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.io.packed.JalviewDataset.AlignmentSet;
import jalview.io.packed.ParsePackedSet;
import jalview.io.packed.SimpleDataProvider;
import jalview.io.packed.DataProvider.JvDataType;
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;
public RestJobThread(RestClient restClient)
{
- super();
+ super(restClient.af, null, restClient._input,
+ restClient.service.postUrl);
this.restClient = restClient; // may not be needed
// Test Code
// minimal job - submit given input and parse result onto alignment as
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
* annotation/features.
*/
/**
- * alignments. New alignments are added to dataset, and subsequently
- * annotated/visualised accordingly. 1. New alignment frame created for new
- * alignment. Decide if any vis settings should be inherited from old
- * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
- * alignment as below:
+ * alignment panels derived from each alignment set returned by service.
*/
+ ArrayList<jalview.gui.AlignmentPanel> destPanels = new ArrayList<jalview.gui.AlignmentPanel>();
/**
- * annotation update to original/newly created context alignment: 1.
- * identify alignment where annotation is to be loaded onto. 2. Add
- * annotation, excluding any duplicates. 3. Ensure annotation is visible on
- * alignment - honouring ordering given by file.
+ * current pane being worked with
*/
+ jalview.gui.AlignmentPanel destPanel;
/**
- * features updated to original or newly created context alignment: 1.
- * Features are(or were already) added to dataset. 2. Feature settings
- * modified to ensure all features are displayed - honouring any ordering
- * given by result file. Consider merging action with the code used by the
- * DAS fetcher to update alignment views with new info.
+ * when false, zeroth pane is panel derived from input deta.
*/
- /**
- * Seq associated data files (PDB files). 1. locate seq association in
- * current dataset/alignment context and add file as normal - keep handle of
- * any created ref objects. 2. decide if new data should be displayed : PDB
- * display: if alignment has PDB display already, should new pdb files be
- * aligned to it ?
- *
- */
- // TODO: check if at least one or more contexts are valid - if so, enable
- // gui
- wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
+ boolean newAlignment = false;
+ 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);
+ }
+ // add the destination panel to frame zero of result panel set
+ destPanels.add(destPanel);
}
-
- });
- wsInfo.mergeResults.addActionListener(new ActionListener()
+ }
+ if (destPanels.size()==0)
{
-
- @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
+ newAlignment = true;
+ }
+ // Now process results, adding/creating new views as necessary.
+ {
+ boolean hsepjobs = restClient.service.isHseparable();
+ boolean vsepjobs = restClient.service.isVseparable();
+ // total number of distinct alignment sets generated by job set.
+ int totalSets = 0, numAlSets = 0;
+ for (int j = 0; j < jobs.length; j++)
{
- // TODO: call method to merge results into existing window
- }
+ RestJob rj = (RestJob) jobs[j];
+ if (rj.hasResults())
+ {
+ JalviewDataset rset = rj.context;
+ numAlSets = rset.hasAlignments() ? 0 : rset.getAl().size();
+ if (numAlSets > 0)
+ {
+ for (int als = 0; als < numAlSets; als++)
+ {
+ // gather data from context
+ if (vsepjobs)
+ {
+ // todo: merge data from each group/sequence onto whole
+ // alignment
+ }
+ else
+ {
+ if (hsepjobs)
+ {
+ // map single result back on to all visible region of original alignment
+ if (als==0 && rj.isInputContextModified())
+ {
+ // transfer features, annotation, groups, etc, from input context to align panel derived from input data
+ new jalview.datamodel.Alignment(new jalview.datamodel.SequenceI[] {null}).getAlignmentAnnotation();
+ }
+
+ }
+ else
+ {
+ // map result onto visible contigs.
+ AlignmentSet alset = rset.getAl().get(als);
+ if (als>0 )
+ if (als == 0)
+ {
+
+ // alignment is added straight to
+ }
+ }
+ }
+ }
+ }
+ }
+ // transfer results onto panel
- });
+ }
+ /**
+ * alignments. New alignments are added to dataset, and subsequently
+ * annotated/visualised accordingly. 1. New alignment frame created for
+ * new alignment. Decide if any vis settings should be inherited from old
+ * alignment frame (e.g. sequence ordering ?). 2. Subsequent data added to
+ * alignment as below:
+ */
+ /**
+ * annotation update to original/newly created context alignment: 1.
+ * identify alignment where annotation is to be loaded onto. 2. Add
+ * annotation, excluding any duplicates. 3. Ensure annotation is visible
+ * on alignment - honouring ordering given by file.
+ */
+ /**
+ * features updated to original or newly created context alignment: 1.
+ * Features are(or were already) added to dataset. 2. Feature settings
+ * modified to ensure all features are displayed - honouring any ordering
+ * given by result file. Consider merging action with the code used by the
+ * DAS fetcher to update alignment views with new info.
+ */
+ /**
+ * Seq associated data files (PDB files). 1. locate seq association in
+ * current dataset/alignment context and add file as normal - keep handle
+ * of any created ref objects. 2. decide if new data should be displayed :
+ * PDB display: if alignment has PDB display already, should new pdb files
+ * be aligned to it ?
+ *
+ */
- wsInfo.setResultsReady();
+ }
+ // destPanel.adjustAnnotationHeight();
}
git://source.jalview.org / jalview.git / blobdiff