Changeset 396 for trunk/uk/ac/ebi

Timestamp:

Aug 15, 2007, 11:56:47 AM (16 years ago)

Author:

dominic

Message:

added util jar files and build file etc

Location:

trunk/uk/ac/ebi/Tab2MageExporter

Files:

• Tab2MageExporter.jar (modified) (previous)
• build.xml (added)
• ebi-plugins-utils.jar (added)
• src/uk/ac/ebi/nugo/common (added)
• src/uk/ac/ebi/nugo/common/Helper.java (added)
• src/uk/ac/ebi/nugo/common/NutribasePluginException.java (added)
• src/uk/ac/ebi/nugo/common/Tab2MageConstants.java (added)
• src/uk/ac/ebi/nugo/common/ValueFormatter.java (added)
• src/uk/ac/ebi/nugo/common/ZipUnpacker.java (added)
• src/uk/ac/ebi/nugo/plugins/Tab2MageExporter.java (modified) (7 diffs)
• src/uk/ac/ebi/nugo/plugins/ta2mageexport/ExporHelper.java (added)
• src/uk/ac/ebi/nugo/plugins/ta2mageexport/Tab2MageValidator.java (added)
• src/uk/ac/ebi/nugo/plugins/ta2mageexport/Tab2MageWriter.java (modified) (14 diffs)
• src/uk/ac/ebi/nugo/plugins/util (deleted)

trunk/uk/ac/ebi/Tab2MageExporter/src/uk/ac/ebi/nugo/plugins/Tab2MageExporter.java

@@ -22 +22 @@
 */
 package uk.ac.ebi.nugo.plugins;
-
 import java.io.Writer;
 import java.util.ArrayList;
@@ -79 +78 @@
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Orders;
-import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageConstants;
-import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageHelper;
+import net.sf.basedb.util.Values;
+import uk.ac.ebi.nugo.common.Helper;
+import uk.ac.ebi.nugo.common.Tab2MageConstants;
+import uk.ac.ebi.nugo.plugins.ta2mageexport.ExporHelper;
 import uk.ac.ebi.nugo.plugins.ta2mageexport.Tab2MageWriter;
-import uk.ac.ebi.nugo.plugins.util.Values;
 
 
@@ -243 +243 @@
     {
       response.setError(ex.getMessage(), Arrays.asList(ex));
-      ex.printStackTrace();
     }   
   }
@@ -305 +304 @@
       if ((Boolean)job.getValue("overwrite") != null) overwrite = (Boolean)job.getValue("overwrite");
       String p = (String)job.getValue("exportPath");
-      File file=Tab2MageHelper.processFilePath(user,overwrite, dc,p);     
+      File file=Helper.processFilePath(user,overwrite, dc,p);     
       String statusp=(String)job.getValue("statusPath");
-      File statusFile=Tab2MageHelper.processFilePath(user,overwrite, dc,statusp);
+      File statusFile=Helper.processFilePath(user,overwrite, dc,statusp);
       Experiment experiment= (Experiment)job.getValue("experiment");
       experiment= Experiment.getById(dc,experiment.getId());
@@ -322 +321 @@
   
       }
-      //intialise, count resources used, create concurrentmap for all parameter headers
+      //initialise, count resources used, create concurrentmap for all parameter headers
       getResourceCounter(experiment,dc);
             
@@ -518 +517 @@
             poolSampleHeader.addAll(hybridizationDataRows);
             
-            bioSources.addAll(Tab2MageHelper.getBiosources(sample, dc));
+            bioSources.addAll(ExporHelper.getBiosources(sample, dc));
           }
           else if (!sample.isPooled())
@@ -858 +857 @@
         newParameterHybSectionHeader.add(annotation.getAnnotationType().getName());
     }
-    //Tab2MageHelper.displayParameterHeader(newParameterHybSectionHeader);
+    //Helper.displayParameterHeader(newParameterHybSectionHeader);
   }
   /**

trunk/uk/ac/ebi/Tab2MageExporter/src/uk/ac/ebi/nugo/plugins/ta2mageexport/Tab2MageWriter.java

@@ -13 +13 @@
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
-import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Experiment;
@@ -23 +22 @@
 import net.sf.basedb.core.plugin.ParameterValues;
 import net.sf.basedb.core.plugin.Response;
-import uk.ac.ebi.nugo.plugins.util.Values;
+import net.sf.basedb.util.Values;
+import uk.ac.ebi.nugo.common.NutribasePluginException;
+import uk.ac.ebi.nugo.common.Tab2MageConstants;
+import uk.ac.ebi.nugo.common.ValueFormatter;
 
 /**
@@ -29 +31 @@
   @author Dominic Oyeniran
   @version 1.0
-  @base.modified $Date
 */
-public class Tab2MageWriter {
+public class Tab2MageWriter 
+{
 
   private static Writer out;
@@ -40 +42 @@
     creates the buffered output stream file writers for the specified files
       @param outputFile, the tab2mage output file
-      @param statusFile, the status fiel for failure, errors and exeptions
+      @param statusFile, the status file for failure, errors and exceptions
    */
   
@@ -54 +56 @@
     catch(UnsupportedEncodingException e)
     {
-      new BaseException(e);
+      new NutribasePluginException(e.getMessage());
     }
     
@@ -107 +109 @@
       out.write(Tab2MageConstants.accession.getName()+"\t"+"E-BASE-"+experiment.getId()+"\n");
       out.write(Tab2MageConstants.quality_control.getName()+"\t\n");
-      out.write(Tab2MageConstants.experiment_design_type.getName()+"\t"+ Tab2MageHelper.getEmptyStringIfNull(experiment.getExperimentDesign())+"\n");
+      out.write(Tab2MageConstants.experiment_design_type.getName()+"\t"+ ValueFormatter.getEmptyStringIfNull(experiment.getExperimentDesign())+"\n");
       out.write(Tab2MageConstants.experiment_name.getName()+"\t"+experiment.getName() +"\n");
-      String description = experiment.getDescription()!=null && experiment.getDescription().length()!=0 ? experiment.getDescription(): Tab2MageHelper.getEmptyStringIfNull(experiment.getAbstract()).toString(); 
+      String description = experiment.getDescription()!=null && experiment.getDescription().length()!=0 ? experiment.getDescription(): ValueFormatter.getEmptyStringIfNull(experiment.getAbstract()).toString(); 
       out.write(Tab2MageConstants.description.getName()+"\t"+description +"\n");
       out.write(Tab2MageConstants.release_date.getName()+"\t"+job.getValue("releaseDate")+"\n");
       out.write(Tab2MageConstants.submission_date.getName()+"\t"+Values.formatDate(new Date())+"\n");
       out.write(Tab2MageConstants.submitter.getName()+"\t"+experiment.getOwner().getName()+"\n");
-      out.write(Tab2MageConstants.submitter_email.getName()+"\t"+Tab2MageHelper.getEmptyStringIfNull(experiment.getOwner().getEmail())+"\n");
-      out.write(Tab2MageConstants.organization.getName()+"\t"+ Tab2MageHelper.getEmptyStringIfNull(experiment.getOwner().getOrganisation()) +"\n");
-      out.write(Tab2MageConstants.publication_title.getName()+"\t"+Tab2MageHelper.getEmptyStringIfNull(experiment.getTitle()) +"\n");
-      out.write(Tab2MageConstants.authors.getName()+"\t"+Tab2MageHelper.getEmptyStringIfNull(experiment.getAuthors())+"\n");
-      out.write(Tab2MageConstants.journal.getName()+"\t"+Tab2MageHelper.getEmptyStringIfNull(experiment.getPublication())+"\n");
+      out.write(Tab2MageConstants.submitter_email.getName()+"\t"+ValueFormatter.getEmptyStringIfNull(experiment.getOwner().getEmail())+"\n");
+      out.write(Tab2MageConstants.organization.getName()+"\t"+ ValueFormatter.getEmptyStringIfNull(experiment.getOwner().getOrganisation()) +"\n");
