2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.io.JalviewFileChooser;
25 import jalview.io.JalviewFileView;
26 import jalview.util.MessageManager;
27 import jalview.ws.params.ParamDatastoreI;
28 import jalview.ws.params.ParamManager;
29 import jalview.ws.params.WsParamSetI;
32 import java.io.FileOutputStream;
33 import java.io.IOException;
34 import java.io.InputStreamReader;
35 import java.io.OutputStreamWriter;
36 import java.io.PrintWriter;
37 import java.util.ArrayList;
38 import java.util.Hashtable;
39 import java.util.List;
40 import java.util.StringTokenizer;
43 * store and retrieve web service parameter sets.
48 public class WsParamSetManager implements ParamManager
50 private static final String WS_PARAM_FILES = "WS_PARAM_FILES";
51 Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
54 public WsParamSetI[] getParameterSet(String name, String serviceUrl,
55 boolean modifiable, boolean unmodifiable)
57 String files = Cache.getProperty(WS_PARAM_FILES);
62 StringTokenizer st = new StringTokenizer(files, "|");
64 ArrayList<WsParamSetI> params = new ArrayList<>();
65 while (st.hasMoreTokens())
67 pfile = st.nextToken();
70 WsParamSetI[] pset = parseParamFile(pfile);
71 for (WsParamSetI p : pset)
74 if (serviceUrl != null)
76 for (String url : p.getApplicableUrls())
78 if (url.equals(serviceUrl))
88 add &= (modifiable == p.isModifiable()
89 || unmodifiable == !p.isModifiable());
90 add &= name == null || p.getName().equals(name);
99 } catch (IOException e)
101 Cache.log.info("Failed to parse parameter file " + pfile
102 + " (Check that all " + WS_PARAM_FILES
103 + " entries are valid!)",
107 return params.toArray(new WsParamSetI[0]);
110 private WsParamSetI[] parseParamFile(String filename) throws IOException
112 List<WsParamSetI> psets = new ArrayList<>();
113 InputStreamReader is = new InputStreamReader(
114 new java.io.FileInputStream(new File(filename)), "UTF-8");
116 jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
118 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
120 unmar.setWhitespacePreserve(true);
123 wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
125 } catch (Exception ex)
127 throw new IOException(ex);
129 if (wspset != null && wspset.getParameters().length() > 0)
131 for (String url : wspset.getServiceURL())
133 ParamDatastoreI parser = paramparsers.get(url);
136 WsParamSetI pset = parser.parseServiceParameterFile(
137 wspset.getName(), wspset.getDescription(),
138 wspset.getServiceURL(), wspset.getParameters());
141 pset.setSourceFile(filename);
149 return psets.toArray(new WsParamSetI[0]);
153 public void storeParameterSet(WsParamSetI parameterSet)
155 String filename = parameterSet.getSourceFile();
159 if (filename != null && !((outfile = new File(filename)).canWrite()))
161 Cache.log.warn("Can't write to " + filename
162 + " - Prompting for new file to write to.");
165 } catch (Exception e)
170 ParamDatastoreI parser = null;
171 for (String urls : parameterSet.getApplicableUrls())
175 parser = paramparsers.get(urls);
180 throw new Error(MessageManager.getString(
181 "error.implementation_error_cannot_find_marshaller_for_param_set"));
183 if (filename == null)
185 JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
186 "Web Service Parameter File");
187 chooser.setFileView(new JalviewFileView());
188 chooser.setDialogTitle(MessageManager
189 .getString("label.choose_filename_for_param_file"));
190 chooser.setToolTipText(MessageManager.getString("action.save"));
191 int value = chooser.showSaveDialog(Desktop.instance);
192 if (value == JalviewFileChooser.APPROVE_OPTION)
194 outfile = chooser.getSelectedFile();
195 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
196 outfile.getParent());
197 filename = outfile.getAbsolutePath();
198 if (!filename.endsWith(".wsparams"))
200 filename = filename.concat(".wsparams");
201 outfile = new File(filename);
207 String paramFiles = jalview.bin.Cache.getDefault(WS_PARAM_FILES,
209 if (paramFiles.indexOf(filename) == -1)
211 if (paramFiles.length() > 0)
213 paramFiles = paramFiles.concat("|");
215 paramFiles = paramFiles.concat(filename);
217 jalview.bin.Cache.setProperty(WS_PARAM_FILES, paramFiles);
219 jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
221 paramxml.setName(parameterSet.getName());
222 paramxml.setDescription(parameterSet.getDescription());
223 paramxml.setServiceURL(parameterSet.getApplicableUrls().clone());
224 paramxml.setVersion("1.0");
227 paramxml.setParameters(
228 parser.generateServiceParameterFile(parameterSet));
229 PrintWriter out = new PrintWriter(new OutputStreamWriter(
230 new FileOutputStream(outfile), "UTF-8"));
231 paramxml.marshal(out);
233 parameterSet.setSourceFile(filename);
234 } catch (Exception e)
236 Cache.log.error("Couldn't write parameter file to " + outfile, e);
243 * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
244 * .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
245 * "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
246 * jalview.io.JalviewFileView());
247 * chooser.setDialogTitle("Load colour scheme");
248 * chooser.setToolTipText("Load");
250 * int value = chooser.showOpenDialog(this);
252 * if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
253 * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
254 * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
255 * "USER_DEFINED_COLOURS", choice.getPath()); if
256 * (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
257 * defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
260 * jalview.ws.params.ParamManager#deleteParameterSet(jalview.ws.params.WsParamSetI
264 public void deleteParameterSet(WsParamSetI parameterSet)
266 String filename = parameterSet.getSourceFile();
267 if (filename == null || filename.trim().length() < 1)
271 String paramFiles = jalview.bin.Cache.getDefault(WS_PARAM_FILES, "");
272 if (paramFiles.indexOf(filename) > -1)
274 String nparamFiles = new String();
275 StringTokenizer st = new StringTokenizer(paramFiles, "|");
276 while (st.hasMoreElements())
278 String fl = st.nextToken();
279 if (!fl.equals(filename))
281 nparamFiles = nparamFiles.concat("|").concat(fl);
284 jalview.bin.Cache.setProperty(WS_PARAM_FILES, nparamFiles);
289 File pfile = new File(filename);
290 if (pfile.exists() && pfile.canWrite())
292 if (JvOptionPane.showConfirmDialog(Desktop.instance,
293 "Delete the preset's file, too ?", "Delete User Preset ?",
294 JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
299 } catch (Exception e)
302 "Exception when trying to delete webservice user preset: ",
308 public void registerParser(String hosturl, ParamDatastoreI paramdataStore)
310 paramparsers.put(hosturl, paramdataStore);