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 Long getExistingDBIdForInChI(String inchi) { // TODO: should this return some UUID type instead of Long?
    if (this.dbChemicals == null)
        return null; // TODO: should this throw an exception instead?

    BasicDBObject query = new BasicDBObject("InChI", inchi);
    BasicDBObject fields = new BasicDBObject("_id", true);
    DBObject o = this.dbChemicals.findOne(query, fields);
    if (o == null) {
        return null;
    }/*  ww w  . jav a  2s .  c  om*/
    // TODO: does this need to be checked?
    return (Long) o.get("_id");
}

---

From source file:act.server.MongoDB.java

License:Open Source License

private long alreadyEntered(Cofactor cof) {
    BasicDBObject query;/*www  .j a  v  a2s. c  o m*/
    String inchi = cof.getInChI();
    long retId = -1;

    if (inchi != null) {
        query = new BasicDBObject();
        query.put("InChI", inchi);
        DBObject o = this.dbCofactors.findOne(query);
        if (o != null)
            retId = (Long) o.get("_id"); // checked: db type IS long
    }
    return retId;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getRxnsWith(Long reactant, Long product) {

    BasicDBObject query = new BasicDBObject();
    query.put("enz_summary.products.pubchem", product);
    query.put("enz_summary.substrates.pubchem", reactant);
    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);/*from   w w  w  .j a  va2s.  co m*/
    }
    cur.close();
    return reactions;
}

---

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("$ne", substrate);
        BasicDBList queryList = new BasicDBList();
        BasicDBObject productQuery = new BasicDBObject();
        productQuery.put("enz_summary.products.pubchem", mainQuery);
        BasicDBObject substrateQuery = new BasicDBObject();
        substrateQuery.put("enz_summary.substrates.pubchem", mainQuery);
        queryList.add(substrateQuery);//from  ww w  .j  a  v a2 s  .c  o m
        queryList.add(productQuery);
        query.put("$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("$ne", enzymeQuery);
    for (Long substrate : substrates) {
        BasicDBList queryList = new BasicDBList();
        DBObject querySubstrate = new BasicDBObject();
        querySubstrate.put("enz_summary.substrates.pubchem", substrate);
        DBObject queryProduct = new BasicDBObject();
        queryProduct.put("enz_summary.products.pubchem", substrate);
        queryList.add(querySubstrate);//w  ww. j  a va  2 s .c o m
        queryList.add(queryProduct);
        query.put("$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 + "$", Pattern.CASE_INSENSITIVE);
        brenda.put("names.brenda", regex);
        pubchem.put("names.pubchem.values", regex);
        synonyms.put("names.synonyms", regex);
    } else {//  w w  w . j  a  va2 s.c  o m
        brenda.put("names.brenda", chemName);
        pubchem.put("names.pubchem.values", chemName);
        synonyms.put("names.synonyms", chemName);
    }
    BasicDBList ors = new BasicDBList();
    ors.add(brenda);
    ors.add(pubchem);
    ors.add(synonyms);
    query.put("$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;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public long getChemicalIDFromExactBrendaName(String chemName) {
    BasicDBObject query = new BasicDBObject();
    query.put("names.brenda", chemName.toLowerCase());
    Long id;/*from w  w  w .j  a va  2 s.c o m*/
    DBObject o = this.dbChemicals.findOne(query);
    if (o != null)
        id = (Long) o.get("_id"); // checked: db type IS Long
    else
        id = -1L;
    return id;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public String getChemicalDBJSON(Long uuid) {
    BasicDBObject query = new BasicDBObject();
    query.put("_id", uuid);

    DBObject o = this.dbChemicals.findOne(query);
    if (o == null)
        return null;

    Set<String> keys = o.keySet();
    String json = "{\n";
    for (String key : keys) {
        json += "\t" + key + " : " + o.get(key) + ",\n";
    }//from w  w  w.j a  v a2s .  c om
    json += "}";
    return json;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Map<String, Long> constructAllInChIs() {
    Map<String, Long> chems = new HashMap<String, Long>();
    BasicDBObject keys = new BasicDBObject();
    keys.append("_id", true);
    keys.append("InChI", true);
    DBCursor cur = constructCursorForMatchingChemicals(null, null, keys);
    while (cur.hasNext()) {
        DBObject o = cur.next();
        long uuid = (Long) o.get("_id"); // checked: db type IS long
        String inchi = (String) o.get("InChI");
        chems.put(inchi, uuid);//w  ww . j a  v  a 2s  .c o  m
    }

