2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
24 import static jalview.util.UrlConstants.DB_ACCESSION;
25 import static jalview.util.UrlConstants.DELIM;
26 import static jalview.util.UrlConstants.SEP;
28 import jalview.util.JSONUtils;
29 import jalview.util.UrlLink;
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;
38 import java.util.StringTokenizer;
40 import org.json.simple.parser.ParseException;
44 * Implements the UrlProviderI interface for a UrlProvider object which serves
45 * URLs from identifiers.org
50 public class IdentifiersUrlProvider extends UrlProviderImpl
53 private static final String LOCAL_KEY = "Local";
55 private static final String ID_ORG_KEY = "identifiers.org";
57 // map of string ids to urls
58 private HashMap<String, UrlLink> urls;
60 // list of selected urls
61 private ArrayList<String> selectedUrls;
63 public IdentifiersUrlProvider(String cachedUrlList)
65 urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
66 selectedUrls = new ArrayList<String>();
67 checkSelectionMatchesUrls(cachedUrlList);
71 * Read data from an identifiers.org download file
74 * name of identifiers.org download file
75 * @return hashmap of identifiers.org data, keyed by MIRIAM id
77 @SuppressWarnings("unchecked")
78 private HashMap<String, UrlLink> readIdentifiers(String idFileName)
80 // identifiers.org data
81 HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
83 String errorMessage = null;
86 // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
88 FileReader reader = new FileReader(idFileName);
90 Map<String, Object> obj = (Map<String, Object>) JSONUtils.parse(reader);
91 if (obj.containsKey(ID_ORG_KEY))
95 else if (obj.containsKey(LOCAL_KEY))
102 "Unexpected key returned from identifiers jalview service");
106 List<Object> jsonarray = (List<Object>) obj.get(key);
108 // loop over each entry in JSON array and build HashMap entry
109 for (int i = 0; i < jsonarray.size(); i++)
111 Map<String, Object> item = (Map<String, Object>) jsonarray.get(i);
113 String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
115 UrlLink link = new UrlLink((String) item.get("name"), url,
116 (String) item.get("prefix"));
117 idData.put((String) item.get("id"), link);
119 } catch (IOException | ParseException e)
121 // unnecessary e.printStackTrace();
122 // Note how in JavaScript we can grab the first bytes from any file reader.
123 // Typical report here is "NetworkError" because the file does not exist.
124 // "https://." is coming from System.getProperty("user.home"), but this could
125 // be set by the page developer to anything, of course.
126 errorMessage = (/** @j2sNative String.fromCharCode.apply(null, reader.$in.is.buf.slice(0,12)) || */e.toString());
129 // BH 2018 -- added more valuable report
130 if (errorMessage != null)
131 System.err.println("IdentifiersUrlProvider: cannot read " + idFileName + ": " + errorMessage);
135 private void checkSelectionMatchesUrls(String cachedUrlList)
137 StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
138 while (st.hasMoreElements())
140 String id = st.nextToken();
144 // this is an identifiers.org MIRIAM id
145 if (urls.containsKey(id))
147 selectedUrls.add(id);
152 // reset defaultUrl in case it is no longer selected
153 setPrimaryUrl(primaryUrl);
157 public boolean setPrimaryUrl(String id)
159 if (urls.containsKey(id))
168 return urls.containsKey(id);
172 public String writeUrlsAsString(boolean selected)
176 return ""; // we don't cache unselected identifiers.org urls
179 StringBuffer links = new StringBuffer();
180 if (!selectedUrls.isEmpty())
182 for (String k : selectedUrls)
188 links.setLength(links.length() - 1);
190 return links.toString();
194 public List<String> getLinksForMenu()
196 List<String> links = new ArrayList<String>();
197 for (String key : selectedUrls)
199 links.add(urls.get(key).toStringWithTarget());
205 public List<UrlLinkDisplay> getLinksForTable()
207 return super.getLinksForTable(urls, selectedUrls, false);
211 public void setUrlData(List<UrlLinkDisplay> links)
213 selectedUrls = new ArrayList<String>();
215 Iterator<UrlLinkDisplay> it = links.iterator();
218 UrlLinkDisplay link = it.next();
220 // Handle links with MIRIAM ids only
221 if (isMiriamId(link.getId()))
223 // select/deselect links accordingly and set default url
224 if (urls.containsKey(link.getId()))
226 if (link.getIsSelected())
228 selectedUrls.add(link.getId());
230 if (link.getIsPrimary())
232 setPrimaryUrl(link.getId());
240 public String getPrimaryUrl(String seqid)
242 return super.getPrimaryUrl(seqid, urls);
246 public String getPrimaryUrlId()
252 public String getPrimaryTarget(String seqid)
258 public String choosePrimaryUrl()
264 public boolean contains(String id)
266 return (urls.containsKey(id));