/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.ebi;
-import java.io.BufferedInputStream;
+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.FileOutputStream;
+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;
/**
*/
public class EBIFetchClient
{
- String format = "default";
-
- String style = "raw";
/**
* Creates a new EBIFetchClient object.
public String[] getSupportedDBs()
{
// TODO - implement rest call for dbfetch getSupportedDBs
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
public String[] getSupportedFormats()
{
// TODO - implement rest call for dbfetch getSupportedFormats
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
/**
public String[] getSupportedStyles()
{
// TODO - implement rest call for dbfetch getSupportedStyles
- throw new Error("Not yet implemented");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
- public File fetchDataAsFile(String ids, String f, String s)
+ /**
+ * 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", ".xml");
+ outFile = File.createTempFile("jalview", "." + ext);
outFile.deleteOnExit();
- fetchData(ids, f, s, outFile);
+ fetchData(ids, format, outFile);
if (outFile.length() == 0)
{
outFile.delete();
}
/**
- * Single DB multiple record retrieval
+ * Fetches queries and either saves the response to a file or returns as
+ * string data
*
* @param ids
- * db:query1;query2;query3
- * @param f
- * raw/xml
- * @param s
- * ?
- *
- * @return Raw string array result of query set
+ * @param format
+ * @param outFile
+ * @return
+ * @throws OutOfMemoryError
*/
- public String[] fetchData(String ids, String f, String s)
+ String[] fetchData(String ids, String format, File outFile)
throws OutOfMemoryError
{
- return fetchData(ids, f, s, null);
+ 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);
}
- public String[] fetchData(String ids, String f, String s, File outFile)
- throws OutOfMemoryError
+ /**
+ * 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)
{
- // Need to split
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
- String[] rslts = new String[0];
+ String database = null;
StringTokenizer queries = new StringTokenizer(ids, ";");
- String db = null;
- StringBuffer querystring = null;
- int nq = 0;
+ boolean appending = queryString.length() > 0;
while (queries.hasMoreTokens())
{
String query = queries.nextToken();
- int p;
- if ((p = query.indexOf(':')) > -1)
+ int p = query.indexOf(':');
+ if (p > -1)
{
- db = query.substring(0, p);
+ 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);
}
- if (querystring == null)
- {
- querystring = new StringBuffer(query);
- nq++;
- }
- else
- {
- querystring.append("," + query);
- nq++;
- }
- }
- if (db == null)
- {
- System.err.println("Invalid Query string : '" + ids
- + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
- return null;
+ queryString.append(appending ? "," : "");
+ queryString.append(query);
+ appending = true;
}
- String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile);
- if (rslt != null)
- {
- String[] nrslts = new String[rslt.length + rslts.length];
- System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
- System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
- rslts = nrslts;
- }
-
- return (rslts.length == 0 ? null : rslts);
+ return database;
}
- public String[] fetchBatch(String ids, String db, String f, String s,
+ /**
+ * 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
{
- long time = System.currentTimeMillis();
- // max 200 ids can be added at one time
+ String url = buildUrl(ids, database, format);
+ InputStream is = null;
+ BufferedReader br = null;
try
{
- URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + db.toLowerCase() + "/" + ids.toLowerCase()
- + (f != null ? "/" + f : ""));
-
- BufferedInputStream is = new BufferedInputStream(rcall.openStream());
- if (outFile != null)
+ URL rcall = new URL(url);
+ HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+ int responseCode = conn.getResponseCode();
+ if (responseCode == 200)
{
- FileOutputStream fio = new FileOutputStream(outFile);
- byte[] bb = new byte[32 * 1024];
- int l;
- while ((l = is.read(bb)) > 0)
+ is = conn.getInputStream();
+ if (outFile != null)
{
- fio.write(bb, 0, l);
+ Platform.streamToFile(is, outFile);
+ return null;
}
- fio.close();
- is.close();
- }
- else
- {
- BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ br = new BufferedReader(new InputStreamReader(is));
String rtn;
- ArrayList<String> arl = new ArrayList<String>();
+ List<String> arl = new ArrayList<>();
while ((rtn = br.readLine()) != null)
{
arl.add(rtn);
}
- return arl.toArray(new String[arl.size()]);
+ 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 " + db
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
+ ":\n" + ids);
throw er;
} catch (Exception ex)
{
- if (ex.getMessage().startsWith(
+ if (!ex.getMessage().startsWith(
"uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
{
- return null;
+ System.err.println("Unexpected exception when retrieving from "
+ + database + "\nQuery was : '" + ids + "'");
+ ex.printStackTrace(System.err);
}
- System.err.println("Unexpected exception when retrieving from " + db
- + "\nQuery was : '" + ids + "'");
- ex.printStackTrace(System.err);
- return null;
} finally
{
- //System.err.println("Took " + (System.currentTimeMillis() - time)
- // / 1000 + " secs for one call.");
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ }
+ }
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ }
+ }
}
return null;
}
-}
+ /**
+ * 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff