2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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.
19 package jalview.ws.jws2;
21 import java.io.IOException;
22 import java.util.ArrayList;
23 import java.util.Arrays;
24 import java.util.Hashtable;
25 import java.util.List;
26 import java.util.StringTokenizer;
28 import org.jmol.util.ArrayUtil;
29 import compbio.metadata.Argument;
30 import compbio.metadata.Option;
31 import compbio.metadata.Parameter;
32 import compbio.metadata.Preset;
33 import compbio.metadata.PresetManager;
34 import compbio.metadata.RunnerConfig;
36 import jalview.ws.jws2.dm.JabaOption;
37 import jalview.ws.jws2.dm.JabaParameter;
38 import jalview.ws.jws2.dm.JabaWsParamSet;
39 import jalview.ws.jws2.jabaws2.Jws2Instance;
40 import jalview.ws.params.ArgumentI;
41 import jalview.ws.params.ParamDatastoreI;
42 import jalview.ws.params.ParamManager;
43 import jalview.ws.params.WsParamSetI;
45 public class JabaParamStore implements ParamDatastoreI
48 Hashtable<String, JabaWsParamSet> editedParams = new Hashtable<String, JabaWsParamSet>();
50 private Jws2Instance service;
52 private RunnerConfig serviceOptions;
54 private Hashtable<String, JabaPreset> servicePresets;
56 public JabaParamStore(Jws2Instance service)
63 public JabaParamStore(Jws2Instance service, ParamManager manager)
65 this.service = service;
66 serviceOptions = service.getRunnerConfig();
67 this.manager = manager;
68 // discover all the user's locally stored presets for this service and
69 // populate the hash table
72 manager.registerParser(service.getUri(), this);
73 WsParamSetI[] prams = manager.getParameterSet(null, service.getUri(),
77 for (WsParamSetI paramset : prams)
79 if (paramset instanceof JabaWsParamSet)
81 editedParams.put(paramset.getName(), (JabaWsParamSet) paramset);
86 .println("Warning: Ignoring parameter set instance of type "
88 + " : Bound but not applicable for service at "
97 public List<WsParamSetI> getPresets()
99 List<WsParamSetI> prefs = new ArrayList();
100 if (servicePresets == null)
102 servicePresets = new Hashtable<String, JabaPreset>();
104 if ((prman = service.getPresets()) != null)
106 List pset = prman.getPresets();
109 for (Object pr : pset)
111 JabaPreset prset = new JabaPreset(service, (Preset) pr);
112 servicePresets.put(prset.getName(), prset);
117 for (JabaPreset pr : servicePresets.values())
121 for (WsParamSetI wspset : editedParams.values())
129 public WsParamSetI getPreset(String name)
131 for (WsParamSetI pr : getPresets())
133 if (pr.getName().equals(name))
141 public static List<ArgumentI> getJwsArgsfromJaba(List jabargs)
143 return getJwsArgsfromJaba(jabargs, true);
146 public static List<ArgumentI> getJwsArgsfromJaba(List jabargs,
149 List<ArgumentI> rgs = new ArrayList<ArgumentI>();
150 List<String> rgnames = new ArrayList<String>();
151 for (Object rg : jabargs)
153 ArgumentI narg = null;
154 String nargstring = null;
155 if (rg instanceof Parameter)
157 narg = new JabaParameter((Parameter) rg);
158 nargstring = narg.getName(); // just sort by name for this
160 else if (rg instanceof Option)
162 narg = new JabaOption((Option) rg);
163 nargstring = (String) ((Option) rg).getOptionNames().get(0);
168 "Implementation Error: Cannot handle Jaba parameter object "
174 rgnames.add(nargstring);
181 ArgumentI[] rgssort = rgs.toArray(new ArgumentI[rgs.size()]);
182 String[] rgssorton = rgnames.toArray(new String[rgs.size()]);
183 jalview.util.QuickSort.sort(rgssorton, rgssort);
186 while (rgssort.length-i>i)
188 tmp1=rgssort[rgssort.length-i-1];
189 rgssort[rgssort.length-i-1] = rgssort[i];
192 return Arrays.asList(rgssort);
195 public static List getJabafromJwsArgs(List<ArgumentI> jwsargs)
197 List rgs = new ArrayList();
198 for (ArgumentI rg : jwsargs)
200 Argument narg = (rg instanceof JabaOption) ? ((JabaOption) rg)
205 "Implementation Error: Cannot handle Jaba parameter object "
217 public List<ArgumentI> getServiceParameters()
219 return getJwsArgsfromJaba(serviceOptions.getArguments());
223 public boolean presetExists(String name)
225 return (editedParams.containsKey(name) || servicePresets
230 public void deletePreset(String name)
232 if (editedParams.containsKey(name))
234 WsParamSetI parameterSet = editedParams.get(name);
235 editedParams.remove(name);
238 manager.deleteParameterSet(parameterSet);
242 if (servicePresets.containsKey(name))
245 "Implementation error: Attempt to delete a service preset!");
250 public void storePreset(String presetName, String text,
251 List<ArgumentI> jobParams)
253 JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
254 jps.setApplicableUrls(new String[]
255 { service.getUri() });
256 editedParams.put(jps.getName(), jps);
259 manager.storeParameterSet(jps);
264 public void updatePreset(String oldName, String presetName, String text,
265 List<ArgumentI> jobParams)
267 JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
268 : getPreset(presetName));
271 throw new Error("Implementation error: Can't locate either oldname ("
272 + oldName + ") or presetName (" + presetName
273 + "in the datastore!");
275 jps.setName(presetName);
276 jps.setDescription(text);
277 jps.setArguments(jobParams);
278 jps.setApplicableUrls(new String[]
279 { service.getUri() });
280 if (oldName != null && !oldName.equals(jps.getName()))
282 editedParams.remove(oldName);
284 editedParams.put(jps.getName(), jps);
288 manager.storeParameterSet(jps);
293 * create a new, empty parameter set for this service
297 WsParamSetI newWsParamSet()
299 return new JabaWsParamSet();
302 private boolean involves(String[] urls)
304 boolean found = false;
305 for (String url : urls)
307 if (service.getServiceTypeURI().equals(url)
308 || service.getUri().equalsIgnoreCase(url))
318 public WsParamSetI parseServiceParameterFile(String name, String descr,
319 String[] urls, String parameterfile) throws IOException
323 throw new IOException(
324 "Implementation error: Cannot find service url in the given url set!");
327 JabaWsParamSet wsp = new JabaWsParamSet();
329 wsp.setDescription(descr);
330 wsp.setApplicableUrls(urls.clone());
332 List<String> lines = new ArrayList<String>();
333 StringTokenizer st = new StringTokenizer(parameterfile, "\n");
334 while (st.hasMoreTokens())
336 lines.add(st.nextToken());
338 wsp.setjabaArguments(ParameterUtils.processParameters(lines,
339 serviceOptions, " "));
344 public String generateServiceParameterFile(WsParamSetI pset)
347 if (!involves(pset.getApplicableUrls()))
349 throw new IOException(
350 "Implementation error: Cannot find service url in the given url set for this service parameter store ("
351 + service.getUri() + ") !");
354 if (!(pset instanceof JabaWsParamSet))
357 "Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
360 StringBuffer rslt = new StringBuffer();
361 for (String ln : ParameterUtils.writeParameterSet(
362 ((JabaWsParamSet) pset).getjabaArguments(), " "))
368 return rslt.toString();