+      out.write(Tab2MageConstants.publication_title.getName()+"\t"+ValueFormatter.getEmptyStringIfNull(experiment.getTitle()) +"\n");
+      out.write(Tab2MageConstants.authors.getName()+"\t"+ValueFormatter.getEmptyStringIfNull(experiment.getAuthors())+"\n");
+      out.write(Tab2MageConstants.journal.getName()+"\t"+ValueFormatter.getEmptyStringIfNull(experiment.getPublication())+"\n");
       out.write(Tab2MageConstants.volume.getName()+"\t\n");
       out.write(Tab2MageConstants.issue.getName()+"\t\n");
       out.write(Tab2MageConstants.pages.getName()+"\t\n");
       out.write(Tab2MageConstants.year.getName()+"\t"+ String.format("%1$tY", experiment.getPublicationDate())+"\n");
-      out.write(Tab2MageConstants.pubmed_id.getName()+"\t"+Tab2MageHelper.getEmptyStringIfNull(experiment.getPubMedId())+"\n");
+      out.write(Tab2MageConstants.pubmed_id.getName()+"\t"+ValueFormatter.getEmptyStringIfNull(experiment.getPubMedId())+"\n");
       out.write("\n");
       out.flush();
@@ -135 +137 @@
     writes Tab2Mage protocol section
     @param protocols, list of protocols to write
-    @param response, the reponse object to return failures or exceptions
+    @param response, the response object to return failures or exceptions
     @param dc, database control object
    */
@@ -152 +154 @@
         {
           out.write("P-BASE-"+protocol.getId()+"\t");
-          out.write(Tab2MageHelper.getEmptyStringIfNull(protocol.getDescription())+"\t");
-          out.write(Tab2MageHelper.getEmptyStringIfNull(protocol.getName())+"\t");
-          out.write(Tab2MageHelper.getEmptyStringIfNull(protocol.getProtocolType().getName())+"\t");
+          out.write(ValueFormatter.getEmptyStringIfNull(protocol.getDescription())+"\t");
+          out.write(ValueFormatter.getEmptyStringIfNull(protocol.getName())+"\t");
+          out.write(ValueFormatter.getEmptyStringIfNull(protocol.getProtocolType().getName())+"\t");
           ItemQuery<AnnotationType> parameterQuery= protocol.getParameters();
           parameterQuery.include(Include.MINE, Include.SHARED,Include.IN_PROJECT);
@@ -165 +167 @@
           }
           length=0;
+          
+          if (parameters.size()==0 || parameters.isEmpty()) 
+          {
+            out.write("");
+          }
           out.write("\t\n");
         }
@@ -180 +187 @@
      writes Tab2Mage hybridization  header section
      @param hybSectionHeader, the header to display
-     @param response, the reponse object to reytun failures or expceptions
+     @param response, the response object to return failures or exceptions
    */
 
@@ -205 +212 @@
      Tab2Mage Hybridization  Channel Line Section
      @param hybDataRow, the data rows to display
-     @param response, the reponse object to return failures or expceptions
+     @param response, the response object to return failures or exceptions
    */
 
@@ -231 +238 @@
       response.setError(ex.getMessage(), Arrays.asList(ex));
     }
-    
   }
   
@@ -254 +260 @@
    * @return
    */
-  public static Writer getOut() {
+  public static Writer getOut() 
+  {
     return out;
   }
 
-  static void setOut(Writer out) {
+  static void setOut(Writer out) 
+  {
     Tab2MageWriter.out = out;
   }
@@ -266 +274 @@
    */
   
-  public static Writer getStatusOut() {
+  public static Writer getStatusOut() 
+  {
     return statusOut;
   }
 
-  static void setStatusOut(Writer statusOut) {
+  static void setStatusOut(Writer statusOut) 
+  {
     Tab2MageWriter.statusOut = statusOut;
   }