Example usage for com.mongodb BasicDBObject getString

List of usage examples for com.mongodb BasicDBObject getString

Introduction

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

Prototype

public String getString(final String key) 

Source Link

Document

Returns the value of a field as a string

Usage

From source file:gMIRC_server.java

public static void HardClean() {
    try {//from   www  .  ja  va2s.c  om
        MongoClient mongoClient = new MongoClient();
        DB db = mongoClient.getDB("mirc");
        DBCollection coll[] = new DBCollection[4];
        coll[0] = db.getCollection("channelCollection");
        coll[1] = db.getCollection("inbox");
        coll[2] = db.getCollection("activeUser");
        coll[3] = db.getCollection("passiveUser");

        DBCursor cursor = coll[3].find();

        try {
            while (cursor.hasNext()) {
                BasicDBObject temp = (BasicDBObject) cursor.next();
                String username = temp.getString("username");
                BasicDBObject query = new BasicDBObject("username", username);
                System.out.println("cleaning " + username);
                for (int i = 0; i < 4; i++) {
                    DBCursor cursor2 = coll[i].find(query);

                    try {
                        while (cursor2.hasNext()) {
                            DBObject temp2 = cursor2.next();
                            coll[i].remove(temp2);
                        }
                    } finally {
                        cursor2.close();
                    }
                }
            }
        } finally {
            cursor.close();
        }

    } catch (UnknownHostException ex) {
        Logger.getLogger(gMIRC_server.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:act.installer.reachablesexplorer.FreemarkerRenderer.java

License:Open Source License

private Object buildReachableModel(Reachable r, List<PathwayDoc> pathwayDocs) {
    /* Freemarker's template language is based on a notion of "hashes," which are effectively just an untyped hierarchy
     * of maps and arrays culminating in scalar values (think of it like a JSON doc done up in plain Java types).
     * There are new facilities to run some Java accessors from within freemarker templates, but the language is
     * sufficiently brittle on its own that complicating things seems like a recipe for much pain.
     *//w  w w . jav  a 2 s.  c  o  m
     * This is just how Freemarker works.  Oh well.
     */
    Map<String, Object> model = new HashMap<>();

    model.put("pageTitle", r.getPageName());

    model.put("inchi", r.getInchi());

    model.put("smiles", r.getSmiles());

    model.put("structureRendering", r.getStructureFilename());

    model.put("cascade", r.getPathwayVisualization());

    if (hidePathways) {
        model.put("hidePathways", true);
        // TODO: is there a cleaner way to make this URL?
        model.put("orderLink",
                String.format("{{SERVER}}%s?%s=%s", ORDER_PATH, ORDER_INCHI_KEY_PARAM, r.getInchiKey()));
    }

    if (r.getWordCloudFilename() != null) {
        model.put("wordcloudRendering", r.getWordCloudFilename());
    }

    List<Object> pathways = new ArrayList<>();
    for (PathwayDoc doc : pathwayDocs) {
        pathways.add(new HashMap<String, String>() {
            {
                put("link", doc.getPageName());
                put("name", doc.getPathText());
                // With help from http://stackoverflow.com/questions/13183982/html-entity-for-check-mark
                put("hasDna", doc.getHasDNA() ? "&#10003;" : "");
            }
        });
    }
    if (pathways.size() > 0) {
        model.put("pathways", pathways);
    }

    List<PatentSummary> patentSummaries = r.getPatentSummaries();
    if (patentSummaries != null && !patentSummaries.isEmpty()) {
        List<Map<String, String>> patentModel = patentSummaries.stream().map(p -> {
            return new HashMap<String, String>() {
                {
                    put("title", p.getTitle());
                    put("link", p.generateUSPTOURL());
                    put("id", p.getId().replaceFirst("-.*$", "")); // Strip date + XML suffix, just leave grant number.
                }
            };
        }).collect(Collectors.toList());
        model.put("patents", patentModel);
    }

