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package jalview.gui; |
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import jalview.bin.Cache; |
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import jalview.bin.Console; |
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import jalview.io.JalviewFileChooser; |
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import jalview.io.JalviewFileView; |
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import jalview.util.MessageManager; |
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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 jalview.xml.binding.jalview.ObjectFactory; |
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import jalview.xml.binding.jalview.WebServiceParameterSet; |
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import java.io.File; |
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import java.io.FileInputStream; |
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import java.io.FileOutputStream; |
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import java.io.IOException; |
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import java.io.InputStreamReader; |
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import java.io.OutputStreamWriter; |
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import java.io.PrintWriter; |
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import java.util.ArrayList; |
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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 javax.xml.bind.JAXBContext; |
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import javax.xml.bind.JAXBElement; |
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import javax.xml.bind.Marshaller; |
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import javax.xml.stream.XMLInputFactory; |
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import javax.xml.stream.XMLStreamReader; |
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@author |
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| 4.3% |
Uncovered Elements: 156 (163) |
Complexity: 37 |
Complexity Density: 0.33 |
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public class WsParamSetManager implements ParamManager |
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{ |
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Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>(); |
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| 12.1% |
Uncovered Elements: 29 (33) |
Complexity: 7 |
Complexity Density: 0.3 |
|
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@Override... |
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public WsParamSetI[] getParameterSet(String name, String serviceUrl, |
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boolean modifiable, boolean unmodifiable) |
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{ |
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String files = Cache.getProperty("WS_PARAM_FILES"); |
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if (files == null) |
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{ |
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return null; |
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} |
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StringTokenizer st = new StringTokenizer(files, "|"); |
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String pfile = null; |
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List<WsParamSetI> params = new ArrayList<>(); |
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while (st.hasMoreTokens()) |
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{ |
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pfile = st.nextToken(); |
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try |
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{ |
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WsParamSetI[] pset = parseParamFile(pfile); |
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for (WsParamSetI p : pset) |
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{ |
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boolean add = false; |
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if (serviceUrl != null) |
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{ |
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for (String url : p.getApplicableUrls()) |
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{ |
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if (url.equals(serviceUrl)) |
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{ |
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add = true; |
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} |
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} |
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} |
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else |
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{ |
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add = true; |
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} |
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add &= (modifiable == p.isModifiable() |
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|| unmodifiable == !p.isModifiable()); |
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add &= name == null || p.getName().equals(name); |
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if (add) |
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{ |
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params.add(p); |
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} |
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} |
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} catch (IOException e) |
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{ |
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Console.info("Failed to parse parameter file " + pfile |
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+ " (Check that all JALVIEW_WSPARAMFILES entries are valid!)", |
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e); |
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} |
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} |
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return params.toArray(new WsParamSetI[0]); |
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} |
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| 0% |
Uncovered Elements: 28 (28) |
Complexity: 6 |
Complexity Density: 0.27 |
|
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private WsParamSetI[] parseParamFile(String filename) throws IOException... |
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{ |
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List<WsParamSetI> psets = new ArrayList<>(); |
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InputStreamReader is = new InputStreamReader( |
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new FileInputStream(new File(filename)), "UTF-8"); |
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WebServiceParameterSet wspset = null; |
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try |
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{ |
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JAXBContext jc = JAXBContext |
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.newInstance("jalview.xml.binding.jalview"); |
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javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); |
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XMLStreamReader streamReader = XMLInputFactory.newInstance() |
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.createXMLStreamReader(is); |
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JAXBElement<WebServiceParameterSet> jbe = um.unmarshal(streamReader, |
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WebServiceParameterSet.class); |
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wspset = jbe.getValue(); |
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} catch (Exception ex) |
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{ |
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throw new IOException(ex); |
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} |
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if (wspset != null && wspset.getParameters().length() > 0) |
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{ |
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List<String> urls = wspset.getServiceURL(); |
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final String[] urlArray = urls.toArray(new String[urls.size()]); |
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for (String url : urls) |
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{ |
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ParamDatastoreI parser = paramparsers.get(url); |
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if (parser != null) |
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{ |
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WsParamSetI pset = parser.parseServiceParameterFile( |
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wspset.getName(), wspset.getDescription(), urlArray, |
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wspset.getParameters()); |
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if (pset != null) |
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{ |
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pset.setSourceFile(filename); |
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psets.add(pset); |
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break; |
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} |
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} |
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} |
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} |
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return psets.toArray(new WsParamSetI[0]); |
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} |
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| 0% |
Uncovered Elements: 66 (66) |
Complexity: 13 |
Complexity Density: 0.27 |
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@Override... |
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public void storeParameterSet(WsParamSetI parameterSet) |
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{ |
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String filename = parameterSet.getSourceFile(); |
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File outfile = null; |
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try |
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{ |
