Examples with NanoWikiRDFReader net.idea.loom.nm.nanowiki.NanoWikiRDFReader used on opensource projects

Example 1 with NanoWikiRDFReader

use of net.idea.loom.nm.nanowiki.NanoWikiRDFReader in project ambit-mirror by ideaconsult.

the class NanoWikiRDFTest method testRead.

@Test
public void testRead() throws Exception {
    NanoWikiRDFReader reader = null;
    int records = 0;
    try {
        reader = new NanoWikiRDFReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(getNanoWikiFile()))));
        while (reader.hasNext()) {
            IStructureRecord record = reader.nextRecord();
            Assert.assertTrue(record instanceof SubstanceRecord);
            System.out.println(((SubstanceRecord) record).getPublicName());
            records++;
        }
    } finally {
        reader.close();
    }
}

Example 2 with NanoWikiRDFReader

use of net.idea.loom.nm.nanowiki.NanoWikiRDFReader in project ambit-mirror by ideaconsult.

the class NanoWikiRDFTest method testWriteNanoWikiRDF.

@Test
public void testWriteNanoWikiRDF() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    IRawReader<IStructureRecord> parser = null;
    try {
        parser = new NanoWikiRDFReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(getNanoWikiFile()))));
        write(parser, c.getConnection(), new ReferenceSubstanceUUID(), false);
    } finally {
        parser.close();
        c.close();
    }
}

Example 3 with NanoWikiRDFReader

use of net.idea.loom.nm.nanowiki.NanoWikiRDFReader in project ambit-mirror by ideaconsult.

the class Export2RDFTest method testNanoWiki2RDF.

@Test
public void testNanoWiki2RDF() throws Exception {
    File nanowiki = NanoWikiRDFTest.getNanoWikiFile();
    Assert.assertTrue(nanowiki.exists());
    Request hack = new Request();
    hack.setRootRef(new Reference("http://localhost/ambit2"));
    SubstanceRDFReporter r = new SubstanceRDFReporter(hack, MediaType.TEXT_RDF_N3);
    Model model = ModelFactory.createDefaultModel();
    r.header(model, null);
    r.setOutput(model);
    NanoWikiRDFReader reader = null;
    OutputStream writer = null;
    StructureRecordValidator validator = new StructureRecordValidator() {

        int idresult = 1;

        int idcompound = 1;

        Map<String, Integer> smileslookup = new TreeMap<String, Integer>();

        @Override
        public IStructureRecord validate(SubstanceRecord record, CompositionRelation rel) throws Exception {
            /**
             * compounds will be assigned ids if imported into database
             * and resource url depends on the ids
             */
            if (rel.getSecondStructure().getIdchemical() <= 0) {
                String smi = rel.getSecondStructure().getSmiles();
                if (smi != null) {
                    Integer index = smileslookup.get(smi);
                    if (index != null)
                        rel.getSecondStructure().setIdchemical(index);
                    else {
                        smileslookup.put(smi, idcompound);
                        rel.getSecondStructure().setIdchemical(idcompound);
                        idcompound++;
                    }
                } else {
                    rel.getSecondStructure().setIdchemical(idcompound);
                    idcompound++;
                }
            }
            return super.validate(record, rel);
        }

