Example usage for com.mongodb BasicDBObject get

Introduction

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

Prototype

public Object get(final String key) 

Source Link

Document

Gets a value from this object

Usage

From source file:org.mybatis.jpetstore.domain.Order.java

License:Apache License

public static Order fromDBObject(@Nonnull final DBObject dbObj) {

    checkNotNull(dbObj, "Argument[dbObj] must not be null");

    BasicDBObject orderObj = (BasicDBObject) dbObj;
    Order order = new Order();

    order.setOrderId(orderObj.getInt("order_id"));
    order.setUsername(orderObj.getString("username"));
    order.setOrderDate(orderObj.getDate("order_date"));
    order.setCourier(orderObj.getString("courier"));

    String totalPrice = orderObj.getString("total_price");
    if (!isNullOrEmpty(totalPrice)) {
        order.setTotalPrice(new BigDecimal(totalPrice));
    }/*from   ww w  .  jav  a2  s  .co m*/
    order.setLocale(orderObj.getString("locale"));
    order.setStatus(orderObj.getString("status"));

    BasicDBObject shipToObj = (BasicDBObject) orderObj.get("shipping_address");
    order.setShipToFirstName(shipToObj.getString("ship_to_firstname"));
    order.setShipToLastName(shipToObj.getString("ship_to_lastname"));
    order.setShipAddress1(shipToObj.getString("ship_address_1"));
    order.setShipAddress2(shipToObj.getString("ship_address_2"));
    order.setShipCity(shipToObj.getString("ship_city"));
    order.setShipState(shipToObj.getString("ship_state"));
    order.setShipZip(shipToObj.getString("ship_zip"));
    order.setShipCountry(shipToObj.getString("ship_country"));

    BasicDBObject billToObj = (BasicDBObject) orderObj.get("billing_address");
    order.setBillToFirstName(billToObj.getString("bill_to_firstname"));
    order.setBillToLastName(billToObj.getString("bill_to_lastname"));
    order.setBillAddress1(billToObj.getString("bill_address_1"));
    order.setBillAddress2(billToObj.getString("bill_address_2"));
    order.setBillCity(billToObj.getString("bill_city"));
    order.setBillState(billToObj.getString("bill_state"));
    order.setBillZip(billToObj.getString("bill_zip"));
    order.setBillCountry(billToObj.getString("bill_country"));

    BasicDBObject paymentInfoObj = (BasicDBObject) orderObj.get("payment_info");
    order.setCreditCard(paymentInfoObj.getString("credit_card"));
    order.setExpiryDate(paymentInfoObj.getString("expiry_date"));
    order.setCardType(paymentInfoObj.getString("card_type"));

    List<DBObject> lineItemObjs = (ArrayList<DBObject>) orderObj.get("line_items");
    List<LineItem> lineItems = new ArrayList<>();

    for (DBObject lineItemObj : lineItemObjs) {
        LineItem lineItem = LineItem.fromDBObject(lineItemObj);
        lineItem.setOrderId(order.getOrderId());
        lineItems.add(lineItem);
    }
    order.setLineItems(lineItems);
    return order;
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private boolean isClinvar(BasicDBObject clinical) {
    return clinical.get("clinvarSet") != null;
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private boolean isGwas(BasicDBObject clinical) {
    return clinical.get("snpIdCurrent") != null;
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private boolean isCosmic(BasicDBObject clinical) {
    return clinical.get("mutationID") != null;
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private Cosmic getCosmic(BasicDBObject clinical) {
    String mutationID = (String) clinical.get("mutationID");
    String primarySite = (String) clinical.get("primarySite");
    String siteSubtype = (String) clinical.get("siteSubtype");
    String primaryHistology = (String) clinical.get("primaryHistology");
    String histologySubtype = (String) clinical.get("histologySubtype");
    String sampleSource = (String) clinical.get("sampleSource");
    String tumourOrigin = (String) clinical.get("tumourOrigin");
    String geneName = (String) clinical.get("geneName");
    String mutationSomaticStatus = (String) clinical.get("mutationSomaticStatus");

    return new Cosmic(mutationID, primarySite, siteSubtype, primaryHistology, histologySubtype, sampleSource,
            tumourOrigin, geneName, mutationSomaticStatus);
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private Gwas getGwas(BasicDBObject clinical) {
    String snpIdCurrent = (String) clinical.get("snpIdCurrent");
    Double riskAlleleFrequency = (Double) clinical.get("riskAlleleFrequency");
    String reportedGenes = (String) clinical.get("reportedGenes");
    List<BasicDBObject> studiesObj = (List<BasicDBObject>) clinical.get("studies");
    Set<String> traitsSet = new HashSet<>();

    for (BasicDBObject studieObj : studiesObj) {
        List<BasicDBObject> traitsObj = (List<BasicDBObject>) studieObj.get("traits");
        for (BasicDBObject traitObj : traitsObj) {
            String trait = (String) traitObj.get("diseaseTrait");
            traitsSet.add(trait);/*from  w  w  w .j ava2  s  .  com*/
        }
    }

