From: Arnaldo <arnaud.gucciardi@gmail.com>
Date: Tue, 2 Mar 2021 15:24:01 +0000 (+0100)
Subject: First commit of 3DB FTS Panel & Restclient
X-Git-Tag: Release_2_11_2_0~39^2~62
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=00974ead1f9b7c9690f33b87bf31c6817446c8aa;p=jalview.git

First commit of 3DB FTS Panel & Restclient
---

diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
new file mode 100644
index 0000000..21034ac
--- /dev/null
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
@@ -0,0 +1,213 @@
+package jalview.fts.service.threedbeacons;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.SequenceFetcher;
+import jalview.util.MessageManager;
+
+@SuppressWarnings("serial")
+public class TDBeaconsFTSPanel extends GFTSPanel
+{       
+  private static String defaultFTSFrameTitle = MessageManager
+          .getString("label.threedb_sequence_fetcher");
+
+  private static Map<String, Integer> tempUserPrefs = new HashMap<>();
+
+  private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
+
+  private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
+  
+  public TDBeaconsFTSPanel(SequenceFetcher fetcher)
+  {
+    super(fetcher);
+    pageLimit = TDBeaconsFTSRestClient.getInstance().getDefaultResponsePageSize();
+    this.seqFetcher = fetcher;
+    this.progressIndicator = (fetcher == null) ? null
+            : fetcher.getProgressIndicator();
+  }
+
+  @Override
+  public void searchAction(boolean isFreshSearch)
+  {
+    mainFrame.requestFocusInWindow();
+    if (isFreshSearch)
+    {
+      offSet = 0;
+    }
+    new Thread()
+    {
+      @Override
+      public void run()
+      {
+        reset();
+        boolean allowEmptySequence = false;
+        if (getTypedText().length() > 0)
+        {
+          setSearchInProgress(true);
+          long startTime = System.currentTimeMillis();
+
+          String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+                  .getSelectedItem()).getCode();
+          wantedFields = TDBeaconsFTSRestClient.getInstance()
+                  .getAllDefaultDisplayedFTSDataColumns();
+          String searchTerm = getTypedText(); // to add : decodeSearchTerm
+
+          FTSRestRequest request = new FTSRestRequest();
+          request.setAllowEmptySeq(allowEmptySequence);
+          request.setResponseSize(100);
+          request.setFieldToSearchBy("(" + searchTarget + ":");
+          request.setSearchTerm(searchTerm + ")");
+          request.setOffSet(offSet);
+          request.setWantedFields(wantedFields);
+          FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient.getInstance();
+          FTSRestResponse resultList;
+          try
+          {
+            resultList = tdbRestClient.executeRequest(request);
+          } catch (Exception e)
+          {
+            setErrorMessage(e.getMessage());
+            checkForErrors();
+            setSearchInProgress(false);
+            return;
+          }
+
+          if (resultList.getSearchSummary() != null
+                  && resultList.getSearchSummary().size() > 0)
+          {
+            getResultTable().setModel(FTSRestResponse.getTableModel(request,
+                    resultList.getSearchSummary()));
+            FTSRestResponse.configureTableColumn(getResultTable(),
+                    wantedFields, tempUserPrefs);
+            getResultTable().setVisible(true);
+          }
+
+          long endTime = System.currentTimeMillis();
+          totalResultSetCount = resultList.getNumberOfItemsFound();
+          resultSetCount = resultList.getSearchSummary() == null ? 0
+                  : resultList.getSearchSummary().size();
+          String result = (resultSetCount > 0)
+                  ? MessageManager.getString("label.results")
+                  : MessageManager.getString("label.result");
+
+          if (isPaginationEnabled() && resultSetCount > 0)
+          {
+            String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
+            String f2 = totalNumberformatter
+                    .format(Integer.valueOf(offSet + resultSetCount));
+            String f3 = totalNumberformatter
+                    .format(Integer.valueOf(totalResultSetCount));
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+                    + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
+                    + (endTime - startTime) + " milli secs)");
+          }
+          else
+          {
+            updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+                    + resultSetCount + " " + result + " ("
+                    + (endTime - startTime) + " milli secs)");
+          }
+
+          setSearchInProgress(false);
+          refreshPaginatorState();
+          updateSummaryTableSelections();
+        }
+        txt_search.updateCache();
+      }
+    }.start();
+  }
+  
+  @Override
+  public void okAction()
