Changeset 6208

Timestamp:

Apr 12, 2021, 4:08:17 PM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1295: Registration of specimen handled by external lab

Added a download link so that it is possible to inspect the JSON file.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/batch/import-external-specimen.js (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/FutureSpecimenServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/batch/import-external-specimen.js

@@ -75 +75 @@
       html += '<td>'+(Strings.encodeTags(item.itemType) || '-')+'</td>';
       html += '<td class="dottedleft">'+(Strings.encodeTags(item.name) || '-')+'</td>';
-      html += '<td class="dottedleft">'+(jsonFile ? Strings.encodeTags(jsonFile.name) : '-')+'</td>';
+      html += '<td class="dottedleft">';
+      if (jsonFile)
+      {
+        html += Strings.encodeTags(jsonFile.name);
+        html += '<span class="link download-file" data-file-no="'+itemNo+'" title="Download and view this file"><img src="../images/download.png"></span>';
+      }
+      html += '</td>';
       html += '<td class="fastq">';
       if (jsonFile && jsonFile.fastq)
@@ -131 +137 @@
     Doc.element('itemTable').innerHTML = html;
     
+    var downloadable = document.getElementsByClassName('download-file');
+    for (var fileNo = 0; fileNo < downloadable.length; fileNo++)
+    {
+      Events.addEventHandler(downloadable[fileNo], 'click', specimen.downloadJsonFile);
+    }
+
+    
     Doc.show('step-1');
     Doc.show('gonext');
+  }
+
+  specimen.downloadJsonFile = function(event)
+  {
+    var itemNo = Data.get(event.currentTarget, 'file-no');
+    var file = importItems[itemNo].jsonFile;
+
+    var url = '../FutureSpecimen.servlet?ID='+App.getSessionId();
+    url += '&cmd=DownloadJsonFile';
+    url += '&file='+encodeURIComponent(file.name);
+    
+    Dialogs.openPopup(url, file.name, 800, 800);
   }
 

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/FutureSpecimenServlet.java

@@ -25 +25 @@
 import net.sf.basedb.opengrid.RemoteSession;
 import net.sf.basedb.opengrid.config.ConnectionInfo;
+import net.sf.basedb.opengrid.filetransfer.ServletResponseDownloadTarget;
 import net.sf.basedb.opengrid.service.OpenGridService;
 import net.sf.basedb.reggie.JsonUtil;
@@ -110 +111 @@
         json.put("importItems", jsonImportItems);
       }
+      else if ("DownloadJsonFile".equals(cmd))
+      {
+        json = null; // No regular JSON output
+        dc = sc.newDbControl();
+        
+        FileServer server = Fileserver.IMPORT_ARCHIVE.load(dc);
+        FileServer fs = Fileserver.IMPORT_ARCHIVE.load(dc);
+        String rootPath = ScriptUtil.checkValidPath(fs.getRootPath(), true, false);
+        String file = ScriptUtil.checkValidFilename(req.getParameter("file"));
+        
+        RemoteSession session = null;
+        try
+        {
+          RemoteHost host = new RemoteHost(new ConnectionInfo(fs));
+          session = host.connect(5);
+          
+          //resp.setHeader("Content-Disposition", "attachment; filename=" + fileName);
+          resp.setContentType("application/json");
+
+          session.downloadFile(rootPath+"/"+file, new ServletResponseDownloadTarget(resp, file));
+        }
+        finally
+        {
+          OpenGrid.close(session);
+        }
+
+        
+      }
     }
     catch (Throwable t)
     {
       t.printStackTrace();
-      json.clear();
-      json.put("status", "error");
-      json.put("message", t.getMessage());
-      json.put("stacktrace", ThrowableUtil.stackTraceToString(t));
+      if (json != null)
+      {
+        json.clear();
+        json.put("status", "error");
+        json.put("message", t.getMessage());
+        json.put("stacktrace", ThrowableUtil.stackTraceToString(t));
+      }
+      else
+      {
+        resp.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR, t.getMessage());
+      }
     }
     finally
     {
       if (dc != null) dc.close();
-      json.writeJSONString(resp.getWriter());
+      if (json != null) json.writeJSONString(resp.getWriter());
     }