Changeset 531

Timestamp:

Jan 10, 2008, 6:18:12 PM (13 years ago)

Author:

mbayer

Message:

had to add in ability for user to configure subject names and tissues against filenames and factors too - this implemented in UI now
also restructured code in writer class and test class

Location:

branches/uk_ac_ebi_Tab2MageImporter

Files:

• Tab2MageImporter.jar (modified) (previous)
• jsp/uk/ac/ebi/nugo/plugins/experiment.jsp (modified) (2 diffs)
• jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp (modified) (2 diffs)
• jsp/uk/ac/ebi/nugo/plugins/mappings.jsp (modified) (9 diffs)
• jsp/uk/ac/ebi/nugo/plugins/protocols.jsp (modified) (1 diff)
• lib/ebi-plugins-utils.jar (modified) (previous)
• src/uk/ac/ebi/nugo/plugins/DataBean.java (modified) (2 diffs)
• src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java (modified) (1 diff)
• src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java (modified) (15 diffs)
• src/uk/ac/ebi/nugo/plugins/Tab2MageWriterTest.java (modified) (1 diff)

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

@@ -4 +4 @@
 <%@ page import="java.util.*"%>
 
-<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session"/>
+<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application"/>
 <!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
 <jsp:setProperty name="inputDataBean" property="*"/>
@@ -32 +32 @@
 <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css">
 <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css">
+
+<script>
+self.resizeTo(800,850);
+</script>
 
 <script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script>

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

@@ -4 +4 @@
 <%@ page import="java.util.*"%>
 
-<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
+<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
 <!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
 <jsp:setProperty name="inputDataBean" property="*" />
@@ -182 +182 @@
   </tr>
   
+  <!-- question 8a -->
+  <tr>
+    <td class="boldText">Subject (replicate) labels:</td>
+    <td class="input"><textarea rows="8" cols="32" name="subjectNames">plant1</textarea></td>
+    <td>Please provide a list of labels(names) for the experimental subjects, one per line,
+     in no particular order (copy and paste from Excel works).</td>
+  </tr> 
+  
   <!-- question 9 -->
   <tr>
     <td class="boldText">Target tissues:</td>
-    <td class="input"><textarea rows="2" cols="32" name="tissues">stem</textarea></td>
-    <td>List all target tissues (as a comma separated list).<br>
-    Example: liver,heart</td>
+    <td class="input"><textarea rows="4" cols="32" name="tissues">stem</textarea></td>
+    <td>List all target tissues one per line, in no particular order (copy and paste from Excel works).</td>
   </tr>
   

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

@@ -7 +7 @@
 <%@ page import="uk.ac.ebi.nugo.plugins.*"%>
 
-<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
+<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
 <!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
 <jsp:setProperty name="inputDataBean" property="*" />
@@ -51 +51 @@
 function gatherValues()
 {
-  var fileString = '';
+  var fileList = '';
+  var subjectList = '';
+  var tissueList = '';
   var frm = document.forms['mappings'];
   var numElements = frm.elements.length;
-  //document.write(numElements);
-  //document.write("<br />");
   for(var i = 0; i < numElements; i++)
   {
     var value = frm.elements[i].value;
     var id = frm.elements[i].id;
-
-    if(id.match("fileinput"))
+    if(id.match("fileInput"))
     {
-      //document.write("id = " + id);
-      //document.write("<br />");
-      //document.write("value = " + value);
-      //document.write("<br />");
-      fileString += frm.elements[i].value + '\t';
-    }
-  }
-  //document.write('combined output = ' + fileString);
-  frm.fileStringParam.value = fileString;
-  //document.write('value of hidden input = ' + frm.fileStringParam.value);
+      fileList += frm.elements[i].value + '\t';
+    }
+    if(id.match("subjectInput"))
+    {
+      subjectList += frm.elements[i].value + '\t';
+    }
+    if(id.match("tissueInput"))
+    {
+      tissueList += frm.elements[i].value + '\t';
+    }
+  }
+  frm.fileList.value = fileList;
+  frm.subjectList.value = subjectList;
+  frm.tissueList.value = tissueList;
 }
 
@@ -88 +91 @@
 <input type="hidden" name="cmd" value="SetParameters"> 
 <input type="hidden" name="requestId" value="<%=requestId%>"> 
-<input type="hidden" id="fileStringParam" name="parameter:fileStringParam" value""/>
+<input type="hidden" id="fileList" name="parameter:fileList" value""/>
+<input type="hidden" id="subjectList" name="parameter:subjectList" value""/>
+<input type="hidden" id="tissueList" name="parameter:tissueList" value""/>
 
 <!-- these are the parameters from the previous input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way -->
@@ -135 +140 @@
 <input type="hidden" name="parameter:pooling" value="<%=inputDataBean.getPooling()%>">
 <input type="hidden" name="parameter:zipFile" value="<%=request.getParameter("path") %>" id="zipFile">
+<input type="hidden" name="parameter:subjectNames" value="<%=inputDataBean.getSubjectNames()%>">
+
 
 <%
@@ -194 +201 @@
   
   dc.close();
+  
+  //next get the subjectNames and make up select boxes with these
+  //they too have to be mapped to filenames
+  String [] subjectNames = request.getParameter("subjectNames").split("\n");
+  
+  //we also need to parse out the tissues string to produce another column of select boxes 
+  String [] tissueNames = request.getParameter("tissues").split("\n");
 %>
 
@@ -201 +215 @@
 
 The table below holds a list of all possible factor value combinations used in your experiment. 
-Please select, for each combination, the appropriate file name from the drop down menu.</p><p>
+Please select, for each combination, the appropriate file, subject and tissue from the drop down menu.</p><p>
 
 <!-- this table holds the combinations of factor values -->
@@ -213 +227 @@
     <!-- file selector header -->
     <td class="header"><h3>File</h3></td>
+    <td class="header"><h3>Subject</h3></td>
+    <td class="header"><h3>Tissue</h3></td>
 
     <!-- factor names -->
@@ -236 +252 @@
     <!-- first we need a cell with a drop down menu where we can select a filename to match the combination of factor values-->
 
-    <td class="input" ><select id="fileinput<%=i %>">
+    <td class="input" ><select id="fileInput<%=i %>">
       <%
           for (int k = 0; k < fileNamesArr.length; k++)
@@ -243 +259 @@
 
       <option><%=fileNamesArr[k]%></option>
+
+      <%
+      }
+      %>
+    </select></td>
+    
+    <!-- next  we need a cell with a drop down menu where we can select a subject name to match the combination of factor values-->
+
+    <td class="input" ><select id="subjectInput<%=i %>">
+      <%
+          for (int k = 0; k < subjectNames.length; k++)
+          {
+      %>
+
+      <option><%=subjectNames[k]%></option>
+
+      <%
+      }
+      %>
+    </select></td>
+    
+    <!-- next  we need a cell with a drop down menu where we can select a tissue name to match the combination of factor values-->
+
+    <td class="input" ><select id="tissueInput<%=i %>">
+      <%
+          for (int k = 0; k < tissueNames.length; k++)
+          {
+      %>
+
+      <option><%=tissueNames[k]%></option>
 
       <%

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

@@ -5 +5 @@
 <%@ page import="java.lang.*"%>
 
-<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
+<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
 <!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
 <jsp:setProperty name="inputDataBean" property="*" />

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

@@ -44 +44 @@
   String zipFile;
   String experimentId;
+  String subjectNames;
   
   
@@ -365 +366 @@
   {
     this.numTreatmentGroups = numTreatmentGroups;
+  }
+  public String getSubjectNames()
+  {
+    return subjectNames;
+  }
+  public void setSubjectNames(String subjectNames)
+  {
+    this.subjectNames = subjectNames;
   }
   

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

@@ -113 +113 @@
           "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
           "numDesigns","dyeSwap","refSample","numTreatmentGroups","expFactors","numReplicates",
-          "tissues","pooling","zipFile", "fileStringParam"};
+          "tissues","pooling","zipFile", "fileList", "subjectList", "tissueList"};
   
 

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

@@ -29 +29 @@
   String[] factorNames;
   String [] fileNames;
-  
-  String domain;
-  String accession;
-  String qualityControl;
-  String experimentalDesign;
-  String experimentName;
-  String description;
-  String releaseDate;
-  String submissionDate;
-  String submitter;
-  String organization;
-  String publicationTitle;
-  String authors;
-  String journal;
-  String volume;
-  String issue;
-  String pages;
-  String year;
-  String pubmedId;
-  String treatmentProtocol;
-  String extractionProtocol;
-  String labelingProtocol;
-  String hybridizationProtocol;
-  String scanningProtocol;
-  String treatmentProtocolParams;
-  String extractionProtocolParams;
-  String labelingProtocolParams;
-  String hybridizationProtocolParams;
-  String scanningProtocolParams;
-  String platform;
-  String organism;
-  String numDesigns;
-  String dyeSwap;
-  String refSample;
-  String numTreatmentGroups;
-  String expFactors;
-  String numReplicates;
-  String tissues;
-  String pooling;
-  String zipFile;
-  String experimentId;
-  String fileStringParam;
-  
+  String [] subjectNames;
+  String [] tissueNames;
+
+  public String domain;
+  public String accession;
+  public String qualityControl;
+  public String experimentalDesign;
+  public String experimentName;
+  public String description;
+  public String releaseDate;
+  public String submissionDate;
+  public String submitter;
+  public String organization;
+  public String publicationTitle;
+  public String authors;
+  public String journal;
+  public String volume;
+  public String issue;
+  public String pages;
+  public String year;
+  public String pubmedId;
+  public String treatmentProtocol;
+  public String extractionProtocol;
+  public String labelingProtocol;
+  public String hybridizationProtocol;
+  public String scanningProtocol;
+  public String treatmentProtocolParams;
+  public String extractionProtocolParams;
+  public String labelingProtocolParams;
+  public String hybridizationProtocolParams;
+  public String scanningProtocolParams;
+  public String platform;
+  public String organism;
+  public String numDesigns;
+  public String dyeSwap;
+  public String refSample;
+  public String numTreatmentGroups;
+  public String expFactors;
+  public String numReplicates;
+  public String tissues;
+  public String pooling;
+  public String zipFile;
+  public String experimentId;
+  public String fileList;
+  public String subjectList;
+  public String tissueList;
+
 
   // ===================================================c'tor================================================
@@ -87 +91 @@
   public Tab2MageWriter()
   {
-    initTestParamValues();
+
   }
 
@@ -104 +108 @@
         field.set(this, job.getValue(paramNames[i]));
       }
-      
+
       //now extract the factor values and store them suitably so we can access them
       makeFactorValueCombinations();
@@ -113 +117 @@
     }
   }
-  
-  // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-    
-  private void makeFactorValueCombinations()
+
+  // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+  public void makeFactorValueCombinations()
   {
     //first extract the factor names and the possible values
@@ -147 +151 @@
       System.out.println();
     }
-    
+
     //now we want the filenames in a separate array so we can add them to their appropriate combinations as selected 
     //by the user in the UI
@@ -153 +157 @@
     //array in the order we find them in the string
     //they then match the order of the combinations in the cartesian product
-    fileNames = fileStringParam.split("\t");
-  }
-  
+    fileNames = fileList.split("\t");
+    //ditto for the lists of subject names and tissues
+    subjectNames = subjectList.split("\t");
+    tissueNames = tissueList.split("\t");
+  }
+
 
   // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
@@ -175 +182 @@
 
     String[] rowHeaders = new String[]
-    { "domain", "accession", "quality_control", "experiment_design_type", "name", "description",
+                                     { "domain", "accession", "quality_control", "experiment_design_type", "name", "description",
             "release_date", "submission_date", "submitter", "organization",
             "publication_title", "authors", "journal", "volume", "issue", "pages",
             "year", "pubmed_id" };
     String[] experimentParams = new String[]
-    { domain, accession, qualityControl, experimentalDesign, experimentName, description, releaseDate,
+                                           { domain, accession, qualityControl, experimentalDesign, experimentName, description, releaseDate,
             submissionDate, submitter, organization, publicationTitle, authors,
             journal, volume, issue, pages, year, pubmedId };
@@ -208 +215 @@
      */
     String[] accessions = new String[]
-    { "P-DIET-1", "P-EXTR-1", "P-LABL-1", "P-HYBR-1", "P-SCAN-1" };
+                                     { "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 };
+                                 { treatmentProtocol, extractionProtocol, labelingProtocol, hybridizationProtocol, scanningProtocol };
     String[] parameters = new String[]
-    { treatmentProtocolParams, extractionProtocolParams, labelingProtocolParams,
+                                     { treatmentProtocolParams, extractionProtocolParams, labelingProtocolParams,
             hybridizationProtocolParams, scanningProtocolParams };
     String[] types = new String[]
-    { "grow", "extraction", "labeling", "hybridization", "scanning" };
+                                { "grow", "extraction", "labeling", "hybridization", "scanning" };
 
     // print header
@@ -241 +248 @@
     // print column headers for the section
     String[] colHeaders = new String[]
-    { "File[raw]", "Array[accession]", "BioSource", "BioMaterialCharacteristics[Organism]",
+                                     { "File[raw]", "Array[accession]", "BioSource", "BioMaterialCharacteristics[Organism]",
             "BioMaterialCharacteristics[OrganismPart]",
             "BioMaterialCharacteristics[CellType]", "Sample", "Protocol[grow]",
@@ -251 +258 @@
       t2mContent += colHeaders[i] + "\t";
     }
-    
+
     //now print the factorvalue headers
     for (int i = 0; i < factorNames.length; i++)
@@ -257 +264 @@
       t2mContent += "FactorValue["+factorNames[i] + "]\t";
     }
-    
+
     //next line will be data
     t2mContent += "\n";
 
-    //single channel data -- currently only Affy
-    //we only need a single record for each tissue in each subject here
+    //determine whether this is a single or dual channel experiment
+    boolean singleChannel = false;
+    //the number of times we have to print the block of data below
+    //with dual channel platforms we have to print each block (row) twice
+    int numPrintRepeats = 2;
     if (platform.equalsIgnoreCase("affymetrix"))
     {
-      int count = 1;
-
-      int numSubjects = Integer.parseInt(numReplicates);
-      String[] allTissues = tissues.split(",");
-      int numTissues = allTissues.length;
-      int numGroups = Integer.parseInt(numTreatmentGroups);
-
-      // for each treatment group
-      for (int i = 1; i <= numGroups; i++)
+      singleChannel = true;
+      numPrintRepeats = 1;
+    }
+
+
+    //we need a single record for each tissue in each subject here
+
+    int count = 1;
+
+    int numSubjects = Integer.parseInt(numReplicates);
+    String[] allTissues = tissues.split(",");
+    int numTissues = allTissues.length;
+    int numGroups = Integer.parseInt(numTreatmentGroups);
+
+    // for each treatment group i.e. factor value combination
+    for (int i = 1; i <= numGroups; i++)
+    {
+      System.out.println("i=" +i);
+      System.out.println("count = " + count);
+      int subjectCount = 0;
+      // for each subject within each group i.e. biological replicate within each factor value combination
+      for (int j = 1; j <= numSubjects; j++)
       {
-        System.out.println("i=" +i);
-        int subjectCount = 0;
-        // for each subject within each group
-        for (int j = 1; j <= numSubjects; j++)
+        subjectCount = (i - 1) * numSubjects + j;
+        System.out.println("subjectCount = "+ subjectCount);
+        // for each target tissue for this subject
+        for (int k = 1; k <= numTissues; k++)
         {
-          subjectCount = (i - 1) * numSubjects + j;
-          // for each target tissue
-          for (int k = 1; k <= numTissues; k++)
+          for(int r = 0; r< numPrintRepeats; r++)
           {
-
+            String subjectName = subjectNames[count-1];
+            
             // file count first
             t2mContent += fileNames[count-1] + "\t" +
+            
             // accession no. i.e the array
             // design
             accession + "\t" +
+            
             // bio source
-            "group-" + i + "-subject-" + subjectCount + "\t" +
+            subjectName + "\t" +
+            
             // BioMaterialCharacteristics[Organism]
             organism + "\t" +
+            
             // BioMaterialCharacteristics[OrganismPart]
-            allTissues[k - 1] + "\t" +
+            tissueNames[count-1] + "\t" +
+            
             // BioMaterialCharacteristics[CellType]
             "" + "\t" +
+            
             // sample
-            "group-" + i + "-subject-" + subjectCount + ".sample-" + k + "\t" +
+            subjectName + ".sample-" + k + "\t" +
+            
             // Protocol[grow]
             "P-DIET-1" + "\t" +
+            
             // Extract
-            "group-" + i + "-subject-" + subjectCount + ".sample-" + k + "-extract" + "\t" +
+            subjectName + ".sample-" + k + "-extract" + "\t" +
+            
             // Protocol[extraction]
             "P-EXTR-1" + "\t" +
+            
             // LabeledExtract
-            "group-" + i + "-subject-" + subjectCount + ".sample-" + k + "-extract-le" + "\t" +
+            subjectName + ".sample-" + k + "-extract-le" + "\t" +
+            
             // Protocol[labeling]
-            "P-LABL-1" + "\t" +
+            "P-LABL-1" + "\t" ;
+            
             // Dye
-            "biotin" + "\t" +
+            //depends on platform and repeat no.
+            if(singleChannel)
+            {
+              t2mContent +="biotin" + "\t";
+            }
+            if(!singleChannel && numPrintRepeats==0)
+            {
+              t2mContent +="Cy3" + "\t";
+            }
+            if(!singleChannel && numPrintRepeats==1)
+            {
+              t2mContent +="Cy5" + "\t";
+            }
+            
             // Hybridization
-            "hybridization-" + count + "\t" +
+            t2mContent += "hybridization-" + count + "\t" +
+            
             // Protocol[hybridization]
             "P-HYBR-1" + "\t" +
+            
             // Scan
             "scan-" + count + "\t" +
+            
             // Protocol[scanning]
             "P-SCAN-1" + "\t";
-            
+
             //now print all the factor values
             // FactorValue[Treatment Type]
@@ -327 +377 @@
             for(int n=0; n< cartesianProduct[0].length; n++)
             {
-              System.out.println("count = " + count);
               System.out.println("n = "+ n);
               t2mContent +=cartesianProduct[i-1][n]+ "\t";
@@ -339 +388 @@
       }
     }
-
-    else //non Affy data, i.e. two channel
-    {
-
-      int count = 1;
-
-      int numSubjects = Integer.parseInt(numReplicates);
-      String[] allTissues = tissues.split(",");
-      int numTissues = allTissues.length;
-      int numGroups = Integer.parseInt(numTreatmentGroups);
-
-      // for each treatment group
-      for (int i = 1; i <= numGroups; i++)
-      {
-        int subjectCount = 0;
-        // for each subject within each group
-        for (int j = 1; j <= numSubjects; j++)
-        {
-          subjectCount = (i - 1) * numSubjects + j;
-          // for each target tissue
-          for (int k = 1; k <= numTissues; k++)
-          {
-            // this whole first block prints
-            // the data for the first
-            // channel
-
-            // file count first
-            t2mContent += fileNames[count-1] + "\t" +
-            // accession no. i.e the array
-            // design
-            accession + "\t" +
-            // bio source
-            "group-" + i + "-subject-" + subjectCount + "\t" +
-            // BioMaterialCharacteristics[Organism]
-            organism + "\t" +
-            // BioMaterialCharacteristics[OrganismPart]
-            allTissues[k - 1] + "\t" +
-            // BioMaterialCharacteristics[CellType]
-            "" + "\t" +
-            // sample
-            "group-" + i + "-subject-" + subjectCount + ".sample-" + k + "\t" +
-            // Protocol[grow]
-            "P-DIET-1" + "\t" +
-            // Extract
-            "group-" + i + "-subject-" + subjectCount + ".sample-" + k + "-extract" + "\t" +
-            // Protocol[extraction]
-            "P-EXTR-1" + "\t" +
-            // LabeledExtract
-            "group-" + i + "-subject-" + subjectCount + ".sample-" + k + "-extract-le" + "\t" +
-            // Protocol[labeling]
-            "P-LABL-1" + "\t" +
-            // Dye
-            "Cy3" + "\t" +
-            // Hybridization
-            "hybridization-" + count + "\t" +
-            // Protocol[hybridization]
-            "P-HYBR-1" + "\t" +
-            // Scan
-            "scan-" + count + "\t" +
-            // Protocol[scanning]
-            "P-SCAN-1" + "\t" +
-            // FactorValue[Treatment Type]
-            "trt_group" + i + "\t";
-
-            // new line
-            t2mContent += "\n";
-
-            // the second block prints the
-            // data for the second channel
-
-            // file count first
-            t2mContent += fileNames[count-1] + "\t" +
-            // accession no. i.e the array
-            // design
-            accession + "\t" +
-            // bio source
-            "reference" + "\t" +
-            // BioMaterialCharacteristics[Organism]
-            organism + "\t" +
-            // BioMaterialCharacteristics[OrganismPart]
-            "multi-tissue" + "\t" +
-            // BioMaterialCharacteristics[CellType]
-            "multi-cell type" + "\t" +
-            // sample
-            "reference" + "\t" +
-            // Protocol[grow]
-            "P-DIET-1" + "\t" +
-            // Extract
-            "reference" + "\t" +
-            // Protocol[extraction]
-            "P-EXTR-1" + "\t" +
-            // LabeledExtract
-            "reference" + "\t" +
-            // Protocol[labeling]
-            "P-LABL-1" + "\t" +
-            // Dye
-            "Cy5" + "\t" +
-            // Hybridization
-            "h" + count + "\t" +
-            // Protocol[hybridization]
-            "P-HYBR-1" + "\t" +
-            // Scan
-            "scan-" + count + "\t" +
-            // Protocol[scanning]
-            "P-SCAN-1" + "\t" +
-            // FactorValue[Treatment Type]
-            "reference" + "\t";
-
-            // new line
-            t2mContent += "\n";
-
-            count++;
-          }
-        }
-      }
-    }
-
-    // //////////////////////////////////////////////////////////////////////////////////////////////////////////
-
   }
 
@@ -468 +398 @@
     {
       // set up a file writer
-       dc = sc.newDbControl();
+      dc = sc.newDbControl();
       net.sf.basedb.core.File t2mFile = net.sf.basedb.core.File.getNew(dc, dir);
       System.out.println("dir for writing new tab2mage file = " + dir.getName());
@@ -543 +473 @@
   // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 
-  private void initTestParamValues()
-  {
-    /*
-     * --org Homo_sapiens --array Agilent1 --single 2 --ref yes
-     * --dye no --trtgroup 6 --factors
-     * compound(aspirin,ibuprofen);dose(none,medium,high) --target
-     * liver,heart,brain --subject 4
-     */
-
-    // experiment section
-    experimentId = "2";
-    domain = "scri.ac.uk";
-    accession = "Affymetrix1";
-    qualityControl = "biological replicate,spike quality control";
-    experimentalDesign = "cell_component_comparison_design,RNA_stability_design,family_history_design,";
-    experimentName = "New experiment";
-    description = "description goes here";
-    releaseDate = "2007-12-03";
-    submissionDate = "2007-12-03";
-    submitter = "Joe Bloggs";
-    organization = "SCRI";
-    publicationTitle = "My Ropey Paper";
-    authors = "Bloggs, Joe";
-    journal = "The Journal of Irreproducible Results";
-    volume = "5";
-    issue = "2";
-    pages = "1234-1235";
-    year = "2007";
-    pubmedId = "11009762";
-
-    // protocols
-    treatmentProtocol = "my treatment protocol text";
-    extractionProtocol = " my extraction protocol text";
-    labelingProtocol = " my labeling protocol text";
-    hybridizationProtocol = "my hybs protocol text";
-    scanningProtocol = " my scanning protocol text";
-    treatmentProtocolParams = "param1";
-    extractionProtocolParams = "param2";
-    labelingProtocolParams = "param3";
-    hybridizationProtocolParams = "param4";
-    scanningProtocolParams = " param5";
-
-    // hybs
-    platform = "Affymetrix";
-    organism = "Solanum tuberosum";
-    numDesigns = "1";
-    dyeSwap = "no";
-    refSample = "yes";
-    numTreatmentGroups = "4";
-    expFactors = "Strain(mutant,wildtype)\nTreatment(treated,control)";
-    numReplicates = "2";
-    tissues = "stem";
-    pooling = "no";
-    zipFile = "/home/michab/potato_small.zip";
-    fileStringParam = "file1.CEL\tfile2.CEL\tfile3.CEL\tfile4.CEL\tfile5.CEL\tfile6.CEL\tfile7.CEL\tfile8.CEL";
-    
-    
-    //now extract the factor values and store them suitably so we can access them
-    makeFactorValueCombinations();
-    
-  }
-  // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 }// end class

