Example usage for com.mongodb DBObject toMap

Introduction

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

Prototype

Map toMap();

Source Link

Document

Returns a map representing this BSONObject.

Usage

From source file:org.mongoj.samples.service.persistence.UserPersistenceImpl.java

License:Open Source License

protected User getDocument(DBObject dbObject) throws SystemException {
    if (dbObject == null) {
        return null;
    }/*  w ww . java  2 s  .  c o  m*/

    User user = new UserImpl(dbObject.toMap());

    return user;
}

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From source file:org.mule.module.mongo.MongoCloudConnector.java

License:Open Source License

/**
 * Convert a DBObject into Map./*w ww.j  ava 2s .  c  o  m*/
 * <p/>
 * {@sample.xml ../../../doc/mongo-connector.xml.sample mongo:dbObjectToMap}
 * 
 * @param input the input for this transformer
 * @return the converted Map representation
 */
@SuppressWarnings("rawtypes")
@Transformer(sourceTypes = { DBObject.class })
public static Map dbObjectToMap(final DBObject input) {
    return input.toMap();
}

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From source file:org.netbeans.modules.mongodb.ui.windows.collectionview.treetable.DBObjectNode.java

License:Open Source License

public DBObjectNode(TreeTableNode parent, DBObject userObject) {
    super(parent, userObject, new ChildrenFactory<DBObject>() {

        @Override/*w w w.ja v  a 2s . com*/
        @SuppressWarnings("unchecked")
        public List<TreeTableNode> createChildren(TreeTableNode parent, DBObject userObject) {
            final Map<String, Object> map = userObject.toMap();
            final List<TreeTableNode> children = new ArrayList<>(map.size());
            for (Map.Entry<String, Object> entry : map.entrySet()) {
                children.add(new JsonPropertyNode(parent, new JsonProperty(entry.getKey(), entry.getValue())));
            }
            return children;
        }
    });
}

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From source file:org.opencb.opencga.storage.mongodb.variant.DBObjectToVariantAnnotationConverter.java

License:Apache License

@Override
public VariantAnnotation convertToDataModelType(DBObject object) {
    VariantAnnotation va = new VariantAnnotation();

    //ConsequenceType
    List<ConsequenceType> consequenceTypes = new LinkedList<>();
    Object cts = object.get(CONSEQUENCE_TYPE_FIELD);
    if (cts != null && cts instanceof BasicDBList) {
        for (Object o : ((BasicDBList) cts)) {
            if (o instanceof DBObject) {
                DBObject ct = (DBObject) o;

                //SO accession name
                List<String> soAccessionNames = new LinkedList<>();
                if (ct.containsField(SO_ACCESSION_FIELD)) {
                    if (ct.get(SO_ACCESSION_FIELD) instanceof List) {
                        List<Integer> list = (List) ct.get(SO_ACCESSION_FIELD);
                        for (Integer so : list) {
                            soAccessionNames.add(ConsequenceTypeMappings.accessionToTerm.get(so));
                        }/*from  ww w. j a  v a2  s. com*/
                    } else {
                        soAccessionNames
                                .add(ConsequenceTypeMappings.accessionToTerm.get(ct.get(SO_ACCESSION_FIELD)));
                    }
                }

                //ProteinSubstitutionScores
                List<Score> proteinSubstitutionScores = new LinkedList<>();
                if (ct.containsField(PROTEIN_SUBSTITUTION_SCORE_FIELD)) {
                    List<DBObject> list = (List) ct.get(PROTEIN_SUBSTITUTION_SCORE_FIELD);
                    for (DBObject dbObject : list) {
                        proteinSubstitutionScores.add(new Score(getDefault(dbObject, SCORE_SCORE_FIELD, 0.0),
                                getDefault(dbObject, SCORE_SOURCE_FIELD, ""),
                                getDefault(dbObject, SCORE_DESCRIPTION_FIELD, "")));
                    }
                }
                if (ct.containsField(POLYPHEN_FIELD)) {
                    DBObject dbObject = (DBObject) ct.get(POLYPHEN_FIELD);
                    proteinSubstitutionScores.add(new Score(getDefault(dbObject, SCORE_SCORE_FIELD, 0.0),
                            "polyphen", getDefault(dbObject, SCORE_DESCRIPTION_FIELD, "")));
                }
                if (ct.containsField(SIFT_FIELD)) {
                    DBObject dbObject = (DBObject) ct.get(SIFT_FIELD);
                    proteinSubstitutionScores.add(new Score(getDefault(dbObject, SCORE_SCORE_FIELD, 0.0),
                            "sift", getDefault(dbObject, SCORE_DESCRIPTION_FIELD, "")));
                }

