ConfigurationException extends Exception {
/**
*
*/
private static final long serialVersionUID = -3810929853461018566L;
public ConfigurationException() {
super();
// TODO Auto-generated constructor stub
}
public ConfigurationException(String message, Throwable cause, boolean enableSuppression,
boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
// TODO Auto-generated constructor stub
}
public ConfigurationException(String message, Throwable cause) {
super(message, cause);
// TODO Auto-generated constructor stub
}
public ConfigurationException(String message) {
super(message);
// TODO Auto-generated constructor stub
}
public ConfigurationException(Throwable cause) {
super(cause);
// TODO Auto-generated constructor stub
}
}

32
src/main/java/org/gcube/application/geoportal/model/vre/SudoOperator.java Normal file
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@ -0,0 +1,32 @@
package org.gcube.application.geoportal.model.vre;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.utils.ISUtils;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.data.transfer.library.utils.ScopeUtils;
import lombok.extern.slf4j.Slf4j;
@Slf4j
public class SudoOperator {
private String token;
private String backupToken;
private String caller;
public SudoOperator() throws ConfigurationException {
this.token=ISUtils.getToken();
this.backupToken=SecurityTokenProvider.instance.get();
this.caller=ScopeUtils.getCurrentCaller();
log.warn("Created SUDO operator by "+caller);
}
public void sudo() {
SecurityTokenProvider.instance.set(token);
log.warn("Starting SUDO operation by "+ScopeUtils.getCurrentCaller());
}
public void reset() {
SecurityTokenProvider.instance.set(backupToken);
}
}

5
src/main/java/org/gcube/application/geoportal/storage/PostgisDBManager.java
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@ -11,6 +11,7 @@ import org.gcube.application.geoportal.model.db.DatabaseConnection;
import org.gcube.application.geoportal.model.db.DatabaseConnection.TYPE;
import org.gcube.application.geoportal.model.db.PostgisTable;
import org.gcube.application.geoportal.model.db.PostgisTable.Field;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.model.fault.DataParsingException;
import org.gcube.application.geoportal.model.gis.BBOX;
import org.gcube.application.geoportal.utils.DBUtils;
@ -22,7 +23,7 @@ import lombok.extern.slf4j.Slf4j;
public class PostgisDBManager implements PostgisDBManagerI {
@Synchronized
public static PostgisDBManager get() throws SQLException {
public static PostgisDBManager get() throws SQLException, ConfigurationException {
if(config==null) {
log.debug("Looking for Default Configuration.. ");
DatabaseConnection defaultConfiguration=DatabaseConnection.get(TYPE.Concessioni);
@ -31,7 +32,7 @@ public class PostgisDBManager implements PostgisDBManagerI {
}
return new PostgisDBManager();
}
public static PostgisDBManagerI get(boolean autocommit) throws SQLException {
public static PostgisDBManagerI get(boolean autocommit) throws SQLException, ConfigurationException {
PostgisDBManager toReturn=get();
toReturn.conn.setAutoCommit(autocommit);
return toReturn;

2
src/main/java/org/gcube/application/geoportal/storage/WorkspaceManager.java
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@ -38,7 +38,7 @@ public class WorkspaceManager {
return sgClient;
}
private FolderContainer getApplicationBaseFolder() throws StorageHubException {
public FolderContainer getApplicationBaseFolder() throws StorageHubException {
if(appBase==null) {
StorageHubClient client=getSGClient();
FolderContainer vre=client.openVREFolder();

