Example usage for com.mongodb DBObject get

Introduction

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

Prototype

Object get(String key);

Source Link

Document

Gets a field from this object by a given name.

Usage

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   w  w  w .ja  v a 2  s.com*/
        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 Reaction convertDBObjectToReaction(DBObject o) {
    long uuid = (Integer) o.get("_id"); // checked: db type IS int
    String ecnum = (String) o.get("ecnum");
    String name_field = (String) o.get("easy_desc");
    Reaction.RxnDetailType type = Reaction.RxnDetailType.valueOf((String) o.get("is_abstract"));
    BasicDBList substrates = (BasicDBList) ((DBObject) o.get("enz_summary")).get("substrates");
    BasicDBList products = (BasicDBList) ((DBObject) o.get("enz_summary")).get("products");
    BasicDBList substrateCofactors = (BasicDBList) ((DBObject) o.get("enz_summary")).get("substrate_cofactors");
    BasicDBList productCofactors = (BasicDBList) ((DBObject) o.get("enz_summary")).get("product_cofactors");
    BasicDBList coenzymes = (BasicDBList) ((DBObject) o.get("enz_summary")).get("coenzymes");
    BasicDBList refs = (BasicDBList) (o.get("references"));
    BasicDBList proteins = (BasicDBList) (o.get("proteins"));
    DBObject mechanisticValidatorResults = (DBObject) (o.get("mechanistic_validator_result"));

    BasicDBList keywords = (BasicDBList) (o.get("keywords"));
    BasicDBList cikeywords = (BasicDBList) (o.get("keywords_case_insensitive"));

    List<Long> substr = new ArrayList<Long>();
    List<Long> prod = new ArrayList<Long>();
    List<Long> substrCofact = new ArrayList<Long>();
    List<Long> prodCofact = new ArrayList<Long>();
    List<Long> coenz = new ArrayList<Long>();

    String conversionDirectionString = (String) o.get("conversion_direction");
    ConversionDirectionType conversionDirection = conversionDirectionString == null ? null
            : ConversionDirectionType.valueOf(conversionDirectionString);

    String pathwayStepDirectionString = (String) o.get("pathway_step_direction");
    StepDirection pathwayStepDirection = pathwayStepDirectionString == null ? null
            : StepDirection.valueOf(pathwayStepDirectionString);

    for (int i = 0; i < substrates.size(); i++) {
        Boolean forBalance = (Boolean) ((DBObject) substrates.get(i)).get("balance");
        if (forBalance != null && forBalance)
            continue;
        substr.add(getEnzSummaryIDAsLong(substrates, i));
    }//from   w w w . ja  va2 s . c  o m
    for (int i = 0; i < products.size(); i++) {
        Boolean forBalance = (Boolean) ((DBObject) products.get(i)).get("balance");
        if (forBalance != null && forBalance)
            continue;
        prod.add(getEnzSummaryIDAsLong(products, i));
    }
    for (int i = 0; i < substrateCofactors.size(); i++) {
        substrCofact.add(getEnzSummaryIDAsLong(substrateCofactors, i));
    }
    for (int i = 0; i < productCofactors.size(); i++) {
        prodCofact.add(getEnzSummaryIDAsLong(productCofactors, i));
    }
    for (int i = 0; i < coenzymes.size(); i++) {
        coenz.add(getEnzSummaryIDAsLong(coenzymes, i));
    }

    Reaction result = new Reaction(uuid, (Long[]) substr.toArray(new Long[0]),
            (Long[]) prod.toArray(new Long[0]), (Long[]) substrCofact.toArray(new Long[0]),
            (Long[]) prodCofact.toArray(new Long[0]), (Long[]) coenz.toArray(new Long[0]), ecnum,
            conversionDirection, pathwayStepDirection, name_field, type);

    for (int i = 0; i < substrates.size(); i++) {
        Integer c = (Integer) ((DBObject) substrates.get(i)).get("coefficient");
        if (c != null)
            result.setSubstrateCoefficient(getEnzSummaryIDAsLong(substrates, i), c);
    }
    for (int i = 0; i < products.size(); i++) {
        Integer c = (Integer) ((DBObject) products.get(i)).get("coefficient");
        if (c != null)
            result.setProductCoefficient(getEnzSummaryIDAsLong(products, i), c);
    }

    Double estimatedEnergy = (Double) o.get("estimateEnergy");
    result.setEstimatedEnergy(estimatedEnergy);

    String datasrc = (String) o.get("datasource");
    if (datasrc != null && !datasrc.equals(""))
        result.setDataSource(Reaction.RxnDataSource.valueOf(datasrc));

    if (mechanisticValidatorResults != null) {
        result.setMechanisticValidatorResult(MongoDBToJSON.conv(mechanisticValidatorResults));
    }

    if (refs != null) {
        for (Object oo : refs) {
            DBObject ref = (DBObject) oo;
            Reaction.RefDataSource src = Reaction.RefDataSource.valueOf((String) ref.get("src"));
            String val = (String) ref.get("val");
            result.addReference(src, val);
        }
    }

    if (proteins != null) {
        for (Object oo : proteins) {
            result.addProteinData(MongoDBToJSON.conv((DBObject) oo));
        }
    }

    if (keywords != null)
        for (Object k : keywords)
            result.addKeyword((String) k);

    if (cikeywords != null)
        for (Object k : cikeywords)
            result.addCaseInsensitiveKeyword((String) k);

    return result;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Cofactor convertDBObjectToCofactor(DBObject o) {
    long uuid = (Long) o.get("_id");
    String inchi = (String) o.get("InChI");
    BasicDBList ns = (BasicDBList) o.get("names");
    List<String> names = new ArrayList<>();
    if (ns != null) {
        for (Object n : ns) {
            names.add((String) n);
        }//from   w  w w  . ja  v  a2 s .  c  o m
    }
    Cofactor cofactor = new Cofactor(uuid, inchi, names);

    return cofactor;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getAllCollectionUUIDs(DBCollection collection) {

