Examples with RawIteratingWrapper ambit2.core.io.RawIteratingWrapper used on opensource projects

Example 1 with RawIteratingWrapper

use of ambit2.core.io.RawIteratingWrapper in project ambit-mirror by ideaconsult.

the class ProteinCoronaPaperReaderTest method test.

@Test
public void test() throws Exception {
    RawIteratingWrapper reader = null;
    try {
        LiteratureEntry entry = new LiteratureEntry("Protein Corona", "http://dx.doi.org/10.1021/nn406018q");
        entry.setType(_type.Dataset);
        File baseDir = new File(System.getProperty("java.io.tmpdir"));
        File datafile = new File(baseDir, "MergedSheets.csv");
        if (!datafile.exists()) {
            URL url = new URL("https://raw.githubusercontent.com/ideaconsult/Protein_Corona/master/MergedSheets.csv");
            DownloadTool.download(url, datafile);
        }
        CSV12Reader chemObjectReader = new CSV12Reader(new FileReader(datafile), entry, "PRCR-");
        reader = new CSV12SubstanceReader(chemObjectReader);
        int r = 0;
        while (reader.hasNext()) {
            IStructureRecord mol = reader.nextRecord();
            Assert.assertTrue(mol instanceof SubstanceRecord);
            System.out.println(((SubstanceRecord) mol).getPublicName());
            System.out.println(((SubstanceRecord) mol).getMeasurements());
            r++;
        }
        Assert.assertTrue(r >= 120);
    } finally {
        reader.close();
    }
}

Example 2 with RawIteratingWrapper

use of ambit2.core.io.RawIteratingWrapper in project ambit-mirror by ideaconsult.

the class RawIteratingWrapperTest method test.

@Test
public void test() throws Exception {
    IIteratingChemObjectReader reader = FileInputState.getReader(RawIteratingWrapperTest.class.getClassLoader().getResourceAsStream("ambit2/core/data/io/test.txt"), "test.txt");
    Assert.assertTrue(reader != null);
    // Assert.assertTrue(reader instanceof IteratingDelimitedFileReader);
    RawIteratingWrapper wrapper = new RawIteratingWrapper(reader);
    int count = 0;
    while (wrapper.hasNext()) {
        IStructureRecord record = (IStructureRecord) wrapper.next();
        count++;
    }
    Assert.assertEquals(11, count);
    wrapper.close();
}

Example 3 with RawIteratingWrapper

use of ambit2.core.io.RawIteratingWrapper in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method testWriteBCFFormat.

@Test
public void testWriteBCFFormat() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(0, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(0, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset");
    Assert.assertEquals(0, srcdataset.getRowCount());
    ITable struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(0, struc_src.getRowCount());
    ITable property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(0, property.getRowCount());
    ITable property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(0, property_values.getRowCount());
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/test/bcf.xls");
    Assert.assertNotNull(in);
    RawIteratingWrapper reader = new RawIteratingWrapper(new EurasBCFReader(in, 0));
    // reader.setReference(LiteratureEntry.getInstance("input.sdf"));
    write(reader, c.getConnection());
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(17, chemicals.getRowCount());
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals where smiles is not null and inchi is not null and formula is not null");
    Assert.assertEquals(0, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(28, strucs.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset where name='TEST INPUT'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(28, struc_src.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM catalog_references");
    Assert.assertEquals(17, property.getRowCount());
    // was 37
    int n = 36;
    property = c.createQueryTable("EXPECTED", "SELECT name,count(idreference) as c FROM properties  group by name");
    Assert.assertEquals(n, property.getRowCount());
    for (int i = 0; i < n; i++) {
        Assert.assertEquals(new BigInteger("14"), property.getValue(i, "c"));
    }
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    // was 518
    Assert.assertEquals(504, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(28 * n, property_values.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset join template_def using(idtemplate) where name='TEST INPUT'");
    Assert.assertEquals(504, srcdataset.getRowCount());
    c.close();
/**
 * Removing redundant properties insert ignore into property_values
 * select id,idproperty,idstructure,idvalue,idtype,user_name,status from
 * property_values where idstructure>3 on duplicate key update
 * idstructure=3 delete from property_values where idstructure>3
 *
 * insert ignore into struc_dataset select idstructure,id_srcdataset
 * from struc_dataset where idstructure>3 on duplicate key update
 * idstructure=3 delete from struc_dataset where idstructure>3
 */
}

