Changeset 516

Timestamp:

Dec 7, 2007, 3:06:52 PM (16 years ago)

Author:

mbayer

Message:

first two sections of tab2mage file now get generated ok

Location:

branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins

Files:

• Tab2MageImporter.java (modified) (3 diffs)
• Tab2MageWriter.java (modified) (3 diffs)

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

@@ -105 +105 @@
   private static final Set<GuiContext> guiContexts = Collections.singleton(experimentItemGuiContext);
   
+  //add all the parameter names to a String array for processing
+  String [] paramNames = new String []{"experimentId","domain","accession","qualityControl","experimentalDesign",
+          "experimentName","description","releaseDate","submissionDate","submitter","organization",
+          "publicationTitle","authors","journal","volume","issue","pages","year","pubmedId","treatmentProtocol",
+          "extractionProtocol","labelingProtocol","hybridizationProtocol","scanningProtocol",
+          "treatmentProtocolParams","extractionProtocolParams","labelingProtocolParams",
+          "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
+          "numDesigns","dyeSwap","refSample","numTreatments","expFactors","numReplicates",
+          "tissues","pooling","zipFile"};
+  
 
 //  =====================================================c'tor==================================  
@@ -123 +133 @@
   private void initParams()
   {   
-    //add all the parameter names to a String array for processing
-    String [] paramNames = new String []{"experimentId","domain","accession","qualityControl","experimentalDesign",
-            "experimentName","description","releaseDate","submissionDate","submitter","organization",
-            "publicationTitle","authors","journal","volume","issue","pages","year","pubmedId","treatmentProtocol",
-            "extractionProtocol","labelingProtocol","hybridizationProtocol","scanningProtocol",
-            "treatmentProtocolParams","extractionProtocolParams","labelingProtocolParams",
-            "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
-            "numDesigns","dyeSwap","refSample","numTreatments","expFactors","numReplicates",
-            "tissues","pooling","zipFile"};
         
-    // next create the parameter type - everyone is a String here
+    //create the parameter type - every parameter is a String 
     StringParameterType stringPT = new StringParameterType(255, null, true);
     
@@ -419 +420 @@
       //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);
+      Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc,paramNames);
       t2mWriter.writeTab2MageFile();
 

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

@@ -1 +1 @@
 package uk.ac.ebi.nugo.plugins;
 
-import java.io.*;
-
-import net.sf.basedb.core.BaseException;
+import java.io.BufferedWriter;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+import java.lang.reflect.Field;
+
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Directory;
-import net.sf.basedb.core.InvalidDataException;
-import net.sf.basedb.core.PermissionDeniedException;
-import net.sf.basedb.core.PluginConfigurationRequest;
 import net.sf.basedb.core.SessionControl;
 import net.sf.basedb.core.plugin.ParameterValues;
-import net.sf.basedb.core.plugin.Request;
 
 public class Tab2MageWriter
 {
-//===================================================vars================================================ 
-  
-  int numReplicates;
-  int numTissues;
-  int numTreatments;
+//  ===================================================vars================================================ 
+
   Directory dir;
   SessionControl sc;
-  
+  String t2mContent = "";
+  ParameterValues job;
+  String [] paramNames;
+
+  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 numTreatments;
+  String expFactors;
+  String numReplicates;
+  String tissues;
+  String pooling;
+  String zipFile;
+  String experimentId;
+  
+  
+
 //  ===================================================c'tor================================================
-  
-  public Tab2MageWriter(ParameterValues job,Directory dir,SessionControl sc)
+
+  public Tab2MageWriter(ParameterValues job,Directory dir,SessionControl sc,String [] paramNames)
   {
     this.dir = dir;
     this.sc = sc;
-
-    //get values for the parameters we need here
-    int numReplicates = Integer.parseInt((String)job.getValue("numReplicates"));
-    int numTreatments = Integer.parseInt((String)job.getValue("numTreatments"));    
-    String tissues = (String)job.getValue("tissues");
-    int numTissues = tissues.split(",").length;
-    
-    System.out.println("numReplicates extracted from job = " +numReplicates);
+    this.job = job;
+    this.paramNames = paramNames;
+    initJobParamValues();
+  }
+
+  //for testing only
+  public Tab2MageWriter()
+  {
+    initTestParamValues();
   }
 
