X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestClient.java;h=195081ba69f8f114ef567861bfee7ff5a44c6d03;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=e618c3f42ea4ac7de5baf80a83c4bcf7bbfa899d;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java index e618c3f..195081b 100644 --- a/src/jalview/ws/rest/RestClient.java +++ b/src/jalview/ws/rest/RestClient.java @@ -1,28 +1,25 @@ -/******************************************************************************* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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. - * + * * 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 java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.Collection; import java.util.Hashtable; import java.util.Vector; @@ -80,9 +77,15 @@ public class RestClient extends WSClient implements WSClientI, public RestClient(RestServiceDescription service2, AlignFrame alignFrame) { + this(service2, alignFrame, false); + } + boolean headless = false; + public RestClient(RestServiceDescription service2, AlignFrame alignFrame, boolean nogui) + { service = service2; af = alignFrame; av = alignFrame.getViewport(); + headless = nogui; constructJob(); } @@ -132,7 +135,8 @@ public class RestClient extends WSClient implements WSClientI, final AlignFrame alignFrame) { JMenuItem submit = new JMenuItem(service.details.Name); - submit.setToolTipText(service.details.Action+" using "+service.details.Name); + submit.setToolTipText(service.details.Action + " using " + + service.details.Name); submit.addActionListener(new ActionListener() { @@ -191,17 +195,19 @@ public class RestClient extends WSClient implements WSClientI, */ protected boolean isAlignmentModified() { - if (undoredo == null || av==null || av.getAlignment()==null) + if (undoredo == null || av == null || av.getAlignment() == null) { - // always return modified if we don't have access to live GUI elements anymore. + // always return modified if we don't have access to live GUI elements + // anymore. return true; } if (av.isUndoRedoHashModified(undoredo)) { - // alignment has been modified in some way. + // alignment has been modified in some way. return true; } - // TODO: look deeper into modification of selection state, etc that may affect RestJobThread.realiseResults(boolean merge); + // TODO: look deeper into modification of selection state, etc that may + // affect RestJobThread.realiseResults(boolean merge); return false; } @@ -220,7 +226,6 @@ public class RestClient extends WSClient implements WSClientI, * informative name for results */ public String viewTitle; - protected void constructJob() { service.setInvolvesFlags(); @@ -234,99 +239,104 @@ public class RestClient extends WSClient implements WSClientI, */ boolean selExists = (av.getSelectionGroup() != null) && (av.getSelectionGroup().getSize() > 1); - // TODO: JAL-715: refactor to alignViewport methods and revise to full focus+context+dataset input data staging model + // TODO: JAL-715: refactor to alignViewport methods and revise to full + // focus+context+dataset input data staging model if (selExists) { if (service.partitiondata) { - if (av.getAlignment().getGroups()!=null && av.getAlignment().getGroups().size() > 0) + if (av.getAlignment().getGroups() != null + && av.getAlignment().getGroups().size() > 0) { // intersect groups with selected region - _input = new AlignmentView(av.getAlignment(), - av.getColumnSelection(), - av.getSelectionGroup(), - av.hasHiddenColumns(), - true, - true); - viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle(); + _input = new AlignmentView(av.getAlignment(), + av.getColumnSelection(), av.getSelectionGroup(), + av.hasHiddenColumns(), true, true); + viewTitle = "selected " + + (av.hasHiddenColumns() ? "visible" : "") + + " region of " + af.getTitle(); } else { // use selected region to partition alignment - _input = new AlignmentView(av.getAlignment(), - av.getColumnSelection(), - av.getSelectionGroup(), - av.hasHiddenColumns(), - false, - true); + _input = new AlignmentView(av.getAlignment(), + av.getColumnSelection(), av.getSelectionGroup(), + av.hasHiddenColumns(), false, true); } - viewTitle = "select and unselected "+(av.hasHiddenColumns() ? "visible" : "") + " regions from "+af.getTitle(); + viewTitle = "select and unselected " + + (av.hasHiddenColumns() ? "visible" : "") + + " regions from " + af.getTitle(); } else { // just take selected region intersection - _input = new AlignmentView(av.getAlignment(), - av.getColumnSelection(), - av.getSelectionGroup(), - av.hasHiddenColumns(), - true, - true); - viewTitle = "selected "+(av.hasHiddenColumns() ? "visible" : "") + " region of "+af.getTitle(); + _input = new AlignmentView(av.getAlignment(), + av.getColumnSelection(), av.getSelectionGroup(), + av.hasHiddenColumns(), true, true); + viewTitle = "selected " + (av.hasHiddenColumns() ? "visible" : "") + + " region of " + af.getTitle(); } - } else { + } + else + { // standard alignment view without selection present - _input = new AlignmentView(av.getAlignment(), - av.getColumnSelection(), - null, - av.hasHiddenColumns(), - false, + _input = new AlignmentView(av.getAlignment(), + av.getColumnSelection(), null, av.hasHiddenColumns(), false, true); - viewTitle = ""+(av.hasHiddenColumns() ? "visible region of " : "") + af.getTitle(); + viewTitle = "" + (av.hasHiddenColumns() ? "visible region of " : "") + + af.getTitle(); } - + RestJobThread jobsthread = new RestJobThread(this); - + if (jobsthread.isValid()) { - setWebserviceInfo(false); - wsInfo.setthisService(this); - jobsthread.setWebServiceInfo(wsInfo); + setWebserviceInfo(headless); + if (!headless) { + wsInfo.setthisService(this); + jobsthread.setWebServiceInfo(wsInfo); + } jobsthread.start(); } else { // TODO: try to tell the user why the job couldn't be started. - JOptionPane.showMessageDialog(Desktop.desktop, - (jobsthread.hasWarnings() ? jobsthread.getWarnings() : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."), - "Unable to start web service analysis", JOptionPane.WARNING_MESSAGE); + JOptionPane + .showMessageDialog( + Desktop.desktop, + (jobsthread.hasWarnings() ? jobsthread.getWarnings() + : "The Job couldn't be started. Please check your input, and the Jalview console for any warning messages."), + "Unable to start web service analysis", + JOptionPane.WARNING_MESSAGE); } } public static RestClient makeShmmrRestClient() { - String action = "Analysis", description = "Sequence Harmony and Multi-Relief (UNSTABLE!)", name = "Sequence Harmony"; + String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony"; Hashtable iparams = new Hashtable(); jalview.ws.rest.params.JobConstant toolp; - //toolp = new jalview.ws.rest.JobConstant("tool","jalview"); - //iparams.put(toolp.token, toolp); - toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr"); - iparams.put(toolp.token, toolp); - toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1"); - iparams.put(toolp.token, toolp); - toolp = new jalview.ws.rest.params.JobConstant("start_search","1"); - iparams.put(toolp.token, toolp); - toolp = new jalview.ws.rest.params.JobConstant("blast","0"); - iparams.put(toolp.token, toolp); - + // toolp = new jalview.ws.rest.JobConstant("tool","jalview"); + // iparams.put(toolp.token, toolp); + // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr"); + // iparams.put(toolp.token, toolp); + // toolp = new + // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1"); + // iparams.put(toolp.token, toolp); + // toolp = new jalview.ws.rest.params.JobConstant("start_search","1"); + // iparams.put(toolp.token, toolp); + // toolp = new jalview.ws.rest.params.JobConstant("blast","0"); + // iparams.put(toolp.token, toolp); + jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment(); - aliinput.token = "ali";//_file"; - aliinput.writeAsFile=false;//true; - //aliinput.token = "ali_file"; - //aliinput.writeAsFile=true; + // SHMR server has a 65K limit for content pasted into the 'ali' parameter, + // so we always upload our files. + aliinput.token = "ali_file"; + aliinput.writeAsFile = true; iparams.put(aliinput.token, aliinput); jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector(); sgroups.setMinsize(2); - sgroups.min=2;// need