Examples with CASKey ambit2.core.processors.structure.key.CASKey used on opensource projects

Example 1 with CASKey

use of ambit2.core.processors.structure.key.CASKey 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 2 with CASKey

use of ambit2.core.processors.structure.key.CASKey in project ambit-mirror by ideaconsult.

the class Context method importI5Z.

protected int importI5Z(IStructureKey keytomatch, boolean i6, StructureRecordValidator validator) throws Exception {
    // validator uses parsertype
    setParserType(i6 ? _parsertype.i6z : _parsertype.i5z);
    logger_cli.log(Level.INFO, "MSG_IMPORT", new Object[] { String.format("i%sz", i6 ? "6" : "5"), inputFile.getAbsolutePath() });
    IZReader reader = null;
    Connection c = null;
    try {
        DBConnectionConfigurable<Context> dbc = null;
        dbc = getConnection(getConfigFile());
        c = dbc.getConnection();
        c.setAutoCommit(true);
        I5Options options = new I5Options();
        options.setMaxReferenceStructures(maxRefSubstances);
        options.setExceptionOnMaxReferenceStructures(false);
        options.setAllowMultipleSubstances(false);
        if (i6)
            reader = new I6ZReader<>(inputFile, options);
        else
            reader = new I5ZReader<>(inputFile, options);
        QASettings qa = new QASettings(false);
        qa.setAll();
        reader.setQASettings(qa);
        matchByKey = keytomatch == null ? new CASKey() : keytomatch;
        return write(reader, c, matchByKey, true, clearMeasurements, clearComposition, validator, null, true, false);
    } catch (Exception x) {
        throw x;
    } finally {
        if (reader != null)
            reader.close();
        try {
            if (c != null)
                c.close();
        } catch (Exception x) {
        }
    }
}

Example 3 with CASKey

use of ambit2.core.processors.structure.key.CASKey in project ambit-mirror by ideaconsult.

the class RepositoryWriterTest method testImportTox21.

@Test
public void testImportTox21() 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/core/pubchem/tox21_excerpt.sdf");
    Assert.assertNotNull(in);
    IRawReader<IStructureRecord> reader = new RawIteratingSDFReader(new InputStreamReader(in));
    // reader.setReference("predictions.sdf");
    write((RawIteratingSDFReader) reader, c.getConnection(), new CASKey());
    reader.close();
    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='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(19, property.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values");
    Assert.assertEquals(57, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = 'PUBCHEM_SID'");
    Assert.assertEquals(3, 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/pubchem/aid720516.csv");
    Assert.assertNotNull(in);
    reader = new RawIteratingWrapper<IIteratingChemObjectReader>(FileInputState.getReader(in, ".csv"));
    // reader.setReference(LiteratureEntry.getDXReference());
    write(reader, c.getConnection(), new PubchemSID(), true);
    reader.close();
    c = getConnection();
    strucs = c.createQueryTable("EXPECTED", "SELECT * FROM structure");
    // Assert.assertEquals(3,strucs.getRowCount());
    property = c.createQueryTable("EXPECTED", "SELECT * FROM properties");
    // does not write
    Assert.assertEquals(19 + 9, property.getRowCount());
    // another
    // PUBCHEM_SID
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = 'PUBCHEM_CID'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = 'PUBCHEM_ACTIVITY_OUTCOME'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = 'PUBCHEM_ACTIVITY_SCORE'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '1^Activity_Summary^STRING^^^^'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '2^ATAD5_Activity^STRING^^^^'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '3^ATAD5 Potency (uM)^FLOAT^uM^AC^^'");
    Assert.assertEquals(0, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '4^ATAD5_Efficacy_(_)^FLOAT^_^^^'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '5^Viability_Activity^STRING^^^^'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '6^Viability_Potency (uM)^FLOAT^uM^^^'");
    Assert.assertEquals(0, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '7^Viability_Efficacy_(_)^FLOAT^_^^^'");
    Assert.assertEquals(3, property_values.getRowCount());
    property_values = c.createQueryTable("EXPECTED", "SELECT * FROM property_values join properties using(idproperty) where name = '8^Sample_Source^STRING^^^^'");
    Assert.assertEquals(3, property_values.getRowCount());
    // Assert.assertEquals(57+9*3,property_values.getRowCount());
    c.close();
}

Example 4 with CASKey

use of ambit2.core.processors.structure.key.CASKey in project ambit-mirror by ideaconsult.

the class CallableStructureEntry method createReference.

@Override
protected TaskResult createReference(Connection connection) throws Exception {
    final RepositoryWriter writer = new RepositoryWriter();
    writer.setUseExistingStructure(isPropertyOnly());
    writer.setPropertyKey(new CASKey());
    SourceDataset dataset;
    if (isPropertyOnly()) {
        dataset = new SourceDataset("Properties registration", LiteratureEntry.getInstance());
    } else
        dataset = new SourceDataset("Chemical structure registration", LiteratureEntry.getInstance());
    dataset.setStars(6);
    writer.setDataset(dataset);
    writer.setConnection(connection);
    writer.setCloseConnection(true);
    try {
        List<IStructureRecord> records = writer.write(record);
        for (IStructureRecord result : records) {
            // what about policies
            if (isPropertyOnly()) {
                return new TaskResult(String.format("%s?feature_uris=%s/dataset/Properties+registration/feature", cmpreporter.getURI(result), applicationRootReference), false);
            } else {
                return new TaskResult(String.format("%s?feature_uris=%s/dataset/Chemical+structure+registration/feature", cmpreporter.getURI(result), applicationRootReference), false);
            }
        }
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND);
    } catch (Exception x) {
        throw x;
    } finally {
        writer.close();
    }
}