+/*
+ * 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;
import javax.swing.JTable;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
* @return the built query string
*/
+ @Override
public String buildQuery(SequenceI seq)
{
List<DBRefEntry> refs = seq.getDBRefs();
* @return
* @throws Exception
*/
+ @Override
public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
Collection<FTSDataColumnI> wantedFields,
FilterOption selectedFilterOpt, boolean b) throws Exception
lastTdbRequest = tdbRequest;
if (resultList != null)
{ // Query the PDB and add additional metadata
- FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+ List<FTSRestResponse> pdbResponse = fetchStructuresMetaDataFor(
getPDBQuerySource(), resultList);
resultList = joinResponses(resultList, pdbResponse);
{
// 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);
* @return
* @throws Exception
*/
+ @Override
public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
Collection<FTSData> collectedResults,
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
+ pdbEntry.setAuthoritative(true);
try
{
pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
} catch (Exception q)
{
- Cache.warn("Unknown filetype for 3D Beacons Model from: "
+ Console.warn("Unknown filetype for 3D Beacons Model from: "
+ strucFormat + " - " + pdbIdStr + " - " + modelPage);
}
* @return
*/
- public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
+ public List<String> buildPDBFTSQueryFor(FTSRestResponse upResponse)
{
+ 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");
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;
}
/**
* @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);
+ 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;
}
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];
+ }
}
}
}