-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws;\r
-\r
-import javax.swing.*;\r
-\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;\r
-\r
-public abstract class WSThread extends Thread\r
-{\r
- /**\r
- * Generic properties for Web Service Client threads.\r
- */\r
- /**\r
- * view that this job was associated with\r
- */\r
- AlignmentI currentView = null;\r
-\r
- /**\r
- * feature settings from view that job was associated with\r
- */\r
- FeatureRendererSettings featureSettings = null;\r
-\r
- /**\r
- * metadata about this web service\r
- */\r
- WebserviceInfo wsInfo = null;\r
-\r
- /**\r
- * original input data for this job\r
- */\r
- AlignmentView input = null;\r
-\r
- /**\r
- * dataset sequence relationships to be propagated onto new results\r
- */\r
- AlignedCodonFrame[] codonframe = null;\r
-\r
- /**\r
- * are there jobs still running in this thread.\r
- */\r
- boolean jobComplete = false;\r
-\r
- abstract class WSJob\r
- {\r
- /**\r
- * Generic properties for an individual job within a Web Service Client\r
- * thread\r
- */\r
- int jobnum = 0; // WebServiceInfo pane for this job\r
-\r
- String jobId; // ws job ticket\r
-\r
- /**\r
- * has job been cancelled\r
- */\r
- boolean cancelled = false;\r
-\r
- /**\r
- * number of exceptions left before job dies\r
- */\r
- int allowedServerExceptions = 3;\r
-\r
- /**\r
- * has job been submitted\r
- */\r
- boolean submitted = false;\r
-\r
- /**\r
- * are all sub-jobs complete\r
- */\r
- boolean subjobComplete = false;\r
-\r
- /**\r
- * \r
- * @return true if job has completed and valid results are available\r
- */\r
- abstract boolean hasResults();\r
-\r
- /**\r
- * \r
- * @return boolean true if job can be submitted.\r
- */\r
- abstract boolean hasValidInput();\r
-\r
- /**\r
- * The last result object returned by the service.\r
- */\r
- vamsas.objects.simple.Result result;\r
- }\r
-\r
- class JobStateSummary\r
- {\r
- /**\r
- * number of jobs running\r
- */\r
- int running = 0;\r
-\r
- /**\r
- * number of jobs queued\r
- */\r
- int queuing = 0;\r
-\r
- /**\r
- * number of jobs finished\r
- */\r
- int finished = 0;\r
-\r
- /**\r
- * number of jobs failed\r
- */\r
- int error = 0;\r
-\r
- /**\r
- * number of jobs stopped due to server error\r
- */\r
- int serror = 0;\r
-\r
- /**\r
- * number of jobs cancelled\r
- */\r
- int cancelled = 0;\r
-\r
- /**\r
- * number of jobs finished with results\r
- */\r
- int results = 0;\r
-\r
- /**\r
- * processes WSJob and updates job status counters and WebService status\r
- * displays\r
- * \r
- * @param wsInfo\r
- * @param OutputHeader\r
- * @param j\r
- */\r
- void updateJobPanelState(WebserviceInfo wsInfo, String OutputHeader,\r
- WSJob j)\r
- {\r
- if (j.result != null)\r
- {\r
- String progheader = "";\r
- // Parse state of job[j]\r
- if (j.result.isRunning())\r
- {\r
- running++;\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);\r
- }\r
- else if (j.result.isQueued())\r
- {\r
- queuing++;\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);\r
- }\r
- else if (j.result.isFinished())\r
- {\r
- finished++;\r
- j.subjobComplete = true;\r
- if (j.hasResults())\r
- {\r
- results++;\r
- }\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else if (j.result.isFailed())\r
- {\r
- progheader += "Job failed.\n";\r
- j.subjobComplete = true;\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- error++;\r
- }\r
- else if (j.result.isServerError())\r
- {\r
- serror++;\r
- j.subjobComplete = true;\r
- wsInfo.setStatus(j.jobnum,\r
- WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- }\r
- else if (j.result.isBroken() || j.result.isFailed())\r
- {\r
- error++;\r
- j.subjobComplete = true;\r
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- // and pass on any sub-job messages to the user\r
