X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FThreeDBStructureChooserQuerySource.java;h=cbc6addea6a872ff6636f0edf003b4404c781297;hb=456e7b01bf201167e0063d0e8b56d4717322d6c0;hp=5a7f7d5cf18a6feee490896d7c44b203f47c7328;hpb=efff0826d9368314db6215e90a856059b86dbea8;p=jalview.git

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index 5a7f7d5..cbc6add 100644
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui.structurechooser;
 
 import java.util.ArrayList;
@@ -12,6 +32,7 @@ import java.util.Set;
 
 import javax.swing.JTable;
 
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -44,8 +65,6 @@ public class ThreeDBStructureChooserQuerySource
 
   private static final String FILTER_SOURCE_PREFIX = "only_";
 
-  private static int MAX_QLENGTH = 7820;
-
   protected FTSRestRequest lastTdbRequest;
 
   protected FTSRestClientI tdbRestClient;
@@ -73,21 +92,12 @@ public class ThreeDBStructureChooserQuerySource
    * @return the built query string
    */
 
+  @Override
   public String buildQuery(SequenceI seq)
   {
-    boolean isPDBRefsFound = false;
-    boolean isUniProtRefsFound = false;
-    StringBuilder queryBuilder = new StringBuilder();
-    Set<String> seqRefs = new LinkedHashSet<>();
-
-    /*
-     * note PDBs as DBRefEntry so they are not duplicated in query
-     */
-    Set<String> pdbids = new HashSet<>();
-
     List<DBRefEntry> refs = seq.getDBRefs();
     int ib = checkUniprotRefs(refs);
-    if (ib>-1)
+    if (ib > -1)
     {
       return getDBRefId(refs.get(ib));
     }
@@ -96,8 +106,10 @@ public class ThreeDBStructureChooserQuerySource
 
   /**
    * Searches DBRefEntry for uniprot refs
+   * 
    * @param seq
-   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of Uniprot canonical DBRefEntry 
+   * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of
+   *         Uniprot canonical DBRefEntry
    */
   public static int checkUniprotRefs(List<DBRefEntry> refs)
   {
@@ -129,7 +141,6 @@ public class ThreeDBStructureChooserQuerySource
    */
   static boolean isValidSeqName(String seqName)
   {
-    // System.out.println("seqName : " + seqName);
     String ignoreList = "pdb,uniprot,swiss-prot";
     if (seqName.length() < 3)
     {
@@ -171,6 +182,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
+  @Override
   public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
           Collection<FTSDataColumnI> wantedFields,
           FilterOption selectedFilterOpt, boolean b) throws Exception
@@ -181,13 +193,14 @@ public class ThreeDBStructureChooserQuerySource
     {
       FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
       resultList = tdbRestClient.executeRequest(tdbRequest);
-      
+
       lastTdbRequest = tdbRequest;
-      if (resultList!=null)
+      if (resultList != null)
       { // Query the PDB and add additional metadata
-        FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+        List<FTSRestResponse> pdbResponse = fetchStructuresMetaDataFor(
                 getPDBQuerySource(), resultList);
-        FTSRestResponse joinedResp = joinResponses(resultList, pdbResponse);
+
+        resultList = joinResponses(resultList, pdbResponse);
       }
       return resultList;
     }
@@ -250,13 +263,12 @@ public class ThreeDBStructureChooserQuerySource
   {
     if (tdbEntries != null && lastTdbRequest != null)
     {
-      int prov_idx = lastTdbRequest.getFieldIndex("Provider");
-      boolean hasPDBe=false;
+      boolean hasPDBe = false;
       for (FTSData _row : tdbEntries)
       {
         // tdb returns custom object
         TDB_FTSData row = (TDB_FTSData) _row;
-        String provider = (String) row.getProvider();
+        String provider = row.getProvider();
         FilterOption providerOpt = new FilterOption(
                 "3DB Provider - " + provider,
                 FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
@@ -266,21 +278,24 @@ public class ThreeDBStructureChooserQuerySource
           tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider);
           if ("PDBe".equalsIgnoreCase(provider))
           {
-            hasPDBe=true;
+            hasPDBe = true;
           }
         }
       }
       if (!hasPDBe)
       {
         // remove the PDBe options from the available filters
-        int op=0;
-        while (op<xtantOptions.size())
+        int op = 0;
+        while (op < xtantOptions.size())
         {
           FilterOption filter = xtantOptions.get(op);
-          if (filter.getQuerySource() instanceof PDBStructureChooserQuerySource)
+          if (filter
+                  .getQuerySource() instanceof PDBStructureChooserQuerySource)
           {
             xtantOptions.remove(op);
-          } else {
+          }
+          else
+          {
             op++;
           }
         }
@@ -332,6 +347,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
+  @Override
   public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
           Collection<FTSData> collectedResults,
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
@@ -370,8 +386,7 @@ public class ThreeDBStructureChooserQuerySource
     int urlColumnIndex = restable.getColumn("Url").getModelIndex();
     int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
-    int categoryColumnIndex = restable.getColumn("Model Category")
-            .getModelIndex();
+    int modelformat = restable.getColumn("Model Format").getModelIndex();
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
     final int up_end_idx = restable.getColumn("Uniprot End")
@@ -408,6 +423,8 @@ public class ThreeDBStructureChooserQuerySource
               .toString();
       String modelPage = humanUrl < 1 ? null
               : (String) restable.getValueAt(row, humanUrl);
+      String strucFormat = restable.getValueAt(row, modelformat).toString();
+
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
@@ -421,17 +438,25 @@ public class ThreeDBStructureChooserQuerySource
       {
         pdbEntry = new PDBEntry();
         pdbEntry.setId(pdbIdStr);
-        boolean hasCif = urlStr.toLowerCase(Locale.ENGLISH).endsWith("cif");
-        boolean probablyPdb = urlStr.toLowerCase(Locale.ENGLISH)
-                .contains("pdb");
-        pdbEntry.setType(hasCif ? PDBEntry.Type.MMCIF
-                : probablyPdb ? PDBEntry.Type.PDB : PDBEntry.Type.FILE);
+        pdbEntry.setAuthoritative(true);
+        try
+        {
+          pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
+        } catch (Exception q)
+        {
+          Console.warn("Unknown filetype for 3D Beacons Model from: "
+                  + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+        }
+
         if (!"PDBe".equalsIgnoreCase(typeColumn))
         {
           pdbEntry.setRetrievalUrl(urlStr);
         }
         pdbEntry.setProvider(typeColumn);
-        pdbEntry.setProviderPage(modelPage);
+        if (modelPage != null)
+        {
+          pdbEntry.setProviderPage(modelPage);
+        }
         selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
       }
       pdbEntriesToView[count++] = pdbEntry;
@@ -453,9 +478,10 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    */
 
-  public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
+  public List<String> buildPDBFTSQueryFor(FTSRestResponse upResponse)
   {
-    List<String> pdbIds = new ArrayList<String>();
+    List<String> ftsQueries = new ArrayList<String>();
+    Set<String> pdbIds = new HashSet<String>();
     int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
     int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
     for (FTSData row : upResponse.getSearchSummary())
@@ -467,7 +493,25 @@ public class ThreeDBStructureChooserQuerySource
         pdbIds.add(id);
       }
     }
-    return String.join(" OR ", pdbIds).toString();
+    StringBuilder sb = new StringBuilder();
+    for (String pdbId : pdbIds)
+    {
+      if (sb.length() > 2500)
+      {
+        ftsQueries.add(sb.toString());
+        sb.setLength(0);
+      }
+      if (sb.length() > 0)
+      {
+        sb.append(" OR ");
+      }
+      sb.append(pdbId);
+    }
+    if (sb.length() > 0)
+    {
+      ftsQueries.add(sb.toString());
+    }
+    return ftsQueries;
   }
 
