package jalview.ws.rest;
import jalview.bin.Cache;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
* @author JimP
*
*/
-public class RestClient extends WSClient implements WSClientI,
- WSMenuEntryProviderI
+public class RestClient extends WSClient
+ implements WSClientI, WSMenuEntryProviderI, ApplicationSingletonI
{
- RestServiceDescription service;
+ public static final String RSBS_SERVICES = "RSBS_SERVICES";
- public RestClient(RestServiceDescription rsd)
- {
- service = rsd;
- }
+ RestServiceDescription service;
/**
* parent alignframe for this job
*/
AlignViewport av;
+ boolean headless = false;
+
+ protected Vector<String> services = null;
+
+ private static RestClient getInstance()
+ {
+ return (RestClient) ApplicationSingletonProvider.getInstance(RestClient.class);
+ }
+
+ public static RestClient makeShmmrRestClient()
+ {
+ String action = "Analysis",
+ description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)",
+ name = MessageManager.getString("label.multiharmony");
+ Hashtable<String, InputType> 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);
+
+ 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(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 = " ";
+ RestServiceDescription shmrService = new RestServiceDescription(action,
+ description, name,
+ "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 static RestClient[] getRestClients()
+ {
+ RestClient c = getInstance();
+
+ if (c.services == null)
+ {
+ c.services = new Vector<>();
+ try
+ {
+ for (RestServiceDescription descr : RestServiceDescription
+ .parseDescriptions(
+ jalview.bin.Cache.getDefault(RSBS_SERVICES,
+ makeShmmrRestClient().service.toString())))
+ {
+ c.services.add(descr.toString());
+ }
+ } catch (Exception ex)
+ {
+ System.err.println(
+ "Serious - RSBS descriptions in user preferences are corrupt!");
+ ex.printStackTrace();
+ }
+
+ }
+ RestClient[] lst = new RestClient[c.services.size()];
+ int i = 0;
+ for (String svc : c.services)
+ {
+ lst[i++] = new RestClient(new RestServiceDescription(svc));
+ }
+ return lst;
+ }
+
+ public static Vector<String> getRsbsDescriptions()
+ {
+ Vector<String> rsbsDescrs = new Vector<>();
+ for (RestClient rsbs : getRestClients())
+ {
+ rsbsDescrs.add(rsbs.getRestDescription().toString());
+ }
+ return rsbsDescrs;
+ }
+
+ public static void setRsbsServices(Vector<String> rsbsUrls)
+ {
+ if (rsbsUrls != null)
+ {
+ // TODO: consider validating services ?
+ RestClient c = getInstance();
+ c.services = new Vector<>(rsbsUrls);
+ StringBuffer sprop = new StringBuffer();
+ for (String s : c.services)
+ {
+ sprop.append(s);
+ }
+ Cache.setProperty(RSBS_SERVICES, sprop.toString());
+ }
+ else
+ {
+ Cache.removeProperty(RSBS_SERVICES);
+ }
+ }
+
/**
* get the alignFrame for the associated input data if it exists.