at least two group defined to make a partition + sgroups.min = 2;// need at least two group defined to make a partition iparams.put("groups", sgroups); sgroups.token = "groups"; sgroups.sep = " "; @@ -334,7 +344,7 @@ public class RestClient extends WSClient implements WSClientI, action, description, name, - "http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1", + "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1", "?tool=jalview", iparams, true, false, '-'); // a priori knowledge of the data returned from the service shmrService.addResultDatatype(JvDataType.ANNOTATION); @@ -343,8 +353,9 @@ public class RestClient extends WSClient implements WSClientI, public AlignmentPanel recoverAlignPanelForView() { - AlignmentPanel[] aps = Desktop.getAlignmentPanels(av.getSequenceSetId()); - for (AlignmentPanel alp:aps) + AlignmentPanel[] aps = Desktop + .getAlignmentPanels(av.getSequenceSetId()); + for (AlignmentPanel alp : aps) { if (alp.av == av) { @@ -360,55 +371,68 @@ public class RestClient extends WSClient implements WSClientI, return true; } - protected static Vector services=null; - public static final String RSBS_SERVICES="RSBS_SERVICES"; + protected static Vector services = null; + + public static final String RSBS_SERVICES = "RSBS_SERVICES"; + public static RestClient[] getRestClients() { - if (services==null) + if (services == null) { services = new Vector(); - try { - for (RestServiceDescription descr: RestServiceDescription.parseDescriptions(jalview.bin.Cache.getDefault(RSBS_SERVICES,makeShmmrRestClient().service.toString()))) + try { - services.add(descr.toString()); - } - } - catch (Exception ex) { - System.err.println("Serious - RSBS descriptions in user preferences are corrupt!"); + for (RestServiceDescription descr : RestServiceDescription + .parseDescriptions(jalview.bin.Cache.getDefault( + RSBS_SERVICES, + makeShmmrRestClient().service.toString()))) + { + services.add(descr.toString()); + } + } catch (Exception ex) + { + System.err + .println("Serious - RSBS descriptions in user preferences are corrupt!"); ex.printStackTrace(); } - + } RestClient[] lst = new RestClient[services.size()]; - int i=0; - for (String svc:services) { + int i = 0; + for (String svc : services) + { lst[i++] = new RestClient(new RestServiceDescription(svc)); } return lst; } + public static void main(String args[]) { - try { + try + { RestClient[] clients = getRestClients(); - System.out.println("Got "+clients.length+" clients."); - int i=0; - Vector urls=new Vector(); - for (RestClient cl:clients) { - System.out.println(""+(++i)+": "+cl.service.toString()); + System.out.println("Got " + clients.length + " clients."); + int i = 0; + Vector urls = new Vector(); + for (RestClient cl : clients) + { + System.out.println("" + (++i) + ": " + cl.service.toString()); urls.add(cl.service.toString()); } setRsbsServices(urls); - if (clients.length!=getRestClients().length) + if (clients.length != getRestClients().length) { - System.err.println("Failed. Differing numbers of clients when stringified and parsed again."); + System.err + .println("Failed. Differing numbers of clients when stringified and parsed again."); } - + } catch (Throwable x) { System.err.println("Failed. Unexpected exception."); x.printStackTrace(); } } + public String getAction() { return service.details.Action; @@ -422,7 +446,7 @@ public class RestClient extends WSClient implements WSClientI, public static Vector getRsbsDescriptions() { Vector rsbsDescrs = new Vector(); - for (RestClient rsbs:getRestClients()) + for (RestClient rsbs : getRestClients()) { rsbsDescrs.add(rsbs.getRestDescription().toString()); } @@ -431,17 +455,17 @@ public class RestClient extends WSClient implements WSClientI, public static void setRsbsServices(Vector rsbsUrls) { - if (rsbsUrls!=null) + if (rsbsUrls != null) { // TODO: consider validating services ? services = new Vector(rsbsUrls); StringBuffer sprop = new StringBuffer(); - for (String s:services) + for (String s : services) { sprop.append(s); } Cache.setProperty(RSBS_SERVICES, sprop.toString()); - } + } else { Cache.removeProperty(RSBS_SERVICES);