Item 6174: New LoadAssayRunCommand to get the runs without a batch

SVN r64467 |2019-09-09 23:48:11 +0000

Author: labkey-ankurj

.gitattributes

@@ -26,6 +26,8 @@ java/src/org/labkey/remoteapi/assay/ImportRunCommand.java -text
 java/src/org/labkey/remoteapi/assay/ImportRunResponse.java -text
 java/src/org/labkey/remoteapi/assay/LoadAssayBatchCommand.java -text
 java/src/org/labkey/remoteapi/assay/LoadAssayBatchResponse.java -text
+java/src/org/labkey/remoteapi/assay/LoadAssayRunCommand.java -text
+java/src/org/labkey/remoteapi/assay/LoadAssayRunResponse.java -text
 java/src/org/labkey/remoteapi/assay/Material.java -text
 java/src/org/labkey/remoteapi/assay/Run.java -text
 java/src/org/labkey/remoteapi/assay/SaveAssayBatchCommand.java -text

java/src/org/labkey/remoteapi/assay/LoadAssayRunCommand.java

@@ -0,0 +1,56 @@
+package org.labkey.remoteapi.assay;
+
+
+import org.json.simple.JSONObject;
+import org.labkey.remoteapi.PostCommand;
+
+/**
+ * Command for obtaining information about a run in a particular folder.
+ */
+public class LoadAssayRunCommand extends PostCommand<LoadAssayRunResponse>
+{
+    private String _lsid;
+
+    public LoadAssayRunCommand(LoadAssayRunCommand source)
+    {
+        super(source);
+        _lsid = source.getLsid();
+    }
+
+    public LoadAssayRunCommand(String lsid)
+    {
+        super("experiment", "loadAssayRun");
+        _lsid = lsid;
+    }
+
+    public String getLsid()
+    {
+        return _lsid;
+    }
+
+    public void setLsid(String lsid)
+    {
+        _lsid = lsid;
+    }
+
+    @Override
+    public LoadAssayRunCommand copy()
+    {
+        return new LoadAssayRunCommand(this);
+    }
+
+    @Override
+    public JSONObject getJsonObject()
+    {
+        JSONObject result = new JSONObject();
+
+        result.put("lsid", _lsid);
+        return result;
+    }
+
+    @Override
+    protected LoadAssayRunResponse createResponse(String text, int status, String contentType, JSONObject json)
+    {
+        return new LoadAssayRunResponse(text, status, contentType, json, this);
+    }
+}

java/src/org/labkey/remoteapi/assay/LoadAssayRunResponse.java

@@ -0,0 +1,40 @@
+package org.labkey.remoteapi.assay;
+
+import org.json.simple.JSONObject;
+import org.labkey.remoteapi.Command;
+import org.labkey.remoteapi.CommandResponse;
+
+public class LoadAssayRunResponse extends CommandResponse
+{
+    private Run _run;
+
+    public Run getRun()
+    {
+        return _run;
+    }
+
+    public void setRun(Run run)
+    {
+        _run = run;
+    }
+
+    /**
+     * Constructs a new CommandResponse, initialized with the provided
+     * response text and status code.
+     *
+     * @param text          The response text
+     * @param statusCode    The HTTP status code
+     * @param contentType   The response content type
+     * @param json          The parsed JSONObject (or null if JSON was not returned).
+     * @param sourceCommand A copy of the command that created this response
+     */
+    public LoadAssayRunResponse(String text, int statusCode, String contentType, JSONObject json, Command sourceCommand)
+    {
+        super(text, statusCode, contentType, json, sourceCommand);
+        JSONObject runJson = (JSONObject) json.get("run");
+        _run = new Run();
+
+        _run.setName((String) runJson.get("name"));
+        _run.setLsid((String) runJson.get("lsid"));
+    }
+}

java/src/org/labkey/remoteapi/assay/Run.java

@@ -34,6 +34,7 @@ public class Run extends ExpObject
     private List<Data> _dataOutputs = new ArrayList<Data>();
     private List<Material> _materialInputs = new ArrayList<>();
     private List<Material> _materialOutputs = new ArrayList<>();
+    private String _lsid;
 
