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perform-service_broken
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git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/application/perform-service@176527 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Fabio Sinibaldi 2019-01-14 13:07:39 +00:00
parent 946e8a4639
commit e0266ddbe0
11 changed files with 182 additions and 54 deletions
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4
src/main/java/org/gcube/application/perform/service/engine/DataBaseManagerImpl.java
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@ -57,7 +57,9 @@ public class DataBaseManagerImpl implements DataBaseManager{
@Override
public Connection getConnection() throws SQLException, InternalException {
DataSource ds=getDataSource();
return ds.getConnection();
Connection conn=ds.getConnection();
conn.setAutoCommit(false);
return conn;
}

9
src/main/java/org/gcube/application/perform/service/engine/MappingManagerImpl.java
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@ -4,6 +4,7 @@ import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.UUID;
import org.gcube.application.perform.service.LocalConfiguration;
import org.gcube.application.perform.service.engine.model.BeanNotFound;
@ -40,6 +41,7 @@ public class MappingManagerImpl implements MappingManager {
public Batch getBatch(DBQueryDescriptor desc) throws SQLException, InternalException{
DataBaseManager db=DataBaseManager.get(getISQueryDescriptor());
Connection conn=db.getConnection();
conn.setAutoCommit(true);
Query getQuery=Queries.GET_BATCH_BY_DESCRIPTIVE_KEY;
PreparedStatement psSearch=getQuery.get(conn, desc);
@ -51,13 +53,10 @@ public class MappingManagerImpl implements MappingManager {
// ID NOT FOUND, TRY TO REGISTER IT
log.trace("Registering new Batch from condition {}",desc);
desc.add(DBField.Batch.fields.get(DBField.Batch.UUID), UUID.randomUUID());
PreparedStatement psInsert=Queries.INSERT_BATCH.get(conn, desc);
boolean inserted=psInsert.executeUpdate()==1;
if(inserted) {
conn.commit();
log.trace("Committed Batch.");
}
psInsert.executeUpdate();
rs=psSearch.executeQuery();
if(rs.next())

