Changeset 518

Timestamp:

Dec 12, 2007, 12:19:07 PM (16 years ago)

Author:

mbayer

Message:

integration of generated tab2mage file with the rest of the code is now partially implemented but not complete (routine check-in for rollback)

Location:

branches/uk_ac_ebi_Tab2MageImporter

Files:

• Tab2MageImporter.jar (modified) (previous)
• jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp (modified) (6 diffs)
• lib/ebi-plugins-utils.jar (modified) (previous)
• src/uk/ac/ebi/nugo/common/Helper.java (modified) (2 diffs)
• src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java (modified) (5 diffs)
• src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java (modified) (15 diffs)
• src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageHybridizationValidation.java (modified) (2 diffs)

branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

@@ -145 +145 @@
   <tr>
     <td class="boldText">Name of the experimental organism:</td>
-    <td class="input"><input type="text" size="60" name="parameter:organism" value="barley"/></td>
+    <td class="input"><input type="text" size="60" name="parameter:organism" value="Solanum tuberosum"/></td>
   </tr>
 
@@ -172 +172 @@
   <tr>
     <td class="boldText">Number of treatment groups:</td>
-    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="12"/></td>
+    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td>
   </tr>
 
@@ -179 +179 @@
     <td class="boldText">Please list your experimental factors and value ranges using the following format (one per
     line):<br>
-    <i>Factor 1(value1,value2,...valueN)<br>
-    Factor 2(value1,value2,...valueN)</i>
+    <i>Factor 1(value1,value2,...valueN)<br></i>
     <p>Example: <i><br>
     Compound(aspirin,ibuprofen,acetaminophen) <br>
     Dose(control,low,medium,high)</i>
     </td>
-    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Factor 1(value1,value2,...valueN)</textarea></td>
+    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
   </tr>
 
@@ -191 +190 @@
   <tr>
     <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
-    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="3"/></td>
+    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
   </tr>
   
@@ -198 +197 @@
     <td class="boldText">List all target tissues (as a comma separated list).<br>
     Example: liver,heart,adipose tissue</td>
-    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">tissues1,tissue2</textarea></td>
+    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">stem</textarea></td>
   </tr>
   
@@ -220 +219 @@
         <div class="buttonclass" onmouseover="this.className='buttonclass_hover';"
           onmouseout="this.className='buttonclass';" onclick="browseOnClick()">
-
-        <table border="0" cellspacing="0" cellpadding="0" class="noBorder">
-          <tr class="noBorder">
-            <td class="centered"><img src="/base/images/browse.png" border="0"></td>
+        <div class="buttonclass_inner">
+        <table border="0" cellspacing="0" cellpadding="0">
+          <tr>
+            <td><img src="/base/images/browse.png" border="0"></td>
             <td>Browse&hellip;</td>
           </tr>
         </table>
-
+        </div>
         </div>
         </td>

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/common/Helper.java

@@ -70 +70 @@
   
     
-   public static File processFilePath (User user,boolean overwrite, SessionControl sc, String pathString)
+   public static File processFilePath (User user,boolean overwrite, SessionControl sc, String pathString) throws Exception
    {
     DbControl dc= null;
@@ -97 +97 @@
     {
       dc.close();
+      throw new Exception(e.getMessage());
     }
     finally

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

@@ -382 +382 @@
       // save the new subDir
       dc.saveItem(subDir);
+      dc.commit();
       
       if(dc==null)
@@ -398 +399 @@
       RawDataType rdt= experiment.getRawDataType(); // experiment platform
 
-//      String statusp=(String)job.getValue("statusPath");
-//      File statusFile=Helper.processFilePath(user,overwrite, sc,statusp);
+      //write a log file in the same directory where the files were unzipped
+//      String statusFilePath = subDir.getPath().toString()+"/importerLog.txt";
+//      System.out.println("statusFile path = "+ statusFilePath);
+//      File statusFile=Helper.processFilePath(user,true, sc,statusFilePath);       
+//      statusFile = File.getById(dc, statusFile.getId());      
+//      System.out.println("statusFile = " +statusFile);
+      
+      
+      ///////////////////////////////////////////////////////////////////////////////////////////////////
+      
+      //now write the tab2mage file to the user's home dir on the server so it can be consumed by the plugin
+      //this takes all the inputs provided by the user on the custom interface (input.jsp)
+      //give the file a unique name so we don't get any conflicts 
+      Tab2MageWriter t2mWriter = new Tab2MageWriter(job, subDir,sc,paramNames);
+      t2mWriter.writeTab2MageFile();
+      File statusFile = t2mWriter.makeStatusFile();
+      System.out.println("statusFile = " +statusFile.getPath());
+      
+      /////////////////////////////////////////////////////////////////////////////////////////////////
+      
 
