Example usage for com.mongodb BasicDBList BasicDBList

Introduction

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

Prototype

BasicDBList

Source Link

Usage

From source file:act.server.MongoDB.java

License:Open Source License

public BasicDBObject createCofactorDoc(Cofactor c, Long ID) {
    BasicDBObject doc = new BasicDBObject();

    doc.put("_id", ID);
    doc.put("InChI", c.getInChI());

    BasicDBList names = new BasicDBList();
    names.addAll(c.getNames());/*  ww  w .j  a  v a 2s.c o  m*/
    doc.put("names", names);

    return doc;
}

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From source file:act.server.MongoDB.java

License:Open Source License

public static BasicDBObject createChemicalDoc(Chemical c, Long ID) {
    BasicDBObject doc = new BasicDBObject();

    doc.put("_id", ID);

    doc.put("canonical", c.getCanon());

    doc.put("SMILES", c.getSmiles());
    doc.put("InChI", c.getInChI());
    doc.put("InChIKey", c.getInChIKey());

    doc.put("isCofactor", c.isCofactor());
    doc.put("isNative", c.isNative());

    BasicDBObject names = new BasicDBObject();
    BasicDBList synonyms = new BasicDBList();
    synonyms.addAll(c.getSynonyms());/* w  w  w  .  ja  v a2s .  c  o  m*/
    names.put("synonyms", synonyms);

    BasicDBList pubchemNames = new BasicDBList();

    for (String type : c.getPubchemNameTypes()) {
        String[] temp = c.getPubchemNames(type);
        BasicDBList dbNames = new BasicDBList();
        for (String t : temp) {
            dbNames.add(t);
        }
        BasicDBObject dbNameObj = new BasicDBObject();
        dbNameObj.put("type", type);
        dbNameObj.put("values", dbNames);
        pubchemNames.add(dbNameObj);
    }
    names.put("pubchem", pubchemNames);
    BasicDBList brendaNames = new BasicDBList(); // will really get its fields later if initial install
    brendaNames.addAll(c.getBrendaNames()); // but for cases where we call it post install, we construct full chem entry
    names.put("brenda", brendaNames);

    doc.put("names", names);

    BasicDBObject xrefs = new BasicDBObject();
    xrefs.put("pubchem", c.getPubchemID());
    int cnt = 0;
    for (REFS xrefTyp : Chemical.REFS.values()) {
        if (c.getRef(xrefTyp) != null) {
            xrefs.put(xrefTyp.name(), MongoDBToJSON.conv((JSONObject) c.getRef(xrefTyp)));
            cnt++;
        }
    }
    doc.put("xref", xrefs);

    doc.put("estimateEnergy", c.getEstimatedEnergy());

    doc.put("keywords", c.getKeywords());
    doc.put("keywords_case_insensitive", c.getCaseInsensitiveKeywords());

    doc.put("csid", c.getChemSpiderID());
    doc.put("num_vendors", c.getChemSpiderNumUniqueVendors());
    doc.put("vendors", MongoDBToJSON.conv(c.getChemSpiderVendorXrefs()));

    return doc;
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateChemicalWithRoBinningInformation(long id, List<Integer> matchedROs) {
    BasicDBObject query = new BasicDBObject("_id", id);
    BasicDBObject createDerivedDataContainer = new BasicDBObject("$set",
            new BasicDBObject("derived_data", new BasicDBObject()));
    this.dbChemicals.update(query, createDerivedDataContainer);

    BasicDBList listOfRos = new BasicDBList();
    listOfRos.addAll(matchedROs);//from  w w  w .  ja v a 2  s  .  c o m

    BasicDBObject updateDerivedDataContainerWithMatchedRos = new BasicDBObject("$set",
            new BasicDBObject("derived_data.matched_ros", listOfRos));
    this.dbChemicals.update(query, updateDerivedDataContainerWithMatchedRos);
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateStoichiometry(Reaction r) {
    BasicDBObject query = new BasicDBObject().append("_id", r.getUUID());
    DBObject obj = this.dbReactions.findOne(query);
    DBObject enz_summary = (DBObject) obj.get("enz_summary");
    BasicDBList substrates = (BasicDBList) enz_summary.get("substrates");
    BasicDBList newSubstrates = new BasicDBList();
    Set<Long> originalSubstrateIDs = new HashSet<Long>();
    for (int i = 0; i < substrates.size(); i++) {
        DBObject substrate = (DBObject) substrates.get(i);
        Long substrateID = (Long) substrate.get("pubchem");
        Boolean isForBalance = (Boolean) substrate.get("balance");
        if (isForBalance != null && isForBalance)
            continue;
        originalSubstrateIDs.add(substrateID);
        substrate.put("coefficient", r.getSubstrateCoefficient(substrateID));
        newSubstrates.add(substrate);//from   w  ww.  jav a2  s .co  m
    }
    Set<Long> substratesNew = r.getSubstrateIdsOfSubstrateCoefficients();
    for (Long s : substratesNew) {
        if (originalSubstrateIDs.contains(s))
            continue;
        if (r.getSubstrateCoefficient(s) == null)
            continue;
        DBObject substrate = new BasicDBObject();
        substrate.put("pubchem", s);
        substrate.put("coefficient", r.getSubstrateCoefficient(s));
        substrate.put("balance", true);
        newSubstrates.add(substrate);
    }

    BasicDBList products = (BasicDBList) enz_summary.get("products");
    BasicDBList newProducts = new BasicDBList();
    Set<Long> originalProductIDs = new HashSet<Long>();
    for (int i = 0; i < products.size(); i++) {
        DBObject product = (DBObject) products.get(i);
        Long productID = (Long) product.get("pubchem");
        Boolean isForBalance = (Boolean) product.get("balance");
        if (isForBalance != null && isForBalance)
            continue;
        originalProductIDs.add(productID);
        product.put("coefficient", r.getProductCoefficient(productID));
        newProducts.add(product);
    }
    Set<Long> productsNew = r.getProductIdsOfProductCoefficients();
    for (Long p : productsNew) {
        if (originalProductIDs.contains(p))
            continue;
        if (r.getProductCoefficient(p) == null)
            continue;
        DBObject product = new BasicDBObject();
        product.put("pubchem", p);
        product.put("coefficient", r.getProductCoefficient(p));
        product.put("balance", true);
        newProducts.add(product);
    }
    enz_summary.put("substrates", newSubstrates);
    enz_summary.put("products", newProducts);
    this.dbReactions.update(query, obj);
}

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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);//from  w ww . j a v  a 2 s  .co  m

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

---

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. ja v a  2 s  .co  m*/
    }

    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 List<Reaction> getRxnsWithAll(List<Long> reactants, List<Long> products) {

    if (reactants.size() == 0 && products.size() == 0) {
        throw new IllegalArgumentException("Reactants and products both empty! Query would return entire DB.");
    }/* ww  w . j  ava2 s  . c  o  m*/
    BasicDBObject query = new BasicDBObject();

    if (!reactants.isEmpty()) {
        BasicDBList substrateIds = new BasicDBList();
        substrateIds.addAll(reactants);
        query.put("enz_summary.substrates.pubchem", new BasicDBObject("$all", substrateIds));
    }

    if (!products.isEmpty()) {
        BasicDBList productIds = new BasicDBList();
        productIds.addAll(products);
        query.put("enz_summary.products.pubchem", new BasicDBObject("$all", productIds));
    }

    DBCursor cur = this.dbReactions.find(query);
    List<Reaction> reactions = new ArrayList<Reaction>();

    try {
        while (cur.hasNext()) {
            DBObject o = cur.next();
            reactions.add(convertDBObjectToReaction(o));
        }
    } finally {
        cur.close();
    }

    return reactions;
}

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From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getRxnsWithEnzyme(String enzyme, Long org, List<Long> substrates) {
    BasicDBObject query = new BasicDBObject();
    query.put("ecnum", enzyme);
    query.put("organisms.id", org);
    for (Long substrate : substrates) {
        BasicDBObject mainQuery = new BasicDBObject();
        mainQuery.put("$ne", substrate);
        BasicDBList queryList = new BasicDBList();
        BasicDBObject productQuery = new BasicDBObject();
        productQuery.put("enz_summary.products.pubchem", mainQuery);
        BasicDBObject substrateQuery = new BasicDBObject();
        substrateQuery.put("enz_summary.substrates.pubchem", mainQuery);
        queryList.add(substrateQuery);//from  w  ww .  j a va2 s  . c  o  m
        queryList.add(productQuery);
        query.put("$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 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("$ne", enzymeQuery);
    for (Long substrate : substrates) {
        BasicDBList queryList = new BasicDBList();
        DBObject querySubstrate = new BasicDBObject();
        querySubstrate.put("enz_summary.substrates.pubchem", substrate);
        DBObject queryProduct = new BasicDBObject();
        queryProduct.put("enz_summary.products.pubchem", substrate);
        queryList.add(querySubstrate);/*from w  w w  . j  a v a2 s .c o m*/
        queryList.add(queryProduct);
        query.put("$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 + "$", Pattern.CASE_INSENSITIVE);
        brenda.put("names.brenda", regex);
        pubchem.put("names.pubchem.values", regex);
        synonyms.put("names.synonyms", regex);
    } else {/*from   w  w  w. j a  v  a2s. c o  m*/
        brenda.put("names.brenda", chemName);
        pubchem.put("names.pubchem.values", chemName);
        synonyms.put("names.synonyms", chemName);
    }
    BasicDBList ors = new BasicDBList();
    ors.add(brenda);
    ors.add(pubchem);
    ors.add(synonyms);
    query.put("$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;
}

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