Examples with DatabaseEntry com.sleepycat.je.DatabaseEntry used on opensource projects

Example 31 with DatabaseEntry

use of com.sleepycat.je.DatabaseEntry in project jvarkit by lindenb.

the class PubmedOrcidGraph method scanArticle.

private void scanArticle(final String rootName, final XMLEventReader r, int depth) throws XMLStreamException, IOException {
    final Article article = new Article();
    boolean PubDate = false;
    final List<Author> authors = new ArrayList<>();
    while (r.hasNext()) {
        final XMLEvent evt = r.nextEvent();
        if (evt.isStartElement()) {
            final StartElement start = evt.asStartElement();
            final String eltName = start.getName().getLocalPart();
            if (article.pmid == null && eltName.equals("PMID")) {
                article.pmid = r.getElementText();
            } else if (article.ISOAbbreviation == null && eltName.equals("ISOAbbreviation")) {
                article.ISOAbbreviation = r.getElementText();
            } else if (article.ArticleTitle == null && eltName.equals("ArticleTitle")) {
                article.ArticleTitle = this.textContent(r);
            } else if (eltName.equals("PubDate")) {
                PubDate = true;
            } else if (article.doi == null && eltName.equals("ArticleId")) {
                final Attribute idType = start.getAttributeByName(new QName("IdType"));
                if (idType != null && idType.getValue().equalsIgnoreCase("doi")) {
                    article.doi = r.getElementText().trim();
                }
            } else if (article.Year == null && PubDate && eltName.equals("Year")) {
                article.Year = r.getElementText();
            } else if (eltName.equals("Author")) {
                final Author author = parseAuthor(r, article.pmid, depth + 1);
                if (author != null && author.orcid != null) {
                    authors.add(author);
                }
            }
        } else if (evt.isEndElement()) {
            final EndElement end = evt.asEndElement();
            final String eltName = end.getName().getLocalPart();
            if (eltName.equals("PubDate")) {
                PubDate = false;
            }
            if (eltName.equals(rootName))
                break;
        }
    }
    if (authors.isEmpty()) {
        // do nothing
        return;
    }
    DatabaseEntry key = new DatabaseEntry();
    DatabaseEntry data = new DatabaseEntry();
    Collections.sort(authors);
    for (int x = 0; x + 1 < authors.size(); ++x) {
        for (int y = x + 1; y < authors.size(); ++y) {
            Link L = null;
            final String orcid1 = authors.get(x).orcid;
            final String orcid2 = authors.get(y).orcid;
            if (this.all_links_between_authors) {
                LongBinding.longToEntry(++ID_GENERATOR, key);
            } else {
                StringBinding.stringToEntry(orcid1 + "~" + orcid2, key);
                if (this.linkDatabase.get(txn, key, data, LockMode.DEFAULT) != OperationStatus.NOTFOUND) {
                    L = this.linkBinding.entryToObject(data);
                }
            }
            if (L == null) {
                L = new Link();
                L.orcid1 = orcid1;
                L.orcid2 = orcid2;
            }
            L.pmids.add(article.pmid);
            this.linkBinding.objectToEntry(L, data);
            if (this.linkDatabase.put(txn, key, data) != OperationStatus.SUCCESS) {
                throw new JvarkitException.BerkeleyDbError("Cannot put in article db");
            }
        }
    }
    // for comparing names
    final Collator collator = Collator.getInstance(Locale.US);
    collator.setStrength(Collator.PRIMARY);
    StringBinding.stringToEntry(article.pmid, key);
    if (this.articleDatabase.get(txn, key, data, LockMode.DEFAULT) != OperationStatus.NOTFOUND) {
        LOG.debug("Article already in database : " + article.pmid);
    } else {
        LOG.debug("inserting article " + article.pmid);
        this.articleBinding.objectToEntry(article, data);
        if (this.articleDatabase.put(txn, key, data) != OperationStatus.SUCCESS) {
            throw new JvarkitException.BerkeleyDbError("Cannot put in article db");
        }
        for (final Author au : authors) {
            StringBinding.stringToEntry(au.orcid, key);
            if (this.authorDatabase.get(txn, key, data, LockMode.DEFAULT) != OperationStatus.NOTFOUND) {
                LOG.debug("Author already in database : " + au.orcid);
                final Author other = this.authorBinding.entryToObject(data);
                if (!StringUtil.isBlank(other.lastName) && !StringUtil.isBlank(au.lastName) && collator.compare(au.lastName, other.lastName) != 0) {
                    this.errPrintWriter.println("Conflict\t" + au.orcid + "\t" + au.foreName + "\t" + other.foreName);
                }
            } else {
                this.authorBinding.objectToEntry(au, data);
                if (this.authorDatabase.put(txn, key, data) != OperationStatus.SUCCESS) {
                    throw new JvarkitException.BerkeleyDbError("Cannot put in author db");
                }
            }
        }
    }
}

Example 32 with DatabaseEntry

use of com.sleepycat.je.DatabaseEntry in project jvarkit by lindenb.

the class PubmedOrcidGraph method dumpGexf.

private void dumpGexf() {
    final XMLOutputFactory xof = XMLOutputFactory.newFactory();
    PrintWriter pw = null;
    XMLStreamWriter w = null;
    DatabaseEntry key = new DatabaseEntry();
    DatabaseEntry data = new DatabaseEntry();
    Cursor c = null;
    try {
        pw = openFileOrStdoutAsPrintWriter(this.outputFile);
        w = xof.createXMLStreamWriter(pw);
        w.writeStartDocument("UTF-8", "1.0");
        w.writeStartElement("gexf");
        w.writeAttribute("xmlns", GexfConstants.XMLNS);
        w.writeAttribute("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
        w.writeAttribute("xsi:schemaLocation", GexfConstants.XSI_SCHEMA_LOCATION);
        w.writeAttribute("version", GexfConstants.VERSION);
        /* meta */
        w.writeStartElement("meta");
        w.writeAttribute("lastmodifieddate", "2017-04-03");
        w.writeStartElement("creator");
        w.writeCharacters("PumedOrcidGraph");
        w.writeEndElement();
        w.writeStartElement("description");
        w.writeCharacters("PumedOrcidGraph");
        w.writeEndElement();
        w.writeEndElement();
        /* graph */
        w.writeStartElement("graph");
        w.writeAttribute("mode", "static");
        w.writeAttribute("defaultedgetype", "undirected");
        /* attributes */
        w.writeStartElement("attributes");
        w.writeAttribute("class", "node");
        w.writeAttribute("mode", "static");
        gexfAttDecl(w, "orcid", "string");
        gexfAttDecl(w, "foreName", "string");
        gexfAttDecl(w, "lastName", "string");
        gexfAttDecl(w, "initials", "string");
        gexfAttDecl(w, "affiliation", "string");
        // attributes
        w.writeEndElement();
        if (!this.hide_edge_attributes) {
            w.writeStartElement("attributes");
            w.writeAttribute("class", "edge");
            w.writeAttribute("mode", "static");
            gexfAttDecl(w, "pmid", "string");
            gexfAttDecl(w, "title", "string");
            gexfAttDecl(w, "doi", "string");
            gexfAttDecl(w, "year", "string");
            gexfAttDecl(w, "journal", "string");
            // attributes
            w.writeEndElement();
        }
        /* nodes */
        w.writeStartElement("nodes");
        c = this.authorDatabase.openCursor(txn, null);
        while (c.getNext(key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
            final Author au = this.authorBinding.entryToObject(data);
            if (NAME_NOT_FOUND.equals(au.foreName)) {
                w.writeComment("Orcid " + au.orcid + " not found in pubmed");
                continue;
            }
            au.gexf(w);
        }
        c.close();
        // nodes
        w.writeEndElement();
        w.writeStartElement("edges");
        key = new DatabaseEntry();
        c = this.linkDatabase.openCursor(txn, null);
        while (c.getNext(key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
            final Link L = this.linkBinding.entryToObject(data);
            w.writeStartElement("edge");
            w.writeAttribute("id", "E" + (++ID_GENERATOR));
            w.writeAttribute("type", "undirected");
            w.writeAttribute("weight", String.valueOf(L.pmids.size()));
            w.writeAttribute("source", L.orcid1);
            w.writeAttribute("target", L.orcid2);
            for (String pmid : L.pmids) {
                DatabaseEntry key2 = new DatabaseEntry();
                DatabaseEntry data2 = new DatabaseEntry();
                StringBinding.stringToEntry(pmid, key2);
                if (this.articleDatabase.get(txn, key2, data2, LockMode.DEFAULT) != OperationStatus.SUCCESS) {
                    throw new JvarkitException.BerkeleyDbError("cannot get article");
                }
                final Article article = this.articleBinding.entryToObject(data2);
                if (this.all_links_between_authors) {
                    w.writeAttribute("label", String.valueOf(L.pmids.size()));
                } else {
                    w.writeAttribute("label", "" + article.ArticleTitle + ". " + article.ISOAbbreviation + ". (" + article.Year + ")");
                }
                if (!this.hide_edge_attributes) {
                    w.writeStartElement("attributes");
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "pmid");
                    w.writeAttribute("value", article.pmid);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "title");
                    w.writeAttribute("value", article.ArticleTitle);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "doi");
                    w.writeAttribute("value", article.doi);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "year");
                    w.writeAttribute("value", article.Year);
                    w.writeEmptyElement("attribute");
                    w.writeAttribute("for", "journal");
                    w.writeAttribute("value", article.ISOAbbreviation);
                    // attributes
                    w.writeEndElement();
                }
                break;
            }
            // 
            // edge
            w.writeEndElement();
        }
        c.close();
        // edges
        w.writeEndElement();
        w.writeEndElement();
        w.writeEndDocument();
        w.flush();
        pw.flush();
        pw.close();
        pw = null;
    } catch (Exception err) {
        throw new RuntimeIOException(err);
    } finally {
        CloserUtil.close(w);
        CloserUtil.close(pw);
    }
}

