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Coverage Report

  1. Project Clover database Mon Nov 11 2024 15:14:12 GMT
  2. Package jalview.urls

File CustomUrlProvider.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

42
100
16
1
355
256
43
0.43
6.25
16
2.69

Classes

Class Line # Actions
CustomUrlProvider 49 100 43
0.924050692.4%
 

Contributing tests

This file is covered by 67 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    import static jalview.util.UrlConstants.SEQUENCE_ID;
28   
29    import jalview.util.MessageManager;
30    import jalview.util.UrlConstants;
31    import jalview.util.UrlLink;
32   
33    import java.util.ArrayList;
34    import java.util.HashMap;
35    import java.util.Iterator;
36    import java.util.List;
37    import java.util.Map;
38    import java.util.Map.Entry;
39    import java.util.StringTokenizer;
40   
41    /**
42    *
43    * Implements the UrlProviderI interface for a UrlProvider object which serves
44    * custom URLs defined by the user
45    *
46    * @author $author$
47    * @version $Revision$
48    */
 
49    public class CustomUrlProvider extends UrlProviderImpl
50    {
51    // Default sequence URL link label for SRS
52    private static final String SRS_LABEL = "SRS";
53   
54    // map of string ids to urlLinks (selected)
55    private HashMap<String, UrlLink> selectedUrls;
56   
57    // map of string ids to urlLinks (not selected)
58    private HashMap<String, UrlLink> nonselectedUrls;
59   
60    /**
61    * Construct UrlProvider for custom (user-entered) URLs
62    *
63    * @param inMenuUrlList
64    * list of URLs set to be displayed in menu, in form stored in Cache.
65    * i.e. SEP delimited string
66    * @param storedUrlList
67    * list of custom URLs entered by user but not currently displayed in
68    * menu, in form stored in Cache
69    */
 
70  43 toggle public CustomUrlProvider(String inMenuUrlList, String storedUrlList)
71    {
72  43 try
73    {
74  43 selectedUrls = parseUrlStrings(inMenuUrlList);
75  43 nonselectedUrls = parseUrlStrings(storedUrlList);
76    } catch (Exception ex)
77    {
78  0 System.out
79    .println(ex.getMessage() + "\nError parsing sequence links");
80    }
81    }
82   
83    /**
84    * Construct UrlProvider for custom (user-entered) URLs
85    *
86    * @param urlList
87    * list of URLs to be displayed in menu, as (label,url) pairs
88    * @param storedUrlList
89    * list of custom URLs entered by user but not currently displayed in
90    * menu, as (label,url) pairs
91    */
 
92  2 toggle public CustomUrlProvider(Map<String, String> inMenuUrlList,
93    Map<String, String> storedUrlList)
94    {
95  2 try
96    {
97  2 selectedUrls = parseUrlList(inMenuUrlList);
98  2 nonselectedUrls = parseUrlList(storedUrlList);
99    } catch (Exception ex)
100    {
101  0 System.out
102    .println(ex.getMessage() + "\nError parsing sequence links");
103    }
104    }
105   
 
106  86 toggle private HashMap<String, UrlLink> parseUrlStrings(String urlStrings)
107    {
108    // cachedUrlList is in form <label>|<url>|<label>|<url>...
109    // parse cachedUrlList into labels (used as id) and url links
110  86 HashMap<String, UrlLink> urls = new HashMap<>();
111   
112  86 StringTokenizer st = new StringTokenizer(urlStrings, SEP);
113  282 while (st.hasMoreElements())
114    {
115  196 String name = st.nextToken().trim();
116   
117  196 if (!isMiriamId(name))
118    {
119    // this one of our custom urls
120  157 String url = st.nextToken();
121    // check for '|' within a regex
122  157 int rxstart = url.indexOf(DELIM + DB_ACCESSION + DELIM);
123  157 if (rxstart == -1)
124    {
125  76 rxstart = url.indexOf(DELIM + SEQUENCE_ID + DELIM);
126    }
127  157 while (rxstart == -1 && url.indexOf("/=" + DELIM) == -1
128    && st.hasMoreTokens())
129    {
130  0 url = url + SEP + st.nextToken();
131    }
132  157 url = url.trim();
133  157 urls.put(name, new UrlLink(name, url, name));
134    }
135    }
136  86 upgradeOldLinks(urls);
137  86 return urls;
138    }
139   
 
