Clover icon

jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.urls

File IdentifiersUrlProvider.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

30
67
13
1
269
185
29
0.43
5.15
13
2.23

Classes

Class Line # Actions
IdentifiersUrlProvider 52 67 29 16
0.854545585.5%
 

Contributing tests

This file is covered by 18 tests. .

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   
22    package jalview.urls;
23   
24    import static jalview.util.UrlConstants.DB_ACCESSION;
25    import static jalview.util.UrlConstants.DELIM;
26    import static jalview.util.UrlConstants.SEP;
27   
28    import jalview.util.UrlLink;
29   
30    import java.io.FileNotFoundException;
31    import java.io.FileReader;
32    import java.io.IOException;
33    import java.util.ArrayList;
34    import java.util.HashMap;
35    import java.util.Iterator;
36    import java.util.List;
37    import java.util.StringTokenizer;
38   
39    import org.json.simple.JSONArray;
40    import org.json.simple.JSONObject;
41    import org.json.simple.parser.JSONParser;
42    import org.json.simple.parser.ParseException;
43   
44    /**
45    *
46    * Implements the UrlProviderI interface for a UrlProvider object which serves
47    * URLs from identifiers.org
48    *
49    * @author $author$
50    * @version $Revision$
51    */
 
52    public class IdentifiersUrlProvider extends UrlProviderImpl
53    {
54   
55    private static final String LOCAL_KEY = "Local";
56   
57    private static final String ID_ORG_KEY = "identifiers.org";
58   
59    // map of string ids to urls
60    private HashMap<String, UrlLink> urls;
61   
62    // list of selected urls
63    private ArrayList<String> selectedUrls;
64   
 
65  29 toggle public IdentifiersUrlProvider(String cachedUrlList)
66    {
67  29 urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
68  29 selectedUrls = new ArrayList<String>();
69  29 checkSelectionMatchesUrls(cachedUrlList);
70    }
71   
72    /**
73    * Read data from an identifiers.org download file
74    *
75    * @param idFileName
76    * name of identifiers.org download file
77    * @return hashmap of identifiers.org data, keyed by MIRIAM id
78    */
 
79  29 toggle private HashMap<String, UrlLink> readIdentifiers(String idFileName)
80    {
81  29 JSONParser parser = new JSONParser();
82   
83    // identifiers.org data
84  29 HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
85   
86  29 String errorMessage = null;
87  29 try
88    {
89  29 FileReader reader = new FileReader(idFileName);
90  29 String key = "";
91  29 JSONObject obj = (JSONObject) parser.parse(reader);
92  29 if (obj.containsKey(ID_ORG_KEY))
93    {
94  0 key = ID_ORG_KEY;
95    }
96  29 else if (obj.containsKey(LOCAL_KEY))
97    {
98  29 key = LOCAL_KEY;
99    }
100    else
101    {
102  0 System.out.println(
103    "Unexpected key returned from identifiers jalview service");
104  0 return idData;
105    }
106   
107  29 JSONArray jsonarray = (JSONArray) obj.get(key);
108   
109    // loop over each entry in JSON array and build HashMap entry
110  8077 for (int i = 0; i < jsonarray.size(); i++)
111    {
112  8048 JSONObject item = (JSONObject) jsonarray.get(i);
113   
114  8048 String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
115    + DELIM;
116  8048 UrlLink link = new UrlLink((String) item.get("name"), url,
117    (String) item.get("prefix"));
118  8048 idData.put((String) item.get("id"), link);
119    }
120    } catch (IOException | ParseException e)
121    {
122    // unnecessary e.printStackTrace();
123    // Note how in JavaScript we can grab the first bytes from any file reader.
124    // Typical report here is "NetworkError" because the file does not exist.
125    // "https://." is coming from System.getProperty("user.home"), but this could
126    // be set by the page developer to anything, of course.
127  0 errorMessage = (/** @j2sNative String.fromCharCode.apply(null, reader.$in.is.buf.slice(0,12)) || */e.toString());
128  0 idData.clear();
129    }
130    // BH 2018 -- added more valuable report
131  29 if (errorMessage != null)
132  0 System.err.println("IdentifiersUrlProvider: cannot read " + idFileName + ": " + errorMessage);
133  29 return idData;
134    }
135   
 
