Examples with Property ambit2.base.data.Property used on opensource projects

Example 96 with Property

use of ambit2.base.data.Property in project ambit-mirror by ideaconsult.

the class CreateAtomEnvironment method getParameters.

@Override
public List<QueryParam> getParameters(int index) throws AmbitException {
    List<QueryParam> params = new ArrayList<QueryParam>();
    params.add(new QueryParam<Integer>(Integer.class, getGroup().getIdchemical()));
    AtomEnvironment ae = ((AtomEnvironmentList) getGroup().getRecordProperty(property)).get(index);
    params.add(new QueryParam<String>(String.class, ae.getCentral_atom()));
    params.add(new QueryParam<Integer>(Integer.class, ae.getFrequency()));
    for (int i = 1; i < 7; i++) {
        String p = ae.getLevel2String(i);
        params.add(new QueryParam<String>(String.class, p == null ? "" : p));
    }
    params.add(new QueryParam<String>(String.class, "valid"));
    return params;
}

Example 97 with Property

use of ambit2.base.data.Property in project ambit-mirror by ideaconsult.

the class ProcessorOntologyEditorTest method testCreateProperty.

@Test
public void testCreateProperty() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/descriptors-datasets.xml");
    IDatabaseConnection c = getConnection();
    ITable names = c.createQueryTable("expected", "SELECT * FROM template_properties where template=\"Physicochemical effects\" and property=\"Boling point\"");
    Assert.assertEquals(0, names.getRowCount());
    editor.setConnection(c.getConnection());
    editor.setOperation(OP.CREATE);
    editor.setTemplate(new Dictionary(null, null), SIDE.LEFT);
    editor.setTemplate(new Dictionary("Physicochemical effects", null), SIDE.RIGHT);
    editor.setCurrentSide(SIDE.RIGHT);
    editor.process(Property.getInstance("Boiling point", "My new reference"));
    names = c.createQueryTable("expected", "SELECT * FROM template_properties where template=\"Physicochemical effects\" and property=\"Boiling point\"");
    Assert.assertEquals(1, names.getRowCount());
    c.close();
}

Example 98 with Property

use of ambit2.base.data.Property in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method testImportDX.

@Test
public void testImportDX() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/dataset-properties.xml");
    IDatabaseConnection c = getConnection();
    ITable chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(5, chemicals.getRowCount());
    ITable strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(5, strucs.getRowCount());
    ITable srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset");
    Assert.assertEquals(1, srcdataset.getRowCount());
    ITable struc_src = c.createQueryTable("EXPECTED", "SELECT * FROM struc_dataset");
    Assert.assertEquals(2, struc_src.getRowCount());
    ITable property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(4, property.getRowCount());
    ITable property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(4, property_values.getRowCount());
    ITable template_def = c.createQueryTable("EXPECTED", "SELECT * FROM template_def");
    Assert.assertEquals(3, template_def.getRowCount());
    InputStream in = this.getClass().getClassLoader().getResourceAsStream("ambit2/core/data/dx/predictions.sdf");
    Assert.assertNotNull(in);
    RawIteratingSDFReader reader = new RawIteratingSDFReader(new InputStreamReader(in));
    // reader.setReference("predictions.sdf");
    write(reader, c.getConnection(), new CASKey());
    reader.close();
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(6, chemicals.getRowCount());
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    Assert.assertEquals(6, 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.assertEquals(31, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(31, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values where idstructure=100215");
    Assert.assertEquals(2, property_values.getRowCount());
    // ITable p_tuples =
    // c.createQueryTable("EXPECTED","SELECT * FROM property_tuples join tuples using(idtuple) join src_dataset using(id_srcdataset) where name='Imported properties'");
    // Assert.assertEquals(66,p_tuples.getRowCount());
    c.close();
    c = getConnection();
    in = this.getClass().getClassLoader().getResourceAsStream("ambit2/core/data/dx/predictions1.sdf");
    Assert.assertNotNull(in);
    reader = new RawIteratingSDFReader(new InputStreamReader(in));
    // reader.setReference(LiteratureEntry.getDXReference());
    write(reader, c.getConnection(), new CASKey());
    reader.close();
    c = getConnection();
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    Assert.assertEquals(31, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(47, property_values.getRowCount());
    template_def = c.createQueryTable("EXPECTED", "SELECT * FROM template_def");
    Assert.assertEquals(30, template_def.getRowCount());
    c.close();
}

Example 99 with Property

use of ambit2.base.data.Property 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 100 with Property

use of ambit2.base.data.Property in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method testWriteMultipleFiles_i5d.

@Test
public void testWriteMultipleFiles_i5d() 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());
    File dir = new File("src/test/resources/ambit2/db/processors/i5d");
    FilenameFilter filter = new FilenameFilter() {

        public boolean accept(File dir, String name) {
            return !name.startsWith(".");
        }
    };
    File[] files = dir.listFiles(filter);
    Assert.assertEquals(3, files.length);
    RawIteratingFolderReader reader = new RawIteratingFolderReader(files);
    write(reader, c.getConnection(), new EINECSKey());
    reader.close();
    c.close();
    c = getConnection();
    chemicals = c.createQueryTable("EXPECTED", "SELECT * FROM chemicals");
    Assert.assertEquals(3, chemicals.getRowCount());
    // there are two empty file without $$$$ sign, which are skipped
    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 join catalog_references using(idreference) where name='Names' and title in ('IUCLID5 SYNONYM#2','IUCLID5')");
    Assert.assertEquals(2, property.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties join catalog_references using(idreference) order by name");
    // Assert.assertEquals(34,property.getRowCount());
    Assert.assertEquals(7, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(19, property_values.getRowCount());
    srcdataset = c.createQueryTable("EXPECTED", "SELECT * FROM src_dataset join template_def using(idtemplate) where name='TEST INPUT'");
    Assert.assertEquals(7, srcdataset.getRowCount());
    ITable p_cas = c.createQueryTable("EXPECTED", "SELECT idchemical,idstructure,value FROM property_values join property_string using(idvalue_string) join properties using(idproperty) where name='CasRN'");
    Assert.assertEquals(3, p_cas.getRowCount());
    ITable p_ec = c.createQueryTable("EXPECTED", "SELECT idchemical,idstructure,value FROM property_values join property_string using(idvalue_string) join properties using(idproperty) where name='EC'");
    Assert.assertEquals(3, p_ec.getRowCount());
    ITable p_uuid = c.createQueryTable("EXPECTED", "SELECT idchemical,idstructure,value FROM property_values join property_string using(idvalue_string) join properties using(idproperty) where name='I5UUID'");
    Assert.assertEquals(3, p_uuid.getRowCount());
    c.close();
}