   /**
@@ -477,34 +521,53 @@ public class ThreeDBStructureChooserQuerySource
    * @param upResponse
    * @return FTSRestResponse via PDBStructureChooserQuerySource
    */
-  public FTSRestResponse fetchStructuresMetaDataFor(
+  public List<FTSRestResponse> fetchStructuresMetaDataFor(
           PDBStructureChooserQuerySource pdbquery,
           FTSRestResponse upResponse) throws Exception
   {
-
-    String pdb_Query = buildPDBFTSQueryFor(upResponse);
-    if (pdb_Query.length() == 0)
+    List<String> pdb_Queries = buildPDBFTSQueryFor(upResponse);
+    if (pdb_Queries.size() == 0)
     {
       return null;
     }
-    FTSRestResponse resultList;
-    FTSRestRequest pdbRequest = new FTSRestRequest();
-    pdbRequest.setAllowEmptySeq(false);
-    pdbRequest.setResponseSize(500);
-    pdbRequest.setFieldToSearchBy("(");
-    // pdbRequest.setFieldToSortBy("pdb_id");
-    pdbRequest.setWantedFields(
-            pdbquery.getDocFieldPrefs().getStructureSummaryFields());
-    pdbRequest.setSearchTerm(pdb_Query + ")");
+    List<FTSRestResponse> results = new ArrayList<FTSRestResponse>();
 
-    resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
+    for (String pdb_Query : pdb_Queries)
+    {
+      FTSRestResponse resultList;
+      FTSRestRequest pdbRequest = new FTSRestRequest();
+      pdbRequest.setAllowEmptySeq(false);
+      pdbRequest.setResponseSize(500);
+      pdbRequest.setFieldToSearchBy("(");
+      // pdbRequest.setFieldToSortBy("pdb_id");
+      pdbRequest.setWantedFields(
+              pdbquery.getDocFieldPrefs().getStructureSummaryFields());
+      pdbRequest.setSearchTerm(pdb_Query + ")");
+
+      // handle exceptions like server errors here - means the threedbeacons
+      // discovery isn't broken by issues to do with the PDBe SOLR api
+      try
+      {
+        resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
+        if (resultList.getNumberOfItemsFound() == 0)
+        {
+          Console.info("Unexpectedly returned no results for pdbe query: "
+                  + pdb_Query);
+        }
+        results.add(resultList);
+        lastPdbRequest = pdbRequest;
+      } catch (Exception ex)
+      {
+        Console.error("PDBFTSQuery failed", ex);
+      }
 
-    lastPdbRequest = pdbRequest;
-    return resultList;
+    }
+
+    return results;
   }
 
   public FTSRestResponse joinResponses(FTSRestResponse upResponse,
-          FTSRestResponse pdbResponse)
+          List<FTSRestResponse> pdbResponses)
   {
     boolean hasPdbResp = lastPdbRequest != null;
 
@@ -516,7 +579,6 @@ public class ThreeDBStructureChooserQuerySource
             : -1;
     int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
 
-    List<FTSData> joinedRows = new ArrayList<FTSData>();
     for (final FTSData row : upResponse.getSearchSummary())
     {
       String id = (String) row.getSummaryData()[idx_modelId];
@@ -530,13 +592,16 @@ public class ThreeDBStructureChooserQuerySource
         }
         else
         {
-          for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+          for (final FTSRestResponse pdbResponse : pdbResponses)
           {
-            String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
-            if (id.equalsIgnoreCase(pdbid))
+            for (final FTSData pdbrow : pdbResponse.getSearchSummary())
             {
-              row.getSummaryData()[tdbTitle_idx] = pdbrow
-                      .getSummaryData()[pdbTitle_idx];
+              String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+              if (id.equalsIgnoreCase(pdbid))
+              {
+                row.getSummaryData()[tdbTitle_idx] = pdbrow
+                        .getSummaryData()[pdbTitle_idx];
+              }
             }
           }
         }
@@ -550,4 +615,22 @@ public class ThreeDBStructureChooserQuerySource
     return upResponse;
   }
 
+  public TDB_FTSData getFTSDataFor(JTable restable, int selectedRow,
+          Collection<FTSData> discoveredStructuresSet)
+  {
+    int idColumnIndex = restable.getColumn("Model id").getModelIndex();
+
+    String modelId = (String) restable.getValueAt(selectedRow,
+            idColumnIndex);
+    for (FTSData row : discoveredStructuresSet)
+    {
+      if (row instanceof TDB_FTSData
+              && ((TDB_FTSData) row).getModelId().equals(modelId))
+      {
+        return ((TDB_FTSData) row);
+      }
+    }
+    return null;
+  }
+
 }
\ No newline at end of file