Examples with RetrieveStructure ambit2.db.readers.RetrieveStructure used on opensource projects

Example 1 with RetrieveStructure

use of ambit2.db.readers.RetrieveStructure in project ambit-mirror by ideaconsult.

the class ARFFIterator method getIterator.

@Override
public Iterator<IStructureRecord> getIterator(File[] target) throws AmbitException {
    try {
        input = new BufferedReader(new FileReader(target[0]));
        results = new BufferedReader(new FileReader(target[1]));
        arffInput = new ArffReader(input, 1);
        arffResults = new ArffReader(results, 1);
        dataInput = arffInput.getStructure();
        dataResults = arffResults.getStructure();
        properties = new Property[dataResults.numAttributes()];
        for (int i = 0; i < dataResults.numAttributes(); i++) {
            Attribute attribute = dataResults.attribute(i);
            RDFPropertyIterator reader = null;
            Property p = null;
            try {
                reader = new RDFPropertyIterator(new Reference(attribute.name()), "arff");
                reader.setBaseReference(baseReference);
                while (reader.hasNext()) {
                    p = reader.next();
                }
            } catch (Exception x) {
                p = null;
            // p.setId((Integer)OpenTox.URI.feature.getId(attribute.name(), baseReference));
            } finally {
                try {
                    reader.close();
                } catch (Exception x) {
                }
            }
            properties[i] = p;
        }
        return new Iterator<IStructureRecord>() {

            public boolean hasNext() {
                try {
                    inputInstance = arffInput.readInstance(dataInput);
                    resultInstance = arffResults.readInstance(dataResults);
                    return (inputInstance != null) && (resultInstance != null);
                } catch (Exception x) {
                    return false;
                }
            }

            public IStructureRecord next() {
                record.clear();
                Object[] ids = OpenTox.URI.conformer.getIds(inputInstance.toString(0), baseReference);
                if ((ids != null) && (ids[0] != null) && (ids[1] != null)) {
                    record.setIdchemical((Integer) ids[0]);
                    record.setIdstructure((Integer) ids[1]);
                } else {
                    Object id = OpenTox.URI.compound.getId(inputInstance.toString(0), baseReference);
                    if (id != null) {
                        record.setIdchemical((Integer) id);
                        record.setIdstructure(-1);
                    } else {
                    // retrieveStructure(uris[index]);
                    }
                }
                for (int i = 0; i < properties.length; i++) if (properties[i] != null) {
                    if (dataResults.attribute(i).isNumeric())
                        record.setRecordProperty(properties[i], resultInstance.value(i));
                    else
                        record.setRecordProperty(properties[i], resultInstance.toString(i));
                }
                return record;
            }

            public void remove() {
            }
        };
    } catch (FileNotFoundException x) {
        throw new AmbitException(x);
    } catch (Exception x) {
        throw new AmbitException(x);
    }
}

Example 2 with RetrieveStructure

use of ambit2.db.readers.RetrieveStructure in project ambit-mirror by ideaconsult.

the class InChIChemicalsTableWriterTest method testProcess.

@Test
public void testProcess() throws Exception {
    StructureNormalizer normalizer = new StructureNormalizer();
    // no inchis as well
    setUpDatabaseFromResource("ambit2/db/processors/test/dataset_nofp.xml");
    IDatabaseConnection dbConnection = getConnection();
    ITable chemicals = dbConnection.createQueryTable("EXPECTED_FP", "SELECT * FROM chemicals where inchi is null");
    Assert.assertEquals(5, chemicals.getRowCount());
    RepositoryReader reader = new RepositoryReader();
    RetrieveStructure molReader = new RetrieveStructure(true);
    reader.setConnection(dbConnection.getConnection());
    InChIChemicalsWriter inchiWriter = new InChIChemicalsWriter();
    inchiWriter.setConnection(dbConnection.getConnection());
    inchiWriter.open();
    reader.open();
    int records = 0;
    IStructureRecord o;
    QueryExecutor<RetrieveStructure> exec = new QueryExecutor<RetrieveStructure>();
    exec.setConnection(dbConnection.getConnection());
    int errors = 0;
    while (reader.hasNext()) {
        o = reader.next();
        String content = reader.getStructure(o.getIdstructure());
        if (content == null)
            continue;
        molReader.setValue(o);
        ResultSet rs = exec.process(molReader);
        while (rs.next()) {
            IStructureRecord record = molReader.getObject(rs);
            try {
                record = normalizer.process(record);
                inchiWriter.process(record);
            } catch (Exception x) {
                errors++;
            }
        }
        rs.close();
        o.clear();
        records++;
    }
    reader.close();
    chemicals = dbConnection.createQueryTable("EXPECTED_FP", "SELECT count(*) as c FROM chemicals where inchi is not null");
    Assert.assertEquals(new BigInteger("4"), chemicals.getValue(0, "c"));
    inchiWriter.close();
}

