Changeset 468 for trunk/uk/ac/ebi

Timestamp:

Nov 12, 2007, 5:47:38 PM (15 years ago)

Author:

dominic

Message:

added newly changed code. This source code is not in sycn with the current released version of the tab2mage importer.

Location:

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation

Files:

• RawDataValidation.java (modified) (1 diff)
• Tab2MageHybridizationValidation.java (modified) (24 diffs)
• Tab2MageImportValidatorUtils.java (modified) (2 diffs)
• Tab2MageProtocolValidation.java (modified) (6 diffs)
• Tab2MageValidationFactory.java (modified) (7 diffs)

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/RawDataValidation.java

@@ -12 +12 @@
   Note: seperate implementation to base1/ baseloader
     @author Dominic Oyeniran
-  @email oyeniran@ebi.ac.uk
+  @email
   @version 1.0
  */

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageHybridizationValidation.java

@@ -61 +61 @@
   protected Path spath;
   
+  // must be added from the HybridizationValidation interface
   protected String path;
   /**
@@ -130 +131 @@
       for(Tab2MAGEHybridization hyb : hybs)
       {
+        // check if the raw data files really exist
         log.info("Checking that file exist.......");
         List<String> fileErrors= checkIfFilesExist(hyb,  spath);
@@ -135 +137 @@
         
         log.info("Checking that file has proper type......");
+        // check if the files have the proper type
+        
         List<String> fileTypesErrors = checkFileTypes(hyb, platform);
         if (!fileTypesErrors.isEmpty())errors.addAll(fileTypesErrors);
@@ -145 +149 @@
         }
       }
+      
       if (!errors.isEmpty())
       {
@@ -172 +177 @@
       Validate the hybridization headers from the Tab2MAGE file. 
       This code MUST be modified for MAGE-TAB implementation. 
+      [TODO] convert all headers to lowercase, to facilitate matching of hyb section header to Tab2mageConstants/Spec
       @param header an <code>ArrayList</code> with all headers from the Tab2MAGE file
       @return true if the headers are valid, false otherwise
@@ -177 +183 @@
   public static boolean validateHeader(ArrayList<String> header, Writer writer)
   {
+    //[TODO] convert all headers to lowercase, to facilitate matching of hyb section header to Tab2mageConstants/Spec
     //header= header2LowerCase(header);
     List<String> headerErrors = new LinkedList<String>();
@@ -185 +192 @@
       {
         log.error("The column \"" + Tab2MageConstants.hybridization.getName() + "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.hybridization.getName() + "\" wasn't found!");
       }
@@ -191 +199 @@
       {
         log.error("The column \"" + Tab2MageConstants.labeledextract.getName() + "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.labeledextract.getName() + "\" wasn't found!");
       }
@@ -197 +206 @@
       {
         log.error("The column \"" + Tab2MageConstants.dye.getName() + "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.dye.getName() + "\" wasn't found!");
       }
@@ -203 +213 @@
       {
         log.error("The column \"" + Tab2MageConstants.extract.getName()+ "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.extract.getName()+ "\" wasn't found!");
       }
@@ -209 +220 @@
       {
         log.error("The column \"" + Tab2MageConstants.sample.getName() + "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.sample.getName() + "\" wasn't found!");
       }
@@ -215 +227 @@
       {
         log.error("The column \"" + Tab2MageConstants.biosource.getName() + "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.biosource.getName() + "\" wasn't found!");
       }
@@ -221 +234 @@
       {
         log.error("The column \"" + Tab2MageConstants.array_accession.getName() + "\" wasn't found!");
+        //valid = false;
         headerErrors.add("The column \"" + Tab2MageConstants.array_accession.getName() + "\" wasn't found!");
       }
+      
+      /*
+         a bit flexible to accommodate non provision of array serial
+       */
+      //if (!header.contains(Tab2MAGEHybridization.ARRAY + "[" + Constants.ARRAY_SERIAL + "]")){
+      //  log.error("The column \"" + Tab2MAGEHybridization.ARRAY + "[" + Constants.ARRAY_SERIAL + "]" + " wasn't found!");
+      //  valid = false;
+      //}
+      
+      /*
+        check for biomaterial characteristics - simply biosource annotation in base2.
+        And exisitence of experimental factors
+        NOTE: "Characteristics" would be used for MAGE-TAB implementation
+       */ 
+    
       