    List<String> traits = new ArrayList<>();
    traits.addAll(traitsSet);
    return new Gwas(snpIdCurrent, traits, riskAlleleFrequency, reportedGenes);
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

private Clinvar getClinvar(BasicDBObject clinical) {
    BasicDBObject clinvarSet = (BasicDBObject) clinical.get("clinvarSet");
    BasicDBObject referenceClinVarAssertion = (BasicDBObject) clinvarSet.get("referenceClinVarAssertion");
    BasicDBObject clinVarAccession = (BasicDBObject) referenceClinVarAssertion.get("clinVarAccession");
    BasicDBObject clinicalSignificance = (BasicDBObject) referenceClinVarAssertion.get("clinicalSignificance");
    BasicDBObject measureSet = (BasicDBObject) referenceClinVarAssertion.get("measureSet");
    List<BasicDBObject> measures = (List<BasicDBObject>) measureSet.get("measure");
    BasicDBObject traitSet = (BasicDBObject) referenceClinVarAssertion.get("traitSet");
    List<BasicDBObject> traits = (List<BasicDBObject>) traitSet.get("trait");

    String acc = (String) clinVarAccession.get("acc");
    String clinicalSignificanceName = (String) clinicalSignificance.get("description");
    String reviewStatus = (String) clinicalSignificance.get("reviewStatus");
    List<String> traitNames = new ArrayList<>();
    Set<String> geneNameSet = new HashSet<>();

    for (BasicDBObject measure : measures) {
        List<BasicDBObject> measureRelationships;
        if ((measureRelationships = (List<BasicDBObject>) measure.get("measureRelationship")) != null) {
            for (BasicDBObject measureRelationship : measureRelationships) {
                List<BasicDBObject> symbols = (List<BasicDBObject>) measureRelationship.get("symbol");
                for (BasicDBObject symbol : symbols) {
                    BasicDBObject elementValue = (BasicDBObject) symbol.get("elementValue");
                    geneNameSet.add((String) elementValue.get("value"));
                }//w w w  . j a va  2s  .c om
            }
        }
    }

    for (BasicDBObject trait : traits) {
        List<BasicDBObject> names = (List<BasicDBObject>) trait.get("name");
        for (BasicDBObject name : names) {
            BasicDBObject elementValue = (BasicDBObject) name.get("elementValue");
            traitNames.add((String) elementValue.get("value"));
        }
    }

    List<String> geneNameList = new ArrayList<>();
    geneNameList.addAll(geneNameSet);
    return new Clinvar(acc, clinicalSignificanceName, traitNames, geneNameList, reviewStatus);
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

public QueryResult getListClinvarAccessions(QueryOptions queryOptions) {
    QueryBuilder builder = QueryBuilder.start("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc")
            .exists(true);// w w w  . j  a v  a2 s.  c  o m
    queryOptions.put("include", Arrays.asList("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc"));
    QueryResult queryResult = executeQuery("", builder.get(), queryOptions);
    List accInfoList = (List) queryResult.getResult();
    List<String> accList = new ArrayList<>(accInfoList.size());
    BasicDBObject accInfo;
    QueryResult listAccessionsToReturn = new QueryResult();

    for (Object accInfoObject : accInfoList) {
        accInfo = (BasicDBObject) accInfoObject;
        accInfo = (BasicDBObject) accInfo.get("clinvarSet");
        accList.add((String) ((BasicDBObject) ((BasicDBObject) ((BasicDBObject) accInfo
                .get("referenceClinVarAssertion"))).get("clinVarAccession")).get("acc"));
    }

    // setting listAccessionsToReturn fields
    listAccessionsToReturn.setId(queryResult.getId());
    listAccessionsToReturn.setDbTime(queryResult.getDbTime());
    listAccessionsToReturn.setNumResults(queryResult.getNumResults());
    listAccessionsToReturn.setNumTotalResults(queryResult.getNumTotalResults());
    listAccessionsToReturn.setResult(accList);

    return listAccessionsToReturn;
}

---

From source file:org.opencb.cellbase.mongodb.db.ClinVarMongoDBAdaptor.java

License:Apache License

public QueryResult getListAccessions(QueryOptions queryOptions) {
    QueryBuilder builder = QueryBuilder.start();
    queryOptions.put("include", Arrays.asList("referenceClinVarAssertion.clinVarAccession.acc"));
    QueryResult queryResult = executeQuery("", builder.get(), queryOptions);
    BasicDBList accInfoList = (BasicDBList) queryResult.getResult();
    List<String> accList = new ArrayList<>(accInfoList.size());
    BasicDBObject accInfo;
    QueryResult listAccessionsToReturn = new QueryResult();

    for (Object accInfoObject : accInfoList) {
        accInfo = (BasicDBObject) accInfoObject;
        accInfo = (BasicDBObject) accInfo.get("referenceClinVarAssertion");
        accInfo = (BasicDBObject) accInfo.get("clinVarAccession");
        accList.add((String) accInfo.get("acc"));
    }// w  w  w .  ja v  a2  s  . com

    // setting listAccessionsToReturn fields
    listAccessionsToReturn.setId(queryResult.getId());
    listAccessionsToReturn.setDbTime(queryResult.getDbTime());
    listAccessionsToReturn.setNumResults(queryResult.getNumResults());
    listAccessionsToReturn.setResult(accList);

    return listAccessionsToReturn;
}

---

From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java

License:Apache License

@Deprecated
@Override/*from  w w  w  .j  av a 2  s .  c o  m*/
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(hunkIds);
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.info(builder.get().toString());
    }

    List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        BasicDBList list = (BasicDBList) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("start") <= region.getEnd()); pos++) {
                //                    System.out.println("valuesList SIZE = " + valuesList.size());
                //                    System.out.println("pos = " + pos);
                //                    System.out.println("DIV " + (chunk.getInt("start") - region.getStart()));
                //                    System.out.println("valuesChunk = " + valuesChunk.get(pos));
                //                    System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart()));
                valuesList.set(pos + chunk.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        ConservedRegionFeature conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

---

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