Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EBIFetchClient	44	71	30	75	0.318181831.8%	Show methods

Class EBIFetchClient

Class EBIFetchClient	Line # 44	Total Statements 71	Complexity 30	Uncovered Elements 75	TOTAL Coverage 0.318181831.8%
EBIFetchClient()   EBIFetchClient()	5050	0.00	1.01	0.00	-1.0 -1.0 -
getSupportedDBs() : String[]   getSupportedDBs() : String[]	5959	1.01	1.01	1.01	0.0 0.00%
getSupportedFormats() : String[]   getSupportedFormats() : String[]	7070	1.01	1.01	1.01	0.0 0.00%
getSupportedStyles() : String[]   getSupportedStyles() : String[]	8181	1.01	1.01	1.01	0.0 0.00%
fetchDataAsFile(String,String,String) : File   fetchDataAsFile(String,String,String) : File	100100	9.09	3.03	11.011	0.0 0.00%
fetchData(String,String,File) : String[]   fetchData(String,String,File) : String[]	130130	8.08	4.04	12.012	0.0 0.00%
parseIds(String,StringBuilder) : String   parseIds(String,StringBuilder) : String	159159	16.016	6.06	0.00	1.0 1.0100%
fetchBatch(String,String,String,File) : String[]   fetchBatch(String,String,String,File) : String[]	199199	30.030	8.08	40.040	0.0 0.00%
buildUrl(String,String,String) : String   buildUrl(String,String,String) : String	278278	5.05	5.05	2.02	0.8181818 0.818181881.8%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.22727273	jalview.ws.ebi.EBIFetchClientTest.testParseIdsjalview.ws.ebi.EBIFetchClientTest.testParseIds	1PASS
	0.09090909	jalview.ws.ebi.EBIFetchClientTest.testBuildUrljalview.ws.ebi.EBIFetchClientTest.testBuildUrl	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.ws.ebi;
22
23		import jalview.datamodel.DBRefSource;
24		import jalview.util.MessageManager;
25
26		import java.io.BufferedInputStream;
27		import java.io.BufferedReader;
28		import java.io.File;
29		import java.io.FileOutputStream;
30		import java.io.InputStream;
31		import java.io.InputStreamReader;
32		import java.net.HttpURLConnection;
33		import java.net.URL;
34		import java.util.ArrayList;
35		import java.util.List;
36		import java.util.StringTokenizer;
37
38		/**
39		* DOCUMENT ME!
40		*
41		* @author $author$
42		* @version $Revision$
43		*/
		31.8% Uncovered Elements: 75 (110) Complexity: 30 Complexity Density: 0.42
44		public class EBIFetchClient
45		{
46
47		/**
48		* Creates a new EBIFetchClient object.
49		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
50	0	public EBIFetchClient()...
51		{
52		}
53
54		/**
55		* DOCUMENT ME!
56		*
57		* @return DOCUMENT ME!
58		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	public String[] getSupportedDBs()...
60		{
61		// TODO - implement rest call for dbfetch getSupportedDBs
62	0	throw new Error(MessageManager.getString("error.not_yet_implemented"));
63		}
64
65		/**
66		* DOCUMENT ME!
67		*
68		* @return DOCUMENT ME!
69		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
70	0	public String[] getSupportedFormats()...
71		{
72		// TODO - implement rest call for dbfetch getSupportedFormats
73	0	throw new Error(MessageManager.getString("error.not_yet_implemented"));
74		}
75
76		/**
77		* DOCUMENT ME!
78		*
79		* @return DOCUMENT ME!
80		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	public String[] getSupportedStyles()...
82		{
83		// TODO - implement rest call for dbfetch getSupportedStyles
84	0	throw new Error(MessageManager.getString("error.not_yet_implemented"));
85		}
86
87		/**
88		* Send an HTTP fetch request to EBI and save the reply in a temporary file.
89		*
90		* @param ids
91		* the query formatted as db:query1;query2;query3
92		* @param format
93		* the format wanted
94		* @param extension
95		* for the temporary file to hold response (without separator)
96		* @return the file holding the response
97		* @throws OutOfMemoryError
98		*/
99
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
100	0	public File fetchDataAsFile(String ids, String format, String ext)...
101		throws OutOfMemoryError
102		{
103	0	File outFile = null;
104	0	try
105		{
106	0	outFile = File.createTempFile("jalview", "." + ext);
107	0	outFile.deleteOnExit();
108	0	fetchData(ids, format, outFile);
109	0	if (outFile.length() == 0)
110		{
111	0	outFile.delete();
112	0	return null;
113		}
114		} catch (Exception ex)
115		{
116		}
117	0	return outFile;
118		}
119
120		/**
121		* Fetches queries and either saves the response to a file or returns as
122		* string data
123		*
124		* @param ids
125		* @param format
126		* @param outFile
127		* @return
128		* @throws OutOfMemoryError
129		*/
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.5
130	0	String[] fetchData(String ids, String format, File outFile)...
131		throws OutOfMemoryError
132		{
133	0	StringBuilder querystring = new StringBuilder(ids.length());
134	0	String database = parseIds(ids, querystring);
135	0	if (database == null)
136		{
137	0	System.err.println("Invalid Query string : '" + ids + "'");
138	0	System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
139	0	return null;
140		}
141
142		// note: outFile is currently always specified, so return value is null
143	0	String[] rslt = fetchBatch(querystring.toString(), database, format,
144		outFile);
145
146	0	return (rslt != null && rslt.length > 0 ? rslt : null);
147		}
148
149		/**
150		* Parses ids formatted as dbname:q1;q2;q3, returns the dbname and adds
151		* queries as comma-separated items to the querystring. dbname must be
152		* specified for at least one queryId. Returns null if a mixture of different
153		* dbnames is found (ignoring case).
154		*
155		* @param ids
156		* @param queryString
157		* @return
158		*/
		100% Uncovered Elements: 0 (24) Complexity: 6 Complexity Density: 0.38
159	7	static String parseIds(String ids, StringBuilder queryString)...
160		{
161	7	String database = null;
162	7	StringTokenizer queries = new StringTokenizer(ids, ";");
163	7	boolean appending = queryString.length() > 0;
164	19	while (queries.hasMoreTokens())
165		{
166	13	String query = queries.nextToken();
167	13	int p = query.indexOf(':');
168	13	if (p > -1)
169		{
170	9	String db = query.substring(0, p);
171	9	if (database != null && !db.equalsIgnoreCase(database))
172		{
173		/*
174		* different databases mixed in together - invalid
175		*/
176	1	return null;
177		}
178	8	database = db;
179	8	query = query.substring(p + 1);
180		}
181	12	queryString.append(appending ? "," : "");
182	12	queryString.append(query);
183	12	appending = true;
184		}
185	6	return database;
186		}
187
188		/**
189		* Fetches queries and either saves the response to a file or (if no file
190		* specified) returns as string data
191		*
192		* @param ids
193		* @param database
194		* @param format
195		* @param outFile
196		* @return
197		* @throws OutOfMemoryError
198		*/
		0% Uncovered Elements: 40 (40) Complexity: 8 Complexity Density: 0.27
199	0	String[] fetchBatch(String ids, String database, String format,...
200		File outFile) throws OutOfMemoryError
201		{
202		// long time = System.currentTimeMillis();
203	0	String url = buildUrl(ids, database, format);
204
205	0	try
206		{
207	0	URL rcall = new URL(url);
208
209	0	HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
210	0	int responseCode = conn.getResponseCode();
211	0	if (responseCode != 200)
212		{
213	0	System.err.println("Warning: response code " + responseCode
214		+ " for " + url);
215		}
216	0	InputStream is = new BufferedInputStream(conn.getInputStream());
217	0	if (outFile != null)
218		{
219		/**@j2sNative
220		* if (outFile._isTemp) {
221		* outFile._bytes = is.$in.$in.buf;
222		* return null;
223		* }
224		*/
225	0	FileOutputStream fio = new FileOutputStream(outFile);
226	0	byte[] bb = new byte[32 * 1024];
227	0	int l;
228	0	while ((l = is.read(bb)) > 0)
229		{
230	0	fio.write(bb, 0, l);
231		}
232	0	fio.close();
233	0	is.close();
234		}
235		else
236		{
237	0	BufferedReader br = new BufferedReader(new InputStreamReader(is));
238	0	String rtn;
239	0	List<String> arl = new ArrayList<String>();
240	0	while ((rtn = br.readLine()) != null)
241		{
242	0	arl.add(rtn);
243		}
244	0	return arl.toArray(new String[arl.size()]);
245		}
246		} catch (OutOfMemoryError er)
247		{
248	0	System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
249		+ ":\n" + ids);
250	0	throw er;
251		} catch (Exception ex)
252		{
253	0	if (ex.getMessage().startsWith(
254		"uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
255		{
256	0	return null;
257		}
258	0	System.err.println("Unexpected exception when retrieving from "
259		+ database + "\nQuery was : '" + ids + "'");
260	0	ex.printStackTrace(System.err);
261	0	return null;
262		} finally
263		{
264		// System.err.println("EBIFetch took " + (System.currentTimeMillis() -
265		// time) + " ms");
266		}
267	0	return null;
268		}
269
270		/**
271		* Constructs the URL to fetch from
272		*
273		* @param ids
274		* @param database
275		* @param format
276		* @return
277		*/
		81.8% Uncovered Elements: 2 (11) Complexity: 5 Complexity Density: 1
278	4	static String buildUrl(String ids, String database, String format)...
279		{
280	4	String url;
281	4	if (database.equalsIgnoreCase(DBRefSource.EMBL)
282		|| database.equalsIgnoreCase(DBRefSource.EMBLCDS))
283		{
284	2	url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
285	2	+ (format != null ? "&" + format : "");
286		}
287		else
288		{
289	2	url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
290		+ database.toLowerCase() + "/" + ids.toLowerCase()
291	2	+ (format != null ? "/" + format : "");
292		}
293	4	return url;
294		}
295		}