                consequenceTypes.add(new ConsequenceType(getDefault(ct, GENE_NAME_FIELD, "") /*.toString()*/,
                        getDefault(ct, ENSEMBL_GENE_ID_FIELD, "") /*.toString()*/,
                        getDefault(ct, ENSEMBL_TRANSCRIPT_ID_FIELD, "") /*.toString()*/,
                        getDefault(ct, STRAND_FIELD, "") /*.toString()*/,
                        getDefault(ct, BIOTYPE_FIELD, "") /*.toString()*/,
                        getDefault(ct, C_DNA_POSITION_FIELD, 0), getDefault(ct, CDS_POSITION_FIELD, 0),
                        getDefault(ct, AA_POSITION_FIELD, 0),
                        getDefault(ct, AA_CHANGE_FIELD, "") /*.toString() */,
                        getDefault(ct, CODON_FIELD, "") /*.toString() */, proteinSubstitutionScores,
                        soAccessionNames, Collections.<ExpressionValue>emptyList()));
            }
        }

    }
    va.setConsequenceTypes(consequenceTypes);

    //Conserved Region Scores
    List<Score> conservedRegionScores = new LinkedList<>();
    if (object.containsField(CONSERVED_REGION_SCORE_FIELD)) {
        List<DBObject> list = (List) object.get(CONSERVED_REGION_SCORE_FIELD);
        for (DBObject dbObject : list) {
            conservedRegionScores.add(new Score(getDefault(dbObject, SCORE_SCORE_FIELD, 0.0),
                    getDefault(dbObject, SCORE_SOURCE_FIELD, ""),
                    getDefault(dbObject, SCORE_DESCRIPTION_FIELD, "")));
        }
    }
    va.setConservationScores(conservedRegionScores);

    //Population frequencies
    List<PopulationFrequency> populationFrequencies = new LinkedList<>();
    if (object.containsField(POPULATION_FREQUENCIES_FIELD)) {
        List<DBObject> list = (List) object.get(POPULATION_FREQUENCIES_FIELD);
        for (DBObject dbObject : list) {
            populationFrequencies.add(new PopulationFrequency(
                    getDefault(dbObject, POPULATION_FREQUENCY_STUDY_FIELD, ""),
                    getDefault(dbObject, POPULATION_FREQUENCY_POP_FIELD, ""),
                    getDefault(dbObject, POPULATION_FREQUENCY_SUPERPOP_FIELD, ""),
                    getDefault(dbObject, POPULATION_FREQUENCY_REFERENCE_ALLELE_FIELD, ""),
                    getDefault(dbObject, POPULATION_FREQUENCY_ALTERNATE_ALLELE_FIELD, ""),
                    (float) getDefault(dbObject, POPULATION_FREQUENCY_REFERENCE_FREQUENCY_FIELD, -1.0),
                    (float) getDefault(dbObject, POPULATION_FREQUENCY_ALTERNATE_FREQUENCY_FIELD, -1.0)));
        }
    }
    va.setPopulationFrequencies(populationFrequencies);

    // Drug-Gene Interactions
    Map<String, List<Object>> drugGeneInteractionMap = new HashMap<>();
    List<Object> drugs = new LinkedList<>();
    if (object.containsField(DRUG_FIELD)) {
        List<DBObject> list = (List) object.get(DRUG_FIELD);
        for (DBObject dbObject : list) {
            drugs.add(dbObject.toMap());
        }
        drugGeneInteractionMap.put("dgidb", drugs);
    }
    va.setGeneDrugInteraction(drugGeneInteractionMap);

    //XREfs
    List<Xref> xrefs = new LinkedList<>();
    Object xrs = object.get(XREFS_FIELD);
    if (xrs != null && xrs instanceof BasicDBList) {
        for (Object o : (BasicDBList) xrs) {
            if (o instanceof DBObject) {
                DBObject xref = (DBObject) o;

                xrefs.add(new Xref((String) xref.get(XREF_ID_FIELD), (String) xref.get(XREF_SOURCE_FIELD)));
            }
        }
    }
    va.setXrefs(xrefs);

    //Clinical Data
    if (object.containsField(CLINICAL_DATA_FIELD)) {
        DBObject clinicalData = ((DBObject) object.get(CLINICAL_DATA_FIELD));
        va.setClinical(clinicalData.toMap());
    }

    return va;
}

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From source file:org.opencb.opencga.storage.mongodb.variant.VariantSourceMongoDBAdaptor.java

