import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider;
import jalview.io.packed.JalviewDataset;
import jalview.ws.AWSThread;
import jalview.ws.AWsJob;
+import java.awt.Desktop;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;
jobs = new RestJob[1];
jobs[0] = new RestJob(0, this,
restClient._input.getVisibleAlignment(restClient.service
- .getGapCharacter()));
+ .getGapCharacter()),
+ restClient._input.getVisibleContigs());
// need a function to get a range on a view/alignment and return both
// annotation, groups and selection subsetted to just that region.
}
else
{
+ int[] viscontig = restClient._input.getVisibleContigs();
AlignmentI[] viscontigals = restClient._input
.getVisibleContigAlignments(restClient.service
.getGapCharacter());
jobs = new RestJob[viscontigals.length];
for (int j = 0; j < jobs.length; j++)
{
+ int[] visc = new int[]
+ { viscontig[j * 2], viscontig[j * 2 + 1] };
if (j != 0)
{
- jobs[j] = new RestJob(j, this, viscontigals[j]);
+ jobs[j] = new RestJob(j, this, viscontigals[j], visc);
}
else
{
- jobs[j] = new RestJob(0, this, viscontigals[j]);
+ jobs[j] = new RestJob(0, this, viscontigals[j], visc);
}
}
}
throws Exception
{
StringBuffer respText = new StringBuffer();
- // con.setContentHandlerFactory(new jalview.ws.io.mime.HttpContentHandler());
+ // con.setContentHandlerFactory(new
+ // jalview.ws.io.mime.HttpContentHandler());
HttpRequestBase request = null;
String messages = "";
if (stg == Stage.SUBMIT)
processResultSet(rj, response, request);
break;
case 202:
- rj.statMessage = "Job submitted successfully. Results available at this URL:\n"
- + rj.getJobId() + "\n";
+ rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
+ + "<a href="
+ + rj.getJobId()
+ + "\">"
+ + rj.getJobId()
+ + "</a><br>";
rj.running = true;
break;
case 302:
rj.setAllowedServerExceptions(0);
rj.setSubjobComplete(true);
rj.error = true;
+ rj.running = false;
completeStatus(rj, response, "" + getStage(stg)
+ "failed. Reason below:\n");
break;
}
HttpEntity en = con.getEntity();
/*
- * Just show the content as a string.
+ * Just append the content as a string.
*/
- rj.statMessage = EntityUtils.toString(en);
+ String f;
+ StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
+ f = f.toLowerCase();
+ int body = f.indexOf("<body");
+ if (body > -1)
+ {
+ content.delete(0, f.indexOf(">", body));
+ }
+ if (body > -1 && sb.length() > 0)
+ {
+ sb.append("\n");
+ content.insert(0, sb);
+ sb = null;
+ }
+ f = null;
+ rj.statMessage = content.toString();
}
@Override
public void parseResult()
{
// crazy users will see this message
- System.err.println("WARNING: Rest job result parser is INCOMPLETE!");
+ // TODO: finish this! and remove the message below!
+ Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
+ int validres = 0;
for (RestJob rj : (RestJob[]) jobs)
{
- // TODO: call each jobs processResults() method and collect valid
- // contexts.
if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid())
{
String ln = null;
- System.out.println("Parsing data for job " + rj.getJobId());
- if (!restClient.isAlignmentModified())
+ try
{
- try
- {
- /*
- * while ((ln=rj.resSet.nextLine())!=null) { System.out.println(ln);
- * } }
- */
- List<DataProvider> dp = new ArrayList<DataProvider>();
- restClient.af.newView_actionPerformed(null);
- dp.add(new SimpleDataProvider(JvDataType.ANNOTATION, rj.resSet, null));
- JalviewDataset context = new JalviewDataset(restClient.av.getAlignment().getDataset(), null, null,restClient.av.getAlignment());
- ParsePackedSet pps = new ParsePackedSet();
- pps.getAlignment(context, dp);
-
- // do an ap.refresh restClient.av.alignmentChanged(Desktop.getAlignmentPanels(restClient.av.getViewId())[0]);
- System.out.println("Finished parsing data for job "
- + rj.getJobId());
-
- } catch (Exception ex)
+ Cache.log.debug("Parsing data for job " + rj.getJobId());
+ rj.parseResultSet();
+ if (rj.hasResults())
{
- System.out.println("Failed to finish parsing data for job "
- + rj.getJobId());
- ex.printStackTrace();
+ validres++;
}
+ Cache.log.debug("Finished parsing data for job " + rj.getJobId());
+
+ } catch (Error ex)
+ {
+ Cache.log.warn("Failed to finish parsing data for job "
+ + rj.getJobId());
+ ex.printStackTrace();
+ } catch (Exception ex)
+ {
+ Cache.log.warn("Failed to finish parsing data for job "
+ + rj.getJobId());
+ ex.printStackTrace();
}
}
}
- /**
- * decisions based on job result content + state of alignFrame that
- * originated the job:
- */
- /*
- * 1. Can/Should this job automatically open a new window for results
- */
- wsInfo.setViewResultsImmediatly(false);
+ if (validres > 0)
+ {
+ // add listeners and activate result display gui elements
+ /**
+ * decisions based on job result content + state of alignFrame that
+ * originated the job:
+ */
+ /*
+ * 1. Can/Should this job automatically open a new window for results
+ */
+ if (true)
+ {
+ wsInfo.setViewResultsImmediatly(false);
+ }
+ else
+ {
+ // realiseResults(true, true);
+ }
+ // otherwise, should automatically view results
+
+ // TODO: check if at least one or more contexts are valid - if so, enable
+ // gui
+ wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ realiseResults(false);
+ }
+
+ });
+ wsInfo.mergeResults.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ realiseResults(true);
+ }
+
+ });
+
+ wsInfo.setResultsReady();
+ }
+ else
+ {
+ // tell the user nothing was returned.
+ }
+ }
+
+ public void realiseResults(boolean merge)
+ {
/*
* 2. Should the job modify the parent alignment frame/view(s) (if they
* still exist and the alignment hasn't been edited) in order to display new
* aligned to it ?
*
*/
- // TODO: check if at least one or more contexts are valid - if so, enable
- // gui
- wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
+ jalview.gui.AlignmentPanel destPanel = null;
+ if (merge)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ if (!restClient.isAlignmentModified())
{
- // TODO: call method to show results in new window
+ destPanel = restClient.recoverAlignPanelForView();
+ if (restClient.isShowResultsInNewView())
+ {
+ destPanel = destPanel.alignFrame.newView(false);
+ }
}
-
- });
- wsInfo.mergeResults.addActionListener(new ActionListener()
+ }
+ if (destPanel == null)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ Object[] idat = input.getAlignmentAndColumnSelection(restClient.av.getGapCharacter());
+ AlignFrame af = new AlignFrame((AlignmentI) idat[0],
+ (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ jalview.gui.Desktop.addInternalFrame(af,
+ "Results for " + restClient.service.details.Name + " "
+ + restClient.service.details.Action + " on "
+ + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ destPanel = af.alignPanel;
+ // create totally new alignment from stashed data/results
+ }
+ else
+ {
+ for (int j = 0; j < jobs.length; j++)
{
- // TODO: call method to merge results into existing window
+ RestJob rj = (RestJob) jobs[j];
+ if (rj.jvresultobj!=null && rj.jvresultobj.length>0) {
+ // transfer results onto panel
+
+ }
}
-
- });
-
- wsInfo.setResultsReady();
+ }
+ destPanel.adjustAnnotationHeight();
+
}
git://source.jalview.org / jalview.git / blobdiff