+import java.util.Locale;
+
+import jalview.datamodel.DBRefSource;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+
+ /**
+ * Creates a new EBIFetchClient object.
+ */
+ public EBIFetchClient()
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedDBs()
+ {
+ // TODO - implement rest call for dbfetch getSupportedDBs
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedFormats()
+ {
+ // TODO - implement rest call for dbfetch getSupportedFormats
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedStyles()
+ {
+ // TODO - implement rest call for dbfetch getSupportedStyles
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
+ }
+
+ /**
+ * Send an HTTP fetch request to EBI and save the reply in a temporary file.
+ *
+ * @param ids
+ * the query formatted as db:query1;query2;query3
+ * @param format
+ * the format wanted
+ * @param ext
+ * for the temporary file to hold response (without separator)
+ * @return the file holding the response
+ * @throws OutOfMemoryError
+ */
+
+ public File fetchDataAsFile(String ids, String format, String ext)
+ throws OutOfMemoryError
+ {
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("jalview", "." + ext);
+ outFile.deleteOnExit();
+ fetchData(ids, format, outFile);
+ if (outFile.length() == 0)
+ {
+ outFile.delete();
+ return null;
+ }
+ } catch (Exception ex)
+ {
+ }
+ return outFile;
+ }
+
+ /**
+ * Fetches queries and either saves the response to a file or returns as
+ * string data
+ *
+ * @param ids
+ * @param format
+ * @param outFile
+ * @return
+ * @throws OutOfMemoryError
+ */
+ String[] fetchData(String ids, String format, File outFile)
+ throws OutOfMemoryError
+ {
+ StringBuilder querystring = new StringBuilder(ids.length());
+ String database = parseIds(ids, querystring);
+ if (database == null)
+ {
+ System.err.println("Invalid Query string : '" + ids + "'");
+ System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
+ return null;
+ }
+
+ // note: outFile is currently always specified, so return value is null
+ String[] rslt = fetchBatch(querystring.toString(), database, format,
+ outFile);
+
+ return (rslt != null && rslt.length > 0 ? rslt : null);
+ }
+
+ /**
+ * Parses ids formatted as dbname:q1;q2;q3, returns the dbname and adds
+ * queries as comma-separated items to the querystring. dbname must be
+ * specified for at least one queryId. Returns null if a mixture of different
+ * dbnames is found (ignoring case).
+ *
+ * @param ids
+ * @param queryString
+ * @return
+ */
+ static String parseIds(String ids, StringBuilder queryString)
+ {
+ String database = null;
+ StringTokenizer queries = new StringTokenizer(ids, ";");
+ boolean appending = queryString.length() > 0;
+ while (queries.hasMoreTokens())
+ {
+ String query = queries.nextToken();
+ int p = query.indexOf(':');
+ if (p > -1)
+ {
+ String db = query.substring(0, p);
+ if (database != null && !db.equalsIgnoreCase(database))
+ {
+ /*
+ * different databases mixed in together - invalid
+ */
+ return null;
+ }
+ database = db;
+ query = query.substring(p + 1);
+ }
+ queryString.append(appending ? "," : "");
+ queryString.append(query);
+ appending = true;
+ }
+ return database;
+ }
+
+ /**
+ * Fetches queries and either saves the response to a file or (if no file
+ * specified) returns as string data
+ *
+ * @param ids
+ * @param database
+ * @param format
+ * @param outFile
+ * @return array of lines from EBI only if outFile is null (which it will not
+ * be)
+ * @throws OutOfMemoryError
+ */
+ String[] fetchBatch(String ids, String database, String format,
+ File outFile) throws OutOfMemoryError
+ {
+ String url = buildUrl(ids, database, format);
+ InputStream is = null;
+ BufferedReader br = null;
+ try
+ {
+ URL rcall = new URL(url);
+ HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+ int responseCode = conn.getResponseCode();
+ if (responseCode == 200)
+ {
+ is = conn.getInputStream();
+ if (outFile != null)
+ {
+ Platform.streamToFile(is, outFile);
+ return null;
+ }
+ br = new BufferedReader(new InputStreamReader(is));
+ String rtn;
+ List<String> arl = new ArrayList<>();
+ while ((rtn = br.readLine()) != null)
+ {
+ arl.add(rtn);
+ }
+ return (String[]) arl.toArray();
+ }
+ System.err.println(
+ "Warning: response code " + responseCode + " for " + url);
+ } catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
+ + ":\n" + ids);
+ throw er;
+ } catch (Exception ex)
+ {
+ if (!ex.getMessage().startsWith(
+ "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+ {
+ System.err.println("Unexpected exception when retrieving from "
+ + database + "\nQuery was : '" + ids + "'");
+ ex.printStackTrace(System.err);
+ }
+ } finally
+ {
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ }
+ }
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ }
+ }
+ }
+ return null;
+ }
+
+ static
+ {
+ Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
+ }
+
+ /**
+ * Constructs the URL to fetch from
+ *
+ * @param ids
+ * @param database
+ * @param format
+ * @return
+ */
+ static String buildUrl(String ids, String database, String format)
+ {
+ String url;
+ if (database.equalsIgnoreCase(DBRefSource.EMBL)
+ || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
+ {
+ url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+ + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
+ }
+ else
+ {
+ url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+ + database.toLowerCase(Locale.ROOT) + "/"
+ + ids.toLowerCase(Locale.ROOT)
+ + (format != null ? "/" + format : "");
+ }
+ return url;
+ }
+}