Changeset 544


Ignore:
Timestamp:
Jan 18, 2008, 10:11:45 AM (13 years ago)
Author:
mbayer
Message:

submission with existing tab2mage file implemented

Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
13 edited

Legend:

Unmodified
Added
Removed
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/configureImporter.jsp

    r543 r544  
    9797
    9898<input type="hidden" name="file_id" value="">
    99 <input type="hidden" name="parameter:zipFile" value=""  id="zipFile">
    100 <input type="hidden" name="parameter:useWizard" value="yes"  id="useWizard">
     99<input type="hidden" name="parameter:path" value=""  id="zipFile">
    101100<input type="hidden" name="parameter:experimentId" value="<%=experimentId %>"  id="experimentId">
     101
     102
     103<input type="hidden"name="parameter:domain" value="<%=inputDataBean.getDomain()%>" />
     104<input type="hidden"name="parameter:accession" value="<%=inputDataBean.getAccession()%>" />
     105<input type="hidden"name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>" />
     106<input type="hidden"name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>" />
     107<input type="hidden"name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>" />
     108<input type="hidden"name="parameter:description" value="<%=inputDataBean.getDescription()%>" />
     109<input type="hidden"name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>" />
     110<input type="hidden"name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>" />
     111<input type="hidden"name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>" />
     112<input type="hidden"name="parameter:organization" value="<%=inputDataBean.getOrganization()%>" />
     113<input type="hidden"name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>" />
     114<input type="hidden"name="parameter:authors" value="<%=inputDataBean.getAuthors()%>" />
     115<input type="hidden"name="parameter:journal" value="<%=inputDataBean.getJournal()%>" />
     116<input type="hidden"name="parameter:volume" value="<%=inputDataBean.getVolume()%>" />
     117<input type="hidden"name="parameter:issue" value="<%=inputDataBean.getIssue()%>" />
     118<input type="hidden"name="parameter:pages" value="<%=inputDataBean.getPages()%>" />
     119<input type="hidden"name="parameter:year" value="<%=inputDataBean.getYear()%>" />
     120<input type="hidden"name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>" />
     121<input type="hidden"name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>" />
     122<input type="hidden"name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>" />
     123<input type="hidden"name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>" />
     124<input type="hidden"name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>" />
     125<input type="hidden"name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>" />
     126<input type="hidden"name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>" />
     127<input type="hidden"name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>" />
     128<input type="hidden"name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>" />
     129<input type="hidden"name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>" />
     130<input type="hidden"name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>" />
     131<input type="hidden"name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>" />
     132<input type="hidden"name="parameter:platform" value="<%=inputDataBean.getPlatform()%>" />
     133<input type="hidden"name="parameter:organism" value="<%=inputDataBean.getOrganism()%>" />
     134<input type="hidden"name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>" />
     135<input type="hidden"name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>" />
     136<input type="hidden"name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>" />
     137<input type="hidden"name="parameter:numTreatmentGroups" value="<%=inputDataBean.getNumTreatmentGroups()%>" />
     138<input type="hidden"name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>" />
     139<input type="hidden"name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>" />
     140<input type="hidden"name="parameter:tissues" value="<%=inputDataBean.getTissues()%>" />
     141<input type="hidden"name="parameter:pooling" value="<%=inputDataBean.getPooling()%>" />
     142<input type="hidden"name="parameter:subjectNames" value="<%=inputDataBean.getSubjectNames()%>" />
     143<input type="hidden"name="parameter:fileList" value="<%=inputDataBean.getFileList()%>" />
     144<input type="hidden"name="parameter:subjectList" value="<%=inputDataBean.getSubjectList()%>" />
     145<input type="hidden"name="parameter:tissueList" value="<%=inputDataBean.getTissueList()%>" />
     146<input type="hidden"name="parameter:useWizard" value="<%=inputDataBean.getUseWizard()%>" />
     147<input type="hidden"name="parameter:legacyData" value="<%=inputDataBean.getLegacyData()%>" />
     148<input type="hidden"name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
     149<input type="hidden"name="parameter:fileList" value=""/>
     150<input type="hidden"name="parameter:subjectList" value=""/>
     151<input type="hidden"name="parameter:tissueList" value=""/>
     152
     153
    102154
    103155<h1>Tab2MAGE Import Wizard -- Select Your Data File</h1>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp

    r543 r544  
    186186        <option>real time PCR quality control</option>
    187187        <option>reverse transcription PCR quality control</option>
    188         <option selected="selected">spike quality control</option>
     188        <option >spike quality control</option>
    189189        <option>technical replicate</option>
    190190      </select></td>
     
