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 java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map.Entry;
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
{
- public IdentifiersUrlProvider(String cachedUrlList)
+ // map of string ids to urls
+ private HashMap<String, HashMap<String, String>> urls;
+
+ // list of selected urls
+ private ArrayList<String> selectedUrls;
+
+ /*
+ * Location of file for identifiers.org download
+ */
+ public static final String ID_ORG_FILE = System.getProperty("user.home")
+ + File.separatorChar + ".jalview_identifiers";
+
+ public IdentifiersUrlProvider(String cachedUrlList, String idFileName)
+ {
+ try
+ {
+ // File idFile = getIdentifiers();
+ urls = readIdentifiers(new FileReader(idFileName));
+ selectedUrls = new ArrayList<String>();
+ checkSelectionMatchesUrls(cachedUrlList);
+
+ } catch (IOException e)
+ {
+ System.out.println("Exception reading URLs from identifiers.org");
+ System.out.println(e.getMessage());
+ }
+ }
+
+ private File getIdentifiers() throws IOException
+ {
+ String identifiersorgUrl = "http://identifiers.org/rest/collections/";
+ String outfile = "identifiers.json";
+ int BUFFER_SIZE = 4096;
+
+ URL url = new URL(identifiersorgUrl);
+ InputStream is = new BufferedInputStream(url.openStream());
+ FileOutputStream os = new FileOutputStream(outfile);
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int bytesRead = -1;
+ while ((bytesRead = is.read(buffer)) != -1)
+ {
+ os.write(buffer, 0, bytesRead);
+ }
+ os.close();
+ is.close();
+
+ return new File(outfile);
+ }
+
+ private HashMap<String, HashMap<String, String>> readIdentifiers(
+ FileReader reader)
{
+ JSONParser parser = new JSONParser();
+ HashMap<String, HashMap<String, String>> idData = new HashMap<String, HashMap<String, String>>();
+
+ try
+ {
+ 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);
+
+ HashMap<String, String> idEntry = new HashMap<String, String>();
+ idEntry.put("name", (String) item.get("name"));
+ idEntry.put("url", (String) item.get("url"));
+ idData.put((String) item.get("id"), idEntry);
+ }
+ } 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)
{
+ String[] prevSelected = cachedUrlList.split("\\" + SEP);
+ for (String id : prevSelected)
+ {
+ if (urls.containsKey(id))
+ {
+ selectedUrls.add(id);
+ }
+ }
+
+ // reset defaultUrl in case it is no longer selected
+ setDefaultUrl(defaultUrl);
}
- @Override
- public String getDefaultUrl()
+ private void checkSelectionMatchesUrls(Vector<String> idList)
{
- // TODO Auto-generated method stub
- return null;
+ String[] prevSelected = new String[idList.size()];
+ idList.toArray(prevSelected);
+ for (String id : prevSelected)
+ {
+ if (urls.containsKey(id))
+ {
+ selectedUrls.add(id);
+ }
+ }
+
+ // reset defaultUrl in case it is no longer selected
+ setDefaultUrl(defaultUrl);
}
@Override
public boolean setDefaultUrl(String id)
{
- return false;
+ if (selectedUrls.contains(id))
+ {
+ defaultUrl = id;
+ }
+ else
+ {
+ defaultUrl = null;
+ }
+ return selectedUrls.contains(id);
}
@Override
public String writeUrlsAsString()
{
+ if (!selectedUrls.isEmpty())
+ {
+ StringBuffer links = new StringBuffer();
+ for (String k : selectedUrls)
+ {
+ links.append(k);
+ links.append(SEP);
+ }
+ // remove last SEP
+ links.setLength(links.length() - 1);
+ return links.toString();
+ }
return "";
}
@Override
- public Vector<String> getLinksForDisplay()
+ public Vector<String> getLinksForMenu()
{
- // TODO Auto-generated method stub
- return null;
+ Vector<String> links = new Vector<String>();
+ for (String key : selectedUrls)
+ {
+ links.add(urls.get(key).get("name") + SEP + urls.get(key).get("url")
+ + "/" + DELIM
+ + DB_ACCESSION + DELIM);
+ }
+ return links;
}
@Override
- public String getDefaultUrl(String seqid)
+ public List<UrlLinkDisplay> getLinksForTable()
{
- // TODO Auto-generated method stub
- return null;
+ ArrayList<UrlLinkDisplay> displayLinks = new ArrayList<UrlLinkDisplay>();
+ for (Entry<String, HashMap<String, String>> entry : urls.entrySet())
+ {
+ String key = entry.getKey();
+ boolean isDefault = (key == defaultUrl);
+ boolean isSelected = (selectedUrls.contains(key));
+ displayLinks.add(new UrlLinkDisplay(key,
+ entry.getValue().get("name"),
+ entry.getValue().get("url")
+ + "/" + DELIM + DB_ACCESSION + DELIM, isSelected, isDefault));
+ }
+ return displayLinks;
}
@Override
- public String getDefaultTarget(String seqid)
+ 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())) // TODO separate use of name and id
+ {
+ // select/deselect links accordingly and set default url
+
+ if (link.getIsSelected())
+ {
+ if (urls.containsKey(link.getId()))
+ {
+ selectedUrls.add(link.getId());
+ }
+ if (link.getIsDefault())
+ {
+ setDefaultUrl(link.getId());
+ }
+
+ }
+ }
+
+ }
+ }
+
+ @Override
+ public String getDefaultUrl(String seqid)
+ {
+ if (seqid.length() < MIN_SUBST_LENGTH)
+ {
+ return null;
+ }
+ else if (defaultUrl == null)
+ {
+ return null;
+ }
+ else
+ {
+ return urls.get(defaultUrl).get("url") + "/" + seqid;
+ }
}
@Override
- public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ public String getDefaultTarget(String seqid)
{
- // deliberately left empty
- // TODO throw exception if called
+ // TODO Auto-generated method stub
+ return null;
}
@Override
git://source.jalview.org / jalview.git / blobdiff