X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestJobThread.java;h=0895f0fff90431425ed8ef8bfca7817b69fa20d4;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=ffbce621fcabafe90891ab8ca48591c7fbed8e9a;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java index ffbce62..0895f0f 100644 --- a/src/jalview/ws/rest/RestJobThread.java +++ b/src/jalview/ws/rest/RestJobThread.java @@ -1,29 +1,34 @@ -/******************************************************************************* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . - *******************************************************************************/ + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.rest; -import jalview.bin.Cache; +import java.util.Locale; + +import jalview.bin.Console; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.Annotation; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; @@ -33,6 +38,7 @@ import jalview.gui.WebserviceInfo; import jalview.io.NewickFile; import jalview.io.packed.JalviewDataset; import jalview.io.packed.JalviewDataset.AlignmentSet; +import jalview.util.MessageManager; import jalview.ws.AWSThread; import jalview.ws.AWsJob; @@ -40,11 +46,9 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.IOException; import java.util.ArrayList; -import java.util.Enumeration; import java.util.Hashtable; import java.util.List; import java.util.Map.Entry; -import java.util.Vector; import org.apache.axis.transport.http.HTTPConstants; import org.apache.http.Header; @@ -57,8 +61,6 @@ import org.apache.http.client.methods.HttpRequestBase; import org.apache.http.entity.mime.HttpMultipartMode; import org.apache.http.entity.mime.MultipartEntity; import org.apache.http.impl.client.DefaultHttpClient; -import org.apache.http.protocol.BasicHttpContext; -import org.apache.http.protocol.HttpContext; import org.apache.http.util.EntityUtils; public class RestJobThread extends AWSThread @@ -88,8 +90,8 @@ public class RestJobThread extends AWSThread { jobs = new RestJob[1]; jobs[0] = new RestJob(0, this, - restClient._input.getVisibleAlignment(restClient.service - .getGapCharacter()), + restClient._input.getVisibleAlignment( + restClient.service.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. @@ -99,15 +101,14 @@ public class RestJobThread extends AWSThread { int[] viscontig = restClient._input.getVisibleContigs(); AlignmentI[] viscontigals = restClient._input - .getVisibleContigAlignments(restClient.service - .getGapCharacter()); + .getVisibleContigAlignments( + restClient.service.getGapCharacter()); if (viscontigals != null && viscontigals.length > 0) { jobs = new RestJob[viscontigals.length]; for (int j = 0; j < jobs.length; j++) { - int[] visc = new int[] - { viscontig[j * 2], viscontig[j * 2 + 1] }; + int[] visc = new int[] { viscontig[j * 2], viscontig[j * 2 + 1] }; if (j != 0) { jobs[j] = new RestJob(j, this, viscontigals[j], visc); @@ -172,9 +173,13 @@ public class RestJobThread extends AWSThread private String getStage(Stage stg) { if (stg == Stage.SUBMIT) + { return "submitting "; + } if (stg == Stage.POLL) + { return "checking status of "; + } return (" being confused about "); } @@ -211,9 +216,6 @@ public class RestJobThread extends AWSThread protected void doHttpReq(Stage stg, RestJob rj, String postUrl) throws Exception { - StringBuffer respText = new StringBuffer(); - // con.setContentHandlerFactory(new - // jalview.ws.io.mime.HttpContentHandler()); HttpRequestBase request = null; String messages = ""; if (stg == Stage.SUBMIT) @@ -228,8 +230,8 @@ public class RestJobThread extends AWSThread { if (input.getValue().validFor(rj)) { - postentity.addPart(input.getKey(), input.getValue() - .formatForInput(rj)); + postentity.addPart(input.getKey(), + input.getValue().formatForInput(rj)); } else { @@ -248,7 +250,6 @@ public class RestJobThread extends AWSThread { DefaultHttpClient httpclient = new DefaultHttpClient(); - HttpContext localContext = new BasicHttpContext(); HttpResponse response = null; try { @@ -261,7 +262,7 @@ public class RestJobThread extends AWSThread + "
See Console output for details."; rj.setAllowedServerExceptions(0);// unrecoverable; rj.error = true; - Cache.log.fatal("Unexpected REST Job " + getStage(stg) + Console.fatal("Unexpected REST Job " + getStage(stg) + "exception for URL " + rj.rsd.postUrl); throw (he); } catch (IOException e) @@ -270,7 +271,7 @@ public class RestJobThread extends AWSThread + "Job.
