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

Examples of org.openbel.framework.common.protonetwork.model.NamespaceTable.TableNamespace


        void readNamespace(ObjectInput in) throws IOException,
                ClassNotFoundException {
            byte nsnull = in.readByte();
            if (nsnull == 1) {
                namespace = new TableNamespace();
                namespace.readExternal(in);
            }
        }
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        EquivalenceLookup[] jArray = new EquivalenceLookup[numParams];
        // Index parameters to their parameter index
        int[] parameterIndices = new int[numParams];
        for (int i = 0; i < numParams; i++) {
            final TableParameter param = params[i];
            TableNamespace ns = param.getNamespace();

            // Sanity check - namespace may be null
            if (ns == null) {
                jArray[i] = null;
                parameterIndices[i] = tpIdx.get(param);
                continue;
            }

            // Resource location is never null
            final String rl = ns.getResourceLocation();

            // Which bucket are we mapped to?
            final EquivalenceLookup bucket = equivs.forResourceLocation(rl);

            // This parameter's namespace is not mapped to the current eqs
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                    "NamespaceIndex", "Value", "(Global ParameterIndex)");

            for (final TableParameter parameter : parameterTable
                    .getTableParameters()) {
                // fetch the namespace value
                TableNamespace tn = parameter.getNamespace();
                Integer nsIndex = nsTable.getNamespaceIndex().get(tn);
                String nsValue = "-";
                if (nsIndex != null) {
                    nsValue = String.valueOf(nsIndex);
                }
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            NamespaceTable nt = pn.getNamespaceTable();

            if (nsg.getDefaultResourceLocation() != null) {
                org.openbel.framework.common.model.Namespace dns =
                        new Namespace("", nsg.getDefaultResourceLocation());
                nt.addNamespace(new TableNamespace(dns), 0);
            }

            // associate namespaces to document id 0
            final List<Namespace> nsl = nsg.getNamespaces();
            if (hasItems(nsl)) {
                for (org.openbel.framework.common.model.Namespace ns : nsl) {
                    nt.addNamespace(new TableNamespace(ns), 0);
                }
            }
        }

        // handle annotation definitions
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        ParameterTable pt = pn.getParameterTable();

        Integer npidx;
        if (p.getNamespace() != null) {
            // add parameter with namespace
            TableNamespace ns = new TableNamespace(p.getNamespace());
            npidx = pt.addTableParameter(new TableParameter(ns, p.getValue()));
        } else if (doc.getNamespaceGroup() != null
                && doc.getNamespaceGroup().getDefaultResourceLocation() != null) {
            // add parameter with user-defined default namespace
            TableNamespace ns = new TableNamespace(doc.getNamespaceGroup()
                    .getDefaultResourceLocation());
            npidx = pt.addTableParameter(new TableParameter(ns, p.getValue()));
        } else {
            // add parameter with TEXT namespace
            npidx = pt.addTableParameter(new TableParameter(p.getValue()));
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                ret[i] = new int[3];
                ret[i][TERM_INDEX] = termIdx;
                ret[i][PARAM_INDEX] = paramIdx;

                final TableParameter tp = myPT.getTableParameter(paramIdx);
                final TableNamespace tn = tp.getNamespace();
                Integer nsIndex = nt.getNamespaceIndex().get(tn);

                if (nsIndex == null)
                    ret[i][NAMESPACE_INDEX] = NO_NAMESPACE;
                else
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    @Before
    public void setUp() {
        pn = new ProtoNetwork();
        er = new TestEquivResource();
        uuids = new ArrayList<SkinnyUUID>(1000);
        TableNamespace ns1 = new TableNamespace("namespace1");
        TableNamespace ns2 = new TableNamespace("namespace2");
        MockEquivLookup lookup1 = new MockEquivLookup();
        MockEquivLookup lookup2 = new MockEquivLookup();
        er.addLookup(ns1.getResourceLocation(), lookup1);
        er.addLookup(ns2.getResourceLocation(), lookup2);

        for (int i = 0; i < 1000; i++) {
            String v1 = "p1" + String.valueOf(i);
            String v2 = "p2" + String.valueOf(i);
            pn.getParameterTable().addTableParameter(
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        assertEquals(3, namespaceTable.getNamespaces().size());
        assertEquals(11, parameterTable.getTableParameters().size());

        assertEquals(9, termTable.getTermValues().size());
        assertTrue(parameterTable.getTableParameters().contains(
                new TableParameter(new TableNamespace(hgncNs), "AIFM1")));
        assertTrue(termTable.getTermValues().contains("proteinAbundance(#)"));
        assertTrue(termTable.getTermValues().contains("geneAbundance(#)"));

        //Test extracted statements
        StatementTable statementTable = protoNetwork.getStatementTable();
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            Integer tid = node2term.get(i);
            String nl = terms.get(tid);
            List<Integer> pids = tpmtidx.get(tid);
            for (Integer pid : pids) {
                TableParameter param = pt.getTableParameter(pid);
                TableNamespace ns = param.getNamespace();
                nl = nl.replaceFirst("#", ns == null ?
                    quoteParameter(param.getValue()) :
                    ns.getPrefix() + ":" + quoteParameter(param.getValue()));
            }

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

            String tf = nl.substring(0, nl.indexOf('('));
            int fv = FunctionEnum.getFunctionEnum(tf).getValue();

            // XXX offset
            knps.setInt(1, eqId + 1);
            knps.setInt(2, fv);
            knps.setInt(3, knl);
            knps.addBatch();
        }

        knps.executeBatch();

        PreparedStatement knpps = getPreparedStatement(KAM_NODE_PARAMETER_SQL);
        PreparedStatement knups = getPreparedStatement(KAM_PARAMETER_UUID_SQL);
        final Map<Integer, Integer> gpi = pt.getGlobalIndex();
        final Map<Integer, SkinnyUUID> guu = pt.getGlobalUUIDs();

        final Set<Integer> seenKamNodes = sizedHashSet(nodes.size());
        final Set<Integer> seenGlobalIds = sizedHashSet(gpi.size());

        // load kam node parameters
        final Map<Integer, Integer> nti = pnt.getNodeTermIndex();
        for (int i = 0, n = nodes.size(); i < n; i++) {
            final Integer ti = nti.get(i);

            // XXX offset
            final Integer eqId = eqn.get(i) + 1;

            // don't add kam node parameters if we have already seen the
            // equivalent node.
            if (seenKamNodes.contains(eqId)) {
                continue;
            }

            List<Integer> gtpl = tpmtidx.get(ti);
            if (hasItems(gtpl)) {
                for (int j = 0; j < gtpl.size(); j++) {
                    // get parameter index, retrieve global parameter, and set
                    Integer parameterIndex = gtpl.get(j);

                    final Integer gid = gpi.get(parameterIndex);

                    // XXX offset
                    knpps.setInt(1, gid + 1);
                    knpps.setInt(2, eqId);
                    knpps.setInt(3, j);
                    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);
                    }
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        TableParameter[] paramArr = paramTbl.getTableParameterArray();
        for (final TableParameter tp : paramArr) {
            if (!validParameter(tp)) {
                continue;
            }
            TableNamespace namespace = tp.getNamespace();
            String value = tp.getValue();
            String rl = namespace.getResourceLocation();
            JDBMEquivalenceLookup jdbmLookup = lookups.get(rl);
            if (jdbmLookup == null) {
                continue;
            }
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