28
src/main/java/org/gcube/application/perform/service/engine/Queries.java
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@ -2,6 +2,7 @@ package org.gcube.application.perform.service.engine;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.UUID;
import org.gcube.application.perform.service.engine.model.DBField;
import org.gcube.application.perform.service.engine.model.DBField.ImportRoutine;
@ -17,23 +18,25 @@ public class Queries {
DBField.Batch.fields.get(DBField.Batch.BATCH_TYPE),
DBField.Batch.fields.get(DBField.Batch.BATCH_NAME)});
public static final Query INSERT_BATCH=new Query("INSERT INTO batches (id,uuid,farmid,type,name) VALUES (SELECT (max(id)+1 from batches),?,?,?,?) ON CONFLICT DO NOTHING",
new DBField[] {});
public static final Query INSERT_BATCH=new Query("INSERT INTO batches (uuid,farmid,type,name) VALUES (?,?,?,?) ON CONFLICT DO NOTHING",
new DBField[] {DBField.Batch.fields.get(DBField.Batch.UUID),
DBField.Batch.fields.get(DBField.Batch.FARM_ID),
DBField.Batch.fields.get(DBField.Batch.BATCH_TYPE),
DBField.Batch.fields.get(DBField.Batch.BATCH_NAME)});
public static final Query GET_FARM_BY_ID=new Query(String.format("SELECT f.farmid as $1%s, f.uuid as %2$s, c.companyid as %3$s, c.uuid as %4$s, a.associationid as %5$s, a.uuid as %6$s FROM "
+ "farms as f INNER JOIN companies as c ON f.companyid=c.companyid INNER JOIN associations as a ON c.associationid=a.associationid WHERE f.farmid = ?",
DBField.Farm.FARM_ID,DBField.Farm.UUID,DBField.Farm.COMPANY_ID,DBField.Farm.COMPANY_UUID,DBField.Farm.ASSOCIATION_ID,DBField.Farm.ASSOCIATION_UUID),
new DBField[] {});
public static final Query GET_FARM_BY_ID=new Query("SELECT * from completefarms WHERE id = ?",
new DBField[] {DBField.Farm.fields.get(DBField.Farm.FARM_ID)});
public static final Query GET_BATCH_BY_ID=new Query("Select * from batches where id = ?",
new DBField[] {});
new DBField[] {DBField.Batch.fields.get(DBField.Batch.BATCH_ID)});
// Imports with lock = hostname or lock == null
public static final Query ORPHAN_IMPORTS=new Query("SELECT * from imports where ",new DBField[]{});
// "acquire"
// set lock = hostname where ID =? and LOCK is null
// Acquired = updated rows == 1
public static final Query ORPHAN_IMPORTS=new Query("",new DBField[]{});
public static final Query ACQUIRE_PS=new Query("",new DBField[]{});
public static final Query ACQUIRE_PS=new Query("Update ",new DBField[]{});
public static final Query GET_BY_ID=new Query("",new DBField[]{});
public static final Query INSERT_ROUTINE=new Query("",new DBField[]{});
@ -49,6 +52,7 @@ public class Queries {
toReturn.setId(rs.getLong(DBField.Batch.BATCH_ID));
toReturn.setName(rs.getString(DBField.Batch.BATCH_NAME));
toReturn.setType(rs.getString(DBField.Batch.BATCH_TYPE));
toReturn.setUuid((UUID)rs.getObject(DBField.Batch.UUID));
return toReturn;
}
@ -56,11 +60,11 @@ public class Queries {
public static Farm rowToFarm(ResultSet rs) throws SQLException {
Farm toReturn=new Farm();
toReturn.setAssociationId(rs.getLong(DBField.Farm.ASSOCIATION_ID));
toReturn.setAssociationUUID(rs.getString(DBField.Farm.ASSOCIATION_UUID));
toReturn.setAssociationUUID((UUID)rs.getObject(DBField.Farm.ASSOCIATION_UUID));
toReturn.setCompanyId(rs.getLong(DBField.Farm.COMPANY_ID));
toReturn.setCompanyUUID(rs.getString(DBField.Farm.COMPANY_UUID));
toReturn.setCompanyUUID((UUID)rs.getObject(DBField.Farm.COMPANY_UUID));
toReturn.setId(rs.getLong(DBField.Farm.FARM_ID));
toReturn.setUUID(rs.getString(DBField.Farm.UUID));
toReturn.setUUID((UUID)rs.getObject(DBField.Farm.UUID));
return toReturn;
}

4
src/main/java/org/gcube/application/perform/service/engine/Query.java
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@ -47,8 +47,12 @@ public class Query {
DBField field=fields.get(i);
if(!desc.getCondition().containsKey(field))
throw new InvalidRequestException("Missing field "+field);
else {
if(field.getType()==Integer.MIN_VALUE) // UUID EXCEPTION
ps.setObject(i+1, desc.getCondition().get(field));
else ps.setObject(i+1, desc.getCondition().get(field), field.getType());
}
}
return ps;
}

