Coverage Report
File IdentifiersUrlProvider.java
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12% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| IdentifiersUrlProvider | 50 | 66 | 29 |
Contributing tests
This file is covered by 63 tests.
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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 | ||
| 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.JSONUtils; | |
| 29 | import jalview.util.UrlLink; | |
| 30 | ||
| 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.Map; | |
| 38 | import java.util.StringTokenizer; | |
| 39 | ||
| 40 | import org.json.simple.parser.ParseException; | |
| 41 | ||
| 42 | /** | |
| 43 | * | |
| 44 | * Implements the UrlProviderI interface for a UrlProvider object which serves | |
| 45 | * URLs from identifiers.org | |
| 46 | * | |
| 47 | * @author $author$ | |
| 48 | * @version $Revision$ | |
| 49 | */ | |
| 50 | public class IdentifiersUrlProvider extends UrlProviderImpl | |
| 51 | { | |
| 52 | ||
| 53 | private static final String LOCAL_KEY = "Local"; | |
| 54 | ||
| 55 | private static final String ID_ORG_KEY = "identifiers.org"; | |
| 56 | ||
| 57 | // map of string ids to urls | |
| 58 | private HashMap<String, UrlLink> urls; | |
| 59 | ||
| 60 | // list of selected urls | |
| 61 | private ArrayList<String> selectedUrls; | |
| 62 | ||
| 63 | 41 |  public IdentifiersUrlProvider(String cachedUrlList) |
| 64 | { | |
| 65 | 41 | urls = readIdentifiers(IdOrgSettings.getDownloadLocation()); |
| 66 | 41 | selectedUrls = new ArrayList<>(); |
| 67 | 41 | checkSelectionMatchesUrls(cachedUrlList); |
| 68 | } | |
| 69 | ||
| 70 | /** | |
| 71 | * Read data from an identifiers.org download file | |
| 72 | * | |
| 73 | * @param idFileName | |
| 74 | * name of identifiers.org download file | |
| 75 | * @return hashmap of identifiers.org data, keyed by MIRIAM id | |
| 76 | */ | |
| 77 | 41 | @SuppressWarnings("unchecked") |
| 78 | private HashMap<String, UrlLink> readIdentifiers(String idFileName) | |
| 79 | { | |
| 80 | // identifiers.org data | |
| 81 | 41 | HashMap<String, UrlLink> idData = new HashMap<>(); |
| 82 | ||
| 83 | 41 | String errorMessage = null; |
| 84 | 41 | try |
| 85 | { | |
| 86 | // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER | |
| 87 | ||
| 88 | 41 | FileReader reader = new FileReader(idFileName); |
| 89 | 41 | String key = ""; |
| 90 | 41 | Map<String, Object> obj = (Map<String, Object>) JSONUtils |
| 91 | .parse(reader); | |
| 92 | 41 | if (obj.containsKey(ID_ORG_KEY)) |
| 93 | { | |
| 94 | 0 | key = ID_ORG_KEY; |
| 95 | } | |
| 96 | 41 | else if (obj.containsKey(LOCAL_KEY)) |
| 97 | { | |
| 98 | 41 | key = LOCAL_KEY; |
| 99 | } | |
| 100 | else | |
| 101 | { | |
| 102 | 0 | jalview.bin.Console.outPrintln( |
| 103 | "Unexpected key returned from identifiers jalview service"); | |
| 104 | 0 | return idData; |
| 105 | } | |
| 106 | ||
| 107 | 41 | List<Object> jsonarray = (List<Object>) obj.get(key); |
| 108 | ||
| 109 | // loop over each entry in JSON array and build HashMap entry | |
| 110 | 15061 | for (int i = 0; i < jsonarray.size(); i++) |
| 111 | { | |
| 112 | 15020 | Map<String, Object> item = (Map<String, Object>) jsonarray.get(i); |
| 113 | ||
| 114 | 15020 | String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION |
| 115 | + DELIM; | |
| 116 | 15020 | UrlLink link = new UrlLink((String) item.get("name"), url, |
| 117 | (String) item.get("prefix")); | |
| 118 | 15020 | 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 | |
| 124 | // reader. | |
| 125 | // Typical report here is "NetworkError" because the file does not exist. | |
| 126 | // "https://." is coming from System.getProperty("user.home"), but this | |
| 127 | // could | |
| 128 | // be set by the page developer to anything, of course. | |
| 129 | 0 | errorMessage = e.toString(); |
| 130 | 0 | idData.clear(); |
| 131 | } | |
| 132 | // BH 2018 -- added more valuable report | |
| 133 | 41 | if (errorMessage != null) |
| 134 | { | |