    cur.close();
    return chems;
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public Chemical convertDBObjectToChemical(DBObject o) {
    long uuid;/*from  w w w.  jav a2  s . c  o  m*/
    // WTF!? Are some chemicals ids int and some long?
    // this code below should not be needed, unless our db is mucked up
    try {
        uuid = (Long) o.get("_id"); // checked: db type IS long
    } catch (ClassCastException e) {
        System.err.println("WARNING: MongoDB.convertDBObjectToChemical ClassCast db.chemicals.id is not Long?");
        uuid = ((Integer) o.get("_id")).longValue(); // this should be dead code
    }

    String chemName = (String) o.get("canonical");
    DBObject xrefs = (DBObject) o.get("xref");
    Long pcid = null;
    try {
        pcid = (Long) (xrefs.get("pubchem"));
    } catch (Exception e) {

    }
    if (pcid == null) {
        pcid = (long) -1;
    }
    String inchi = (String) o.get("InChI");
    String inchiKey = (String) o.get("InChIKey");
    String smiles = (String) o.get("SMILES");
    Chemical c = new Chemical(uuid, pcid, chemName, smiles);
    c.setInchi(inchi);
    c.setCanon((String) o.get("canonical"));
    try {
        for (String typ : xrefs.keySet()) {
            if (typ.equals("pubchem"))
                continue;
            c.putRef(Chemical.REFS.valueOf(typ), MongoDBToJSON.conv((DBObject) xrefs.get(typ)));
        }
    } catch (Exception e) {

    }

    if (o.get("derived_data") != null) {
        BasicDBList matchedRos = (BasicDBList) ((DBObject) o.get("derived_data")).get("matched_ros");
        if (matchedRos != null) {
            for (Object roId : matchedRos) {
                c.addSubstructureRoId((Integer) roId);
            }
        }
    }

    BasicDBList names = (BasicDBList) ((DBObject) o.get("names")).get("brenda");
    if (names != null) {
        for (Object n : names) {
            c.addBrendaNames((String) n);
        }
    }
    if (names != null) {
        names = (BasicDBList) ((DBObject) o.get("names")).get("synonyms");
        for (Object n : names) {
            c.addSynonym((String) n);
        }
    }
    if (names != null) {
        names = (BasicDBList) ((DBObject) o.get("names")).get("pubchem");
        for (Object n : names) {
            String typ = (String) ((DBObject) n).get("type");
            BasicDBList pnames = (BasicDBList) ((DBObject) n).get("values");
            List<String> s = new ArrayList<String>();
            for (Object os : pnames)
                s.add((String) os);
            c.addNames(typ, s.toArray(new String[0]));
        }
    }
    if ((Boolean) o.get("isCofactor"))
        c.setAsCofactor();
    if ((Boolean) o.get("isNative"))
        c.setAsNative();
    if ((Double) o.get("estimateEnergy") != null)
        c.setEstimatedEnergy((Double) o.get("estimateEnergy"));
    BasicDBList keywords = (BasicDBList) o.get("keywords");
    if (keywords != null)
        for (Object k : keywords)
            c.addKeyword((String) k);
    BasicDBList cikeywords = (BasicDBList) o.get("keywords_case_insensitive");
    if (cikeywords != null)
        for (Object k : cikeywords)
            c.addCaseInsensitiveKeyword((String) k);

    BasicDBList vendors = (BasicDBList) o.get("vendors");
    Integer num_vendors = (Integer) o.get("num_vendors");
    Integer chemspiderid = (Integer) o.get("csid");

    c.setChemSpiderVendorXrefs(vendors == null ? null : MongoDBToJSON.conv(vendors));
    c.setChemSpiderNumUniqueVendors(num_vendors);
    c.setChemSpiderID(chemspiderid);

    /**
     * Shortest name  is most useful so just use that.
     */
    //TODO: what are we doing with shortest name here?
    String shortestName = c.getCanon();

    for (String name : c.getBrendaNames()) {
        if (shortestName == null || name.length() < shortestName.length())
            shortestName = name;
    }
    for (String name : c.getSynonyms()) {
        if (shortestName == null || name.length() < shortestName.length())
            shortestName = name;
    }

    return c;
}

---

• «
• 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
• 34
• 35
• 36
• 37
• 38
• 39
• 40
• 41
• 42
• 43
• 44
• 45
• 46
• 47
• 48
• 49
• 50
• »