Clover icon

Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.gui

File WsParamSetManager.java

 

Coverage histogram

../../img/srcFileCovDistChart1.png
57% of files have more coverage

Code metrics

46
112
5
1
336
265
37
0.33
22.4
5
7.4

Classes

Class Line # Actions
WsParamSetManager 58 112 37
0.0429447854.3%
 

Contributing tests

This file is covered by 80 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.gui;
22   
23    import jalview.bin.Cache;
24    import jalview.bin.Console;
25    import jalview.io.JalviewFileChooser;
26    import jalview.io.JalviewFileView;
27    import jalview.util.MessageManager;
28    import jalview.ws.params.ParamDatastoreI;
29    import jalview.ws.params.ParamManager;
30    import jalview.ws.params.WsParamSetI;
31    import jalview.xml.binding.jalview.ObjectFactory;
32    import jalview.xml.binding.jalview.WebServiceParameterSet;
33   
34    import java.io.File;
35    import java.io.FileInputStream;
36    import java.io.FileOutputStream;
37    import java.io.IOException;
38    import java.io.InputStreamReader;
39    import java.io.OutputStreamWriter;
40    import java.io.PrintWriter;
41    import java.util.ArrayList;
42    import java.util.Hashtable;
43    import java.util.List;
44    import java.util.StringTokenizer;
45   
46    import javax.xml.bind.JAXBContext;
47    import javax.xml.bind.JAXBElement;
48    import javax.xml.bind.Marshaller;
49    import javax.xml.stream.XMLInputFactory;
50    import javax.xml.stream.XMLStreamReader;
51   
52    /**
53    * store and retrieve web service parameter sets.
54    *
55    * @author JimP
56    *
57    */
 
58    public class WsParamSetManager implements ParamManager
59    {
60    private static final String WS_PARAM_FILES = "WS_PARAM_FILES";
61    Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
62   
 
63  481 toggle @Override
64    public WsParamSetI[] getParameterSet(String name, String serviceUrl,
65    boolean modifiable, boolean unmodifiable)
66    {
67  481 String files = Cache.getProperty(WS_PARAM_FILES);
68  481 if (files == null)
69    {
70  481 return null;
71    }
72  0 StringTokenizer st = new StringTokenizer(files, "|");
73  0 String pfile = null;
74  0 List<WsParamSetI> params = new ArrayList<>();
75  0 while (st.hasMoreTokens())
76    {
77  0 pfile = st.nextToken();
78  0 try
79    {
80  0 WsParamSetI[] pset = parseParamFile(pfile);
81  0 for (WsParamSetI p : pset)
82    {
83  0 boolean add = false;
84  0 if (serviceUrl != null)
85    {
86  0 for (String url : p.getApplicableUrls())
87    {
88  0 if (url.equals(serviceUrl))
89    {
90  0 add = true;
91    }
92    }
93    }
94    else
95    {
96  0 add = true;
97    }
98  0 add &= (modifiable == p.isModifiable()
99    || unmodifiable == !p.isModifiable());
100  0 add &= name == null || p.getName().equals(name);
101   
102  0 if (add)
103    {
104   
105  0 params.add(p);
106    }
107   
108    }
109    } catch (IOException e)
110    {
111  0 Console.info("Failed to parse parameter file " + pfile
112    + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
113    e);
114    }
115    }
116  0 return params.toArray(new WsParamSetI[0]);
117    }
118   
 
119  0 toggle private WsParamSetI[] parseParamFile(String filename) throws IOException
120    {
121  0 List<WsParamSetI> psets = new ArrayList<>();
122  0 InputStreamReader is = new InputStreamReader(
123    new FileInputStream(new File(filename)), "UTF-8");
124   
125  0 WebServiceParameterSet wspset = null;
126  0 try
127    {
128  0 JAXBContext jc = JAXBContext
129    .newInstance("jalview.xml.binding.jalview");
130  0 javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
131  0 XMLStreamReader streamReader = XMLInputFactory.newInstance()
132    .createXMLStreamReader(is);
133  0 JAXBElement<WebServiceParameterSet> jbe = um.unmarshal(streamReader,
134    WebServiceParameterSet.class);
135  0 wspset = jbe.getValue();
136    } catch (Exception ex)
137    {
138  0 throw new IOException(ex);
139    }
140   
141  0 if (wspset != null && wspset.getParameters().length() > 0)
142    {
143  0 List<String> urls = wspset.getServiceURL();
144  0 final String[] urlArray = urls.toArray(new String[urls.size()]);
145   
146  0 for (String url : urls)
147    {
148  0 ParamDatastoreI parser = paramparsers.get(url);
149  0 if (parser != null)
150    {
151  0 WsParamSetI pset = parser.parseServiceParameterFile(
152    wspset.getName(), wspset.getDescription(),
153    urlArray, wspset.getParameters());
154  0 if (pset != null)
155    {
156  0 pset.setSourceFile(filename);
157  0 psets.add(pset);
158  0 break;
159    }
160    }
161    }
162    }
163   
164  0 return psets.toArray(new WsParamSetI[0]);
165    }
166   
 
