JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API

[jalview.git] / src / jalview / fts / service / uniprot / UniprotFTSPanel.java

diff --git a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index 33ad8c4..0d9767c 100644 (file)
--- a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@ -21,6 +21,13 @@
 
 package jalview.fts.service.uniprot;
 
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.help.HelpSetException;
+
+import jalview.bin.Console;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestRequest;
@@ -31,12 +38,6 @@ import jalview.gui.Help.HelpId;
 import jalview.gui.SequenceFetcher;
 import jalview.util.MessageManager;
 
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-
-import javax.help.HelpSetException;
-
 @SuppressWarnings("serial")
 public class UniprotFTSPanel extends GFTSPanel
 {
@@ -69,10 +70,19 @@ public class UniprotFTSPanel extends GFTSPanel
   @Override
   public void searchAction(boolean isFreshSearch)
   {
+    searchAction(null, isFreshSearch);
+  }
+
+  public void searchAction(String cursor, boolean isFreshSearch)
+  {
     mainFrame.requestFocusInWindow();
     if (isFreshSearch)
     {
       offSet = 0;
+      UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+      c.clearCursors();
+      c.setCursorPage(0);
+      c.setCursor(0, "");
     }
     new Thread()
     {
@@ -97,12 +107,12 @@ public class UniprotFTSPanel extends GFTSPanel
           request.setSearchTerm(searchTerm);
           request.setOffSet(offSet);
           request.setWantedFields(wantedFields);
-          FTSRestClientI uniProtRestClient = UniProtFTSRestClient
+          UniProtFTSRestClient uniProtRestClient = UniProtFTSRestClient
                   .getInstance();
           FTSRestResponse resultList;
           try
           {
-            resultList = uniProtRestClient.executeRequest(request);
+            resultList = uniProtRestClient.executeRequest(request, cursor);
           } catch (Exception e)
           {
             setErrorMessage(e.getMessage());
@@ -268,4 +278,68 @@ public class UniprotFTSPanel extends GFTSPanel
       e1.printStackTrace();
     }
   }
+
+  /*
+   * 2022-07-20 bsoares
+   * The new Uniprot API has a strange pagination process described at
+   * https://www.uniprot.org/help/pagination
+   * When a successful request returns results, with more results past the size
+   * limit, the response sends a "Link" header with a URL containing the a "cursor"
+   * parameter with an opaque string that refers to the next page of results.
+   * These are store as nextCursor in the UniProtFTSRestClient along with the currCursor.
+   * When navigation across pages occurs these should be swapped around.
+   */
+  @Override
+  public void refreshPaginatorState()
+  {
+    UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+    setNextPageButtonEnabled(c.getNextCursor() != null);
+    setPrevPageButtonEnabled(c.getPrevCursor() != null);
+  }
+
+  @Override
+  public void prevPageAction()
+  {
+    updatePaginatorCart();
+    UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+    String prevCursor = c.getPrevCursor();
+    if (prevCursor != null)
+    {
+      if (offSet >= pageLimit)
+      {
+        offSet -= pageLimit;
+      }
+      else
+      {
+        // not sure what's happening if we get here though it wouldn't surprise
+        // me
+        Console.warn(
+                "UniprotFTSPanel: prevCursor exists but offset < pageLimit. This probably shouldn't be happening.");
+      }
+      c.setPrevCursorPage();
+      searchAction(prevCursor, false);
+    }
+    else
+    {
+      refreshPaginatorState();
+    }
+  }
+
+  @Override
+  public void nextPageAction()
+  {
+    UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+    String nextCursor = c.getNextCursor();
+    if (nextCursor != null)
+    {
+      offSet += pageLimit;
+      c.setNextCursorPage();
+      searchAction(nextCursor, false);
+    }
+    else
+    {
+      refreshPaginatorState();
+    }
+  }
+
 }