       cont:
@@ -244 +273 @@
       {
         log.error("At least one BioMaterial Characteristics should be provided!");
+        //valid = false;
         headerErrors.add("At least one BioMaterial Characteristics should be provided!");
       }
@@ -250 +280 @@
       {
         log.error("At least one Experimental Factor should be provided!");
+        //valid = false;
         headerErrors.add("At least one Experimental Factor should be provided!");
       }
@@ -275 +306 @@
           {
             log.error("The protocol column \"" + head + "\" is not a valid protocol format allowed in the tab2mage specification!");
+            //valid = false;
             headerErrors.add("The protocol column \"" + head + "\" is not a valid protocol format allowed in the tab2mage specification!");
           }
@@ -282 +314 @@
       if(!tmpValid1 || !tmpValid2 || !tmpValid3){
         log.error("The protocol columns of the Tab2MAGE hybridization section aren't valid!");
+        //valid = false;
         headerErrors.add("The protocol columns of the Tab2MAGE hybridization section aren't valid!");
       }
@@ -294 +327 @@
           {
             log.error("The parameter " + head + " does not match parameters specified in the protocol section!");
+            //valid = false;
             headerErrors.add("The parameter: [" + head + "] does not match parameters specified in the protocol section!");
           }
@@ -352 +386 @@
         {
           log.error("The raw data file [" + hyb.getFileRaw() + "] doesn't exist or couldn't be accessed!");
+          //return false;
           errs.add("The raw data file [" + hyb.getFileRaw() + "] doesn't exist or couldn't be accessed!");
         }
+        
       }
       
@@ -361 +397 @@
         {
           log.error("The image file [" + hyb.getFileImage() + "] doesn't exist or couldn't be accessed!");
+          //return false;
           errs.add("The image file [" + hyb.getFileImage() + "] doesn't exist or couldn't be accessed!");
         }
       }
+    /*
+      Uncomment to ADD support for cdf and chp file 
+     */
+      //System.out.println("cheking the cdf file.....");
+      //if(hyb.getFileCDF() != null)
+      //{
+      //  if(!File.exists(dc, dir, hyb.getFileCDF()))
+      //  {
+      //    log.error("The cdf file " + hyb.getFileCDF() + " doesn't exist or couldn't be accessed!");
+      //    return false;
+      //  }
+      //}
+      //System.out.println("cheking the chp file.....");
+      //if(hyb.getFileCHP() != null && !hyb.getFileCHP().equals("NA"))
+      //{
+      //  if (!File.exists(dc, dir, hyb.getFileCHP()))
+      //  {
+      //    log.error("The chp file " + hyb.getFileCHP() + " doesn't exist or couldn't be accessed!");
+      //    return false;
+      //  }
+      //}
+      
+      /*
+        code to be used for support of file[normalised], file[transformed] not supported yet in Base2
+        hyb.getFileTransformed and hyb.getFileNormalised should be added to Tab2MAGEHybridization Class.
+      
+      
+      //if(hyb.getFileTransformed() != null )
+      //{
+      //  if (!File.exists(dc, directory, hyb.getFileTransformed()))
+      //  {
+      //    log.error("The transformed file " + hyb.getFileTransformed() + " doesn't exist or couldn't be accessed!");
+      //    return false;
+      //  }
+      //}
+      
+      //if(hyb.getFileNormalised() != null )
+      //{
+      //  if (!File.exists(dc, directory, hyb.getFileNormalised()))
+      //  {
+      //    log.error("The normalised file " + hyb.getFileNormalised() + " doesn't exist or couldn't be accessed!");
+      //    return false;
+      //  }
+      //}
+      
+      END OF THE SECTION TO ADD FUNCTIONALITY ADD-ONS.
+     */
     }
     catch (Throwable tr)
@@ -390 +474 @@
       {
         log.error("The raw data file from the hybridization [" + hyb.getName() + "] has not the proper type.");
+        //return false;
         er.add("The raw data file from the hybridization [" + hyb.getName() + "] has not the proper type.");
       }
@@ -401 +486 @@
         {
           log.error("The CHP file from the hybridization [" + hyb.getName() + "] has not the proper type.");
+          //return false;
           er.add("The CHP file from the hybridization [" + hyb.getName() + "] has not the proper type.");
         }
@@ -412 +498 @@
       {
         log.error("The GPR file from the hybridization [" + hyb.getName() + "] has not the proper type.");
+        //return false;
         er.add("The GPR file from the hybridization [" + hyb.getName() + "] has not the proper type.");
       }
     }
+    
+    //add code to check other raw data file here, do extend the experiment platform enum class too
+    
     return er;
   }
@@ -521 +611 @@
   }
   
+  
   public void setAllowSlideCreation(boolean allowSlideCreation) 
   {

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageImportValidatorUtils.java

@@ -186 +186 @@
         if (parameterAnnotationType.containsKey(e.getKey()))
         {
-          log.info("Found Parameter key : [" + e.getKey()+ "] and value is :" + parameterAnnotationType.get(e.getKey()));
+          //log.info("Found Parameter key : [" + e.getKey()+ "] and value is :" + parameterAnnotationType.get(e.getKey()));
           parameter="true";
         }
+        //log.info(".....checking biomat map");
         if (bioMaterialAnnotationType.containsKey(e.getKey())) 
         {
-          log.info("Found BioMat key: [" + e.getKey()+ "] and value is :" + bioMaterialAnnotationType.get(e.getKey()));
+          //log.info("Found BioMat key: [" + e.getKey()+ "] and value is :" + bioMaterialAnnotationType.get(e.getKey()));
           items.add("biosource");
         }
-          
+        //log.info(".....checking factor value map"); 
         if (factorValueAnnotationType.containsKey(e.getKey())) 
         {
-          log.info("Found Factor Value key: [" + e.getKey()+ "] and value is :" + factorValueAnnotationType.get(e.getKey()));
+          //log.info("Found Factor Value key: [" + e.getKey()+ "] and value is :" + factorValueAnnotationType.get(e.getKey()));
           items.add("rawbioassay");
         }
@@ -228 +229 @@
   }
   /**
-    creates a simple flatfile into a specified directory using the format of existing similar file
+    creates a simple flatfile into a specified directory using the format of exisiting similar file
       @param dc, the db control
       @param dir, the directory- parent directory

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageProtocolValidation.java

@@ -79 +79 @@
                 log.error("The protocol type is empty. Must be provided");
                 errors.add("Protocol Type for protocol with accession number: [" + protocol.getAccession()+ "] is empty. Must be provided");
+                //return false;
             }
            
             //check if protocol is allowed in tab2mage.
+          
             Set<Tab2MageConstants> allowedProtocols = Collections.unmodifiableSet(Tab2MageConstants.protocolContants());
           for  (Tab2MageConstants  allowedProtocol : allowedProtocols  )
@@ -93 +95 @@
           if(!allowed)
             {
+                // if it is not reachable log the error message and stop
                 log.error("The protocol : " + protocol.getName() + " isn't permissible in the tab2mage specification.!");
+                //return false;
                 errors.add("The protocol : [" + protocol.getName() + "] isn't permissible in the tab2mage specification.!");
             }
           
           // check if all protocol types are reachable in base2
+          
           ItemQuery<ProtocolType> protocolTypesQuery = ProtocolType.getQuery();
           ItemResultList<ProtocolType> protocolTypes =protocolTypesQuery.list(dc);
@@ -111 +116 @@
           }
           if(!found)
-          {
+           {
+                // if it is not reachable log the error message and stop
                 log.warn("The protocol type: " + protocol.getType() + " isn't existing in BASE.!\n The importer may FAIL and your experiment may not be loaded");
                 errors.add("The protocol type: [" + protocol.getType() + "] isn't existing in BASE.!\n The importer may FAIL and your experiment may not be loaded");
-          }
+                //    return false;
+           }
           
