Example usage for com.mongodb BasicDBObject get

List of usage examples for com.mongodb BasicDBObject get

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Introduction

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

Prototype

public Object get(final String key)

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Gets a value from this object

Usage

From source file:act.installer.bing.BingSearchRanker.java

License:Open Source License

/**
 * This function is used to write out the conditional reachability results with data on target chemical, root chemical,
 * depth of steps from root to target chemical, the bing search results, all the other names associated with the target
 * and inchi of the target in a tsv file. This function is not scalable since it has to have an in-memory representation
 * of the target and root molecule's bing results to input the data into the TSV file.
 * @param descendantInchiToRootInchi mapping of chemical to its root chemical in the conditional reachability tree
 * @param depthOfPathFromRootToMolecule Since a chemical can be associated with only one root, there is a unique mapping between
 *                        the chemical and it's depth from the root. This structure holds that information.
 * @param outputPath The output path of the tsv file.
 * @throws IOException//w  w  w .  j av a 2 s  . com
 */
public void writeBingSearchRanksAsTSVUsingConditionalReachabilityFormat(Set<String> inchisToProcess,
        Map<String, String> descendantInchiToRootInchi, Map<String, Integer> depthOfPathFromRootToMolecule,
        String outputPath) throws IOException {

    // Define headers
    List<String> bingRankerHeaderFields = new ArrayList<>();
    addChemicalHeaders(bingRankerHeaderFields);
    bingRankerHeaderFields.add(ConditionalReachabilityHeaderFields.DEPTH.name());
    bingRankerHeaderFields.add(ConditionalReachabilityHeaderFields.ROOT_MOLECULE_BEST_NAME.name());
    bingRankerHeaderFields.add(ConditionalReachabilityHeaderFields.TOTAL_COUNT_SEARCH_RESULTS_ROOT.name());
    bingRankerHeaderFields.add(ConditionalReachabilityHeaderFields.ROOT_INCHI.name());

    LOGGER.info("The total number of inchis are: %d", inchisToProcess.size());

    LOGGER.info("Creating mappings between inchi and it's DB object");
    DBCursor cursor = mongoDB.fetchNamesAndUsageForInchis(inchisToProcess);

    // TODO: We have to do an in-memory calculation of all the inchis since we need to pair up the descendant and root
    // db objects. This can take up a lot of memory.
    Map<String, BasicDBObject> inchiToDBObject = new HashMap<>();

    int cursorCounter = 0;
    while (cursor.hasNext()) {
        cursorCounter++;
        BasicDBObject o = (BasicDBObject) cursor.next();
        String inchi = o.get("InChI").toString();

        if (inchi == null) {
            LOGGER.error("Inchi could not be parsed.");
            continue;
        }

        inchiToDBObject.put(inchi, o);
    }

    LOGGER.info("The total number of inchis found in the db is: %d", cursorCounter);

    LOGGER.info("Going to write to TSV file.");
    try (TSVWriter<String, String> tsvWriter = new TSVWriter<>(bingRankerHeaderFields)) {
        tsvWriter.open(new File(outputPath));

        int counter = 0;

        for (String descendantInchi : descendantInchiToRootInchi.keySet()) {
            // Add all the descendant field results
            BasicDBObject descendentDBObject = inchiToDBObject.get(descendantInchi);
            if (descendentDBObject == null) {
                LOGGER.info("Could not find info on inchi %s", descendantInchi);
                continue;
            }

            // Add all descendant molecule fields
            Map<String, String> row = new HashMap<>();
            updateRowWithChemicalInformation(descendentDBObject, row);

            // Add all the root molecule fields
            String rootInchi = descendantInchiToRootInchi.get(descendantInchi);
            row.put(ConditionalReachabilityHeaderFields.ROOT_INCHI.name(), rootInchi);
            BasicDBObject rootDBObject = inchiToDBObject.get(rootInchi);
            if (rootDBObject != null) {
                BasicDBObject rootXref = (BasicDBObject) rootDBObject.get("xref");
                BasicDBObject rootBing = (BasicDBObject) rootXref.get("BING");
                BasicDBObject rootMetadata = (BasicDBObject) rootBing.get("metadata");

