X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Frest%2FRestClient.java;h=18be1c1eec3678e15d52ec57729b113a8f619482;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=5a4cf615b9a0fd078bd629d30bed7a7bd7fee583;hpb=c762d9525db36ffd5d3fca49fb5e7d506d13401a;p=jalview.git
diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 5a4cf61..18be1c1 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -1,3 +1,20 @@
+/*******************************************************************************
+ * 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
+ *
+ * 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 .
+ *******************************************************************************/
/**
*
*/
@@ -5,6 +22,7 @@ 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;
@@ -14,14 +32,14 @@ import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-import com.sun.org.apache.bcel.internal.generic.ISHL;
-
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
+import jalview.io.packed.DataProvider.JvDataType;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
@@ -82,6 +100,7 @@ public class RestClient extends WSClient implements WSClientI,
{
wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
+ WebServiceReference);
+ wsInfo.setRenderAsHtml(true);
}
}
@@ -113,7 +132,8 @@ 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()
{
@@ -172,14 +192,19 @@ public class RestClient extends WSClient implements WSClientI,
*/
protected boolean isAlignmentModified()
{
- if (undoredo == null)
+ if (undoredo == null || av == null || av.getAlignment() == null)
{
+ // 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.
+ return true;
}
+ // TODO: look deeper into modification of selection state, etc that may
+ // affect RestJobThread.realiseResults(boolean merge);
return false;
}
@@ -194,10 +219,14 @@ public class RestClient extends WSClient implements WSClientI,
*/
jalview.io.packed.JalviewDataset jds;
+ /**
+ * informative name for results
+ */
+ public String viewTitle;
+
protected void constructJob()
{
service.setInvolvesFlags();
-
// record all aspects of alignment view so we can merge back or recreate
// later
undoredo = av.getUndoRedoHash();
@@ -208,55 +237,56 @@ public class RestClient extends WSClient implements WSClientI,
*/
boolean selExists = (av.getSelectionGroup() != null)
&& (av.getSelectionGroup().getSize() > 1);
- // TODO: 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);
+ _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);
}
- // TODO: verify that some kind of partition can be constructed from input
+ 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);
+ _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();
}
-
+
RestJobThread jobsthread = new RestJobThread(this);
-
+
if (jobsthread.isValid())
{
setWebserviceInfo(false);
@@ -266,33 +296,43 @@ public class RestClient extends WSClient implements WSClientI,
}
else
{
- JOptionPane.showMessageDialog(Desktop.desktop,
- "Unable to start web service analysis",
- "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
+ // 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);
}
}
public static RestClient makeShmmrRestClient()
{
- String action = "Analyse", description = "Sequence Harmony and Multi-Relief", name = "SHMR";
+ 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();
+ // 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("ali_file", aliinput);
+ 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
iparams.put("groups", sgroups);
sgroups.token = "groups";
sgroups.sep = " ";
@@ -300,9 +340,132 @@ 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);
return new RestClient(shmrService);
}
+ public AlignmentPanel recoverAlignPanelForView()
+ {
+ AlignmentPanel[] aps = Desktop
+ .getAlignmentPanels(av.getSequenceSetId());
+ for (AlignmentPanel alp : aps)
+ {
+ if (alp.av == av)
+ {
+ return alp;
+ }
+ }
+ return null;
+ }
+
+ public boolean isShowResultsInNewView()
+ {
+ // TODO make this a property of the service
+ return true;
+ }
+
+ protected static Vector services = null;
+
+ public static final String RSBS_SERVICES = "RSBS_SERVICES";
+
+ public static RestClient[] getRestClients()
+ {
+ if (services == null)
+ {
+ services = new Vector();
+ try
+ {
+ 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)
+ {
+ lst[i++] = new RestClient(new RestServiceDescription(svc));
+ }
+ return lst;
+ }
+
+ public static void main(String args[])
+ {
+ 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());
+ urls.add(cl.service.toString());
+ }
+ setRsbsServices(urls);
+ if (clients.length != getRestClients().length)
+ {
+ 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;
+ }
+
+ public RestServiceDescription getRestDescription()
+ {
+ return service;
+ }
+
+ public static Vector getRsbsDescriptions()
+ {
+ Vector rsbsDescrs = new Vector();
+ for (RestClient rsbs : getRestClients())
+ {
+ rsbsDescrs.add(rsbs.getRestDescription().toString());
+ }
+ return rsbsDescrs;
+ }
+
+ public static void setRsbsServices(Vector rsbsUrls)
+ {
+ if (rsbsUrls != null)
+ {
+ // TODO: consider validating services ?
+ services = new Vector(rsbsUrls);
+ StringBuffer sprop = new StringBuffer();
+ for (String s : services)
+ {
+ sprop.append(s);
+ }
+ Cache.setProperty(RSBS_SERVICES, sprop.toString());
+ }
+ else
+ {
+ Cache.removeProperty(RSBS_SERVICES);
+ }
+ }
+
}