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package jalview.fts.service.threedbeacons; |
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import java.net.URI; |
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import java.util.ArrayList; |
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import java.util.Collection; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import javax.ws.rs.core.MediaType; |
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import org.json.simple.parser.ParseException; |
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import com.sun.jersey.api.client.Client; |
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import com.sun.jersey.api.client.ClientResponse; |
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import com.sun.jersey.api.client.WebResource; |
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import com.sun.jersey.api.client.config.DefaultClientConfig; |
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import jalview.datamodel.SequenceI; |
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import jalview.fts.api.FTSData; |
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import jalview.fts.api.FTSDataColumnI; |
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import jalview.fts.api.FTSRestClientI; |
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import jalview.fts.api.StructureFTSRestClientI; |
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import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource; |
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import jalview.fts.core.FTSRestClient; |
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import jalview.fts.core.FTSRestRequest; |
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import jalview.fts.core.FTSRestResponse; |
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import jalview.util.JSONUtils; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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| 75% |
Uncovered Elements: 40 (160) |
Complexity: 43 |
Complexity Density: 0.4 |
|
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public class TDBeaconsFTSRestClient extends FTSRestClient |
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implements StructureFTSRestClientI |
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{ |
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private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/"; |
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private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/"; |
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private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API; |
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public static FTSRestClientI instance = null; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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5 |
protected TDBeaconsFTSRestClient()... |
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{ |
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} |
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| 55.2% |
Uncovered Elements: 26 (58) |
Complexity: 14 |
Complexity Density: 0.35 |
|
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14 |
@SuppressWarnings("unchecked")... |
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@Override |
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public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest) |
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throws Exception |
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{ |
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try |
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{ |
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String query = tdbRestRequest.getSearchTerm(); |
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Client client; |
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Class<ClientResponse> clientResponseClass; |
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if (Platform.isJS()) |
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{ |
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|
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client = (Client) (Object) new jalview.javascript.web.Client(); |
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clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class; |
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} |
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else |
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{ |
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client = Client.create(new DefaultClientConfig()); |
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clientResponseClass = ClientResponse.class; |
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} |
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WebResource webResource; |
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webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query); |
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URI uri = webResource.getURI(); |
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jalview.bin.Console.outPrintln(uri.toString()); |
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ClientResponse clientResponse; |
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14 |
if (isMocked()) |
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{ |
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clientResponse = null; |
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} |
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else |
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{ |
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clientResponse = webResource.accept(MediaType.APPLICATION_JSON) |
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.get(clientResponseClass); |
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} |
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Map<String, Object> jsonObj = null; |
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String responseString = null; |
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int responseStatus = isMocked() |
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? (mockQueries.containsKey(query) ? 200 : 404) |
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: clientResponse.getStatus(); |
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switch (responseStatus) |
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{ |
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case 200: |
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if (Platform.isJS()) |
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{ |
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jsonObj = clientResponse.getEntity(Map.class); |
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} |
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else |
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{ |
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responseString = isMocked() ? mockQueries.get(query) |
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: clientResponse.getEntity(String.class); |
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} |
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break; |
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case 400: |
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throw new Exception(parseJsonExceptionString(responseString)); |
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case 404: |
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return emptyTDBeaconsJsonResponse(); |
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default: |
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throw new Exception( |
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getMessageByHTTPStatusCode(responseStatus, "3DBeacons")); |
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} |
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return parseTDBeaconsJsonResponse(responseString, jsonObj, |
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tdbRestRequest); |
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} catch (Exception e) |
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{ |
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String exceptionMsg = e.getMessage(); |
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0 |
if (exceptionMsg != null) |
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{ |
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if (exceptionMsg.contains("SocketException")) |
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{ |
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throw new Exception(MessageManager.getString( |
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"exception.unable_to_detect_internet_connection")); |
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} |
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else if (exceptionMsg.contains("UnknownHostException")) |
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{ |
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throw new Exception(MessageManager.formatMessage( |
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"exception.fts_server_unreachable", "3DB Hub")); |
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} |
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} |
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throw e; |
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} |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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1 |
private FTSRestResponse emptyTDBeaconsJsonResponse()... |
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{ |
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return null; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public String setSearchTerm(String term)... |
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{ |
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return term; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public static FTSRestResponse parseTDBeaconsJsonResponse(... |
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String tdbJsonResponseString, FTSRestRequest tdbRestRequest) |
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{ |
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return parseTDBeaconsJsonResponse(tdbJsonResponseString, |
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(Map<String, Object>) null, tdbRestRequest); |
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} |
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| 90.5% |
Uncovered Elements: 2 (21) |
Complexity: 4 |
Complexity Density: 0.24 |
|
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13 |
@SuppressWarnings("unchecked")... |
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public static FTSRestResponse parseTDBeaconsJsonResponse( |
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String tdbJsonResponseString, Map<String, Object> jsonObj, |
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FTSRestRequest tdbRestRequest) |
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{ |
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FTSRestResponse searchResult = new FTSRestResponse(); |
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List<FTSData> result = null; |
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try |
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{ |
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13 |
if (jsonObj == null) |
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{ |
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jsonObj = (Map<String, Object>) JSONUtils |
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.parse(tdbJsonResponseString); |
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} |
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Object uniprot_entry = jsonObj.get("uniprot_entry"); |
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List<Object> structures = (List<Object>) jsonObj.get("structures"); |
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result = new ArrayList<>(); |
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int numFound = 0; |
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5106 |
for (Iterator<Object> strucIter = structures.iterator(); strucIter |
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.hasNext();) |
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{ |
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5093 |
Map<String, Object> structure = (Map<String, Object>) strucIter |
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.next(); |
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result.add(getFTSData(structure, tdbRestRequest)); |
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numFound++; |
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} |
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searchResult.setNumberOfItemsFound(numFound); |
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searchResult.setSearchSummary(result); |
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} catch (ParseException e) |
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{ |
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e.printStackTrace(); |
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} |
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return searchResult; |
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} |
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| 97.4% |
Uncovered Elements: 1 (39) |
Complexity: 10 |
Complexity Density: 0.4 |
|
244 |
5093 |
private static FTSData getFTSData(... |
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Map<String, Object> tdbJsonStructureSummary, |
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FTSRestRequest tdbRequest) |
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{ |
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5093 |
String primaryKey = null; |
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5093 |
Object[] summaryRowData; |
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5093 |
SequenceI associatedSequence; |
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5093 |
Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields(); |
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5093 |
SequenceI associatedSeq = tdbRequest.getAssociatedSequence(); |
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5093 |
int colCounter = 0; |
256 |
5093 |
summaryRowData = new Object[(associatedSeq != null) |
257 |
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? displayFields.size() + 1 |
258 |
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: displayFields.size()]; |
259 |
5093 |
if (associatedSeq != null) |
260 |
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{ |
261 |
5030 |
associatedSequence = associatedSeq; |
262 |
5030 |
summaryRowData[0] = associatedSequence; |
263 |
5030 |
colCounter = 1; |
264 |
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} |
265 |
5093 |
Map<String, Object> tdbJsonStructure = (Map<String, Object>) tdbJsonStructureSummary |
266 |
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.get("summary"); |
267 |
5093 |
for (FTSDataColumnI field : displayFields) |
268 |
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{ |
269 |
75702 |
String fieldData = (tdbJsonStructure.get(field.getCode()) == null) |
270 |
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? " " |
271 |
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: tdbJsonStructure.get(field.getCode()).toString(); |
272 |
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|
273 |
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|
274 |
75702 |
if (field.isPrimaryKeyColumn()) |
275 |
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{ |
276 |
5093 |
primaryKey = fieldData; |
277 |
5093 |
summaryRowData[colCounter++] = primaryKey; |
278 |
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} |
279 |
70609 |
else if (fieldData == null || fieldData.trim().isEmpty()) |
280 |
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{ |
281 |
20088 |
summaryRowData[colCounter++] = null; |
282 |
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} |
283 |
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else |
284 |
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{ |
285 |
50521 |
try |
286 |
|
{ |
287 |
50521 |
summaryRowData[colCounter++] = (field.getDataType() |
288 |
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.getDataTypeClass() == Integer.class) |
289 |
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? Integer.valueOf(fieldData) |
290 |
40461 |
: (field.getDataType() |
291 |
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.getDataTypeClass() == Double.class) |
292 |
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? Double.valueOf(fieldData) |
293 |
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: fieldData; |
294 |
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} catch (Exception e) |
295 |
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{ |
296 |
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|
297 |
0 |
jalview.bin.Console |
298 |
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.outPrintln("offending value:" + fieldData + fieldData); |
299 |
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} |
300 |
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} |
301 |
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} |
302 |
5093 |
final String primaryKey1 = primaryKey; |
303 |
5093 |
final Object[] summaryRowData1 = summaryRowData; |
304 |
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|
305 |
5093 |
return new TDB_FTSData(primaryKey, tdbJsonStructure, summaryRowData1); |
306 |
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} |
307 |
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310 |
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311 |
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315 |
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322 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
323 |
0 |
private String parseJsonExceptionString(String jsonErrorString)... |
324 |
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{ |
325 |
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|
326 |
0 |
return null; |
327 |
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} |
328 |
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|
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
329 |
5 |
@Override... |
330 |
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public String getColumnDataConfigFileName() |
331 |
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{ |
332 |
5 |
return "/fts/tdbeacons_data_columns.txt"; |
333 |
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} |
334 |
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|
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
335 |
166 |
public static FTSRestClientI getInstance()... |
336 |
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{ |
337 |
166 |
if (instance == null) |
338 |
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{ |
339 |
5 |
instance = new TDBeaconsFTSRestClient(); |
340 |
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} |
341 |
166 |
return instance; |
342 |
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} |
343 |
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private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns; |
345 |
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|
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
346 |
70 |
@Override... |
347 |
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public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns() |
348 |
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{ |
349 |
70 |
if (allDefaultDisplayedStructureDataColumns == null |
350 |
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|| allDefaultDisplayedStructureDataColumns.isEmpty()) |
351 |
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{ |
352 |
5 |
allDefaultDisplayedStructureDataColumns = new ArrayList<>(); |
353 |
5 |
allDefaultDisplayedStructureDataColumns |
354 |
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.addAll(super.getAllDefaultDisplayedFTSDataColumns()); |
355 |
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} |
356 |
70 |
return allDefaultDisplayedStructureDataColumns; |
357 |
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} |
358 |
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|
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| 64.3% |
Uncovered Elements: 5 (14) |
Complexity: 4 |
Complexity Density: 0.29 |
|
359 |
71 |
@Override... |
360 |
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public String[] getPreferencesColumnsFor(PreferenceSource source) |
361 |
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{ |
362 |
71 |
String[] columnNames = null; |
363 |
71 |
switch (source) |
364 |
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{ |
365 |
1 |
case SEARCH_SUMMARY: |
366 |
1 |
columnNames = new String[] { "", "Display", "Group" }; |
367 |
1 |
break; |
368 |
70 |
case STRUCTURE_CHOOSER: |
369 |
70 |
columnNames = new String[] { "", "Display", "Group" }; |
370 |
70 |
break; |
371 |
0 |
case PREFERENCES: |
372 |
0 |
columnNames = new String[] { "3DB Beacons Field", |
373 |
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"Show in search summary", "Show in structure summary" }; |
374 |
0 |
break; |
375 |
0 |
default: |
376 |
0 |
break; |
377 |
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} |
378 |
71 |
return columnNames; |
379 |
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} |
380 |
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} |