public class TDBeaconsFTSRestClient extends FTSRestClient
{
private static final String DEFAULT_THREEDBEACONS_DOMAIN =
- "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
+ "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
private static FTSRestClientI instance = null;
{
try
{
- String query = tdbRestRequest.getFieldToSearchBy()
- + tdbRestRequest.getSearchTerm();
+ String query = tdbRestRequest.getSearchTerm();
Client client;
Class<ClientResponse> clientResponseClass;
if (Platform.isJS())
{
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<>();
+ // 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();)
+ for (Iterator<Object> strucIter = structures.iterator(); strucIter.hasNext();)
{
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.setSearchSummary(result);
- searchResult.setSequenceLength(seqLength);
} catch (ParseException e)
{
Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
int colCounter = 0;
summaryRowData = new Object[displayFields.size()];
+
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;
}
: fieldData;
} catch (Exception e)
{
- e.printStackTrace();
- System.out.println("offending value:" + fieldData);
+ //e.printStackTrace();
+ System.out.println("offending value:" + fieldData + fieldData);
}
}
}