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 void updateEstimatedEnergy(Chemical chemical) {
    BasicDBObject query = new BasicDBObject().append("_id", chemical.getUuid());
    DBObject obj = this.dbChemicals.findOne(query);
    obj.put("estimateEnergy", chemical.getEstimatedEnergy());
    this.dbChemicals.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateEstimatedEnergy(Reaction reaction) {
    BasicDBObject query = new BasicDBObject().append("_id", reaction.getUUID());
    DBObject obj = this.dbReactions.findOne(query);
    obj.put("estimateEnergy", reaction.getEstimatedEnergy());
    this.dbReactions.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateReactionRefsOf(Seq seq) {
    BasicDBObject query = new BasicDBObject().append("_id", seq.getUUID());
    DBObject obj = this.dbSeq.findOne(query);
    BasicDBList refs = new BasicDBList();
    for (Long r : seq.getReactionsCatalyzed())
        refs.add(r);/*  w w  w  .  java2s.co  m*/

    obj.put("rxn_refs", refs);
    this.dbSeq.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateKeywordsCascade(Long id, Set<String> kwrds, Set<String> ciKwrds) {
    BasicDBObject query = new BasicDBObject().append("_id", id);
    DBObject obj = this.dbCascades.findOne(query);
    obj.put("keywords", kwrds);
    obj.put("keywords_case_insensitive", ciKwrds);
    this.dbCascades.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateKeywordsWaterfall(Long id, Set<String> kwrds, Set<String> ciKwrds) {
    BasicDBObject query = new BasicDBObject().append("_id", id);
    DBObject obj = this.dbWaterfalls.findOne(query);
    obj.put("keywords", kwrds);
    obj.put("keywords_case_insensitive", ciKwrds);
    this.dbWaterfalls.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateKeywords(Reaction reaction) {
    BasicDBObject query = new BasicDBObject().append("_id", reaction.getUUID());
    DBObject obj = this.dbReactions.findOne(query);
    obj.put("keywords", reaction.getKeywords());
    obj.put("keywords_case_insensitive", reaction.getCaseInsensitiveKeywords());
    this.dbReactions.update(query, obj);
}

From source file:act.server.MongoDB.java

License:Open Source License

public void updateActReaction(Reaction r, int id) {
    // db.collection.update(query, update, options)
    // updates document(s) that match query with the update doc
    // Ref: http://docs.mongodb.org/manual/reference/method/db.collection.update/
    ///*from  w w  w  . j a va 2s  .  c  om*/
    // Update doc: Can be { $set : { <field> : <val> } }
    // in case you need to keep the old document, but just update
    // some fields inside of it.
    // Ref: http://docs.mongodb.org/manual/reference/operator/update/set/
    //
    // But here (and in updateActChemical) we want to overwrite
    // the entire document with a new one, and so
    // a simple update call with the new document is what we need.

    BasicDBObject doc = createReactionDoc(r, id);
    DBObject query = new BasicDBObject();
    query.put("_id", id);
    this.dbReactions.update(query, doc);
}

From source file:act.server.MongoDB.java

License:Open Source License

public static BasicDBObject createReactionDoc(Reaction r, int id) {
    BasicDBObject doc = new BasicDBObject();
    doc.put("_id", id);
    doc.put("ecnum", r.getECNum());
    doc.put("easy_desc", r.getReactionName());

    BasicDBList substr = new BasicDBList();
    Long[] ss = r.getSubstrates();
    for (int i = 0; i < ss.length; i++) {
        DBObject o = getObject("pubchem", ss[i]);
        o.put("coefficient", r.getSubstrateCoefficient(ss[i]));
        substr.put(i, o);/*  w  ww . j  av  a  2s. c om*/
    }

    BasicDBList prods = new BasicDBList();
    Long[] pp = r.getProducts();
    for (int i = 0; i < pp.length; i++) {
        DBObject o = getObject("pubchem", pp[i]);
        o.put("coefficient", r.getProductCoefficient(pp[i]));
        prods.put(i, o);
    }

    BasicDBList prodCofactors = new BasicDBList();
    Long[] ppc = r.getProductCofactors();
    for (int i = 0; i < ppc.length; i++) {
        DBObject o = getObject("pubchem", ppc[i]);
        prodCofactors.put(i, o);
    }

    BasicDBList substrCofactors = new BasicDBList();
    Long[] ssc = r.getSubstrateCofactors();
    for (int i = 0; i < ssc.length; i++) {
        DBObject o = getObject("pubchem", ssc[i]);
        substrCofactors.put(i, o);
    }

    BasicDBList coenzymes = new BasicDBList();
    Long[] coenz = r.getCoenzymes();
    for (int i = 0; i < coenz.length; i++) {
        DBObject o = getObject("pubchem", coenz[i]);
        coenzymes.put(i, o);
    }

    BasicDBObject enz = new BasicDBObject();
    enz.put("products", prods);
    enz.put("substrates", substr);
    enz.put("product_cofactors", prodCofactors);
    enz.put("substrate_cofactors", substrCofactors);
    enz.put("coenzymes", coenzymes);
    doc.put("enz_summary", enz);

    doc.put("is_abstract", r.getRxnDetailType().name());

    if (r.getDataSource() != null)
        doc.put("datasource", r.getDataSource().name());

    if (r.getMechanisticValidatorResult() != null) {
        doc.put("mechanistic_validator_result", MongoDBToJSON.conv(r.getMechanisticValidatorResult()));
    }

    BasicDBList refs = new BasicDBList();
    for (P<Reaction.RefDataSource, String> ref : r.getReferences()) {
        BasicDBObject refEntry = new BasicDBObject();
        refEntry.put("src", ref.fst().toString());
        refEntry.put("val", ref.snd());
        refs.add(refEntry);
    }
    doc.put("references", refs);

    BasicDBList proteins = new BasicDBList();
    for (JSONObject proteinData : r.getProteinData()) {
        proteins.add(MongoDBToJSON.conv(proteinData));
    }
    doc.put("proteins", proteins);
    ConversionDirectionType cd = r.getConversionDirection();
    doc.put("conversion_direction", cd == null ? null : cd.toString());
    StepDirection psd = r.getPathwayStepDirection();
    doc.put("pathway_step_direction", psd == null ? null : psd.toString());

    return doc;
}

From source file:act.server.MongoDB.java

License:Open Source License

public void submitToActOrganismDB(Organism o) {
    BasicDBObject doc = new BasicDBObject();
    doc.put("_id", o.getUUID());
    doc.put("parent_id", o.getParent());
    doc.put("rank", o.getRank());

    if (this.dbOrganisms == null) {
        System.out.print("Organism: " + o);
    } else {/*from   w  w w  .  j  av  a  2s.c  o m*/
        this.dbOrganisms.insert(doc);
    }
}

From source file:act.server.MongoDB.java

License:Open Source License

public void submitToActOrganismNameDB(Organism o) {
    BasicDBObject doc = new BasicDBObject();
    doc.put("org_id", o.getUUID());
    doc.put("name", o.getName());
    // TODO: support NCBI ids too.
    if (this.dbOrganismNames == null) {
        System.out.print("Organism: " + o);
    } else {/*from www  .java  2s .  c o m*/
        this.dbOrganismNames.insert(doc);
    }
}