From 2bf65e89ad86e9900a4891a0d0e9bb2cdd54cd5b Mon Sep 17 00:00:00 2001
From: Mateusz Warowny <mmzwarowny@dundee.ac.uk>
Date: Wed, 10 May 2023 11:23:01 +0200
Subject: [PATCH] JAL-3954 Implement job dispatcher service discoverer

---
 .../ws2/client/ebi/JobDispatcherWSDiscoverer.java  |  106 ++++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java

diff --git a/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java b/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java
new file mode 100644
index 0000000..11fbf2a
--- /dev/null
+++ b/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java
@@ -0,0 +1,106 @@
+package jalview.ws2.client.ebi;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.List;
+
+import jalview.bin.Console;
+import jalview.ws.params.ParamManager;
+import jalview.ws2.actions.NullAction;
+import jalview.ws2.actions.api.ActionI;
+import jalview.ws2.api.WebService;
+import jalview.ws2.client.api.AbstractWebServiceDiscoverer;
+import uk.ac.dundee.compbio.hmmerclient.PhmmerClient;
+
+public final class JobDispatcherWSDiscoverer extends AbstractWebServiceDiscoverer
+{
+
+  private static final URL DEFAULT_URL;
+  static
+  {
+    try
+    {
+      DEFAULT_URL = new URL("https://www.ebi.ac.uk/Tools/services/rest/hmmer3_phmmer/");
+    } catch (MalformedURLException e)
+    {
+      throw new ExceptionInInitializerError(e);
+    }
+  }
+  
+  private static JobDispatcherWSDiscoverer instance = null;
+  private static ParamManager paramManager = null;
+  
+  private JobDispatcherWSDiscoverer() {}
+  
+  public static JobDispatcherWSDiscoverer getInstance() {
+    if (instance == null)
+      instance = new JobDispatcherWSDiscoverer();
+    return instance;
+  }
+  
+  public static void setParamManager(ParamManager manager)
+  {
+    paramManager = manager;
+  }
+  
+  @Override
+  public int getStatusForUrl(URL url)
+  {
+    try
+    {
+      return new PhmmerClient(url).testEndpoint() ? STATUS_OK : STATUS_INVALID;
+    } catch (URISyntaxException e)
+    {
+      Console.error(e.getMessage());
+      return STATUS_INVALID;
+    } 
+  }
+
+  @Override
+  protected String getUrlsPropertyKey()
+  {
+    return null;
+  }
+
+  @Override
+  protected URL getDefaultUrl()
+  {
+    return DEFAULT_URL;
+  }
+
+  @Override
+  protected List<WebService<?>> fetchServices(URL url) throws IOException
+  {
+    PhmmerClient client;
+    try {
+      client = new PhmmerClient(url);
+    }
+    catch (URISyntaxException e) {
+      throw new MalformedURLException(e.getMessage());
+    }
+    if (!client.testEndpoint())
+      throw new IOException(
+              "unable to reach dispatcher server at " + url);
+    // TODO change once a concrete action is implemented
+    var wsBuilder = WebService.<NullAction> newBuilder();
+    wsBuilder.url(url);
+    wsBuilder.clientName("job dispatcher");
+    wsBuilder.category("Database search");
+    wsBuilder.name("pHMMER");
+    wsBuilder.description("Hmmer3 phmmer is used to search one or more query sequences against a sequence database.");
+    wsBuilder.interactive(false);
+    wsBuilder.paramDatastore(ParamStores.newPhmmerDatastore(url, paramManager));
+    wsBuilder.actionClass(NullAction.class);
+    var webService = wsBuilder.build(); 
+    
+    var actionBuilder = NullAction.newBuilder();
+    actionBuilder.webService(webService);
+    actionBuilder.name("");
+    webService.addAction(actionBuilder.build());
+    
+    return List.of(webService);
+  }
+
+}
-- 
1.7.10.2