package jalview.fts.service.uniprot;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestClient;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
-import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
public class UniProtFTSRestClient extends FTSRestClient
{
+ private static final String DEFAULT_UNIPROT_DOMAIN = "https://legacy.uniprot.org";
+
+ static
+ {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
+ }
+
private static FTSRestClientI instance = null;
- public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+ public final String uniprotSearchEndpoint;
+
+ public UniProtFTSRestClient()
+ {
+ super();
+ uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
+ DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
+ }
+ @SuppressWarnings("unchecked")
@Override
- public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+ public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest)
+ throws Exception
{
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
- String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
- .getWantedFields());
- int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
- : uniportRestRequest.getResponseSize();
-
- String query = uniportRestRequest.getFieldToSearchBy() + ":"
- + uniportRestRequest.getSearchTerm();
- // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
- // : " AND status:REL");
- // System.out.println(">>>>> Query : " + query);
- // System.out.println(">>>>> Columns : " + wantedFields);
- WebResource webResource = null;
- webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
- .queryParam("format", "tab")
- .queryParam("columns", wantedFields)
- .queryParam("limit", String.valueOf(responseSize))
- .queryParam("query", query);
- // Execute the REST request
- ClientResponse clientResponse = webResource
- .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
- String uniProtTabDelimittedResponseString = clientResponse
- .getEntity(String.class);
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
- // System.out.println(">>>>> response : "
- // + uniProtTabDelimittedResponseString);
- return parseUniprotResponse(uniProtTabDelimittedResponseString,
- uniportRestRequest);
+ try
+ {
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
+ uniprotRestRequest.getWantedFields());
+ int responseSize = (uniprotRestRequest.getResponseSize() == 0)
+ ? getDefaultResponsePageSize()
+ : uniprotRestRequest.getResponseSize();
+
+ int offSet = uniprotRestRequest.getOffSet();
+ String query;
+ if (isAdvancedQuery(uniprotRestRequest.getSearchTerm()))
+ {
+ query = uniprotRestRequest.getSearchTerm();
+ }
+ else
+ {
+ query = uniprotRestRequest.getFieldToSearchBy()
+ .equalsIgnoreCase("Search All")
+ ? uniprotRestRequest.getSearchTerm()
+ + " or mnemonic:"
+ + uniprotRestRequest.getSearchTerm()
+ : uniprotRestRequest.getFieldToSearchBy() + ":"
+ + uniprotRestRequest.getSearchTerm();
+ }
+
+ // BH 2018 the trick here is to coerce the classes in Javascript to be
+ // different from the ones in Java yet still allow this to be correct for
+ // Java
+ Client client;
+ Class<ClientResponse> clientResponseClass;
+ if (Platform.isJS())
+ {
+ // JavaScript only -- coerce types to Java types for Java
+ client = (Client) (Object) new jalview.javascript.web.Client();
+ clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ // Java only
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
+ }
+
+ WebResource webResource = null;
+ webResource = client.resource(uniprotSearchEndpoint)
+ .queryParam("format", "tab")
+ .queryParam("columns", wantedFields)
+ .queryParam("limit", String.valueOf(responseSize))
+ .queryParam("offset", String.valueOf(offSet))
+ .queryParam("sort", "score").queryParam("query", query);
+ if (Console.isDebugEnabled())
+ {
+ Console.debug("Uniprot FTS Request: " + webResource.toString());
+ }
+ // Execute the REST request
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
+ String uniProtTabDelimittedResponseString = clientResponse
+ .getEntity(String.class);
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ // System.out.println(">>>>> response : "
+ // + uniProtTabDelimittedResponseString);
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = getMessageByHTTPStatusCode(
+ clientResponse.getStatus(), "Uniprot");
+ throw new Exception(errorMessage);
+
+ }
+ int xTotalResults = Platform.isJS() ? 1
+ : Integer.valueOf(clientResponse.getHeaders()
+ .get("X-Total-Results").get(0));
+ clientResponse = null;
+ client = null;
+ return parseUniprotResponse(uniProtTabDelimittedResponseString,
+ uniprotRestRequest, xTotalResults);
+ } 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 'http://www.uniprot.org' is unreachable
+ throw new Exception(MessageManager.formatMessage(
+ "exception.fts_server_unreachable", "Uniprot"));
+ }
+ else
+ {
+ throw e;
+ }
+ }
+ }
+ public boolean isAdvancedQuery(String query)
+ {
+ if (query.contains(" AND ") || query.contains(" OR ")
+ || query.contains(" NOT ") || query.contains(" ! ")
+ || query.contains(" || ") || query.contains(" && ")
+ || query.contains(":") || query.contains("-"))
+ {
+ return true;
+ }
+ return false;
}
public FTSRestResponse parseUniprotResponse(
String uniProtTabDelimittedResponseString,
- FTSRestRequest uniprotRestRequest)
+ FTSRestRequest uniprotRestRequest, int xTotalResults)
{
FTSRestResponse searchResult = new FTSRestResponse();
List<FTSData> result = null;
+ if (uniProtTabDelimittedResponseString == null
+ || uniProtTabDelimittedResponseString.trim().isEmpty())
+ {
+ searchResult.setNumberOfItemsFound(0);
+ return searchResult;
+ }
String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
if (foundDataRow != null && foundDataRow.length > 0)
{
- result = new ArrayList<FTSData>();
- String titleRow = getDataColumnsFieldsAsTabDelimitedString(uniprotRestRequest
- .getWantedFields());
- // System.out.println(">>>>Title row : " + titleRow);
+ result = new ArrayList<>();
+ boolean firstRow = true;
for (String dataRow : foundDataRow)
{
- if (dataRow.equalsIgnoreCase(titleRow))
+ // The first data row is usually the header data. This should be
+ // filtered out from the rest of the data See: JAL-2485
+ if (firstRow)
{
- // System.out.println(">>>>>>>>>> matched!!!");
+ firstRow = false;
continue;
}
// System.out.println(dataRow);
result.add(getFTSData(dataRow, uniprotRestRequest));
}
- searchResult.setNumberOfItemsFound(result.size());
+ searchResult.setNumberOfItemsFound(xTotalResults);
searchResult.setSearchSummary(result);
}
return searchResult;
}
+ // /**
+ // * Takes a collection of FTSDataColumnI and converts its 'code' values into
+ // a
+ // * tab delimited string.
+ // *
+ // * @param dataColumnFields
+ // * the collection of FTSDataColumnI to process
+ // * @return the generated comma delimited string from the supplied
+ // * FTSDataColumnI collection
+ // */
+ // private String getDataColumnsFieldsAsTabDelimitedString(
+ // Collection<FTSDataColumnI> dataColumnFields)
+ // {
+ // String result = "";
+ // if (dataColumnFields != null && !dataColumnFields.isEmpty())
+ // {
+ // StringBuilder returnedFields = new StringBuilder();
+ // for (FTSDataColumnI field : dataColumnFields)
+ // {
+ // if (field.getName().equalsIgnoreCase("Uniprot Id"))
+ // {
+ // returnedFields.append("\t").append("Entry");
+ // }
+ // else
+ // {
+ // returnedFields.append("\t").append(field.getName());
+ // }
+ // }
+ // returnedFields.deleteCharAt(0);
+ // result = returnedFields.toString();
+ // }
+ // return result;
+ // }
+
public static FTSData getFTSData(String tabDelimittedDataStr,
FTSRestRequest request)
{
{
try
{
- summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer
- .valueOf(fieldData)
- : (field.getDataColumnClass() == Double.class) ? Double
- .valueOf(fieldData) : fieldData;
+ summaryRowData[colCounter++] = (field.getDataType()
+ .getDataTypeClass() == Integer.class)
+ ? Integer.valueOf(fieldData.replace(",", ""))
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? Double.valueOf(fieldData)
+ : fieldData;
} catch (Exception e)
{
e.printStackTrace();
- System.out.println("offending value:" + fieldData);
+ System.out.println("offending value:" + fieldData);
}
}
} catch (Exception e)
{
return Objects.hash(primaryKey1, this.toString());
}
+
+ @Override
+ public boolean equals(Object that)
+ {
+ return this.toString().equals(that.toString());
+ }
};
}
-
public static FTSRestClientI getInstance()
{
if (instance == null)
@Override
public String getColumnDataConfigFileName()
{
- return getResourceFile("/fts/uniprot_data_columns.conf");
+ return "/fts/uniprot_data_columns.txt";
}
}
git://source.jalview.org / jalview.git / blobdiff