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.JSONUtils;
+import jalview.util.UrlLink;
+
+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.Vector;
+import java.util.StringTokenizer;
+
+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;
+
+ // list of selected urls
+ private ArrayList<String> selectedUrls;
+
public IdentifiersUrlProvider(String cachedUrlList)
{
+ urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
+ selectedUrls = new ArrayList<>();
+ 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
+ */
+ @SuppressWarnings("unchecked")
+ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
+ {
+ // identifiers.org data
+ 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;
+ }
+ 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++)
+ {
+ 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"), url,
+ (String) item.get("prefix"));
+ idData.put((String) item.get("id"), link);
+ }
+ } catch (IOException | 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)
+ {
+ jalview.bin.Console.errPrintln("IdentifiersUrlProvider: cannot read " + idFileName
+ + ": " + errorMessage);
+ }
+ 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
+ setPrimaryUrl(primaryUrl);
}
@Override
- public String getDefaultUrl()
+ public boolean setPrimaryUrl(String id)
{
- // TODO Auto-generated method stub
- return null;
+ if (urls.containsKey(id))
+ {
+ primaryUrl = id;
+ }
+ else
+ {
+ primaryUrl = null;
+ }
+
+ return urls.containsKey(id);
}
@Override
- public boolean setDefaultUrl(String id)
+ public String writeUrlsAsString(boolean selected)
{
- return false;
+ 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 String writeUrlsAsString()
+ public List<String> getLinksForMenu()
{
- return "";
+ List<String> links = new ArrayList<>();
+ for (String key : selectedUrls)
+ {
+ links.add(urls.get(key).toStringWithTarget());
+ }
+ return links;
}
@Override
- public Vector<String> getLinksForDisplay()
+ public List<UrlLinkDisplay> getLinksForTable()
{
- // TODO Auto-generated method stub
- return null;
+ return super.getLinksForTable(urls, selectedUrls, false);
}
@Override
- public String getDefaultUrl(String seqid)
+ public void setUrlData(List<UrlLinkDisplay> links)
{
- // TODO Auto-generated method stub
- return null;
+ selectedUrls = new ArrayList<>();
+
+ 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 getDefaultTarget(String seqid)
+ public String getPrimaryUrl(String seqid)
{
- // TODO Auto-generated method stub
- return null;
+ return super.getPrimaryUrl(seqid, urls);
}
@Override
- public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ public String getPrimaryUrlId()
{
- // deliberately left empty
- // TODO throw exception if called
+ return primaryUrl;
}
@Override
- public String chooseDefaultUrl()
+ public String getPrimaryTarget(String seqid)
{
- // TODO Auto-generated method stub
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