package jalview.urls;
-//import static jalview.util.UrlConstants.EMBLEBI_LABEL;
-//import static jalview.util.UrlConstants.EMBLEBI_STRING;
-//import static jalview.util.UrlConstants.SRS_LABEL;
-
-
import static jalview.util.UrlConstants.DB_ACCESSION;
import static jalview.util.UrlConstants.DELIM;
import static jalview.util.UrlConstants.SEP;
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.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
{
+ // map of string ids to urls
+ private HashMap<String, HashMap<String, String>> urls;
+
+ // list of selected urls
+ private ArrayList<String> selectedUrls;
+
public IdentifiersUrlProvider(String cachedUrlList, String idFileName)
{
+ try
+ {
+ // File idFile = getIdentifiers();
+ urls = readIdentifiers(new FileReader(idFileName));
+ checkSelectionMatchesUrls(cachedUrlList);
+
+ } catch (IOException e)
+ {
+
+ }
+ }
+
+ 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,
- String idFileName)
+ private void checkSelectionMatchesUrls(String cachedUrlList)
{
+ selectedUrls = new ArrayList<String>();
+ 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);
+ }
+ private void checkSelectionMatchesUrls(Vector<String> idList)
+ {
+ selectedUrls = new ArrayList<String>();
+ 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 String getDefaultUrl()
{
- // TODO Auto-generated method stub
- return null;
+ return 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()
{
- return "";
+ StringBuffer links = new StringBuffer();
+ for (String k : selectedUrls)
+ {
+ links.append(k);
+ }
+ return links.toString();
}
@Override
public Vector<String> getLinksForDisplay()
{
- // TODO Auto-generated method stub
- return null;
+ Vector<String> links = new Vector<String>();
+ for (String key : selectedUrls)
+ {
+ links.add(key + SEP + urls.get(key).get("url") + "/" + DELIM
+ + DB_ACCESSION + DELIM);
+ }
+ return links;
}
@Override
public String getDefaultUrl(String seqid)
{
- // TODO Auto-generated method stub
- return null;
+ return urls.get(defaultUrl).get("url") + "/" + seqid;
}
@Override
@Override
public void setUrlLinks(Vector<String> names, Vector<String> urls)
{
- // deliberately left empty
- // TODO throw exception if called
+ // ignores urls, only uses names (as ids)
+ checkSelectionMatchesUrls(names);
}
@Override
UrlProviderI idProvider = new IdentifiersUrlProvider(cachedUrlList,
ID_ORG_FILE);
customProvider = new CustomUrlProvider(cachedUrlList);
- providers.add(idProvider);
+ // providers.add(idProvider);
providers.add(customProvider);
// check that the defaultUrl still exists
// create all the UrlProviders we need
providers = new ArrayList<UrlProviderI>();
- UrlProviderI idProvider = new IdentifiersUrlProvider(urlList,
+ UrlProviderI idProvider = new IdentifiersUrlProvider(null,
ID_ORG_FILE);
customProvider = new CustomUrlProvider(urlList);
providers.add(idProvider);
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.File;
+import java.io.FileWriter;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class IdentifiersUrlProviderTest
"MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
"MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$"};
+ private static final String[] dlinks1 = {
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$",
+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$" };
+
+ private static final String[] dlinks2 = {
+ "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$",
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$" };
+
private static final String stringLinks = "MIR:00000005|http://identifiers.org/uniprot/$DB_ACCESSION$"
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
-
private static final Vector<String> displayLinks = new Vector<String>(
Arrays.asList(dlinks));
+ private static final Vector<String> displayLinks1 = new Vector<String>(
+ Arrays.asList(dlinks1));
+
+ private static final Vector<String> displayLinks2 = new Vector<String>(
+ Arrays.asList(dlinks2));
+
private static final HashMap<String, String> urlMap = new HashMap<String, String>()
{
{
}
};
+ private String testfile = "";
+
+
+ @BeforeClass(alwaysRun = true)
+ public void setup()
+ {
+ // setup test ids in a file
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("testidsfile", "txt");
+ outFile.deleteOnExit();
+
+ FileWriter fw = new FileWriter(outFile);
+ fw.write(testIdOrgFile);
+ fw.close();
+
+ testfile = outFile.getAbsolutePath();
+
+ } catch (Exception ex)
+ {
+ System.err.println(ex);
+ }
+ }
+
/*
* Test urls are set and returned correctly
*/
{
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
- UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+ UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
assertTrue(displayLinks.containsAll(idProv.getLinksForDisplay()));
// because UrlProvider does not guarantee order of links, we can't just
// compare the output of writeUrlsAsString to a string, hence the hoops here
String result = idProv.writeUrlsAsString();
- UrlProviderI up = new IdentifiersUrlProvider(result, testIdOrgFile);
+ UrlProviderI up = new IdentifiersUrlProvider(result, testfile);
assertTrue(displayLinks.containsAll(up.getLinksForDisplay()));
}
{
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
- UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+ UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
// initially no default
assertEquals(null, idProv.getDefaultUrl());
{
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
- UrlProviderI idProv = new IdentifiersUrlProvider(idList, testIdOrgFile);
+ UrlProviderI idProv = new IdentifiersUrlProvider(idList, testfile);
// set url links
String[] ids = { "MIR:00000372", "MIR:00000011" };
Vector<String> names = new Vector<String>(Arrays.asList(ids));
Vector<String> urls = null;
idProv.setUrlLinks(names, urls);
- assertEquals(names, idProv.getLinksForDisplay());
+ Vector<String> result = idProv.getLinksForDisplay();
+ assertEquals(displayLinks1.size(), result.size());
+ assertTrue(displayLinks1.containsAll(result));
//set default url then reset url links, default should be unset if not present
String[] moreids = { "MIR:00000005", "MIR:00000011" };
names = new Vector<String>(Arrays.asList(moreids));
idProv.setDefaultUrl("MIR:00000372");
idProv.setUrlLinks(names, urls);
- assertEquals(names, idProv.getLinksForDisplay());
+ result = idProv.getLinksForDisplay();
+ assertEquals(displayLinks2.size(), result.size());
+ assertTrue(displayLinks2.containsAll(result));
assertEquals(null, idProv.getDefaultUrl());
}
git://source.jalview.org / jalview.git / commitdiff