Example usage for com.mongodb BasicDBList get

Introduction

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

Prototype

public Object get(final String key) 

Source Link

Document

Gets a value at an index.

Usage

From source file:achmad.rifai.erp1.entity.Suplier.java

public static Suplier of(Db d, String kode) throws Exception {
    Suplier v = null;//from   ww  w  .  ja  v a 2s.c  om
    achmad.rifai.erp1.util.RSA r = achmad.rifai.erp1.util.Work.loadRSA();
    com.mongodb.DBObject p = new com.mongodb.BasicDBObject();
    p.put("berkas", kode);
    com.mongodb.DBCursor c = d.getD().getCollectionFromString("suplier").find(p);
    while (c.hasNext()) {
        com.mongodb.DBObject o = c.next();
        com.mongodb.BasicDBList l = (com.mongodb.BasicDBList) o.get("bin");
        String json = "";
        for (int x = 0; x < l.size(); x++)
            json += r.decrypt("" + l.get(x));
        v = new Suplier(json);
        break;
    }
    return v;
}

---

From source file:achmad.rifai.erp1.entity.Terima.java

public static Terima of(Db d, String kode) throws Exception {
    Terima t = null;/*from w w w. jav a  2 s . com*/
    achmad.rifai.erp1.util.RSA r = achmad.rifai.erp1.util.Work.loadRSA();
    com.mongodb.DBObject p = new com.mongodb.BasicDBObject();
    p.put("berkas", kode);
    com.mongodb.DBCursor c = d.getD().getCollectionFromString("terima").find(p);
    if (c.hasNext()) {
        com.mongodb.BasicDBList l = (com.mongodb.BasicDBList) c.next().get("bin");
        String json = "";
        for (int x = 0; x < l.size(); x++)
            json += r.decrypt("" + l.get(x));
        t = new Terima(json);
    }
    return t;
}

---

From source file:achmad.rifai.erp1.entity.Tracks.java

public static Tracks of(Db d, String kode) throws Exception {
    Tracks v = null;/*  www.  j  a va 2  s.c  o m*/
    achmad.rifai.erp1.util.RSA r = achmad.rifai.erp1.util.Work.loadRSA();
    com.mongodb.DBObject p = new com.mongodb.BasicDBObject();
    p.put("berkas", kode);
    com.mongodb.DBCursor c = d.getD().getCollectionFromString("tracks").find(p);
    while (c.hasNext()) {
        com.mongodb.DBObject o = c.next();
        com.mongodb.BasicDBList l = (com.mongodb.BasicDBList) o.get("bin");
        String json = "";
        for (int x = 0; x < l.size(); x++)
            json += r.decrypt("" + l.get(x));
        v = new Tracks(json);
        break;
    }
    return v;
}

---

From source file:achmad.rifai.erp1.entity.Tugas.java

public static Tugas of(Db d, String kode) throws Exception {
    Tugas t = null;//from  w w  w  .j  a v a 2 s.c  o  m
    achmad.rifai.erp1.util.RSA r = achmad.rifai.erp1.util.Work.loadRSA();
    com.mongodb.DBObject p = new com.mongodb.BasicDBObject();
    p.put("berkas", kode);
    com.mongodb.DBCursor c = d.getD().getCollection("tugas").find(p);
    while (c.hasNext()) {
        com.mongodb.DBObject o = c.next();
        com.mongodb.BasicDBList l = (com.mongodb.BasicDBList) o.get("bin");
        String json = "";
        for (int x = 0; x < l.size(); x++)
            json += r.decrypt("" + l.get(x));
        t = new Tugas(json);
        break;
    }
    return t;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

private String getReactantFromMongoDocument(BasicDBObject family, String which, int i) {
    BasicDBList o = (BasicDBList) ((DBObject) family.get("enz_summary")).get(which);
    if (i >= o.size())
        return "";
    return "" + (Long) ((DBObject) o.get(i)).get("pubchem");
}

---

From source file:act.server.MongoDB.java

License:Open Source License

private static BasicDBList compare(BasicDBList l, BasicDBList refl, boolean listsAreSet) {
    boolean different = false;
    BasicDBList diff = new BasicDBList();

    if (!listsAreSet) {
        // lists are to be treated as ordered sets and so we can compare element by element
        for (int i = 0; i < l.size(); i++) {
            Object val = l.get(i);
            Object refv = refl.get(i);
            Object d;//from ww w .  j  a v a  2 s. c om
            if ((d = compare(val, refv, listsAreSet)) != null) {
                different = true;
                diff.add(d);
            } else {
                // elements at this index are identical, but we don't want to muck up the order
                // in case future elements are not identical... so add a null to the diff,
                // BUT IMP: do not set the flag that the list is different
                diff.add(null);
            }
        }
    } else {
        // lists are to be treated as unordered sets: we try to match each element best
        // effort to any one of the list elements, and if it does proceed greedily

        // we keep this as a list as opposed to a true set because the original (ref)
        // and the current (new) might have (identical) replicates, and so should not
        // be flagged different because of that.
        List<Object> refset = new ArrayList<Object>();
        refset.addAll(refl);

        for (Object e : l) {
            boolean matches_some = false;
            for (Object eref : refset) {
                if (compare(e, eref, listsAreSet) == null) {
                    // this object matches something, great, lets move to the next object
                    // also remove the matched object from the ref list, so that we have
                    // a 1-1 mapping between this and the ref list object
                    matches_some = true;
                    refset.remove(eref);
                    break;
                }
            }
            if (!matches_some) {
                // if this object in new list could not be matched against something,
                // the lists are different
                different = true;
                diff.add(e);
            }
        }

        if (refset.size() != 0) {
            // still some elements remain in the ref list, i.e., sets different
            different = true;
            diff.addAll(refset);
        }

    }

    return different ? diff : null;
}

---

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 ww w .  ja va2s .  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);
}

---

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));
    }//  www.j a v a 2  s.  co  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

private Long getEnzSummaryIDAsLong(BasicDBList reactant, int i) {
    try {//from w ww. j a  v a  2  s . c  o m
        return (Long) ((DBObject) reactant.get(i)).get("pubchem");
    } catch (ClassCastException e) {
        return ((Integer) ((DBObject) reactant.get(i)).get("pubchem")).longValue();
    }
}

---

From source file:act.shared.helpers.MongoDBToJSON.java

License:Open Source License

public static JSONArray conv(BasicDBList a) {
    JSONArray result = new JSONArray();
    for (int i = 0; i < a.size(); ++i) {
        Object o = a.get(i);
        if (o instanceof DBObject) {
            result.put(conv((DBObject) o));
        } else if (o instanceof BasicDBList) {
            result.put(conv((BasicDBList) o));
        } else {/*from ww w .j  a v  a2  s. com*/
            result.put(o);
        }
    }
    return result;
}

---

• «
• 1
• 2
• 3
• 4
• 5
• 6
• 7
• 8
• 9
• 10
• 11
• 12
• 13
• 14
• 15
• 16
• 17
• 18
• 19
• 20
• 21
• 22
• 23
• 24
• 25
• 26
• 27
• 28
• 29
• 30
• 31
• 32
• 33
• »