X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=50151d962f92fa0c1810d19485712c373985c5a9;hb=504b9bf9450187df0937d8a1be03c3680e739dc9;hp=074b76c19984898df0c75cfe652e15e19b129400;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 074b76c..50151d9 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,30 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.ebi;
+import jalview.datamodel.DBRefSource;
+import jalview.util.MessageManager;
+
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
+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;
/**
@@ -35,9 +43,6 @@ import java.util.StringTokenizer;
*/
public class EBIFetchClient
{
- String format = "default";
-
- String style = "raw";
/**
* Creates a new EBIFetchClient object.
@@ -54,7 +59,7 @@ public class EBIFetchClient
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"));
}
/**
@@ -65,7 +70,7 @@ public class EBIFetchClient
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"));
}
/**
@@ -76,18 +81,31 @@ public class EBIFetchClient
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 extension
+ * 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();
@@ -100,83 +118,102 @@ public class EBIFetchClient
}
/**
- * 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++;
- }
+ queryString.append(appending ? "," : "");
+ queryString.append(query);
+ appending = true;
}
- if (db == null)
- {
- System.err.println("Invalid Query string : '" + ids
- + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
- return null;
- }
- 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
+ * @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
+ // long time = System.currentTimeMillis();
+ String url = buildUrl(ids, database, format);
+
try
{
- URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + db.toLowerCase() + "/" + ids.toLowerCase()
- + (f != null ? "/" + f : ""));
+ URL rcall = new URL(url);
- BufferedInputStream is = new BufferedInputStream(rcall.openStream());
+ HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
+ int responseCode = conn.getResponseCode();
+ if (responseCode != 200)
+ {
+ System.out.println("Warning: response code " + responseCode
+ + " for " + url);
+ }
+ InputStream is = new BufferedInputStream(conn.getInputStream());
if (outFile != null)
{
FileOutputStream fio = new FileOutputStream(outFile);
@@ -193,7 +230,7 @@ public class EBIFetchClient
{
BufferedReader br = new BufferedReader(new InputStreamReader(is));
String rtn;
- ArrayList arl = new ArrayList();
+ List arl = new ArrayList();
while ((rtn = br.readLine()) != null)
{
arl.add(rtn);
@@ -202,8 +239,7 @@ public class EBIFetchClient
}
} 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)
@@ -213,16 +249,41 @@ public class EBIFetchClient
{
return null;
}
- System.err.println("Unexpected exception when retrieving from " + db
- + "\nQuery was : '" + ids + "'");
+ System.err.println("Unexpected exception when retrieving from "
+ + database + "\nQuery was : '" + ids + "'");
ex.printStackTrace(System.err);
return null;
} finally
{
- //System.err.println("Took " + (System.currentTimeMillis() - time)
- // / 1000 + " secs for one call.");
+ // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
+ // time) + " ms");
}
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/data/view/" + ids.toLowerCase()
+ + (format != null ? "&" + format : "");
+ }
+ else
+ {
+ url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+ + database.toLowerCase() + "/" + ids.toLowerCase()
+ + (format != null ? "/" + format : "");
+ }
+ return url;
+ }
+}