Example usage for com.mongodb BasicDBObject BasicDBObject

Introduction

In this page you can find the example usage for com.mongodb BasicDBObject BasicDBObject.

Prototype

public BasicDBObject(final String key, final Object value)

Source Link

Document

Creates an object with the given key/value

Usage

From source file:act.installer.reachablesexplorer.Loader.java

License:Open Source License

Reachable queryById(Long id) {
    DBObject query = new BasicDBObject(Reachable.ID_FIELD_NAME, id);
    return jacksonReachablesCollection.findOne(query);
}

From source file:act.installer.reachablesexplorer.WordCloudGenerator.java

License:Open Source License

public Set<String> getBingInchis() {

    BasicDBObject query = new BasicDBObject("xref.BING.metadata.usage_terms.0",
            new BasicDBObject(MongoKeywords.EXISTS$.MODULE$.value(), true));
    BasicDBObject keys = new BasicDBObject(ChemicalKeywords.INCHI$.MODULE$.value(), true);

    DBIterator ite = bingDb.getIteratorOverChemicals(query, keys);
    Set<String> bingSet = new HashSet<>();
    while (ite.hasNext()) {
        BasicDBObject o = (BasicDBObject) ite.next();
        String inchi = o.getString(ChemicalKeywords.INCHI$.MODULE$.value());
        if (inchi != null) {
            bingSet.add(inchi);//from   w w w .ja v a  2  s  .  c  o m
        }
    }
    return bingSet;
}

From source file:act.server.MongoDB.java

License:Open Source License

/**
 * Appends XRef data for the chemical with the specified inchi.  Might only apply to Metacyc for now.  Does not crash
 * if idPath or metaPath are null.//from  w  w w. jav a 2  s. c  o m
 *
 * This uses Mongo's query mechanism to add new ids to a set of xref ids only if they don't already exist, and to
 * append (without comparison) new xref metadata to an existing list without having to read/de-serialize/add/serialize
 * the object ourselves.  This results in a significant performance improvement, especially towards the end of the
 * Metacyc installation process.
 *
 * TODO: this API is awful.  Fix it up to be less Metacyc-specific and more explicit in its behavior.
 *
 * @param inchi The inchi of the chemical to update in Mongo.
 * @param idPath The path to the field where ids should be added, like xref.METACYC.id.
 * @param id The id for this chemical reference to write.
 * @param metaPath The path to the field where metadata blobs should be stored, like xref.METACYC.meta.
 * @param metaObjects A list of metadata objects to append to the metadata list in Mongo.
 */
public void appendChemicalXRefMetadata(String inchi, String idPath, String id, String metaPath,
        BasicDBList metaObjects) {
    if (idPath == null && metaPath == null) {
        return;
    }

    // Get chemical by InChI.
    BasicDBObject query = new BasicDBObject("InChI", inchi);
    BasicDBObject update = new BasicDBObject();
    if (idPath != null) {
        // Add to set will add an id to the array of xref ids only if it doesn't already exist in the array.
        update.put("$addToSet", new BasicDBObject(idPath, id));
    }

    if (metaPath != null) {
        /* Add all metadata objects to the xref list containing metadata for this source.
         * Note: $push + $each applied to an array of objects is like $pushAll, which is now deprecated. */
        update.put("$push", new BasicDBObject(metaPath, new BasicDBObject("$each", metaObjects)));
    }
    // Run exactly one query to update, which should save a lot of time over the course of the installation.
    this.dbChemicals.update(query, update);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateChemicalWithRoBinningInformation(long id, List<Integer> matchedROs) {
    BasicDBObject query = new BasicDBObject("_id", id);
    BasicDBObject createDerivedDataContainer = new BasicDBObject("$set",
            new BasicDBObject("derived_data", new BasicDBObject()));
    this.dbChemicals.update(query, createDerivedDataContainer);