36
src/main/java/org/gcube/application/geoportal/utils/ISUtils.java
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@ -3,7 +3,10 @@ package org.gcube.application.geoportal.utils;
import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.util.List;
import org.gcube.application.geoportal.model.db.DatabaseConnection;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.common.encryption.encrypter.StringEncrypter;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.resources.gcore.ServiceEndpoint.AccessPoint;
@ -12,7 +15,7 @@ import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
public class ISUtils {
public static DatabaseConnection queryForDB(String platform,String flag) {
public static DatabaseConnection queryForDB(String platform,String flag) throws ConfigurationException {
SimpleQuery query = queryFor(ServiceEndpoint.class);
@ -22,14 +25,41 @@ public class ISUtils {
.setResult("$resource/Profile/AccessPoint");
DiscoveryClient<AccessPoint> client = clientFor(AccessPoint.class);
AccessPoint point=client.submit(query).get(0);
List<AccessPoint> found=client.submit(query);
if(found.size()>1) {
throw new ConfigurationException("Multiple SE found ["+found.size()+"] for platform : "+platform+" flag : "+flag);
}else if (found.isEmpty()){
throw new ConfigurationException("No SE found for platform : "+platform+" flag : "+flag);
}
AccessPoint point=found.get(0);
return new DatabaseConnection(point.username(),decryptString(point.password()),point.address());
}
public static String getToken() throws ConfigurationException {
SimpleQuery query = queryFor(ServiceEndpoint.class);
query.addCondition("$resource/Profile/Category/text() eq 'Application'")
.addCondition("$resource/Profile/Name/text() eq 'GNA-APP'")
.setResult("$resource/Profile/AccessPoint");
DiscoveryClient<AccessPoint> client = clientFor(AccessPoint.class);
List<AccessPoint> found= client.submit(query);
if(found.size()>1) {
throw new ConfigurationException("Multiple Token SE found ["+found.size()+"] for Category : Application name : GNA-APP");
}else if (found.isEmpty()){
throw new ConfigurationException("No Token SE found ["+found.size()+"] for Category : Application name : GNA-APP");
}
AccessPoint point=found.get(0);
return decryptString(point.password());
}
public static String decryptString(String toDecrypt){
try{
return StringEncrypter.getEncrypter().decrypt(toDecrypt);

40
src/test/java/org/gcube/application/geoportal/CheckContextConfiguration.java
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@ -4,16 +4,24 @@ package org.gcube.application.geoportal;
import org.gcube.application.geoportal.managers.ConcessioneManager;
import org.gcube.application.geoportal.managers.ManagerFactory;
import org.gcube.application.geoportal.model.concessioni.Concessione;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.model.fault.PersistenceException;
import org.gcube.application.geoportal.model.fault.PublishException;
import org.gcube.application.geoportal.model.fault.ValidationException;
import org.gcube.application.geoportal.storage.WorkspaceManager;
import org.gcube.application.geoportal.utils.ISUtils;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.data.transfer.library.utils.ScopeUtils;
public class CheckContextConfiguration {
public static void main(String[] args) {
// TokenSetter.set("/gcube/devNext/NextNext");
TokenSetter.set("/pred4s/preprod/preVRE");
public static void main(String[] args) throws ConfigurationException, StorageHubException {
TokenSetter.set("/gcube/devNext/NextNext");
// TokenSetter.set("/pred4s/preprod/preVRE");
// TokenSetter.set("/d4science.research-infrastructures.eu/D4OS/GeoNA-Prototype");
// System.out.println("Checking for internal .. ");
// ConcessioneManager manager=ManagerFactory.getByRecord(new Concessione());
// try {
@ -24,11 +32,37 @@ public class CheckContextConfiguration {
// }finally {
// manager.shutdown();
// }
// Checking token validity
// only from 1.0.3
// System.out.println("Checking for token ");
// String token = ISUtils.getToken();
// System.out.println("Token Found ");
//
// String toRestore= (SecurityTokenProvider.instance.get());
// System.out.println("Current Identity : "+ScopeUtils.getCurrentCaller());
// SecurityTokenProvider.instance.set(token);
// System.out.println("Current Identity : "+ScopeUtils.getCurrentCaller());
//
// SecurityTokenProvider.instance.set(toRestore);
// System.out.println("Current Identity : "+ScopeUtils.getCurrentCaller());
//
//
System.out.println(ISUtils.queryForDB("postgresql", "internal-db"));
System.out.println("Checking for postgis .. ");
System.out.println(ISUtils.queryForDB("postgis", "Concessioni"));
System.out.println("Base folder path : "+new WorkspaceManager(null).getApplicationBaseFolder().get().getPath());
System.out.println("Inspecting internal DB ");
System.out.println("Found "+ManagerFactory.getList().size()+" records");
// INIT APP
// INTERNAL DB // ******* IS ******** SE platform : "postgresql" AP."GNA_DB"="internal-db"
// WORKSPACE ROOT FOLDER

