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Coverage Report

  1. Project Clover database Thu Dec 4 2025 16:11:35 GMT
  2. Package jalview.ws2.params

File SimpleParamDatastore.java

 

Coverage histogram

../../../img/srcFileCovDistChart2.png
54% of files have more coverage

Code metrics

30
97
13
1
257
220
32
0.33
7.46
13
2.46

Classes

Class Line # Actions
SimpleParamDatastore 31 97 32
0.11428571511.4%
 

Contributing tests

This file is covered by 456 tests. .

Source view

1    package jalview.ws2.params;
2   
3    import java.io.ByteArrayOutputStream;
4    import java.io.IOException;
5    import java.io.StringReader;
6    import java.net.URL;
7    import java.util.ArrayList;
8    import java.util.Collections;
9    import java.util.List;
10   
11    import javax.xml.bind.JAXBContext;
12    import javax.xml.bind.JAXBException;
13    import javax.xml.bind.Marshaller;
14    import javax.xml.bind.Unmarshaller;
15   
16    import jalview.bin.Cache;
17    import jalview.bin.Console;
18    import jalview.util.MessageManager;
19    import jalview.ws.params.ArgumentI;
20    import jalview.ws.params.ParamDatastoreI;
21    import jalview.ws.params.ParamManager;
22    import jalview.ws.params.WsParamSetI;
23   
24    /**
25    * A web client agnostic parameters datastore that provides view of the
26    * parameters and delegates parameters storage to {@link ParamManager}
27    * if given. Parameter datastore maintains the applicable service url
28    * the list of service parameters and both presets and user defined
29    * parameter sets
30    */
 
31    public class SimpleParamDatastore implements ParamDatastoreI
32    {
33    protected URL serviceUrl;
34    protected List<ArgumentI> parameters;
35    protected List<SimpleParamSet> servicePresets;
36    protected List<SimpleParamSet> userPresets = new ArrayList<>();
37    protected ParamManager manager;
38   
39    /**
40    * Create new parameter datastore bound to the specified url with
41    * given service parameters and presets. Additionally, a parameters
42    * manager may be provided that will be used to load and store
43    * user parameter sets.
44    *
45    * @param serviceUrl applicable url
46    * @param parameters service parameters
47    * @param presets unmodifiable service presets
48    * @param manager parameter manager used to load and store user presets
49    */
 
50  1651 toggle public SimpleParamDatastore(URL serviceUrl, List<ArgumentI> parameters,
51    List<? extends WsParamSetI> presets, ParamManager manager)
52    {
53  1651 this.serviceUrl = serviceUrl;
54  1651 this.parameters = Collections.unmodifiableList(new ArrayList<>(parameters));
55  1651 this.servicePresets = new ArrayList<>(presets.size());
56  1651 for (var preset : presets)
57    {
58  0 if (preset instanceof SimpleParamSet)
59  0 servicePresets.add((SimpleParamSet) preset);
60    else
61  0 servicePresets.add(new SimpleParamSet(preset));
62    }
63  1651 this.servicePresets = Collections.unmodifiableList(this.servicePresets);
64  1651 this.manager = manager;
65  1651 if (manager != null)
66  0 _initManager(manager);
67    }
68   
 
69  0 toggle private void _initManager(ParamManager manager)
70    {
71  0 manager.registerParser(serviceUrl.toString(), this);
72  0 WsParamSetI[] paramSets = manager.getParameterSet(null, serviceUrl.toString(),
73    true, false);
74  0 if (paramSets != null)
75    {
76  0 for (WsParamSetI paramSet : paramSets)
77    {
78    // TODO: handle mismatch between preset and current parameters
79  0 if (paramSet instanceof SimpleParamSet)
80  0 userPresets.add((SimpleParamSet) paramSet);
81    else
82    {
83  0 userPresets.add(new SimpleParamSet(paramSet));
84  0 Console.warn(String.format(
85    "Parameter set instance type %s is not applicable to service"
86    + "at %s.", paramSet.getClass(), serviceUrl));
87    }
88    }
89    }
90    }
91   
 
92  111498 toggle @Override
93    public List<WsParamSetI> getPresets()
94    {
95  111498 List<WsParamSetI> presets = new ArrayList<>();
96  111498 presets.addAll(servicePresets);
97  111499 presets.addAll(userPresets);
98  111499 return presets;
99    }
100   
 
101  0 toggle @Override
102    public SimpleParamSet getPreset(String name)
103    {
104  0 SimpleParamSet preset = null;
105  0 preset = getUserPreset(name);
106  0 if (preset != null)
107  0 return preset;
108  0 preset = getServicePreset(name);
109  0 if (preset != null)
110  0 return preset;
111  0 return null;
112    }
113   
 