    213213          <div id="BiologicalProperty" style="display:none"><select
    214214            multiple="multiple" name="biologicalProperty" size="16">
    215             <option selected="selected">cell_component_comparison_design</option>
     215            <option>cell_component_comparison_design</option>
    216216            <option>cell_cycle_design</option>
    217217            <option>cell_type_comparison_design</option>
     
    227227            <option>sex_design</option>
    228228            <option>species_design</option>
    229             <option>strain_or_line_design</option>
     229            <option selected="selected">strain_or_line_design</option>
    230230            <option>unknown_experiment_design_type</option>
    231231          </select></div>
     
    243243          <div id="BioMolecularAnnotation" style="display:none"><select
    244244            multiple="multiple" name="bioMolecularAnnotation"  size="11">
    245             <option selected="selected">RNA_stability_design</option>
     245            <option>RNA_stability_design</option>
    246246            <option>binding_site_identification_design</option>
    247247            <option>co-expression_design</option>
     
    270270            <option>clinical_history_design</option>
    271271            <option>disease_state_design</option>
    272             <option selected="selected">family_history_design</option>
     272            <option>family_history_design</option>
    273273            <option>unknown_experiment_design_type</option>
    274274          </select></div>
     
    379379      <td class="boldText">Experiment Description:</td>
    380380      <td class="input"><textarea rows="4" cols="30"
    381         name="description">This is a totally contrived example experiment.</textarea></td>
     381        name="description">my test description</textarea></td>
    382382      <td class="helpText">A short paragraph describing the purpose of the experiment.</td>
    383383    </tr>
     
    387387      <td class="boldText">Release Date:</td>
    388388      <td class="input"><input type="text" size="10"
    389         name="releaseDate" value="2007-12-03" /></td>
     389        name="releaseDate" value="2007-05-15" /></td>
    390390      <td class="helpText">Date for public release, in the format YYYY-MM-DD.</td>
    391391    </tr>
     
    394394      <td class="boldText">Submission Date:</td>
    395395      <td class="input"><input type="text" size="10"
    396         name="submissionDate" value="2007-12-03" /></td>
     396        name="submissionDate" value="2007-05-30" /></td>
    397397      <td class="helpText">Date of submission, in the format YYYY-MM-DD.</td>
    398398    </tr>
     
    401401      <td class="boldText">Submitter:</td>
    402402      <td class="input"><input type="text" size="45" name="submitter"
    403         value="Joe Bloggs" /></td>
     403        value="Micha Bayer" /></td>
    404404      <td class="helpText">The name of the person responsible for submitting the
    405405      experiment to the database.</td>
     
    424424      <td class="plainLabel" style="border-style: none;">Title:</td>
    425425      <td class="input" style="border-style: none;"><textarea rows="3" cols="30"
    426         name="publicationTitle" >My Ropey Paper</textarea></td>
     426        name="publicationTitle" >My crazy title</textarea></td>
    427427      <td style="border-style: none;"></td>
    428428    </tr>
     
    430430    <tr>
    431431      <td class="plainLabel" style="border-style: none;">Authors:</td>
    432       <td class="input" style="border-style: none;"><textarea rows="3" cols="30" name="authors">Bloggs, Joe</textarea></td>
     432      <td class="input" style="border-style: none;"><textarea rows="3" cols="30" name="authors">Micha Bayer; Joe Bloggs</textarea></td>
    433433      <td  class="helpText" style="border-style: none;">The authors list is a semicolon-delimited list of names.</td>
    434434    </tr>
     
    444444      <td class="plainLabel" style="border-style: none;">Volume:</td>
    445445      <td class="input" style="border-style: none;"><input type="text" size="10" name="volume"
    446         value="5" /></td>
     446        value="1" /></td>
    447447      <td style="border-style: none;"></td>
    448448    </tr>
     
    451451      <td class="plainLabel" style="border-style: none;">Issue:</td>
    452452      <td class="input" style="border-style: none;"><input type="text" size="10" name="issue"
    453         value="2" /></td>
     453        value="1" /></td>
    454454      <td style="border-style: none;"></td>
    455455    </tr>
     
    458458      <td class="plainLabel" style="border-style: none;">Pages:</td>
    459459      <td class="input" style="border-style: none;"><input type="text" size="10" name="pages"
    460         value="123-135" /></td>
     460        value="112-122" /></td>
    461461      <td style="border-style: none;"></td>
    462462    </tr>
     
