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Commit 9f18bd15 authored by Davide Lagoa's avatar Davide Lagoa
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initial commit

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<projectDescription>
<name>biosynth</name>
<comment></comment>
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<modelVersion>4.0.0</modelVersion>
<groupId>Biosynth</groupId>
<artifactId>biosynth</artifactId>
<version>0.0.1-SNAPSHOT</version>
<description>
</description>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
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<configuration>
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<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
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</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-chebi</artifactId>
<version>0.9.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-biodb-reactome</artifactId>
<version>0.9.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-chemanalysis</artifactId>
<version>0.9.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-core</artifactId>
<version>0.9.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-genome</artifactId>
<version>0.9.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
</exclusion>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-integration</artifactId>
<version>0.9.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.biosynthframework</groupId>
<artifactId>biosynth-visualization</artifactId>
<version>0.9.0-SNAPSHOT</version>
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<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>3.17</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>6.0.6</version>
</dependency>
<dependency>
<groupId>pt.uminho.sysbio.common</groupId>
<artifactId>bioapis</artifactId>
<version>0.0.1-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
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<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.5.3</version>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
<artifactId>jsoup</artifactId>
<version>1.11.2</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>5.0.0</version>
</dependency>
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.8.0-beta1</version>
</dependency>
</dependencies>
</project>
package biosynth;
import java.io.File;
import org.neo4j.graphdb.GraphDatabaseService;
import pt.uminho.sysbio.biosynth.integration.GraphMetaboliteEntity;
import pt.uminho.sysbio.biosynth.integration.etl.CentralMetaboliteEtlDataCleansing;
import pt.uminho.sysbio.biosynth.integration.etl.DefaultMetaboliteEtlExtract;
import pt.uminho.sysbio.biosynth.integration.etl.EtlTransform;
import pt.uminho.sysbio.biosynth.integration.etl.HbmNeo4jHybridMetaboliteEtlPipeline;
import pt.uminho.sysbio.biosynth.integration.etl.HeterogenousMetaboliteEtlLoad;
import pt.uminho.sysbio.biosynth.integration.etl.biodb.bigg.BiggMetaboliteTransform;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.Neo4jGraphMetaboliteDaoImpl;
import pt.uminho.sysbio.biosynthframework.Metabolite;
import pt.uminho.sysbio.biosynthframework.chemanalysis.cdk.CdkWrapper;
import pt.uminho.sysbio.biosynthframework.core.data.io.dao.biodb.bigg.CsvBiggMetaboliteDaoImpl;
import pt.uminho.sysbio.biosynthframework.core.data.io.factory.BiggDaoFactory;
import pt.uminho.sysbio.biosynthframework.io.MetaboliteDao;
public class BIGG1 {
// public static void main(String[] args) {
//
// EtlTransform<BiggMetaboliteEntity, GraphMetaboliteEntity> t = getBiggMetaboliteTransform();
// MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
//// MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc = Metacyc.getMetacycMetaboliteDao();
// etl(daoBigg , t);
//
// }
public static CsvBiggMetaboliteDaoImpl getBigg1MetaboliteDatabase() {
CsvBiggMetaboliteDaoImpl dao =
