Package org.openbel.framework.common.protonetwork.model

Examples of org.openbel.framework.common.protonetwork.model.SkinnyUUID

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        /**
         * {@inheritDoc}
         */
        @Override
        public EquivalentParameter convert(Parameter src) {
            SkinnyUUID bucket = null;
            Namespace ns = src.getNamespace();
            String val = src.getValue();
            if (ns != null) {
                String rl = ns.getResourceLocation();
                EquivalenceLookup el = lookup.forResourceLocation(rl);
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        // get uuids for namespaceValues
        Set<SkinnyUUID> uuids = new LinkedHashSet<SkinnyUUID>();
        // resource location : values
        Map<String, Set<String>> noEquivs = new HashMap<String, Set<String>>();
        for (NamespaceValue nv : nvs) {
            SkinnyUUID uuid = nv.getEquivalence() != null ? new SkinnyUUID(nv
                    .getEquivalence().getMsb(), nv.getEquivalence().getLsb())
                    : equivalencer
                            .getUUID(Converter.convert(nv.getNamespace()),
                                    nv.getValue());
            if (uuid != null) {
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        default:
            throw new UnsupportedOperationException("Unknown domain: " + domain);
        }

        try {
            SkinnyUUID uuid = equivalencer.getUUID(
                    getNamespace(orig.getNamespace()), orig.getValue());
            if (uuid == null) {
                // no equivalents anywhere
                return orig;
            }
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            String v2 = "p2" + String.valueOf(i);
            pn.getParameterTable().addTableParameter(
                    new TableParameter(ns1, v1));
            pn.getParameterTable().addTableParameter(
                    new TableParameter(ns2, v2));
            SkinnyUUID u = new SkinnyUUID(UUID.randomUUID());
            uuids.add(u);
            lookup1.addLookup(v1, u);
            lookup2.addLookup(v2, u);
        }
        be = new BucketEquivalencer(pn, er);
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    @Before
    public void setup() {
        try {
            indexPath = tempFolder.newFolder();
            value = new SkinnyUUID(UUID.randomUUID());

            RecordManager recman = RecordManagerFactory.createRecordManager(
                    indexPath.getAbsolutePath(), new Properties());
            PrimaryTreeMap<String, SkinnyUUID> tree =
                    recman.treeMap(IndexerConstants.INDEX_TREE_KEY,
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            JDBMEquivalenceLookup jdbmLookup =
                    new JDBMEquivalenceLookup(indexPath.getAbsolutePath());
            jdbmLookup.open();

            assertEquals(1, jdbmLookup.getRecordCount());
            assertNull(jdbmLookup.reverseLookup(new SkinnyUUID(UUID
                    .randomUUID())));

            jdbmLookup.close();
        } catch (Exception e) {
            e.printStackTrace();
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                    recman.treeMap(IndexerConstants.INDEX_TREE_KEY,
                            new SkinnyUUIDSerializer());
            tree.inverseHashView(IndexerConstants.INVERSE_KEY);

            for (int i = 0; i < numToTest; i++) {
                SkinnyUUID uuid = new SkinnyUUID(UUID.randomUUID());
                tree.put(String.valueOf(i), uuid);
                uuids.add(uuid);
            }

            recman.commit();
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            JDBMEquivalenceLookup jdbmLookup =
                    new JDBMEquivalenceLookup(indexPath.getAbsolutePath());
            jdbmLookup.open();

            for (int i = 0; i < numToTest; i++) {
                SkinnyUUID uuid = uuids.get(i);
                assertEquals("Failed for " + i, uuid,
                        jdbmLookup.lookup(String.valueOf(i)));
            }

            jdbmLookup.close();
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                    knpps.addBatch();

                    if (seenGlobalIds.contains(gid)) {
                        continue;
                    }
                    SkinnyUUID uuid = guu.get(gid);
                    if (uuid != null) {
                        // XXX offset
                        knups.setInt(1, gid + 1);
                        knups.setLong(2, uuid.getMostSignificantBits());
                        knups.setLong(3, uuid.getLeastSignificantBits());
                        knups.addBatch();
                    }
                    seenGlobalIds.add(gid);
                }
            }

            // track equivalent kam node
            seenKamNodes.add(eqId);
        }

        knpps.executeBatch();

        PreparedStatement pps = getPreparedStatement(TERM_PARAMETER_SQL);
        PreparedStatement tps = getPreparedStatement(TERM_SQL);
        final Map<Integer, Integer> termNodes = pnt.getTermNodeIndex();
        // load term parameters and terms
        int tpindex = 0;
        for (int ti = 0; ti < terms.size(); ti++) {
            String t = terms.get(ti);

            // find node equivalence
            Integer nodeId = termNodes.get(ti);
            // XXX offset
            final Integer eqId = eqn.get(nodeId) + 1;

            Integer ctl = valueIndexMap.get(t);
            if (ctl == null) {
                ctl = saveObject(1, t);
                valueIndexMap.put(t, ctl);
            }

            // XXX offset
            tps.setInt(1, ti + 1);
            // XXX offset
            tps.setInt(2, eqId);
            tps.setInt(3, ctl);
            tps.addBatch();

            int ord = 0;
            List<Integer> pl = tpmtidx.get(ti);
            if (hasItems(pl)) {
                for (Integer pi : pl) {
                    TableParameter p = pt.getIndexTableParameter().get(pi);
                    Integer cpv = valueIndexMap.get(p.getValue());
                    if (cpv == null) {
                        cpv = saveObject(1, p.getValue());
                        valueIndexMap.put(p.getValue(), cpv);
                    }

                    final Integer gid = gpi.get(pi);

                    // XXX offset
                    pps.setInt(1, tpindex + 1);
                    // XXX offset
                    pps.setInt(2, gid + 1);
                    // XXX offset
                    pps.setInt(3, ti + 1);

                    // find index for the parameter's namespace
                    TableNamespace tn = p.getNamespace();
                    Integer ni = null;
                    if (tn != null) {
                        ni = nt.getNamespaceIndex().get(tn);
                    }

                    if (ni == null) {
                        pps.setNull(4, Types.INTEGER);
                    } else {
                        // XXX offset
                        pps.setInt(4, ni + 1);
                    }

                    pps.setInt(5, cpv);
                    pps.setInt(6, ord);
                    pps.addBatch();

                    ord++;
                    tpindex++;

                    if (seenGlobalIds.contains(gid)) {
                        continue;
                    }
                    SkinnyUUID uuid = guu.get(gid);
                    if (uuid != null) {
                        // XXX offset
                        knups.setInt(1, gid + 1);
                        knups.setLong(2, uuid.getMostSignificantBits());
                        knups.setLong(3, uuid.getLeastSignificantBits());
                        knups.addBatch();
                    }
                    seenGlobalIds.add(gid);
                }
            }
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                    String rl = ns.getResourceLocation();

                    // ... do we have set membership?
                    JDBMEquivalenceLookup jdbmLookup = lookups.get(rl);
                    if (jdbmLookup != null) {
                        SkinnyUUID uuid = jdbmLookup.lookup(val);
                        // Check for set membership, uuid ∊ uuids
                        if (uuids.contains(uuid)) {

                            // This indicates equivalent parameters are
                            // used by both document and network. This
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Related Classes of org.openbel.framework.common.protonetwork.model.SkinnyUUID

  • org.openbel.framework.api.internal.KAMStoreDaoImpl
  • org.openbel.framework.api.Resolver
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.compiler.PhaseThreeImpl
  • org.openbel.framework.core.equivalence.BucketEquivalencer
  • org.openbel.framework.core.equivalence.BucketEquivalencerTest
  • org.openbel.framework.core.equivalence.DefaultParameterEquivalencer
  • org.openbel.framework.core.equivalence.EquivalenceConverter$ParameterConverter
  • org.openbel.framework.core.indexer.JDBMEquivalenceLookupTest
  • org.openbel.framework.core.indexer.SkinnyUUIDSerializer
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