Example 4 with RawIteratingWrapper

use of ambit2.core.io.RawIteratingWrapper in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method testWriteTXT.

public void testWriteTXT() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(0, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(0, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset");
    Assert.assertEquals(0, srcdataset.getRowCount());
    ITable struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(0, struc_src.getRowCount());
    ITable property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(0, property.getRowCount());
    ITable property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(0, property_values.getRowCount());
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/txt/test.txt");
    Assert.assertNotNull(in);
    IIteratingChemObjectReader reader1 = FileInputState.getReader(in, "test.txt");
    RawIteratingWrapper reader = new RawIteratingWrapper(reader1);
    reader.setReference(LiteratureEntry.getInstance("test.txt"));
    write(reader, c.getConnection());
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    // 8 or 9
    Assert.assertEquals(9, chemicals.getRowCount());
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals where smiles is not null and inchi is not null and formula is not null");
    Assert.assertEquals(9, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(9, strucs.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT id_srcdataset,idtemplate FROM src_dataset where name='TEST INPUT'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    // verifies if trigger insert_dataset_template works ok
    Assert.assertNotNull(srcdataset.getValue(0, "idtemplate"));
    struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(9, struc_src.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(5, property.getRowCount());
    // verifies if insert_property_tuple works ok
    property = c.createQueryTable("EXPECTED", "SELECT * FROM template_def join src_dataset using(idtemplate) where name='TEST INPUT'");
    Assert.assertEquals(5, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(45, property_values.getRowCount());
    ITable tuples = c.createQueryTable("EXPECTED", "SELECT * FROM tuples");
    Assert.assertEquals(9, tuples.getRowCount());
    ITable p_tuples = c.createQueryTable("EXPECTED", "SELECT * FROM property_tuples");
    Assert.assertEquals(45, p_tuples.getRowCount());
    c.close();
/**
 * Removing redundant properties insert ignore into property_values
 * select id,idproperty,idstructure,idvalue,idtype,user_name,status from
 * property_values where idstructure>3 on duplicate key update
 * idstructure=3 delete from property_values where idstructure>3
 *
 * insert ignore into struc_dataset select idstructure,id_srcdataset
 * from struc_dataset where idstructure>3 on duplicate key update
 * idstructure=3 delete from struc_dataset where idstructure>3
 */
}

Example 5 with RawIteratingWrapper

use of ambit2.core.io.RawIteratingWrapper in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method testImport3Same.

@Test
public void testImport3Same() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/match/99-72-9.sdf");
    Assert.assertNotNull(in);
    RawIteratingSDFReader reader = new RawIteratingSDFReader(new InputStreamReader(in));
    reader.setReference(LiteratureEntry.getInstance("input.sdf"));
    write(reader, c.getConnection());
    c.close();
    c = getConnection();
    ITable chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(1, chemicals.getRowCount());
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals where smiles is not null and inchi is not null and formula is not null");
    Assert.assertEquals(1, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(2, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT id_srcdataset,idtemplate FROM src_dataset where name='TEST INPUT'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/match/99-72-9.csv");
    Assert.assertNotNull(in);
    IIteratingChemObjectReader reader1 = FileInputState.getReader(in, "99-72-9.csv");
    RawIteratingWrapper wrapper = new RawIteratingWrapper(reader1);
    wrapper.setReference(LiteratureEntry.getInstance("input.csv"));
    write(wrapper, c.getConnection());
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(3, chemicals.getRowCount());
    // Should be 2, but structures from SDF and SMILES come with different
    // stereo ...
    // Assert.assertEquals(2,chemicals.getRowCount());
    c.close();
}