    Map<Chemical.REFS, BasicDBObject> xrefs = r.getXref();
    // We check that xrefs is not null to avoid NPEs when a Reachable does not have xrefs (cross-references) populated.
    // It is expected that projections such as L3 or L4 are in that situation.
    if (xrefs != null) {
        // Each XREF being populated in a Reachable as DBObjects, serialization and deserialization causes funky problems
        // to appear. In particular, casting to BasicDBObjects fails because Jackson deserialized it as a LinkedHashMap
        // See http://stackoverflow.com/questions/28821715/java-lang-classcastexception-java-util-linkedhashmap-cannot-be-cast-to-com-test
        if (xrefs.containsKey(Chemical.REFS.BING)) {
            BasicDBObject bingXref = xrefs.get(Chemical.REFS.BING);
            Map<String, Object> bingMetadata = (Map) bingXref.get("metadata");
            List<Map> bingUsageTerms = (List) bingMetadata.get("usage_terms");
            if (bingUsageTerms.size() > 0) {
                List<Map<String, Object>> bingUsageTermsModel = bingUsageTerms.stream()
                        .map(usageTerm -> new HashMap<String, Object>() {
                            {
                                put("usageTerm", usageTerm.get("usage_term"));
                                put("urls", usageTerm.get("urls"));
                            }
                        }).collect(Collectors.toList());
                Collections.sort(bingUsageTermsModel,
                        (o1, o2) -> ((ArrayList) o2.get("urls")).size() - ((ArrayList) o1.get("urls")).size());
                model.put("bingUsageTerms", bingUsageTermsModel);
            }
        }

        if (xrefs.containsKey(Chemical.REFS.WIKIPEDIA)) {
            BasicDBObject wikipediaXref = xrefs.get(Chemical.REFS.WIKIPEDIA);
            String wikipediaUrl = wikipediaXref.getString("dbid");
            model.put("wikipediaUrl", wikipediaUrl);
        }
    }

    if (r.getSynonyms() != null) {
        if (r.getSynonyms().getPubchemSynonyms() != null) {
            List<Map<String, Object>> pubchemSynonymModel = r.getSynonyms().getPubchemSynonyms().entrySet()
                    .stream().map(entry -> new HashMap<String, Object>() {
                        {
                            put("synonymType", entry.getKey().toString());
                            put("synonyms", entry.getValue().stream().collect(Collectors.toList()));
                        }
                    }).collect(Collectors.toList());
            model.put("pubchemSynonyms", pubchemSynonymModel);
        }
        if (r.getSynonyms().getMeshHeadings() != null) {
            List<Map<String, Object>> meshHeadingModel = r.getSynonyms().getMeshHeadings().entrySet().stream()
                    .map(entry -> new HashMap<String, Object>() {
                        {
                            String key = entry.getKey().toString();
                            put("synonymType", "NONE".equals(key) ? "MeSH" : key);
                            put("synonyms", entry.getValue().stream().collect(Collectors.toList()));
                        }
                    }).collect(Collectors.toList());

            model.put("meshHeadings", meshHeadingModel);
        }
    }

    if (r.getPhysiochemicalProperties() != null) {
        PhysiochemicalProperties physiochemicalProperties = r.getPhysiochemicalProperties();
        model.put("physiochemicalProperties", new HashMap<String, String>() {
            {
                put("pka", String.format("%.2f", physiochemicalProperties.getPkaAcid1()));
                put("logp", String.format("%.2f", physiochemicalProperties.getLogPTrue()));
                put("hlb", String.format("%.2f", physiochemicalProperties.getHlbVal()));
            }
        });
    }

    return model;
}

From source file:act.installer.reachablesexplorer.WordCloudGenerator.java

License:Open Source License

public Set<String> getBingInchis() {

    BasicDBObject query = new BasicDBObject("xref.BING.metadata.usage_terms.0",
            new BasicDBObject(MongoKeywords.EXISTS$.MODULE$.value(), true));
    BasicDBObject keys = new BasicDBObject(ChemicalKeywords.INCHI$.MODULE$.value(), true);