 //  ===================================================methods================================================  
-  
-  public static void main(String [] args)
-  {
-  }
-  
+
+  //sets all the values of the local variables to those found in the job object
+  private void initJobParamValues()
+  {
+    try
+    {
+      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.set(this, job.getValue(paramNames[i]));
+      }
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+//  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
+
+  public String generateFileContents()
+  {
+    makeExperimentSection();
+    makeProtocolSection();
+    makeHybridizationsSection();
+    return t2mContent;
+  }
+
+//  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   
+  
+  private void makeExperimentSection()
+  {
+    //header for this section
+    t2mContent += "Experiment section\n";
+    
+    String [] rowHeaders = new String [] {"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,submissionDate,submitter,organization,publicationTitle,authors,journal,volume,issue,pages,year,pubmedId};
+    
+    for (int i = 0; i < rowHeaders.length; i++)
+    {
+      t2mContent += rowHeaders[i] + "\t" + experimentParams[i] + "\n";
+    }
+    
+    //separate from next section by a blank line
+    t2mContent += "\n\n";
+  }
+  
+//  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   
+  
+  private void makeProtocolSection()
+  {
+    //header for this section
+    t2mContent += "Protocol section\n";
+    
+    //section needs to look like this:
+    /*
+    accession name      text    parameters    type
+    P-DIET-1  treatment   text            grow
+    P-EXTR-1  extraction    text            extraction
+    P-LABL-1  labeling      text            labeling
+    P-HYBR-1  hybridization text            hybridization
+    P-SCAN-1  scanning    text            scanning
+    */
+    String [] accessions = new String [] {"P-DIET-1","P-EXTR-1","P-LABL-1","P-HYBR-1","P-SCAN-1"};
+    String [] names = new String [] {"treatment","extraction","labeling","hybridization","scanning"};
+    String [] values = new String [] { treatmentProtocol, extractionProtocol, labelingProtocol, hybridizationProtocol, scanningProtocol};
+    String [] parameters = new String [] {treatmentProtocolParams, extractionProtocolParams,labelingProtocolParams,hybridizationProtocolParams,scanningProtocolParams};
+    String [] types = new String [] {"grow","extraction","labeling","hybridization","scanning"};
+    
+    //print header
+    t2mContent += "accession\tname\ttext\tparameters\ttype\n";
+    
+    //print rows
+    for (int i = 0; i < accessions.length; i++)
+    {
+      t2mContent += accessions[i] + "\t" + names[i] + "\t" + values[i] + "\t" + parameters[i] + "\t" + types[i] + "\n";
+    }
+    
+    //separate from next section by a blank line
+    t2mContent += "\n\n";
+  }
+
+//  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   
+  
+  private void makeHybridizationsSection()
+  {
+    //header for this section
+    t2mContent += "Hybridization section\n";
+  }
+  
+//  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
+
   public void writeTab2MageFile()
   {
@@ -55 +185 @@
       t2mFile.setName("tab2mage.txt");      
       dc.saveItem(t2mFile);
-      
+
       if(dc==null)
         dc = sc.newDbControl();
-      
+
       Writer out= new BufferedWriter(new OutputStreamWriter(t2mFile.getUploadStream(false),"ISO-8859-1"));
-      
-      //write stuff to file
-      out.write("test String");
-      
+
+      //write content to file
+      out.write(t2mContent);
+
       //close writer
       if (out!= null) out.close();
-      
+
       dc.commit();
       if(dc!=null)
@@ -76 +206 @@
     }   
   }
+
+//  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
   
   private int calcNumHybs()
   {
+    //get values for the parameters we need here
+    int numReps = Integer.parseInt(numReplicates);
+    int numTreats = Integer.parseInt(numTreatments);    
+    int numTissues = tissues.split(",").length;
     //Number of hybridizations (NH) = Number of subjects (NS) x Number of Target Tissue (NTT) x Number of Study groups (NSG)
-    return numReplicates * numTissues * numTreatments;
-
-  }
-
-}
+    return numReps * numTissues * numTreats;
+  }
+
+//  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 
+
+  private void initTestParamValues()
+  {
+    experimentId = "2";
+    domain = "scri.ac.uk";
+    accession = "E-SCRI-001";
+    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";
+    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";
+    platform = "Affymetrix";
+    organism = "barley";
+    numDesigns = "1";
+    dyeSwap = "no";
+    refSample = "no";
+    numTreatments = "2";
+    expFactors = "Factor 1(value1,value2,...valueN)";
+    numReplicates = "3";
+    tissues = "tissues1,tissue2";
+    pooling = "no";
+    zipFile = "/home/michab/potato_small.zip";
+
+  }
+//-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+}//end class