         //FILE UNZIP MODULE: unzip the files into user specified directory
@@ -414 +433 @@
 
       // -- end of file unzip module
-      
-      ///////////////////////////////////////////////////////////////////////////////////////////////////
-      
-      //now write the tab2mage file to the user's home dir on the server so it can be consumed by the plugin
-      //this takes all the inputs provided by the user on the custom interface (input.jsp)
-      //give the file a unique name so we don't get any conflicts 
-      Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc,paramNames);
-      t2mWriter.writeTab2MageFile();
-
-      
-      /////////////////////////////////////////////////////////////////////////////////////////////////
-      
-/*
 
         //VALIDATION MODULE
@@ -461 +467 @@
         return;
       }
-
+      
+      
       Map<ValidationConstants, Boolean> validations= validator.validateTab2MageFile();
       StringBuffer failureMessage = new StringBuffer();
@@ -555 +562 @@
       // -- end of experiment configuration and loading module
 
-        //MESSAGING MODULE
-        
-      //  send an email to the user on the success of the experiment (if email server name and email address are provided) 
-      if (hostName!= null && hostName.length()>=5)
-      {
-        if (!user.getEmail().equals("") && user.getEmail()!=null )
-        {
-          Tab2MageEMessaging message= new Tab2MageEMessaging(writtenExp,"", user.getEmail(),tab2MageFileName, user.getName(), experiment.getName(),hostName );
-          message.sendEmail();
-        }
-      }
-      // -- end of messaging module
-      */
-      //dc.commit();
+
+      dc.commit();
       response.setDone("Import plugin ended successfully");
     }

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java

@@ -8 +8 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Directory;
+import net.sf.basedb.core.File;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.plugin.ParameterValues;
@@ -76 +77 @@
   public Tab2MageWriter()
   {
-    initTestParamValues();
-  }
+  }
+  
+  
 
   // ===================================================methods================================================
@@ -86 +88 @@
     try
     {
-      Class cls = Class.forName("uk.ac.ebi.nugo.plugins.Tab2MageWriter");
+      Tab2MageWriter writer = new Tab2MageWriter();
+      
+      Class cls = writer.getClass();
+      //Class cls = Class.forName("uk.ac.ebi.nugo.plugins.Tab2MageWriter");
+      
       for (int i = 0; i < paramNames.length; i++)
       {
-        Field field = cls.getField(paramNames[i]);
+        Field field = cls.getDeclaredField(paramNames[i]);
         field.set(this, job.getValue(paramNames[i]));
       }
-    }
+            
+      //chop off any potential commas at the end of the experimentalDesign String
+      //these arise because we string together values form multiple inputs in the web forms
+      if(experimentalDesign.endsWith(","))
+      {
+        experimentalDesign = experimentalDesign.substring(0, experimentalDesign.length()-2);
+      }
+    } 
     catch (Exception e)
     {
@@ -150 +163 @@
     { "P-DIET-1", "P-EXTR-1", "P-LABL-1", "P-HYBR-1", "P-SCAN-1" };
     String[] names = new String[]
-    { "treatment", "extraction", "labeling", "hybridization", "scanning" };
+    { "Treatment", "Extraction", "Labeling", "Hybridization", "Scanning" };
     String[] values = new String[]
     { treatmentProtocol, extractionProtocol, labelingProtocol, hybridizationProtocol, scanningProtocol };
@@ -157 +170 @@
             hybridizationProtocolParams, scanningProtocolParams };
     String[] types = new String[]
-    { "grow", "extraction", "labeling", "hybridization", "scanning" };
+    { "Sampling", "Extraction", "Labeling", "Hybridization", "Scanning" };
 
     // print header
@@ -180 +193 @@
     
     // print column headers for the section
-    String [] colHeaders  = new String [] {"File[raw]"," array[accession]"," BioSource"," BioMaterialCharacteristics[Organism]"," BioMaterialCharacteristics[OrganismPart]"," BioMaterialCharacteristics[CellType]"," Sample"," Protocol[grow]"," Extract"," Protocol[extraction]"," LabeledExtract"," Protocol[labeling]"," Dye"," Hybridization"," Protocol[hybridization]"," Scan"," Protocol[scanning]"," FactorValue[Treatment Type]"};
+    String [] colHeaders  = new String [] {"File[raw]"," Array[accession]"," BioSource"," BioMaterialCharacteristics[Organism]"," BioMaterialCharacteristics[OrganismPart]"," BioMaterialCharacteristics[CellType]"," Sample"," Protocol[Sampling]"," Extract"," Protocol[Extraction]"," LabeledExtract"," Protocol[Labeling]"," Dye"," Hybridization"," Protocol[Hybridization]"," Scan"," Protocol[Scanning]"," FactorValue[Treatment Type]"};
     for (int i = 0; i < colHeaders.length; i++)
     {
@@ -187 +200 @@
     t2mContent += "\n";
 
-
-// //////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-
+    //the following is a direct translation of Philippe's Perl script code
     int count = 1;
     
@@ -212 +222 @@
           
           // file count first
-          t2mContent += "file-" + count + ".txt" + "\t" + 
+          t2mContent += "file-" + count + ".gpr" + "\t" + 
           // accession no. i.e the array design
           accession + "\t" + 
@@ -254 +264 @@
           
           // file count first
-          t2mContent += "file-" + count + ".txt" + "\t" + 
+          t2mContent += "file-" + count + ".gpr" + "\t" + 
           // accession no. i.e the array design
           accession + "\t" + 
@@ -296 +306 @@
         }
       }
-    }
-    
-            
-// //////////////////////////////////////////////////////////////////////////////////////////////////////////
-        
+    }     
   }
 
@@ -316 +322 @@
       dc.saveItem(t2mFile);
 
-      if (dc == null)
-        dc = sc.newDbControl();
-
       Writer out = new BufferedWriter(new OutputStreamWriter(t2mFile.getUploadStream(false), "ISO-8859-1"));
 
       // write content to file
+      generateFileContents();
       out.write(t2mContent);
 
@@ -337 +341 @@
     }
   }
+  
+  // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+  public File makeStatusFile()
+  {
+    net.sf.basedb.core.File statusFile = null;
+    try
+    {
+      DbControl dc = sc.newDbControl();
+      statusFile = net.sf.basedb.core.File.getNew(dc, dir);
+      statusFile.setName("importerLog.txt");
+      dc.saveItem(statusFile);
+      dc.commit();
+      if (dc != null)
+        dc.close();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    return statusFile;
+  }
+  
+  
 
   // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
@@ -352 +380 @@
   // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 
-  private void initTestParamValues()
+  public void initTestParamValues()
   {
     /*
+     * Philippe's hybs params for testing (rest is made up):
+     * 
     --org Homo_sapiens 
     --array Agilent1 
@@ -370 +400 @@
     domain = "scri.ac.uk";
     accession = "Agilent1";
-    qualityControl = "biological replicate,spike quality control";
-    experimentalDesign = "cell_component_comparison_design,RNA_stability_design,family_history_design,";
+    qualityControl = "biological replicate";
+    experimentalDesign = "strain_or_line_design";
     experimentName = "New experiment";
     description = "description goes here";
@@ -400 +430 @@
     
     //hybs
-    platform = "Agilent";
-    organism = "Homo_sapiens";
+    platform = "Genepix";
+    organism = "Solanum tuberosum";
     numDesigns = "1";
     dyeSwap = "no";
     refSample = "yes";
-    numTreatmentGroups = "6";
+    numTreatmentGroups = "2";
     expFactors = "compound(aspirin,ibuprofen);dose(none,medium,high) )";
-    numReplicates = "4";
-    tissues = "liver,heart,brain";
+    numReplicates = "2";
+    tissues = "stem";
     pooling = "no";
     zipFile = "/home/michab/potato_small.zip";

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageHybridizationValidation.java

@@ -183 +183 @@
   public static boolean validateHeader(ArrayList<String> header, Writer writer)
   {
+    System.out.println("/////////////////////////////////////////////");
+    System.out.println("hybs headers:");
+    for (String string : header)
+    {
+      System.out.println(string);
+    }
+    System.out.println("/////////////////////////////////////////////");
+    
+    
     //[TODO] convert all headers to lowercase, to facilitate matching of hyb section header to Tab2mageConstants/Spec
     //header= header2LowerCase(header);
@@ -189 +198 @@
     try
     {
-      if(!header.contains(Tab2MageConstants.hybridization.getName()))
+      if(!header.contains(Tab2MageConstants.hybridization.getName().trim()))
       {
         log.error("The column \"" + Tab2MageConstants.hybridization.getName() + "\" wasn't found!");