-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-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)
- {
- String[] data = fetchData(ids, f, s);
- 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)
- {
- // 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)
- {
- // 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);
- }
- 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;
- }
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.ws.ebi;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+import javax.xml.namespace.*;\r
+import javax.xml.rpc.*;\r
+\r
+import org.apache.axis.client.Call;\r
+import org.apache.axis.client.Service;\r
+import org.apache.axis.encoding.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class EBIFetchClient\r
+{\r
+ Call call;\r
+\r
+ String format = "default";\r
+\r
+ String style = "raw";\r
+\r
+ /**\r
+ * Creates a new EBIFetchClient object.\r
+ */\r
+ public EBIFetchClient()\r
+ {\r
+ try\r
+ {\r
+ call = (Call) new Service().createCall();\r
+ call.setTargetEndpointAddress(new java.net.URL(\r
+ "http://www.ebi.ac.uk/ws/services/Dbfetch"));\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String[] getSupportedDBs()\r
+ {\r
+ try\r
+ {\r
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
+\r
+ return (String[]) call.invoke(new Object[]\r
+ {});\r
+ } catch (Exception ex)\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String[] getSupportedFormats()\r
+ {\r
+ try\r
+ {\r
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
+\r
+ return (String[]) call.invoke(new Object[]\r
+ {});\r
+ } catch (Exception ex)\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String[] getSupportedStyles()\r
+ {\r
+ try\r
+ {\r
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
+\r
+ return (String[]) call.invoke(new Object[]\r
+ {});\r
+ } catch (Exception ex)\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+\r
+ public File fetchDataAsFile(String ids, String f, String s)\r
+ throws OutOfMemoryError\r
+ {\r
+ String[] data = fetchData(ids, f, s);\r
+ // TODO: after JV 2.4 - test data==null and pass error(s) back up if\r
+ // possible (OutOfMemoryErrors are usual problem)\r
+ if (data == null)\r
+ {\r
+ return null;\r
+ }\r
+ File outFile = null;\r
+ try\r
+ {\r
+ outFile = File.createTempFile("jalview", ".xml");\r
+ outFile.deleteOnExit();\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ int index = 0;\r
+ while (index < data.length)\r
+ {\r
+ out.println(data[index]);\r
+ index++;\r
+ }\r
+ out.close();\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ return outFile;\r
+ }\r
+\r
+ /**\r
+ * Single DB multiple record retrieval\r
+ * \r
+ * @param ids\r
+ * db:query1;query2;query3\r
+ * @param f\r
+ * raw/xml\r
+ * @param s\r
+ * ?\r
+ * \r
+ * @return Raw string array result of query set\r
+ */\r
+ public String[] fetchData(String ids, String f, String s)\r
+ throws OutOfMemoryError\r
+ {\r
+ // Need to split\r
+ // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
+ StringTokenizer queries = new StringTokenizer(ids, ";");\r
+ String db = null;\r
+ StringBuffer querystring = null;\r
+ while (queries.hasMoreTokens())\r
+ {\r
+ String query = queries.nextToken();\r
+ int p;\r
+ if ((p = query.indexOf(':')) > -1)\r
+ {\r
+ db = query.substring(0, p);\r
+ query = query.substring(p + 1);\r
+ }\r
+ if (querystring == null)\r
+ {\r
+ querystring = new StringBuffer(query);\r
+ }\r
+ else\r
+ {\r
+ querystring.append("," + query);\r
+ }\r
+ }\r
+ if (db == null)\r
+ {\r
+ System.err.println("Invalid Query string : '" + ids\r
+ + "'\nShould be of form 'dbname:q1;q2;q3;q4'");\r
+ }\r
+ return fetchBatch(querystring.toString(), db, f, s);\r
+ }\r
+\r
+ public String[] fetchBatch(String ids, String db, String f, String s)\r
+ throws OutOfMemoryError\r
+ {\r
+ // max 50 ids can be added at one time\r
+ try\r
+ {\r
+ // call.setOperationName(new QName("urn:Dbfetch", "fetchData"));\r
+ call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));\r
+ call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
+ call.setReturnType(XMLType.SOAP_ARRAY);\r
+\r
+ if (f != null)\r
+ {\r
+ format = f;\r
+ }\r
+\r
+ if (s != null)\r
+ {\r
+ style = s;\r
+ }\r
+\r
+ try\r
+ {\r
+ return (String[]) call.invoke(new Object[]\r
+ { ids.toLowerCase(), db.toLowerCase(), format, style });\r
+ } catch (OutOfMemoryError er)\r
+ {\r
+\r
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db\r
+ + ":\n" + ids);\r
+ throw er;\r
+ }\r
+ // return null;\r
+ } catch (Exception ex)\r
+ {\r
+ if (ex.getMessage().startsWith(\r
+ "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))\r
+ {\r
+ return null;\r
+ }\r
+ System.err.println("Unexpected exception when retrieving from " + db\r
+ + "\nQuery was : '" + ids + "'");\r
+ ex.printStackTrace(System.err);\r
+ return null;\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff