X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FIdentifiersUrlProvider.java;h=850a2308c6d8692fe8d441f85e57528e604984f0;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hp=45d3863fd19ef61a4e65566d379b2a3b59eeef2c;hpb=e63a4d52c27252dfb83efeeee1bda6c89b6dddec;p=jalview.git

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 45d3863..850a230 100644
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -25,21 +25,18 @@ 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.FileNotFoundException;
 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.StringTokenizer;
-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;
 
 /**
@@ -53,6 +50,10 @@ 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;
 
@@ -62,7 +63,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   public IdentifiersUrlProvider(String cachedUrlList)
   {
     urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
-    selectedUrls = new ArrayList<String>();
+    selectedUrls = new ArrayList<>();
     checkSelectionMatchesUrls(cachedUrlList);
   }
 
@@ -73,39 +74,66 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
    *          name of identifiers.org download file
    * @return hashmap of identifiers.org data, keyed by MIRIAM id
    */
-  private HashMap<String, UrlLink> readIdentifiers(
-          String idFileName)
+  @SuppressWarnings("unchecked")
+  private HashMap<String, UrlLink> readIdentifiers(String idFileName)
   {
-    JSONParser parser = new JSONParser();
-
     // identifiers.org data
-    HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+    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
+      {
+        System.out.println(
+                "Unexpected key returned from identifiers jalview service");
+        return idData;
+      }
 
-      JSONArray jsonarray = (JSONArray) parser.parse(reader);
+      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);
 
         String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
                 + DELIM;
-        UrlLink link = new UrlLink((String) item.get("name") + SEP + url);
+        UrlLink link = new UrlLink((String) item.get("name"), url,
+                (String) item.get("prefix"));
         idData.put((String) item.get("id"), link);
       }
-    } catch (FileNotFoundException e)
+    } catch (IOException | ParseException e)
     {
-      e.printStackTrace();
-    } catch (IOException 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;
   }
@@ -128,21 +156,22 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
     }
 
     // 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
@@ -168,12 +197,12 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   }
 
   @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).toString());
+      links.add(urls.get(key).toStringWithTarget());
     }
     return links;
   }
@@ -187,7 +216,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   @Override
   public void setUrlData(List<UrlLinkDisplay> links)
   {
-    selectedUrls = new ArrayList<String>();
+    selectedUrls = new ArrayList<>();
 
     Iterator<UrlLinkDisplay> it = links.iterator();
     while (it.hasNext())
@@ -198,48 +227,48 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
       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 super.getDefaultUrl(seqid, urls);
+    return super.getPrimaryUrl(seqid, urls);
   }
 
   @Override
-  public String getDefaultUrlId()
+  public String getPrimaryUrlId()
   {
-    return defaultUrl;
+    return primaryUrl;
   }
 
   @Override
-  public String getDefaultTarget(String seqid)
+  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));
+  }
 }