JAL-3829 proof in principle 3d-beacons sequence fetcher - still some TODOs !

diff --git a/resources/fts/tdbeacons_data_columns.txt b/resources/fts/tdbeacons_data_columns.txt
index 4eb9b98..5cd9f0d 100644 (file)
--- a/resources/fts/tdbeacons_data_columns.txt
+++ b/resources/fts/tdbeacons_data_columns.txt
@@ -24,11 +24,12 @@ tdbeacons_data_columns
 _group.id
 _group.name
 _group.sort_order
-g1;Miscellaneous;2
-g2;Name;1
-g3;Quality;3
+g1;ModelInfo;1
+g2;Quality;2
+g3;Miscellaneous;3
+
 #
-_data_column.primary_key;model_identifier
+_data_column.primary_key;model_url
 _data_column.default_response_page_size;100
 #
 _data_column.name
@@ -40,18 +41,18 @@ _data_column.max_col_width
 _data_column.preferred_col_width
 _data_column.is_shown_by_default
 _data_column.is_searchable
-Model id;model_identifier;String;g2;80;150;85;true;false
-Sequence;aligned_sequence;String;g1;80;150;85;false;false
+Model id;model_identifier;String;g3;80;150;85;true;false
+Sequence;aligned_sequence;String;g3;80;150;85;false;false
 Provider;provider;String;g1;80;150;85;true;false
-Uniprot Id;id;String;g2;80;150;85;false;false
-UniProt Accession;uniprot_accession;String;g2;50;400;95;false;true
-Entry Name;entry_name;String;g2;100;150;105;true;false 
-Url;model_url;String;g1;100;150;105;false;false
+Model Category;model_category;String;g1;80;150;85;true;false
+Uniprot Id;id;String;g1;80;150;85;false;false
+Uniprot Start;uniprot_start;Integer;g1;80;150;85;true;false
+Uniprot End;uniprot_end;Integer;g1;80;150;85;true;false
+Resolution;resolution;double;g2;80;150;85;true;false
 Qmean;qmean_avg_local_score;double;g2;100;150;105;true;false
-Uniprot Start;uniprot_start;Integer;g3;3;8;3;true;false
-Uniprot End;uniprot_end;Integer;g3;3;8;3;true;false
-Resolution;resolution;double;g3;3;8;3;true;false
-Coverage;coverage;double;g3;3;8;3;true;false
-Sequence Identity;sequence_identity;Float;g3;3;8;3;false;false
-Model Category;model_category;String;g3;3;8;3;true;false
-Created Date;created;string;g3;3;8;3;true;false
\ No newline at end of file
+Coverage;coverage;double;g2;80;150;85;true;false
+Sequence Identity;sequence_identity;Float;g2;80;150;85;false;false
+Created Date;created;string;g3;80;150;85;true;false
+UniProt Accession;uniprot_accession;String;g1;50;400;95;false;true
+Entry Name;entry_name;String;g3;100;150;105;true;false 
+Url;model_url;String;g3;100;150;105;true;false

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
index c368e7b..7fa6aa5 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
@@ -10,9 +10,13 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 
+import javax.swing.SwingUtilities;
+
 import org.json.JSONArray;
 import org.json.JSONObject;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestRequest;
@@ -20,11 +24,16 @@ import jalview.fts.core.FTSRestResponse;
 import jalview.fts.core.GFTSPanel;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.gui.SequenceFetcher;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
 @SuppressWarnings("serial")
 public class TDBeaconsFTSPanel extends GFTSPanel
-{       
+{
   private static String defaultFTSFrameTitle = MessageManager
           .getString("label.pdb_sequence_fetcher");
 