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if (filename != null && !((outfile = new File(filename)).canWrite())) |
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{ |
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Console.warn("Can't write to " + filename |
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+ " - Prompting for new file to write to."); |
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filename = null; |
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} |
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} catch (Exception e) |
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{ |
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filename = null; |
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} |
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ParamDatastoreI parser = null; |
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for (String urls : parameterSet.getApplicableUrls()) |
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{ |
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if (parser == null) |
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{ |
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parser = paramparsers.get(urls); |
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} |
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} |
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if (parser == null) |
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{ |
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throw new Error(MessageManager.getString( |
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"error.implementation_error_cannot_find_marshaller_for_param_set")); |
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} |
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if (filename == null) |
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{ |
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JalviewFileChooser chooser = new JalviewFileChooser("wsparams", |
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"Web Service Parameter File"); |
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chooser.setFileView(new JalviewFileView()); |
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chooser.setDialogTitle(MessageManager |
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.getString("label.choose_filename_for_param_file")); |
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chooser.setToolTipText(MessageManager.getString("action.save")); |
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int value = chooser.showSaveDialog(Desktop.instance); |
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if (value == JalviewFileChooser.APPROVE_OPTION) |
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{ |
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outfile = chooser.getSelectedFile(); |
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Cache.setProperty("LAST_DIRECTORY", outfile.getParent()); |
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filename = outfile.getAbsolutePath(); |
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if (!filename.endsWith(".wsparams")) |
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{ |
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filename = filename.concat(".wsparams"); |
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outfile = new File(filename); |
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} |
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} |
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} |
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if (outfile != null) |
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{ |
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String paramFiles = Cache.getDefault("WS_PARAM_FILES", filename); |
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if (paramFiles.indexOf(filename) == -1) |
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{ |
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if (paramFiles.length() > 0) |
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{ |
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paramFiles = paramFiles.concat("|"); |
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} |
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paramFiles = paramFiles.concat(filename); |
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} |
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Cache.setProperty("WS_PARAM_FILES", paramFiles); |
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WebServiceParameterSet paramxml = new WebServiceParameterSet(); |
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paramxml.setName(parameterSet.getName()); |
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paramxml.setDescription(parameterSet.getDescription()); |
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for (String url : parameterSet.getApplicableUrls()) |
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{ |
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paramxml.getServiceURL().add(url); |
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} |
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paramxml.setVersion("1.0"); |
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try |
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{ |
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paramxml.setParameters( |
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parser.generateServiceParameterFile(parameterSet)); |
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PrintWriter out = new PrintWriter(new OutputStreamWriter( |
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new FileOutputStream(outfile), "UTF-8")); |
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JAXBContext jaxbContext = JAXBContext |
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.newInstance(WebServiceParameterSet.class); |
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Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); |
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jaxbMarshaller.marshal( |
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new ObjectFactory().createWebServiceParameterSet(paramxml), |
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out); |
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out.close(); |
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parameterSet.setSourceFile(filename); |
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} catch (Exception e) |
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{ |
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Console.error("Couldn't write parameter file to " + outfile, e); |
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} |
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} |
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} |
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@see |
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| 0% |
Uncovered Elements: 30 (30) |
Complexity: 10 |
Complexity Density: 0.56 |
|
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0 |
@Override... |
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public void deleteParameterSet(WsParamSetI parameterSet) |
287 |
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{ |
288 |
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String filename = parameterSet.getSourceFile(); |
289 |
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if (filename == null || filename.trim().length() < 1) |
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{ |
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return; |
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} |
293 |
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String paramFiles = Cache.getDefault("WS_PARAM_FILES", ""); |
294 |
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if (paramFiles.indexOf(filename) > -1) |
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{ |
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String nparamFiles = new String(); |
297 |
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StringTokenizer st = new StringTokenizer(paramFiles, "|"); |
298 |
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while (st.hasMoreElements()) |
299 |
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{ |
300 |
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String fl = st.nextToken(); |
301 |
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if (!fl.equals(filename)) |
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{ |
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nparamFiles = nparamFiles.concat("|").concat(fl); |
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} |
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} |
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Cache.setProperty("WS_PARAM_FILES", nparamFiles); |
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} |
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try |
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{ |
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File pfile = new File(filename); |
312 |
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if (pfile.exists() && pfile.canWrite()) |
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{ |
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if (JvOptionPane.showConfirmDialog(Desktop.instance, |
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"Delete the preset's file, too ?", "Delete User Preset ?", |
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JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION) |
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{ |
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pfile.delete(); |
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} |
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} |
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} catch (Exception e) |
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{ |
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Console.error( |
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"Exception when trying to delete webservice user preset: ", |
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e); |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
329 |
681 |
@Override... |
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public void registerParser(String hosturl, ParamDatastoreI paramdataStore) |
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{ |
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paramparsers.put(hosturl, paramdataStore); |
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} |
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} |