--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.DELIM;
+import static jalview.util.UrlConstants.SEP;
+
+import jalview.util.UrlLink;
+
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.StringTokenizer;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+/**
+ *
+ * Implements the UrlProviderI interface for a UrlProvider object which serves
+ * URLs from identifiers.org
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifiersUrlProvider extends UrlProviderImpl
+{
+
+ private static final String LOCAL_KEY = "Local";
+
+ private static final String ID_ORG_KEY = "identifiers.org";
+
+ // map of string ids to urls
+ private HashMap<String, UrlLink> urls;
+
+ // list of selected urls
+ private ArrayList<String> selectedUrls;
+
+ public IdentifiersUrlProvider(String cachedUrlList)
+ {
+ urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
+ selectedUrls = new ArrayList<String>();
+ checkSelectionMatchesUrls(cachedUrlList);
+ }
+
+ /**
+ * Read data from an identifiers.org download file
+ *
+ * @param idFileName
+ * name of identifiers.org download file
+ * @return hashmap of identifiers.org data, keyed by MIRIAM id
+ */
+ private HashMap<String, UrlLink> readIdentifiers(
+ String idFileName)
+ {
+ JSONParser parser = new JSONParser();
+
+ // identifiers.org data
+ HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+
+ try
+ {
+ FileReader reader = new FileReader(idFileName);
+ String key = "";
+ JSONObject obj = (JSONObject) parser.parse(reader);
+ if (obj.containsKey(ID_ORG_KEY))
+ {
+ key = ID_ORG_KEY;
+ }
+ else if (obj.containsKey(LOCAL_KEY))
+ {
+ key = LOCAL_KEY;
+ }
+ else
+ {
+ System.out
+ .println("Unexpected key returned from identifiers jalview service");
+ return idData;
+ }
+
+ JSONArray jsonarray = (JSONArray) obj.get(key);
+
+ // loop over each entry in JSON array and build HashMap entry
+ for (int i = 0; i < jsonarray.size(); i++)
+ {
+ JSONObject item = (JSONObject) jsonarray.get(i);
+
+ String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
+ + DELIM;
+ UrlLink link = new UrlLink((String) item.get("name"), url,
+ (String) item.get("prefix"));
+ idData.put((String) item.get("id"), link);
+ }
+ } catch (FileNotFoundException e)
+ {
+ e.printStackTrace();
+ idData.clear();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ idData.clear();
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ idData.clear();
+ }
+ return idData;
+ }
+
+ private void checkSelectionMatchesUrls(String cachedUrlList)
+ {
+ StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
+ while (st.hasMoreElements())
+ {
+ String id = st.nextToken();
+
+ if (isMiriamId(id))
+ {
+ // this is an identifiers.org MIRIAM id
+ if (urls.containsKey(id))
+ {
+ selectedUrls.add(id);
+ }
+ }
+ }
+
+ // reset defaultUrl in case it is no longer selected
+ setPrimaryUrl(primaryUrl);
+ }
+
+ @Override
+ public boolean setPrimaryUrl(String id)
+ {
+ if (urls.containsKey(id))
+ {
+ primaryUrl = id;
+ }
+ else
+ {
+ primaryUrl = null;
+ }
+
+ return urls.containsKey(id);
+ }
+
+ @Override
+ public String writeUrlsAsString(boolean selected)
+ {
+ if (!selected)
+ {
+ return ""; // we don't cache unselected identifiers.org urls
+ }
+
+ StringBuffer links = new StringBuffer();
+ if (!selectedUrls.isEmpty())
+ {
+ for (String k : selectedUrls)
+ {
+ links.append(k);
+ links.append(SEP);
+ }
+ // remove last SEP
+ links.setLength(links.length() - 1);
+ }
+ return links.toString();
+ }
+
+ @Override
+ public List<String> getLinksForMenu()
+ {
+ List<String> links = new ArrayList<String>();
+ for (String key : selectedUrls)
+ {
+ links.add(urls.get(key).toStringWithTarget());
+ }
+ return links;
+ }
+
+ @Override
+ public List<UrlLinkDisplay> getLinksForTable()
+ {
+ return super.getLinksForTable(urls, selectedUrls, false);
+ }
+
+ @Override
+ public void setUrlData(List<UrlLinkDisplay> links)
+ {
+ selectedUrls = new ArrayList<String>();
+
+ Iterator<UrlLinkDisplay> it = links.iterator();
+ while (it.hasNext())
+ {
+ UrlLinkDisplay link = it.next();
+
+ // Handle links with MIRIAM ids only
+ if (isMiriamId(link.getId()))
+ {
+ // select/deselect links accordingly and set default url
+ if (urls.containsKey(link.getId()))
+ {
+ if (link.getIsSelected())
+ {
+ selectedUrls.add(link.getId());
+ }
+ if (link.getIsPrimary())
+ {
+ setPrimaryUrl(link.getId());
+ }
+ }
+ }
+ }
+ }
+
+ @Override
+ public String getPrimaryUrl(String seqid)
+ {
+ return super.getPrimaryUrl(seqid, urls);
+ }
+
+ @Override
+ public String getPrimaryUrlId()
+ {
+ return primaryUrl;
+ }
+
+ @Override
+ public String getPrimaryTarget(String seqid)
+ {
+ return null;
+ }
+
+ @Override
+ public String choosePrimaryUrl()
+ {
+ return null;
+ }
+
+ @Override
+ public boolean contains(String id)
+ {
+ return (urls.containsKey(id));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff