Examples with DBBundleStudyWriter ambit2.db.substance.processor.DBBundleStudyWriter used on opensource projects

Example 1 with DBBundleStudyWriter

use of ambit2.db.substance.processor.DBBundleStudyWriter in project ambit-mirror by ideaconsult.

the class SubstanceWriterTest method delete.

public int delete(SubstanceEndpointsBundle bundle, IRawReader<IStructureRecord> reader, Connection connection) throws Exception {
    /*
		 * DBSubstanceWriter writer; if (bundle != null) writer = new
		 * DBBundleStudyWriter(bundle, DBSubstanceWriter.datasetMeta(), new
		 * SubstanceRecord()); else writer = new
		 * DBSubstanceWriter(DBSubstanceWriter.datasetMeta(), new
		 * SubstanceRecord(), clearMeasurements, clearComposition);
		 * writer.setSplitRecord(splitRecord); writer.setConnection(connection);
		 * writer.open();
		 */
    UpdateExecutor<IQueryUpdate> writer = new UpdateExecutor<IQueryUpdate>();
    writer.setConnection(connection);
    DeleteMatrixValue q = new DeleteMatrixValue();
    q.setGroup(bundle);
    int records = 0;
    while (reader.hasNext()) {
        Object record = reader.next();
        if (record == null)
            continue;
        Assert.assertTrue(record instanceof SubstanceRecord);
        Assert.assertEquals("IUC4-efdb21bb-e79f-3286-a988-b6f6944d3734", ((SubstanceRecord) record).getSubstanceUUID());
        for (ProtocolApplication pa : ((SubstanceRecord) record).getMeasurements()) {
            Assert.assertTrue(pa instanceof ProtocolApplicationAnnotated);
            // System.out.println(((ProtocolApplicationAnnotated) pa)getRecords_to_delete());
            ProtocolApplicationAnnotated paa = (ProtocolApplicationAnnotated) pa;
            List<ValueAnnotated> vaa = paa.getRecords_to_delete();
            for (ValueAnnotated va : vaa) {
                q.setObject(va);
                writer.process(q);
            }
        }
        // writer.setImportedRecord((SubstanceRecord) record);
        // writer.process((IStructureRecord) record);
        records++;
    }
    writer.close();
    return records;
}

Example 2 with DBBundleStudyWriter

use of ambit2.db.substance.processor.DBBundleStudyWriter in project ambit-mirror by ideaconsult.

the class SubstanceWriterTest method write.

public int write(SubstanceEndpointsBundle bundle, IRawReader<IStructureRecord> reader, Connection connection, PropertyKey key, boolean splitRecord, boolean clearMeasurements, boolean clearComposition) throws Exception {
    DBSubstanceWriter writer;
    if (bundle != null)
        writer = new DBBundleStudyWriter(bundle, DBSubstanceWriter.datasetMeta(), new SubstanceRecord());
    else
        writer = new DBSubstanceWriter(DBSubstanceWriter.datasetMeta(), new SubstanceRecord(), clearMeasurements, clearComposition);
    writer.setSplitRecord(splitRecord);
    writer.setConnection(connection);
    writer.open();
    int records = 0;
    while (reader.hasNext()) {
        Object record = reader.next();
        if (record == null)
            continue;
        Assert.assertTrue(record instanceof IStructureRecord);
        if (record instanceof SubstanceRecord)
            writer.setImportedRecord((SubstanceRecord) record);
        writer.process((IStructureRecord) record);
        records++;
    }
    writer.close();
    return records;
}