    472472      <td class="plainLabel" style="border-style: none;">Pubmed ID:</td>
    473473      <td class="input" style="border-style: none;"><input type="text" size="30" name="pubmedId"
    474         value="11009762" /></td>
     474        value=" " /></td>
    475475      <td style="border-style: none;"></td>
    476476
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

    r543 r544  
    9191
    9292<input type="hidden" name="file_id" value="">
    93 <input type="hidden" name="zipFile" value="/home/michab/affyTestFiles.zip"  id="zipFile">
     93<input type="hidden" name="zipFile" value="/home/michab/potato_small.zip"  id="zipFile">
    9494
    9595<h1>Tab2MAGE Import Wizard -- Your Hybridizations</h1>
     
    109109    <option >BZScan</option>
    110110    <option >ChipSkipper</option>
    111     <option >GenePix</option>
     111    <option selected="selected">GenePix</option>
    112112    <option >GeneTAC</option>
    113113    <option >Illumina</option>
     
    124124  <tr>
    125125    <td class="boldText">Experimental organism:</td>
    126     <td class="input"><input type="text" size="50" name="organism" value="Solanum tuberosum"/></td>
     126    <td class="input"><input type="text" size="50" name="organism" value="Hordeum vulgare"/></td>
    127127    <td>The full scientific name of the experimental organism used.</td>
    128128  </tr>
     
    139139  <tr>
    140140    <td class="boldText">Dye-swap</td>
    141     <td class="input">yes <input type="radio" name="dyeSwap" value="yes"> no <input type="radio"
    142       name="dyeSwap" value="no" checked="checked"> <br>
    143      
     141    <td class="input">
     142    <table class="noBorder" cellpadding="4">
     143      <tr>
     144        <td class="noBorder"><input type="radio" name="dyeSwap" value="yes"></td>
     145        <td class="noBorder">yes</td>
     146      </tr>
     147
     148      <tr>
     149        <td class="noBorder"><input type="radio" name="dyeSwap" value="no" checked="checked"></td>
     150        <td class="noBorder">no</td>
     151      </tr>
     152    </table>     
    144153    </td>
    145154    <td>If you used a dye-swap design please indicate this here.</td>
     
    149158  <tr>
    150159    <td class="boldText">Reference sample</td>
    151     <td class="input">yes <input type="radio" name="refSample" value="yes" > no <input type="radio"
    152       name="refSample" value="no" checked="checked"></td>
     160    <td class="input"> 
     161    <table class="noBorder" cellpadding="4">
     162      <tr>
     163        <td class="noBorder"><input type="radio" name="refSample" value="yes"></td>
     164        <td class="noBorder">yes</td>
     165      </tr>
     166
     167      <tr>
     168        <td class="noBorder"><input type="radio"name="refSample" value="no"  checked="checked"></td>
     169        <td class="noBorder">no</td>
     170      </tr>
     171    </table>       
     172    </td>
    153173    <td>If you used a reference sample please indicate this here.</td>
    154174  </tr>
     
    186206  <tr>
    187207    <td class="boldText">Subject (replicate) labels:</td>
    188     <td class="input"><textarea rows="8" cols="32" name="subjectNames">plant1</textarea></td>
     208    <td class="input"><textarea rows="8" cols="32" name="subjectNames"></textarea></td>
    189209    <td>Please provide a list of labels(names) for the experimental subjects, one per line,
    190210     in no particular order (copy and paste from Excel works).</td>
     
    201221  <tr>
    202222    <td class="boldText">Sample pooling:</td>
    203     <td class="input">yes <input type="radio" name="pooling" value="yes"> no <input type="radio"
    204       name="pooling" value="no" checked="checked"></td>
     223    <td class="input">
     224    <table class="noBorder" cellpadding="4">
     225      <tr>
     226        <td class="noBorder"><input type="radio" name="pooling" value="yes"></td>
     227        <td class="noBorder">yes</td>
     228      </tr>
     229      <tr>
     230        <td class="noBorder"><input type="radio" name="pooling" value="no" checked="checked"></td>
     231        <td class="noBorder">no</td>
     232      </tr>
     233    </table>   
     234    </td>
    205235    <td>If the samples were pooled please indicate this here.</td>
    206236  </tr>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp

    r543 r544  
    160160  //we also need to parse out the tissues string to produce another column of select boxes
    161161  String [] tissueNames = inputDataBean.getTissues().split("\n");
     162 
     163 
     164  //work out the number of hybridizations
     165  int numReplicates = Integer.parseInt(inputDataBean.getNumReplicates());
     166  int numTreatmentGroups =Integer.parseInt(inputDataBean.getNumTreatmentGroups());
     167  int numTissues = inputDataBean.getTissues().split("\n").length;
     168  int numHybs = Tab2MageWriter.calcNumHybs( numReplicates, numTreatmentGroups,  numTissues);
     169  System.out.println("numHybs = " + numHybs);
     170  System.out.println("products.length = " + products.length);
    162171%>
    163172
     