        @Override
        public IStructureRecord validate(SubstanceRecord record, ProtocolApplication<Protocol, IParams, String, IParams, String> papp) throws Exception {
            /*
				 * EffectRecords resource URL depends on th eidresult, when
				 * imported into DB it's automatically assigned, here it's set
				 * to subsequent numbers
				 */
            for (EffectRecord<String, IParams, String> effect : papp.getEffects()) {
                if (effect.getIdresult() <= 0)
                    effect.setIdresult(idresult++);
            }
            return super.validate(record, papp);
        }
    };
    int records = 0;
    try {
        reader = new NanoWikiRDFReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(nanowiki))));
        while (reader.hasNext()) {
            IStructureRecord record = reader.nextRecord();
            Assert.assertTrue(record instanceof SubstanceRecord);
            validator.validate((SubstanceRecord) record);
            r.processItem((SubstanceRecord) record);
            records++;
        }
        r.footer(model, null);
        // one substance
        ResIterator substances = model.listSubjectsWithProperty(RDF.type, RDFTermsSubstance.CHEBI_59999.getResource(model));
        Assert.assertTrue(countResources(substances) >= 404);
        // asssay
        ResIterator assays = model.listSubjectsWithProperty(RDF.type, RDFTermsSubstance.BAO_0000015.getResource(model));
        Assert.assertTrue(countResources(assays) >= 866);
        // measure groups
        ResIterator measuregroups = model.listSubjectsWithProperty(RDF.type, RDFTermsSubstance.BAO_0000040.getResource(model));
        Assert.assertTrue(countResources(measuregroups) >= 86);
        // protocols
        ResIterator protocols = model.listSubjectsWithProperty(RDF.type, RDFTermsSubstance.OBI_0000272.getResource(model));
        Assert.assertTrue(countResources(protocols) >= 65);
        // endpoint
        ResIterator endpoints = model.listSubjectsWithProperty(RDF.type, RDFTermsSubstance.BAO_0000179.getResource(model));
        // thanks to the validator result ids are set and we have > 1 entry,
        // otherwise all endpoints collapse into one
        Assert.assertTrue(countResources(endpoints) >= 866);
        File output = new File(System.getProperty("java.io.tmpdir") + "/" + "nanowiki_export.ttl");
        System.out.println("Exported to " + output.getAbsolutePath());
        writer = new FileOutputStream(output);
        RDFDataMgr.write(writer, model, RDFFormat.TURTLE);
    } finally {
        reader.close();
        if (writer != null)
            writer.close();
    }
}

Example 4 with NanoWikiRDFReader

use of net.idea.loom.nm.nanowiki.NanoWikiRDFReader in project ambit-mirror by ideaconsult.

the class NanoWikiRDFTest method testRoundtrip.

@Test
public void testRoundtrip() throws Exception {
    NanoWikiRDFReader reader = null;
    Request hack = new Request();
    hack.setRootRef(new Reference("http://localhost/ambit2"));
    SubstanceRDFReporter r = new SubstanceRDFReporter(hack, MediaType.TEXT_RDF_N3);
    Model model = ModelFactory.createDefaultModel();
    r.header(model, null);
    r.setOutput(model);
    try {
        reader = new NanoWikiRDFReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(getNanoWikiFile()))));
        while (reader.hasNext()) {
            IStructureRecord record = reader.nextRecord();
            Assert.assertTrue(record instanceof SubstanceRecord);
            r.processItem((SubstanceRecord) record);
        }
        r.footer(model, null);
        File output = new File(System.getProperty("java.io.tmpdir") + "/" + "nanordf_enm-export.ttl");
        System.out.println("Exported to " + output.getAbsolutePath());
        OutputStream writer = new FileOutputStream(output);
        RDFDataMgr.write(writer, model, RDFFormat.TURTLE);
    } finally {
        if (reader != null)
            reader.close();
    }
}

Example 5 with NanoWikiRDFReader

use of net.idea.loom.nm.nanowiki.NanoWikiRDFReader in project ambit-mirror by ideaconsult.

the class Context method createParser.

protected IRawReader<IStructureRecord> createParser(InputStream stream, boolean xlsx) throws Exception {
    _parsertype mode = getParserType();
    InputStream in = null;
    if (gzipped)
        in = new GZIPInputStream(stream);
    else
        in = stream;
    if (mode == null) {
        logger_cli.log(Level.INFO, "MSG_IMPORT", new Object[] { "parser type not specified, assuming", xlsx ? "xlsx" : "xls" });
        return new GenericExcelParser(in, jsonConfig, xlsx);
    } else
        switch(mode) {
            case enmrdf:
                return new ENanoMapperRDFReader(new InputStreamReader(in), "ENM3");
            case nanowiki:
                return new NanoWikiRDFReader(new InputStreamReader(in));
            default:
                if (jsonConfig == null)
                    throw new FileNotFoundException("JSON config file not specified!");
                return new GenericExcelParser(in, jsonConfig, xlsx, prefix);
        }
}