import static jalview.util.UrlConstants.DELIM;
import static jalview.util.UrlConstants.SEP;
-import java.io.BufferedInputStream;
-import java.io.File;
+import jalview.util.UrlLink;
+
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.StringTokenizer;
import java.util.Vector;
import org.json.simple.JSONArray;
{
// 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;
- /*
- * 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
+ public IdentifiersUrlProvider(String cachedUrlList)
{
- 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<String>();
+ 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
+ */
+ 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, UrlLink>();
try
{
+ FileReader reader = new FileReader(idFileName);
+
JSONArray jsonarray = (JSONArray) parser.parse(reader);
// loop over each entry in JSON array and build HashMap entry
{
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);
+ 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)
{
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);
+ }
}
}
}
@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
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);
+ links.add(urls.get(key).toString());
}
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
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
@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;
- }
+ return super.getDefaultUrl(seqid, urls);
+ }
+
+ @Override
+ public String getDefaultUrlId()
+ {
+ return defaultUrl;
}
@Override
git://source.jalview.org / jalview.git / blobdiff