136  29 toggle private void checkSelectionMatchesUrls(String cachedUrlList)
137    {
138  29 StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
139  259 while (st.hasMoreElements())
140    {
141  230 String id = st.nextToken();
142   
143  230 if (isMiriamId(id))
144    {
145    // this is an identifiers.org MIRIAM id
146  44 if (urls.containsKey(id))
147    {
148  44 selectedUrls.add(id);
149    }
150    }
151    }
152   
153    // reset defaultUrl in case it is no longer selected
154  29 setPrimaryUrl(primaryUrl);
155    }
156   
 
157  45 toggle @Override
158    public boolean setPrimaryUrl(String id)
159    {
160  45 if (urls.containsKey(id))
161    {
162  2 primaryUrl = id;
163    }
164    else
165    {
166  43 primaryUrl = null;
167    }
168   
169  45 return urls.containsKey(id);
170    }
171   
 
172  5 toggle @Override
173    public String writeUrlsAsString(boolean selected)
174    {
175  5 if (!selected)
176    {
177  2 return ""; // we don't cache unselected identifiers.org urls
178    }
179   
180  3 StringBuffer links = new StringBuffer();
181  3 if (!selectedUrls.isEmpty())
182    {
183  3 for (String k : selectedUrls)
184    {
185  9 links.append(k);
186  9 links.append(SEP);
187    }
188    // remove last SEP
189  3 links.setLength(links.length() - 1);
190    }
191  3 return links.toString();
192    }
193   
 
194  16 toggle @Override
195    public List<String> getLinksForMenu()
196    {
197  16 List<String> links = new ArrayList<String>();
198  16 for (String key : selectedUrls)
199    {
200  15 links.add(urls.get(key).toStringWithTarget());
201    }
202  16 return links;
203    }
204   
 
205  12 toggle @Override
206    public List<UrlLinkDisplay> getLinksForTable()
207    {
208  12 return super.getLinksForTable(urls, selectedUrls, false);
209    }
210   
 
211  9 toggle @Override
212    public void setUrlData(List<UrlLinkDisplay> links)
213    {
214  9 selectedUrls = new ArrayList<String>();
215   
216  9 Iterator<UrlLinkDisplay> it = links.iterator();
217  99 while (it.hasNext())
218    {
219  90 UrlLinkDisplay link = it.next();
220   
221    // Handle links with MIRIAM ids only
222  90 if (isMiriamId(link.getId()))
223    {
224    // select/deselect links accordingly and set default url
225  35 if (urls.containsKey(link.getId()))
226    {
227  35 if (link.getIsSelected())
228    {
229  26 selectedUrls.add(link.getId());
230    }
231  35 if (link.getIsPrimary())
232    {
233  0 setPrimaryUrl(link.getId());
234    }
235    }
236    }
237    }
238    }
239   
 
240  7 toggle @Override
241    public String getPrimaryUrl(String seqid)
242    {
243  7 return super.getPrimaryUrl(seqid, urls);
244    }
245   
 
246  5 toggle @Override
247    public String getPrimaryUrlId()
248    {
249  5 return primaryUrl;
250    }
251   
 
252  0 toggle @Override
253    public String getPrimaryTarget(String seqid)
254    {
255  0 return null;
256    }
257   
 
258  1 toggle @Override
259    public String choosePrimaryUrl()
260    {
261  1 return null;
262    }
263   
 
264  25 toggle @Override
265    public boolean contains(String id)
266    {
267  25 return (urls.containsKey(id));
268    }
269    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.