import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Objects;
import javax.ws.rs.core.MediaType;
private static FTSRestClientI instance = null;
+ protected TDBeaconsFTSRestClient()
+ {
+ }
+
@SuppressWarnings("unchecked")
@Override
public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
{
try
{
- // Removed wantedFields, sortParam & facetPivot from PDBFTSRClient
- String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
- tdbRestRequest.getWantedFields());
- int responseSize = (tdbRestRequest.getResponseSize() == 0)
- ? getDefaultResponsePageSize()
- : tdbRestRequest.getResponseSize();
-
String query = tdbRestRequest.getFieldToSearchBy()
+ tdbRestRequest.getSearchTerm();
Client client;
}
WebResource webResource;
webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN)
- .queryParam("P",query);
+ .path(query);
URI uri = webResource.getURI();
-
- System.out.println(uri);
+ System.out.println(uri.toString());
// Execute the REST request
ClientResponse clientResponse = webResource
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
+ // if success
case 200:
if (Platform.isJS())
{
}
+ public String setSearchTerm(String term) {
+ return term;
+ }
+
public static FTSRestResponse parseTDBeaconsJsonResponse(
String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
{
Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
{
FTSRestResponse searchResult = new FTSRestResponse();
- //searchResult.setNumberOfItemsFound(1);
List<FTSData> result = null;
try
{
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);
-//
-// }
+ Object uniprot_entry = jsonObj.get("uniprot_entry");
+ Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
+ //System.out.println(uniprot_entry);
+ //System.out.println(jsonObj);
+ //System.out.println("seqLenght :" + seqLength);
+
+ //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
+ List<Object> structures = (List<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();
+ 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)
{
e.printStackTrace();
return searchResult;
}
+private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
+ FTSRestRequest tdbRequest)
+ {
+ // TODO Auto-generated method stub
+ String primaryKey = null;
+ Object[] summaryRowData;
+ Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
+ int colCounter = 0;
+ summaryRowData = new Object[displayFields.size()];
+
+ for (FTSDataColumnI field : displayFields) {
+ System.out.println("Field " + field);
+ String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " "
+ : tdbJsonStructure.get(field.getCode()).toString();
+ System.out.println("Field Data : " + fieldData);
+ if (field.isPrimaryKeyColumn())
+ {
+ primaryKey = fieldData;
+ summaryRowData[colCounter++] = primaryKey;
+ }
+ else if (fieldData == null || fieldData.isEmpty())
+ {
+ summaryRowData[colCounter++] = null;
+ }
+ else
+ {
+ try
+ {
+ summaryRowData[colCounter++] = (field.getDataType()
+ .getDataTypeClass() == Integer.class)
+ ? Integer.valueOf(fieldData)
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? Double.valueOf(fieldData)
+ : fieldData;
+ } catch (Exception e)
+ {
+ //e.printStackTrace();
+ System.out.println("offending value:" + 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());
+ }
+ };
+ }
+
// private static FTSData getFTSData(Map<String, Object> doc,
// FTSRestRequest tdbRestRequest)
// {
@Override
public String getColumnDataConfigFileName()
{
- // TODO Auto-generated method stub
- return null;
+ return "/fts/tdbeacons_data_columns.txt";
}
public static FTSRestClientI getInstance()
git://source.jalview.org / jalview.git / blobdiff