Changeset 543


Ignore:
Timestamp:
Jan 17, 2008, 12:51:57 PM (13 years ago)
Author:
mbayer
Message:

submit mechanism has been changed to interactive -- submit.jsp now requires user to review and accept the current set of parameter values; this is because jsp forwarding was causing endless problems

Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
15 edited

Legend:

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

    r540 r543  
    9191
    9292
    93 <form name="hybridizations"action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
     93<form name="hybridizations"action="<%= request.getContextPath()%>/common/plugin/index.jsp?ID=<%=ID%>" method="post">
    9494<input type="hidden" name="ID" value="<%=ID%>">
    9595<input type="hidden" name="cmd" value="SetParameters">
     
    109109  <!-- file upload -->
    110110  <tr>
    111     <td class="boldText">Zip file:</td>
     111    <td class="boldText">File:</td>
    112112
    113113    <td class="input">
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp

    r532 r543  
    3434
    3535<script>
    36 self.resizeTo(800,850);
     36self.resizeTo(800,800);
    3737</script>
    3838
     
    131131<p>
    132132
    133 <form name="experimentData" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
     133<form name="experimentData" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp?ID=<%=ID%>" method="post">
    134134<input type="hidden" name="ID" value="<%=ID%>">
    135135<input type="hidden"name="requestId" value="<%=requestId%>">
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

    r532 r543  
    8585
    8686
    87 <form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice2.jsp" method="post">
     87<form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice2.jsp?ID=<%=ID%>" method="post">
    8888<input type="hidden" name="ID" value="<%=ID%>">
    8989<input type="hidden" name="cmd" value="SetParameters">
     
    9191
    9292<input type="hidden" name="file_id" value="">
    93 <input type="hidden" name="zipFile" value=""  id="zipFile">
     93<input type="hidden" name="zipFile" value="/home/michab/affyTestFiles.zip"  id="zipFile">
    9494
    9595<h1>Tab2MAGE Import Wizard -- Your Hybridizations</h1>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/mappings.jsp

    r532 r543  
    1515  final String ID = sc.getId();
    1616  final String requestId = request.getParameter("requestId");
     17 
     18  System.out.println("mappings.jsp: inputDataBean = " + inputDataBean.toString());
     19  System.out.println("mappings.jsp: ID = " + ID);
    1720%>
    1821
     
    8689
    8790
    88 <form name="mappings" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp" method="post">
     91<form name="mappings" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp?ID=<%=ID%>" method="post">
    8992
    9093<input type="hidden" name="ID" value="<%=ID%>">
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r532 r543  
    118118 %>
    119119
    120 <form name="protocols" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hybridizations.jsp" method="post">
     120<form name="protocols" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hybridizations.jsp?ID=<%=ID%>" method="post">
    121121<input type="hidden" name="ID" value="<%=ID%>">
    122122<input type="hidden"name="requestId" value="<%=requestId%>">
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/spreadsheetdata.jsp

    r539 r543  
    3737<h1>Tab2MAGE Import Wizard -- Enter Spreadsheet Data for Mappings</h1>
    3838
    39 <form id="spreadSheetMappings" name="spreadSheetMappings" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp">
     39<form id="spreadSheetMappings" name="spreadSheetMappings" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp?ID=<%=ID%>">
    4040
    4141<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters">
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/submit.jsp

    r540 r543  
    66<%@ page import="java.lang.reflect.*"%>
    77
    8 <!-- this page never actually loads - it simply gathers up all the parameters we need to send and forwards the request
    9 to the submission page, /common/plugin/index.jsp -->
    108
    119<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
    1210
     11<html>
     12
     13<head>
     14
     15<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
     16<link rel="stylesheet" type="text/css" href="/base/include/styles/main.css">
     17<link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css">
     18
     19<script type="text/javascript">
     20  //submits form
     21  function submit()
     22  {
     23    document.paramValues.submit();
     24  }
     25</script>
     26
     27</head>
     28
     29<body>
     30
     31<h1>Tab2MAGE Import Wizard -- Summary</h1>
     32<p>
     33
     34Please review the values you have entered and if you are happy with these, click 'Submit'.
     35<p>
     36
     37<table cellpadding="5">
     38
     39  <tr>
     40  <td>Parameter>
     41  </td>
     42  <td class="input">Value
     43  </td>
     44  </tr>
    1345
    1446<%
     
