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package jalview.ws.jws2; |
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import jalview.util.MessageManager; |
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import jalview.ws.jws2.dm.JabaOption; |
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import jalview.ws.jws2.dm.JabaParameter; |
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import jalview.ws.jws2.dm.JabaWsParamSet; |
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import jalview.ws.jws2.jabaws2.Jws2Instance; |
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import jalview.ws.params.ArgumentI; |
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import jalview.ws.params.ParamDatastoreI; |
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import jalview.ws.params.ParamManager; |
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import jalview.ws.params.WsParamSetI; |
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import java.io.IOException; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.StringTokenizer; |
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import compbio.metadata.Argument; |
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import compbio.metadata.Option; |
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import compbio.metadata.Parameter; |
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import compbio.metadata.Preset; |
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import compbio.metadata.PresetManager; |
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import compbio.metadata.RunnerConfig; |
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| 14.6% |
Uncovered Elements: 164 (192) |
Complexity: 45 |
Complexity Density: 0.37 |
|
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public class JabaParamStore implements ParamDatastoreI |
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{ |
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Hashtable<String, JabaWsParamSet> editedParams = new Hashtable<String, JabaWsParamSet>(); |
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private Jws2Instance service; |
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private RunnerConfig serviceOptions; |
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private Hashtable<String, JabaPreset> servicePresets; |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public JabaParamStore(Jws2Instance service)... |
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{ |
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this(service, null); |
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} |
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ParamManager manager; |
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| 52.9% |
Uncovered Elements: 8 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
|
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public JabaParamStore(Jws2Instance service, ParamManager manager)... |
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{ |
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this.service = service; |
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serviceOptions = service.getRunnerConfig(); |
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this.manager = manager; |
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|
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|
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if (manager != null) |
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{ |
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manager.registerParser(service.getUri(), this); |
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WsParamSetI[] prams = manager.getParameterSet(null, service.getUri(), |
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true, false); |
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if (prams != null) |
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{ |
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for (WsParamSetI paramset : prams) |
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{ |
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if (paramset instanceof JabaWsParamSet) |
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{ |
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editedParams.put(paramset.getName(), (JabaWsParamSet) paramset); |
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} |
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else |
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{ |
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jalview.bin.Console.errPrintln( |
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"Warning: Ignoring parameter set instance of type " |
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+ paramset.getClass() |
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+ " : Bound but not applicable for service at " |
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+ service.getUri()); |
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} |
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} |
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} |
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} |
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} |
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| 81% |
Uncovered Elements: 4 (21) |
Complexity: 4 |
Complexity Density: 0.27 |
|
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5042 |
@Override... |
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public List<WsParamSetI> getPresets() |
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{ |
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5042 |
List<WsParamSetI> prefs = new ArrayList<>(); |
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5042 |
if (servicePresets == null) |
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{ |
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servicePresets = new Hashtable<String, JabaPreset>(); |
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PresetManager prman; |
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if ((prman = service.getPresets()) != null) |
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{ |
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164 |
List pset = prman.getPresets(); |
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if (pset != null) |
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{ |
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for (Object pr : pset) |
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{ |
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JabaPreset prset = new JabaPreset(service, (Preset) pr); |
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servicePresets.put(prset.getName(), prset); |
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} |
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} |
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} |
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} |
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5042 |
for (JabaPreset pr : servicePresets.values()) |
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{ |
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18061 |
prefs.add(pr); |
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} |