new BiggDaoFactory().withFile(new File("C:\\Users\\Davide\\Downloads\\metaboliteList.tsv"))
.buildCsvBiggMetaboliteDao();
// AnnotationEntityToGraphEntityTransform<BiggReactionEntity> entityTransform =
// new AnnotationEntityToGraphEntityTransform<BiggReactionEntity>();
// GraphReactionEntity graphReactionEntity = entityTransform.etlTransform(biggReactionEntity);
// System.out.println(graphReactionEntity);
return dao;
}
public static BiggMetaboliteTransform getBiggMetaboliteTransform() {
BiggMetaboliteTransform t = new BiggMetaboliteTransform();
return t;
}
public static<M extends Metabolite> void etl(MetaboliteDao<M> src, EtlTransform<M, GraphMetaboliteEntity> t, GraphDatabaseService graphDatabaseService) {
// logger.info("Load database {}", src.getClass().getSimpleName());
// GraphDatabaseService graphDatabaseService = HelperNeo4jConfigInitializer.initializeNeo4jDataDatabaseConstraints("C:\\Users\\Davide\\Documents\\BASE DE DADOS BIOSYNTH\\db");
System.out.println("Load database " + src.getClass().getSimpleName());
Neo4jGraphMetaboliteDaoImpl dst = new Neo4jGraphMetaboliteDaoImpl(graphDatabaseService);
HbmNeo4jHybridMetaboliteEtlPipeline<M, GraphMetaboliteEntity> etlPipeline =
new HbmNeo4jHybridMetaboliteEtlPipeline<>();
etlPipeline.exclude.add("D05511");
etlPipeline.setSkipLoad(false);
etlPipeline.setGraphDatabaseService(graphDatabaseService);
etlPipeline.setSessionFactory(null);
etlPipeline.setEtlDataCleasingSubsystem(new CentralMetaboliteEtlDataCleansing(new CdkWrapper()));
etlPipeline.setExtractSubsystem(new DefaultMetaboliteEtlExtract<M>(src));
etlPipeline.setLoadSubsystem(new HeterogenousMetaboliteEtlLoad<GraphMetaboliteEntity>(dst));
etlPipeline.setTransformSubsystem(t);
etlPipeline.etl();
}
}
package biosynth;
import java.io.File;
import org.neo4j.graphdb.GraphDatabaseService;
import pt.uminho.sysbio.biosynth.integration.GraphMetaboliteEntity;
import pt.uminho.sysbio.biosynth.integration.etl.CentralMetaboliteEtlDataCleansing;
import pt.uminho.sysbio.biosynth.integration.etl.DefaultMetaboliteEtlExtract;
import pt.uminho.sysbio.biosynth.integration.etl.EtlTransform;
import pt.uminho.sysbio.biosynth.integration.etl.HbmNeo4jHybridMetaboliteEtlPipeline;
import pt.uminho.sysbio.biosynth.integration.etl.HeterogenousMetaboliteEtlLoad;
import pt.uminho.sysbio.biosynth.integration.etl.biodb.bigg.Bigg2MetaboliteTransform;
import pt.uminho.sysbio.biosynth.integration.io.dao.neo4j.Neo4jGraphMetaboliteDaoImpl;
import pt.uminho.sysbio.biosynthframework.Metabolite;
import pt.uminho.sysbio.biosynthframework.chemanalysis.cdk.CdkWrapper;
import pt.uminho.sysbio.biosynthframework.core.data.io.dao.biodb.bigg.CsvBiggMetaboliteDaoImpl;
import pt.uminho.sysbio.biosynthframework.core.data.io.factory.BiggDaoFactory;
import pt.uminho.sysbio.biosynthframework.io.MetaboliteDao;
import pt.uminho.sysbio.biosynthframework.io.biodb.RestBigg2MetaboliteDaoImpl;
public class BIGG2 {
// public static void main(String[] args) {
//
//// EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t = getMetacycMetaboliteTransform();
//// // MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
//// MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc = getMetacycMetaboliteDao();
//// etl(daoBiocyc , t);
//
// System.out.println("requesting...");
//
// EtlTransform<Bigg2MetaboliteEntity, GraphMetaboliteEntity> t = getBIGG2MetaboliteTransform();
// MetaboliteDao<Bigg2MetaboliteEntity> daoBigg2 = getBigg2MetaboliteDao();
// etl(daoBigg2 , t);
//
// System.out.println("done...");
//
//
// }
public static RestBigg2MetaboliteDaoImpl getBigg2MetaboliteDao() {
RestBigg2MetaboliteDaoImpl dao = new RestBigg2MetaboliteDaoImpl();
return dao;
}
public static CsvBiggMetaboliteDaoImpl getBigg1MetaboliteDatabase() {
CsvBiggMetaboliteDaoImpl source =
new BiggDaoFactory().withFile(new File("C:\\Users\\Davide\\Downloads\\metaboliteList.tsv"))
.buildCsvBiggMetaboliteDao();
System.out.println(source.getAllMetaboliteEntries());