                String bestNameForRootMolecule = rootMetadata.get("best_name").toString();
                row.put(ConditionalReachabilityHeaderFields.ROOT_MOLECULE_BEST_NAME.name(),
                        bestNameForRootMolecule.equals("") ? rootInchi : bestNameForRootMolecule);

                row.put(ConditionalReachabilityHeaderFields.TOTAL_COUNT_SEARCH_RESULTS_ROOT.name(),
                        rootMetadata.get("total_count_search_results").toString());
            } else {
                row.put(ConditionalReachabilityHeaderFields.ROOT_MOLECULE_BEST_NAME.name(), rootInchi);
                row.put(ConditionalReachabilityHeaderFields.TOTAL_COUNT_SEARCH_RESULTS_ROOT.name(),
                        DEFAULT_COUNT.toString());
            }
            row.put(ConditionalReachabilityHeaderFields.DEPTH.name(),
                    depthOfPathFromRootToMolecule.get(descendantInchi).toString());

            tsvWriter.append(row);
            tsvWriter.flush();
            counter++;
        }

        LOGGER.info("Wrote %d rows to %s", counter, outputPath);
    }
}

From source file:act.installer.bing.BingSearchResults.java

License:Open Source License

/** This key function caches in a MongoDB collection and returns a set of SearchResults.
 * If present, the results are returned from the cache. If not, the results are queried and returned after updating
 * the cache./*from w  w  w. j  av a2s . c o  m*/
 * @param name (String) the name to return results for. Will be normalized to lower case.
 * @return a set of SearchResults
 * @throws IOException
 */
public Set<SearchResult> getAndCacheTopSearchResults(String name) throws IOException {

    String formattedName = name.toLowerCase();
    BasicDBObject nameSearchResultDBObject = bingCacheMongoDB
            .getNameSearchResultDBObjectFromName(formattedName);
    Set<SearchResult> searchResults = new HashSet<>();

    // There are 3 cases:
    // 1) There is a corresponding entry in the cache AND the topSearchResults are populated.
    //    In this case, we read from the cache and return the results.
    // 2) There is a corresponding entry in the cache BUT the topSearchResults are not populated.
    //    This case occurs when only totalCountSearchResults is populated.
    //    In this case, perform the relevant query, update the cache and return the results
    // 3) There is no corresponding entry in the cache.
    //    In this case, perform the relevant query, create a new entry in the cache and return the results.

    if (nameSearchResultDBObject == null) {
        // Case 3)
        LOGGER.debug("No corresponding entry in the cache. Fetching results and populating cache.");
        // Query the results
        searchResults = fetchTopSearchResults(formattedName, TOP_N);
        // Create new object and update it
        NameSearchResults nameSearchResults = new NameSearchResults(formattedName);
        nameSearchResults.setTopSearchResults(searchResults);
        // Save new document in the cache
        bingCacheMongoDB.cacheNameSearchResult(nameSearchResults);
        return searchResults;
    }

    // There is an existing entry in the DB
    BasicDBList topSearchResultsList = (BasicDBList) nameSearchResultDBObject.get("topSearchResults");
    if (topSearchResultsList == null) {
        // Case 2)
        LOGGER.debug(
                "Existing entry in the cache, with empty topSearchResults. Fetching results and updating cache.");
        // Query the results
        searchResults = fetchTopSearchResults(formattedName, TOP_N);
        // Create new object and update its instance variable
        NameSearchResults nameSearchResults = new NameSearchResults(formattedName);
        nameSearchResults.setTopSearchResults(searchResults);
        // Update the cache
        bingCacheMongoDB.updateTopSearchResults(formattedName, nameSearchResults);
        return searchResults;
    }

    // Case 1)
    LOGGER.debug("Existing entry in the cache, with populated topSearchResults. Returning from the cache.");
    for (Object topSearchResult : topSearchResultsList) {
        SearchResult searchResult = new SearchResult();
        BasicDBObject topSearchResultDBObject = (BasicDBObject) topSearchResult;
        searchResult.populateFromBasicDBObject(topSearchResultDBObject);
        searchResults.add(searchResult);
    }
    return searchResults;
}

From source file:act.installer.bing.BingSearchResults.java

License:Open Source License

public Set<SearchResult> getTopSearchResultsFromCache(String name) {
    Set<SearchResult> searchResults = new HashSet<>();
    String formattedName = name.toLowerCase();
    BasicDBObject nameSearchResultDBObject = bingCacheMongoDB
            .getNameSearchResultDBObjectFromName(formattedName);
    if (nameSearchResultDBObject == null) {
        return searchResults;
    }//  w ww. j a  va  2  s . c  o  m
    BasicDBList topSearchResultsList = (BasicDBList) nameSearchResultDBObject.get("topSearchResults");
    if (topSearchResultsList == null) {
        return searchResults;
    }
    for (Object topSearchResult : topSearchResultsList) {
        SearchResult searchResult = new SearchResult();
        BasicDBObject topSearchResultDBObject = (BasicDBObject) topSearchResult;
        searchResult.populateFromBasicDBObject(topSearchResultDBObject);
        searchResults.add(searchResult);
    }
    return searchResults;
}