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5042 |
for (WsParamSetI wspset : editedParams.values()) |
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{ |
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prefs.add(wspset); |
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} |
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5042 |
return prefs; |
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} |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
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0 |
@Override... |
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public WsParamSetI getPreset(String name) |
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{ |
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for (WsParamSetI pr : getPresets()) |
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{ |
135 |
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if (pr.getName().equals(name)) |
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{ |
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return pr; |
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} |
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} |
140 |
0 |
return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
143 |
0 |
public static List<ArgumentI> getJwsArgsfromJaba(List jabargs)... |
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{ |
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return getJwsArgsfromJaba(jabargs, true); |
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} |
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| 0% |
Uncovered Elements: 37 (37) |
Complexity: 6 |
Complexity Density: 0.22 |
|
148 |
0 |
public static List<ArgumentI> getJwsArgsfromJaba(List jabargs,... |
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boolean sortByOpt) |
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{ |
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List<ArgumentI> rgs = new ArrayList<ArgumentI>(); |
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List<String> rgnames = new ArrayList<String>(); |
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for (Object rg : jabargs) |
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{ |
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ArgumentI narg = null; |
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String nargstring = null; |
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0 |
if (rg instanceof Parameter) |
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{ |
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narg = new JabaParameter((Parameter) rg); |
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nargstring = narg.getName(); |
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} |
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else if (rg instanceof Option) |
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{ |
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narg = new JabaOption((Option) rg); |
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nargstring = (String) ((Option) rg).getOptionNames().get(0); |
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} |
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if (narg == null) |
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{ |
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throw new Error(MessageManager.formatMessage( |
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"error.implementation_error_cannot_handle_jaba_param", |
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new String[] |
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{ rg.getClass().toString() })); |
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} |
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else |
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{ |
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rgs.add(narg); |
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rgnames.add(nargstring); |
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} |
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} |
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if (!sortByOpt) |
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{ |
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return rgs; |
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} |
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0 |
ArgumentI[] rgssort = rgs.toArray(new ArgumentI[rgs.size()]); |
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String[] rgssorton = rgnames.toArray(new String[rgs.size()]); |
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jalview.util.QuickSort.sort(rgssorton, rgssort); |
187 |
0 |
ArgumentI tmp1; |
188 |
0 |
int i = 0; |
189 |
0 |
while (rgssort.length - i > i) |
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{ |
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0 |
tmp1 = rgssort[rgssort.length - i - 1]; |
192 |
0 |
rgssort[rgssort.length - i - 1] = rgssort[i]; |
193 |
0 |
rgssort[i++] = tmp1; |
194 |
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} |
195 |
0 |
return Arrays.asList(rgssort); |
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} |
197 |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
198 |
0 |
public static List getJabafromJwsArgs(List<ArgumentI> jwsargs)... |
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{ |
200 |
0 |
List rgs = new ArrayList(); |
201 |
0 |
for (ArgumentI rg : jwsargs) |
202 |
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{ |
203 |
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Argument narg = (rg instanceof JabaOption) |
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? ((JabaOption) rg).getOption() |
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: null; |
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0 |
if (narg == null) |
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{ |
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throw new Error(MessageManager.formatMessage( |
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"error.implementation_error_cannot_handle_jaba_param", |
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new String[] |
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{ rg.getClass().toString() })); |
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} |
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else |
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{ |
215 |
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rgs.add(narg); |
216 |
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} |
217 |
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} |
218 |
0 |
return rgs; |
219 |
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} |
220 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
221 |
0 |
@Override... |
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public List<ArgumentI> getServiceParameters() |
223 |
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{ |
224 |
0 |
return getJwsArgsfromJaba(serviceOptions.getArguments()); |
225 |
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} |
226 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
227 |
0 |
@Override... |
228 |
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public boolean presetExists(String name) |
229 |
