X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FIdentifiersUrlProvider.java;h=850a2308c6d8692fe8d441f85e57528e604984f0;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hp=3501169ada665b9ea75647166aeb9856901b6fbd;hpb=a889a61789f15e79ecde7043cddfdea18ad00166;p=jalview.git

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 3501169..850a230 100644
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -25,24 +25,18 @@ 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 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;
 
 /**
@@ -56,140 +50,141 @@ 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;
 
-  /*
-   * 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)
+  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
+      {
+        System.out.println(
+                "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();
+      System.err.println("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);
-      }
-    }
+      String id = st.nextToken();
 
-    // reset defaultUrl in case it is no longer selected
-    setDefaultUrl(defaultUrl);
-  }
-
-  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);
+    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);
@@ -197,20 +192,17 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
       }
       // remove last SEP
       links.setLength(links.length() - 1);
-      return links.toString();
     }
-    return "";
+    return links.toString();
   }
 
   @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).get("name") + SEP + urls.get(key).get("url")
-              + "/" + DELIM
-              + DB_ACCESSION + DELIM);
+      links.add(urls.get(key).toStringWithTarget());
     }
     return links;
   }
@@ -218,24 +210,13 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   @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())
@@ -243,56 +224,51 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
       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)
   {
-    if (seqid.length() < MIN_SUBST_LENGTH)
-    {
-      return null;
-    }
-    else if (defaultUrl == null)
-    {
-      return null;
-    }
-    else
-    {
-      return urls.get(defaultUrl).get("url") + "/" + seqid;
-    }
+    return super.getPrimaryUrl(seqid, urls);
   }
 
   @Override
-  public String getDefaultTarget(String seqid)
+  public String getPrimaryUrlId()
+  {
+    return primaryUrl;
+  }
+
+  @Override
+  public String getPrimaryTarget(String seqid)
   {
-    // TODO Auto-generated method stub
     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));
+  }
 }