uk.ac.manchester.cs.owl.semspreadsheets.repository.bioportal.BioPortalRepositoryAccessor.java Source code

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Here is the source code for uk.ac.manchester.cs.owl.semspreadsheets.repository.bioportal.BioPortalRepositoryAccessor.java

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/*******************************************************************************
 * Copyright (c) 2009-2012, University of Manchester
 * 
 * Licensed under the New BSD License. 
 * Please see LICENSE file that is distributed with the source code
 ******************************************************************************/
package uk.ac.manchester.cs.owl.semspreadsheets.repository.bioportal;

import java.io.IOException;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.SocketTimeoutException;
import java.net.URL;
import java.net.UnknownHostException;
import java.util.ArrayList;
import java.util.Collection;

import org.apache.log4j.Logger;

import uk.ac.manchester.cs.owl.semspreadsheets.repository.Repository;
import uk.ac.manchester.cs.owl.semspreadsheets.repository.RepositoryAccessor;
import uk.ac.manchester.cs.owl.semspreadsheets.repository.RepositoryItem;
import uk.ac.manchester.cs.owl.semspreadsheets.ui.ErrorHandler;

import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;

/**
 * @author Matthew Horridge
 * @author Stuart Owen
 */
public class BioPortalRepositoryAccessor implements RepositoryAccessor {

    private static Logger logger = Logger.getLogger(BioPortalRepositoryAccessor.class);

    private final int CONNECT_TIMEOUT = 120000;

    private final boolean SAVE_PROPERTIES_CACHE = false;

    private BioPortalRepository repository;

    public String getRepositoryName() {
        return BioPortalRepository.NAME;
    }

    public synchronized Repository getRepository() {
        if (repository == null) {
            repository = new BioPortalRepository();
        }
        return repository;
    }

    public String fetchOntologyFormat(String ontologyAcronym) {
        logger.debug("Fetching format for " + ontologyAcronym);
        BioPortalCache cache = BioPortalCache.getInstance();
        String format = cache.getFormat(ontologyAcronym);
        if (format != null) {
            if (logger.isDebugEnabled()) {
                logger.debug("The ontology format for " + ontologyAcronym + " was found in the cache as " + format);
            }
        } else {
            logger.info("The format for " + ontologyAcronym + " not found in cache, fetching");
            try {
                URL url = new URL(BioPortalRepository.ONTOLOGY_LIST + "/" + ontologyAcronym + "/"
                        + BioPortalRepository.LATEST_SUBMISSION + "?format=json&apikey="
                        + BioPortalRepository.readAPIKey());
                logger.info("About to fetch more ontology information from " + url.toExternalForm());
                HttpURLConnection connection = (HttpURLConnection) url.openConnection();
                connection.setConnectTimeout(CONNECT_TIMEOUT);
                connection.setReadTimeout(CONNECT_TIMEOUT);
                int responseCode = connection.getResponseCode();
                logger.info("BioPortal http response: " + responseCode);

                if (responseCode == 400 || responseCode == 403) {
                    throw new BioPortalAccessDeniedException();
                }

                JsonParser parser = new JsonFactory().createParser(connection.getInputStream());
                while (format == null && parser.nextToken() != null) {
                    String name = parser.getCurrentName();
                    if ("hasOntologyLanguage".equals(name)) {
                        parser.nextToken();
                        format = parser.getText();
                    }
                }
                if (format == null) {
                    format = "unknown";
                }
                cache.storeFormat(ontologyAcronym, format);
            } catch (UnknownHostException e) {
                ErrorHandler.getErrorHandler().handleError(e);
            } catch (MalformedURLException e) {
                logger.error("Error with URL for BioPortal rest API", e);
            } catch (SocketTimeoutException e) {
                logger.error("Timeout connecting to BioPortal", e);
                ErrorHandler.getErrorHandler().handleError(e);
            } catch (IOException e) {
                logger.error("Error communiciating with BioPortal rest API", e);
            } catch (BioPortalAccessDeniedException e) {
                ErrorHandler.getErrorHandler().handleError(e);
            }
        }

        return format;
    }

    public Collection<RepositoryItem> getOntologies() {
        final Collection<RepositoryItem> items = new ArrayList<RepositoryItem>();
        URL url = null;
        try {

            url = new URL(
                    BioPortalRepository.ONTOLOGY_LIST + "?format=json&apikey=" + BioPortalRepository.readAPIKey());

            logger.debug("Contacting BioPortal REST API at: " + url.toExternalForm());

            HttpURLConnection connection = (HttpURLConnection) url.openConnection();
            connection.setConnectTimeout(CONNECT_TIMEOUT);
            connection.setReadTimeout(CONNECT_TIMEOUT);
            int responseCode = connection.getResponseCode();
            logger.info("BioPortal http response: " + responseCode);

            if (responseCode == 400 || responseCode == 403) {
                throw new BioPortalAccessDeniedException();
            }
            ObjectMapper mapper = new ObjectMapper();

            JsonNode node = mapper.readTree(connection.getInputStream());
            for (final JsonNode item : node) {
                String name = item.get("name").asText();
                String id = item.get("acronym").asText();

                BioPortalRepositoryItem repositoryItem = new BioPortalRepositoryItem(id, name, this);
                if (repositoryItem.isCompatible()) {
                    items.add(repositoryItem);
                }
            }
            if (SAVE_PROPERTIES_CACHE) {
                BioPortalCache.getInstance().dumpStoredProperties();
            }
        } catch (UnknownHostException e) {
            ErrorHandler.getErrorHandler().handleError(e);
        } catch (MalformedURLException e) {
            logger.error("Error with URL for BioPortal rest API", e);
        } catch (SocketTimeoutException e) {
            logger.error("Timeout connecting to BioPortal", e);
            ErrorHandler.getErrorHandler().handleError(e);
        } catch (IOException e) {
            logger.error("Error communiciating with BioPortal rest API", e);
        } catch (BioPortalAccessDeniedException e) {
            ErrorHandler.getErrorHandler().handleError(e);
        }
        return items;
    }
}