+  {
+    // mainFrame.dispose();
+    disableActionButtons();
+    StringBuilder selectedIds = new StringBuilder();
+    HashSet<String> selectedIdsSet = new HashSet<>();
+    int primaryKeyColIndex = 0;
+    try
+    {
+      primaryKeyColIndex = getFTSRestClient()
+              .getPrimaryKeyColumIndex(wantedFields, false);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    int[] selectedRows = getResultTable().getSelectedRows();
+    String searchTerm = getTypedText();
+    for (int summaryRow : selectedRows)
+    {
+      String idStr = getResultTable()
+              .getValueAt(summaryRow, primaryKeyColIndex).toString();
+      selectedIdsSet.add(searchTerm);
+    }
+
+    for (String idStr : paginatorCart)
+    {
+      selectedIdsSet.add(searchTerm);
+    }
+
+    for (String selectedId : selectedIdsSet)
+    {
+      selectedIds.append(selectedId).append(";");
+    }
+
+    String ids = selectedIds.toString();
+    seqFetcher.setQuery(ids);
+    Thread worker = new Thread(seqFetcher);
+    worker.start();
+    delayAndEnableActionButtons();
+  }
+  
+  @Override
+  public FTSRestClientI getFTSRestClient()
+  {
+    return TDBeaconsFTSRestClient.getInstance();
+  }
+  
+  @Override
+  public String getFTSFrameTitle()
+  {
+    return defaultFTSFrameTitle;
+  }
+
+  @Override
+  public boolean isPaginationEnabled()
+  {
+    return true;
+  }
+
+  @Override
+  public Map<String, Integer> getTempUserPrefs()
+  {
+    return tempUserPrefs;
+  }
+
+  @Override
+  public String getCacheKey()
+  {
+    return THREEDB_FTS_CACHE_KEY;
+  }
+
+  @Override
+  public String getAutosearchPreference()
+  {
+    return THREEDB_AUTOSEARCH;
+  }
+
+  @Override
+  protected void showHelp()
+  {
+    System.out.println("No help implemented yet.");
+    
+  }
+
+}
diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
new file mode 100644
index 0000000..967fb2d
--- /dev/null
+++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java
@@ -0,0 +1,240 @@
+package jalview.fts.service.threedbeacons;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import javax.ws.rs.core.MediaType;
+
+import org.json.simple.parser.ParseException;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.util.JSONUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class TDBeaconsFTSRestClient extends FTSRestClient
+{
+  private static final String DEFAULT_THREEDBEACONS_DOMAIN = 
+          "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
+  
+  private static FTSRestClientI instance = null;
+  
+  @SuppressWarnings("unchecked")
+  @Override
+  public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
+          throws Exception
+  {
+    try
+    {
+      // Removed wantedFields, sortParam & facetPivot from PDBFTSRClient
+      
+      int responseSize = (tdbRestRequest.getResponseSize() == 0)
+              ? getDefaultResponsePageSize()
+              : tdbRestRequest.getResponseSize();
+      
+      String query = tdbRestRequest.getFieldToSearchBy()
+              + tdbRestRequest.getSearchTerm();
+      Client client;
+      Class<ClientResponse> clientResponseClass;
+      if (Platform.isJS())
+      {
+        // JavaScript only
+        client = (Client) (Object) new jalview.javascript.web.Client();
+        clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+      }
+      else
+      /**
+       * Java only
+       * @j2sIgnore
+       */
+      {
+        client = Client.create(new DefaultClientConfig());
+        clientResponseClass = ClientResponse.class;
+      }
+      WebResource webResource;
+      webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN);
+      URI uri = webResource.getURI();
+        
+      System.out.println(uri);
+        
+      // Execute the REST request
+      ClientResponse clientResponse = webResource
+              .accept(MediaType.APPLICATION_JSON).get(clientResponseClass);
+  
+      // Get the JSON string from the response object or directly from the
+      // client (JavaScript)
+      Map<String, Object> jsonObj = null;
+      String responseString = null;
+  
+      System.out.println("query >>>>>>> " + tdbRestRequest.toString());
+        
+      // Check the response status and report exception if one occurs
+      int responseStatus = clientResponse.getStatus();
+      switch (responseStatus)
+      {
+      // if succesful
+      case 200:
+        if (Platform.isJS())
+        {
+          jsonObj = clientResponse.getEntity(Map.class);
+        }
+        else
+        {
+          responseString = clientResponse.getEntity(String.class);
+        }
+        break;
+      case 400:
+        throw new Exception(parseJsonExceptionString(responseString));
+      default:
+        throw new Exception(
+                getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
+      }
+      // Process the response and return the result to the caller.
+      return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest);
+    } catch (Exception e)
+    {
+      String exceptionMsg = e.getMessage();
+      if (exceptionMsg.contains("SocketException"))
+      {
+        // No internet connection
+        throw new Exception(MessageManager.getString(
+                "exception.unable_to_detect_internet_connection"));
+      }
+      else if (exceptionMsg.contains("UnknownHostException"))
+      {
+        // The server is unreachable
+        throw new Exception(MessageManager.formatMessage(
+                "exception.fts_server_unreachable", "3DB Hub"));
+      }
+      else
+      {
+        throw e;
+      }
+    }
+      
+  }
+  
+  public static FTSRestResponse parseTDBeaconsJsonResponse(
+          String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
+  {
+    return parseTDBeaconsJsonResponse(tdbJsonResponseString,
+            (Map<String, Object>) null, tdbRestRequest);
+  }
+  
+  @SuppressWarnings("unchecked")
+  public static FTSRestResponse parseTDBeaconsJsonResponse(String tdbJsonResponseString,
+          Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
+  {
+    FTSRestResponse searchResult = new FTSRestResponse();
+    //searchResult.setNumberOfItemsFound(1);
+    List<FTSData> result = null;
+    
+    try
+    {
+      if (jsonObj == null)
+      {
+        jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
+      }
+      Map<String, Object> tdbEntry = (Map<String, Object>) jsonObj.get("uniprot_entry");
+      //String seqLength = tdbEntry.get("sequence_length").toString();
+      int seqLength = Integer.valueOf(tdbEntry.get("sequence_length").toString());
+      
+      // tdbStructures is the list of found structures
+//      Map<String, Object> tdbStructures = (Map<String, Object>) jsonObj.get("structures");
+      Object[] structures = (Object[]) jsonObj.get("structures");
+      String accessName = ((Map<String, Object>) jsonObj.get("uniprot_entry"))
+              .get("ac").toString();
+      // this is to be modified
+      int numFound = structures.length;
+//      if (numFound > 0)
+//      {
+//        
+//        result = new ArrayList<>();
+//        List<String> models;
+//        //= ((Map<String, Object>) jsonObj.get("structures"))
+//                //.get("model_identifier").toString();
+//        for (Iterator<String> modelsIter = models.iterator(); modelsIter.hasNext();)
+//                .hasNext();)
+//        {
+//          Map<String, Object> doc = (Map<String, Object>) docIter.next();
+//          result.add(getFTSData(doc, tdbRestRequest));
+//        }
+        searchResult.setNumberOfItemsFound(numFound); 
+        // searchResult.setAccessionName(accessName); ?usefulness?       
+//        searchResult.setSearchSummary(result);
+//        
+//      }
+    } catch (ParseException e)
+    {
+      e.printStackTrace();
+    }
+    return searchResult;
+  }
+
+//  private static FTSData getFTSData(Map<String, Object> doc,
+//          FTSRestRequest tdbRestRequest)
+//  {
+//    String primaryKey = null;
+//
+//    Object[] summaryRowData;
+//
+//    Collection<FTSDataColumnI> displayFields = tdbRestRequest.getWantedFields();
+//    int colCounter = 0;
+//    summaryRowData = new Object[displayFields.size() + 1];
+// 
+//    return null;
+//  }
+
+  private String parseJsonExceptionString(String jsonErrorString)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getColumnDataConfigFileName()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+  
+  public static FTSRestClientI getInstance()
+  {
+    if (instance == null)
+    {
+      instance = new TDBeaconsFTSRestClient();
+    }
+    return instance;
+  }
+  
+  private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
+
+  public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
+  {
+    if (allDefaultDisplayedStructureDataColumns == null
+            || allDefaultDisplayedStructureDataColumns.isEmpty())
+    {
+      allDefaultDisplayedStructureDataColumns = new ArrayList<>();
+      allDefaultDisplayedStructureDataColumns
+              .addAll(super.getAllDefaultDisplayedFTSDataColumns());
+    }
+    return allDefaultDisplayedStructureDataColumns;
+  }
+  
+}