    List<Long> ids = new ArrayList<Long>();

    BasicDBObject query = new BasicDBObject();
    BasicDBObject keys = new BasicDBObject();
    keys.put("_id", 1); // 0 means exclude, rest are included
    DBCursor cur = collection.find(query, keys);

    while (cur.hasNext()) {
        DBObject o = cur.next();
        long uuid = (Integer) o.get("_id"); // checked: db type IS int
        ids.add(uuid);/*from ww  w .ja v  a 2 s . co  m*/
    }
    cur.close();

    return ids;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Seq convertDBObjectToSeq(DBObject o) {
    long id = (Integer) o.get("_id"); // checked: db type IS int
    String ecnum = (String) o.get("ecnum");
    String org_name = (String) o.get("org");
    Long org_id = (Long) o.get("org_id");
    String aa_seq = (String) o.get("seq");
    String srcdb = (String) o.get("src");

    BasicDBList refs = (BasicDBList) o.get("references");
    DBObject meta = (DBObject) o.get("metadata");
    BasicDBList rxn_refs = (BasicDBList) (o.get("rxn_refs"));

    if (srcdb == null)
        srcdb = Seq.AccDB.swissprot.name();
    Seq.AccDB src = Seq.AccDB.valueOf(srcdb); // genbank | uniprot | trembl | embl | swissprot

    List<JSONObject> references = new ArrayList<>();
    if (refs != null)
        for (Object r : refs)
            references.add(MongoDBToJSON.conv((DBObject) r));

    String dummyString = ""; // for type differentiation in overloaded method
    Long dummyLong = 0L; // for type differentiation in overloaded method

    Set<Long> rxns_catalyzed = from_dblist(rxn_refs, dummyLong);

    return Seq.rawInit(id, ecnum, org_id, org_name, aa_seq, references, meta, src,
            // the rest of the params are the ones that are typically
            // "constructed". But since we are reading from the DB, we manually init
            rxns_catalyzed);//from w  w  w .  j a  v a 2s.  c  o m
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Organism convertDBObjectToOrg(DBObject o) {
    Long id = (long) o.get("org_id");
    String name = (String) o.get("name");

    return new Organism(id, name);
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public String getOrganismNameFromId(Long id) {
    BasicDBObject query = new BasicDBObject();
    query.put("org_id", id);
    BasicDBObject keys = new BasicDBObject();
    keys.put("name", 1);

    if (this.dbOrganismNames != null) {
        DBObject cur = this.dbOrganismNames.findOne(query, keys);
        if (cur == null) {
            //System.out.println("Did not find in organismnames: " + name);
            return null;
        }/*from ww  w.  j ava2 s .com*/
        return (String) cur.get("name");
    } else {
        //System.out.println("no organism names collection");
    }
    return null;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public long getOrganismId(String name) {
    BasicDBObject query = new BasicDBObject();
    query.put("name", name);
    BasicDBObject keys = new BasicDBObject();
    keys.put("org_id", 1);

    if (this.dbOrganismNames != null) {
        DBObject cur = this.dbOrganismNames.findOne(query, keys);
        if (cur == null) {
            //System.out.println("Did not find in organismnames: " + name);
            return -1;
        }// w w  w . ja  va  2 s . c o  m
        return (Long) cur.get("org_id"); // checked: db type IS long
    } else {
        //System.out.println("no organism names collection");
    }
    return -1;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Set<Long> getOrganismIDs() {
    DBIterator iterator = getIteratorOverReactions(new BasicDBObject(), null);
    Set<Long> ids = new HashSet<Long>();
    while (iterator.hasNext()) {
        DBObject r = iterator.next();
        BasicDBList orgs = (BasicDBList) r.get("organisms");
        for (Object o : orgs) {
            ids.add((Long) ((DBObject) o).get("id")); // checked: db type IS Long
        }/*from  w ww .j a va2  s . c  o m*/
    }
    return ids;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Set<Long> getOrganismIDs(Long reactionID) {
    if (reactionID < 0) {
        reactionID = Reaction.reverseID(reactionID);
    }// w ww  .  ja  v a 2  s  . co m
    DBObject query = new BasicDBObject();
    query.put("_id", reactionID);
    Set<Long> ids = new HashSet<Long>();
    DBObject reaction = this.dbReactions.findOne(query);
    if (reaction != null) {
        BasicDBList orgs = (BasicDBList) reaction.get("organisms");
        for (Object o : orgs) {
            ids.add((Long) ((DBObject) o).get("id")); // checked: db type IS long
        }
    }
    return ids;
}

---

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