- wsInfo.setProgressText(j.jobnum, OutputHeader);\r
- wsInfo.appendProgressText(j.jobnum, progheader);\r
- if (j.result.getStatus() != null)\r
- {\r
- wsInfo.appendProgressText(j.jobnum, j.result.getStatus());\r
- }\r
- }\r
- else\r
- {\r
- if (j.submitted && j.subjobComplete)\r
- {\r
- if (j.allowedServerExceptions == 0)\r
- {\r
- serror++;\r
- }\r
- else if (j.result == null)\r
- {\r
- error++;\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * one or more jobs being managed by this thread.\r
- */\r
- WSJob jobs[] = null;\r
-\r
- /**\r
- * full name of service\r
- */\r
- String WebServiceName = null;\r
-\r
- String OutputHeader;\r
-\r
- String WsUrl = null;\r
-\r
- /**\r
- * query web service for status of job. on return, job.result must not be null\r
- * - if it is then it will be assumed that the job status query timed out and\r
- * a server exception will be logged.\r
- * \r
- * @param job\r
- * @throws Exception\r
- * will be logged as a server exception for this job\r
- */\r
- abstract void pollJob(WSJob job) throws Exception;\r
-\r
- public void run()\r
- {\r
- JobStateSummary jstate = null;\r
- if (jobs == null)\r
- {\r
- jobComplete = true;\r
- }\r
- while (!jobComplete)\r
- {\r
- jstate = new JobStateSummary();\r
- for (int j = 0; j < jobs.length; j++)\r
- {\r
-\r
- if (!jobs[j].submitted && jobs[j].hasValidInput())\r
- {\r
- StartJob(jobs[j]);\r
- }\r
-\r
- if (jobs[j].submitted && !jobs[j].subjobComplete)\r
- {\r
- try\r
- {\r
- pollJob(jobs[j]);\r
- if (jobs[j].result == null)\r
- {\r
- throw (new Exception(\r
- "Timed out when communicating with server\nTry again later.\n"));\r
- }\r
- jalview.bin.Cache.log.debug("Job " + j + " Result state "\r
- + jobs[j].result.getState() + "(ServerError="\r
- + jobs[j].result.isServerError() + ")");\r
- } catch (Exception ex)\r
- {\r
- // Deal with Transaction exceptions\r
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName\r
- + " Server exception!\n" + ex.getMessage());\r
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum\r
- + ") Server exception: " + ex.getMessage());\r
-\r
- if (jobs[j].allowedServerExceptions > 0)\r
- {\r
- jobs[j].allowedServerExceptions--;\r
- Cache.log.debug("Sleeping after a server exception.");\r
- try\r
- {\r
- Thread.sleep(5000);\r
- } catch (InterruptedException ex1)\r
- {\r
- }\r
- }\r
- else\r
- {\r
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);\r
- jobs[j].subjobComplete = true;\r
- wsInfo.setStatus(jobs[j].jobnum,\r
- WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- }\r
- } catch (OutOfMemoryError er)\r
- {\r
- jobComplete = true;\r
- jobs[j].subjobComplete = true;\r
- jobs[j].result = null; // may contain out of date result object\r
- wsInfo.setStatus(jobs[j].jobnum,\r
- WebserviceInfo.STATE_STOPPED_ERROR);\r
- Cache.log.error("Out of memory when retrieving Job " + j\r
- + " id:" + WsUrl + "/" + jobs[j].jobId, er);\r
- new jalview.gui.OOMWarning("retrieving result for "\r
- + WebServiceName, er);\r
- System.gc();\r
- }\r
- }\r
- jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
- }\r
- // Decide on overall state based on collected jobs[] states\r
- if (jstate.running > 0)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
- }\r
- else if (jstate.queuing > 0)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
- }\r
- else\r
- {\r
- jobComplete = true;\r
- if (jstate.finished > 0)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
- }\r
- else if (jstate.error > 0)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
- }\r
- else if (jstate.serror > 0)\r
- {\r
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
- }\r
- }\r
- if (!jobComplete)\r
- {\r
- try\r
- {\r
- Thread.sleep(5000);\r
- } catch (InterruptedException e)\r
- {\r
- Cache.log\r