From source file:act.installer.bing.BingSearchResults.java

License:Open Source License

public Long getTotalCountSearchResultsFromCache(String name) {
    String formattedName = name.toLowerCase();
    BasicDBObject nameSearchResultDBObject = bingCacheMongoDB
            .getNameSearchResultDBObjectFromName(formattedName);
    Long totalCountSearchResults;
    if (nameSearchResultDBObject == null) {
        return -1L;
    }/*from  www  .  j  a  v  a  2 s .c om*/
    totalCountSearchResults = (Long) nameSearchResultDBObject.get("totalCountSearchResults");
    if (totalCountSearchResults == null) {
        return -1L;
    }
    return totalCountSearchResults;
}

From source file:act.installer.bing.BingSearchResults.java

License:Open Source License

/** This key function caches in a MongoDB collection and returns the total count of Bing search results.
 * If present, the results are returned from the cache. If not, the results are queried and returned after updating
 * the cache./*from w  w  w  .  j av a 2s  . c  o  m*/
 * @param name (String) the name to return results for. Will be normalized to lower case.
 * @return the total search result count
 * @throws IOException
 */
public Long getAndCacheTotalCountSearchResults(String name) throws IOException {

    String formattedName = name.toLowerCase();
    BasicDBObject nameSearchResultDBObject = bingCacheMongoDB
            .getNameSearchResultDBObjectFromName(formattedName);
    Long totalCountSearchResults;

    // There are 3 cases:
    // 1) There is a corresponding entry in the cache AND the totalCountSearchResults are populated.
    //    In this case, we read from the cache and return the results.
    // 2) There is a corresponding entry in the cache BUT the totalCountSearchResults are not populated.
    //    This case occurs when only topSearchResults is populated.
    //    In this case, perform the relevant query, update the cache and return the total count
    // 3) There is no corresponding entry in the cache.
    //    In this case, perform the relevant query, create a new entry in the cache and return the total count.

    if (nameSearchResultDBObject == null) {
        // Case 3)
        LOGGER.debug("No corresponding entry in the cache. Fetching results and populating cache.");
        // Query the results
        totalCountSearchResults = fetchTotalCountSearchResults(formattedName);
        // Create new object and update it
        NameSearchResults nameSearchResults = new NameSearchResults(formattedName);
        nameSearchResults.setTotalCountSearchResults(totalCountSearchResults);
        // Save new document in the cache
        bingCacheMongoDB.cacheNameSearchResult(nameSearchResults);
        return totalCountSearchResults;
    }

    // There is an existing entry in the cache
    totalCountSearchResults = (Long) nameSearchResultDBObject.get("totalCountSearchResults");

    if (totalCountSearchResults == null || totalCountSearchResults < 0) {
        // Case 2)
        LOGGER.debug("Existing entry in the cache, with empty totalCountSearchResults. "
                + "Fetching results and updating cache.");
        // Query the results
        totalCountSearchResults = fetchTotalCountSearchResults(formattedName);
        // Create new object and update its instance variable
        NameSearchResults nameSearchResults = new NameSearchResults(formattedName);
        nameSearchResults.setTotalCountSearchResults(totalCountSearchResults);
        // Update the cache
        bingCacheMongoDB.updateTotalCountSearchResults(formattedName, nameSearchResults);
        return totalCountSearchResults;
    }

    // Case 1)
    LOGGER.debug(
            "Existing entry in the cache, with populated totalCountSearchResults. Returning from the cache.");
    return totalCountSearchResults;
}

From source file:act.installer.bing.SearchResult.java

License:Open Source License

public void populateFromBasicDBObject(BasicDBObject result) {
    setDescription((String) result.get("description"));
    setTitle((String) result.get("title"));
    setUrl((String) result.get("url"));
}

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.
     */*from  ww w.j  a  va 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.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

public NamesOfMolecule getNamesFromBasicDBObject(BasicDBObject c) {

    String inchi = (String) c.get("InChI");

