Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...

[jalview.git] / src / jalview / urls / IdentifiersUrlProvider.java

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 51d181d..c298639 100644 (file)
--- 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
+      {
+        jalview.bin.Console.outPrintln(
+                "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)
-    {
-      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;
   }
@@ -169,12 +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;
   }
@@ -188,7 +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())