- .debug("Interrupted sleep waiting for next job poll.", e);\r
- }\r
- // System.out.println("I'm alive "+alTitle);\r
- }\r
- }\r
- if (jobComplete && jobs != null)\r
- {\r
- parseResult(); // tidy up and make results available to user\r
- }\r
- else\r
- {\r
- Cache.log\r
- .debug("WebServiceJob poll loop finished with no jobs created.");\r
- wsInfo.setFinishedNoResults();\r
- }\r
- }\r
-\r
- /**\r
- * submit job to web service\r
- * \r
- * @param job\r
- */\r
- abstract void StartJob(WSJob job);\r
-\r
- /**\r
- * process the set of WSJob objects into a set of results, and tidy up.\r
- */\r
- abstract void parseResult();\r
-\r
- /**\r
- * helper function to conserve dataset references to sequence objects returned\r
- * from web services 1. Propagates AlCodonFrame data from\r
- * <code>codonframe</code> to <code>al</code>\r
- * \r
- * @param al\r
- */\r
- protected void propagateDatasetMappings(Alignment al)\r
- {\r
- if (codonframe != null)\r
- {\r
- SequenceI[] alignment = al.getSequencesArray();\r
- for (int sq = 0; sq < alignment.length; sq++)\r
- {\r
- for (int i = 0; i < codonframe.length; i++)\r
- {\r
- if (codonframe[i] != null\r
- && codonframe[i].involvesSequence(alignment[sq]))\r
- {\r
- al.addCodonFrame(codonframe[i]);\r
- codonframe[i] = null;\r
- break;\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * @param alignFrame\r
- * reference for copying mappings across\r
- * @param wsInfo\r
- * gui attachment point\r
- * @param input\r
- * input data for the calculation\r
- * @param webServiceName\r
- * name of service\r
- * @param wsUrl\r
- * url of the service being invoked\r
- */\r
- public WSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,\r
- AlignmentView input, String webServiceName, String wsUrl)\r
- {\r
- this(alignFrame, wsinfo, input, wsUrl);\r
- WebServiceName = webServiceName;\r
- }\r
-\r
- char defGapChar = '-';\r
-\r
- /**\r
- * \r
- * @return gap character to use for any alignment generation\r
- */\r
- public char getGapChar()\r
- {\r
- return defGapChar;\r
- }\r
-\r
- /**\r
- * \r
- * @param alframe\r
- * - reference for copying mappings and display styles across\r
- * @param wsinfo2\r
- * - gui attachment point\r
- * @param alview\r
- * - input data for the calculation\r
- * @param wsurl2\r
- * - url of the service being invoked\r
- */\r
- public WSThread(AlignFrame alframe, WebserviceInfo wsinfo2,\r
- AlignmentView alview, String wsurl2)\r
- {\r
- super();\r
- // this.alignFrame = alframe;\r
- currentView = alframe.getCurrentView().getAlignment();\r
- featureSettings = alframe.getFeatureRenderer().getSettings();\r
- defGapChar = alframe.getViewport().getGapCharacter();\r
- this.wsInfo = wsinfo2;\r
- this.input = alview;\r
- WsUrl = wsurl2;\r
- if (alframe != null)\r
- {\r
- AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()\r
- .getCodonFrames();\r
- if (cf != null)\r
- {\r
- codonframe = new AlignedCodonFrame[cf.length];\r
- System.arraycopy(cf, 0, codonframe, 0, cf.length);\r
- }\r
- }\r
- }\r
-}\r
+package jalview.ws;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.WebserviceInfo;
+import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+
+public abstract class AWSThread extends Thread
+{
+
+ /**
+ * view that this job was associated with
+ */
+ protected AlignmentI currentView = null;
+ /**
+ * feature settings from view that job was associated with
+ */
+ protected FeatureRendererSettings featureSettings = null;
+ /**
+ * metadata about this web service
+ */
+ protected WebserviceInfo wsInfo = null;
+ /**
+ * original input data for this job
+ */
+ protected AlignmentView input = null;
+ /**
+ * dataset sequence relationships to be propagated onto new results
+ */
+ protected AlignedCodonFrame[] codonframe = null;
+ /**
+ * are there jobs still running in this thread.
