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package jalview.fts.service.pdb; |
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import java.io.File; |
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import java.io.FileInputStream; |
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import java.io.FileReader; |
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import java.net.URI; |
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import java.nio.CharBuffer; |
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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 java.util.Objects; |
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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; |
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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.fts.service.alphafold.AlphafoldRestClient; |
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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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60 |
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@author |
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| 65.1% |
Uncovered Elements: 80 (229) |
Complexity: 60 |
Complexity Density: 0.4 |
|
64 |
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public class PDBFTSRestClient extends FTSRestClient |
65 |
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implements StructureFTSRestClientI |
66 |
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{ |
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68 |
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private static FTSRestClientI instance = null; |
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public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?"; |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
72 |
5 |
protected PDBFTSRestClient()... |
73 |
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{ |
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} |
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@param |
80 |
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@return |
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@throws |
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| 66% |
Uncovered Elements: 32 (94) |
Complexity: 24 |
Complexity Density: 0.41 |
|
84 |
34 |
@SuppressWarnings({ "unused", "unchecked" })... |
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@Override |
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public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest) |
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throws Exception |
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{ |
89 |
34 |
try |
90 |
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{ |
91 |
34 |
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString( |
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pdbRestRequest.getWantedFields()); |
93 |
34 |
int responseSize = (pdbRestRequest.getResponseSize() == 0) |
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? getDefaultResponsePageSize() |
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: pdbRestRequest.getResponseSize(); |
96 |
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int offSet = pdbRestRequest.getOffSet(); |
97 |
34 |
String sortParam = null; |
98 |
34 |
if (pdbRestRequest.getFieldToSortBy() == null |
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|| pdbRestRequest.getFieldToSortBy().trim().isEmpty()) |
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{ |
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32 |
sortParam = ""; |
102 |
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} |
103 |
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else |
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{ |
105 |
2 |
if (pdbRestRequest.getFieldToSortBy() |
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.equalsIgnoreCase("Resolution")) |
107 |
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{ |
108 |
0 |
sortParam = pdbRestRequest.getFieldToSortBy() |
109 |
0 |
+ (pdbRestRequest.isAscending() ? " asc" : " desc"); |
110 |
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} |
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else |
112 |
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{ |
113 |
2 |
sortParam = pdbRestRequest.getFieldToSortBy() |
114 |
2 |
+ (pdbRestRequest.isAscending() ? " desc" : " asc"); |
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} |
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} |
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|
118 |
34 |
String facetPivot = (pdbRestRequest.getFacetPivot() == null |
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|| pdbRestRequest.getFacetPivot().isEmpty()) ? "" |
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: pdbRestRequest.getFacetPivot(); |
121 |
34 |
String facetPivotMinCount = String |
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.valueOf(pdbRestRequest.getFacetPivotMinCount()); |
