Examples with ItemFactory org.intermine.xml.full.ItemFactory used on opensource projects

Example 1 with ItemFactory

use of org.intermine.xml.full.ItemFactory in project intermine by intermine.

the class DataSourceUpdater method execute.

/**
 * For each data set in the objectstore, retreive it's details from UniProt data file
 * @throws BuildException if an error occurs
 */
@Override
public void execute() {
    // Needed so that STAX can find it's implementation classes
    ClassLoader cl = Thread.currentThread().getContextClassLoader();
    Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
    if (osAlias == null) {
        throw new BuildException("osAlias attribute is not set");
    }
    if (outputFile == null) {
        throw new BuildException("outputFile attribute is not set");
    }
    if (dataSourceFile == null) {
        throw new BuildException("dataSourceFile attribute is not set");
    }
    LOG.info("Starting DataSourceUpdater");
    Writer writer = null;
    try {
        writer = new FileWriter(outputFile);
        ObjectStore os = ObjectStoreFactory.getObjectStore(osAlias);
        // get the data sources already in the database
        dataSourceNames = getDataSources(os);
        // parse the uniprot data source file
        Map<String, DataSourceHolder> allDataSources = parseDataFile(new FileReader(dataSourceFile));
        ItemFactory itemFactory = new ItemFactory(os.getModel(), "-1_");
        writer.write(FullRenderer.getHeader() + "\n");
        // write the relevant data sources to file
        for (DataSourceHolder holder : allDataSources.values()) {
            Item datasource = itemFactory.makeItemForClass("DataSource");
            datasource.setAttribute("name", holder.name);
            if (holder.descr != null) {
                datasource.setAttribute("description", holder.descr);
            }
            if (holder.url != null) {
                datasource.setAttribute("url", holder.url);
            }
            if (holder.pubMedId != null) {
                Item publication = itemFactory.makeItemForClass("Publication");
                publication.setAttribute("pubMedId", holder.pubMedId);
                writer.write(FullRenderer.render(publication));
                datasource.addToCollection("publications", publication);
            }
            writer.write(FullRenderer.render(datasource));
        }
        writer.write(FullRenderer.getFooter() + "\n");
    } catch (Exception e) {
        throw new BuildException("exception while retrieving data sets", e);
    } finally {
        Thread.currentThread().setContextClassLoader(cl);
        if (writer != null) {
            try {
                writer.close();
            } catch (Exception e) {
            // ignore
            }
        }
    }
}

Example 2 with ItemFactory

use of org.intermine.xml.full.ItemFactory in project intermine by intermine.

the class GoConverterTest method testCreateWithObjects.

public void testCreateWithObjects() throws Exception {
    ItemFactory tgtItemFactory = new ItemFactory(Model.getInstanceByName("genomic"));
    Item organism = tgtItemFactory.makeItem("3_1", "Organism", "");
    organism.setAttribute("taxonId", "7227");
    Set<String> expected = new HashSet<String>();
    expected.add("4_1");
    expected.add("4_2");
    converter.initialiseMapsForFile();
    assertEquals(expected, new HashSet<String>(converter.createWithObjects("FLYBASE:Grip84; FB:FBgn0026430, FLYBASE:l(1)dd4; FB:FBgn0001612", organism)));
}

Example 3 with ItemFactory

use of org.intermine.xml.full.ItemFactory in project intermine by intermine.

the class CreateChromosomeLocationsProcessTest method setUp.

public void setUp() throws Exception {
    osw = ObjectStoreWriterFactory.getObjectStoreWriter("osw.bio-test");
    osw.getObjectStore().flushObjectById();
    model = Model.getInstanceByName("genomic");
    itemFactory = new ItemFactory(model);
}

Example 4 with ItemFactory

use of org.intermine.xml.full.ItemFactory in project intermine by intermine.

the class MakeSpanningLocationsProcessTest method setUp.

public void setUp() throws Exception {
    osw = ObjectStoreWriterFactory.getObjectStoreWriter("osw.bio-test");
    osw.getObjectStore().flushObjectById();
    model = Model.getInstanceByName("genomic");
    itemFactory = new ItemFactory(model);
}

Example 5 with ItemFactory

use of org.intermine.xml.full.ItemFactory in project intermine by intermine.

the class GFF3RecordHandlerTest method setUp.

public void setUp() throws Exception {
    tgtModel = Model.getInstanceByName("genomic");
    itemFactory = new ItemFactory(tgtModel);
}