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 jalview.util.JSONUtils;
+import jalview.util.UrlLink;
+
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 java.util.Map;
+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;
/**
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, HashMap<String, String>> urls;
+ private HashMap<String, UrlLink> urls;
// list of selected urls
private ArrayList<String> selectedUrls;
- public IdentifiersUrlProvider(String cachedUrlList, String idFileName)
+ public IdentifiersUrlProvider(String cachedUrlList)
{
- 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);
+ urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
+ selectedUrls = new ArrayList<>();
+ checkSelectionMatchesUrls(cachedUrlList);
}
- private HashMap<String, HashMap<String, String>> readIdentifiers(
- FileReader reader)
+ /**
+ * 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)
{
- JSONParser parser = new JSONParser();
- HashMap<String, HashMap<String, String>> idData = new HashMap<String, HashMap<String, String>>();
+ // identifiers.org data
+ HashMap<String, UrlLink> idData = new HashMap<>();
+ String errorMessage = null;
try
{
- JSONArray jsonarray = (JSONArray) parser.parse(reader);
+ // 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++)
{
- JSONObject item = (JSONObject) jsonarray.get(i);
+ Map<String, Object> item = (Map<String, Object>) 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);
+ 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();
- } catch (IOException e)
+ } catch (IOException | ParseException 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;
}
private void checkSelectionMatchesUrls(String cachedUrlList)
{
-
- String[] prevSelected = cachedUrlList.split("\\" + SEP);
- for (String id : prevSelected)
+ StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
+ while (st.hasMoreElements())
{
- if (urls.containsKey(id))
- {
- selectedUrls.add(id);
- }
- }
-
- // reset defaultUrl in case it is no longer selected
- setDefaultUrl(defaultUrl);
- }
+ String id = st.nextToken();
- private void checkSelectionMatchesUrls(Vector<String> idList)
- {
- String[] prevSelected = new String[idList.size()];
- idList.toArray(prevSelected);
- for (String id : prevSelected)
- {
- if (urls.containsKey(id))
+ if (isMiriamId(id))
{
- selectedUrls.add(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 String getDefaultUrl()
- {
- return defaultUrl;
+ setPrimaryUrl(primaryUrl);
}
@Override
- public boolean setDefaultUrl(String id)
+ public boolean setPrimaryUrl(String id)
{
- if (selectedUrls.contains(id))
+ if (urls.containsKey(id))
{
- defaultUrl = id;
+ primaryUrl = id;
}
else
{
- defaultUrl = null;
+ primaryUrl = null;
}
- return selectedUrls.contains(id);
+
+ return urls.containsKey(id);
}
@Override
- public String writeUrlsAsString()
+ public String writeUrlsAsString(boolean selected)
{
+ if (!selected)
+ {
+ return ""; // we don't cache unselected identifiers.org urls
+ }
+
+ StringBuffer links = new StringBuffer();
if (!selectedUrls.isEmpty())
{
- StringBuffer links = new StringBuffer();
for (String k : selectedUrls)
{
links.append(k);
}
// remove last SEP
links.setLength(links.length() - 1);
- return links.toString();
}
- return "";
+ return links.toString();
}
@Override
- public Vector<String> getLinksForDisplay()
+ public List<String> getLinksForMenu()
{
- Vector<String> links = new Vector<String>();
+ List<String> links = new ArrayList<>();
for (String key : selectedUrls)
{
- links.add(urls.get(key).get("name") + SEP + urls.get(key).get("url")
- + "/" + DELIM
- + DB_ACCESSION + DELIM);
+ links.add(urls.get(key).toStringWithTarget());
}
return links;
}
@Override
public List<UrlLinkDisplay> getLinksForTable()
{
- 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;
+ return super.getLinksForTable(urls, selectedUrls, false);
}
@Override
public void setUrlData(List<UrlLinkDisplay> links)
{
- selectedUrls = new ArrayList<String>();
+ 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())) // TODO separate use of name and id
+ if (isMiriamId(link.getId()))
{
// select/deselect links accordingly and set default url
-
- if (link.getIsSelected())
+ if (urls.containsKey(link.getId()))
{
- if (urls.containsKey(link.getId()))
+ if (link.getIsSelected())
{
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 urls.get(defaultUrl).get("url") + "/" + seqid;
+ return super.getPrimaryUrl(seqid, urls);
}
@Override
- public String getDefaultTarget(String seqid)
+ public String getPrimaryUrlId()
{
- // TODO Auto-generated method stub
- return null;
+ return primaryUrl;
}
@Override
- public void setUrlLinks(Vector<String> names, Vector<String> urls)
+ public String getPrimaryTarget(String seqid)
{
- // ignores urls, only uses names (as ids)
- checkSelectionMatchesUrls(names);
+ return null;
}
@Override
- public String chooseDefaultUrl()
+ public String choosePrimaryUrl()
{
- // TODO Auto-generated method stub
return null;
}
+ @Override
+ public boolean contains(String id)
+ {
+ return (urls.containsKey(id));
+ }
}
git://source.jalview.org / jalview.git / blobdiff