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124 |
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String query = pdbRestRequest.getFieldToSearchBy() |
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+ pdbRestRequest.getSearchTerm() |
126 |
34 |
+ (pdbRestRequest.isAllowEmptySeq() ? "" |
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: " AND molecule_sequence:['' TO *]") |
128 |
34 |
+ (pdbRestRequest.isAllowUnpublishedEntries() ? "" |
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: " AND status:REL"); |
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136 |
34 |
Client client; |
137 |
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Class<ClientResponse> clientResponseClass; |
138 |
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if (Platform.isJS()) |
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{ |
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0 |
client = (Client) (Object) new jalview.javascript.web.Client(); |
142 |
0 |
clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class; |
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} |
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else |
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148 |
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149 |
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{ |
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client = Client.create(new DefaultClientConfig()); |
152 |
34 |
clientResponseClass = ClientResponse.class; |
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} |
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155 |
34 |
WebResource webResource; |
156 |
34 |
if (pdbRestRequest.isFacet()) |
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{ |
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0 |
webResource = client.resource(PDB_SEARCH_ENDPOINT) |
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.queryParam("wt", "json").queryParam("fl", wantedFields) |
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.queryParam("rows", String.valueOf(responseSize)) |
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.queryParam("q", query) |
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.queryParam("start", String.valueOf(offSet)) |
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.queryParam("sort", sortParam).queryParam("facet", "true") |
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.queryParam("facet.pivot", facetPivot) |
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.queryParam("facet.pivot.mincount", facetPivotMinCount); |
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} |
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else |
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{ |
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webResource = client.resource(PDB_SEARCH_ENDPOINT) |
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.queryParam("wt", "json").queryParam("fl", wantedFields) |
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.queryParam("rows", String.valueOf(responseSize)) |
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.queryParam("start", String.valueOf(offSet)) |
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.queryParam("q", query).queryParam("sort", sortParam); |
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} |
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URI uri = webResource.getURI(); |
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|
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jalview.bin.Console.outPrintln(uri); |
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ClientResponse clientResponse = null; |
180 |
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int responseStatus = -1; |
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|
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183 |
34 |
Map<String, Object> jsonObj = null; |
184 |
34 |
String responseString = null; |
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|
186 |
34 |
jalview.bin.Console |
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.outPrintln("query >>>>>>> " + pdbRestRequest.toString()); |
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|
189 |
34 |
if (!isMocked()) |
190 |
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{ |
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|
192 |
0 |
clientResponse = webResource.accept(MediaType.APPLICATION_JSON) |
193 |
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.get(clientResponseClass); |
194 |
0 |
responseStatus = clientResponse.getStatus(); |
195 |
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} |
196 |
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else |
197 |
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{ |
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|
199 |
34 |
if (mockQueries.containsKey(uri.toString())) |
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{ |
201 |
32 |
responseStatus = 200; |
202 |
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} |
203 |
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else |
