2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 import java.io.FileOutputStream;
23 import java.io.IOException;
24 import java.io.InputStreamReader;
25 import java.io.OutputStreamWriter;
26 import java.io.PrintWriter;
27 import java.util.ArrayList;
28 import java.util.Hashtable;
29 import java.util.List;
30 import java.util.StringTokenizer;
32 import javax.swing.JOptionPane;
34 import jalview.bin.Cache;
35 import jalview.io.JalviewFileChooser;
36 import jalview.util.MessageManager;
37 import jalview.ws.params.ParamDatastoreI;
38 import jalview.ws.params.ParamManager;
39 import jalview.ws.params.WsParamSetI;
42 * store and retrieve web service parameter sets.
47 public class WsParamSetManager implements ParamManager
49 Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<String, ParamDatastoreI>();
52 public WsParamSetI[] getParameterSet(String name, String serviceUrl,
53 boolean modifiable, boolean unmodifiable)
55 String files = Cache.getProperty("WS_PARAM_FILES");
60 StringTokenizer st = new StringTokenizer(files, "|");
62 ArrayList<WsParamSetI> params = new ArrayList<WsParamSetI>();
63 while (st.hasMoreTokens())
65 pfile = st.nextToken();
68 WsParamSetI[] pset = parseParamFile(pfile);
69 for (WsParamSetI p : pset)
72 if (serviceUrl != null)
74 for (String url : p.getApplicableUrls())
76 if (url.equals(serviceUrl))
86 add &= (modifiable == p.isModifiable() || unmodifiable == !p
88 add &= name == null || p.getName().equals(name);
97 } catch (IOException e)
100 .info("Failed to parse parameter file "
102 + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
106 return params.toArray(new WsParamSetI[0]);
109 private WsParamSetI[] parseParamFile(String filename) throws IOException
111 List<WsParamSetI> psets = new ArrayList<WsParamSetI>();
112 InputStreamReader is = new InputStreamReader(
113 new java.io.FileInputStream(new File(filename)), "UTF-8");
115 jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
117 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
119 unmar.setWhitespacePreserve(true);
122 wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
124 } catch (Exception ex)
126 throw new IOException(ex);
128 if (wspset != null && wspset.getParameters().length() > 0)
130 for (String url : wspset.getServiceURL())
132 ParamDatastoreI parser = paramparsers.get(url);
135 WsParamSetI pset = parser.parseServiceParameterFile(
136 wspset.getName(), wspset.getDescription(),
137 wspset.getServiceURL(), wspset.getParameters());
140 pset.setSourceFile(filename);
148 return psets.toArray(new WsParamSetI[0]);
152 public void storeParameterSet(WsParamSetI parameterSet)
154 String filename = parameterSet.getSourceFile();
158 if (filename != null && !((outfile = new File(filename)).canWrite()))
160 Cache.log.info("Can't write to " + filename
161 + " - Prompting for new file to write to.");
164 } catch (Exception e)
169 ParamDatastoreI parser = null;
170 for (String urls : parameterSet.getApplicableUrls())
174 parser = paramparsers.get(urls);
180 "Implementation error: Can't find a marshaller for the parameter set");
182 if (filename == null)
184 JalviewFileChooser chooser = new JalviewFileChooser(
185 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
186 { "wsparams" }, new String[]
187 { "Web Service Parameter File" },
188 "Web Service Parameter File");
189 chooser.setFileView(new jalview.io.JalviewFileView());
190 chooser.setDialogTitle("Choose a filename for this parameter file");
191 chooser.setToolTipText(MessageManager.getString("action.save"));
192 int value = chooser.showSaveDialog(Desktop.instance);
193 if (value == JalviewFileChooser.APPROVE_OPTION)
195 outfile = chooser.getSelectedFile();
197 .setProperty("LAST_DIRECTORY", outfile.getParent());
198 filename = outfile.getAbsolutePath();
199 if (!filename.endsWith(".wsparams"))
201 filename = filename.concat(".wsparams");
202 outfile = new File(filename);
208 String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
210 if (paramFiles.indexOf(filename) == -1)
212 if (paramFiles.length() > 0)
214 paramFiles = paramFiles.concat("|");
216 paramFiles = paramFiles.concat(filename);
218 jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles);
220 jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
222 paramxml.setName(parameterSet.getName());
223 paramxml.setDescription(parameterSet.getDescription());
224 paramxml.setServiceURL(parameterSet.getApplicableUrls().clone());
225 paramxml.setVersion("1.0");
228 paramxml.setParameters(parser
229 .generateServiceParameterFile(parameterSet));
230 PrintWriter out = new PrintWriter(new OutputStreamWriter(
231 new FileOutputStream(outfile), "UTF-8"));
232 paramxml.marshal(out);
234 parameterSet.setSourceFile(filename);
235 } catch (Exception e)
237 Cache.log.error("Couldn't write parameter file to " + outfile, e);
244 * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
245 * .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
246 * "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
247 * jalview.io.JalviewFileView());
248 * chooser.setDialogTitle("Load colour scheme");
249 * chooser.setToolTipText("Load");
251 * int value = chooser.showOpenDialog(this);
253 * if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
254 * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
255 * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
256 * "USER_DEFINED_COLOURS", choice.getPath()); if
257 * (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
258 * defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
261 * jalview.ws.params.ParamManager#deleteParameterSet(jalview.ws.params.WsParamSetI
265 public void deleteParameterSet(WsParamSetI parameterSet)
267 String filename = parameterSet.getSourceFile();
268 if (filename == null || filename.trim().length() < 1)
272 String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
273 if (paramFiles.indexOf(filename) > -1)
275 String nparamFiles = new String();
276 StringTokenizer st = new StringTokenizer(paramFiles, "|");
277 while (st.hasMoreElements())
279 String fl = st.nextToken();
280 if (!fl.equals(filename))
282 nparamFiles = nparamFiles.concat("|").concat(fl);
285 jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
290 File pfile = new File(filename);
291 if (pfile.exists() && pfile.canWrite())
293 if (JOptionPane.showConfirmDialog(Desktop.instance,
294 "Delete the preset's file, too ?", "Delete User Preset ?",
295 JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION)
300 } catch (Exception e)
303 .error("Exception when trying to delete webservice user preset: ",
309 public void registerParser(String hosturl, ParamDatastoreI paramdataStore)
311 paramparsers.put(hosturl, paramdataStore);