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package jalview.ws.ebi; |
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import jalview.datamodel.DBRefSource; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import java.io.BufferedReader; |
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import java.io.File; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.io.InputStreamReader; |
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import java.net.HttpURLConnection; |
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import java.net.URL; |
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import java.util.ArrayList; |
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import java.util.List; |
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import java.util.StringTokenizer; |
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@author |
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@version |
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| 32.7% |
Uncovered Elements: 72 (107) |
Complexity: 31 |
Complexity Density: 0.46 |
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public class EBIFetchClient |
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{ |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
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public EBIFetchClient()... |
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{ |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public String[] getSupportedDBs()... |
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{ |
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throw new Error(MessageManager.getString("error.not_yet_implemented")); |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public String[] getSupportedFormats()... |
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{ |
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throw new Error(MessageManager.getString("error.not_yet_implemented")); |
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} |
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@return |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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public String[] getSupportedStyles()... |
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{ |
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throw new Error(MessageManager.getString("error.not_yet_implemented")); |
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} |
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@param |
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@param |
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@param |
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@return |
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@throws |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 3 |
Complexity Density: 0.33 |
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public File fetchDataAsFile(String ids, String format, String ext)... |
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throws OutOfMemoryError |
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{ |
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File outFile = null; |
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try |
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{ |
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outFile = File.createTempFile("jalview", "." + ext); |
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outFile.deleteOnExit(); |
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fetchData(ids, format, outFile); |
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if (outFile.length() == 0) |
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{ |
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outFile.delete(); |
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return null; |
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} |
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} catch (Exception ex) |
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{ |
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} |
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return outFile; |
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} |
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@param |
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@param |
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@param |
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@return |
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@throws |
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| 0% |
Uncovered Elements: 12 (12) |
Complexity: 4 |
Complexity Density: 0.5 |
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String[] fetchData(String ids, String format, File outFile)... |
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throws OutOfMemoryError |
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{ |
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StringBuilder querystring = new StringBuilder(ids.length()); |
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String database = parseIds(ids, querystring); |
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if (database == null) |
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{ |
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System.err.println("Invalid Query string : '" + ids + "'"); |
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System.err.println("Should be of form 'dbname:q1;q2;q3;q4'"); |
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return null; |
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} |
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String[] rslt = fetchBatch(querystring.toString(), database, format, |
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outFile); |
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return (rslt != null && rslt.length > 0 ? rslt : null); |
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} |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (24) |
Complexity: 6 |
Complexity Density: 0.38 |
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static String parseIds(String ids, StringBuilder queryString)... |
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{ |
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String database = null; |
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StringTokenizer queries = new StringTokenizer(ids, ";"); |
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boolean appending = queryString.length() > 0; |
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while (queries.hasMoreTokens()) |
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{ |
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String query = queries.nextToken(); |
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int p = query.indexOf(':'); |
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if (p > -1) |
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{ |
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String db = query.substring(0, p); |
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if (database != null && !db.equalsIgnoreCase(database)) |
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{ |
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return null; |
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} |
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database = db; |
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query = query.substring(p + 1); |
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} |
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queryString.append(appending ? "," : ""); |
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queryString.append(query); |
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appending = true; |
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} |
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return database; |
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} |
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@param |
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@param |
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@param |
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@param |
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@return |
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@throws |
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| 0% |
Uncovered Elements: 37 (37) |
Complexity: 9 |
Complexity Density: 0.33 |
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String[] fetchBatch(String ids, String database, String format,... |
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File outFile) throws OutOfMemoryError |
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{ |
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String url = buildUrl(ids, database, format); |
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InputStream is = null; |
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try |
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{ |
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URL rcall = new URL(url); |
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HttpURLConnection conn = (HttpURLConnection) rcall.openConnection(); |
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int responseCode = conn.getResponseCode(); |
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if (responseCode == 200) |
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{ |
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is = conn.getInputStream(); |
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if (outFile != null) |
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{ |
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Platform.streamToFile(is, outFile); |
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return null; |
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} |
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BufferedReader br = new BufferedReader(new InputStreamReader(is)); |
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String rtn; |
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List<String> arl = new ArrayList<>(); |
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while ((rtn = br.readLine()) != null) |
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{ |
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arl.add(rtn); |
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} |
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return (String[]) arl.toArray(); |
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} |
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System.err.println( |
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"Warning: response code " + responseCode + " for " + url); |
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} catch (OutOfMemoryError er) |
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{ |
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System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database |
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+ ":\n" + ids); |
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throw er; |
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} catch (Exception ex) |
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{ |
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if (!ex.getMessage().startsWith( |
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"uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException")) |
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{ |
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System.err.println("Unexpected exception when retrieving from " |
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+ database + "\nQuery was : '" + ids + "'"); |
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ex.printStackTrace(System.err); |
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} |
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} finally |
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{ |
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if (is != null) |
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{ |
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try |
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{ |
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is.close(); |
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} catch (IOException e) |
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{ |
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} |
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} |
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} |
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0 |
return null; |
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} |
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259 |
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260 |
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261 |
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@param |
262 |
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@param |
263 |
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@param |
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@return |
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| 81.8% |
Uncovered Elements: 2 (11) |
Complexity: 5 |
Complexity Density: 1 |
|
266 |
4 |
static String buildUrl(String ids, String database, String format)... |
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{ |
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String url; |
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4 |
if (database.equalsIgnoreCase(DBRefSource.EMBL) |
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|| database.equalsIgnoreCase(DBRefSource.EMBLCDS)) |
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{ |
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url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase() |
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+ (format != null ? "&" + format : ""); |
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} |
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else |
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{ |
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url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/" |
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+ database.toLowerCase() + "/" + ids.toLowerCase() |
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2 |
+ (format != null ? "/" + format : ""); |
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} |
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4 |
return url; |
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} |
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} |