import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.StringTokenizer;
import compbio.metadata.Argument;
import compbio.metadata.Option;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParamManager;
import jalview.ws.params.WsParamSetI;
public class JabaParamStore implements ParamDatastoreI
public JabaParamStore(Jws2Instance service)
{
- this.service = service;
- serviceOptions = service.getRunnerConfig();
- // TODO: discover all the user's locally sored presets for this service and populate the hash table
- // TODO: for JAL-632
+ this(service, null);
}
- /**
- * store the given parameters in the user parameter set database.
- *
- * @param storeSetName
- * - lastParmSet
- * @param descr
- * - setDescr.getText()
- * @param jobParams
- * - getJobParams()
- */
- private void _storeUserPreset(String storeSetName, String descr,
- List<Argument> jobParams)
- {
- // this is a simple hash store.
- editedParams.put(storeSetName, new JabaWsParamSet(storeSetName, descr,
- JabaParamStore.getJwsArgsfromJaba(jobParams)));
- // writeParam("Saving " + storeSetName + ": ", jobParams);
- }
+ ParamManager manager;
- private void writeParam(String nm, List<Argument> params)
+ public JabaParamStore(Jws2Instance service, ParamManager manager)
{
- for (Argument p : params)
+ this.service = service;
+ serviceOptions = service.getRunnerConfig();
+ this.manager = manager;
+ // discover all the user's locally stored presets for this service and
+ // populate the hash table
+ if (manager != null)
{
- System.out.println(nm + ":" + System.identityHashCode(p) + " Name: "
- + p.getName() + " Value: " + p.getDefaultValue());
+ manager.registerParser(service.getUri(), this);
+ WsParamSetI[] prams = manager.getParameterSet(null, service.getUri(),
+ true, false);
+ if (prams != null)
+ {
+ for (WsParamSetI paramset : prams)
+ {
+ if (paramset instanceof JabaWsParamSet)
+ {
+ editedParams.put(paramset.getName(), (JabaWsParamSet) paramset);
+ }
+ else
+ {
+ System.err
+ .println("Warning: Ignoring parameter set instance of type "
+ + paramset.getClass()
+ + " : Bound but not applicable for service at "
+ + service.getUri());
+ }
+ }
+ }
}
}
- private JabaWsParamSet _getUserPreset(String setName)
- {
- JabaWsParamSet pset = editedParams.get(setName);
- return pset;
- }
-
- /**
- * remove the given user preset from the preset stash
- *
- * @param setName
- */
- private void _deleteUserPreset(String setName)
- {
- editedParams.remove(setName);
- }
-
@Override
public List<WsParamSetI> getPresets()
{
{
if (editedParams.containsKey(name))
{
+ WsParamSetI parameterSet = editedParams.get(name);
editedParams.remove(name);
+ if (manager != null)
+ {
+ manager.deleteParameterSet(parameterSet);
+ }
return;
}
if (servicePresets.containsKey(name))
}
}
-
@Override
public void storePreset(String presetName, String text,
List<ArgumentI> jobParams)
{
JabaWsParamSet jps = new JabaWsParamSet(presetName, text, jobParams);
+ jps.setApplicableUrls(new String[]
+ { service.getUri() });
editedParams.put(jps.getName(), jps);
+ if (manager != null)
+ {
+ manager.storeParameterSet(jps);
+ }
}
@Override
- public boolean readParamSet(WsParamSetI wsp,
- Reader reader) throws IOException
+ public void updatePreset(String oldName, String presetName, String text,
+ List<ArgumentI> jobParams)
{
- if (!(wsp instanceof JabaWsParamSet))
+ JabaWsParamSet jps = (JabaWsParamSet) ((oldName != null) ? getPreset(oldName)
+ : getPreset(presetName));
+ if (jps == null)
{
- throw new Error("Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+ throw new Error("Implementation error: Can't locate either oldname ("
+ + oldName + ") or presetName (" + presetName
+ + "in the datastore!");
}
- List<String> lines=new ArrayList<String>();
- String line;
- BufferedReader br = new BufferedReader(reader);
- while ((line=br.readLine())!=null)
+ jps.setName(presetName);
+ jps.setDescription(text);
+ jps.setArguments(jobParams);
+ jps.setApplicableUrls(new String[]
+ { service.getUri() });
+ if (oldName != null && !oldName.equals(jps.getName()))
{
- lines.add(line);
+ editedParams.remove(oldName);
+ }
+ editedParams.put(jps.getName(), jps);
+
+ if (manager != null)
+ {
+ manager.storeParameterSet(jps);
}
- ((JabaWsParamSet) wsp).setjabaArguments(ParameterUtils.processParameters(lines, serviceOptions, " "));
- return true;
+ }
+
+ /**
+ * create a new, empty parameter set for this service
+ *
+ * @return
+ */
+ WsParamSetI newWsParamSet()
+ {
+ return new JabaWsParamSet();
+ };
+
+ private boolean involves(String[] urls)
+ {
+ boolean found = false;
+ for (String url : urls)
+ {
+ if (service.getUri().equalsIgnoreCase(url))
+ {
+ found = true;
+ break;
+ }
+ }
+ return found;
}
@Override
- public boolean writeParamSet(WsParamSetI wsp,
- Writer writer) throws IOException
+ public WsParamSetI parseServiceParameterFile(String name, String descr,
+ String[] urls, String parameterfile) throws IOException
{
- if (!(wsp instanceof JabaWsParamSet))
- {
- throw new Error("Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
- }
- writer.write(ParameterUtils.writeParameterSet(((JabaWsParamSet)wsp).getjabaArguments(), " ")
- .toString());
- return true;
+ if (!involves(urls))
+ {
+ throw new IOException(
+ "Implementation error: Cannot find service url in the given url set!");
+
+ }
+ JabaWsParamSet wsp = new JabaWsParamSet();
+ wsp.setName(name);
+ wsp.setDescription(descr);
+ wsp.setApplicableUrls(urls.clone());
+
+ List<String> lines = new ArrayList<String>();
+ StringTokenizer st = new StringTokenizer(parameterfile, "\n");
+ while (st.hasMoreTokens())
+ {
+ lines.add(st.nextToken());
+ }
+ wsp.setjabaArguments(ParameterUtils.processParameters(lines,
+ serviceOptions, " "));
+ return wsp;
+ }
+
+ @Override
+ public String generateServiceParameterFile(WsParamSetI pset)
+ throws IOException
+ {
+ if (!involves(pset.getApplicableUrls()))
+ {
+ throw new IOException(
+ "Implementation error: Cannot find service url in the given url set for this service parameter store ("
+ + service.getUri() + ") !");
+
+ }
+ if (!(pset instanceof JabaWsParamSet))
+ {
+ throw new Error(
+ "Implementation error: JabaWsParamSets can only be handled by JabaParamStore");
+ }
+
+ StringBuffer rslt = new StringBuffer();
+ for (String ln : ParameterUtils.writeParameterSet(
+ ((JabaWsParamSet) pset).getjabaArguments(), " "))
+ {
+ rslt.append(ln);
+ rslt.append("\n");
+ }
+ ;
+ return rslt.toString();
}
}
git://source.jalview.org / jalview.git / blobdiff