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()

Source Link

Document

Creates an empty object.

Usage

From source file:act.server.MongoDB.java

License:Open Source License

/**
 * establishes new numbering system for organisms not already in our database
 * @param name the name of the organism to be added to the database
 * @return the id of the new organism added to the database
 *///from   w ww .j av  a  2 s .co m
public Long submitToActOrganismNameDB(String name) {
    BasicDBObject doc = new BasicDBObject();
    Long id = this.dbOrganismNames.count() + ORG_ID_BASE;
    doc.put("org_id", id);
    doc.put("name", name);
    // TODO: support NCBI ids too.
    if (this.dbOrganismNames == null) {
        System.out.print("Organism: " + name);
        return null;
    } else {
        this.dbOrganismNames.insert(doc);
        return id;
    }
}

From source file:act.server.MongoDB.java

License:Open Source License

private static BasicDBObject getObject(String field, Long val) {
    BasicDBObject singularObj = new BasicDBObject();
    singularObj.put(field, val);
    return singularObj;
}

From source file:act.server.MongoDB.java

License:Open Source License

private BasicDBObject getObject(String f1, Long v1, String f2, Float v2) {
    BasicDBObject o = new BasicDBObject();
    o.put(f1, v1);/*from   w w  w.j  a v  a 2s  .co  m*/
    o.put(f2, v2);
    return o;
}

From source file:act.server.MongoDB.java

License:Open Source License

private long alreadyEntered(Chemical c) {
    BasicDBObject query;/* ww w. j  a va 2  s  .  co  m*/
    String inchi = c.getInChI();
    long retId = -1;

    if (inchi != null) {
        query = new BasicDBObject();
        query.put("InChI", inchi);
        DBObject o = this.dbChemicals.findOne(query);
        if (o != null)
            retId = (Long) o.get("_id"); // checked: db type IS long
    }
    return retId;
}

From source file:act.server.MongoDB.java

License:Open Source License

private long alreadyEntered(Cofactor cof) {
    BasicDBObject query;//from   w ww.  j  a  v  a2  s. co  m
    String inchi = cof.getInChI();
    long retId = -1;

    if (inchi != null) {
        query = new BasicDBObject();
        query.put("InChI", inchi);
        DBObject o = this.dbCofactors.findOne(query);
        if (o != null)
            retId = (Long) o.get("_id"); // checked: db type IS long
    }
    return retId;
}

From source file:act.server.MongoDB.java

License:Open Source License

private boolean alreadyEntered(Reaction r) {
    BasicDBObject query = new BasicDBObject();
    query.put("_id", r.getUUID());

    DBObject o = this.dbReactions.findOne(query);
    return o != null; // meaning there is at least one document that matches
}

From source file:act.server.MongoDB.java

License:Open Source License

private boolean alreadyEntered(PubmedEntry entry, int pmid) {
    BasicDBObject query = new BasicDBObject();
    query.put("_id", pmid);

    DBObject o = this.dbPubmed.findOne(query);
    return o != null;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getRxnsWith(Long reactant, Long product) {

    BasicDBObject query = new BasicDBObject();
    query.put("enz_summary.products.pubchem", product);
    query.put("enz_summary.substrates.pubchem", reactant);
    DBCursor cur = this.dbReactions.find(query);

    List<Long> reactions = new ArrayList<Long>();
    while (cur.hasNext()) {
        DBObject o = cur.next();/* w ww .j av a 2s.  co m*/
        long id = (Integer) o.get("_id"); // checked: db type IS int
        reactions.add(id);
    }
    cur.close();
    return reactions;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Reaction> getRxnsWithAll(List<Long> reactants, List<Long> products) {

    if (reactants.size() == 0 && products.size() == 0) {
        throw new IllegalArgumentException("Reactants and products both empty! Query would return entire DB.");
    }/*  ww w. j  a v  a  2s .c o  m*/
    BasicDBObject query = new BasicDBObject();

    if (!reactants.isEmpty()) {
        BasicDBList substrateIds = new BasicDBList();
        substrateIds.addAll(reactants);
        query.put("enz_summary.substrates.pubchem", new BasicDBObject("$all", substrateIds));
    }

    if (!products.isEmpty()) {
        BasicDBList productIds = new BasicDBList();
        productIds.addAll(products);
        query.put("enz_summary.products.pubchem", new BasicDBObject("$all", productIds));
    }

    DBCursor cur = this.dbReactions.find(query);
    List<Reaction> reactions = new ArrayList<Reaction>();

    try {
        while (cur.hasNext()) {
            DBObject o = cur.next();
            reactions.add(convertDBObjectToReaction(o));
        }
    } finally {
        cur.close();
    }

    return reactions;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getRxnsWithEnzyme(String enzyme, Long org, List<Long> substrates) {
    BasicDBObject query = new BasicDBObject();
    query.put("ecnum", enzyme);
    query.put("organisms.id", org);
    for (Long substrate : substrates) {
        BasicDBObject mainQuery = new BasicDBObject();
        mainQuery.put("$ne", substrate);
        BasicDBList queryList = new BasicDBList();
        BasicDBObject productQuery = new BasicDBObject();
        productQuery.put("enz_summary.products.pubchem", mainQuery);
        BasicDBObject substrateQuery = new BasicDBObject();
        substrateQuery.put("enz_summary.substrates.pubchem", mainQuery);
        queryList.add(substrateQuery);/*from w w  w. j a  v  a  2  s . c  o  m*/
        queryList.add(productQuery);
        query.put("$or", queryList);
    }
    DBCursor cur = this.dbReactions.find(query);

    List<Long> reactions = new ArrayList<Long>();
    while (cur.hasNext()) {
        DBObject o = cur.next();
        long id = (Integer) o.get("_id"); // checked: db type IS int
        reactions.add(id);
    }
    cur.close();
    return reactions;
}