    NamesOfMolecule moleculeNames = new NamesOfMolecule(inchi);
    BasicDBObject names = (BasicDBObject) c.get("names");
    if (names != null) {
        BasicDBList brendaNamesList = (BasicDBList) names.get("brenda");
        if (brendaNamesList != null) {
            Set<String> brendaNames = new HashSet<>();
            for (Object brendaName : brendaNamesList) {
                brendaNames.add((String) brendaName);
            }/*from  w ww.  j ava2  s.c om*/
            moleculeNames.setBrendaNames(brendaNames);
        }
    }
    // XREF
    BasicDBObject xref = (BasicDBObject) c.get("xref");
    if (xref != null) {
        // CHEBI
        BasicDBObject chebi = (BasicDBObject) xref.get("CHEBI");
        if (chebi != null) {
            Set<String> chebiNames = new HashSet<>();
            BasicDBObject chebiMetadata = (BasicDBObject) chebi.get("metadata");
            BasicDBList chebiSynonymsList = (BasicDBList) chebiMetadata.get("Synonym");
            if (chebiSynonymsList != null) {
                for (Object chebiName : chebiSynonymsList) {
                    chebiNames.add((String) chebiName);
                }
                moleculeNames.setChebiNames(chebiNames);
            }
        }
        // METACYC
        BasicDBObject metacyc = (BasicDBObject) xref.get("METACYC");
        if (metacyc != null) {
            Set<String> metacycNames = new HashSet<>();
            BasicDBList metacycMetadata = (BasicDBList) metacyc.get("meta");
            if (metacycMetadata != null) {
                for (Object metaCycMeta : metacycMetadata) {
                    BasicDBObject metaCycMetaDBObject = (BasicDBObject) metaCycMeta;
                    String metaCycName = (String) metaCycMetaDBObject.get("sname");
                    if (metaCycName == null) {
                        continue;
                    }
                    metacycNames.add(metaCycName);
                }
                moleculeNames.setMetacycNames(metacycNames);
            }
        }
        // DRUGBANK
        BasicDBObject drugbank = (BasicDBObject) xref.get("DRUGBANK");
        if (drugbank != null) {
            Set<String> drugbankNames = new HashSet<>();
            BasicDBObject drugbankMetadata = (BasicDBObject) drugbank.get("metadata");
            drugbankNames.add((String) drugbankMetadata.get("name"));
            BasicDBObject drugbankSynonyms = (BasicDBObject) drugbankMetadata.get("synonyms");
            if (drugbankSynonyms != null) {
                if (drugbankSynonyms.get("synonym") instanceof String) {
                    drugbankNames.add((String) drugbankSynonyms.get("synonym"));
                    moleculeNames.setDrugbankNames(drugbankNames);
                } else {
                    BasicDBList drugbankSynonymsList = (BasicDBList) drugbankSynonyms.get("synonym");
                    if (drugbankSynonymsList != null) {
                        for (Object drugbankSynonym : drugbankSynonymsList) {
                            drugbankNames.add((String) drugbankSynonym);
                        }
                        moleculeNames.setDrugbankNames(drugbankNames);
                    }
                }
            }
            Set<String> drugbankBrands = new HashSet<>();
            BasicDBObject drugbankBrandsObject = (BasicDBObject) drugbankMetadata.get("brands");
            if (drugbankBrandsObject != null) {
                if (drugbankBrandsObject.get("brand") instanceof String) {
                    drugbankBrands.add((String) drugbankBrandsObject.get("brand"));
                    moleculeNames.setDrugbankBrands(drugbankBrands);
                } else {
                    BasicDBList drugbankBrandsList = (BasicDBList) drugbankBrandsObject.get("brand");
                    if (drugbankBrandsList != null) {
                        for (Object drugbankBrand : drugbankBrandsList) {
                            drugbankBrands.add((String) drugbankBrand);
                        }
                        moleculeNames.setDrugbankBrands(drugbankBrands);
                    }
                }
            }
        }
        // WIKIPEDIA
        BasicDBObject wikipedia = (BasicDBObject) xref.get("WIKIPEDIA");
        if (wikipedia != null) {
            BasicDBObject wikipediaMetadata = (BasicDBObject) wikipedia.get("metadata");
            if (wikipediaMetadata != null) {
                String wikipediaName = (String) wikipediaMetadata.get("article");
                moleculeNames.setWikipediaName(wikipediaName);
            }
        }
    }
    return moleculeNames;
}

From source file:act.server.MongoDB.java

License:Open Source License

/**
 * This function retrieves the ChEBI ID corresponding to an InChI. In the (frequent) case where no ChEBI xref is
 * present, null is returned.//from   ww w  . j ava  2  s .c o m
 * @param inchi input InChI representation of the chemical
 * @return String: the ChEBI ID corresponding to the InChI representation provided
 */
public String getChebiIDFromInchi(String inchi) {
    BasicDBObject whereQuery = new BasicDBObject("InChI", inchi);
    BasicDBObject existsQuery = new BasicDBObject("$exists", true);
    whereQuery.put("xref.CHEBI", existsQuery);
    BasicDBObject c = (BasicDBObject) dbChemicals.findOne(whereQuery, new BasicDBObject());
    if (c == null) {
        return null;
    } else {
        BasicDBObject xref = (BasicDBObject) c.get("xref");
        BasicDBObject chebi = (BasicDBObject) xref.get("CHEBI");
        return (String) chebi.get("dbid");
    }
}