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{ |
230 |
0 |
return (editedParams.containsKey(name) |
231 |
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|| servicePresets.containsKey(name)); |
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} |
233 |
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| 0% |
Uncovered Elements: 14 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
234 |
0 |
@Override... |
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public void deletePreset(String name) |
236 |
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{ |
237 |
0 |
if (editedParams.containsKey(name)) |
238 |
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{ |
239 |
0 |
WsParamSetI parameterSet = editedParams.get(name); |
240 |
0 |
editedParams.remove(name); |
241 |
0 |
if (manager != null) |
242 |
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{ |
243 |
0 |
manager.deleteParameterSet(parameterSet); |
244 |
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} |
245 |
0 |
return; |
246 |
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} |
247 |
0 |
if (servicePresets.containsKey(name)) |
248 |
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{ |
249 |
0 |
throw new Error(MessageManager.getString( |
250 |
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"error.implementation_error_attempt_to_delete_service_preset")); |
251 |
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} |
252 |
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} |
253 |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
254 |
0 |
@Override... |
255 |
|
public void storePreset(String presetName, String text, |
256 |
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List<ArgumentI> jobParams) |
257 |
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{ |
258 |
0 |
JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams); |
259 |
0 |
jps.setApplicableUrls(new String[] { service.getUri() }); |
260 |
0 |
editedParams.put(jps.getName(), jps); |
261 |
0 |
if (manager != null) |
262 |
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{ |
263 |
0 |
manager.storeParameterSet(jps); |
264 |
|
} |
265 |
|
} |
266 |
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|
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| 0% |
Uncovered Elements: 20 (20) |
Complexity: 6 |
Complexity Density: 0.5 |
|
267 |
0 |
@Override... |
268 |
|
public void updatePreset(String oldName, String presetName, String text, |
269 |
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List<ArgumentI> jobParams) |
270 |
|
{ |
271 |
0 |
JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) |
272 |
|
? getPreset(oldName) |
273 |
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: getPreset(presetName)); |
274 |
0 |
if (jps == null) |
275 |
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{ |
276 |
0 |
throw new Error(MessageManager.formatMessage( |
277 |
|
"error.implementation_error_cannot_locate_oldname_presetname", |
278 |
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new String[] |
279 |
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{ oldName, presetName })); |
280 |
|
} |
281 |
0 |
jps.setName(presetName); |
282 |
0 |
jps.setDescription(text); |
283 |
0 |
jps.setArguments(jobParams); |
284 |
0 |
jps.setApplicableUrls(new String[] { service.getUri() }); |
285 |
0 |
if (oldName != null && !oldName.equals(jps.getName())) |
286 |
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{ |
287 |
0 |
editedParams.remove(oldName); |
288 |
|
} |
289 |
0 |
editedParams.put(jps.getName(), jps); |
290 |
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|
291 |
0 |
if (manager != null) |
292 |
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{ |
293 |
0 |
manager.storeParameterSet(jps); |
294 |
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} |
295 |
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} |
296 |
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|
297 |
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|
298 |
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|
299 |
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|
300 |
|
@return |
301 |
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|
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|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
302 |
0 |
WsParamSetI newWsParamSet()... |
303 |
|
{ |
304 |
0 |
return new JabaWsParamSet(); |
305 |
|
}; |
306 |
|
|
|
|
| 0% |
Uncovered Elements: 8 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
307 |
0 |
private boolean involves(String[] urls)... |
308 |
|
{ |
309 |
0 |
boolean found = false; |
310 |
0 |
for (String url : urls) |
311 |
|
{ |
312 |
0 |
if (service.getServiceTypeURI().equals(url) |
313 |
|
|| service.getUri().equalsIgnoreCase(url)) |
314 |
|
{ |
315 |
0 |
found = true; |
316 |
0 |
break; |
317 |
|
} |
318 |
|
} |
319 |
0 |
return found; |
320 |
|
} |
321 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
322 |
0 |
@Override... |
323 |
|
public WsParamSetI parseServiceParameterFile(String name, String descr, |
324 |
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String[] urls, String parameterfile) throws IOException |
325 |
|
{ |
326 |
0 |
if (!involves(urls)) |
327 |
|
{ |
328 |
0 |
throw new IOException(MessageManager.getString( |
329 |
|
"error.implementation_error_cannot_find_service_url_in_given_set")); |
330 |
|
|
331 |
|
} |
332 |
0 |
JabaWsParamSet wsp = new JabaWsParamSet(); |
333 |
0 |
wsp.setName(name); |
334 |
0 |
wsp.setDescription(descr); |
335 |
0 |
wsp.setApplicableUrls(urls.clone()); |
336 |
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|
337 |
0 |
List<String> lines = new ArrayList<String>(); |
338 |
0 |
StringTokenizer st = new StringTokenizer(parameterfile, "\n"); |
339 |
0 |
while (st.hasMoreTokens()) |
340 |
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{ |
341 |
0 |
lines.add(st.nextToken()); |
342 |
|
} |
343 |
0 |
wsp.setjabaArguments( |
344 |
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ParameterUtils.processParameters(lines, serviceOptions, " ")); |
345 |
0 |
return wsp; |
346 |
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} |
347 |
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|
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|
| 0% |
Uncovered Elements: 14 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
|
348 |
0 |
@Override... |
349 |
|
public String generateServiceParameterFile(WsParamSetI pset) |
350 |
|
throws IOException |
351 |
|
{ |
352 |
0 |
if (!involves(pset.getApplicableUrls())) |
353 |
|
{ |
354 |
0 |
throw new IOException(MessageManager.formatMessage( |
355 |
|
"error.implementation_error_cannot_find_service_url_in_given_set_param_store", |
356 |
|
new String[] |
357 |
|
{ service.getUri() })); |
358 |
|
} |
359 |
0 |
if (!(pset instanceof JabaWsParamSet)) |
360 |
|
{ |
361 |
0 |
throw new Error(MessageManager.getString( |
362 |
|
"error.implementation_error_jabaws_param_set_only_handled_by")); |
363 |
|
} |
364 |
|
|
365 |
0 |
StringBuffer rslt = new StringBuffer(); |
366 |
0 |
for (String ln : ParameterUtils.writeParameterSet( |
367 |
|
((JabaWsParamSet) pset).getjabaArguments(), " ")) |
368 |
|
{ |
369 |
0 |
rslt.append(ln); |
370 |
0 |
rslt.append("\n"); |
371 |
|
} |
372 |
0 |
; |
373 |
0 |
return rslt.toString(); |
374 |
|
} |
375 |
|
|
376 |
|
} |