+/*
+ * 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.fts.service.threedbeacons;
import java.net.URI;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
public class TDBeaconsFTSRestClient extends FTSRestClient
+ implements StructureFTSRestClientI
{
- private static final String DEFAULT_THREEDBEACONS_DOMAIN =
- "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
-
- private static FTSRestClientI instance = null;
-
+ /**
+ * production server URI
+ */
+ private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+ /**
+ * dev server URI
+ */
+ private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+ private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
+
+ public static FTSRestClientI instance = null;
+
protected TDBeaconsFTSRestClient()
- {
+ {
}
-
+
@SuppressWarnings("unchecked")
@Override
public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
{
try
{
- String query = tdbRestRequest.getFieldToSearchBy()
- + tdbRestRequest.getSearchTerm();
+ String query = tdbRestRequest.getSearchTerm();
Client client;
Class<ClientResponse> clientResponseClass;
if (Platform.isJS())
else
/**
* Java only
+ *
* @j2sIgnore
*/
{
client = Client.create(new DefaultClientConfig());
clientResponseClass = ClientResponse.class;
}
+
WebResource webResource;
- webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN)
- .path(query);
+ webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
+
URI uri = webResource.getURI();
System.out.println(uri.toString());
-
+
// Execute the REST request
- ClientResponse clientResponse = webResource
- .accept(MediaType.APPLICATION_JSON).get(clientResponseClass);
-
+ ClientResponse clientResponse;
+ if (isMocked())
+ {
+ clientResponse = null;
+ }
+ else
+ {
+ 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;
-
+
// Check the response status and report exception if one occurs
- int responseStatus = clientResponse.getStatus();
+ int responseStatus = isMocked()
+ ? (mockQueries.containsKey(query) ? 200 : 404)
+ : clientResponse.getStatus();
switch (responseStatus)
{
// if success
}
else
{
- responseString = clientResponse.getEntity(String.class);
+ responseString = isMocked() ? mockQueries.get(query)
+ : clientResponse.getEntity(String.class);
}
break;
case 400:
throw new Exception(parseJsonExceptionString(responseString));
+ case 404:
+ return emptyTDBeaconsJsonResponse();
default:
throw new Exception(
getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
}
// Process the response and return the result to the caller.
- return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest);
+ 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
+ if (exceptionMsg != null)
{
- throw e;
+ 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"));
+ }
}
+ throw e;
+
}
-
+
+ }
+
+ /**
+ * returns response for when the 3D-Beacons service doesn't have a record for
+ * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
+ *
+ * @return null
+ */
+ private FTSRestResponse emptyTDBeaconsJsonResponse()
+ {
+ return null;
}
-
- public String setSearchTerm(String term) {
+
+ public String setSearchTerm(String term)
+ {
return term;
}
-
+
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)
+ public static FTSRestResponse parseTDBeaconsJsonResponse(
+ String tdbJsonResponseString, Map<String, Object> jsonObj,
+ FTSRestRequest tdbRestRequest)
{
FTSRestResponse searchResult = new FTSRestResponse();
List<FTSData> result = null;
-
+
try
{
if (jsonObj == null)
{
- jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
+ jsonObj = (Map<String, Object>) JSONUtils
+ .parse(tdbJsonResponseString);
}
- //System.out.println(jsonObj);
-
- Object uniprot_entry = jsonObj.get("uniprot_entry");
- System.out.println(uniprot_entry);
-
- Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
- System.out.println("seqLenght :" + seqLength);
-
- result = new ArrayList<>();
+
+ Object uniprot_entry = jsonObj.get("uniprot_entry");
+ // TODO: decide if anything from uniprot_entry needs to be reported via
+ // the FTSRestResponse object
+ // Arnaud added seqLength = (Long) ((Map<String, Object>)
+ // jsonObj.get("uniprot_entry")).get("sequence_length");
+
List<Object> structures = (List<Object>) jsonObj.get("structures");
- //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
-
+ result = new ArrayList<>();
+
int numFound = 0;
for (Iterator<Object> strucIter = structures.iterator(); strucIter
.hasNext();)
{
- Map<String, Object> structure = (Map<String, Object>) strucIter.next();
+ Map<String, Object> structure = (Map<String, Object>) strucIter
+ .next();
result.add(getFTSData(structure, tdbRestRequest));
numFound++;
- //System.out.println(structure);
}
-
- System.out.println("1 : " + structures.get(1));
- searchResult.setNumberOfItemsFound(numFound);
+
+ searchResult.setNumberOfItemsFound(numFound);
searchResult.setSearchSummary(result);
- searchResult.setSequenceLength(seqLength);
-
+
} catch (ParseException e)
{
e.printStackTrace();
return searchResult;
}
-private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
+ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
FTSRestRequest tdbRequest)
{
- // TODO Auto-generated method stub
String primaryKey = null;
Object[] summaryRowData;
+
+ SequenceI associatedSequence;
+
Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
+ SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
int colCounter = 0;
- summaryRowData = new Object[displayFields.size()];
- for (FTSDataColumnI field : displayFields) {
- String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " "
+ summaryRowData = new Object[(associatedSeq != null)
+ ? displayFields.size() + 1
+ : displayFields.size()];
+ if (associatedSeq != null)
+ {
+ associatedSequence = associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (FTSDataColumnI field : displayFields)
+ {
+ String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
+ ? " "
: tdbJsonStructure.get(field.getCode()).toString();
+ // System.out.println("Field : " + field + " Data : " + fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
summaryRowData[colCounter++] = primaryKey;
}
- else if (fieldData == null || fieldData.isEmpty())
+ else if (fieldData == null || fieldData.trim().isEmpty())
{
summaryRowData[colCounter++] = null;
}
- else
+ else
{
try
{
: fieldData;
} catch (Exception e)
{
- e.printStackTrace();
- System.out.println("offending value:" + fieldData);
+ // e.printStackTrace();
+ System.out.println("offending value:" + fieldData + fieldData);
}
}
}
final String primaryKey1 = primaryKey;
final Object[] summaryRowData1 = summaryRowData;
-
- return new FTSData()
- {
-
- @Override
- public Object[] getSummaryData()
- {
- return summaryRowData1;
- }
- @Override
- public Object getPrimaryKey()
- {
- return primaryKey1;
- }
-
- /**
- * Returns a string representation of this object;
- */
- @Override
- public String toString()
- {
- StringBuilder summaryFieldValues = new StringBuilder();
- for (Object summaryField : summaryRowData1)
- {
- summaryFieldValues.append(
- summaryField == null ? " " : summaryField.toString())
- .append("\t");
- }
- return summaryFieldValues.toString();
- }
-
- /**
- * Returns hash code value for this object
- */
- @Override
- public int hashCode()
- {
- return Objects.hash(primaryKey1, this.toString());
- }
-
- @Override
- public boolean equals(Object that)
- {
- return this.toString().equals(that.toString());
- }
- };
+ return new TDB_FTSData(primaryKey, tdbJsonStructure, summaryRowData1);
}
-// 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 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)
{
{
return "/fts/tdbeacons_data_columns.txt";
}
-
+
public static FTSRestClientI getInstance()
{
if (instance == null)
}
return instance;
}
-
+
private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
}
return allDefaultDisplayedStructureDataColumns;
}
-
+
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source)
+ {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[] { "3DB Beacons Field",
+ "Show in search summary", "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+ return columnNames;
+ }
}
git://source.jalview.org / jalview.git / blobdiff