           // check name and accession
@@ -121 +128 @@
                 log.error("A protocol accession is empty.");
                 errors.add("A protocol accession is empty in the protocol section. Must be provided to proceed");
+                //return false;
             }
             if(protocol.getName().equals("") || protocol.getName() == null)
@@ -126 +134 @@
                 log.error("A protocol name is empty.");
                 errors.add("A protocol name is empty in the protocol section. Must be provided to proceed");
-            }
+                //return false;
+            }
+            
             getAllProtocolParameters(protocol);
         }
@@ -196 +206 @@
     Tab2MageProtocolValidation.protocolParameters = protocolParameters;
   }
+
 }

trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/validation/Tab2MageValidationFactory.java

@@ -132 +132 @@
     response = resp;
     statusFile = file;  
+    //this calls the Tab2mage file validation routine
+    //validateTab2MageFile();
     createWriter();
   }
@@ -198 +200 @@
    */
   @SuppressWarnings("static-access")
+  //public void validateTab2MageFile()
   public Map<ValidationConstants, Boolean> validateTab2MageFile()
   {
@@ -246 +249 @@
       }
                   
+      // Display the protocols only for debugging     
+      //log.info("\n+++++++++++++++++++++++ALL THE PROTOCOLS++++++++++++++++++++++++++++++++++++++\n");
+      //for (Tab2MAGEProtocol p : protocols)
+      //{
+      //  log.warn(p.getAccession()+ "\t" +p.getText()+ "\t" +p.getName() + "\t" +p.getType()+ "\t" +p.getParameters());
+      //}
+      //Display all the parameters, only for debugging
+      
+      //log.info("\n++++++++++++++++++++ The parameters ++++++++++++++\n");
+      //List<String> params= protocolVal.getProtocolParameters();
+      //for (String p : params)
+      //{
+      //  log.warn(p);
+      //}
+            
       log.info( doneProtocol ? " \n.... Protocol validation is SUCCESSFUL .... \n" :" \n.... Protocol validation FAILED .... \n");
       statusOut.write( doneProtocol ? " \n.... Protocol validation is SUCCESSFUL .... \n" :" \n.... Protocol validation FAILED .... \n");
@@ -263 +281 @@
       {
         log.error("SORRY: The header for the hybridization section of the tab2mage file: " +filename+ " is invalid. Must be rectified to proceed. See the log file for more details");
+        //throw new NutribasePluginException("The header for the hybridization section of the tab2mage file: " +filename+ " is invalid. Must be rectified to proceed. See the log file for more details");
         statusOut.write("Sorry the header for the hybridization section of the tab2mage file: " +filename+ " is invalid. Must be rectified to proceed.");
         doneHybridizationHeaders = false;
       }
       statusOut.write( doneHybridizationHeaders ? " \n.... Hybridization header validation is SUCCESSFUL .... \n" :" \n.... Hybridization header validation FAILED .... \n");
-            
-        //validate rows /lines
+      //statusOut.flush();
+      
+      //validate rows /lines
       
       Tab2MageHybridizationValidation validateHyb = new Tab2MageHybridizationValidation(dir, platform, hybs, reader, sc);
@@ -286 +306 @@
          
        */
+      // check if the dc is closed, or disconnected and create a new one if yes
       if (dc == null || !dc.isConnected() || dc.isClosed()) dc = sc.newDbControl();
       dir= Directory.getByPath(dc, dir.getPath());
@@ -317 +338 @@
         {
           log.error("Sorry the agilent files cannot be validated. Mandatory Columns are missing. Must be rectified to proceed. See the log file for more details");
+          //throw new ValidationException("An agilent file is missing once or more mandatory columns!");
           statusOut.write("Sorry the agilent files cannot be validated. Mandatory Columns are missing. Must be rectified to proceed.");
           doneAgilent =false;
@@ -386 +408 @@
       
       statusOut.close();
+      //dc.commit();
     }
     catch(Throwable tr)