114  0 toggle public SimpleParamSet getUserPreset(String name)
115    {
116  0 for (SimpleParamSet preset : userPresets)
117    {
118  0 if (name.equals(preset.getName()))
119  0 return preset;
120    }
121  0 return null;
122    }
123   
 
124  0 toggle public SimpleParamSet getServicePreset(String name)
125    {
126  0 for (SimpleParamSet preset : servicePresets)
127    {
128  0 if (name.equals(preset.getName()))
129  0 return preset;
130    }
131  0 return null;
132    }
133   
 
134  162277 toggle @Override
135    public List<ArgumentI> getServiceParameters()
136    {
137  162277 return parameters;
138    }
139   
 
140  0 toggle @Override
141    public boolean presetExists(String name)
142    {
143  0 return getPreset(name) != null;
144    }
145   
 
146  0 toggle @Override
147    public void deletePreset(String name)
148    {
149  0 var userPreset = getUserPreset(name);
150  0 if (userPreset != null)
151    {
152  0 userPresets.remove(userPreset);
153  0 if (manager != null)
154    {
155  0 manager.deleteParameterSet(userPreset);
156    }
157    }
158  0 else if (getServicePreset(name) != null)
159    {
160  0 throw new RuntimeException(MessageManager.getString(
161    "error.implementation_error_attempt_to_delete_service_preset"));
162    }
163    else
164    {
165  0 Console.warn("Implementation error: no preset to delete");
166    }
167    }
168   
 
169  0 toggle @Override
170    public void storePreset(String presetName, String text, List<ArgumentI> jobParams)
171    {
172  0 var builder = SimpleParamSet.newBuilder();
173  0 builder.name(presetName);
174  0 builder.description(text);
175  0 builder.arguments(jobParams);
176  0 builder.url(serviceUrl.toString());
177  0 builder.modifiable(true);
178  0 var preset = builder.build();
179  0 userPresets.add(preset);
180  0 if (manager != null)
181  0 manager.storeParameterSet(preset);
182    }
183   
 
184  0 toggle @Override
185    public void updatePreset(String oldName, String newName, String text, List<ArgumentI> jobParams)
186    {
187  0 var preset = getPreset(oldName != null ? oldName : newName);
188  0 if (preset == null)
189  0 throw new RuntimeException(MessageManager.formatMessage(
190    "error.implementation_error_cannot_locate_oldname_presetname",
191    oldName, newName));
192  0 preset.setName(newName);
193  0 preset.setDescription(text);
194  0 preset.setArguments(jobParams);
195  0 preset.setApplicableUrls(new String[] { serviceUrl.toString() });
196  0 if (manager != null)
197  0 manager.storeParameterSet(preset);
198    }
199   
 
200  0 toggle @Override
201    public WsParamSetI parseServiceParameterFile(String name, String description,
202    String[] serviceURL, String parameters)
203    throws IOException
204    {
205  0 var builder = SimpleParamSet.newBuilder();
206  0 builder.name(name);
207  0 builder.description(description);
208  0 builder.urls(serviceURL);
209  0 builder.modifiable(true);
210  0 Unmarshaller unmarshaller;
211  0 try
212    {
213  0 var ctx = JAXBContext.newInstance(ArgumentBeanList.class);
214  0 unmarshaller = ctx.createUnmarshaller();
215    } catch (JAXBException e)
216    {
217  0 throw new RuntimeException(e);
218    }
219  0 ArgumentBeanList argList;
220  0 try
221    {
222  0 argList = (ArgumentBeanList) unmarshaller.unmarshal(new StringReader(parameters));
223    } catch (JAXBException | ClassCastException e)
224    {
225  0 throw new IOException("Unable to load parameters from file", e);
226    }
227  0 builder.arguments(argList.arguments);
228  0 return builder.build();
229    }
230   
 
231  0 toggle @Override
232    public String generateServiceParameterFile(WsParamSetI pset) throws IOException
233    {
234  0 Marshaller marshaller;
235  0 try
236    {
237  0 var ctx = JAXBContext.newInstance(ArgumentBeanList.class);
238  0 marshaller = ctx.createMarshaller();
239  0 marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
240  0 marshaller.setProperty(Marshaller.JAXB_FRAGMENT, true);
241    } catch (JAXBException e)
242    {
243  0 throw new RuntimeException(e);
244    }
245  0 ArgumentBeanList argList = ArgumentBeanList.fromList(pset.getArguments());
246  0 var out = new ByteArrayOutputStream();
247  0 try
248    {
249  0 marshaller.marshal(argList, out);
250    } catch (JAXBException e)
251    {
252  0 throw new IOException("Unable to generate parameters file", e);
253    }
254  0 return out.toString();
255    }
256   
257    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.