X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FIdentifiersUrlProvider.java;fp=src%2Fjalview%2Furls%2FIdentifiersUrlProvider.java;h=c9386666168df27674d0aeaa82440c5c35b480c6;hb=9eabd6dffd6d19b2826b887a5def80351b9bceed;hp=0000000000000000000000000000000000000000;hpb=9debcac658224e1a84ddff4c4fd9f696e812913f;p=jalview.git

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
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+++ b/src/jalview/urls/IdentifiersUrlProvider.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.urls;
+
+import static jalview.util.UrlConstants.DB_ACCESSION;
+import static jalview.util.UrlConstants.DELIM;
+import static jalview.util.UrlConstants.SEP;
+
+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.StringTokenizer;
+
+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
+ * URLs from identifiers.org
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+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;
+
+  // list of selected urls
+  private ArrayList<String> selectedUrls;
+
+  public IdentifiersUrlProvider(String cachedUrlList)
+  {
+    urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
+    selectedUrls = new ArrayList<String>();
+    checkSelectionMatchesUrls(cachedUrlList);
+  }
+
+  /**
+   * 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();
+
+    // identifiers.org data
+    HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+
+    try
+    {
+      FileReader reader = new FileReader(idFileName);
+      String key = "";
+      JSONObject obj = (JSONObject) parser.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) 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);
+
+        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();
+      idData.clear();
+    } catch (IOException e)
+    {
+      e.printStackTrace();
+      idData.clear();
+    } catch (ParseException e)
+    {
+      e.printStackTrace();
+      idData.clear();
+    }
+    return idData;
+  }
+
+  private void checkSelectionMatchesUrls(String cachedUrlList)
+  {
+    StringTokenizer st = new StringTokenizer(cachedUrlList, SEP);
+    while (st.hasMoreElements())
+    {
+      String id = st.nextToken();
+
+      if (isMiriamId(id))
+      {
+        // this is an identifiers.org MIRIAM id
+        if (urls.containsKey(id))
+        {
+          selectedUrls.add(id);
+        }
+      }
+    }
+
+    // reset defaultUrl in case it is no longer selected
+    setPrimaryUrl(primaryUrl);
+  }
+
+  @Override
+  public boolean setPrimaryUrl(String id)
+  {
+    if (urls.containsKey(id))
+    {
+      primaryUrl = id;
+    }
+    else
+    {
+      primaryUrl = null;
+    }
+
+    return urls.containsKey(id);
+  }
+
+  @Override
+  public String writeUrlsAsString(boolean selected)
+  {
+    if (!selected)
+    {
+      return ""; // we don't cache unselected identifiers.org urls
+    }
+
+    StringBuffer links = new StringBuffer();
+    if (!selectedUrls.isEmpty())
+    {
+      for (String k : selectedUrls)
+      {
+        links.append(k);
+        links.append(SEP);
+      }
+      // remove last SEP
+      links.setLength(links.length() - 1);
+    }
+    return links.toString();
+  }
+
+  @Override
+  public List<String> getLinksForMenu()
+  {
+    List<String> links = new ArrayList<String>();
+    for (String key : selectedUrls)
+    {
+      links.add(urls.get(key).toStringWithTarget());
+    }
+    return links;
+  }
+
+  @Override
+  public List<UrlLinkDisplay> getLinksForTable()
+  {
+    return super.getLinksForTable(urls, selectedUrls, false);
+  }
+
+  @Override
+  public void setUrlData(List<UrlLinkDisplay> links)
+  {
+    selectedUrls = new ArrayList<String>();
+
+    Iterator<UrlLinkDisplay> it = links.iterator();
+    while (it.hasNext())
+    {
+      UrlLinkDisplay link = it.next();
+
+      // Handle links with MIRIAM ids only
+      if (isMiriamId(link.getId()))
+      {
+        // select/deselect links accordingly and set default url
+        if (urls.containsKey(link.getId()))
+        {
+          if (link.getIsSelected())
+          {
+            selectedUrls.add(link.getId());
+          }
+          if (link.getIsPrimary())
+          {
+            setPrimaryUrl(link.getId());
+          }
+        }
+      }
+    }
+  }
+
+  @Override
+  public String getPrimaryUrl(String seqid)
+  {
+    return super.getPrimaryUrl(seqid, urls);
+  }
+
+  @Override
+  public String getPrimaryUrlId()
+  {
+    return primaryUrl;
+  }
+
+  @Override
+  public String getPrimaryTarget(String seqid)
+  {
+    return null;
+  }
+
+  @Override
+  public String choosePrimaryUrl()
+  {
+    return null;
+  }
+
+  @Override
+  public boolean contains(String id)
+  {
+    return (urls.containsKey(id));
+  }
+}