Biological_Data_Migration_Example.java

public class Main {
    public static void main(String[] args) {

        SimpleURI localGrakn = new SimpleURI("127.0.0.1", 48555);
        Keyspace keyspace = Keyspace.of("gene-disease-associations");
        Grakn grakn = new Grakn(localGrakn);
        Grakn.Session session = grakn.session(keyspace);

        migrateDiseases(session);
        migrateGenes(session);
        migrateGeneDiseaseAssociations(session);

        session.close();
    }

    public static void migrateGenes(Grakn.Session session) {
        try {
            BufferedReader reader = Files.newBufferedReader(Paths.get("PATH_TO_CSV_FILE"));
            CSVParser csvParser = new CSVParser(reader, CSVFormat.DEFAULT);

            for (CSVRecord csvRecord: csvParser) {

                // skip header
                if (csvRecord.getRecordNumber() == 1) {
                    continue;
                }

                String geneId = csvRecord.get(0);
                String geneSymbol = csvRecord.get(1);

                InsertQuery insertQuery = Graql.insert(var("g").isa("gene")
                        .has("gene-id", geneId)
                        .has("gene-symbol", geneSymbol));

                Grakn.Transaction writeTransaction = session.transaction(GraknTxType.WRITE);
                List<ConceptMap> insertedId = insertQuery.withTx(writeTransaction).execute();
                System.out.println("Inserted a gene with ID: " + insertedId.get(0).get("g").id());
                writeTransaction.commit();
            }

            System.out.println("-----genes have been migrated-----");
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    public static void migrateDiseases(Grakn.Session session) {
        try {
            BufferedReader reader = Files.newBufferedReader(Paths.get("PATH_TO_CSV_FILE"));
            CSVParser csvParser = new CSVParser(reader, CSVFormat.DEFAULT);

            for (CSVRecord csvRecord: csvParser) {

                // skip header
                if (csvRecord.getRecordNumber() == 1) {
                    continue;
                }

                String diseaseName = csvRecord.get(0);
                String source = csvRecord.get(1);
                String diseaseId = csvRecord.get(2);
                double dieaseMim = Double.parseDouble(csvRecord.get(3));
                double lastModified = Double.parseDouble(csvRecord.get(4));

                InsertQuery insertQuery = Graql.insert(var("d").isa("disease")
                        .has("diease-name", diseaseName)
                        .has("source", source)
                        .has("disease-id", diseaseId)
                        .has("disease-mim", dieaseMim)
                        .has("last-modified", lastModified));

                Grakn.Transaction writeTransaction = session.transaction(GraknTxType.WRITE);
                List<ConceptMap> insertedId = insertQuery.withTx(writeTransaction).execute();
                System.out.println("Inserted a disease with ID: " + insertedId.get(0).get("v").id());
                writeTransaction.commit();
            }

            System.out.println("-----diseases have been migrated-----");
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    public static void migrateGeneDiseaseAssociations(Grakn.Session session) {
        try {
            BufferedReader reader = Files.newBufferedReader(Paths.get("PATH_TO_CSV_FILE"));
            CSVParser csvParser = new CSVParser(reader, CSVFormat.DEFAULT);

            for (CSVRecord csvRecord: csvParser) {

                // skip header
                if (csvRecord.getRecordNumber() == 1) {
                    continue;
                }

                double geneId = Double.parseDouble(csvRecord.get(0));
                String diseaseId = csvRecord.get(2);

                InsertQuery insertQuery = Graql.match(
                        var("g").isa("gene").has("gene-id", geneId),
                        var("d").isa("disease").has("disease-id", diseaseId))
                        .insert(var("gda").isa("gene-disease-association").rel("associated-gene", "g").rel("associated-disease", "d"));

                Grakn.Transaction writeTransaction = session.transaction(GraknTxType.WRITE);
                List<ConceptMap> insertedId = insertQuery.withTx(writeTransaction).execute();
                System.out.println("Inserted a gene disease associaiton with ID: " + insertedId.get(0).get("gda").id());
                writeTransaction.commit();
            }

            System.out.println("-----gene disease associations have been migrated-----");
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}