21
src/main/java/org/gcube/application/perform/service/engine/model/DBField.java
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@ -8,6 +8,9 @@ import java.util.Map;
public class DBField {
public static class Batch{
public static final String TABLE="batches";
public static final Map<String,DBField> fields=new HashMap<>();
public static final String BATCH_ID="id";
@ -18,7 +21,7 @@ public class DBField {
static {
fields.put(BATCH_ID, new DBField(Types.BIGINT,BATCH_ID));
fields.put(UUID, new DBField(Types.VARCHAR,UUID));
fields.put(UUID, new DBField(Integer.MIN_VALUE,UUID));
fields.put(FARM_ID, new DBField(Types.BIGINT,FARM_ID));
fields.put(BATCH_TYPE, new DBField(Types.VARCHAR,BATCH_TYPE));
fields.put(BATCH_NAME, new DBField(Types.VARCHAR,BATCH_NAME));
@ -26,6 +29,9 @@ public class DBField {
}
public static class Farm{
public static final String TABLE="completefarms";
public static final Map<String,DBField> fields=new HashMap<>();
public static final String FARM_ID="id";
@ -39,7 +45,7 @@ public class DBField {
fields.put(FARM_ID, new DBField(Types.BIGINT,FARM_ID));
fields.put(COMPANY_ID, new DBField(Types.BIGINT,COMPANY_ID));
fields.put(ASSOCIATION_ID, new DBField(Types.BIGINT,ASSOCIATION_ID));
fields.put(UUID, new DBField(Types.NVARCHAR,UUID));
fields.put(UUID, new DBField(Integer.MIN_VALUE,UUID));
fields.put(COMPANY_UUID, new DBField(Types.NVARCHAR,COMPANY_UUID));
fields.put(ASSOCIATION_UUID, new DBField(Types.NVARCHAR,ASSOCIATION_UUID));
@ -47,6 +53,8 @@ public class DBField {
}
public static class ImportRoutine{
public static final String TABLE="imports";
public static final Map<String,DBField> fields=new HashMap<>();
public static final String ID="id";
@ -55,8 +63,8 @@ public class DBField {
public static final String SOURCE_URL="sourceurl";
public static final String SOURCE_VERSION="sourceversion";
public static final String START="start";
public static final String END="end";
public static final String START="start_time";
public static final String END="end_time";
public static final String STATUS="status";
public static final String CALLER="caller";
public static final String COMPUTATION_ID="computation_id";
@ -132,6 +140,11 @@ public class DBField {
return true;
}
@Override
public String toString() {
return "DBField ["+fieldName+"]";
}
}

5
src/main/java/org/gcube/application/perform/service/engine/model/DatabaseConnectionDescriptor.java
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@ -8,6 +8,11 @@ public class DatabaseConnectionDescriptor {
@Override
public String toString() {
return "DatabaseConnectionDescriptor [username=" + username + ", url=" + url + "]";
}
public DatabaseConnectionDescriptor(String username, String url, String password) {
super();
this.username = username;

10
src/main/java/org/gcube/application/perform/service/engine/model/anagraphic/Batch.java
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@ -1,5 +1,7 @@
package org.gcube.application.perform.service.engine.model.anagraphic;
import java.util.UUID;
public class Batch {
@ -11,10 +13,10 @@ public class Batch {
public void setId(Long id) {
this.id = id;
}
public String getUuid() {
public UUID getUuid() {
return uuid;
}
public void setUuid(String uuid) {
public void setUuid(UUID uuid) {
this.uuid = uuid;
}
public String getName() {
@ -39,7 +41,7 @@ public class Batch {
public Batch() {
// TODO Auto-generated constructor stub
}
public Batch(Long id, String uuid, String name, String type, Long farmId) {
public Batch(Long id, UUID uuid, String name, String type, Long farmId) {
super();
this.id = id;
this.uuid = uuid;
@ -48,7 +50,7 @@ public class Batch {
this.farmId = farmId;
}
private Long id;
private String uuid;
private UUID uuid;
private String name;
private String type;
private Long farmId;