204 |
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{ |
205 |
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206 |
2 |
responseStatus = 400; |
207 |
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} |
208 |
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} |
209 |
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210 |
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211 |
34 |
switch (responseStatus) |
212 |
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{ |
213 |
32 |
case 200: |
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|
215 |
32 |
if (isMocked()) |
216 |
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{ |
217 |
32 |
responseString = mockQueries.get(uri.toString()); |
218 |
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} |
219 |
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else |
220 |
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{ |
221 |
0 |
if (Platform.isJS()) |
222 |
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{ |
223 |
0 |
jsonObj = clientResponse.getEntity(Map.class); |
224 |
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} |
225 |
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else |
226 |
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{ |
227 |
0 |
responseString = clientResponse.getEntity(String.class); |
228 |
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} |
229 |
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} |
230 |
32 |
break; |
231 |
2 |
case 400: |
232 |
2 |
throw new Exception(isMocked() ? "400 response (Mocked)" |
233 |
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: parseJsonExceptionString(responseString)); |
234 |
0 |
default: |
235 |
0 |
throw new Exception( |
236 |
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getMessageByHTTPStatusCode(responseStatus, "PDB")); |
237 |
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} |
238 |
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|
239 |
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|
240 |
32 |
return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest); |
241 |
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} catch (Exception e) |
242 |
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{ |
243 |
2 |
if (e.getMessage() == null) |
244 |
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{ |
245 |
0 |
throw (e); |
246 |
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} |
247 |
2 |
String exceptionMsg = e.getMessage(); |
248 |
2 |
if (exceptionMsg.contains("SocketException")) |
249 |
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{ |
250 |
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|
251 |
0 |
throw new Exception(MessageManager.getString( |
252 |
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"exception.unable_to_detect_internet_connection")); |
253 |
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} |
254 |
2 |
else if (exceptionMsg.contains("UnknownHostException")) |
255 |
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{ |
256 |
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|
257 |
0 |
throw new Exception(MessageManager.formatMessage( |
258 |
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"exception.fts_server_unreachable", "PDB Solr")); |
259 |
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} |
260 |
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else |
261 |
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{ |
262 |
2 |
throw e; |
263 |
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} |
264 |
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} |
265 |
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} |
266 |
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267 |
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268 |
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269 |
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|
270 |
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@param |
271 |
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|
272 |
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@return |
273 |
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| 0% |
Uncovered Elements: 16 (16) |
Complexity: 2 |
Complexity Density: 0.12 |
|
274 |
0 |
@SuppressWarnings("unchecked")... |
275 |
|
public static String parseJsonExceptionString(String jsonErrorResponse) |
276 |
|
{ |
277 |
0 |
StringBuilder errorMessage = new StringBuilder( |
278 |
|
"\n============= PDB Rest Client RunTime error =============\n"); |
279 |
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|
280 |
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281 |
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282 |
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283 |
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284 |
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285 |
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286 |
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287 |
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288 |