Example 33 with DatabaseEntry

use of com.sleepycat.je.DatabaseEntry in project jvarkit by lindenb.

the class PubmedOrcidGraph method getAuthorByOrcid.

private Author getAuthorByOrcid(final String orcid) {
    final DatabaseEntry key = new DatabaseEntry();
    final DatabaseEntry data = new DatabaseEntry();
    StringBinding.stringToEntry(orcid, key);
    if (this.authorDatabase.get(txn, key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
        return this.authorBinding.entryToObject(data);
    } else {
        return null;
    }
}

Example 34 with DatabaseEntry

use of com.sleepycat.je.DatabaseEntry in project bboxdb by jnidzwetzki.

the class BDBTupleStore method readTuple.

@Override
public Tuple readTuple(final String key) throws IOException {
    final DatabaseEntry keyEntry = new DatabaseEntry(key.getBytes());
    final DatabaseEntry value = new DatabaseEntry();
    Transaction txn = null;
    if (USE_TRANSACTIONS) {
        txn = environment.beginTransaction(null, null);
    }
    final OperationStatus result = database.get(null, keyEntry, value, LockMode.DEFAULT);
    if (result != OperationStatus.SUCCESS) {
        throw new RuntimeException("Data fetch got status " + result + " for " + key);
    }
    if (txn != null) {
        txn.commit();
    }
    final ByteBuffer byteBuffer = ByteBuffer.wrap(value.getData());
    return TupleHelper.decodeTuple(byteBuffer);
}

Example 35 with DatabaseEntry

use of com.sleepycat.je.DatabaseEntry in project voldemort by voldemort.

the class BdbStorageEngine method getAndLock.

@Override
public KeyLockHandle<byte[]> getAndLock(ByteArray key) {
    long startTimeNs = -1;
    if (logger.isTraceEnabled())
        startTimeNs = System.nanoTime();
    StoreUtils.assertValidKey(key);
    DatabaseEntry keyEntry = new DatabaseEntry(key.get());
    DatabaseEntry valueEntry = new DatabaseEntry();
    Transaction transaction = null;
    List<Versioned<byte[]>> vals = null;
    KeyLockHandle<byte[]> handle;
    try {
        transaction = environment.beginTransaction(null, null);
        // do a get for the existing values
        OperationStatus status = getBdbDatabase().get(transaction, keyEntry, valueEntry, LockMode.RMW);
        if (OperationStatus.SUCCESS == status) {
            vals = StoreBinaryFormat.fromByteArray(valueEntry.getData());
        } else {
            vals = new ArrayList<Versioned<byte[]>>(0);
        }
        handle = new KeyLockHandle<byte[]>(vals, transaction);
    } catch (DatabaseException e) {
        this.bdbEnvironmentStats.reportException(e);
        // Unless we return out properly from this method, we need to ensure
        // the transaction handle is closed on exception..
        attemptAbort(transaction);
        logger.error("Error in getAndLock for store " + this.getName(), e);
        throw new PersistenceFailureException(e);
    } finally {
        if (logger.isTraceEnabled()) {
            logger.trace("Completed getAndLock (" + getName() + ") to key " + key + " (keyRef: " + System.identityHashCode(key) + " in " + (System.nanoTime() - startTimeNs) + " ns at " + System.currentTimeMillis());
        }
    }
    return handle;
}