+ */
+ protected boolean jobComplete = false;
+ /**
+ * one or more jobs being managed by this thread.
+ */
+ protected AWsJob jobs[] = null;
+ /**
+ * full name of service
+ */
+ protected String WebServiceName = null;
+ protected char defGapChar = '-';
+ /**
+ * header prepended to all output from job
+ */
+ protected String OutputHeader;
+
+ /**
+ * only used when reporting a web service out of memory error - the job ID will be concatenated to the URL
+ */
+ protected String WsUrl = null;
+
+ /**
+ * generic web service job/subjob poll loop
+ */
+ public void run()
+ {
+ JobStateSummary jstate = null;
+ if (jobs == null)
+ {
+ jobComplete = true;
+ }
+ while (!jobComplete)
+ {
+ jstate = new JobStateSummary();
+ for (int j = 0; j < jobs.length; j++)
+ {
+
+ if (!jobs[j].submitted && jobs[j].hasValidInput())
+ {
+ StartJob(jobs[j]);
+ }
+
+ if (jobs[j].submitted && !jobs[j].subjobComplete)
+ {
+ try
+ {
+ pollJob(jobs[j]);
+ if (!jobs[j].hasResponse())
+ {
+ throw (new Exception(
+ "Timed out when communicating with server\nTry again later.\n"));
+ }
+ jalview.bin.Cache.log.debug("Job " + j + " Result state "
+ + jobs[j].getState() + "(ServerError="
+ + jobs[j].isServerError() + ")");
+ } catch (Exception ex)
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug(ex);
+ }
+ // Deal with Transaction exceptions
+ wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
+ + " Server exception!\n" + ex.getMessage());
+ Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ + ") Server exception: " + ex.getMessage());
+
+ if (jobs[j].allowedServerExceptions > 0)
+ {
+ jobs[j].allowedServerExceptions--;
+ Cache.log.debug("Sleeping after a server exception.");
+ try
+ {
+ Thread.sleep(5000);
+ } catch (InterruptedException ex1)
+ {
+ }
+ }
+ else
+ {
+ Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ jobs[j].subjobComplete = true;
+ wsInfo.setStatus(jobs[j].jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ } catch (OutOfMemoryError er)
+ {
+ jobComplete = true;
+ jobs[j].subjobComplete = true;
+ jobs[j].clearResponse(); // may contain out of date result data
+ wsInfo.setStatus(jobs[j].jobnum,
+ WebserviceInfo.STATE_STOPPED_ERROR);
+ Cache.log.error("Out of memory when retrieving Job " + j
+ + " id:" + WsUrl + "/" + jobs[j].jobId, er);
+ new jalview.gui.OOMWarning("retrieving result for "
+ + WebServiceName, er);
+ System.gc();
+ }
+ }
+ jstate.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+ }
+ // Decide on overall state based on collected jobs[] states
+ if (jstate.running > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+ }
+ else if (jstate.queuing > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+ }
+ else
+ {
+ jobComplete = true;
+ if (jstate.finished > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (jstate.error > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ else if (jstate.serror > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ }
+ if (!jobComplete)
+ {
+ try
+ {
+ Thread.sleep(5000);
+ } catch (InterruptedException e)
+ {
+ Cache.log
+ .debug("Interrupted sleep waiting for next job poll.", e);
+ }
+ // System.out.println("I'm alive "+alTitle);
+ }
+ }
+ if (jobComplete && jobs != null)
+ {
+ parseResult(); // tidy up and make results available to user
+ }
+ else
+ {
+ Cache.log
+ .debug("WebServiceJob poll loop finished with no jobs created.");
+ wsInfo.setFinishedNoResults();
+ }
+ }
+
+
+ public AWSThread()
+ {
+ super();
+ }
+
+ public AWSThread(Runnable target)
+ {
+ super(target);
+ }
+
+ public AWSThread(String name)
+ {
+ super(name);
+ }
+
+ public AWSThread(ThreadGroup group, Runnable target)
+ {
+ super(group, target);
+ }
+
+ public AWSThread(ThreadGroup group, String name)
+ {
+ super(group, name);
+ }
+
+ public AWSThread(Runnable target, String name)
+ {
+ super(target, name);
+ }
+
+ public AWSThread(ThreadGroup group, Runnable target, String name)
+ {
+ super(group, target, name);
+ }
+
+ /**
+ * query web service for status of job. on return, job.result must not be null
+ * - if it is then it will be assumed that the job status query timed out and
+ * a server exception will be logged.
