Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EBIFetchClient	46	73	33	0.00%	Show methods

Class EBIFetchClient

Class EBIFetchClient	Line # 46	Total Statements 73	Complexity 33	TOTAL Coverage 0.00%
EBIFetchClient()   EBIFetchClient()	5252	0.00	1.01	-1.0 -1.0 -
getSupportedDBs() : String[]   getSupportedDBs() : String[]	6161	1.01	1.01	0.0 0.00%
getSupportedFormats() : String[]   getSupportedFormats() : String[]	7272	1.01	1.01	0.0 0.00%
getSupportedStyles() : String[]   getSupportedStyles() : String[]	8383	1.01	1.01	0.0 0.00%
fetchDataAsFile(String,String,String) : File   fetchDataAsFile(String,String,String) : File	102102	9.09	3.03	0.0 0.00%
fetchData(String,String,File) : String[]   fetchData(String,String,File) : String[]	132132	8.08	4.04	0.0 0.00%
parseIds(String,StringBuilder) : String   parseIds(String,StringBuilder) : String	163163	16.016	6.06	0.0 0.00%
fetchBatch(String,String,String,File) : String[]   fetchBatch(String,String,String,File) : String[]	204204	31.031	11.011	0.0 0.00%
<clinit>, line 274()   <clinit>, line 274()	274274	1.01	1.01	0.0 0.00%
buildUrl(String,String,String) : String   buildUrl(String,String,String) : String	287287	5.05	4.04	0.0 0.00%

 

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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 java.io.BufferedReader;
24		import java.io.File;
25		import java.io.IOException;
26		import java.io.InputStream;
27		import java.io.InputStreamReader;
28		import java.net.HttpURLConnection;
29		import java.net.URL;
30		import java.util.ArrayList;
31		import java.util.List;
32		import java.util.Locale;
33		import java.util.StringTokenizer;
34
35		import jalview.datamodel.DBRefSource;
36		import jalview.util.HttpUtils;
37		import jalview.util.MessageManager;
38		import jalview.util.Platform;
39
40		/**
41		* DOCUMENT ME!
42		*
43		* @author $author$
44		* @version $Revision$
45		*/
		0% Uncovered Elements: 113 (113) Complexity: 33 Complexity Density: 0.45
46		public class EBIFetchClient
47		{
48
49		/**
50		* Creates a new EBIFetchClient object.
51		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
52	0	public EBIFetchClient()...
53		{
54		}
55
56		/**
57		* DOCUMENT ME!
58		*
59		* @return DOCUMENT ME!
60		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
61	0	public String[] getSupportedDBs()...
62		{
63		// TODO - implement rest call for dbfetch getSupportedDBs
64	0	throw new Error(MessageManager.getString("error.not_yet_implemented"));
65		}
66
67		/**
68		* DOCUMENT ME!
69		*
70		* @return DOCUMENT ME!
71		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	public String[] getSupportedFormats()...
73		{
74		// TODO - implement rest call for dbfetch getSupportedFormats
75	0	throw new Error(MessageManager.getString("error.not_yet_implemented"));
76		}
77
78		/**
79		* DOCUMENT ME!
80		*
81		* @return DOCUMENT ME!
82		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	public String[] getSupportedStyles()...
84		{
85		// TODO - implement rest call for dbfetch getSupportedStyles
86	0	throw new Error(MessageManager.getString("error.not_yet_implemented"));
87		}
88
89		/**
90		* Send an HTTP fetch request to EBI and save the reply in a temporary file.
91		*
92		* @param ids
93		* the query formatted as db:query1;query2;query3
94		* @param format
95		* the format wanted
96		* @param ext
97		* for the temporary file to hold response (without separator)
98		* @return the file holding the response
99		* @throws OutOfMemoryError
100		*/
101
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.33
102	0	public File fetchDataAsFile(String ids, String format, String ext)...
103		throws OutOfMemoryError
104		{
105	0	File outFile = null;
106	0	try
107		{
108	0	outFile = File.createTempFile("jalview", "." + ext);
109	0	outFile.deleteOnExit();
110	0	fetchData(ids, format, outFile);
111	0	if (outFile.length() == 0)
112		{
113	0	outFile.delete();
114	0	return null;
115		}
116		} catch (Exception ex)
117		{
118		}
119	0	return outFile;
120		}
121
122		/**
123		* Fetches queries and either saves the response to a file or returns as
124		* string data
125		*
126		* @param ids
127		* @param format
128		* @param outFile
129		* @return
130		* @throws OutOfMemoryError
131		*/
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.5
132	0	String[] fetchData(String ids, String format, File outFile)...
133		throws OutOfMemoryError
134		{
135	0	StringBuilder querystring = new StringBuilder(ids.length());
136	0	String database = parseIds(ids, querystring);
137	0	if (database == null)
138		{
139	0	jalview.bin.Console
140		.errPrintln("Invalid Query string : '" + ids + "'");
141	0	jalview.bin.Console
142		.errPrintln("Should be of form 'dbname:q1;q2;q3;q4'");
143	0	return null;
144		}
145
146		// note: outFile is currently always specified, so return value is null
147	0	String[] rslt = fetchBatch(querystring.toString(), database, format,
148		outFile);
149
150	0	return (rslt != null && rslt.length > 0 ? rslt : null);
151		}
152
153		/**
154		* Parses ids formatted as dbname:q1;q2;q3, returns the dbname and adds
155		* queries as comma-separated items to the querystring. dbname must be
156		* specified for at least one queryId. Returns null if a mixture of different
157		* dbnames is found (ignoring case).
158		*
159		* @param ids
160		* @param queryString
161		* @return
162		*/
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.38
163	0	static String parseIds(String ids, StringBuilder queryString)...
164		{
165	0	String database = null;
166	0	StringTokenizer queries = new StringTokenizer(ids, ";");
167	0	boolean appending = queryString.length() > 0;
168	0	while (queries.hasMoreTokens())
169		{
170	0	String query = queries.nextToken();
171	0	int p = query.indexOf(':');
172	0	if (p > -1)
173		{
174	0	String db = query.substring(0, p);
175	0	if (database != null && !db.equalsIgnoreCase(database))
176		{
177		/*
178		* different databases mixed in together - invalid
179		*/
180	0	return null;
181		}
182	0	database = db;
183	0	query = query.substring(p + 1);
184		}
185	0	queryString.append(appending ? "," : "");
186	0	queryString.append(query);
187	0	appending = true;
188		}
189	0	return database;
190		}
191
192		/**
193		* Fetches queries and either saves the response to a file or (if no file
194		* specified) returns as string data
195		*
196		* @param ids
197		* @param database
198		* @param format
199		* @param outFile
200		* @return array of lines from EBI only if outFile is null (which it will not
201		* be)
202		* @throws OutOfMemoryError
203		*/
		0% Uncovered Elements: 43 (43) Complexity: 11 Complexity Density: 0.35
204	0	String[] fetchBatch(String ids, String database, String format,...
205		File outFile) throws OutOfMemoryError
206		{
207	0	String url = buildUrl(ids, database, format);
208	0	InputStream is = null;
209	0	BufferedReader br = null;
210	0	try
211		{
212	0	URL rcall = new URL(url);
213	0	HttpURLConnection conn = (HttpURLConnection) HttpUtils
214		.openConnection(rcall);
215	0	int responseCode = conn.getResponseCode();
216	0	if (responseCode == 200)
217		{
218	0	is = conn.getInputStream();
219	0	if (outFile != null)
220		{
221	0	Platform.streamToFile(is, outFile);
222	0	return null;
223		}
224	0	br = new BufferedReader(new InputStreamReader(is));
225	0	String rtn;
226	0	List<String> arl = new ArrayList<>();
227	0	while ((rtn = br.readLine()) != null)
228		{
229	0	arl.add(rtn);
230		}
231	0	return (String[]) arl.toArray();
232		}
233	0	jalview.bin.Console.errPrintln(
234		"Warning: response code " + responseCode + " for " + url);
235		} catch (OutOfMemoryError er)
236		{
237	0	jalview.bin.Console.outPrintln("OUT OF MEMORY DOWNLOADING QUERY FROM "
238		+ database + ":\n" + ids);
239	0	throw er;
240		} catch (Exception ex)
241		{
242	0	if (!ex.getMessage().startsWith(
243		"uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
244		{
245	0	jalview.bin.Console
246		.errPrintln("Unexpected exception when retrieving from "
247		+ database + "\nQuery was : '" + ids + "'");
248	0	ex.printStackTrace(System.err);
249		}
250		} finally
251		{
252	0	if (is != null)
253		{
254	0	try
255		{
256	0	is.close();
257		} catch (IOException e)
258		{
259		}
260		}
261	0	if (br != null)
262		{
263	0	try
264		{
265	0	br.close();
266		} catch (IOException e)
267		{
268		}
269		}
270		}
271	0	return null;
272		}
273
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
274	0	static...
275		{
276	0	Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
277		}
278
279		/**
280		* Constructs the URL to fetch from
281		*
282		* @param ids
283		* @param database
284		* @param format
285		* @return
286		*/
		0% Uncovered Elements: 9 (9) Complexity: 4 Complexity Density: 0.8
287	0	static String buildUrl(String ids, String database, String format)...
288		{
289	0	String url;
290	0	if (database.equalsIgnoreCase(DBRefSource.EMBL)
291		|| database.equalsIgnoreCase(DBRefSource.EMBLCDS))
292		{
293	0	url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
294		+ ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
295		}
296		else
297		{
298	0	url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
299		+ database.toLowerCase(Locale.ROOT) + "/"
300		+ ids.toLowerCase(Locale.ROOT)
301	0	+ (format != null ? "/" + format : "");
302		}
303	0	return url;
304		}
305		}