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

Example 6 with RawIteratingSDFReader

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

the class RepositoryWriterTest method testImportByInChI.

@Test
public void testImportByInChI() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/match/atropine.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(1, strucs.getRowCount());
    ITable 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"));
    ITable struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(1, struc_src.getRowCount());
    ITable property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(2, property.getRowCount());
    ITable property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(2, property_values.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset join template_def using(idtemplate) where name='TEST INPUT'");
    Assert.assertEquals(2, srcdataset.getRowCount());
    c.close();
    c = getConnection();
    // now import properties and match by inchi
    in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/match/props.csv");
    Assert.assertNotNull(in);
    IIteratingChemObjectReader reader1 = FileInputState.getReader(in, ".csv");
    importProperties(reader1, c.getConnection(), new InchiKey());
    // importProperties(reader1,c.getConnection(),new InchiPropertyKey());
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(1, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(1, strucs.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset where name='Imported properties'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset join src_dataset using(id_srcdataset) where name='Imported properties'");
    Assert.assertEquals(1, struc_src.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertTrue(property.getRowCount() >= 6);
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(6, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name='chiSquared'");
    Assert.assertEquals(1, property_values.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset join template_def using(idtemplate) where name='Imported properties'");
    Assert.assertEquals(4, srcdataset.getRowCount());
    c.close();
}

Example 7 with RawIteratingSDFReader

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

the class RepositoryWriterTest method testZeroLeadingCAS.

@Test
public void testZeroLeadingCAS() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/test/weirdcasformatting.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(10, 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(10, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(10, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT id_srcdataset,idtemplate FROM src_dataset where name='TEST INPUT'");
    Assert.assertEquals(1, srcdataset.getRowCount());
    ITable table = c.createQueryTable("EXPECTED", "SELECT value from property_string where value='1728-95-6'");
    Assert.assertEquals(1, table.getRowCount());
    table = c.createQueryTable("Z0", "SELECT value,name FROM property_values left join property_string using(idvalue_string) join properties using(idproperty) join catalog_references using(idreference) where comments='http://www.opentox.org/api/1.1#CASRN' and !(value regexp '^0')");
    Assert.assertEquals(10, table.getRowCount());
    c.close();
}

Example 8 with RawIteratingSDFReader

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

the class RepositoryWriterTest method testSeekByCID.

@Test
public void testSeekByCID() 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/cid/712.sdf");
    Assert.assertNotNull(in);
    RawIteratingSDFReader reader = new RawIteratingSDFReader(new InputStreamReader(in));
    reader.setReference(LiteratureEntry.getInstance("712.sdf"));
    write(reader, c.getConnection(), new PubchemCID());
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(1, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(3, 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(3, struc_src.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(38, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(63, property_values.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset join template_def using(idtemplate) where name='TEST INPUT'");
    Assert.assertEquals(38, 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 9 with RawIteratingSDFReader

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

the class RepositoryWriterTest method main.

public static void main(String[] args) {
    if (args == null || args.length == 0)
        System.exit(-1);
    RepositoryWriterTest w = new RepositoryWriterTest();
    File file = new File(args[0]);
    RawIteratingSDFReader reader = null;
    IDatabaseConnection c = null;
    long now = System.currentTimeMillis();
    try {
        w.setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
        c = w.getConnection();
        reader = new RawIteratingSDFReader(new FileReader(file));
        reader.setReference(LiteratureEntry.getInstance(file.getName()));
        w.write(reader, c.getConnection(), new NoneKey(), false, 1000000);
        c.close();
    } catch (Exception x) {
        x.printStackTrace();
    } finally {
        try {
            if (reader != null)
                reader.close();
        } catch (Exception x) {
        }
        try {
            if (c != null)
                c.close();
        } catch (Exception x) {
        }
        System.out.print("Elapsed ");
        System.out.println(System.currentTimeMillis() - now);
    }
}

Example 10 with RawIteratingSDFReader

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

the class QuerySmartsTest method testMatchNoAccelerator.

@Test
public void testMatchNoAccelerator() throws Exception {
    Preferences.setProperty(Preferences.FASTSMARTS, "false");
    QuerySMARTS q = new QuerySMARTS();
    q.setValue(new FunctionalGroup("aromatic aldehyde example", "c1ccccc1[$(C(C)C(=O)),$(CC(C)C(=O))]", ""));
    // "c1ccccc1C(C)C(=O)",""));
    RawIteratingSDFReader reader = new RawIteratingSDFReader(new InputStreamReader(getClass().getClassLoader().getResourceAsStream("ambit2/db/processors/test/smartssearch.sdf")));
    int count = 0;
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        Assert.assertEquals(1.0, q.calculateMetric(record));
        count++;
    }
    Assert.assertEquals(2, count);
}