45
src/main/java/org/gcube/application/perform/service/engine/model/anagraphic/Farm.java
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@ -1,12 +1,24 @@
package org.gcube.application.perform.service.engine.model.anagraphic;
import java.util.UUID;
public class Farm {
public Farm() {
// TODO Auto-generated constructor stub
}
public Farm(Long id, Long companyId, Long associationId, java.util.UUID uUID, java.util.UUID companyUUID,
java.util.UUID associationUUID) {
super();
this.id = id;
this.companyId = companyId;
this.associationId = associationId;
UUID = uUID;
this.companyUUID = companyUUID;
this.associationUUID = associationUUID;
}
public Farm() {
// TODO Auto-generated constructor stub
}
public Long getId() {
return id;
}
@ -25,37 +37,28 @@ public class Farm {
public void setAssociationId(Long associationId) {
this.associationId = associationId;
}
public String getUUID() {
public UUID getUUID() {
return UUID;
}
public void setUUID(String uUID) {
public void setUUID(UUID uUID) {
UUID = uUID;
}
public String getCompanyUUID() {
public UUID getCompanyUUID() {
return companyUUID;
}
public void setCompanyUUID(String companyUUID) {
public void setCompanyUUID(UUID companyUUID) {
this.companyUUID = companyUUID;
}
public String getAssociationUUID() {
public UUID getAssociationUUID() {
return associationUUID;
}
public void setAssociationUUID(String associationUUID) {
this.associationUUID = associationUUID;
}
public Farm(Long id, Long companyId, Long associationId, String uUID, String companyUUID, String associationUUID) {
super();
this.id = id;
this.companyId = companyId;
this.associationId = associationId;
UUID = uUID;
this.companyUUID = companyUUID;
public void setAssociationUUID(UUID associationUUID) {
this.associationUUID = associationUUID;
}
private Long id;
private Long companyId;
private Long associationId;
private String UUID;
private String companyUUID;
private String associationUUID;
private UUID UUID;
private UUID companyUUID;
private UUID associationUUID;
}

4
src/main/java/org/gcube/application/perform/service/rest/Mappings.java
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@ -80,7 +80,7 @@ public class Mappings {
return mappings.getBatch(desc);
}catch(BeanNotFound e) {
log.debug("Exception while getting Batch",e);
throw new WebApplicationException("Unable to find Batch with condition "+desc,Response.Status.BAD_REQUEST);
throw new WebApplicationException("Unable to find Batch with condition "+desc,Response.Status.NOT_FOUND);
}catch(SQLException e) {
log.debug("Exception while getting Batch",e);
throw new WebApplicationException("Unexpected Exception occurred while dealing with database.", e,Response.Status.INTERNAL_SERVER_ERROR);
@ -130,7 +130,7 @@ public class Mappings {
return mappings.getFarm(desc);
}catch(BeanNotFound e) {
log.debug("Exception while getting Farm",e);
throw new WebApplicationException("Unable to find Farm with condition "+desc,Response.Status.BAD_REQUEST);
throw new WebApplicationException("Unable to find Farm with condition "+desc,Response.Status.NOT_FOUND);
}catch(SQLException e) {
log.debug("Exception while getting Farm",e);
throw new WebApplicationException("Unexpected Exception occurred while dealing with database.", e,Response.Status.INTERNAL_SERVER_ERROR);

4
src/test/java/org/gcube/application/perform/service/AnagraphicTests.java
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@ -44,7 +44,7 @@ public class AnagraphicTests extends JerseyTest{
path(ServiceConstants.Mappings.BATCHES_METHOD).
queryParam(ServiceConstants.Mappings.BATCH_NAME_PARAMETER, "gino").
queryParam(ServiceConstants.Mappings.BATCH_TYPE_PARAMETER, "pino").
queryParam(ServiceConstants.Mappings.FARM_ID_PARAMETER, 1234);
queryParam(ServiceConstants.Mappings.FARM_ID_PARAMETER, 12682549);
System.out.println(target.getUri());
Response resp=target.request().get();
@ -58,7 +58,7 @@ public class AnagraphicTests extends JerseyTest{
// path(ServiceConstants.APPLICATION_PATH).
target(ServiceConstants.Mappings.PATH).
path(ServiceConstants.Mappings.FARM_METHOD).
queryParam(ServiceConstants.Mappings.FARM_ID_PARAMETER, 12334).
queryParam(ServiceConstants.Mappings.FARM_ID_PARAMETER, 126825).
queryParam(ServiceConstants.Mappings.FARM_UUID_PARAMETER, "pino");
System.out.println(target.getUri());