Example 3 with RetrieveStructure

use of ambit2.db.readers.RetrieveStructure in project ambit-mirror by ideaconsult.

the class Structure_crud_test method createVerify.

@Override
protected void createVerify(IQueryUpdate<Object, IStructureRecord> query) throws Exception {
    IDatabaseConnection c = getConnection();
    QueryStructure q = new QueryStructure();
    q.setFieldname(ExactStructureSearchMode.idchemical);
    q.setValue("10");
    RetrieveStructure r = new RetrieveStructure();
    // structure
    r.setFieldname(false);
    QueryExecutor execR = new QueryExecutor();
    execR.setConnection(c.getConnection());
    QueryExecutor exec = new QueryExecutor();
    exec.setConnection(c.getConnection());
    ResultSet rs = exec.process(q);
    int count = 0;
    while (rs.next()) {
        IStructureRecord record = q.getObject(rs);
        r.setValue(record);
        ResultSet rs1 = execR.process(r);
        while (rs1.next()) {
            record = r.getObject(rs1);
            if ("content".equals(record.getContent()))
                count++;
        }
        execR.closeResults(rs1);
    }
    exec.closeResults(rs);
    Assert.assertEquals(1, count);
    c.close();
}

Example 4 with RetrieveStructure

use of ambit2.db.readers.RetrieveStructure in project ambit-mirror by ideaconsult.

the class Structure_crud_test method createVerifyNew.

@Override
protected void createVerifyNew(IQueryUpdate<Object, IStructureRecord> query) throws Exception {
    IDatabaseConnection c = getConnection();
    ITable table = c.createQueryTable("EXPECTED", "SELECT idstructure,idchemical,type_structure FROM structure");
    Assert.assertTrue(table.getRowCount() > 0);
    RetrieveStructure r = new RetrieveStructure();
    r.setPreferedStructure(false);
    r.setFieldname(false);
    QueryExecutor execR = new QueryExecutor();
    execR.setConnection(c.getConnection());
    int count = 0;
    for (int i = 0; i < table.getRowCount(); i++) {
        IStructureRecord record = new StructureRecord();
        record.setIdstructure(Integer.parseInt(table.getValue(i, "idstructure").toString()));
        try {
            Object t = table.getValue(i, "type_structure");
            for (STRUC_TYPE type : STRUC_TYPE.values()) if (type.toString().equals(t)) {
                record.setType(type);
                break;
            }
        } catch (Exception x) {
            record.setType(STRUC_TYPE.NA);
        }
        r.setValue(record);
        ResultSet rs1 = execR.process(r);
        while (rs1.next()) {
            record = r.getObject(rs1);
            if ("content".equals(record.getContent()))
                count++;
        }
        execR.closeResults(rs1);
    }
    Assert.assertEquals(1, count);
    c.close();
}

Example 5 with RetrieveStructure

use of ambit2.db.readers.RetrieveStructure in project ambit-mirror by ideaconsult.

the class StructureRecordXLSXReporter method configureProcessors.

@Override
protected void configureProcessors(String baseRef, boolean includeMol) {
    if (includeMol) {
        RetrieveStructure r = new RetrieveStructure();
        r.setPage(0);
        r.setPageSize(1);
        getProcessors().add(new ProcessorStructureRetrieval(r));
    }
    configurePropertyProcessors();
    getProcessors().add(new ProcessorStructureRetrieval(new QuerySmilesByID()));
    // configureCollectionProcessors(baseRef);
    getProcessors().add(new DefaultAmbitProcessor<IStructureRecord, IStructureRecord>() {

        private static final long serialVersionUID = -7316415661186235101L;

        @Override
        public IStructureRecord process(IStructureRecord target) throws Exception {
            processItem(target);
            return target;
        }
    });
}