X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FWsParamSetManager.java;h=4c767146effb76e7aa57514e51113fb83ddcbcc2;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=a8265039e4c4e38b58c6f16f08bef0117b8460ea;hpb=7534e6f358b2bba0db179cb2f496bd2e5a4da43d;p=jalview.git diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java index a826503..4c76714 100644 --- a/src/jalview/gui/WsParamSetManager.java +++ b/src/jalview/gui/WsParamSetManager.java @@ -27,8 +27,11 @@ import jalview.util.MessageManager; import jalview.ws.params.ParamDatastoreI; import jalview.ws.params.ParamManager; import jalview.ws.params.WsParamSetI; +import jalview.xml.binding.jalview.ObjectFactory; +import jalview.xml.binding.jalview.WebServiceParameterSet; import java.io.File; +import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStreamReader; @@ -39,6 +42,12 @@ import java.util.Hashtable; import java.util.List; import java.util.StringTokenizer; +import javax.xml.bind.JAXBContext; +import javax.xml.bind.JAXBElement; +import javax.xml.bind.Marshaller; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLStreamReader; + /** * store and retrieve web service parameter sets. * @@ -47,7 +56,7 @@ import java.util.StringTokenizer; */ public class WsParamSetManager implements ParamManager { - Hashtable paramparsers = new Hashtable(); + Hashtable paramparsers = new Hashtable<>(); @Override public WsParamSetI[] getParameterSet(String name, String serviceUrl, @@ -60,7 +69,7 @@ public class WsParamSetManager implements ParamManager } StringTokenizer st = new StringTokenizer(files, "|"); String pfile = null; - ArrayList params = new ArrayList(); + List params = new ArrayList<>(); while (st.hasMoreTokens()) { pfile = st.nextToken(); @@ -97,7 +106,7 @@ public class WsParamSetManager implements ParamManager } } catch (IOException e) { - Cache.log.info("Failed to parse parameter file " + pfile + Cache.info("Failed to parse parameter file " + pfile + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)", e); } @@ -107,33 +116,39 @@ public class WsParamSetManager implements ParamManager private WsParamSetI[] parseParamFile(String filename) throws IOException { - List psets = new ArrayList(); + List psets = new ArrayList<>(); InputStreamReader is = new InputStreamReader( - new java.io.FileInputStream(new File(filename)), "UTF-8"); - - jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet(); + new FileInputStream(new File(filename)), "UTF-8"); - org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller( - wspset); - unmar.setWhitespacePreserve(true); + WebServiceParameterSet wspset = null; try { - wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar - .unmarshal(is); + JAXBContext jc = JAXBContext + .newInstance("jalview.xml.binding.jalview"); + javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); + XMLStreamReader streamReader = XMLInputFactory.newInstance() + .createXMLStreamReader(is); + JAXBElement jbe = um.unmarshal(streamReader, + WebServiceParameterSet.class); + wspset = jbe.getValue(); } catch (Exception ex) { throw new IOException(ex); } + if (wspset != null && wspset.getParameters().length() > 0) { - for (String url : wspset.getServiceURL()) + List urls = wspset.getServiceURL(); + final String[] urlArray = urls.toArray(new String[urls.size()]); + + for (String url : urls) { ParamDatastoreI parser = paramparsers.get(url); if (parser != null) { WsParamSetI pset = parser.parseServiceParameterFile( wspset.getName(), wspset.getDescription(), - wspset.getServiceURL(), wspset.getParameters()); + urlArray, wspset.getParameters()); if (pset != null) { pset.setSourceFile(filename); @@ -156,7 +171,7 @@ public class WsParamSetManager implements ParamManager { if (filename != null && !((outfile = new File(filename)).canWrite())) { - Cache.log.warn("Can't write to " + filename + Cache.warn("Can't write to " + filename + " - Prompting for new file to write to."); filename = null; } @@ -192,8 +207,7 @@ public class WsParamSetManager implements ParamManager if (value == JalviewFileChooser.APPROVE_OPTION) { outfile = chooser.getSelectedFile(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - outfile.getParent()); + Cache.setProperty("LAST_DIRECTORY", outfile.getParent()); filename = outfile.getAbsolutePath(); if (!filename.endsWith(".wsparams")) { @@ -204,7 +218,7 @@ public class WsParamSetManager implements ParamManager } if (outfile != null) { - String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", + String paramFiles = Cache.getDefault("WS_PARAM_FILES", filename); if (paramFiles.indexOf(filename) == -1) { @@ -214,13 +228,16 @@ public class WsParamSetManager implements ParamManager } paramFiles = paramFiles.concat(filename); } - jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles); + Cache.setProperty("WS_PARAM_FILES", paramFiles); - jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet(); + WebServiceParameterSet paramxml = new WebServiceParameterSet(); paramxml.setName(parameterSet.getName()); paramxml.setDescription(parameterSet.getDescription()); - paramxml.setServiceURL(parameterSet.getApplicableUrls().clone()); + for (String url : parameterSet.getApplicableUrls()) + { + paramxml.getServiceURL().add(url); + } paramxml.setVersion("1.0"); try { @@ -228,19 +245,24 @@ public class WsParamSetManager implements ParamManager parser.generateServiceParameterFile(parameterSet)); PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(outfile), "UTF-8")); - paramxml.marshal(out); + JAXBContext jaxbContext = JAXBContext + .newInstance(WebServiceParameterSet.class); + Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); + jaxbMarshaller.marshal( + new ObjectFactory().createWebServiceParameterSet(paramxml), + out); out.close(); parameterSet.setSourceFile(filename); } catch (Exception e) { - Cache.log.error("Couldn't write parameter file to " + outfile, e); + Cache.error("Couldn't write parameter file to " + outfile, e); } } } /* * - * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache + * JalviewFileChooser chooser = new JalviewFileChooser(Cache * .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] { * "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new * jalview.io.JalviewFileView()); @@ -250,8 +272,8 @@ public class WsParamSetManager implements ParamManager * int value = chooser.showOpenDialog(this); * * if (value == JalviewFileChooser.APPROVE_OPTION) { File choice = - * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", - * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault( + * chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY", + * choice.getParent()); String defaultColours = Cache.getDefault( * "USER_DEFINED_COLOURS", choice.getPath()); if * (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours = * defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc) @@ -268,7 +290,7 @@ public class WsParamSetManager implements ParamManager { return; } - String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", ""); + String paramFiles = Cache.getDefault("WS_PARAM_FILES", ""); if (paramFiles.indexOf(filename) > -1) { String nparamFiles = new String(); @@ -281,7 +303,7 @@ public class WsParamSetManager implements ParamManager nparamFiles = nparamFiles.concat("|").concat(fl); } } - jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles); + Cache.setProperty("WS_PARAM_FILES", nparamFiles); } try @@ -298,7 +320,7 @@ public class WsParamSetManager implements ParamManager } } catch (Exception e) { - Cache.log.error( + Cache.error( "Exception when trying to delete webservice user preset: ", e); }