// BiggMetaboliteEntity metabEntity = source.getMetaboliteByEntry("5mta");
//
// System.out.println(metabEntity.getCompartments());
// AnnotationEntityToGraphEntityTransform<BiggReactionEntity> entityTransform =
// new AnnotationEntityToGraphEntityTransform<BiggReactionEntity>();
// GraphReactionEntity graphReactionEntity = entityTransform.etlTransform(biggReactionEntity);
// System.out.println(graphReactionEntity);
return source;
}
public static Bigg2MetaboliteTransform getBIGG2MetaboliteTransform() {
// Map<String, String> map = new HashMap<> ();
//
// CsvBiggMetaboliteDaoImpl bigg1MetabDatabase = getBigg1MetaboliteDatabase();
//
// for (String cpdEntry : bigg1MetabDatabase.getAllMetaboliteEntries()) {
// BiggMetaboliteEntity cpd = bigg1MetabDatabase.getMetaboliteByEntry(cpdEntry);
// map.put(cpd.getInternalId().toString(), cpdEntry);
// }
// BiocycMetaboliteTransform t = new BiocycMetaboliteTransform(MetaboliteMajorLabel.MetaCyc.toString(), map);
Bigg2MetaboliteTransform t = new Bigg2MetaboliteTransform();
return t;
}
public static<M extends Metabolite> void etl(MetaboliteDao<M> src, EtlTransform<M, GraphMetaboliteEntity> t, GraphDatabaseService graphDatabaseService) {
// logger.info("Load database {}", src.getClass().getSimpleName());
// GraphDatabaseService graphDatabaseService =
// HelperNeo4jConfigInitializer.initializeNeo4jDataDatabaseConstraints("C:\\Users\\Davide\\Documents\\BASE DE DADOS BIOSYNTH\\db");
System.out.println("Load database " + src.getClass().getSimpleName());
Neo4jGraphMetaboliteDaoImpl dst = new Neo4jGraphMetaboliteDaoImpl(graphDatabaseService);
HbmNeo4jHybridMetaboliteEtlPipeline<M, GraphMetaboliteEntity> etlPipeline =
new HbmNeo4jHybridMetaboliteEtlPipeline<>();
// etlPipeline.exclude.add("D05511");
etlPipeline.setSkipLoad(false);
etlPipeline.setGraphDatabaseService(graphDatabaseService);
etlPipeline.setSessionFactory(null);
etlPipeline.setEtlDataCleasingSubsystem(new CentralMetaboliteEtlDataCleansing(new CdkWrapper()));
etlPipeline.setExtractSubsystem(new DefaultMetaboliteEtlExtract<M>(src));
etlPipeline.setLoadSubsystem(new HeterogenousMetaboliteEtlLoad<GraphMetaboliteEntity>(dst));
etlPipeline.setTransformSubsystem(t);
etlPipeline.etl();
}
}
package biosynth;
import org.neo4j.graphdb.GraphDatabaseService;
import edu.uminho.biosynth.core.data.integration.neo4j.HelperNeo4jConfigInitializer;
import pt.uminho.sysbio.biosynth.integration.GraphMetaboliteEntity;
import pt.uminho.sysbio.biosynth.integration.etl.EtlTransform;
import pt.uminho.sysbio.biosynthframework.biodb.biocyc.BioCycMetaboliteEntity;
import pt.uminho.sysbio.biosynthframework.io.MetaboliteDao;
public class BuildDatabase {
public static void main(String[] args) {
System.out.println("setting GraphDatabaseService...");
GraphDatabaseService graphDatabaseService = HelperNeo4jConfigInitializer
.initializeNeo4jDataDatabaseConstraints("C:\\Users\\Davide\\Documents\\BASE DE DADOS BIOSYNTH\\db3_0");
// System.out.println("opening ModelSEED...");
//
// EtlTransform<ModelSeedMetaboliteEntity, GraphMetaboliteEntity> t0 = ModelSEED.getMetaboliteTransform();
//
// MetaboliteDao<ModelSeedMetaboliteEntity> dao0 = ModelSEED.getMetaboliteDatabase();
//
// System.out.println("transforming...");
//
// ModelSEED.etl(dao0 , t0, graphDatabaseService);
//
// System.out.println("ModelSEED complete...");
//
// ///////////////////////////////////////////////////////////
// System.out.println();
// System.out.println("requesting kegg compounds...");
//
// KEGG.etl(KEGG.getKeggCompoundMetaboliteDao() , KEGG.getKeggCompoundTransform(), graphDatabaseService);
//
// System.out.println("requesting kegg glycans...");
//
// KEGG.etl(KEGG.getKeggGlycanMetaboliteDao() , KEGG.getKeggGlycanTransform(), graphDatabaseService);
//
// ///////////////////////////////////////////////////////////
//
// System.out.println();
// System.out.println("opening BIGG1...");
//