| 135 | 0 | jalview.bin.Console.errPrintln("IdentifiersUrlProvider: cannot read " |
| 136 | + idFileName + ": " + errorMessage); | |
| 137 | } | |
| 138 | 41 | return idData; |
| 139 | } | |
| 140 | ||
| 141 | 41 | private void checkSelectionMatchesUrls(String cachedUrlList) |
| 142 | { | |
| 143 | 41 | StringTokenizer st = new StringTokenizer(cachedUrlList, SEP); |
| 144 | 307 | while (st.hasMoreElements()) |
| 145 | { | |
| 146 | 266 | String id = st.nextToken(); |
| 147 | ||
| 148 | 266 | if (isMiriamId(id)) |
| 149 | { | |
| 150 | // this is an identifiers.org MIRIAM id | |
| 151 | 44 | if (urls.containsKey(id)) |
| 152 | { | |
| 153 | 44 | selectedUrls.add(id); |
| 154 | } | |
| 155 | } | |
| 156 | } | |
| 157 | ||
| 158 | // reset defaultUrl in case it is no longer selected | |
| 159 | 41 | setPrimaryUrl(primaryUrl); |
| 160 | } | |
| 161 | ||
| 162 | 79 | @Override |
| 163 | public boolean setPrimaryUrl(String id) | |
| 164 | { | |
| 165 | 79 | if (urls.containsKey(id)) |
| 166 | { | |
| 167 | 2 | primaryUrl = id; |
| 168 | } | |
| 169 | else | |
| 170 | { | |
| 171 | 77 | primaryUrl = null; |
| 172 | } | |
| 173 | ||
| 174 | 79 | return urls.containsKey(id); |
| 175 | } | |
| 176 | ||
| 177 | 5 | @Override |
| 178 | public String writeUrlsAsString(boolean selected) | |
| 179 | { | |
| 180 | 5 | if (!selected) |
| 181 | { | |
| 182 | 2 | return ""; // we don't cache unselected identifiers.org urls |
| 183 | } | |
| 184 | ||
| 185 | 3 | StringBuffer links = new StringBuffer(); |
| 186 | 3 | if (!selectedUrls.isEmpty()) |
| 187 | { | |
| 188 | 3 | for (String k : selectedUrls) |
| 189 | { | |
| 190 | 9 | links.append(k); |
| 191 | 9 | links.append(SEP); |
| 192 | } | |
| 193 | // remove last SEP | |
| 194 | 3 | links.setLength(links.length() - 1); |
| 195 | } | |
| 196 | 3 | return links.toString(); |
| 197 | } | |
| 198 | ||
| 199 | 103 | @Override |
| 200 | public List<String> getLinksForMenu() | |
| 201 | { | |
| 202 | 103 | List<String> links = new ArrayList<>(); |
| 203 | 103 | for (String key : selectedUrls) |
| 204 | { | |
| 205 | 15 | links.add(urls.get(key).toStringWithTarget()); |
| 206 | } | |
| 207 | 103 | return links; |
| 208 | } | |
| 209 | ||
| 210 | 21 | @Override |
| 211 | public List<UrlLinkDisplay> getLinksForTable() | |
| 212 | { | |
| 213 | 21 | return super.getLinksForTable(urls, selectedUrls, false); |
| 214 | } | |
| 215 | ||
| 216 | 9 | @Override |
| 217 | public void setUrlData(List<UrlLinkDisplay> links) | |
| 218 | { | |
| 219 | 9 | selectedUrls = new ArrayList<>(); |
| 220 | ||
| 221 | 9 | Iterator<UrlLinkDisplay> it = links.iterator(); |
| 222 | 99 | while (it.hasNext()) |
| 223 | { | |
| 224 | 90 | UrlLinkDisplay link = it.next(); |
| 225 | ||
| 226 | // Handle links with MIRIAM ids only | |
| 227 | 90 | if (isMiriamId(link.getId())) |
| 228 | { | |
| 229 | // select/deselect links accordingly and set default url | |
| 230 | 35 | if (urls.containsKey(link.getId())) |
| 231 | { | |
| 232 | 35 | if (link.getIsSelected()) |
| 233 | { | |
| 234 | 26 | selectedUrls.add(link.getId()); |
| 235 | } | |
| 236 | 35 | if (link.getIsPrimary()) |
| 237 | { | |
| 238 | 0 | setPrimaryUrl(link.getId()); |
| 239 | } | |
| 240 | } | |
| 241 | } | |
| 242 | } | |
| 243 | } | |
| 244 | ||
| 245 | 7 | @Override |
| 246 | public String getPrimaryUrl(String seqid) | |
| 247 | { | |
| 248 | 7 | return super.getPrimaryUrl(seqid, urls); |
| 249 | } | |
| 250 | ||
| 251 | 5 | @Override |
| 252 | public String getPrimaryUrlId() | |
| 253 | { | |
| 254 | 5 | return primaryUrl; |
| 255 | } | |
| 256 | ||
| 257 | 0 | @Override |
| 258 | public String getPrimaryTarget(String seqid) | |
| 259 | { | |
| 260 | 0 | return null; |
| 261 | } | |
| 262 | ||
| 263 | 1 | @Override |
| 264 | public String choosePrimaryUrl() | |
| 265 | { | |
| 266 | 1 | return null; |
| 267 | } | |
| 268 | ||
| 269 | 37 | @Override |
| 270 | public boolean contains(String id) | |
| 271 | { | |
| 272 | 37 | return (urls.containsKey(id)); |
| 273 | } | |
| 274 | } |