@@ -33,81 +42,19 @@ public class TDBeaconsFTSPanel extends GFTSPanel
   private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
 
   private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
-  
+
   private static HttpURLConnection connection;
-  
+
   public TDBeaconsFTSPanel(SequenceFetcher fetcher)
   {
-    super(fetcher);
-    pageLimit = TDBeaconsFTSRestClient.getInstance().getDefaultResponsePageSize();
+    // no ID retrieval option for TD Beacons just now
+    super(null);
+    pageLimit = TDBeaconsFTSRestClient.getInstance()
+            .getDefaultResponsePageSize();
     this.seqFetcher = fetcher;
     this.progressIndicator = (fetcher == null) ? null
             : fetcher.getProgressIndicator();
   }
-  
-//  public int TDBeaconsFTSPanel2(String result)
-//  {
-//    int seqlength = executeParse(result);
-//    return seqlength;
-//  }
-  
-  public static int executeParse(String query) {
-    BufferedReader reader;
-    String line;
-    StringBuffer responseContent = new StringBuffer();
-    try {
-      URL url = new URL("https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/" + query + ".json");
-      connection = (HttpURLConnection) url.openConnection();
-      connection.setRequestMethod("GET");
-      connection.setConnectTimeout(5000); // <=>5seconds
-      connection.setReadTimeout(5000);
-      // Status check up, 200 = connection succesful
-      int status = connection.getResponseCode();
-      // System.out.println(status);
-
-      if (status > 299) {
-              reader = new BufferedReader(new InputStreamReader(connection.getErrorStream()));
-              while ((line = reader.readLine()) != null) {
-                      responseContent.append(line);
-              }
-              reader.close();
-      } else {
-              reader = new BufferedReader(new InputStreamReader(connection.getInputStream()));
-              while ((line = reader.readLine()) != null) {
-                      responseContent.append(line);
-              }
-              reader.close();
-      }
-      //System.out.println(responseContent.toString());
-      int seq = parse(responseContent.toString());
-      return seq;
-
-      } catch (MalformedURLException e) {
-        e.printStackTrace();
-      } catch (IOException e) {
-        e.printStackTrace();
-      } finally {
-      connection.disconnect();
-      }
-      return (Integer) null;
-      
-  }
-  
-  public static int parse(String jsonString) {
-    JSONObject entry = new JSONObject(jsonString);
-    System.out.println(entry);
-    int length = entry.getJSONObject("uniprot_entry").getInt("sequence_length");
-    String  ac = entry.getJSONObject("uniprot_entry").getString("ac");
-    
-    JSONArray structures = entry.getJSONArray("structures");
-    for (int i=0 ; i < structures.length() ; i++) {
-            String id = structures.getJSONObject(i).getString("model_identifier");
-            //System.out.println("identifier num " + i + " : " + id);
-    }
-    System.out.println("length : " + length + "; access name : " + ac);
-    return length;
-    
-}
 
   @Override
   public void searchAction(boolean isFreshSearch)
@@ -138,11 +85,12 @@ public class TDBeaconsFTSPanel extends GFTSPanel
           FTSRestRequest request = new FTSRestRequest();
           request.setAllowEmptySeq(allowEmptySequence);
           request.setResponseSize(100);
-          request.setFieldToSearchBy("(" + searchTarget + ":");
-          request.setSearchTerm(searchTerm + ")");
+          // expect it to be uniprot accesssion
+          request.setSearchTerm(searchTerm + ".json");
           request.setOffSet(offSet);
           request.setWantedFields(wantedFields);
-          FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient.getInstance();
+          FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient
+                  .getInstance();
           FTSRestResponse resultList;
           try
           {
@@ -175,7 +123,8 @@ public class TDBeaconsFTSPanel extends GFTSPanel
 