    BasicDBList listOfRos = new BasicDBList();
    listOfRos.addAll(matchedROs);/*from  w  w  w.j  ava2s.c  o  m*/

    BasicDBObject updateDerivedDataContainerWithMatchedRos = new BasicDBObject("$set",
            new BasicDBObject("derived_data.matched_ros", listOfRos));
    this.dbChemicals.update(query, updateDerivedDataContainerWithMatchedRos);
}

From source file:act.server.MongoDB.java

License:Open Source License

public boolean alreadyEnteredChemical(String inchi) {
    if (this.dbChemicals == null)
        return false; // TODO: should this throw an exception instead?

    BasicDBObject query = new BasicDBObject("InChI", inchi);
    long c = this.dbChemicals.count(query);
    return c > 0;
}

From source file:act.server.MongoDB.java

License:Open Source License

public Long getExistingDBIdForInChI(String inchi) { // TODO: should this return some UUID type instead of Long?
    if (this.dbChemicals == null)
        return null; // TODO: should this throw an exception instead?

    BasicDBObject query = new BasicDBObject("InChI", inchi);
    BasicDBObject fields = new BasicDBObject("_id", true);
    DBObject o = this.dbChemicals.findOne(query, fields);
    if (o == null) {
        return null;
    }// w  ww .ja  v a 2  s  .  c o m
    // TODO: does this need to be checked?
    return (Long) o.get("_id");
}

From source file:act.server.MongoDB.java

License:Open Source License

public Iterator<String> getIteratorOverInchis(BasicDBObject matchCriterion) {
    BasicDBObject keys = new BasicDBObject(ChemicalKeywords.INCHI$.MODULE$.toString(), true);
    final DBIterator iter = getIteratorOverChemicals(matchCriterion, keys);

    return new Iterator<String>() {
        @Override/*from ww w  . j ava2s.c  o  m*/
        public boolean hasNext() {
            boolean hasNext = iter.hasNext();
            if (!hasNext)
                iter.close();
            return hasNext;
        }

        @Override
        public String next() {
            DBObject o = iter.next();
            return (String) o.get("InChI");
        }
    };
}

From source file:act.server.MongoDB.java

License:Open Source License

public Iterator<Chemical> getChemicalsbyIds(List<Long> ids, boolean notimeout) {
    BasicDBList queryList = new BasicDBList();
    for (Long id : ids) {
        queryList.add(new BasicDBObject(ChemicalKeywords.ID$.MODULE$.toString(), id));
    }/* w  w  w  . j  a v a 2s.com*/

    return getJavaIteratorOverChemicals(new BasicDBObject(MongoKeywords.OR$.MODULE$.toString(), queryList));
}

From source file:act.server.MongoDB.java

License:Open Source License

public Iterator<Reaction> getReactionsIteratorById(List<Long> ids, boolean notimeout) {
    BasicDBList reactionList = new BasicDBList();

    for (Long id : ids) {
        reactionList.add(new BasicDBObject(ChemicalKeywords.ID$.MODULE$.toString(), id));
    }/*  ww w . j av  a2  s  .  com*/

    BasicDBObject query = new BasicDBObject(MongoKeywords.OR$.MODULE$.toString(), reactionList);

    final DBIterator iter = getIteratorOverReactions(query, null);

    return new Iterator<Reaction>() {
        @Override
        public boolean hasNext() {
            boolean hasNext = iter.hasNext();
            if (!hasNext)
                iter.close();
            return hasNext;
        }

        @Override
        public Reaction next() {
            DBObject o = iter.next();
            return convertDBObjectToReaction(o);
        }
    };
}

From source file:act.server.MongoDB.java

License:Open Source License

public Seq getSeqFromSequence(String seq) {
    DBObject o = this.dbSeq.findOne(new BasicDBObject("seq", seq), new BasicDBObject());
    if (o == null)
        return null;
    return convertDBObjectToSeq(o);
}