3
src/test/java/org/gcube/application/geoportal/UploadGpkgTable.java
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@ -7,6 +7,7 @@ import java.util.Map;
import org.gcube.application.geoportal.model.db.DBInteractionException;
import org.gcube.application.geoportal.model.db.DatabaseConnection;
import org.gcube.application.geoportal.model.fault.ConfigurationException;
import org.gcube.application.geoportal.model.fault.DataParsingException;
import org.gcube.application.geoportal.model.fault.GeoPackageInteractionException;
import org.gcube.application.geoportal.storage.PostgisDBManager;
@ -30,7 +31,7 @@ public class UploadGpkgTable {
+ "--TABLENAME";
public static void main(String[] args) throws SQLException, IOException, GeoPackageInteractionException, DBInteractionException, DataParsingException {
public static void main(String[] args) throws SQLException, IOException, GeoPackageInteractionException, DBInteractionException, DataParsingException, ConfigurationException {
if(args.length<1) {
System.out.println(USAGE);

11
src/test/java/org/gcube/application/geoportal/UseCases.java
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@ -4,6 +4,7 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.gcube.application.geoportal.managers.AbstractRecordManager;
import org.gcube.application.geoportal.managers.ConcessioneManager;
import org.gcube.application.geoportal.managers.ManagerFactory;
import org.gcube.application.geoportal.model.InputStreamDescriptor;
@ -54,6 +55,8 @@ public class UseCases {
}catch(Throwable t) {
System.err.println("ALERT "+t.getMessage());
throw t;
}finally {
AbstractRecordManager.shutdown();
}
@ -62,7 +65,6 @@ public class UseCases {
public static Concessione registerNewConcessione() throws FileNotFoundException, IOException{
ConcessioneManager manager=null;
try {
//Preparo l'istanza del modello con i vari campi compilati e senza gli allegati
Concessione conc=TestModel.prepareEmptyConcessione();
@ -138,20 +140,13 @@ public class UseCases {
return registered;
//--- FINALLY --/
}finally{
manager.shutdown();
}
}
public static void readConcessione(long id) {
ConcessioneManager manager=ManagerFactory.getByRecordID(id);
try{
System.out.println(manager.getRecord());
}finally {
manager.shutdown();
}
}

39
src/test/java/org/gcube/application/geoportal/WSTests.java Normal file
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@ -0,0 +1,39 @@
package org.gcube.application.geoportal;
import org.gcube.application.geoportal.utils.Workspace;
import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.storagehub.client.dsl.ItemContainer;
import org.gcube.common.storagehub.client.dsl.ListResolver;
import org.gcube.common.storagehub.client.dsl.StorageHubClient;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.common.storagehub.model.items.Item;
public class WSTests {
public static void main(String[] args) throws StorageHubException {
TokenSetter.set("/gcube/devNext/NextNext");
StorageHubClient client=Workspace.getClient();
String id="9e397c1f-0b52-4b59-b247-e5ef301978ed";
ItemContainer item=client.open(id).asItem();
System.out.println(item.get().getPath());
// switch(item.getType()) {
// case FILE :
// FileContainer file=(FileContainer) item;
// file.getAnchestors();
// }
System.out.println(path(item));
}
public static String path(ItemContainer item) throws StorageHubException {
StringBuilder builder=new StringBuilder();
ListResolver resolver=item.getAnchestors();
for(Item i:resolver.getItems()) {
builder.append(i.getName()+" ID : "+i.getId()+"\n");
}
return builder.toString();
}
}