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriterTest.java

@@ -17 +17 @@
       //get the tab2mage output gerenated by the writer
       Tab2MageWriter writer = new Tab2MageWriter();
+      
+      //set parameters for testing
+      writer.experimentId = "2";
+      writer.domain = "scri.ac.uk";
+      writer.accession = "Affymetrix1";
+      writer.qualityControl = "biological replicate,spike quality control";
+      writer.experimentalDesign = "cell_component_comparison_design,RNA_stability_design,family_history_design,";
+      writer.experimentName = "New experiment";
+      writer.description = "description goes here";
+      writer.releaseDate = "2007-12-03";
+      writer.submissionDate = "2007-12-03";
+      writer.submitter = "Joe Bloggs";
+      writer.organization = "SCRI";
+      writer.publicationTitle = "My Ropey Paper";
+      writer.authors = "Bloggs, Joe";
+      writer.journal = "The Journal of Irreproducible Results";
+      writer.volume = "5";
+      writer.issue = "2";
+      writer.pages = "1234-1235";
+      writer.year = "2007";
+      writer.pubmedId = "11009762";
+
+      // protocols
+      writer.treatmentProtocol = "my treatment protocol text";
+      writer.extractionProtocol = " my extraction protocol text";
+      writer.labelingProtocol = " my labeling protocol text";
+      writer.hybridizationProtocol = "my hybs protocol text";
+      writer.scanningProtocol = " my scanning protocol text";
+      writer.treatmentProtocolParams = "param1";
+      writer.extractionProtocolParams = "param2";
+      writer.labelingProtocolParams = "param3";
+      writer.hybridizationProtocolParams = "param4";
+      writer.scanningProtocolParams = " param5";
+
+      // hybs
+      writer.platform = "Genepix";
+      writer.organism = "Solanum tuberosum";
+      writer.numDesigns = "1";
+      writer.dyeSwap = "no";
+      writer.refSample = "yes";
+      writer.numTreatmentGroups = "4";
+      writer.expFactors = "Strain(mutant,wildtype)\nTreatment(treated,control)";
+      writer.numReplicates = "2";
+      writer.tissues = "stem";
+      writer.pooling = "no";
+      writer.zipFile = "/home/michab/potato_small.zip";
+      writer.fileList = "file1.CEL\tfile2.CEL\tfile3.CEL\tfile4.CEL\tfile5.CEL\tfile6.CEL\tfile7.CEL\tfile8.CEL";
+      writer.subjectList = "plant1\tplant2\tplant3\tplant4\tplant5\tplant6\tplant7\tplant8";
+      writer.tissueList = "stem\tleaf\troot\tstem\tleaf\troot\tstem\tleaf";
+      
+      writer.makeFactorValueCombinations();
+      
+      
       String t2mContent = writer.generateFileContents();
       System.out.println("t2mContent = \n\n" + t2mContent);