    195204
    196205  <%
    197     for (int i = 0; i < products.length; i++)
     206    for (int i = 0; i < numHybs; i++)
    198207    {
    199208  %>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r543 r544  
    144144  <tr>
    145145    <td class="boldText">Treatment</td>
    146     <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">my treatment protocol text </textarea></td>
    147     <td class="input_topaligned"><textarea rows="3" cols="35" name="treatmentProtocolParams">param1</textarea></td>
     146    <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">All chemicals tested were supplied by Merck (Darmstadt, Germany) or Aldrich (Hannover, Germany). All were of highest purity grade.</textarea></td>
     147    <td class="input_topaligned"><textarea rows="3" cols="35" name="treatmentProtocolParams">medium;CO2;antibiotics</textarea></td>
    148148  </tr>
    149149
    150150  <tr>
    151151    <td class="boldText">Extraction</td>
    152     <td class="input"><textarea rows="8" cols="35" name="extractionProtocol"> my extraction protocol text  </textarea></td>
    153     <td class="input_topaligned"><textarea rows="3" cols="35" name="extractionProtocolParams">param2</textarea></td>
     152    <td class="input"><textarea rows="8" cols="35" name="extractionProtocol">RNA was isolated using a FastPrep instrument (Q-Biogene, Irvine USA) and Rneasy reagents (Qiagen, Hilden Germany). RNA quality was checked with a 2100 Bioanalyser (Agilent Technologies, Palo Alto USA) by assessing the 28S/18S rRNA ratio.</textarea></td>
     153    <td class="input_topaligned"><textarea rows="3" cols="35" name="extractionProtocolParams"></textarea></td>
    154154  </tr>
    155155
    156156  <tr>
    157157    <td class="boldText">Labeling</td>
    158     <td class="input"><textarea rows="8" cols="35" name="labelingProtocol"> my labeling protocol text  </textarea></td>
    159     <td class="input_topaligned"><textarea rows="3" cols="35" name="labelingProtocolParams">param3</textarea></td>
     158    <td class="input"><textarea rows="8" cols="35" name="labelingProtocol">labeling protocol text  </textarea></td>
     159    <td class="input_topaligned"><textarea rows="3" cols="35" name="labelingProtocolParams"></textarea></td>
    160160  </tr>
    161161
    162162  <tr>
    163163    <td class="boldText">Hybridization</td>
    164     <td class="input"><textarea rows="8" cols="35" name="hybridizationProtocol">my hybs protocol text   </textarea></td>
    165     <td class="input_topaligned"><textarea rows="3" cols="35" name="hybridizationProtocolParams">param4</textarea></td>
     164    <td class="input"><textarea rows="8" cols="35" name="hybridizationProtocol">hybs protocol text   </textarea></td>
     165    <td class="input_topaligned"><textarea rows="3" cols="35" name="hybridizationProtocolParams">temperature(degree_C) ; duration(hr)</textarea></td>
    166166  </tr>
    167167
    168168  <tr>
    169169    <td class="boldText">Scanning</td>
    170     <td class="input"><textarea rows="8" cols="35"name="scanningProtocol"> my scanning protocol text </textarea></td>
    171     <td class="input_topaligned"><textarea rows="3" cols="35" name="scanningProtocolParams"> param5</textarea></td>
     170    <td class="input"><textarea rows="8" cols="35"name="scanningProtocol">scanning protocol text </textarea></td>
     171    <td class="input_topaligned"><textarea rows="3" cols="35" name="scanningProtocolParams"></textarea></td>
    172172  </tr>
    173173
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/submit.jsp

    r543 r544  
    5959    String value = (String)field.get(inputDataBean);
    6060    String fieldName = field.getName();
     61   
     62    if(!value.trim().equals("default"))
     63    {
    6164%>   
    6265 
     