167  0 toggle @Override
168    public void storeParameterSet(WsParamSetI parameterSet)
169    {
170  0 String filename = parameterSet.getSourceFile();
171  0 File outfile = null;
172  0 try
173    {
174  0 if (filename != null && !((outfile = new File(filename)).canWrite()))
175    {
176  0 Console.warn("Can't write to " + filename
177    + " - Prompting for new file to write to.");
178  0 filename = null;
179    }
180    } catch (Exception e)
181    {
182  0 filename = null;
183    }
184   
185  0 ParamDatastoreI parser = null;
186  0 for (String urls : parameterSet.getApplicableUrls())
187    {
188  0 if (parser == null)
189    {
190  0 parser = paramparsers.get(urls);
191    }
192    }
193  0 if (parser == null)
194    {
195  0 throw new Error(MessageManager.getString(
196    "error.implementation_error_cannot_find_marshaller_for_param_set"));
197    }
198  0 if (filename == null)
199    {
200    // TODO: JAL-3048 webservice - not required for Jalview-JS
201   
202  0 JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
203    "Web Service Parameter File");
204  0 chooser.setFileView(new JalviewFileView());
205  0 chooser.setDialogTitle(MessageManager
206    .getString("label.choose_filename_for_param_file"));
207  0 chooser.setToolTipText(MessageManager.getString("action.save"));
208  0 int value = chooser.showSaveDialog(Desktop.getInstance());
209  0 if (value == JalviewFileChooser.APPROVE_OPTION)
210    {
211  0 outfile = chooser.getSelectedFile();
212  0 Cache.setProperty("LAST_DIRECTORY", outfile.getParent());
213  0 filename = outfile.getAbsolutePath();
214  0 if (!filename.endsWith(".wsparams"))
215    {
216  0 filename = filename.concat(".wsparams");
217  0 outfile = new File(filename);
218    }
219    }
220    }
221  0 if (outfile != null)
222    {
223  0 String paramFiles = Cache.getDefault("WS_PARAM_FILES", filename);
224  0 if (paramFiles.indexOf(filename) == -1)
225    {
226  0 if (paramFiles.length() > 0)
227    {
228  0 paramFiles = paramFiles.concat("|");
229    }
230  0 paramFiles = paramFiles.concat(filename);
231    }
232  0 Cache.setProperty(WS_PARAM_FILES, paramFiles);
233   
234  0 WebServiceParameterSet paramxml = new WebServiceParameterSet();
235   
236  0 paramxml.setName(parameterSet.getName());
237  0 paramxml.setDescription(parameterSet.getDescription());
238  0 for (String url : parameterSet.getApplicableUrls())
239    {
240  0 paramxml.getServiceURL().add(url);
241    }
242  0 paramxml.setVersion("1.0");
243  0 try
244    {
245  0 paramxml.setParameters(
246    parser.generateServiceParameterFile(parameterSet));
247  0 PrintWriter out = new PrintWriter(new OutputStreamWriter(
248    new FileOutputStream(outfile), "UTF-8"));
249  0 JAXBContext jaxbContext = JAXBContext
250    .newInstance(WebServiceParameterSet.class);
251  0 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
252  0 jaxbMarshaller.marshal(
253    new ObjectFactory().createWebServiceParameterSet(paramxml),
254    out);
255  0 out.close();
256  0 parameterSet.setSourceFile(filename);
257    } catch (Exception e)
258    {
259  0 Console.error("Couldn't write parameter file to " + outfile, e);
260    }
261    }
262    }
263   
264    /*
265    *
266    * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
267    * .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
268    * "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
269    * jalview.io.JalviewFileView());
270    * chooser.setDialogTitle("Load colour scheme");
271    * chooser.setToolTipText("Load");
272    *
273    * int value = chooser.showOpenDialog(this);
274    *
275    * if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
276    * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
277    * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
278    * "USER_DEFINED_COLOURS", choice.getPath()); if
279    * (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
280    * defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
281    *
282    * @see
283    * jalview.ws.params.ParamManager#deleteParameterSet(jalview.ws.params.WsParamSetI
284    * )
285    */
 
286  0 toggle @Override
287    public void deleteParameterSet(WsParamSetI parameterSet)
288    {
289  0 String filename = parameterSet.getSourceFile();
290  0 if (filename == null || filename.trim().length() < 1)
291    {
292  0 return;
293    }
294  0 String paramFiles = Cache.getDefault(WS_PARAM_FILES, "");
295  0 if (paramFiles.indexOf(filename) > -1)
296    {
297  0 String nparamFiles = new String();
298  0 StringTokenizer st = new StringTokenizer(paramFiles, "|");
299  0 while (st.hasMoreElements())
300    {
301  0 String fl = st.nextToken();
302  0 if (!fl.equals(filename))
303    {
304  0 nparamFiles = nparamFiles.concat("|").concat(fl);
305    }
306    }
307  0 Cache.setProperty(WS_PARAM_FILES, nparamFiles);
308    }
309   
310  0 try
311    {
312  0 File pfile = new File(filename);
313  0 if (pfile.exists() && pfile.canWrite())
314    {
315  0 if (JvOptionPane.showConfirmDialog(Desktop.getInstance(),
316    "Delete the preset's file, too ?", "Delete User Preset ?",
317    JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
318    {
319  0 pfile.delete();
320    }
321    }
322    } catch (Exception e)
323    {
324  0 Console.error(
325    "Exception when trying to delete webservice user preset: ",
326    e);
327    }
328    }
329   
 
330  481 toggle @Override
331    public void registerParser(String hosturl, ParamDatastoreI paramdataStore)
332    {
333  481 paramparsers.put(hosturl, paramdataStore);
334    }
335   
336    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
  • OpenClover is free and open-source software.