+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.service.uniprot;
+import jalview.bin.Cache;
+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 java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
import javax.ws.rs.core.MediaType;
import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
-public class UniProtRestClient extends FTSRestClient
+public class UniProtFTSRestClient extends FTSRestClient
{
+ private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
private static FTSRestClientI instance = null;
- public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+ public final String uniprotSearchEndpoint;
- private static int DEFAULT_RESPONSE_SIZE = 200;
+ public UniProtFTSRestClient()
+ {
+ super();
+ uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
+ DEFAULT_UNIPROT_DOMAIN) + "/uniprot/?";
+ }
@Override
public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+ throws Exception
{
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
- @SuppressWarnings("unchecked")
- // String wantedFields =
- // getUniProtDocFieldsAsCommaDelimitedString((Collection<UniProtDocField>)
- // uniportRestRequest
- // .getWantedFields());
- int responseSize = (uniportRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
- : uniportRestRequest.getResponseSize();
-
- WebResource webResource = null;
-
- webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
- .queryParam("format", "tab")
- // .queryParam("columns", wantedFields)
- .queryParam("limit", String.valueOf(responseSize))
- .queryParam("query", "name:filaggrin");
- // Execute the REST request
- ClientResponse clientResponse = webResource
- .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
- String responseString = clientResponse.getEntity(String.class);
- String[] results = responseString.split("\n");
- for (String result : results)
+ try
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ Client client = Client.create(clientConfig);
+
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
+ uniportRestRequest.getWantedFields());
+ int responseSize = (uniportRestRequest.getResponseSize() == 0)
+ ? getDefaultResponsePageSize()
+ : uniportRestRequest.getResponseSize();
+
+ int offSet = uniportRestRequest.getOffSet();
+ String query;
+ if (isAdvancedQuery(uniportRestRequest.getSearchTerm()))
+ {
+ query = uniportRestRequest.getSearchTerm();
+ }
+ else
+ {
+ query = uniportRestRequest.getFieldToSearchBy()
+ .equalsIgnoreCase("Search All")
+ ? uniportRestRequest.getSearchTerm()
+ + " or mnemonic:"
+ + uniportRestRequest.getSearchTerm()
+ : uniportRestRequest.getFieldToSearchBy() + ":"
+ + uniportRestRequest.getSearchTerm();
+ }
+
+ 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);
+ // 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
+ // System.out.println(">>>>> response : "
+ // + uniProtTabDelimittedResponseString);
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = getMessageByHTTPStatusCode(
+ clientResponse.getStatus(), "Uniprot");
+ throw new Exception(errorMessage);
+
+ }
+ int xTotalResults = Integer.valueOf(
+ clientResponse.getHeaders().get("X-Total-Results").get(0));
+ clientResponse = null;
+ client = null;
+ return parseUniprotResponse(uniProtTabDelimittedResponseString,
+ uniportRestRequest, xTotalResults);
+ } catch (Exception e)
{
- String[] columns = result.split("\t");
- System.out.println("Entry : " + columns[0]);
- System.out.println("Entry name : " + columns[1]);
- System.out.println("Status : " + columns[2]);
- System.out.println("Protein names : " + columns[3]);
- System.out.println("Gene name : " + columns[4]);
- System.out.println("Organism : " + columns[5]);
- System.out.println("Lenght : " + columns[6]);
- System.out.println("");
+ 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;
+ }
}
+ }
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
- return null;
+ 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;
+ }
- // Process the response and return the result to the caller.
- // return parsePDBJsonResponse(responseString, pdbRestRequest);
- // System.out.println(">>>>> " + responseString);
+ public FTSRestResponse parseUniprotResponse(
+ String uniProtTabDelimittedResponseString,
+ 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<>();
+ boolean firstRow = true;
+ for (String dataRow : foundDataRow)
+ {
+ // 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)
+ {
+ firstRow = false;
+ continue;
+ }
+ // System.out.println(dataRow);
+ result.add(getFTSData(dataRow, uniprotRestRequest));
+ }
+ 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)
+ {
+ String primaryKey = null;
+
+ Object[] summaryRowData;
+
+ Collection<FTSDataColumnI> diplayFields = request.getWantedFields();
+ int colCounter = 0;
+ summaryRowData = new Object[diplayFields.size()];
+ String[] columns = tabDelimittedDataStr.split("\t");
+ for (FTSDataColumnI field : diplayFields)
+ {
+ try
+ {
+ String fieldData = columns[colCounter];
+ 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.replace(",", ""))
+ : (field.getDataType()
+ .getDataTypeClass() == Double.class)
+ ? Double.valueOf(fieldData)
+ : fieldData;
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.out.println("offending value:" + fieldData);
+ }
+ }
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ }
+ }
+
+ 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());
+ }
+ };
+ }
public static FTSRestClientI getInstance()
{
if (instance == null)
{
- instance = new UniProtRestClient();
+ instance = new UniProtFTSRestClient();
}
return instance;
}
@Override
- public String getColumnDataConfigFile()
+ public String getColumnDataConfigFileName()
{
- return "fts/uniprot_data_columns.conf";
+ return "/fts/uniprot_data_columns.txt";
}
}
git://source.jalview.org / jalview.git / blobdiff