96
src/test/java/org/gcube/application/perform/service/InitializeDataBase.java Normal file
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@ -0,0 +1,96 @@
package org.gcube.application.perform.service;
import java.net.MalformedURLException;
import java.nio.file.Paths;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import org.gcube.application.perform.service.engine.DataBaseManager;
import org.gcube.application.perform.service.engine.model.DBField.Batch;
import org.gcube.application.perform.service.engine.model.DBField.Farm;
import org.gcube.application.perform.service.engine.model.DBField.ImportRoutine;
import org.gcube.application.perform.service.engine.model.ISQueryDescriptor;
import org.gcube.application.perform.service.engine.model.InternalException;
public class InitializeDataBase {
public static void main(String[] args) throws MalformedURLException, SQLException, InternalException {
TokenSetter.set("/gcube/preprod/preVRE");
LocalConfiguration.init(Paths.get("src/main/webapp/WEB-INF/config.properties").toUri().toURL());
ISQueryDescriptor desc= new ISQueryDescriptor(
LocalConfiguration.getProperty(LocalConfiguration.MAPPING_DB_ENDPOINT_NAME), null,
LocalConfiguration.getProperty(LocalConfiguration.MAPPING_DB_ENDPOINT_CATEGORY));
DataBaseManager db=DataBaseManager.get(desc);
Connection conn=db.getConnection();
Statement stmt=conn.createStatement();
// CREATE BATCHES
stmt.executeUpdate("CREATE TABLE IF NOT EXISTS "+Batch.TABLE+" ("
+ Batch.BATCH_ID+" bigserial NOT NULL,"
+ Batch.UUID+" uuid NOT NULL,"
+ Batch.FARM_ID+" bigint NOT NULL,"
+ Batch.BATCH_TYPE+" varchar(100),"
+ Batch.BATCH_NAME+" text,"
+ "PRIMARY KEY ("+Batch.BATCH_ID+"),"
+ "FOREIGN KEY ("+Batch.FARM_ID+") REFERENCES farms(farmid))"
);
// CREATE IMPORT ROUTINE
stmt.executeUpdate("CREATE TABLE IF NOT EXISTS "+ImportRoutine.TABLE+" ("
+ ImportRoutine.ID+" bigserial NOT NULL,"
+ ImportRoutine.FARM_ID+" bigint NOT NULL,"
+ ImportRoutine.BATCH_TYPE+" varchar(100) NOT NULL,"
+ ImportRoutine.SOURCE_URL+" text,"
+ ImportRoutine.SOURCE_VERSION+" text,"
+ ImportRoutine.START+" timestamp with time zone,"
+ ImportRoutine.END+" timestamp with time zone,"
+ ImportRoutine.STATUS+" varchar(20),"
+ ImportRoutine.CALLER+" text,"
+ ImportRoutine.COMPUTATION_ID+" text,"
+ ImportRoutine.COMPUTATION_URL+" text,"
+ ImportRoutine.COMPUTATION_OPID+" text,"
+ ImportRoutine.COMPUTATION_OPNAME+" text,"
+ ImportRoutine.COMPUTATION_REQ+" text,"
+ ImportRoutine.LOCK+" varchar(200),"
+ "primary key ("+ImportRoutine.ID+"))");
// CREATE FARM VIEW
try {
ResultSet rs=stmt.executeQuery("Select * from "+Farm.TABLE);
if(rs.next()) {
// table already present
}
}catch(SQLException e) {
// Expected error on table not found, trying to create it
stmt.executeUpdate("CREATE VIEW "+Farm.TABLE+" AS ("
+ "Select f.farmid as "+Farm.FARM_ID+", f.uuid as "+Farm.UUID+", c.companyid as "+Farm.COMPANY_ID+", "
+ "c.uuid as "+Farm.COMPANY_UUID+", a.associationid as "+Farm.ASSOCIATION_ID+", a.uuid as "+Farm.ASSOCIATION_UUID+" "
+ "FROM farms as f INNER JOIN companies as c ON f.companyid=c.companyid "
+ "INNER JOIN associations as a ON c.associationid = a. associationid)");
}
// stmt.executeQuery("CREATE VIEW suca as SELECT 1");
// CREATE ANAGRAPHIC OUTPUT
// CREATE PUBLIC OUTPUT VIEW
// CREATE IMPORTED TABLES
conn.commit();
}
}