// EtlTransform<BiggMetaboliteEntity, GraphMetaboliteEntity> t1 = BIGG1.getBiggMetaboliteTransform();
//
// MetaboliteDao<BiggMetaboliteEntity> daoBigg1 = BIGG1.getBigg1MetaboliteDatabase();
//
// System.out.println("transforming...");
//
// BIGG1.etl(daoBigg1, t1, graphDatabaseService);
//
// System.out.println("BIGG1 complete...");
//
// ///////////////////////////////////////////////////////////
// System.out.println();
// System.out.println("opening BIGG2...");
//
// EtlTransform<Bigg2MetaboliteEntity, GraphMetaboliteEntity> t2 = BIGG2.getBIGG2MetaboliteTransform();
// MetaboliteDao<Bigg2MetaboliteEntity> daoBigg2 = BIGG2.getBigg2MetaboliteDao();
//
// System.out.println("transforming...");
//
// BIGG2.etl(daoBigg2 , t2, graphDatabaseService);
//
// System.out.println("BIGG2 complete...");
//
// ///////////////////////////////////////////////////////////
// System.out.println();
// System.out.println("opening Metacyc META...");
//
// EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t3 = Metacyc.getMetacycMetaboliteTransform();
//// MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
// MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc3 = Metacyc.getMetacycMetaboliteDao("META");
//
// System.out.println("transforming...");
//
// Metacyc.etl(daoBiocyc3 , t3, graphDatabaseService);
//
// System.out.println("Metacyc META complete...");
//
// ///////////////////////////////////////////////////////////
// System.out.println();
System.out.println("opening Metacyc ECOLI...");
EtlTransform<BioCycMetaboliteEntity, GraphMetaboliteEntity> t4 = Metacyc.getMetacycMetaboliteTransform();
// MetaboliteDao<BiggMetaboliteEntity> daoBigg = getBigg1MetaboliteDatabase();
MetaboliteDao<BioCycMetaboliteEntity> daoBiocyc4 = Metacyc.getMetacycMetaboliteDao("ECOLI");
System.out.println("transforming...");
Metacyc.etl(daoBiocyc4 , t4, graphDatabaseService);
System.out.println("Metacyc ECOLI complete...");
// System.out.println("requesting kegg drugs...");
//
// etl(getKeggDrugMetaboliteDao() , getKeggDrugTransform(), graphDatabaseService);
System.out.println("database load complete...");
graphDatabaseService.shutdown();
System.out.println("shutdown...");
}
}
package biosynth;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.Resource;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.type.MapType;
import pt.uminho.sysbio.biosynthframework.ReferenceType;
import pt.uminho.sysbio.biosynthframework.biodb.seed.ModelSeedMetaboliteCrossreferenceEntity;
import pt.uminho.sysbio.biosynthframework.biodb.seed.ModelSeedMetaboliteEntity;
import pt.uminho.sysbio.biosynthframework.io.MetaboliteDao;
public class Json2ModelSeedMetaboliteDaoImpl implements MetaboliteDao<ModelSeedMetaboliteEntity> {
private static final Logger logger = LoggerFactory.getLogger(Json2ModelSeedMetaboliteDaoImpl.class);
private Map<String, ModelSeed2Compound> data = new HashMap<> ();
public static Boolean integerToBoolean(Integer i) {
if ( i == null) {
return null;
}
return i == 0 ? false : true;
}
public Function<ModelSeed2Compound, ModelSeedMetaboliteEntity> function =
new Function<ModelSeed2Compound, ModelSeedMetaboliteEntity>() {
@Override
public ModelSeedMetaboliteEntity apply(ModelSeed2Compound t) {
ModelSeedMetaboliteEntity cpd = new ModelSeedMetaboliteEntity();
cpd.setEntry(t.id);
cpd.setName(t.name);
cpd.setFormula(t.formula);
cpd.setAbbreviation(t.abbreviation);
cpd.setSeedSource(t.source);
cpd.setSearchInchi(t.search_inchi);
cpd.setStructure(t.structure);
cpd.setCore(integerToBoolean(t.is_core));
cpd.setCofactor(integerToBoolean(t.is_cofactor));
cpd.setObsolete(integerToBoolean(t.is_obsolete));
cpd.setDefaultCharge(t.charge);
cpd.setDeltaG(t.deltag);
cpd.setDeltaGErr(t.deltagerr);
cpd.setMass(t.mass);
//probably should leave the transformer to fix it ...
List<ModelSeedMetaboliteCrossreferenceEntity> refs = new ArrayList<> ();
for (String bigg : t.bigg_aliases) {