Changeset 548

Timestamp:

Jan 22, 2008, 10:42:12 AM (15 years ago)

Author:

mbayer

Message:

new page added to gather additional info needed for autogeneration of t2m file

Location:

branches/uk_ac_ebi_Tab2MageImporter

Files:

• TODO.txt (modified) (1 diff)
• Tab2MageImporter.jar (modified) (previous)
• html/autogenerate.html (added)
• jsp/uk/ac/ebi/nugo/plugins/autogenerate.jsp (added)
• jsp/uk/ac/ebi/nugo/plugins/configureImporter.jsp (modified) (1 diff)
• jsp/uk/ac/ebi/nugo/plugins/experiment.jsp (modified) (1 diff)
• jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp (modified) (1 diff)
• jsp/uk/ac/ebi/nugo/plugins/mappings.jsp (modified) (1 diff)
• jsp/uk/ac/ebi/nugo/plugins/submit.jsp (modified) (2 diffs)
• jsp/uk/ac/ebi/nugo/plugins/userchoice2.jsp (modified) (2 diffs)
• 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) (6 diffs)
• test cases.xlsx (added)

branches/uk_ac_ebi_Tab2MageImporter/TODO.txt

@@ -1 +1 @@
 - naming of plugin and classes?
-- sort out copy right and ownership issues
+- sort out copyright and ownership issues
 - check in Charles' code
 - implement more complex use cases (pooling, dyeswap, no ref sample)
 - status report does not get written in all cases
+- add support for users using their own name bases for samples and perhaps extracts
+- adapt no of rows in table in mappings.jsp so it matches the correct number required
+- error handling, checks and validation
+- throw an error if dye-swap and reference set both to yes
+- if pooling, include a pooling protocol in the pooling section
+- implement failure conditions i.e. unsupported cases 

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

@@ -148 +148 @@
 <input type="hidden"name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
 <input type="hidden"name="parameter:spreadSheetMappings" value="<%= inputDataBean.getSpreadSheetMappings()%>"/>
+<input type="hidden"name="parameter:samplePairing" value="<%= inputDataBean.getSamplePairing()%>"/>
+<input type="hidden"name="parameter:timeCourse" value="<%= inputDataBean.getTimeCourse()%>"/>
+<input type="hidden"name="parameter:timePoints" value="<%= inputDataBean.getTimePoints()%>"/>
+<input type="hidden"name="parameter:proceed" value="<%= inputDataBean.getProceed()%>"/>
 
 <input type="hidden"name="parameter:fileList" value=""/>

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

@@ -34 +34 @@
 
 <script>
-self.resizeTo(800,800);
+self.resizeTo(800,1100);
 </script>
 

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

@@ -178 +178 @@
     <td class="boldText">Number of treatment groups:</td>
     <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td>
-    <td>The number of permutations of factor values. <p>
+    <td>The number of discrete combinations of factor values, i.e. the product of the number of factor levels(values) from all factors. <p>
     Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
     </td>

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

@@ -165 +165 @@
 
   //work out the number of hybridizations
+  String platform = inputDataBean.getPlatform();
+  //work out whether this is a single or dual channel experiment
+  boolean singleChannel = false;
+  if (platform.equalsIgnoreCase("affymetrix"))
+  {
+    singleChannel = true;
+  } 
   int numReplicates = Integer.parseInt(inputDataBean.getNumReplicates());
   int numTreatmentGroups = Integer.parseInt(inputDataBean.getNumTreatmentGroups());
   int numTissues = inputDataBean.getTissues().split("\n").length;
-  int numHybs = Tab2MageWriter.calcNumHybs(numReplicates, numTreatmentGroups, numTissues);
+  int numHybs = Tab2MageWriter.calcNumHybs(singleChannel,numReplicates, numTreatmentGroups, numTissues);
   System.out.println("numHybs = " + numHybs);
   System.out.println("products.length = " + products.length);

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

@@ -58 +58 @@
     "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
     "numDesigns","dyeSwap","refSample","numTreatmentGroups","expFactors","numReplicates",
-    "tissues","pooling","path"};
+    "tissues","pooling","path","samplePairing","timeCourse","timePoints"};
     
     String [] friendlyNames = new String []{"Domain","Accession","Quality Control","Experimental Design",
     "Experiment Name","Description","Release Date","Submission Date","Submitter","Organization",
-    "Publication Title","Authors","Journal","Volume","Issue","Pages","Year","Pubmed ID","Treatment SProtocol",
+    "Publication Title","Authors","Journal","Volume","Issue","Pages","Year","Pubmed ID","Treatment Protocol",
     "Extraction Protocol","Labeling Protocol","Hybridization Protocol","Scanning Protocol",
     "Treatment Protocol Parameters","Extraction Protocol Parameters","Labeling Protocol Parameters",
     "Hybridization Protocol Parameters","Scanning Protocol Parameters","Platform","Organism",
     "Number of Array Designs","Dye Swap","Reference Sample","Number of Treatment Groups","Experimental Factors","Number of Replicates per Group",
-    "Tissues","Pooling","Zip File"};
+    "Tissues","Pooling","Zip File","Sample Pairing Rationale","Time Course","Time Points"};
 
   //print out all relevant parameter values in the bean
@@ -149 +149 @@
 <input type="hidden"name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
 <input type="hidden"name="parameter:spreadSheetMappings" value="<%= inputDataBean.getSpreadSheetMappings()%>"/>
+<input type="hidden"name="parameter:samplePairing" value="<%= inputDataBean.getSamplePairing()%>"/>
+<input type="hidden"name="parameter:timeCourse" value="<%= inputDataBean.getTimeCourse()%>"/>
+<input type="hidden"name="parameter:timePoints" value="<%= inputDataBean.getTimePoints()%>"/>
+<input type="hidden"name="parameter:proceed" value="<%= inputDataBean.getProceed()%>"/>
 
 <input type="hidden"name="parameter:fileList" value=""/>

branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/userchoice2.jsp

@@ -41 +41 @@
   if(document.getElementById("legacyDataNo").checked)
   {
-    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp?ID=<%=ID%>";
+    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/autogenerate.jsp?ID=<%=ID%>";
   }
 
@@ -84 +84 @@
 <p>If you choose 'yes' you will be asked for mappings between filenames, samples and factor value combinations on the next pages.
 </p>
-<p>If you choose 'no' the Tab2MAGE importer will autogenerate names for files and samples on your behalf and proceed with the import automatically.
+<p>If you choose 'no' the Tab2MAGE importer will autogenerate names for files and samples on your behalf.
 </p>
 

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

@@ -55 +55 @@
   public String mappingsMode;
   public String spreadSheetMappings;
+  public String samplePairing;
+  public String timeCourse;
+  public String timePoints;
+  public String proceed;
   
   public DataBean()
@@ -468 +472 @@
     this.spreadSheetMappings = spreadSheetMappings;
   }
+
+  public String getProceed()
+  {
+    return proceed;
+  }
+
+  public void setProceed(String proceed)
+  {
+    this.proceed = proceed;
+  }
+
+  public String getSamplePairing()
+  {
+    return samplePairing;
+  }
+
+  public void setSamplePairing(String samplePairing)
+  {
+    this.samplePairing = samplePairing;
+  }
+
+  public String getTimeCourse()
+  {
+    return timeCourse;
+  }
+
+  public void setTimeCourse(String timeCourse)
+  {
+    this.timeCourse = timeCourse;
+  }
+
+  public String getTimePoints()
+  {
+    return timePoints;
+  }
+
+  public void setTimePoints(String timePoints)
+  {
+    this.timePoints = timePoints;
+  }
   
   

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

@@ -99 +99 @@
     "numDesigns","dyeSwap","refSample","numTreatmentGroups","expFactors","numReplicates",
     "tissues","pooling","path", "subjectNames", "fileList", "subjectList", "tissueList","combinationList", "useWizard",
-    "legacyData","mappingsMode","spreadSheetMappings"};
+    "legacyData","mappingsMode","spreadSheetMappings","samplePairing","timeCourse","timePoints","proceed"};
 
 

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

@@ -26 +26 @@
   String t2mContent = "";
   ParameterValues job;
+  boolean singleChannel = false;
+  
   String[] paramNames;
-
   String[] factorNames;
   String [] fileNames;
@@ -82 +83 @@
   public String mappingsMode;
   public String spreadSheetMappings;
+  public String samplePairing;
+  public String timeCourse;
+  public String timePoints;
+  public String proceed;
 
 
@@ -122 +127 @@
       }
 
-      //this extracts the individaul factor names from the String that comes from the web page
+      //work out whether this is a single or dual channel experiment
+      if (platform.equalsIgnoreCase("affymetrix"))
+      {
+        singleChannel = true;
+      }
+      //this extracts the individual factor names from the String that comes from the web page
       extractFactorNames();
       //now extract the factor values and store them suitably so we can access them
@@ -182 +192 @@
       combinations = new String [entries.length][];
       
+      //now populate the 2d array of factor value combinations as above
       for (int i = 0; i < entries.length; i++)
       {
@@ -319 +330 @@
     t2mContent += "\n";
 
-    //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"))
-    {
-      singleChannel = true;
+    if (singleChannel)
+    {     
       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(",");
@@ -518 +524 @@
   // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 
-  public static int calcNumHybs(int numReplicates, int numTreatmentGroups, int numTissues)
-  {
-    // Number of hybridizations (NH) = Number of subjects (NS) x
-    // Number of Target Tissue (NTT) x Number of Study groups (NSG)
-    return numReplicates * numTissues * numTreatmentGroups;
+  public static int calcNumHybs(boolean dyeSwap, boolean pooling, int numDesigns, int numReplicates, int numTreatmentGroups, int numTissues)
+  {
+    int numHybs = 0;
+
+    /*
+    Basic assumption: 
+      no pooling, one source ->one sample->one extract->one labeled extract->one hyb
+      Number of hybridizations (NH) = Number of subjects (NS) x Number of Target Tissue (NTT) x Number of Study groups (NSG)
+     */
+    numHybs = numReplicates * numTissues * numTreatmentGroups;
+
+    //a number of conditions can then modify the basic number of hybs:
+
+    //dye swap results in twice the number of hybs
+    //NHdye-swap=2 x NH
+    if(dyeSwap)
+    {     
+      numHybs = numHybs *2;
+    }
+    
+    //if several array designs are used all hybs must be applied to each of them
+    //NHmultiple designs=Nad x NH
+    if(numDesigns > 1)
+    {
+      numHybs = numHybs * numDesigns;
+    }
+    
+    //pooling reduces the number of hybs as the biological replication gets cancelled out
+    //NH(if pooling)= NH/Number of subjects (NS)
+    if(pooling)
+    {
+      numHybs = numHybs/numReplicates;
+    }
+
+
+
+    return numHybs; 
   }