    DBIterator ite = bingDb.getIteratorOverChemicals(query, keys);
    Set<String> bingSet = new HashSet<>();
    while (ite.hasNext()) {
        BasicDBObject o = (BasicDBObject) ite.next();
        String inchi = o.getString(ChemicalKeywords.INCHI$.MODULE$.value());
        if (inchi != null) {
            bingSet.add(inchi);//  ww  w .  j a va 2  s  .co  m
        }
    }
    return bingSet;
}

From source file:at.oneminutedistraction.mongodbrealm.UserCollection.java

public String[] authenticate(final String username, final String password) throws LoginException {

    BasicDBObject user = find(username);
    if (null == user)
        throw new LoginException(username + " does not exist");

    if (!(user.containsField(ATTR_PASSWORD) && passwordMgr.isValid(user.getString(ATTR_PASSWORD), password)))
        throw new LoginException("Invalid password");

    return (groups(user));

    //      BasicDBList groups = (BasicDBList)user.get(ATTR_GROUPS);
    //      if (null == groups)
    //         return (new String[]{});
    ////from w w  w.ja va 2s . c  om
    //      
    //      List<String> g = groups.stream()
    //            .map(e -> { return (e.toString()); })
    //            .collect(Collectors.toList());
    //      return (g.toArray(new String[g.size()]));
}

From source file:at.oneminutedistraction.mongodbrealm.UserCollection.java

public void insert(BasicDBObject insertUser) throws MongoDBRealmException {

    String username = insertUser.getString(ATTR_USERNAME);
    if (null != find(username))
        throw new MongoDBRealmException("User exists: " + username);

    try {//from   ww  w .j av a2 s .  c o m
        users.insert(insertUser);
    } catch (MongoException ex) {
        throw new MongoDBRealmException("Inserting user " + username, ex);
    }

}

From source file:at.oneminutedistraction.mongodbrealm.UserCollection.java

public void update(BasicDBObject updateUser) throws MongoDBRealmException {

    String username = updateUser.getString(ATTR_USERNAME);
    verify(updateUser, "Cannot find user: " + username);

    try {/* w w  w.  j  a  v a  2 s.  com*/
        users.update(new BasicDBObject(ATTR_USERNAME, username), updateUser);
    } catch (MongoException ex) {
        throw new MongoDBRealmException("Updating user " + username, ex);
    }
}

From source file:at.oneminutedistraction.mongodbrealm.UserCollection.java

public void remove(BasicDBObject deleteUser) throws MongoDBRealmException {

    String username = deleteUser.getString(ATTR_USERNAME);
    verify(deleteUser, "Cannot find user: " + username);

    try {/* www .  j a v a  2s. c o m*/
        users.remove(deleteUser);
    } catch (MongoException ex) {
        throw new MongoDBRealmException("Deleting user " + username, ex);
    }
}

From source file:at.oneminutedistraction.mongodbrealm.UserCollection.java

private void verify(final BasicDBObject obj, final String exceptionMsg) throws MongoDBRealmException {
    final String username = obj.getString(ATTR_USERNAME);
    if (null == find(username))
        throw new MongoDBRealmException(exceptionMsg);
}

From source file:bd.DArticulo.java

@Override
public String insertar(Object o) {
    CArticulo x = (CArticulo) o;/*from www .ja va2s  .  c  om*/

    String ver = verificar(x);
    if (ver.compareTo(MSG_ACEPTADO) != 0)
        return ver;

    conecion con = new conecion(table);
    BasicDBObject datos = new BasicDBObject(x.get_datos());
    con.get_colletion().insert(datos);
    con.end();
    return datos.getString("_id");
}

From source file:bd.DArticulo.java

@Override
public String eliminar(Object o) {
    CArticulo x = (CArticulo) o;//  w  ww  .j av  a  2 s  .  c o m
    conecion con = new conecion(table);
    BasicDBObject datos = new BasicDBObject("_id", x.getId());
    con.get_colletion().remove(datos);
    con.end();
    return datos.getString("_id");
}