package jalview.urls;
-import java.util.Map;
+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 java.util.Vector;
+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
public class IdentifiersUrlProvider extends UrlProviderImpl
{
+ // 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);
+
+ JSONArray jsonarray = (JSONArray) parser.parse(reader);
+
+ // 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") + SEP + url);
+ idData.put((String) item.get("id"), link);
+ }
+ } catch (FileNotFoundException e)
+ {
+ e.printStackTrace();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return idData;
}
- public IdentifiersUrlProvider(Map<String, String> urlList)
+ 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
+ setDefaultUrl(defaultUrl);
+ }
+ @Override
+ public boolean setDefaultUrl(String id)
+ {
+ if (urls.containsKey(id))
+ {
+ defaultUrl = id;
+ }
+ else
+ {
+ defaultUrl = null;
+ }
+
+ return urls.containsKey(id);
}
@Override
- public String getDefaultUrl()
+ public String writeUrlsAsString(boolean selected)
{
- // TODO Auto-generated method stub
- return null;
+ 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 boolean setDefaultUrl(String id)
+ public Vector<String> getLinksForMenu()
{
- return false;
+ Vector<String> links = new Vector<String>();
+ for (String key : selectedUrls)
+ {
+ links.add(urls.get(key).toString());
+ }
+ return links;
}
@Override
- public String writeUrlsAsString()
+ public List<UrlLinkDisplay> getLinksForTable()
{
- return "";
+ return super.getLinksForTable(urls, selectedUrls, false);
}
@Override
- public Vector<String> getLinksForDisplay()
+ public void setUrlData(List<UrlLinkDisplay> links)
{
- // TODO Auto-generated method stub
- return null;
+ 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.getIsDefault())
+ {
+ setDefaultUrl(link.getId());
+ }
+ }
+ }
+ }
}
@Override
public String getDefaultUrl(String seqid)
{
- // TODO Auto-generated method stub
- return null;
+ return super.getDefaultUrl(seqid, urls);
}
@Override
- public String getDefaultTarget(String seqid)
+ public String getDefaultUrlId()
{
- // TODO Auto-generated method stub
- return null;
+ return defaultUrl;
}
@Override
- public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ public String getDefaultTarget(String seqid)
{
- // deliberately left empty
- // TODO throw exception if called
+ return null;
}
@Override
public String chooseDefaultUrl()
{
- // TODO Auto-generated method stub
return null;
}
-
}