Changeset 497 for branches


Ignore:
Timestamp:
Nov 28, 2007, 5:13:18 PM (14 years ago)
Author:
mbayer
Message:
  • various specification related documents added (from Philippe)
  • have modified the structure of the extension -- now uses 3 separate JSP pages to collect data from user, one per tab2mage section, and data from these is stored in a data bean in the background and then retrieved in the last page
Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
10 added
4 edited

Legend:

Unmodified
Added
Removed

  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/input.jsp

    r486 r497  
    2323 %>
    2424
    25 
     25<h2>Tab2MAGE Importer -- Experiment Configuration</h2>
    2626
    2727<form action="index.jsp" method="get">
    … …  
    115115      name="parameter:pooling" value="no" checked="checked"></td>
    116116  </tr>
     117 
     118  <tr>
     119  <td align="center" colspan="2">
     120  <input type="submit" value="Continue" />
     121  </td>
     122  </tr>
     123 
    117124
    118125
    119126</table>
    120127
    121 <p><input type="submit" value="Submit" />
    122128</form>
    123129

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

    r486 r497  
    1212import java.util.LinkedList;
    1313import java.util.List;
     14import java.util.Map;
    1415import java.util.Set;
    1516import java.util.zip.ZipEntry;
    … …  
    2223import net.sf.basedb.core.Experiment;
    2324import net.sf.basedb.core.File;
    24 import net.sf.basedb.core.FileParameterType;
    25 import net.sf.basedb.core.IntegerParameterType;
    2625import net.sf.basedb.core.Item;
    2726import net.sf.basedb.core.Job;
    … …  
    3231import net.sf.basedb.core.RequestInformation;
    3332import net.sf.basedb.core.StringParameterType;
     33import net.sf.basedb.core.User;
    3434import net.sf.basedb.core.plugin.About;
    3535import net.sf.basedb.core.plugin.AboutImpl;
    … …  
    4141import net.sf.basedb.core.plugin.Request;
    4242import net.sf.basedb.core.plugin.Response;
     43import uk.ac.ebi.nugo.common.Helper;
     44import uk.ac.ebi.nugo.common.ZipUnpacker;
     45import uk.ac.ebi.nugo.plugins.tab2mageimport.ValidationConstants;
     46import uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter;
     47import uk.ac.ebi.nugo.plugins.tab2mageimport.io.Tab2MageDataImportFactory;
     48import uk.ac.ebi.nugo.plugins.tab2mageimport.io.Tab2MageExperimentWriter;
     49import uk.ac.ebi.nugo.plugins.tab2mageimport.io.Tab2MageWriterFactory;
     50import uk.ac.ebi.nugo.plugins.tab2mageimport.mail.Tab2MageEMessaging;
     51import uk.ac.ebi.nugo.plugins.tab2mageimport.validation.Tab2MageValidationFactory;
    4352import uk.ac.ebi.nugo.plugins.util.tab2mage.Tab2MageHelper;
    4453
    … …  
    5261public class Tab2MageImporter extends AbstractPlugin implements InteractivePlugin, AutoDetectingImporter
    5362{
     63
     64//  =======================================================vars=================================== 
     65
    5466  //
    5567  private RequestInformation configureJob;
    … …  
    93105  PluginParameter tissues;
    94106  PluginParameter pooling;
    95 
     107  PluginParameter experimentName;
     108  PluginParameter treatmentProtocol;
     109
     110  //holds the plugin/job config parameters
     111  LinkedList<PluginParameter<?>> params;
    96112
    97113  private static final About about = new AboutImpl("Tab2Mage Importer", "This plugin is used to import raw data files and an experiment in the tab2mage format specfication. The tab2mage specification " + "is provided by the microarray informatics team at the EBI, Cambridge. The imported experiment can later be " + "exported by the corresponding tab2mage export plugin.", "1.0", "@Copyright 2007, The EBI NutriBase development team", "Dominic Oyeniran", "oyeniran@ebi.ac.uk", "http://www.ebi.ac.uk/~oyeniran");
    … …  
    100116
    101117  private static final Set<GuiContext> guiContexts = Collections.singleton(experimentItemGuiContext);
     118
     119//  =====================================================c'tor================================== 
    102120
    103121  /**
    … …  
    107125  public Tab2MageImporter()
    108126  {
    109   }
     127    initParams();
     128  }
     129
     130
     131//  ================================================methods====================================
     132
     133
     134  private void initParams()
     135  {   
     136    // first create the parameter types
     137    StringParameterType stringPT = new StringParameterType(255, null, true);
     138
     139    // create the plugin parameter objects here
     140    experimentName = new PluginParameter<String>("experimentName", "experimentName", "experimentName", stringPT);
     141    treatmentProtocol = new PluginParameter<String>("treatmentProtocol", "treatmentProtocol", "treatmentProtocol", stringPT);
     142//    zipFile = new PluginParameter<String>("zipFile", " Zip file", "Contains raw data files", stringPT);