License:Apache License

/**
 * Populates the dictionary relating sources and samples.
 *
 * @return The QueryResult with information of how long the query took
 *///  w  ww  .  j av a 2s .c  o  m
private QueryResult populateSamplesInSources() {
    MongoDBCollection coll = db.getCollection(collectionName);
    DBObject projection = new BasicDBObject(DBObjectToVariantSourceConverter.FILEID_FIELD, true)
            .append(DBObjectToVariantSourceConverter.SAMPLES_FIELD, true);
    QueryResult queryResult = coll.find((DBObject) null, projection, null);

    List<DBObject> result = queryResult.getResult();
    for (DBObject dbo : result) {
        if (!dbo.containsField(DBObjectToVariantSourceConverter.FILEID_FIELD)) {
            continue;
        }
        String key = dbo.get(DBObjectToVariantSourceConverter.FILEID_FIELD).toString();
        DBObject value = (DBObject) dbo.get(DBObjectToVariantSourceConverter.SAMPLES_FIELD);
        samplesInSources.put(key, new ArrayList(value.toMap().keySet()));
    }

    return queryResult;
}

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From source file:org.restlet.example.ext.oauth.mongo.MongoClient.java

License:Open Source License

@SuppressWarnings("unchecked")
public Map<String, Object> getProperties() {
    DBObject properties = (DBObject) client.get(PROPERTIES);
    return properties.toMap();
}

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From source file:org.restlet.example.ext.oauth.mongo.MongoTokenManager.java

License:Open Source License

@SuppressWarnings("unchecked")
public AuthSession restoreSession(String code) throws OAuthException {
    DBObject sessionObj = sessions.findOne(new BasicDBObject("_id", code));

    if (sessionObj == null) {
        throw new OAuthException(OAuthError.invalid_grant, "Invalid code.", null);
    }//from w w  w. ja  v a 2s  . c o m

    return AuthSession.toAuthSession((Map<String, Object>) sessionObj.toMap());
}

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From source file:org.s1.mongodb.MongoDBFormat.java

License:Apache License

/**
 *
 * @param obj/*from   ww  w.  ja va  2  s  . c o  m*/
 * @return
 */
public static Map<String, Object> toMap(DBObject obj) {
    if (obj == null)
        return null;
    Map<String, Object> m = obj.toMap();
    /*if(m.get("_id")!=null) {
    m.put("_id", m.get("_id").toString());
    }*/
    m.remove("_id");

    m = Objects.iterate(m, new Closure<ObjectIterator.IterateBean, Object>() {
        @Override
        public Object call(ObjectIterator.IterateBean input) {
            Object o = input.getValue();
            if (o instanceof Map) {
                Map m = (Map) o;
                if (m.containsKey("$date") && m.size() == 1) {
                    o = m.get("$date");
                }
                if (m.containsKey("_serializable") && m.size() == 1) {
                    try {
                        byte[] b = (byte[]) m.get("_serializable");
                        ByteArrayInputStream bin = new ByteArrayInputStream(b);
                        ObjectInputStream ois = new ObjectInputStream(bin);
                        o = ois.readObject();
                    } catch (Exception e) {
                        throw S1SystemError.wrap(e);
                    }
                }
            }
            return o;
        }
    });
    return m;
}

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From source file:org.shenjitang.mongodbutils.MongoDbOperater.java

public <T> T findOneObj(String dbName, String collName, Map queryMap, Class<T> clazz)
        throws InstantiationException, IllegalAccessException, InvocationTargetException {
    DB db = mongoClient.getDB(dbName);/*from   w  ww  .j a v  a 2  s  .  c  om*/
    DBCollection coll = db.getCollection(collName);
    BasicDBObject query = new BasicDBObject(queryMap);
    DBObject map = coll.findOne(query);
    if (map == null) {
        return null;
    }
    T obj = clazz.newInstance();
    ConvertUtils.register(new DateConverter(null), Date.class);
    ConvertUtils.register(new IntegerConverter(null), Integer.class);
    BeanUtils.populate(obj, map.toMap());
    return obj;
}

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From source file:org.slc.sli.ingestion.util.IndexObject.java

License:Apache License

@SuppressWarnings("boxing")
public final void setKeys(DBObject obj) {
    //This DBObject.toMap returns a LinkedHashMap, so order
    // is preserved
    @SuppressWarnings("unchecked")
    Map<String, Object> objMap = obj.toMap();
    for (Map.Entry<String, Object> entry : objMap.entrySet()) {
        Object value = entry.getValue();
        if (value instanceof Double) {
            keys.put(entry.getKey(), ((Double) value).intValue());
        } else {/*from w ww.j  a  va2  s  . c  om*/
            keys.put(entry.getKey(), (Integer) value);
        }
    }
}

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