     // Used when inserting new data via SaveAssayBatchAction
     private List<Map<String, Object>> _resultData;
@@ -83,6 +84,12 @@ public Run(JSONObject json)
             }
         }
         _comment = (String)json.get("comment");
+
+        if (json.containsKey("lsid"))
+        {
+            _lsid = (String) json.get("lsid");
+        }
+
     }
 
     @Override
@@ -103,6 +110,7 @@ public JSONObject toJSONObject()
         }
         result.put("dataOutputs", dataOutputs);
         result.put("comment", _comment);
+        result.put("lsid", _lsid);
 
         JSONArray materialInputs = new JSONArray();
         JSONArray materialOutputs = new JSONArray();
@@ -198,4 +206,14 @@ public void setResultData(List<Map<String, Object>> resultData)
     {
         _resultData = resultData;
     }
+
+    public String getLsid()
+    {
+        return _lsid;
+    }
+
+    public void setLsid(String lsid)
+    {
+        _lsid = lsid;
+    }
 }

java/src/org/labkey/remoteapi/assay/SaveAssayRunCommand.java

@@ -13,15 +13,17 @@
  */
 public class SaveAssayRunCommand extends PostCommand<SaveAssayRunResponse>
 {
-    private List<Run> _runs = new ArrayList<Run>();
+    private List<Run> _runs;
+    private String _protocolName;
 
     /**
      * @param runs the runs to be saved
      */
-    public SaveAssayRunCommand(List<Run> runs)
+    public SaveAssayRunCommand(String protocolName, List<Run> runs)
     {
         super("assay", "saveAssayRun");
         _runs = runs;
+        _protocolName = protocolName;
     }
 
     public SaveAssayRunCommand(SaveAssayRunCommand source)
@@ -46,6 +48,33 @@ public JSONObject getJsonObject()
             runs.add(run.toJSONObject());
         }
         result.put("runs", runs);
+        result.put("protocolName", getProtocolName());
         return result;
     }
+
+    @Override
+    protected SaveAssayRunResponse createResponse(String text, int status, String contentType, JSONObject json)
+    {
+        return new SaveAssayRunResponse(text, status, contentType, json, this);
+    }
+
+    public List<Run> getRuns()
+    {
+        return _runs;
+    }
+
+    public void setRuns(List<Run> runs)
+    {
+        _runs = runs;
+    }
+
+    public String getProtocolName()
+    {
+        return _protocolName;
+    }
+
+    public void setProtocolName(String protocolName)
+    {
+        _protocolName = protocolName;
+    }
 }

java/src/org/labkey/remoteapi/assay/SaveAssayRunResponse.java

@@ -1,11 +1,17 @@
 package org.labkey.remoteapi.assay;
 
+import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 import org.labkey.remoteapi.Command;
 import org.labkey.remoteapi.CommandResponse;
 
+import java.util.ArrayList;
+import java.util.List;
+
 public class SaveAssayRunResponse extends CommandResponse
 {
+    private List<Run> _runs = new ArrayList<>();
+
     /**
      * Constructs a new CommandResponse, initialized with the provided
      * response text and status code.
@@ -19,5 +25,21 @@ public class SaveAssayRunResponse extends CommandResponse
     public SaveAssayRunResponse(String text, int statusCode, String contentType, JSONObject json, Command sourceCommand)
     {
         super(text, statusCode, contentType, json, sourceCommand);
+        JSONArray array = (JSONArray)json.get("runs");
+        for (Object o : array)
+        {
+            JSONObject run = (JSONObject) o;
+            _runs.add(new Run(run));
+        }
+    }
+
+    public List<Run> getRuns()
+    {
+        return _runs;
+    }
+
+    public void setRuns(List<Run> runs)
+    {
+        _runs = runs;
     }
 }