Problematic url was " + request.getURI() + "
See Console output for details."; - Cache.log.warn("IO Exception for REST Job " + getStage(stg) + Console.warn("IO Exception for REST Job " + getStage(stg) + "exception for URL " + rj.rsd.postUrl); throw (e); @@ -279,52 +280,27 @@ public class RestJobThread extends AWSThread { case 200: rj.running = false; - Cache.log.debug("Processing result set."); + Console.debug("Processing result set."); processResultSet(rj, response, request); break; case 202: - rj.statMessage = "
Job submitted successfully. Results available at this URL:\n" - + "" - + rj.getJobId() - + "
"; - rj.running = true; + markJobAsRunning(rj); break; + case 201: + // Created - redirect may be present. Fallthrough to 302 case 302: - Header[] loc; - if (!rj.isSubmitted() - && (loc = response - .getHeaders(HTTPConstants.HEADER_LOCATION)) != null - && loc.length > 0) - { - if (loc.length > 1) - { - Cache.log - .warn("Ignoring additional " - + (loc.length - 1) - + " location(s) provided in response header ( next one is '" - + loc[1].getValue() + "' )"); - } - rj.setJobId(loc[0].getValue()); - rj.setSubmitted(true); - } + extractJobId(rj, response); completeStatus(rj, response); break; case 500: - // Failed. - rj.setSubmitted(true); - rj.setAllowedServerExceptions(0); - rj.setSubjobComplete(true); - rj.error = true; - rj.running = false; + markAsFailed(rj, response); completeStatus(rj, response, "" + getStage(stg) + "failed. Reason below:\n"); break; default: // Some other response. Probably need to pop up the content in a window. // TODO: deal with all other HTTP response codes from server. - Cache.log.warn("Unhandled response status when " + getStage(stg) + Console.warn("Unhandled response status when " + getStage(stg) + "for " + postUrl + ": " + response.getStatusLine()); rj.error = true; rj.setAllowedServerExceptions(0); @@ -332,26 +308,75 @@ public class RestJobThread extends AWSThread rj.setSubmitted(true); try { - completeStatus( - rj, - response, - "" - + getStage(stg) - + " resulted in an unexpected server response.
Url concerned was " - + request.getURI() - + "
Filtered response content below:
"); + completeStatus(rj, response, "" + getStage(stg) + + " resulted in an unexpected server response.
Url concerned was " + request.getURI() + + "
Filtered response content below:
"); } catch (IOException e) { - Cache.log.debug("IOException when consuming unhandled response", - e); + Console.debug("IOException when consuming unhandled response", e); } ; } } } + private void markAsFailed(RestJob rj, HttpResponse response) + { + // Failed. + rj.setSubmitted(true); + rj.setAllowedServerExceptions(0); + rj.setSubjobComplete(true); + rj.error = true; + rj.running = false; + } + + /** + * set the jobRunning flag and post a link to the physical result page encoded + * in rj.getJobId() + * + * @param rj + */ + private void markJobAsRunning(RestJob rj) + { + rj.statMessage = "
Job submitted successfully. Results available at this URL:\n" + + "" + + rj.getJobId() + + "
"; + rj.running = true; + } + + /** + * extract the job ID URL from the redirect page. Does nothing if job is + * already running. + * + * @param rj + * @param response + */ + private void extractJobId(RestJob rj, HttpResponse response) + { + Header[] loc; + if (!rj.isSubmitted()) + { + + // redirect URL - typical for IBIVU type jobs. + if ((loc = response.getHeaders(HTTPConstants.HEADER_LOCATION)) != null + && loc.length > 0) + { + if (loc.length > 1) + { + Console.warn("Ignoring additional " + + (loc.length - 1) + + " location(s) provided in response header ( next one is '" + + loc[1].getValue() + "' )"); + } + rj.setJobId(loc[0].getValue()); + rj.setSubmitted(true); + } + } + } /** * job has completed. Something valid should be available from con * @@ -407,7 +432,7 @@ public class RestJobThread extends AWSThread */ String f; StringBuffer content = new StringBuffer(f = EntityUtils.toString(en)); - f = f.toLowerCase(); + f = f.toLowerCase(Locale.ROOT); int body = f.indexOf(" -1) { @@ -451,7 +476,7 @@ public class RestJobThread extends AWSThread { job.setSubjobComplete(true); job.setAllowedServerExceptions(-1); - Cache.log.error("Exception when trying to start Rest Job.", ex); + Console.error("Exception when trying to start Rest Job.", ex); } } @@ -460,7 +485,7 @@ public class RestJobThread extends AWSThread { // crazy users will see this message // TODO: finish this! and remove the message below! - Cache.log.warn("Rest job result parser is currently INCOMPLETE!"); + Console.warn("Rest job result parser is currently INCOMPLETE!"); int validres = 0; for (RestJob rj : (RestJob[]) jobs) { @@ -469,31 +494,29 @@ public class RestJobThread extends AWSThread String ln = null; try { - Cache.log.debug("Parsing data for job " + rj.getJobId()); + Console.debug("Parsing data for job " + rj.getJobId()); rj.parseResultSet(); if (rj.hasResults()) { validres++; } - Cache.log.debug("Finished parsing data for job " + rj.getJobId()); + Console.debug("Finished parsing data for job " + rj.getJobId()); } catch (Error ex) { - Cache.log.warn("Failed to finish parsing data for job " - + rj.getJobId()); + Console.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()); + Console.warn( + "Failed to finish parsing data for job " + rj.getJobId()); ex.printStackTrace(); } finally { rj.error = true; rj.statMessage = "Error whilst parsing data for this job.
URL for job response is :" - + rj.resSet.getUrl() + + rj.resSet.getUrl() + "\">" + rj.resSet.getUrl() + "
"; } } @@ -608,7 +631,7 @@ public class RestJobThread extends AWSThread // total number of distinct alignment sets generated by job set. int numAlSets = 0, als = 0; List destAls = new ArrayList(); - List destColsel = new ArrayList(); + List destColsel = new ArrayList(); List> trees = new ArrayList>(); do @@ -714,7 +737,7 @@ public class RestJobThread extends AWSThread RestJob rj = (RestJob) jobs[nrj]; int contigs[] = input.getVisibleContigs(); AlignmentI destAl = null; - jalview.datamodel.ColumnSelection destCs = null; + jalview.datamodel.HiddenColumns destHCs = null; // Resolve destAl for this data. if (als == 0 && rj.isInputContextModified()) { @@ -730,10 +753,10 @@ public class RestJobThread extends AWSThread if (!restClient.isAlignmentModified() && merge) { destAl = restClient.av.getAlignment(); - destCs = restClient.av.getColumnSelection(); - resultDest - .add(restClient.isShowResultsInNewView() ? AddDataTo.newView - : AddDataTo.currentView); + destHCs = restClient.av.getAlignment().getHiddenColumns(); + resultDest.add(restClient.isShowResultsInNewView() + ? AddDataTo.newView + : AddDataTo.currentView); destPanels.add(restClient.recoverAlignPanelForView()); } else @@ -741,15 +764,15 @@ public class RestJobThread extends AWSThread newAlignment = true; // recreate the input alignment data Object[] idat = input - .getAlignmentAndColumnSelection(gapCharacter); + .getAlignmentAndHiddenColumns(gapCharacter); destAl = new Alignment((SequenceI[]) idat[0]); - destCs = (ColumnSelection) idat[1]; + destHCs = (HiddenColumns) idat[1]; resultDest.add(AddDataTo.newAlignment); // but do not add to the alignment panel list - since we need to // create a whole new alignFrame set. } destAls.add(destAl); - destColsel.add(destCs); + destColsel.add(destHCs); } } else @@ -762,13 +785,13 @@ public class RestJobThread extends AWSThread { // TODO: decide if multiple multiple alignments returned by // non-vseparable services are allowed. - Cache.log - .warn("dealing with multiple alignment products returned by non-vertically separable service."); + Console.warn( + "dealing with multiple alignment products returned by non-vertically separable service."); } // recover reference to last alignment created for this rest frame // ready for extension destAl = destAls.get(als); - destCs = destColsel.get(als); + destHCs = destColsel.get(als); } else { @@ -797,14 +820,16 @@ public class RestJobThread extends AWSThread newview = input.getUpdatedView(rseqs, orders, gapCharacter); } destAl = new Alignment((SequenceI[]) newview[0]); - destCs = (ColumnSelection) newview[1]; + destHCs = (HiddenColumns) newview[1]; newAlignment = true; // TODO create alignment from result data with propagated // references. destAls.add(destAl); - destColsel.add(destCs); + destColsel.add(destHCs); resultDest.add(AddDataTo.newAlignment); - throw new Error("Impl. Error! TODO: "); + throw new Error( + MessageManager.getString("error.implementation_error") + + "TODO: "); } } /** @@ -860,10 +885,8 @@ public class RestJobThread extends AWSThread // TODO: cope with recovering hidden sequences from // resultContext { - Vector sqs = sg.getSequences(null); - for (int sqsi = 0, iSize = sqs.size(); sqsi < iSize; sqsi++) + for (SequenceI oseq : sg.getSequences(null)) { - SequenceI oseq = (SequenceI) sqs.get(sqsi); SequenceI nseq = getNewSeq(oseq, rseqs[nrj], ordermap[nrj], destAl); if (nseq != null) @@ -876,8 +899,8 @@ public class RestJobThread extends AWSThread } else { - Cache.log - .warn("Couldn't resolve original sequence for new sequence."); + Console.warn( + "Couldn't resolve original sequence for new sequence."); } } if (sg.hasSeqrep()) @@ -899,8 +922,8 @@ public class RestJobThread extends AWSThread { // adjust boundaries of recovered group w.r.t. new group being // merged on to original alignment. - int start = sg.getStartRes() + contigs[ncnt], end = sg - .getEndRes() + contigs[ncnt]; + int start = sg.getStartRes() + contigs[ncnt], + end = sg.getEndRes() + contigs[ncnt]; if (start < exsg.getStartRes()) { exsg.setStartRes(start); @@ -954,8 +977,8 @@ public class RestJobThread extends AWSThread grass = groupNames.get(alan[nrj][an].groupRef.getName()); if (grass == null) { - Cache.log - .error("Couldn't relocate group referemce for group " + Console.error( + "Couldn't relocate group referemce for group " + alan[nrj][an].groupRef.getName()); } } @@ -981,7 +1004,8 @@ public class RestJobThread extends AWSThread visan.sequenceRef = sqass; visAlAn.add(visan); } - if (contigs[ncnt] + alan[nrj][an].annotations.length > visan.annotations.length) + if (contigs[ncnt] + + alan[nrj][an].annotations.length > visan.annotations.length) { // increase width of annotation row Annotation[] newannv = new Annotation[contigs[ncnt] @@ -1004,8 +1028,8 @@ public class RestJobThread extends AWSThread { // TODO: process each newick file, lifting over sequence refs to // current alignment, if necessary. - Cache.log - .error("Tree recovery from restjob not yet implemented."); + Console.error( + "Tree recovery from restjob not yet implemented."); } } } @@ -1041,10 +1065,12 @@ public class RestJobThread extends AWSThread for (AddDataTo action : resultDest) { AlignmentI destal; - ColumnSelection destcs; - String alTitle = restClient.service.details.Action + " using " - + restClient.service.details.Name + " on " - + restClient.viewTitle; + HiddenColumns destcs; + String alTitle = MessageManager + .formatMessage("label.webservice_job_title_on", new String[] + { restClient.service.details.getAction(), + restClient.service.details.getName(), + restClient.viewTitle }); switch (action) { case newAlignment: @@ -1052,8 +1078,8 @@ public class RestJobThread extends AWSThread destcs = destColsel.get(als); destaf = new AlignFrame(destal, destcs, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - PaintRefresher.Refresh(destaf, destaf.getViewport() - .getSequenceSetId()); + PaintRefresher.Refresh(destaf, + destaf.getViewport().getSequenceSetId()); // todo transfer any feature settings and colouring /* * destaf.getFeatureRenderer().transferSettings(this.featureSettings); @@ -1181,8 +1207,8 @@ public class RestJobThread extends AWSThread { if (start + width < end) { - blocks[c][s] = sequenceIs[s].getSubSequence(start, start - + width); + blocks[c][s] = sequenceIs[s].getSubSequence(start, + start + width); } else {