+ *
+ * @param job
+ * @throws Exception
+ * will be logged as a server exception for this job
+ */
+ public abstract void pollJob(AWsJob job) throws Exception;
+
+ /**
+ * submit job to web service
+ *
+ * @param job
+ */
+ public abstract void StartJob(AWsJob job);
+
+ /**
+ * process the set of AWsJob objects into a set of results, and tidy up.
+ */
+ public abstract void parseResult();
+
+ /**
+ * helper function to conserve dataset references to sequence objects returned
+ * from web services 1. Propagates AlCodonFrame data from
+ * <code>codonframe</code> to <code>al</code>
+ * TODO: refactor to datamodel
+ * @param al
+ */
+ public void propagateDatasetMappings(Alignment al)
+ {
+ if (codonframe != null)
+ {
+ SequenceI[] alignment = al.getSequencesArray();
+ for (int sq = 0; sq < alignment.length; sq++)
+ {
+ for (int i = 0; i < codonframe.length; i++)
+ {
+ if (codonframe[i] != null
+ && codonframe[i].involvesSequence(alignment[sq]))
+ {
+ al.addCodonFrame(codonframe[i]);
+ codonframe[i] = null;
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ public AWSThread(ThreadGroup group, Runnable target, String name,
+ long stackSize)
+ {
+ super(group, target, name, stackSize);
+ }
+
+ /**
+ *
+ * @return gap character to use for any alignment generation
+ */
+ public char getGapChar()
+ {
+ return defGapChar;
+ }
+
+ /**
+ *
+ * @param alignFrame
+ * reference for copying mappings across
+ * @param wsInfo
+ * gui attachment point
+ * @param input
+ * input data for the calculation
+ * @param webServiceName
+ * name of service
+ * @param wsUrl
+ * url of the service being invoked
+ */
+ public AWSThread(AlignFrame alignFrame, WebserviceInfo wsinfo,
+ AlignmentView input, String webServiceName, String wsUrl)
+ {
+ this(alignFrame, wsinfo, input, wsUrl);
+ WebServiceName = webServiceName;
+ }
+
+ /**
+ *
+ * @param alframe
+ * - reference for copying mappings and display styles across
+ * @param wsinfo2
+ * - gui attachment point
+ * @param alview
+ * - input data for the calculation
+ * @param wsurl2
+ * - url of the service being invoked
+ */
+ public AWSThread(AlignFrame alframe, WebserviceInfo wsinfo2,
+ AlignmentView alview, String wsurl2)
+ {
+ super();
+ // this.alignFrame = alframe;
+ currentView = alframe.getCurrentView().getAlignment();
+ featureSettings = alframe.getFeatureRenderer().getSettings();
+ defGapChar = alframe.getViewport().getGapCharacter();
+ this.wsInfo = wsinfo2;
+ this.input = alview;
+ WsUrl = wsurl2;
+ if (alframe != null)
+ {
+ AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ .getCodonFrames();
+ if (cf != null)
+ {
+ codonframe = new AlignedCodonFrame[cf.length];
+ System.arraycopy(cf, 0, codonframe, 0, cf.length);
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff