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

public List<Long> getRxnsWithSubstrate(String enzyme, Long org, List<Long> substrates) {
    BasicDBObject query = new BasicDBObject();
    query.put("organisms.id", org);
    BasicDBObject enzymeQuery = new BasicDBObject();
    enzymeQuery.put("ecnum", enzyme);
    query.put("$ne", enzymeQuery);
    for (Long substrate : substrates) {
        BasicDBList queryList = new BasicDBList();
        DBObject querySubstrate = new BasicDBObject();
        querySubstrate.put("enz_summary.substrates.pubchem", substrate);
        DBObject queryProduct = new BasicDBObject();
        queryProduct.put("enz_summary.products.pubchem", substrate);
        queryList.add(querySubstrate);/*w  ww.j  ava2s  .  c  om*/
        queryList.add(queryProduct);
        query.put("$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;
}

From source file:act.server.MongoDB.java

License:Open Source License

public long getChemicalIDFromName(String chemName, boolean caseInsensitive) {
    BasicDBObject query = new BasicDBObject();
    DBObject brenda = new BasicDBObject();
    DBObject pubchem = new BasicDBObject();
    DBObject synonyms = new BasicDBObject();
    if (caseInsensitive) {
        String escapedName = Pattern.quote(chemName);
        Pattern regex = Pattern.compile("^" + escapedName + "$", Pattern.CASE_INSENSITIVE);
        brenda.put("names.brenda", regex);
        pubchem.put("names.pubchem.values", regex);
        synonyms.put("names.synonyms", regex);
    } else {// w  w  w.  j  a v a2s .  c o m
        brenda.put("names.brenda", chemName);
        pubchem.put("names.pubchem.values", chemName);
        synonyms.put("names.synonyms", chemName);
    }
    BasicDBList ors = new BasicDBList();
    ors.add(brenda);
    ors.add(pubchem);
    ors.add(synonyms);
    query.put("$or", ors);
    Long id;
    DBObject o = this.dbChemicals.findOne(query);
    if (o != null)
        id = (Long) o.get("_id"); // checked: db type IS Long
    else
        id = -1L;
    return id;
}

From source file:act.server.MongoDB.java

License:Open Source License

public long getChemicalIDFromExactBrendaName(String chemName) {
    BasicDBObject query = new BasicDBObject();
    query.put("names.brenda", chemName.toLowerCase());
    Long id;// w w  w.ja  v  a2s.  co  m
    DBObject o = this.dbChemicals.findOne(query);
    if (o != null)
        id = (Long) o.get("_id"); // checked: db type IS Long
    else
        id = -1L;
    return id;
}

From source file:act.server.MongoDB.java

License:Open Source License

public String getChemicalDBJSON(Long uuid) {
    BasicDBObject query = new BasicDBObject();
    query.put("_id", uuid);

    DBObject o = this.dbChemicals.findOne(query);
    if (o == null)
        return null;

    Set<String> keys = o.keySet();
    String json = "{\n";
    for (String key : keys) {
        json += "\t" + key + " : " + o.get(key) + ",\n";
    }/*ww  w.ja v a 2 s  .  co  m*/
    json += "}";
    return json;
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> getChemicalsThatHaveField(String field) {
    DBObject val = new BasicDBObject();
    val.put("$exists", "true");
    return constructAllChemicalsFromActData(field, val);
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> getDrugbankChemicals() {
    DBObject val = new BasicDBObject();
    val.put("$ne", null);
    String field = "xref.DRUGBANK";

    return constructAllChemicalsFromActData(field, val);
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> getSigmaChemicals() {
    DBObject val = new BasicDBObject();
    val.put("$ne", null);
    String field = "xref.SIGMA";

    return constructAllChemicalsFromActData(field, val);
}

From source file:act.server.MongoDB.java

License:Open Source License

public List<Chemical> constructAllChemicalsFromActData(String field, Object val) {
    return constructAllChemicalsFromActData(field, val, new BasicDBObject());
}

From source file:act.server.MongoDB.java

License:Open Source License

public DBIterator getIdCursorForFakeChemicals() {
    DBObject fakeRegex = new BasicDBObject();
    DBObject abstractInchi = new BasicDBObject();
    fakeRegex.put(ChemicalKeywords.INCHI$.MODULE$.toString(),
            new BasicDBObject(MongoKeywords.REGEX$.MODULE$.toString(), "^InChI=/FAKE"));

    abstractInchi.put(ChemicalKeywords.INCHI$.MODULE$.toString(),
            new BasicDBObject(MongoKeywords.REGEX$.MODULE$.toString(), "^InChI=.*R.*"));

    BasicDBList conditionList = new BasicDBList();
    conditionList.add(fakeRegex);// w ww.jav  a2s . c om
    conditionList.add(abstractInchi);

    BasicDBObject conditions = new BasicDBObject(MongoKeywords.OR$.MODULE$.toString(), conditionList);

    return getIteratorOverChemicals(conditions,
            new BasicDBObject(ChemicalKeywords.ID$.MODULE$.toString(), true));
}

From source file:act.server.MongoDB.java

License:Open Source License

private DBCursor constructCursorForMatchingChemicals(String field, Object val, BasicDBObject keys) {
    DBCursor cur;/*from  w w w .j a v a 2s  .  co  m*/
    if (field != null) {
        BasicDBObject query;
        query = new BasicDBObject();
        query.put(field, val);
        if (keys == null) {
            cur = this.dbChemicals.find(query);
        } else {
            cur = this.dbChemicals.find(query, keys);
        }
    } else if (keys != null) {
        cur = this.dbChemicals.find(new BasicDBObject(), keys);
    } else {
        /* Ensure a default ordering when iterating over a whole collection.
         * This helps maintain result stability and should have minimal performance cost since we're iterating over
         * the primary keys in their natural order. */
        cur = this.dbChemicals.find(DEFAULT_CURSOR_ORDER_BY_ID);
    }

    return cur;
}