From: Mateusz Warowny Date: Wed, 3 Feb 2021 18:48:32 +0000 (+0100) Subject: JAL-3809 - Fixed param edit dialog for jalviewjs. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=433801a3edef339c0d679eb87e07498ab1325457;p=jalview.git JAL-3809 - Fixed param edit dialog for jalviewjs. Edit settings dialog now works asynchronously. Annotation services still do not add annotations to the sequences. --- diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9d8407a..db6870e 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1141,16 +1141,18 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMBuild(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMBuild(this, args)).start(); } - new Thread(new HMMBuild(this, args)).start(); } @Override @@ -1172,16 +1174,18 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMAlign(this, args2)).start(); + } + }); + } + else + { + new Thread(new HMMAlign(this, args)).start(); } - new Thread(new HMMAlign(this, args)).start(); } @Override @@ -1203,17 +1207,20 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new HMMSearch(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new HMMSearch(this, args)).start(); + alignPanel.repaint(); } - new Thread(new HMMSearch(this, args)).start(); - alignPanel.repaint(); } @Override @@ -1232,18 +1239,20 @@ public class AlignFrame extends GAlignFrame { WsParamSetI set = new HMMERPreset(); WsJobParameters params = new WsJobParameters(store, set, args); - if (params.showRunDialog()) - { - args = params.getJobParams(); - } - else - { - return; // user cancelled - } + params.showRunDialog().thenAccept((startJob) -> { + if (startJob) + { + var args2 = params.getJobParams(); + new Thread(new JackHMMER(this, args2)).start(); + alignPanel.repaint(); + } + }); + } + else + { + new Thread(new JackHMMER(this, args)).start(); + alignPanel.repaint(); } - new Thread(new JackHMMER(this, args)).start(); - alignPanel.repaint(); - } /** diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java index 719b7d9..88819e4 100644 --- a/src/jalview/gui/WsJobParameters.java +++ b/src/jalview/gui/WsJobParameters.java @@ -48,14 +48,18 @@ import java.awt.event.ItemListener; import java.util.Hashtable; import java.util.List; import java.util.Vector; +import java.util.concurrent.CompletableFuture; +import java.util.concurrent.CompletionStage; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JDialog; +import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTextArea; +import javax.swing.WindowConstants; import javax.swing.border.TitledBorder; import javax.swing.event.DocumentEvent; import javax.swing.event.DocumentListener; @@ -93,6 +97,9 @@ public class WsJobParameters extends JPanel implements ItemListener, // TODO ABSRACT FROM JABAWS CLASSES + // completion stage representing whether start was clicked + private final CompletableFuture completionStage = new CompletableFuture<>(); + /** * manager for options and parameters. */ @@ -123,13 +130,22 @@ public class WsJobParameters extends JPanel implements ItemListener, JTextArea setDescr = new JTextArea(); JScrollPane paramPane = new JScrollPane(); + + JButton startjob = JvSwingUtils.makeButton( + MessageManager.getString("action.start_job"), + MessageManager.getString("label.start_job_current_settings"), + this::startjob_actionPerformed); + JButton canceljob = JvSwingUtils.makeButton( + MessageManager.getString("action.cancel_job"), + MessageManager.getString("label.cancel_job_close_dialog"), + this::canceljob_actionPerformed); ParamDatastoreI paramStore; // set true when 'Start Job' is clicked boolean startJob = false; - JDialog frame = null; + JFrame frame = null; UIinfo service; @@ -195,10 +211,10 @@ public class WsJobParameters extends JPanel implements ItemListener, * * @return */ - public boolean showRunDialog() + public CompletionStage showRunDialog() { - - frame = new JDialog(Desktop.getInstance(), true); + frame = new JFrame(); + frame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); if (service != null) { frame.setTitle(MessageManager.formatMessage("label.edit_params_for", @@ -228,9 +244,9 @@ public class WsJobParameters extends JPanel implements ItemListener, } }); + frame.setVisible(true); - - return startJob; + return completionStage; } private void jbInit() @@ -254,75 +270,21 @@ public class WsJobParameters extends JPanel implements ItemListener, updatepref = JvSwingUtils.makeButton( MessageManager.getString("action.update"), MessageManager.getString("label.update_user_parameter_set"), - new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - update_actionPerformed(); - } - }); + this::update_actionPerformed); deletepref = JvSwingUtils.makeButton( MessageManager.getString("action.delete"), MessageManager.getString("label.delete_user_parameter_set"), - new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - delete_actionPerformed(); - } - }); + this::delete_actionPerformed); createpref = JvSwingUtils.makeButton( MessageManager.getString("action.create"), MessageManager.getString("label.create_user_parameter_set"), - new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - create_actionPerformed(); - } - }); + this::create_actionPerformed); revertpref = JvSwingUtils.makeButton( MessageManager.getString("action.revert"), MessageManager .getString("label.revert_changes_user_parameter_set"), - new ActionListener() - { + this::revert_actionPerformed); - @Override - public void actionPerformed(ActionEvent e) - { - revert_actionPerformed(); - } - }); - - JButton startjob = JvSwingUtils.makeButton( - MessageManager.getString("action.start_job"), - MessageManager.getString("label.start_job_current_settings"), - new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - startjob_actionPerformed(); - } - }); - JButton canceljob = JvSwingUtils.makeButton( - MessageManager.getString("action.cancel_job"), - MessageManager.getString("label.cancel_job_close_dialog"), - new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - canceljob_actionPerformed(); - } - }); JPanel setDetails = new JPanel(); setDetails.setBorder( @@ -424,13 +386,13 @@ public class WsJobParameters extends JPanel implements ItemListener, validate(); } - protected void revert_actionPerformed() + protected void revert_actionPerformed(ActionEvent e) { reInitDialog(lastParmSet); updateWebServiceMenus(); } - protected void update_actionPerformed() + protected void update_actionPerformed(ActionEvent e) { if (isUserPreset) { @@ -448,7 +410,7 @@ public class WsJobParameters extends JPanel implements ItemListener, paramStore.deletePreset(lastParmSet2); } - protected void delete_actionPerformed() + protected void delete_actionPerformed(ActionEvent e) { if (isUserPreset) { @@ -459,7 +421,7 @@ public class WsJobParameters extends JPanel implements ItemListener, updateWebServiceMenus(); } - protected void create_actionPerformed() + protected void create_actionPerformed(ActionEvent e) { String curname = ((String) setName.getSelectedItem()).trim(); if (curname.length() > 0) @@ -478,22 +440,24 @@ public class WsJobParameters extends JPanel implements ItemListener, } } - protected void canceljob_actionPerformed() + protected void canceljob_actionPerformed(ActionEvent e) { startJob = false; if (frame != null) { frame.setVisible(false); } + completionStage.complete(false); } - protected void startjob_actionPerformed() + protected void startjob_actionPerformed(ActionEvent e) { startJob = true; if (frame != null) { frame.setVisible(false); } + completionStage.complete(true); } void initForService(WsParamSetI paramSet, List jobArgset) diff --git a/src/jalview/ws/WSClient.java b/src/jalview/ws/WSClient.java index 33aea90..a68f3f3 100755 --- a/src/jalview/ws/WSClient.java +++ b/src/jalview/ws/WSClient.java @@ -20,6 +20,7 @@ */ package jalview.ws; +import jalview.bin.Cache; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.WebserviceInfo; @@ -32,6 +33,8 @@ import jalview.ws.params.ParamDatastoreI; import jalview.ws.params.WsParamSetI; import java.util.List; +import java.util.concurrent.CompletableFuture; +import java.util.concurrent.CompletionStage; public abstract class WSClient // implements WSMenuEntryProviderI { @@ -116,7 +119,7 @@ public abstract class WSClient // implements WSMenuEntryProviderI * @param arguments */ public WSClient(AlignFrame _alignFrame, WsParamSetI preset, - List arguments) + List arguments) { alignFrame = _alignFrame; this.preset = preset; @@ -131,12 +134,12 @@ public abstract class WSClient // implements WSMenuEntryProviderI if (!b) { return new WebserviceInfo(WebServiceJobTitle, - WebServiceJobTitle + " using service hosted at " - + WsURL + "\n" - + (serv.getDescription() != null - ? serv.getDescription() - : ""), - false); + WebServiceJobTitle + " using service hosted at " + + WsURL + "\n" + + (serv.getDescription() != null + ? serv.getDescription() + : ""), + false); } return null; } @@ -148,15 +151,14 @@ public abstract class WSClient // implements WSMenuEntryProviderI * @param editParams * @return */ - protected boolean processParams(ServiceWithParameters sh, - boolean editParams) + protected CompletionStage processParams(ServiceWithParameters sh, + boolean editParams) { return processParams(sh, editParams, false); } - protected boolean processParams(ServiceWithParameters sh, - boolean editParams, - boolean adjustingExisting) + protected CompletionStage processParams(ServiceWithParameters sh, + boolean editParams, boolean adjustingExisting) { if (editParams) @@ -165,35 +167,38 @@ public abstract class WSClient // implements WSMenuEntryProviderI sh.initParamStore(Desktop.getUserParameterStore()); WsJobParameters jobParams = (preset == null && paramset != null - && paramset.size() > 0) - ? new WsJobParameters((ParamDatastoreI) null, sh, - (WsParamSetI) null, paramset) - : new WsJobParameters((ParamDatastoreI) null, sh, - preset, (List) null); + && paramset.size() > 0) + ? new WsJobParameters((ParamDatastoreI) null, sh, + (WsParamSetI) null, paramset) + : new WsJobParameters((ParamDatastoreI) null, sh, + preset, (List) null); if (adjustingExisting) { jobParams.setName(MessageManager - .getString("label.adjusting_parameters_for_calculation")); + .getString("label.adjusting_parameters_for_calculation")); } - if (!jobParams.showRunDialog()) - { - return false; // dialog cancelled - } - - WsParamSetI prset = jobParams.getPreset(); - if (prset == null) - { - paramset = jobParams.isServiceDefaults() ? null + var stage = jobParams.showRunDialog(); + return stage.thenApply((startJob) -> { + if (startJob) + { + WsParamSetI prset = jobParams.getPreset(); + if (prset == null) + { + paramset = jobParams.isServiceDefaults() ? null : jobParams.getJobParams(); - this.preset = null; - } - else - { - this.preset = prset; // ((JabaPreset) prset).p; - paramset = null; // no user supplied parameters. - } + this.preset = null; + } + else + { + this.preset = prset; // ((JabaPreset) prset).p; + paramset = null; // no user supplied parameters. + } + } + return startJob; + }); + } - return true; + return CompletableFuture.completedFuture(true); } } diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index e44381c..3123078 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -110,42 +110,41 @@ public class MsaWSClient extends Jws2Client implements WSMenuEntryProviderI AlignFrame _alignFrame) { super(_alignFrame, preset, arguments); - if (!processParams(sh, editParams)) - { - return; - } - - if (!(sh instanceof JalviewServiceEndpointProviderI - && ((JalviewServiceEndpointProviderI) sh) - .getEndpoint() instanceof MultipleSequenceAlignmentI)) - { - // redundant at mo - but may change - JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), - MessageManager.formatMessage( - "label.service_called_is_not_msa_service", - new String[] - { sh.getName() }), - MessageManager.getString("label.internal_jalview_error"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - serviceHandle = sh; - server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh) - .getEndpoint(); - if ((wsInfo = setWebService(sh, false)) == null) - { - JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager - .formatMessage("label.msa_service_is_unknown", new String[] - { sh.getName() }), - MessageManager.getString("label.internal_jalview_error"), - JvOptionPane.WARNING_MESSAGE); - - return; - } - - startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); - + processParams(sh, editParams).thenAccept((startJob) -> { + if (!startJob) + return; + + if (!(sh instanceof JalviewServiceEndpointProviderI + && ((JalviewServiceEndpointProviderI) sh) + .getEndpoint() instanceof MultipleSequenceAlignmentI)) + { + // redundant at mo - but may change + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + MessageManager.formatMessage( + "label.service_called_is_not_msa_service", + new String[] + { sh.getName() }), + MessageManager.getString("label.internal_jalview_error"), + JvOptionPane.WARNING_MESSAGE); + + return; + } + serviceHandle = sh; + server = (MultipleSequenceAlignmentI) ((JalviewServiceEndpointProviderI) sh) + .getEndpoint(); + if ((wsInfo = setWebService(sh, false)) == null) + { + JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager + .formatMessage("label.msa_service_is_unknown", new String[] + { sh.getName() }), + MessageManager.getString("label.internal_jalview_error"), + JvOptionPane.WARNING_MESSAGE); + + return; + } + + startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset); + }); } public MsaWSClient() diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 6939db4..838ea60 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -61,8 +61,8 @@ public class SequenceAnnotationWSClient extends Jws2Client // dan think. Do I need to change this method to run RNAalifold through the // GUI - public void initSequenceAnnotationWSClient(final ServiceWithParameters sh, - AlignFrame alignFrame, WsParamSetI preset, boolean editParams) + private void initSequenceAnnotationWSClient(final ServiceWithParameters sh, + AlignFrame alignFrame, final WsParamSetI preset, boolean editParams) { // dan changed! dan test. comment out if conditional // if (alignFrame.getViewport().getAlignment().isNucleotide()) @@ -82,74 +82,97 @@ public class SequenceAnnotationWSClient extends Jws2Client // columns List clnts = alignFrame.getViewport() - .getCalcManager() - .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class); + .getCalcManager() + .getWorkersOfClass(SeqAnnotationServiceCalcWorker.class); - SeqAnnotationServiceCalcWorker worker = null; + SeqAnnotationServiceCalcWorker tmpworker = null; if (clnts != null) { for (AlignCalcWorkerI _worker : clnts) { - worker = (SeqAnnotationServiceCalcWorker) _worker; - if (worker.hasService() - && worker.getService().getClass().equals(clientClass)) + tmpworker = (SeqAnnotationServiceCalcWorker) _worker; + if (tmpworker.hasService() + && tmpworker.getService().getClass().equals(clientClass)) { break; } - worker = null; + tmpworker = null; } } + final var worker = tmpworker; if (worker == null) { - if (!processParams(sh, editParams)) - { - return; - } - try - { - worker = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset, + processParams(sh, editParams).thenAccept((startJob) -> { + if (startJob) + { + final SeqAnnotationServiceCalcWorker worker_; + try + { + worker_ = new SeqAnnotationServiceCalcWorker(sh, alignFrame, this.preset, paramset); - } catch (Exception x) - { - x.printStackTrace(); - throw new Error( + } catch (Exception x) + { + x.printStackTrace(); + throw new Error( MessageManager.getString("error.implementation_error"), x); - } - alignFrame.getViewport().getCalcManager().registerWorker(worker); // also - // starts - // the - // worker + } + alignFrame.getViewport().getCalcManager().registerWorker(worker_); + // also starts the worker + startSeqAnnotationWorker(sh, alignFrame, preset, editParams); + } + }); } else { + WsParamSetI preset_; if (editParams) { paramset = worker.getArguments(); - preset = worker.getPreset(); + preset_ = worker.getPreset(); + } + else + { + preset_ = preset; } + processParams(sh, editParams, true).thenAccept((startJob) -> { + if (startJob) + { + // reinstate worker if it was blacklisted (might have happened due + // to + // invalid parameters) + alignFrame.getViewport().getCalcManager().enableWorker(worker); + worker.updateParameters(this.preset, paramset); + startSeqAnnotationWorker(sh, alignFrame, preset_, editParams); + } + }); - if (!processParams(sh, editParams, true)) + if (!processParams(sh, editParams, true).toCompletableFuture().join()) { return; } - // reinstate worker if it was blacklisted (might have happened due to - // invalid parameters) - alignFrame.getViewport().getCalcManager().enableWorker(worker); - worker.updateParameters(this.preset, paramset); } } + else + { + startSeqAnnotationWorker(sh, alignFrame, preset, editParams); + } + } + + private void startSeqAnnotationWorker(ServiceWithParameters sh, + AlignFrame alignFrame, WsParamSetI preset, boolean editParams) + { if (!sh.isInteractiveUpdate()) { // build IUPred style client. take sequences, returns annotation per // sequence. - if (!processParams(sh, editParams)) - { - return; - } - - alignFrame.getViewport().getCalcManager().startWorker( + processParams(sh, editParams).thenAccept((startJob) -> { + if (startJob) + { + alignFrame.getViewport().getCalcManager().startWorker( new SeqAnnotationServiceCalcWorker(sh, alignFrame, preset, paramset)); + } + }); } }