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289 |
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290 |
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291 |
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292 |
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293 |
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294 |
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295 |
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|
296 |
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|
297 |
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|
298 |
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|
299 |
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|
300 |
0 |
try |
301 |
|
{ |
302 |
0 |
Map<String, Object> jsonObj = (Map<String, Object>) JSONUtils |
303 |
|
.parse(jsonErrorResponse); |
304 |
0 |
Map<String, Object> errorResponse = (Map<String, Object>) jsonObj |
305 |
|
.get("error"); |
306 |
|
|
307 |
0 |
Map<String, Object> responseHeader = (Map<String, Object>) jsonObj |
308 |
|
.get("responseHeader"); |
309 |
0 |
Map<String, Object> paramsObj = (Map<String, Object>) responseHeader |
310 |
|
.get("params"); |
311 |
0 |
String status = responseHeader.get("status").toString(); |
312 |
0 |
String message = errorResponse.get("msg").toString(); |
313 |
0 |
String query = paramsObj.get("q").toString(); |
314 |
0 |
String fl = paramsObj.get("fl").toString(); |
315 |
|
|
316 |
0 |
errorMessage.append("Status: ").append(status).append("\n"); |
317 |
0 |
errorMessage.append("Message: ").append(message).append("\n"); |
318 |
0 |
errorMessage.append("query: ").append(query).append("\n"); |
319 |
0 |
errorMessage.append("fl: ").append(fl).append("\n"); |
320 |
|
|
321 |
|
} catch (ParseException e) |
322 |
|
{ |
323 |
0 |
e.printStackTrace(); |
324 |
|
} |
325 |
0 |
return errorMessage.toString(); |
326 |
|
} |
327 |
|
|
328 |
|
|
329 |
|
|
330 |
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|
331 |
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|
332 |
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|
333 |
|
@param |
334 |
|
|
335 |
|
@param |
336 |
|
|
337 |
|
|
338 |
|
@return |
339 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
340 |
0 |
public static FTSRestResponse parsePDBJsonResponse(... |
341 |
|
String pdbJsonResponseString, FTSRestRequest pdbRestRequest) |
342 |
|
{ |
343 |
0 |
return parsePDBJsonResponse(pdbJsonResponseString, |
344 |
|
(Map<String, Object>) null, pdbRestRequest); |
345 |
|
} |
346 |
|
|
|
|
| 88% |
Uncovered Elements: 3 (25) |
Complexity: 5 |
Complexity Density: 0.26 |
|
347 |
32 |
@SuppressWarnings("unchecked")... |
348 |
|
public static FTSRestResponse parsePDBJsonResponse( |
349 |
|
String pdbJsonResponseString, Map<String, Object> jsonObj, |
350 |
|
FTSRestRequest pdbRestRequest) |
351 |
|
{ |
352 |
32 |
FTSRestResponse searchResult = new FTSRestResponse(); |
353 |
32 |
List<FTSData> result = null; |
354 |
32 |
try |
355 |
|
{ |
356 |
32 |
if (jsonObj == null) |
357 |
|
{ |
358 |
32 |
jsonObj = (Map<String, Object>) JSONUtils |
359 |
|
.parse(pdbJsonResponseString); |
360 |
|
} |
361 |
32 |
Map<String, Object> pdbResponse = (Map<String, Object>) jsonObj |
362 |
|
.get("response"); |
363 |
32 |
String queryTime = ((Map<String, Object>) jsonObj |
364 |
|
.get("responseHeader")).get("QTime").toString(); |
365 |
32 |
int numFound = Integer |
366 |
|
.valueOf(pdbResponse.get("numFound").toString()); |
367 |
32 |
List<Object> docs = (List<Object>) pdbResponse.get("docs"); |
368 |
|
|
369 |
32 |
result = new ArrayList<FTSData>(); |
370 |
32 |
if (numFound > 0) |
371 |
|
{ |
372 |
|
|
373 |
8278 |
for (Iterator<Object> docIter = docs.iterator(); docIter.hasNext();) |
374 |
|
{ |
375 |
8246 |
Map<String, Object> doc = (Map<String, Object>) docIter.next(); |
376 |
8246 |
result.add(getFTSData(doc, pdbRestRequest)); |
377 |
|
} |
378 |
|
} |
379 |
|
|
380 |
|
|
381 |
32 |
searchResult.setNumberOfItemsFound(numFound); |
382 |
32 |
searchResult.setResponseTime(queryTime); |
383 |
32 |
searchResult.setSearchSummary(result); |
384 |
|
|
385 |
|
} catch (ParseException e) |
386 |
|
{ |
387 |
0 |
e.printStackTrace(); |
388 |
|
} |
389 |
32 |
return searchResult; |
390 |
|
} |
391 |
|
|
|
|
| 79.5% |
Uncovered Elements: 8 (39) |
Complexity: 10 |
Complexity Density: 0.4 |
|
392 |
8246 |
public static FTSData getFTSData(Map<String, Object> pdbJsonDoc,... |
393 |
|
FTSRestRequest request) |
394 |
|
{ |
395 |
|
|
396 |
8246 |
String primaryKey = null; |
397 |
|
|
398 |
8246 |
Object[] summaryRowData; |
399 |
|
|
400 |
8246 |
SequenceI associatedSequence; |
401 |
|
|
402 |
8246 |
Collection<FTSDataColumnI> diplayFields = request.getWantedFields(); |
403 |
8246 |
SequenceI associatedSeq = request.getAssociatedSequence(); |
404 |
8246 |
int colCounter = 0; |
405 |
8246 |
summaryRowData = new Object[(associatedSeq != null) |
406 |
|
? diplayFields.size() + 1 |
407 |
|
: diplayFields.size()]; |
408 |
8246 |
if (associatedSeq != null) |
409 |
|
{ |
410 |
0 |
associatedSequence = associatedSeq; |
411 |
0 |
summaryRowData[0] = associatedSequence; |
412 |
0 |
colCounter = 1; |
413 |
|
} |
414 |
|
|
415 |
8246 |
for (FTSDataColumnI field : diplayFields) |
416 |
|
{ |
417 |
|
|
418 |
32984 |
String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? "" |
419 |
|
: pdbJsonDoc.get(field.getCode()).toString(); |
420 |
|
|
421 |
32984 |
if (field.isPrimaryKeyColumn()) |
422 |
|
{ |
423 |
8246 |
primaryKey = fieldData; |
424 |
8246 |
summaryRowData[colCounter++] = primaryKey; |
425 |
|
} |
426 |
24738 |
else if (fieldData == null || fieldData.isEmpty()) |
427 |
|
{ |
428 |
480 |
summaryRowData[colCounter++] = null; |
429 |
|
} |
430 |
|
else |
431 |
|
{ |
432 |
24258 |
try |
433 |
|
{ |
434 |
24258 |
summaryRowData[colCounter++] = (field.getDataType() |
435 |
|
.getDataTypeClass() == Integer.class) |
436 |
|
? Integer.valueOf(fieldData) |
437 |
24258 |
: (field.getDataType() |
438 |
|
.getDataTypeClass() == Double.class) |
439 |
|
? Double.valueOf(fieldData) |
440 |
|
: sanitiseData(fieldData); |
441 |
|
} catch (Exception e) |
442 |
|
{ |
443 |
0 |
e.printStackTrace(); |
444 |
0 |
jalview.bin.Console.outPrintln("offending value:" + fieldData); |
445 |
|
} |
446 |
|
} |
447 |
|
} |
448 |
|
|
449 |
8246 |
final String primaryKey1 = primaryKey; |
450 |
|
|
451 |
8246 |
final Object[] summaryRowData1 = summaryRowData; |
452 |
8246 |
return new FTSData() |
453 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
454 |
11201663 |
@Override... |
455 |
|
public Object[] getSummaryData() |
456 |
|
{ |
457 |
11201663 |
return summaryRowData1; |
458 |
|
} |
459 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
460 |
0 |
@Override... |
461 |
|
public Object getPrimaryKey() |
462 |
|
{ |
463 |
0 |
return primaryKey1; |
464 |
|
} |
465 |
|
|
466 |
|
|
467 |
|
|
468 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
469 |
0 |
@Override... |
470 |
|
public String toString() |
471 |
|
{ |
472 |
0 |
StringBuilder summaryFieldValues = new StringBuilder(); |
473 |
0 |
for (Object summaryField : summaryRowData1) |
474 |
|
{ |
475 |
0 |
summaryFieldValues.append( |
476 |
0 |
summaryField == null ? " " : summaryField.toString()) |
477 |
|
.append("\t"); |
478 |
|
} |
479 |
0 |
return summaryFieldValues.toString(); |
480 |
|
} |
481 |
|
|
482 |
|
|
483 |
|
|
484 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
485 |
0 |
@Override... |
486 |
|
public int hashCode() |
487 |
|
{ |
488 |
0 |
return Objects.hash(primaryKey1, this.toString()); |
489 |
|
} |
490 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
491 |
0 |
@Override... |
492 |
|
public boolean equals(Object that) |
493 |
|
{ |
494 |
0 |
return this.toString().equals(that.toString()); |
495 |
|
} |
496 |
|
}; |
497 |
|
} |
498 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
499 |
16492 |
private static String sanitiseData(String data)... |
500 |
|
{ |
501 |
16492 |
String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "") |
502 |
|
.replaceAll("\\[", "").replaceAll("\\]", "") |
503 |
|
.replaceAll("\",\"", ", ").replaceAll("\"", ""); |
504 |
16492 |
return cleanData; |
505 |
|
} |
506 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
507 |
5 |
@Override... |
508 |
|
public String getColumnDataConfigFileName() |
509 |
|
{ |
510 |
5 |
return "/fts/pdb_data_columns.txt"; |
511 |
|
} |
512 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
513 |
163 |
public static FTSRestClientI getInstance()... |
514 |
|
{ |
515 |
163 |
if (instance == null) |
516 |
|
{ |
517 |
5 |
instance = new PDBFTSRestClient(); |
518 |
|
} |
519 |
163 |
return instance; |
520 |
|
} |
521 |
|
|
522 |
|
private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns; |
523 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
524 |
68 |
@Override... |
525 |
|
public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns() |
526 |
|
{ |
527 |
68 |
if (allDefaultDisplayedStructureDataColumns == null |
528 |
|
|| allDefaultDisplayedStructureDataColumns.isEmpty()) |
529 |
|
{ |
530 |
5 |
allDefaultDisplayedStructureDataColumns = new ArrayList<>(); |
531 |
5 |
allDefaultDisplayedStructureDataColumns |
532 |
|
.addAll(super.getAllDefaultDisplayedFTSDataColumns()); |
533 |
|
} |
534 |
68 |
return allDefaultDisplayedStructureDataColumns; |
535 |
|
} |
536 |
|
|
|
|
| 64.3% |
Uncovered Elements: 5 (14) |
Complexity: 4 |
Complexity Density: 0.29 |
|
537 |
69 |
@Override... |
538 |
|
public String[] getPreferencesColumnsFor(PreferenceSource source) |
539 |
|
{ |
540 |
69 |
String[] columnNames = null; |
541 |
69 |
switch (source) |
542 |
|
{ |
543 |
1 |
case SEARCH_SUMMARY: |
544 |
1 |
columnNames = new String[] { "", "Display", "Group" }; |
545 |
1 |
break; |
546 |
68 |
case STRUCTURE_CHOOSER: |
547 |
68 |
columnNames = new String[] { "", "Display", "Group" }; |
548 |
68 |
break; |
549 |
0 |
case PREFERENCES: |
550 |
0 |
columnNames = new String[] { "PDB Field", "Show in search summary", |
551 |
|
"Show in structure summary" }; |
552 |
0 |
break; |
553 |
0 |
default: |
554 |
0 |
break; |
555 |
|
} |
556 |
69 |
return columnNames; |
557 |
|
} |
558 |
|
} |