Changeset 1546 for extensions/net.sf.basedb.reggie

Timestamp:

Mar 2, 2012, 1:19:02 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #366: Import annotations and other information from Caliper output

The important features has been implemented. There is still some more to do on the error handling side and maybe also on the usability side.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/css/reggie.css (modified) (1 diff)
• resources/rnaqc_plate_import.jsp (added)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/Mimetype.java (added)
• src/net/sf/basedb/reggie/plugins/CaliperPlateImporter.java (added)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/RnaQcServlet.java (modified) (4 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/css/reggie.css

@@ -109 +109 @@
   list-style-image: url('../images/ok.png');
 }
+.failure ul
+{
+  list-style-image: url('../images/error.png');
+}
 
 .reporttable

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/Reggie.java

@@ -221 +221 @@
   */
   public static final String ANNOTATION_QC_OPERATOR = "QCOperator";
+
+  /**
+    The name of the "BA_RIN" annotation, used
+    for extract (RNAQC). It is a float annotation type
+    @since 2.4
+  */
+  public static final String ANNOTATION_BA_RIN = "BA_RIN";
+
   
   /**

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

@@ -25 +25 @@
 import net.sf.basedb.core.ItemKey;
 import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.MimeType;
 import net.sf.basedb.core.MultiPermissions;
 import net.sf.basedb.core.Permission;
@@ -34 +35 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.dao.BioplateType;
+import net.sf.basedb.reggie.dao.Mimetype;
 import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.EqualsHelper;
@@ -117 +119 @@
         jsonChecks.add(checkBioplateType(dc, BioplateType.CALIPER_RNAQC, createIfMissing));
         
+        // MIME types
+        jsonChecks.add(checkMimeType(dc, Mimetype.GDX, createIfMissing));
+        
         // Annotation type checks 
         // -- the first batch need to be shared to the PatientCurator group
@@ -179 +184 @@
             null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_QC_OPERATOR, new Item[] { Item.BIOPLATE}, Type.STRING, 1, 
+            null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_BA_RIN, new Item[] { Item.EXTRACT }, Type.FLOAT, 1, 
             null, effectiveOptions, createIfMissing));
         
@@ -209 +216 @@
             Reggie.ANNOTATION_QC_RUN_DATE, Reggie.ANNOTATION_QC_OPERATOR));
         
-
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.DNA, createIfMissing));
 
-        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNAQC, createIfMissing));
+        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.RNAQC, createIfMissing,
+            Reggie.ANNOTATION_BA_RIN));
         
         json.put("checks", jsonChecks);
@@ -854 +861 @@
   }
 
+  /**
+    Create a MIME type with the given options. The type is created in
+    a separate transaction.
+    @since 2.4
+  */
+  public MimeType createMimeType(SessionControl sc, Mimetype def)
+  {
+    MimeType type = null;
+    DbControl dc = sc.newDbControl();
+    try
+    {
+      type = MimeType.getNew(dc);
+      type.setName(def.getMimeType());
+      type.setExtension(def.getExtension());
+      type.setDescription(def.getDescription());
+      if (def.getFileType() != null)
+      {
+        type.setFileType(def.getFileType().load(dc));
+      }
+      
+      dc.saveItem(type);
+      dc.commit();
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+    return type;
+  }
+
+  
+  /**
+    Check for an existing MIME type with the given options.
+    A JSONObject is returned with the result. The following 
+    keys are used:
+    <ul>
+    <li>itemType: MIMETYPE
+    <li>name: The name of the subtype
+    <li>id: The id of the subtype if it exists
+    <li>mainType: The main item type that the subtype applies to
+    <li>status: ok, error, or missing
+    <li>message: A descriptive message in case of an error
+    </ul>
+    @since 2.4
+  */
+  @SuppressWarnings("unchecked")
+  public JSONObject checkMimeType(DbControl dc, Mimetype mimeType, 
+    boolean createIfMissing)
+  {
+  
+    JSONObject json = new JSONObject();
+    JSONArray jsonMessages = new JSONArray();
+    json.put("itemType", Item.MIMETYPE.name());
+    json.put("name", mimeType.getDescription());
+    json.put("mimeType", mimeType.getMimeType());
+    json.put("extension", mimeType.getExtension());
+      
+    List<MimeType> result = mimeType.list(dc);
+    if (result.size() == 0)
+    {
+      if (createIfMissing)
+      {
+        MimeType type = createMimeType(dc.getSessionControl(), mimeType);
+        json.put("id", type.getId());
+        json.put("status", "ok");
+        jsonMessages.add("Created");
+      }
+      else
+      {
+        json.put("status", "missing");
+        jsonMessages.add("Not found");
+      }
+    }
+    else if (result.size() > 1)
+    {
+      json.put("status", "error");
+      jsonMessages.add("Found > 1 MIME type");
+    }
+    else
+    {
+      MimeType s = result.get(0);
+      json.put("id", s.getId());
+      json.put("status", "ok"); // For now -- more checks below
+      
+      if (!s.getName().equals(mimeType.getMimeType()))
+      {
+        json.put("status", "error");
+        jsonMessages.add("Should have '" + mimeType.getMimeType() + "' as MIME type.");
+      }
+      
+    }
+    if (jsonMessages.size() == 0) jsonMessages.add("Ok");
+    json.put("messages", jsonMessages);
+    return json;
+  
+  }
+
 
