X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=b5a732894aa5e55324f917b8c63fd7bc748b4d97;hb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;hp=b83735481335327c152c43bce987c5b179be2884;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index b837354..b5a7328 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,242 +1,283 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * 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.
- *
- * 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 .
- */
-package jalview.ws.ebi;
-
-import java.io.*;
-import java.util.*;
-import javax.xml.namespace.*;
-import javax.xml.rpc.*;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.axis.encoding.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class EBIFetchClient
-{
- Call call;
-
- String format = "default";
-
- String style = "raw";
-
- /**
- * Creates a new EBIFetchClient object.
- */
- public EBIFetchClient()
- {
- try
- {
- call = (Call) new Service().createCall();
- call.setTargetEndpointAddress(new java.net.URL(
- "http://www.ebi.ac.uk/ws/services/Dbfetch"));
- } catch (Exception ex)
- {
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String[] getSupportedDBs()
- {
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[]
- {});
- } catch (Exception ex)
- {
- return null;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String[] getSupportedFormats()
- {
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[]
- {});
- } catch (Exception ex)
- {
- return null;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String[] getSupportedStyles()
- {
- try
- {
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- return (String[]) call.invoke(new Object[]
- {});
- } catch (Exception ex)
- {
- return null;
- }
- }
-
- public File fetchDataAsFile(String ids, String f, String s)
- throws OutOfMemoryError
- {
- String[] data = fetchData(ids, f, s);
- // TODO: after JV 2.4 - test data==null and pass error(s) back up if
- // possible (OutOfMemoryErrors are usual problem)
- if (data == null)
- {
- return null;
- }
- File outFile = null;
- try
- {
- outFile = File.createTempFile("jalview", ".xml");
- outFile.deleteOnExit();
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- int index = 0;
- while (index < data.length)
- {
- out.println(data[index]);
- index++;
- }
- out.close();
- } catch (Exception ex)
- {
- }
- return outFile;
- }
-
- /**
- * Single DB multiple record retrieval
- *
- * @param ids
- * db:query1;query2;query3
- * @param f
- * raw/xml
- * @param s
- * ?
- *
- * @return Raw string array result of query set
- */
- public String[] fetchData(String ids, String f, String s)
- throws OutOfMemoryError
- {
- // Need to split
- // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
- StringTokenizer queries = new StringTokenizer(ids, ";");
- String db = null;
- StringBuffer querystring = null;
- while (queries.hasMoreTokens())
- {
- String query = queries.nextToken();
- int p;
- if ((p = query.indexOf(':')) > -1)
- {
- db = query.substring(0, p);
- query = query.substring(p + 1);
- }
- if (querystring == null)
- {
- querystring = new StringBuffer(query);
- }
- else
- {
- querystring.append("," + query);
- }
- }
- if (db == null)
- {
- System.err.println("Invalid Query string : '" + ids
- + "'\nShould be of form 'dbname:q1;q2;q3;q4'");
- }
- return fetchBatch(querystring.toString(), db, f, s);
- }
-
- public String[] fetchBatch(String ids, String db, String f, String s)
- throws OutOfMemoryError
- {
- // max 50 ids can be added at one time
- try
- {
- // call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
- call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
- call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
- call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
- call.setReturnType(XMLType.SOAP_ARRAY);
-
- if (f != null)
- {
- format = f;
- }
-
- if (s != null)
- {
- style = s;
- }
-
- try
- {
- return (String[]) call.invoke(new Object[]
- { ids.toLowerCase(), db.toLowerCase(), format, style });
- } catch (OutOfMemoryError er)
- {
-
- System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
- + ":\n" + ids);
- throw er;
- }
- // return null;
- } catch (Exception ex)
- {
- if (ex.getMessage().startsWith(
- "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
- {
- return null;
- }
- System.err.println("Unexpected exception when retrieving from " + db
- + "\nQuery was : '" + ids + "'");
- ex.printStackTrace(System.err);
- return null;
- }
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.ebi;
+
+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 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", "." + 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;
+ 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;
+ }
+ BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ String rtn;
+ List 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)
+ {
+ }
+ }
+ }
+ 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;
+ }
+}