     143    platform = new PluginParameter<String>("platform", "Platform", "chip platform used", stringPT);
     144//    organism = new PluginParameter<String>("organism", "Organism", "First string", stringPT);
     145//    numDesigns = new PluginParameter<String>("numDesigns", "NumDesigns", "Second string", stringPT);
     146//    dyeSwap = new PluginParameter<String>("dyeSwap", "dyeSwap", "dyeSwap", stringPT);
     147//    refSample = new PluginParameter<String>("refSample","refSample","refSample", stringPT);
     148//    numTreatments = new PluginParameter<String>("numTreatments","numTreatments","numTreatments", stringPT);
     149//    expFactors = new PluginParameter<String>("expFactors","expFactors","expFactors",stringPT);
     150//    numReplicates = new PluginParameter<String>("numReplicates","numReplicates","numReplicates", stringPT);
     151//    tissues = new PluginParameter<String>("tissues","tissues","tissues", stringPT);
     152//    pooling = new PluginParameter<String>("pooling","pooling","pooling",stringPT);
     153
     154    //add them all to a list
     155    params = new LinkedList<PluginParameter<?>>();
     156    params.add(experimentName);
     157    params.add(treatmentProtocol);
     158//    params.add(zipFile);
     159    params.add(platform);
     160//    params.add(organism);
     161//    params.add(numDesigns);
     162//    params.add(dyeSwap);
     163//    params.add(refSample);
     164//    params.add(numTreatments);
     165//    params.add(expFactors);
     166//    params.add(numReplicates);
     167//    params.add(tissues);
     168//    params.add(pooling);
     169  }
     170
     171//  ---------------------------------------------------------------------------------------------------------------------------------------------- 
    110172
    111173  public void configure(GuiContext context, Request request, Response response)
    … …  
    117179    try
    118180    {
    119       if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
    120       {
    121 
    122       }
    123       else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
     181      if (command.equals(Request.COMMAND_CONFIGURE_JOB))
    124182      {
    125183        //validation
    126 //        List<Throwable> errors = validateRequestParameters (getConfigureJobParameters().getParameters(), request);
    127 //        if (errors != null)
    128 //        {
    129 //        response.setError(errors.size() + " invalid parameters were found in the request",errors);
    130 //        return;
     184        List<Throwable> errors = validateRequestParameters (params, request);
     185        if (errors != null)
     186        {
     187          response.setError(errors.size() + " invalid parameters were found in the request",errors);
     188          return;
     189        }
    131190
    132191        //store the parameter values in the database
    133         storeValue(job, request, zipFile);
    134         storeValue(job, request, platform);
    135         storeValue(job, request, organism);
    136         storeValue(job, request, numDesigns);
    137         storeValue(job, request, dyeSwap);
    138         storeValue(job, request, refSample);
    139         storeValue(job, request, numTreatments);
    140         storeValue(job, request, expFactors);
    141         storeValue(job, request, numReplicates);
    142         storeValue(job, request, tissues);
    143         storeValue(job, request, pooling);
    144 
    145         // set the response as done
    146         response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
     192        for(PluginParameter<?> param : params)
     193        {
     194          storeValue(job, request, param);
     195        }
     196
     197        //for speedy testing
     198        //requires plugin to be set up so that immediate execution is allowed
     199        response.setExecuteImmediately("Job configuration complete", Job.ExecutionTime.SHORT,true);
     200       
     201        //set the response as done
     202        //response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
    147203
    148204        //print out current values
     205        System.out.println("current parameter values:");
    149206        PluginConfigurationRequest pcRequest = (PluginConfigurationRequest) sc.getSessionSetting("plugin.configure.request");
    150         String zipFile = (String)pcRequest.getCurrentParameterValue("zipFile");
    151         String platform = (String) pcRequest.getCurrentParameterValue("platform");
    152         String organism = (String) pcRequest.getCurrentParameterValue("organism");
    153         String numDesigns = (String) pcRequest.getCurrentParameterValue("numDesigns");
    154         String dyeSwap = (String) pcRequest.getCurrentParameterValue("dyeSwap");
    155         String refSample = (String) pcRequest.getCurrentParameterValue("refSample");
    156         String numTreatments = (String) pcRequest.getCurrentParameterValue("numTreatments");
    157         String expFactors = (String) pcRequest.getCurrentParameterValue("expFactors");
    158         String numReplicates = (String) pcRequest.getCurrentParameterValue("numReplicates");
    159         String tissues = (String) pcRequest.getCurrentParameterValue("tissues");
    160         String pooling = (String) pcRequest.getCurrentParameterValue("pooling");
    161 
    162         System.out.println("zipFile = " + zipFile);
    163         System.out.println("platform = " + platform);
    164         System.out.println("numDesigns = " + numDesigns);
    165         System.out.println("numTreatments = " + numTreatments);
    166         System.out.println("numReplicates = " + numReplicates);
    167         System.out.println("dyeSwap = " + dyeSwap);
    168         System.out.println("organism = " + organism);
    169         System.out.println("refSample = " + refSample);
    170         System.out.println("expFactors = " + expFactors);
    171         System.out.println("numReplicates = " + numReplicates);
    172         System.out.println("tissues = " + tissues);
    173         System.out.println("pooling = " + pooling);
    174        
     207        for(PluginParameter<?> param : params)
     208        {
     209          String value = (String)pcRequest.getCurrentParameterValue(param.getName());
     210          System.out.println(param.getName() + " = " + value);
     211        }
    175212      }
    176213    }
    … …  
    183220  }
    184221
    185   /*
    186    * From the InteractivePlugin interface -------------------------------------------
    187    */
     222//  ----------------------------------------------------------------------------------------------------------------------------------------------   
     223
    188224  /**
    189225   * Return a set containing the context:s [ARRAY DESIGN, LIST],
    … …  
    194230  }
    195231
     232//  ----------------------------------------------------------------------------------------------------------------------------------------------     
     233
    196234  /**
    197235   * checks that the we are using the experiment object and that it is not null returns null if we are not working on an ITEM but a LIST
    … …  
    221259  }
    222260
     261//  ----------------------------------------------------------------------------------------------------------------------------------------------     
     262
    223263  public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
    224264  {
    … …  
    229269    try
    230270    {
    231       // first create the parameter types
    232       StringParameterType stringPT = new StringParameterType(255, null, true);
    233 
    234       // create the plugin parameter objects here
    235       zipFile = new PluginParameter<String>("zipFile", " Zip file", "Contains raw data files", stringPT);
    236       platform = new PluginParameter<String>("platform", "Platform", "chip platform used", stringPT);
    237       organism = new PluginParameter<String>("organism", "Organism", "First string", stringPT);
    238       numDesigns = new PluginParameter<String>("numDesigns", "NumDesigns", "Second string", stringPT);
    239       dyeSwap = new PluginParameter<String>("dyeSwap", "dyeSwap", "dyeSwap", stringPT);
    240       refSample = new PluginParameter<String>("refSample","refSample","refSample", stringPT);
    241       numTreatments = new PluginParameter<String>("numTreatments","numTreatments","numTreatments", stringPT);
    242       expFactors = new PluginParameter<String>("expFactors","expFactors","expFactors",stringPT);
    243       numReplicates = new PluginParameter<String>("numReplicates","numReplicates","numReplicates", stringPT);
    244       tissues = new PluginParameter<String>("tissues","tissues","tissues", stringPT);
    245       pooling = new PluginParameter<String>("pooling","pooling","pooling",stringPT);
    246 
    247       // add them all to our list
    248       List<PluginParameter<?>> parameters = new LinkedList<PluginParameter<?>>();
    249       parameters.add(zipFile);
    250       parameters.add(platform);
    251       parameters.add(organism);
    252       parameters.add(numDesigns);
    253       parameters.add(dyeSwap);
    254       parameters.add(refSample);
    255       parameters.add(numTreatments);
    256       parameters.add(expFactors);
    257       parameters.add(numReplicates);
    258       parameters.add(tissues);
    259       parameters.add(pooling);
    260 
    261271      //the request information object provides the parameter list and the name of the custom input page to navigate to for
    262272      //the configuration of the plugin run
    263       requestInformation = new RequestInformation(Request.COMMAND_CONFIGURE_JOB, null, null, parameters, "input.jsp");
    264     }
    265     catch (Throwable e)
     273      requestInformation = new RequestInformation(Request.COMMAND_CONFIGURE_JOB, null, null, params, "experiment.jsp");
     274    }
     275    catch (Exception e)
    266276    {
    267277      e.printStackTrace();
    … …  
    271281  }
    272282
    273   /*
    274    * From the Plugin interface --------------------------------
    275    */
     283//  ----------------------------------------------------------------------------------------------------------------------------------------------     
     284
    276285  public About getAbout()
    277286  {
    … …  
    279288  }
    280289
     290//  ----------------------------------------------------------------------------------------------------------------------------------------------     
     291
    281292  public MainType getMainType()
    282293  {
    283294    return Plugin.MainType.IMPORT;
    284295  }
    285 
    286   public void run(Request request, Response response, ProgressReporter progress)
    287   {
    288     // DbControl dc=null;
    289     // String hostName="";
    290     // boolean validPlatform=false, validateImageFile, validTab2mageFile, validTab2mageFileName=false;
    291     // boolean overwrite= false, validation = false;
    292     // try
    293     // {
    294     // //who is using this plugin
    295     // dc= sc.newDbControl();
    296     // User user= User.getById(dc, sc.getLoggedInUserId());
    297 
    298     // /*
    299     // obtain all job parameters
    300     // */
    301     // File file = (File) job.getValue("file");
    302     // file= File.getById(dc, file.getId());
    303 
    304     // String directoryName = (String)job.getValue("directory");
    305 
    306     // String tab2MageFileName= (String) job.getValue("tab2mageFileName");
    307     // hostName= (String) job.getValue("emailHost");
    308 
    309     // if ((Boolean)job.getValue("overwrite") != null) overwrite = (Boolean)job.getValue("overwrite");
    310     // if ((Boolean)job.getValue("validation") != null) validation = (Boolean)job.getValue("validation");
    311 
    312     // Experiment experiment= (Experiment)job.getValue("experiment");
    313     // experiment= Experiment.getById(dc,experiment.getId());
    314     // RawDataType rdt= experiment.getRawDataType(); // experiment platform
    315 
    316     // String statusp=(String)job.getValue("statusPath");
    317     // File statusFile=Helper.processFilePath(user,overwrite, sc,statusp);
    318 
    319     // /*
    320     // FILE UNZIP MODULE: unzip the files into user specified directory
    321     // */
    322 
    323     // ZipUnpacker importUnpacker = new ZipUnpacker(file, user, sc);
    324     // importUnpacker.unpack(directoryName);
    325     // Directory dir= importUnpacker.getUnzippedFilesDirectory(); // this may return the id of the unzipped file directory instead
    326     // if (dir==null)
    327     // {
    328     // response.setError("IMPORT FAILS: The zip file cannot be unzipped. You may NOT have sufficient Disk Space or " +
    329     // "Lack permission to read or use the Directory" ,Arrays.asList(new Throwable()));
    330     // return;
    331     // }
    332 
    333     // // -- end of file unzip module
    334 
    335     // /*
    336     // VALIDATION MODULE
    337     // */
    338 
    339     // if (dc == null || !dc.isConnected()|| dc.isClosed()) dc = sc.newDbControl();
    340 
    341     // // validate files supplied to platform
    342     // validPlatform=Tab2MageHelper.validatePlatform(dir, dc, rdt);
    343     // if (!validPlatform)
    344     // {
    345     // response.setError("IMPORT FAILS: Invalid File format: files supplied not appropriate for the experiment platform: [ " + rdt.getId() +" ]" ,Arrays.asList(new Throwable()));
    346     // return;
    347     // }
    348 
    349     // // validate image file
    350     // List<File> imageFiles=Tab2MageHelper.getImageFiles(dir, dc) ;
    351     // if (!imageFiles.isEmpty()|| imageFiles==null)
    352     // {
    353     // validateImageFile= Tab2MageHelper.validateImages(imageFiles, rdt);
    354     // if (!validateImageFile)
    355     // {
    356     // response.setError("IMPORT FAILS: Invalid Image File format: image files supplied not appropriate for the experiment platform: [ " + rdt.getId() +" ]" ,Arrays.asList(new
    357     // Throwable()));
    358     // return;
    359     // }
    360     // }
    361     // // validate the tab2mage file (do initialisation here too)
    362 
    363     // Tab2MageValidationFactory validator = new Tab2MageValidationFactory(tab2MageFileName, sc, dir, rdt.getId(), response, statusFile);
    364     // validTab2mageFileName = validator.validateTab2MageFileName();
    365     // if (!validTab2mageFileName)
    366     // {
    367     // response.setError("IMPORT FAILS: The Tab2Mage filename provided as parameter on the GUI : [ " + tab2MageFileName+ " ] does not match that contained in the zip file"
    368     // ,Arrays.asList(new Throwable()));
    369     // return;
    370     // }
    371 
    372     // Map<ValidationConstants, Boolean> validations= validator.validateTab2MageFile();
    373     // StringBuffer failureMessage = new StringBuffer();
    374     // if (!validations.isEmpty())
    375     // {
    376     // for (ValidationConstants key : validations.keySet())
    377     // {
    378     // failureMessage.append(key.getKeyMessage()+";") ;
    379     // }
    380     // response.setError("IMPORT FAILS: Tab2Mage file validation is UNSUCCESSFUL. The ['"+ failureMessage.substring(0, failureMessage.length()-1)+ "'] Failed. " +
    381     // "Check the Validation ReportFile ["+statusFile.getPath().toString()+"] on BASE File System for Details" ,Arrays.asList(new Throwable()));
    382     // return;
    383     // }
    384 
    385     // // -- end of validation module
    386     // if (validation)
    387     // {
    388     // Directory delDir =Directory.getById(dc, dir.getId());
    389     // response.setDone("Validation Successful. Check the Validation File [ "+statusFile.getPath().toString()+" ] for annotations warning. The unzipped directory " +
    390     // "name [ "+delDir.getName()+" ] CANNOT be re-used as a parameter to re-run the tab2mage importer.");
    391     // return;
    392     // }
    393 
    394     // /*
    395     // TAB2MAGE FILE IMPORT MODULE.
    396     // */
    397     // // create annotation types
    398     // AnnotationTypesWriter atWriter= new AnnotationTypesWriter (sc, validator.getAtFile(),progress);
    399     // boolean writtenAT =atWriter.write(); // note if this action failed the transaction is completely rolled back
    400     // if (!writtenAT)
    401     // {
    402     // response.setError("IMPORT FAILS: Annotation Type was not written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
    403     // return;
    404     // }
    405 
    406     // // write protocols and hybs
    407     // Tab2MageWriterFactory hibernateItemsWriter = new Tab2MageWriterFactory
    408     // (sc,Tab2MageValidationFactory.getCatchedProtocol(),
    409     // Tab2MageValidationFactory.getCatchedHybs(),rdt,
    410     // validator.getSampleExtractMap(),
    411     // validator.getBioSourceSampleMap(),
    412     // validator.getExtractLabeledExtractMap());
    413 
    414     // // if the protocol type is not found, write it into the database.
    415     // // alternative is to fail at validation instead of a warning, if the protocol type
    416     // // provided in tab2mage file is not in Base2 database.
    417 
    418     // hibernateItemsWriter.writeProtocolTypes();
    419 
    420     // boolean writtenHibItems = hibernateItemsWriter.write();
    421     // if (!writtenHibItems)
    422     // {
    423     // response.setError("IMPORT FAILS: Protocol and Hybridization items were not written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
    424     // return;
    425     // }
    426 
    427     // boolean writtenPoolItems = hibernateItemsWriter.writePooledMetaData();
    428     // if (!writtenPoolItems)
    429     // {
    430     // response.setError("IMPORT FAILS: Pooled items were not written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
    431     // return;
    432     // }
    433     // // -- end of Tab2Mage file import module
    434 
    435     // /*
    436     // RAW DATA IMPORT MODULE
    437 
    438     // */
    439 
    440     // if (dc == null || !dc.isConnected()|| dc.isClosed()) dc = sc.newDbControl();
    441 
    442     // // get raw data files
    443     // List<File> rawDataFiles= Tab2MageHelper.getRawDataFiles(dir, dc, rdt.getId(), tab2MageFileName);
    444 
    445     // // do data import
    446     // Tab2MageDataImportFactory dataImport = new Tab2MageDataImportFactory(sc,rdt.getId(),rawDataFiles,
    447     // hibernateItemsWriter.getRbas(), progress);
    448     // boolean writtenRawData = dataImport.importData();
    449     // if (!writtenRawData)
    450     // {
    451     // response.setError("IMPORT FAILS: Raw Data cannot not be written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
    452     // return;
    453     // }
    454     // // -- end of raw data import module
    455 
    456     // /*
    457     // EXPERIMENT CONFIGURATION AND LOADING MODULE
    458 
    459     // */
    460     // //write experiment, attaching raw bio-assays
    461     // Tab2MageExperimentWriter expWriter= new Tab2MageExperimentWriter(hibernateItemsWriter.getRbas(),sc,
    462     // experiment,hibernateItemsWriter.getExpFactors(),
    463     // validator.getTExperiment());
    464     // boolean writtenExp= expWriter.LoadExperiment();
    465     // // -- end of experiment configuration and loading module
    466 
    467     // /*
    468     // MESSAGING MODULE
    469     // */
    470     // // send an email to the user on the success of the experiment (if email server name and email address are provided)
    471     // if (hostName!= null && hostName.length()>=5)
    472     // {
    473     // if (!user.getEmail().equals("") && user.getEmail()!=null )
    474     // {
    475     // Tab2MageEMessaging message= new Tab2MageEMessaging(writtenExp,"", user.getEmail(),tab2MageFileName, user.getName(), experiment.getName(),hostName );
    476     // message.sendEmail();
    477     // }
    478     // }
    479     // // -- end of messaging module
    480     // dc.commit();
    481     // response.setDone("Import plugin ended successfully");
    482     // }
    483     // catch(Throwable tr)
    484     // {
    485     // response.setError(tr.getMessage(), Arrays.asList(tr));
    486     // }
    487     // finally
    488     // {
    489     // if (dc!=null)
    490     // dc.close();
    491     // }
    492 
    493     System.out.println("running Tab2MageImporter plugin (testing run method only)");
    494     response.setDone("Plugin ended successfully");
    495   }
    496 
    497   /*
    498    * From AutoDetectionImporter interface
    499    */
    500   /**
    501    * checks whether the zip file supplied by the user is actually a zip file.
    502    */
    503   public boolean isImportable(InputStream in) throws BaseException
    504   {
    505     ZipInputStream zin = null;
    506     try
    507     {
    508       zin = new ZipInputStream(in);
    509       // if this is not a zip file, this will throw an exception:
    510       ZipEntry zn = zin.getNextEntry();
    511     }
    512     catch (Exception e)
    513     {
    514       return false;
    515     }
    516     finally
    517     {
    518       try
    519       {
    520         zin.close();
    521       }
    522       catch (IOException ex)
    523       {
    524         throw new BaseException(ex);
    525       }
    526     }
    527     return true;
    528   }
     296 
     297//  ----------------------------------------------------------------------------------------------------------------------------------------------     
    529298
    530299  public void doImport(InputStream in, ProgressReporter progress) throws BaseException
    531300  {
    532301  }
     302
     303//  ----------------------------------------------------------------------------------------------------------------------------------------------     
    533304
    534305  /**
    … …  
    555326    }
    556327  }
    557 }
     328 
     329
     330//  ----------------------------------------------------------------------------------------------------------------------------------------------     
     331
     332  /**
     333   * checks whether the zip file supplied by the user is actually a zip file.
     334   */
     335  public boolean isImportable(InputStream in) throws BaseException
     336  {
     337    ZipInputStream zin = null;
     338    try
     339    {
     340      zin = new ZipInputStream(in);
     341      // if this is not a zip file, this will throw an exception:
     342      ZipEntry zn = zin.getNextEntry();
     343    }
     344    catch (Exception e)
     345    {
     346      return false;
     347    }
     348    finally
     349    {
     350      try
     351      {
     352        zin.close();
     353      }
     354      catch (IOException ex)
     355      {
     356        throw new BaseException(ex);
     357      }
     358    }
     359    return true;
     360  }
     361
     362//  ----------------------------------------------------------------------------------------------------------------------------------------------     
     363
     364  public void run(Request request, Response response, ProgressReporter progress)
     365  {
     366    System.out.println("running Tab2MageImporter plugin");
     367    response.setDone("Import plugin ended successfully");
     368    /*
     369   
     370    DbControl dc=null;
     371    String hostName="";
     372    boolean validPlatform=false, validateImageFile, validTab2mageFile, validTab2mageFileName=false;
     373    boolean overwrite= false, validation = false;
     374    try
     375    {
     376      //who is using this plugin
     377      dc= sc.newDbControl();
     378      User user= User.getById(dc, sc.getLoggedInUserId());
     379
     380
     381       //obtain all job parameters
     382
     383      File file = (File) job.getValue("file");
     384      file= File.getById(dc, file.getId());
     385
     386      String directoryName = (String)job.getValue("directory");
     387
     388      String tab2MageFileName= (String) job.getValue("tab2mageFileName");
     389      hostName= (String) job.getValue("emailHost");
     390
     391      if ((Boolean)job.getValue("overwrite") != null) overwrite = (Boolean)job.getValue("overwrite");
     392      if ((Boolean)job.getValue("validation") != null)  validation = (Boolean)job.getValue("validation");
     393
     394      Experiment experiment= (Experiment)job.getValue("experiment");
     395      experiment= Experiment.getById(dc,experiment.getId());
     396      RawDataType rdt= experiment.getRawDataType(); // experiment platform
     397
     398      String statusp=(String)job.getValue("statusPath");
     399      File statusFile=Helper.processFilePath(user,overwrite, sc,statusp);
     400
     401        //FILE UNZIP MODULE: unzip the files into user specified directory
     402         
     403      ZipUnpacker importUnpacker = new ZipUnpacker(file, user, sc);
     404      importUnpacker.unpack(directoryName);
     405      Directory dir= importUnpacker.getUnzippedFilesDirectory(); // this may return the id of the unzipped file directory instead
     406      if (dir==null)
     407      {
     408        response.setError("IMPORT FAILS: The zip file cannot be unzipped. You may NOT have sufficient Disk Space or " +
     409                "Lack permission to read or use the Directory" ,Arrays.asList(new Throwable()));
     410        return;
     411      }
     412
     413      // -- end of file unzip module
     414     
     415      ///////////////////////////////////////////////////////////////////////////////////////////////////
     416     
     417      //now write the tab2mage file to the user's home dir on the server so it can be consumed by the plugin
     418      //this takes all the inputs provided by the user on the custom interface (input.jsp)
     419      //give the file a unique name so we don't get any conflicts
     420      //use code from tab2mage exporter to do so
     421     
     422      /////////////////////////////////////////////////////////////////////////////////////////////////
     423     
     424
     425
     426        //VALIDATION MODULE
     427
     428
     429      if (dc == null || !dc.isConnected()|| dc.isClosed()) dc = sc.newDbControl();
     430
     431      // validate files supplied to platform
     432      validPlatform=Tab2MageHelper.validatePlatform(dir, dc, rdt);
     433      if (!validPlatform)
     434      {
     435        response.setError("IMPORT FAILS: Invalid File format: files supplied not appropriate for the experiment platform: [ " + rdt.getId() +" ]" ,Arrays.asList(new Throwable()));
     436        return;
     437      }
     438
     439      // validate image file
     440      List<File> imageFiles=Tab2MageHelper.getImageFiles(dir, dc) ;
     441      if (!imageFiles.isEmpty()|| imageFiles==null)
     442      {
     443        validateImageFile= Tab2MageHelper.validateImages(imageFiles, rdt);
     444        if (!validateImageFile)
     445        {
     446          response.setError("IMPORT FAILS: Invalid Image File format: image files supplied not appropriate for the experiment platform: [ " + rdt.getId() +" ]" ,Arrays.asList(new Throwable()));
     447          return;
     448        }
     449      }
     450      // validate the tab2mage file (do initialisation here too)
     451
     452      Tab2MageValidationFactory validator = new Tab2MageValidationFactory(tab2MageFileName, sc, dir, rdt.getId(), response, statusFile);
     453      validTab2mageFileName = validator.validateTab2MageFileName();
     454      if (!validTab2mageFileName)
     455      {
     456        response.setError("IMPORT FAILS: The Tab2Mage filename provided as parameter on the GUI : [ " + tab2MageFileName+ " ] does not match that contained in the zip file" ,Arrays.asList(new Throwable()));
     457        return;
     458      }
     459
     460      Map<ValidationConstants, Boolean> validations= validator.validateTab2MageFile();
     461      StringBuffer failureMessage = new StringBuffer();
     462      if (!validations.isEmpty())
     463      {
     464        for (ValidationConstants key : validations.keySet())
     465        {
     466          failureMessage.append(key.getKeyMessage()+";")  ;
     467        }
     468        response.setError("IMPORT FAILS: Tab2Mage file validation is UNSUCCESSFUL. The ['"+ failureMessage.substring(0, failureMessage.length()-1)+ "'] Failed. " +
     469                "Check the Validation ReportFile ["+statusFile.getPath().toString()+"] on BASE File System for Details" ,Arrays.asList(new Throwable()));
     470        return;
     471      }
     472
     473      // -- end of validation module
     474      if (validation)
     475      {
     476        Directory delDir =Directory.getById(dc, dir.getId());
     477        response.setDone("Validation Successful. Check the Validation File [ "+statusFile.getPath().toString()+" ] for annotations warning. The unzipped directory " +
     478                "name [ "+delDir.getName()+" ] CANNOT be re-used as a parameter to re-run the tab2mage importer.");
     479        return;
     480      }
     481
     482
     483        //TAB2MAGE FILE IMPORT MODULE.
     484
     485      //  create annotation types
     486      AnnotationTypesWriter atWriter= new AnnotationTypesWriter (sc, validator.getAtFile(),progress);
     487      boolean writtenAT =atWriter.write(); // note if this action failed the transaction is completely rolled back
     488      if (!writtenAT)
     489      {
     490        response.setError("IMPORT FAILS: Annotation Type was not written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
     491        return;
     492      }
     493
     494      // write protocols and hybs
     495      Tab2MageWriterFactory hibernateItemsWriter = new Tab2MageWriterFactory
     496      (sc,Tab2MageValidationFactory.getCatchedProtocol(),
     497              Tab2MageValidationFactory.getCatchedHybs(),rdt,
     498              validator.getSampleExtractMap(),
     499              validator.getBioSourceSampleMap(),
     500              validator.getExtractLabeledExtractMap());
     501
     502      // if the protocol type is not found, write it into the database.
     503      // alternative is to fail at validation instead of a warning, if the protocol type
     504      // provided in tab2mage file is not in Base2 database.
     505
     506      hibernateItemsWriter.writeProtocolTypes();
     507
     508      boolean writtenHibItems = hibernateItemsWriter.write();
     509      if (!writtenHibItems)
     510      {
     511        response.setError("IMPORT FAILS: Protocol and Hybridization items were not written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
     512        return;
     513      }
     514
     515      boolean writtenPoolItems = hibernateItemsWriter.writePooledMetaData();
     516      if (!writtenPoolItems)
     517      {
     518        response.setError("IMPORT FAILS: Pooled items were not written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
     519        return;
     520      }
     521      // -- end of Tab2Mage file import module
     522
     523 
     524        //RAW DATA IMPORT MODULE
     525
     526
     527      if (dc == null || !dc.isConnected()|| dc.isClosed()) dc = sc.newDbControl();
     528
     529      // get raw data files
     530      List<File> rawDataFiles= Tab2MageHelper.getRawDataFiles(dir, dc, rdt.getId(), tab2MageFileName);
     531
     532      // do data import
     533      Tab2MageDataImportFactory dataImport = new Tab2MageDataImportFactory(sc,rdt.getId(),rawDataFiles,
     534              hibernateItemsWriter.getRbas(), progress);
     535      boolean writtenRawData = dataImport.importData();
     536      if (!writtenRawData)
     537      {
     538        response.setError("IMPORT FAILS: Raw Data cannot not be written to the Database. Check Log error for details" ,Arrays.asList(new Throwable()));
     539        return;
     540      }
     541      // -- end of raw data import module
     542
     543
     544        //EXPERIMENT CONFIGURATION AND LOADING MODULE
     545 
     546      //write experiment, attaching raw bio-assays
     547      Tab2MageExperimentWriter expWriter= new Tab2MageExperimentWriter(hibernateItemsWriter.getRbas(),sc,
     548              experiment,hibernateItemsWriter.getExpFactors(),
     549              validator.getTExperiment());
     550      boolean writtenExp= expWriter.LoadExperiment();
     551      // -- end of experiment configuration and loading module
     552
     553        //MESSAGING MODULE
     554       
     555      //  send an email to the user on the success of the experiment (if email server name and email address are provided)
     556      if (hostName!= null && hostName.length()>=5)
     557      {
     558        if (!user.getEmail().equals("") && user.getEmail()!=null )
     559        {
     560          Tab2MageEMessaging message= new Tab2MageEMessaging(writtenExp,"", user.getEmail(),tab2MageFileName, user.getName(), experiment.getName(),hostName );
     561          message.sendEmail();
     562        }
     563      }
     564      // -- end of messaging module
     565     
     566      dc.commit();
     567      response.setDone("Import plugin ended successfully");
     568    }
     569    catch(Throwable tr)
     570    {
     571      response.setError(tr.getMessage(), Arrays.asList(tr));
     572    }
     573    finally
     574    {
     575      if (dc!=null)
     576        dc.close();
     577    }
     578   
     579    */
     580
     581  }
     582
     583
     584//  ---------------------------------------------------------------------------------------------------------------------------------------------- 
     585
     586}//end class
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