140  4 toggle private HashMap<String, UrlLink> parseUrlList(Map<String, String> urlList)
141    {
142  4 HashMap<String, UrlLink> urls = new HashMap<>();
143  4 if (urlList == null)
144    {
145  1 return urls;
146    }
147   
148  3 Iterator<Map.Entry<String, String>> it = urlList.entrySet().iterator();
149  11 while (it.hasNext())
150    {
151  8 Map.Entry<String, String> pair = it.next();
152  8 urls.put(pair.getKey(),
153    new UrlLink(pair.getKey(), pair.getValue(), pair.getKey()));
154    }
155  3 upgradeOldLinks(urls);
156  3 return urls;
157    }
158   
159    /*
160    * Upgrade any legacy links which may have been left lying around
161    */
 
162  89 toggle private void upgradeOldLinks(HashMap<String, UrlLink> urls)
163    {
164  89 boolean upgrade = false;
165    // upgrade old SRS link
166  89 if (urls.containsKey(SRS_LABEL))
167    {
168  12 urls.remove(SRS_LABEL);
169  12 upgrade = true;
170    }
171    // upgrade old EBI link - easier just to remove and re-add than faffing
172    // around checking exact url
173  89 if (urls.containsKey(UrlConstants.DEFAULT_LABEL))
174    {
175    // note because this is called separately for selected and nonselected
176    // urls, the default url will not always be present
177  25 urls.remove(UrlConstants.DEFAULT_LABEL);
178  25 upgrade = true;
179    }
180  89 if (upgrade)
181    {
182  37 UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
183  37 link.setLabel(UrlConstants.DEFAULT_LABEL);
184  37 urls.put(UrlConstants.DEFAULT_LABEL, link);
185    }
186    }
187   
 
188  108 toggle @Override
189    public List<String> getLinksForMenu()
190    {
191  108 List<String> links = new ArrayList<>();
192  108 Iterator<Map.Entry<String, UrlLink>> it = selectedUrls.entrySet()
193    .iterator();
194  377 while (it.hasNext())
195    {
196  269 Map.Entry<String, UrlLink> pair = it.next();
197  269 links.add(pair.getValue().toString());
198    }
199  108 return links;
200    }
201   
 
202  22 toggle @Override
203    public List<UrlLinkDisplay> getLinksForTable()
204    {
205  22 ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<>();
206  22 displayLinks = getLinksForTable(selectedUrls, true);
207  22 displayLinks.addAll(getLinksForTable(nonselectedUrls, false));
208  22 return displayLinks;
209    }
210   
 
211  44 toggle private ArrayList<UrlLinkDisplay> getLinksForTable(
212    HashMap<String, UrlLink> urlList, boolean selected)
213    {
214  44 return super.getLinksForTable(urlList, null, selected);
215    }
216   
 
217  47 toggle @Override
218    public boolean setPrimaryUrl(String id)
219    {
220  47 if (selectedUrls.containsKey(id))
221    {
222  44 primaryUrl = id;
223    }
224  3 else if (nonselectedUrls.containsKey(id))
225    {
226  0 primaryUrl = id;
227    }
228    else
229    {
230  3 primaryUrl = null;
231    }
232   
233  47 return (primaryUrl != null);
234    }
235   
 