*
return jalview.gui.Desktop.getAlignFrameFor(av);
}
+ private RestClient()
+ {
+
+ }
+
+ public RestClient(RestServiceDescription rsd)
+ {
+ service = rsd;
+ }
+
public RestClient(RestServiceDescription service2, AlignFrame alignFrame)
{
this(service2, alignFrame, false);
}
- boolean headless = false;
-
public RestClient(RestServiceDescription service2, AlignFrame alignFrame,
boolean nogui)
{
public void setWebserviceInfo(boolean headless)
{
- WebServiceJobTitle = MessageManager.formatMessage("label.webservice_job_title", new String[]{service.details.Action,service.details.Name});
+ WebServiceJobTitle = MessageManager
+ .formatMessage("label.webservice_job_title", new String[]
+ { service.details.Action, service.details.Name });
WebServiceName = service.details.Name;
WebServiceReference = "No reference - go to url for more info";
if (service.details.description != null)
}
if (!headless)
{
- wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
- + WebServiceReference, true);
+ wsInfo = new WebserviceInfo(WebServiceJobTitle,
+ WebServiceName + "\n" + WebServiceReference, true);
wsInfo.setRenderAsHtml(true);
}
final AlignFrame alignFrame)
{
JMenuItem submit = new JMenuItem(service.details.Name);
- submit.setToolTipText(MessageManager.formatMessage("label.rest_client_submit", new String[]{service.details.Action,service.details.Name}));
+ submit.setToolTipText(MessageManager
+ .formatMessage("label.rest_client_submit", new String[]
+ { service.details.Action, service.details.Name }));
submit.addActionListener(new ActionListener()
{
{
// intersect groups with selected region
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
- viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true,
+ true);
+ viewTitle = MessageManager.formatMessage(
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
+ af.getTitle() });
}
else
{
// use selected region to partition alignment
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), false, true);
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), false,
+ true);
}
- viewTitle = MessageManager.formatMessage("label.select_unselect_visible_regions_from", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ viewTitle = MessageManager.formatMessage(
+ "label.select_unselect_visible_regions_from", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
+ af.getTitle() });
}
else
{
// just take selected region intersection
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), av.getSelectionGroup(),
- av.hasHiddenColumns(), true, true);
- viewTitle = MessageManager.formatMessage("label.select_visible_region_of", new String[]{(av.hasHiddenColumns() ? MessageManager.getString("label.visible") : ""),af.getTitle()});
+ av.getAlignment().getHiddenColumns(),
+ av.getSelectionGroup(), av.hasHiddenColumns(), true, true);
+ viewTitle = MessageManager.formatMessage(
+ "label.select_visible_region_of", new String[]
+ { (av.hasHiddenColumns()
+ ? MessageManager.getString("label.visible")
+ : ""),
+ af.getTitle() });
}
}
else
{
// standard alignment view without selection present
_input = new AlignmentView(av.getAlignment(),
- av.getColumnSelection(), null, av.hasHiddenColumns(), false,
- true);
- viewTitle = "" + (av.hasHiddenColumns() ? (new StringBuffer(" ").append(MessageManager.getString("label.visible_region_of")).toString()) : "")
+ av.getAlignment().getHiddenColumns(), null,
+ av.hasHiddenColumns(), false, true);
+ viewTitle = ""
+ + (av.hasHiddenColumns()
+ ? (new StringBuffer(" ")
+ .append(MessageManager
+ .getString("label.visible_region_of"))
+ .toString())
+ : "")
+ af.getTitle();
}
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
- (jobsthread.hasWarnings() ? jobsthread.getWarnings()
- : MessageManager.getString("label.job_couldnt_be_started_check_input")),
- MessageManager.getString("label.unable_start_web_service_analysis"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ (jobsthread.hasWarnings() ? jobsthread.getWarnings()
+ : MessageManager.getString(
+ "label.job_couldnt_be_started_check_input")),
+ MessageManager
+ .getString("label.unable_start_web_service_analysis"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager.getString("label.multiharmony");
- Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
- 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);
-
- 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(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 = " ";
- RestServiceDescription shmrService = new RestServiceDescription(
- action,
- description,
- name,
- "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
return true;
}
- protected static Vector<String> services = null;
-
- public static final String RSBS_SERVICES = "RSBS_SERVICES";
-
- public static RestClient[] getRestClients()
- {
- if (services == null)
- {
- services = new Vector<String>();
- 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<String> urls = new Vector<String>();
- 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;
return service;
}
- public static Vector<String> getRsbsDescriptions()
- {
- Vector<String> rsbsDescrs = new Vector<String>();
- for (RestClient rsbs : getRestClients())
- {
- rsbsDescrs.add(rsbs.getRestDescription().toString());
- }
- return rsbsDescrs;
- }
-
- public static void setRsbsServices(Vector<String> rsbsUrls)
- {
- if (rsbsUrls != null)
- {
- // TODO: consider validating services ?
- services = new Vector<String>(rsbsUrls);
- StringBuffer sprop = new StringBuffer();
- for (String s : services)
- {
- sprop.append(s);
- }
- Cache.setProperty(RSBS_SERVICES, sprop.toString());
- }
- else
- {
- Cache.removeProperty(RSBS_SERVICES);
- }
- }
-
}
git://source.jalview.org / jalview.git / blobdiff