   /**

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

@@ -15 +15 @@
 import org.json.simple.parser.JSONParser;
 
+import net.sf.basedb.core.AnnotationSet;
+import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
 import net.sf.basedb.core.BioPlate;
@@ -23 +25 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
+import net.sf.basedb.core.File;
+import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.ItemQuery;
@@ -33 +37 @@
 import net.sf.basedb.reggie.dao.Rna;
 import net.sf.basedb.reggie.dao.Subtype;
+import net.sf.basedb.reggie.plugins.CaliperPlateImporter;
 import net.sf.basedb.reggie.plugins.CaliperSampleNameExporter;
 import net.sf.basedb.util.Coordinate;
@@ -267 +272 @@
         }
         
+        dc.commit();
+      }
+      else if ("PreValidateCaliperResults".equals(cmd))
+      {
+        int csvId = Values.getInt(req.getParameter("csv"));
+        
+        dc = sc.newDbControl();
+        File csv = File.getById(dc, csvId);
+        
+        CaliperPlateImporter cpi = new CaliperPlateImporter();
+        cpi.setAnnotationMapping("RNA Quality Score", null); // safe to use 'null' when validating
+        
+        if (cpi.doPreValidate(dc, csv.getDownloadStream(0)))
+        {
+          // The validation was ok
+          BioPlate plate = cpi.getBioPlate();
+          ReactionPlate rnaQc = ReactionPlate.getById(dc, plate.getId());
+          AnnotationType qcRunDate = Reggie.findAnnotationType(dc, Item.BIOPLATE, Reggie.ANNOTATION_QC_RUN_DATE, false);
+          AnnotationType qcOperator = Reggie.findAnnotationType(dc, Item.BIOPLATE, Reggie.ANNOTATION_QC_OPERATOR, false);
+          if (qcRunDate != null) 
+          {
+            rnaQc.loadAnnotations("QCRunDate", qcRunDate, Reggie.CONVERTER_DATE_TO_STRING);
+          }
+          if (qcOperator != null)
+          {
+            rnaQc.loadAnnotations("QCOperator", qcOperator, null);
+          }
+          JSONObject jsonPlate = rnaQc.asJSONObject();
+          
+          json.put("plate", jsonPlate);
+        }
+        else
+        {
+          json.put("status", "error");
+          json.put("message", "Validation failed");
+          jsonMessages.addAll(cpi.getErrorMessages());
+        }
+        
+      }
+      else if ("ImportCaliperResults".equals(cmd))
+      {
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());
+
+        Number csvId = (Number)jsonReq.get("csv");
+        Number gxdId = (Number)jsonReq.get("gxd");
+        Number pdfId = (Number)jsonReq.get("pdf");
+        
+        dc = sc.newDbControl();
+        AnnotationType qcRunDate = Reggie.findAnnotationType(dc, Item.BIOPLATE, Reggie.ANNOTATION_QC_RUN_DATE, true);
+        AnnotationType qcOperator = Reggie.findAnnotationType(dc, Item.BIOPLATE, Reggie.ANNOTATION_QC_OPERATOR, true);
+        AnnotationType rin = Reggie.findAnnotationType(dc, Item.EXTRACT, Reggie.ANNOTATION_BA_RIN, true);
+        
+        File csv = File.getById(dc, csvId.intValue());
+        
+        CaliperPlateImporter cpi = new CaliperPlateImporter();
+        cpi.setAnnotationMapping("RNA Quality Score", rin);
+        
+        if (cpi.doImport(dc, csv.getDownloadStream(0)))
+        {
+          // The import was successful
+          BioPlate plate = cpi.getBioPlate();
+          jsonMessages.add("Imported data to " + cpi.getNumImported() + " extracts on plate " + plate.getName());
+          
+          // Attach the files we used to the bioplate
+          cpi.attachFile(dc, csv, "CSV file");
+          jsonMessages.add("Attached file '" + csv.getName() + "' to plate " + plate.getName());
+          if (gxdId != null)
+          {
+            File gxd = File.getById(dc, gxdId.intValue());
+            cpi.attachFile(dc, gxd, "LabView GX raw data");
+            jsonMessages.add("Attached file '" + gxd.getName() + "' to plate " + plate.getName());
+          }
+          if (pdfId != null)
+          {
+            File pdf = File.getById(dc, pdfId.intValue());
+            cpi.attachFile(dc, pdf, "PDF printout");
+            jsonMessages.add("Attached file '" + pdf.getName() + "' to plate " + plate.getName());
+          }
+          
+          AnnotationSet as = plate.getAnnotationSet();
+          as.getAnnotation(qcRunDate).setValue(Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("QCRunDate")));
+          as.getAnnotation(qcOperator).setValue(jsonReq.get("QCOperator"));
+          
+          plate.setDestroyed(true);
+          dc.commit();
+          
+        }
+        else
+        {
+          jsonMessages.addAll(cpi.getErrorMessages());
+          json.put("status", "error");
+          json.put("message", "Import failed from file: " + csv.getName());
+        }
+        
       }
       
-      dc.commit();
+
       json.put("messages", jsonMessages);
-
       
     }