236  7 toggle @Override
237    public String writeUrlsAsString(boolean selected)
238    {
239  7 StringBuffer links = new StringBuffer();
240  7 HashMap<String, UrlLink> urls;
241  7 if (selected)
242    {
243  4 urls = selectedUrls;
244    }
245    else
246    {
247  3 urls = nonselectedUrls;
248    }
249  7 if (urls.size() > 0)
250    {
251  7 for (Entry<String, UrlLink> entry : urls.entrySet())
252    {
253  22 links.append(entry.getValue().toString());
254  22 links.append(SEP);
255    }
256   
257    // remove last SEP
258  7 links.setLength(links.length() - 1);
259    }
260    else
261    {
262  0 urls.clear();
263    }
264  7 return links.toString();
265    }
266   
 
267  12 toggle @Override
268    public String getPrimaryUrl(String seqid)
269    {
270  12 String result = super.getPrimaryUrl(seqid, selectedUrls);
271  12 if (result == null)
272    {
273  2 result = super.getPrimaryUrl(seqid, nonselectedUrls);
274    }
275  12 return result;
276    }
277   
 
278  8 toggle @Override
279    public String getPrimaryUrlId()
280    {
281  8 return primaryUrl;
282    }
283   
 
284  0 toggle @Override
285    public String getPrimaryTarget(String seqid)
286    {
287  0 return selectedUrls.get(primaryUrl).getTarget();
288    }
289   
 
290  9 toggle @Override
291    public void setUrlData(List<UrlLinkDisplay> links)
292    {
293  9 HashMap<String, UrlLink> unselurls = new HashMap<>();
294  9 HashMap<String, UrlLink> selurls = new HashMap<>();
295   
296  9 Iterator<UrlLinkDisplay> it = links.iterator();
297  99 while (it.hasNext())
298    {
299  90 UrlLinkDisplay link = it.next();
300   
301    // MIRIAM ids will be handled by a different UrlProvider class
302  90 if (!isMiriamId(link.getId()))
303    {
304    // don't allow duplicate key names as entries will be overwritten
305  55 if (unselurls.containsKey(link.getId())
306    || selurls.containsKey(link.getId()))
307    {
308  0 throw new IllegalArgumentException(MessageManager.formatMessage(
309    "exception.url_cannot_have_duplicate_id", link.getId()));
310    }
311  55 if (link.getIsSelected())
312    {
313  37 selurls.put(link.getId(), new UrlLink(link.getDescription(),
314    link.getUrl(), link.getDescription()));
315    }
316    else
317    {
318  18 unselurls.put(link.getId(), new UrlLink(link.getDescription(),
319    link.getUrl(), link.getDescription()));
320    }
321    // sort out primary and selected ids
322  55 if (link.getIsPrimary())
323    {
324  8 setPrimaryUrl(link.getId());
325    }
326    }
327   
328    }
329  9 nonselectedUrls = unselurls;
330  9 selectedUrls = selurls;
331    }
332   
 
333  5 toggle @Override
334    public String choosePrimaryUrl()
335    {
336    // unilaterally set the primary id to the EMBL_EBI link
337  5 if ((!nonselectedUrls.containsKey(UrlConstants.DEFAULT_LABEL))
338    && (!selectedUrls.containsKey(UrlConstants.DEFAULT_LABEL)))
339    {
340  4 UrlLink link = new UrlLink(UrlConstants.DEFAULT_STRING);
341  4 link.setLabel(UrlConstants.DEFAULT_LABEL);
342  4 selectedUrls.put(UrlConstants.DEFAULT_LABEL, link);
343    }
344  5 primaryUrl = UrlConstants.DEFAULT_LABEL;
345  5 return UrlConstants.DEFAULT_LABEL;
346    }
347   
 
348  38 toggle @Override
349    public boolean contains(String id)
350    {
351  38 return (selectedUrls.containsKey(id)
352    || nonselectedUrls.containsKey(id));
353    }
354   
355    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 15:21:34 GMT using coverage data from Mon Nov 11 2024 15:21:19 GMT.
  • OpenClover is free and open-source software.