Package org.openbel.framework.core.indexer

Examples of org.openbel.framework.core.indexer.JDBMEquivalenceLookup.lookup()

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    public SkinnyUUID getUUID(Parameter param) throws ResourceDownloadError,
            IndexingFailure, IOException {
        String srl = param.getNamespace().getResourceLocation();
        openEquivalence(srl);
        JDBMEquivalenceLookup lookup = openEquivalences.get(srl);
        return lookup.lookup(param.getValue());
    }

    /**
     * Obtain the destinationNamespace equivalent value of sourceValue in sourceNamespace
     * @param sourceNamespace resourceLocation of source namespace
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        JDBMEquivalenceLookup sourceLookup =
                openEquivalences.get(sourceNamespace);
        if (sourceLookup == null) {
            return null;
        }
        final SkinnyUUID sourceUUID = sourceLookup.lookup(sourceValue);

        if (sourceUUID == null) {
            return null;
        }
        return doFindEquivalence(destinationNamespace, sourceUUID);
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            JDBMEquivalenceLookup jdbmLookup =
                    new JDBMEquivalenceLookup(indexPath.getAbsolutePath());
            jdbmLookup.open();

            assertEquals(1, jdbmLookup.getRecordCount());
            assertEquals(value, jdbmLookup.lookup(key));

            jdbmLookup.close();
        } catch (Exception e) {
            e.printStackTrace();
            fail(e.getMessage());
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            JDBMEquivalenceLookup jdbmLookup =
                    new JDBMEquivalenceLookup(indexPath.getAbsolutePath());
            jdbmLookup.open();

            assertEquals(1, jdbmLookup.getRecordCount());
            assertNull(jdbmLookup.lookup("0"));

            jdbmLookup.close();
        } catch (Exception e) {
            e.printStackTrace();
            fail(e.getMessage());
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            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();
        } catch (Exception e) {
            e.printStackTrace();
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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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                            // lookup UUID for protein family member
                            JDBMEquivalenceLookup jdbmLookup = lookups.get(mrl);
                            if (jdbmLookup == null) {
                                continue;
                            }
                            SkinnyUUID uuid = jdbmLookup.lookup(mval);

                            // do we have protein family member parameter uuid
                            // in molecular activity function entries?
                            if (eu.contains(uuid)) {
                                // construct member term
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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 being
                            // used by both document and network. This
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                JDBMEquivalenceLookup jdbmLookup = lookups.get(rl);
                if (jdbmLookup == null) {
                    continue;
                }

                SkinnyUUID uuid = jdbmLookup.lookup(val);
                if (uuid != null) {
                    uuids.add(uuid);
                }
            }
        }
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            JDBMEquivalenceLookup jdbmLookup = lookups.get(rl);
            if (jdbmLookup == null) {
                continue;
            }

            SkinnyUUID uuid = jdbmLookup.lookup(value);
            if (uuid != null) {
                pnUUIDs.add(uuid);
            }
        }
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