           if (isPaginationEnabled() && resultSetCount > 0)
           {
-            String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
+            String f1 = totalNumberformatter
+                    .format(Integer.valueOf(offSet + 1));
             String f2 = totalNumberformatter
                     .format(Integer.valueOf(offSet + resultSetCount));
             String f3 = totalNumberformatter
@@ -199,14 +148,14 @@ public class TDBeaconsFTSPanel extends GFTSPanel
       }
     }.start();
   }
-  
+
   @Override
   public void okAction()
   {
     // mainFrame.dispose();
     disableActionButtons();
     StringBuilder selectedIds = new StringBuilder();
-    HashSet<String> selectedIdsSet = new HashSet<>();
+    final HashSet<String> selectedIdsSet = new HashSet<>();
     int primaryKeyColIndex = 0;
     try
     {
@@ -222,12 +171,12 @@ public class TDBeaconsFTSPanel extends GFTSPanel
     {
       String idStr = getResultTable()
               .getValueAt(summaryRow, primaryKeyColIndex).toString();
-      selectedIdsSet.add(searchTerm);
+      selectedIdsSet.add(idStr);
     }
 
     for (String idStr : paginatorCart)
     {
-      selectedIdsSet.add(searchTerm);
+      selectedIdsSet.add(idStr);
     }
 
     for (String selectedId : selectedIdsSet)
@@ -235,19 +184,57 @@ public class TDBeaconsFTSPanel extends GFTSPanel
       selectedIds.append(selectedId).append(";");
     }
 
-    String ids = selectedIds.toString();
-    seqFetcher.setQuery(ids);
-    Thread worker = new Thread(seqFetcher);
-    worker.start();
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        AlignmentI allSeqs = null;
+        FormatAdapter fl = new jalview.io.FormatAdapter();
+        for (String tdbURL : selectedIdsSet)
+        {
+          try
+          {
+            // retrieve the structure via its URL
+            AlignmentI tdbAl = fl.readFile(tdbURL, DataSourceType.URL,
+                    FileFormat.MMCif);
+
+            // TODO: pad structure according to its Uniprot Start so all line up w.r.t. the Uniprot reference sequence
+            // TODO: give the structure a sensible name (not the giant URL *:o) )
+            if (tdbAl != null)
+            {
+              if (allSeqs != null)
+              {
+                allSeqs.append(tdbAl);
+              }
+              else
+              {
+                allSeqs = tdbAl;
+              }
+            }
+          } catch (Exception x)
+          {
+            Cache.log.warn(
+                    "Couldn't retrieve 3d-beacons model for uniprot id"
+                            + searchTerm + " : " + tdbURL,
+                    x);
+          }
+        }
+        seqFetcher.parseResult(allSeqs,
+                "3D-Beacons models for " + searchTerm, FileFormat.MMCif,
+                null);
+
+      }
+    });
     delayAndEnableActionButtons();
   }
-  
+
   @Override
   public FTSRestClientI getFTSRestClient()
   {
     return TDBeaconsFTSRestClient.getInstance();
   }
-  
+
   @Override
   public String getFTSFrameTitle()
   {
@@ -282,10 +269,11 @@ public class TDBeaconsFTSPanel extends GFTSPanel
   protected void showHelp()
   {
     System.out.println("No help implemented yet.");
-    
+
   }
-  
-  public static String decodeSearchTerm(String enteredText) {
+
+  public static String decodeSearchTerm(String enteredText)
+  {
     // no multiple query support yet
     return enteredText;
   }

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
index 7a556b5..e956461 100644 (file)
--- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -47,8 +47,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient
   {
     try
     {
-      String query = tdbRestRequest.getFieldToSearchBy()
-              + tdbRestRequest.getSearchTerm();
+      String query = tdbRestRequest.getSearchTerm();
       Client client;
       Class<ClientResponse> clientResponseClass;
       if (Platform.isJS())
@@ -190,7 +189,7 @@ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
     for (FTSDataColumnI field : displayFields) {
       String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " " 
               : tdbJsonStructure.get(field.getCode()).toString();
-      System.out.println("Field : " + field + "  Data : " + fieldData);
+      // System.out.println("Field : " + field + "  Data : " + fieldData);
       if (field.isPrimaryKeyColumn())
       {
         primaryKey = fieldData;