    6972   
    7073  <% 
     74    }
    7175  }
    7276%>
     
    8084<input type="hidden" name="requestId" value="<%=requestId%>"/>
    8185<input type="hidden"name="parameter:domain" value="<%=inputDataBean.getDomain()%>" />
    82 <input type="hidden"name="parameter:accession" value="E-SCRI-002" />
     86<input type="hidden"name="parameter:accession" value="<%=inputDataBean.getAccession()%>" />
    8387<input type="hidden"name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>" />
    8488<input type="hidden"name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>" />
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/userchoice1.jsp

    r543 r544  
    1313final String requestId = request.getParameter("requestId");
    1414
    15 System.out.println("userchoice1.jsp: inputDataBean = " + inputDataBean.toString());
    16 System.out.println("userchoice1.jsp: ID = " + ID);
    1715 %>
    1816 
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/CartesianProduct.java

    r528 r544  
    1010            {"1h","12h", "24h"}
    1111    };
    12     getCartesianProduct (values);
    1312   
     13    String [][] products = getCartesianProduct (values);
     14   
     15    for (int i = 0; i < products.length; i++)
     16    {
     17      for (int j = 0; j < products[i].length; j++)
     18      {
     19        System.out.print (products[i][j] + "   ");
     20      }
     21      System.out.println();
     22    }
    1423  }
    1524 
     25  //returns a 2d array of Strings where each outer element represents a distinct factor value combination
     26  //and each inner element represents a factor value
    1627  public static String [][] getCartesianProduct (String[][] values)
    1728  {
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/DataBean.java

    r532 r544  
    11package uk.ac.ebi.nugo.plugins;
     2
     3import java.lang.reflect.Field;
    24
    35public class DataBean
     
    5254  public String mappingsMode;
    5355 
     56  public DataBean()
     57  {
     58    initDefaults();
     59  }
     60 
     61  private void initDefaults()
     62  {   
     63    try
     64    {
     65      Class cls = Class.forName("uk.ac.ebi.nugo.plugins.DataBean");
     66      Field [] fields = cls.getDeclaredFields();
     67      for (int i = 0; i < fields.length; i++)
     68      {
     69          fields[i].set(this, "default");
     70      }
     71    }
     72    catch (Exception e)
     73    {
     74      e.printStackTrace();
     75    }
     76  }
     77 
    5478 
    5579  public String getAccession()
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

    r543 r544  
    66package uk.ac.ebi.nugo.plugins;
    77
     8import java.io.BufferedWriter;
    89import java.io.IOException;
    910import java.io.InputStream;
     11import java.io.OutputStreamWriter;
     12import java.io.Writer;
    1013import java.util.Arrays;
    1114import java.util.Calendar;
     
    117120    for (int i = 0; i < paramNames.length; i++)
    118121    {
    119       PluginParameter<String> param = new PluginParameter<String>(paramNames[i],paramNames[i],paramNames[i],stringPT);
     122      PluginParameter<String> param = new PluginParameter<String>(paramNames[i],paramNames[i],paramNames[i],null, stringPT);
    120123      params.add(param);
    121124    }
     
    381384
    382385      //if we are in wizard mode, generate the tab2mage file automatically
    383       Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc,paramNames);
     386      File statusFile= null;
    384387      if(useWizard.equals("yes"))
    385388      {
     389        Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc,paramNames);
    386390        //now write the tab2mage file to the user's home dir on the server so it can be consumed by the plugin
    387391        //this takes all the inputs provided by the user on the custom interface (input.jsp)
    388392        //give the file a unique name so we don't get any conflicts         
    389         t2mWriter.writeTab2MageFile();       
    390       }
    391       t2mWriter.writeStatusFile();
    392       File statusFile = File.getByPath(dc, new Path(dir.getPath()+"/statusReport.txt",Path.Type.FILE ), false);
     393        t2mWriter.writeTab2MageFile(); 
     394        t2mWriter.writeStatusFile();
     395      }
     396      else
     397      {
     398        //need to write the status file here
     399        String statusPath = dir.getName() + "/statusReport.txt";
     400        statusFile=Helper.processFilePath(user,overwrite, sc,statusPath);
     401      }
     402     
     403      statusFile = File.getByPath(dc, new Path(dir.getPath()+"/statusReport.txt",Path.Type.FILE ), false);
    393404      System.out.println("statusFile = "+ statusFile.getPath());
    394405
    395      
    396406     
    397407      //VALIDATION MODULE
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java

    r543 r544  
    476476  // -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    477477
    478   private int calcNumHybs()
    479   {
    480     // get values for the parameters we need here
    481     int numReps = Integer.parseInt(numReplicates);
    482     int numTreats = Integer.parseInt(numTreatmentGroups);
    483     int numTissues = tissues.split(",").length;
     478  public static int calcNumHybs(int numReplicates, int numTreatmentGroups, int numTissues)
     479  {
    484480    // Number of hybridizations (NH) = Number of subjects (NS) x
    485481    // Number of Target Tissue (NTT) x Number of Study groups (NSG)
    486     return numReps * numTissues * numTreats;
     482    return numReplicates * numTissues * numTreatmentGroups;
    487483  }
    488484
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