import static jalview.util.UrlConstants.DELIM;
import static jalview.util.UrlConstants.SEP;
+import jalview.util.JSONUtils;
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.Map;
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;
/**
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;
public IdentifiersUrlProvider(String cachedUrlList)
{
urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
- selectedUrls = new ArrayList<String>();
+ selectedUrls = new ArrayList<>();
checkSelectionMatchesUrls(cachedUrlList);
}
* name of identifiers.org download file
* @return hashmap of identifiers.org data, keyed by MIRIAM id
*/
- private HashMap<String, UrlLink> readIdentifiers(
- String idFileName)
+ @SuppressWarnings("unchecked")
+ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
{
- JSONParser parser = new JSONParser();
-
// identifiers.org data
- HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+ HashMap<String, UrlLink> idData = new HashMap<>();
+ String errorMessage = null;
try
{
+ // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
+
FileReader reader = new FileReader(idFileName);
+ String key = "";
+ Map<String, Object> obj = (Map<String, Object>) JSONUtils
+ .parse(reader);
+ if (obj.containsKey(ID_ORG_KEY))
+ {
+ key = ID_ORG_KEY;
+ }
+ else if (obj.containsKey(LOCAL_KEY))
+ {
+ key = LOCAL_KEY;
+ }
+ else
+ {
+ jalview.bin.Console.outPrintln(
+ "Unexpected key returned from identifiers jalview service");
+ return idData;
+ }
- JSONArray jsonarray = (JSONArray) parser.parse(reader);
+ List<Object> jsonarray = (List<Object>) 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);
+ Map<String, Object> item = (Map<String, Object>) jsonarray.get(i);
String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
+ DELIM;
- UrlLink link = new UrlLink((String) item.get("name") + SEP + url);
+ UrlLink link = new UrlLink((String) item.get("name"), url,
+ (String) item.get("prefix"));
idData.put((String) item.get("id"), link);
}
- } catch (FileNotFoundException e)
+ } catch (IOException | ParseException e)
{
- e.printStackTrace();
- } catch (IOException e)
- {
- e.printStackTrace();
- } catch (ParseException e)
+ // unnecessary e.printStackTrace();
+ // Note how in JavaScript we can grab the first bytes from any file
+ // reader.
+ // Typical report here is "NetworkError" because the file does not exist.
+ // "https://." is coming from System.getProperty("user.home"), but this
+ // could
+ // be set by the page developer to anything, of course.
+ errorMessage = e.toString();
+ idData.clear();
+ }
+ // BH 2018 -- added more valuable report
+ if (errorMessage != null)
{
- e.printStackTrace();
+ jalview.bin.Console.errPrintln("IdentifiersUrlProvider: cannot read " + idFileName
+ + ": " + errorMessage);
}
return idData;
}
}
// reset defaultUrl in case it is no longer selected
- setDefaultUrl(defaultUrl);
+ setPrimaryUrl(primaryUrl);
}
@Override
- public boolean setDefaultUrl(String id)
+ public boolean setPrimaryUrl(String id)
{
if (urls.containsKey(id))
{
- defaultUrl = id;
+ primaryUrl = id;
}
else
{
- defaultUrl = null;
+ primaryUrl = null;
}
return urls.containsKey(id);
}
@Override
- public Vector<String> getLinksForMenu()
+ public List<String> getLinksForMenu()
{
- Vector<String> links = new Vector<String>();
+ List<String> links = new ArrayList<>();
for (String key : selectedUrls)
{
- links.add(urls.get(key).toString());
+ links.add(urls.get(key).toStringWithTarget());
}
return links;
}
@Override
public void setUrlData(List<UrlLinkDisplay> links)
{
- selectedUrls = new ArrayList<String>();
+ selectedUrls = new ArrayList<>();
Iterator<UrlLinkDisplay> it = links.iterator();
while (it.hasNext())
{
selectedUrls.add(link.getId());
}
- if (link.getIsDefault())
+ if (link.getIsPrimary())
{
- setDefaultUrl(link.getId());
+ setPrimaryUrl(link.getId());
}
}
}
}
@Override
- public String getDefaultUrl(String seqid)
+ public String getPrimaryUrl(String seqid)
{
- return super.getDefaultUrl(seqid, urls);
+ return super.getPrimaryUrl(seqid, urls);
}
@Override
- public String getDefaultUrlId()
+ public String getPrimaryUrlId()
{
- return defaultUrl;
+ return primaryUrl;
}
@Override
- public String getDefaultTarget(String seqid)
+ public String getPrimaryTarget(String seqid)
{
return null;
}
@Override
- public String chooseDefaultUrl()
+ public String choosePrimaryUrl()
{
return null;
}
+
+ @Override
+ public boolean contains(String id)
+ {
+ return (urls.containsKey(id));
+ }
}