    2153
    2254  //print out all current parameter values in the bean
    23   System.out.println("=================================");
    24   System.out.println("current parameter values in the data bean:");
    25   System.out.println("=================================");
    2655  Class cls = inputDataBean.getClass();
    2756  for (int i = 0; i < paramNames.length; i++)
     
    3059    String value = (String)field.get(inputDataBean);
    3160    String fieldName = field.getName();
    32     System.out.println(fieldName + " = " + value);
    33   }
    34   System.out.println("=================================");
    35   System.out.println("end parameters:");
    36   System.out.println("=================================");
     61%>   
     62 
     63  <tr>
     64  <td><%=fieldName %>
     65  </td>
     66  <td class="input"><%=value %>
     67  </td>
     68  </tr>
     69   
     70  <% 
     71  }
    3772%>
    3873
     74</table>
    3975
    40 <jsp:forward page="/common/plugin/index.jsp">
     76<form name="paramValues" id="paramValues" action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
    4177
    42 <jsp:param name="parameter:domain" value="<%=inputDataBean.getDomain()%>" />
    43 <jsp:param name="parameter:accession" value="<%=inputDataBean.getAccession()%>" />
    44 <jsp:param name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>" />
    45 <jsp:param name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>" />
    46 <jsp:param name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>" />
    47 <jsp:param name="parameter:description" value="<%=inputDataBean.getDescription()%>" />
    48 <jsp:param name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>" />
    49 <jsp:param name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>" />
    50 <jsp:param name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>" />
    51 <jsp:param name="parameter:organization" value="<%=inputDataBean.getOrganization()%>" />
    52 <jsp:param name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>" />
    53 <jsp:param name="parameter:authors" value="<%=inputDataBean.getAuthors()%>" />
    54 <jsp:param name="parameter:journal" value="<%=inputDataBean.getJournal()%>" />
    55 <jsp:param name="parameter:volume" value="<%=inputDataBean.getVolume()%>" />
    56 <jsp:param name="parameter:issue" value="<%=inputDataBean.getIssue()%>" />
    57 <jsp:param name="parameter:pages" value="<%=inputDataBean.getPages()%>" />
    58 <jsp:param name="parameter:year" value="<%=inputDataBean.getYear()%>" />
    59 <jsp:param name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>" />
    60 <jsp:param name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>" />
    61 <jsp:param name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>" />
    62 <jsp:param name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>" />
    63 <jsp:param name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>" />
    64 <jsp:param name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>" />
    65 <jsp:param name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>" />
    66 <jsp:param name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>" />
    67 <jsp:param name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>" />
    68 <jsp:param name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>" />
    69 <jsp:param name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>" />
    70 <jsp:param name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>" />
    71 <jsp:param name="parameter:platform" value="<%=inputDataBean.getPlatform()%>" />
    72 <jsp:param name="parameter:organism" value="<%=inputDataBean.getOrganism()%>" />
    73 <jsp:param name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>" />
    74 <jsp:param name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>" />
    75 <jsp:param name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>" />
    76 <jsp:param name="parameter:numTreatmentGroups" value="<%=inputDataBean.getNumTreatmentGroups()%>" />
    77 <jsp:param name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>" />
    78 <jsp:param name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>" />
    79 <jsp:param name="parameter:tissues" value="<%=inputDataBean.getTissues()%>" />
    80 <jsp:param name="parameter:pooling" value="<%=inputDataBean.getPooling()%>" />
    81 <jsp:param name="parameter:path" value="<%=inputDataBean.getPath() %>" />
    82 <jsp:param name="parameter:subjectNames" value="<%=inputDataBean.getSubjectNames()%>" />
    83 <jsp:param name="parameter:fileList" value="<%=inputDataBean.getFileList()%>" />
    84 <jsp:param name="parameter:subjectList" value="<%=inputDataBean.getSubjectList()%>" />
    85 <jsp:param name="parameter:tissueList" value="<%=inputDataBean.getTissueList()%>" />
    86 <jsp:param name="parameter:useWizard" value="<%=inputDataBean.getUseWizard()%>" />
    87 <jsp:param name="parameter:legacyData" value="<%=inputDataBean.getLegacyData()%>" />
    88 <jsp:param name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
    89 
    90 <jsp:param name="parameter:fileList" value=""/>
    91 <jsp:param name="parameter:subjectList" value=""/>
    92 <jsp:param name="parameter:tissueList" value=""/>
    93 
    94 <jsp:param name="cmd" value="SetParameters"/>
    95 
    96 </jsp:forward>
     78<input type="hidden"name="cmd" value="SetParameters"/>
     79<input type="hidden" name="ID" value="<%=ID%>"/>
     80<input type="hidden" name="requestId" value="<%=requestId%>"/>
     81<input type="hidden"name="parameter:domain" value="<%=inputDataBean.getDomain()%>" />
     82<input type="hidden"name="parameter:accession" value="E-SCRI-002" />
     83<input type="hidden"name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>" />
     84<input type="hidden"name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>" />
     85<input type="hidden"name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>" />
     86<input type="hidden"name="parameter:description" value="<%=inputDataBean.getDescription()%>" />
     87<input type="hidden"name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>" />
     88<input type="hidden"name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>" />
     89<input type="hidden"name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>" />
     90<input type="hidden"name="parameter:organization" value="<%=inputDataBean.getOrganization()%>" />
     91<input type="hidden"name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>" />
     92<input type="hidden"name="parameter:authors" value="<%=inputDataBean.getAuthors()%>" />
     93<input type="hidden"name="parameter:journal" value="<%=inputDataBean.getJournal()%>" />
     94<input type="hidden"name="parameter:volume" value="<%=inputDataBean.getVolume()%>" />
     95<input type="hidden"name="parameter:issue" value="<%=inputDataBean.getIssue()%>" />
     96<input type="hidden"name="parameter:pages" value="<%=inputDataBean.getPages()%>" />
     97<input type="hidden"name="parameter:year" value="<%=inputDataBean.getYear()%>" />
     98<input type="hidden"name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>" />
     99<input type="hidden"name="parameter:experimentId" value="<%=inputDataBean.getExperimentId()%>" />
     100<input type="hidden"name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>" />
     101<input type="hidden"name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>" />
     102<input type="hidden"name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>" />
     103<input type="hidden"name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>" />
     104<input type="hidden"name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>" />
     105<input type="hidden"name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>" />
     106<input type="hidden"name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>" />
     107<input type="hidden"name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>" />
     108<input type="hidden"name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>" />
     109<input type="hidden"name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>" />
     110<input type="hidden"name="parameter:platform" value="<%=inputDataBean.getPlatform()%>" />
     111<input type="hidden"name="parameter:organism" value="<%=inputDataBean.getOrganism()%>" />
     112<input type="hidden"name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>" />
     113<input type="hidden"name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>" />
     114<input type="hidden"name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>" />
     115<input type="hidden"name="parameter:numTreatmentGroups" value="<%=inputDataBean.getNumTreatmentGroups()%>" />
     116<input type="hidden"name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>" />
     117<input type="hidden"name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>" />
     118<input type="hidden"name="parameter:tissues" value="<%=inputDataBean.getTissues()%>" />
     119<input type="hidden"name="parameter:pooling" value="<%=inputDataBean.getPooling()%>" />
     120<input type="hidden"name="parameter:path" value="<%=inputDataBean.getPath() %>" />
     121<input type="hidden"name="parameter:subjectNames" value="<%=inputDataBean.getSubjectNames()%>" />
     122<input type="hidden"name="parameter:fileList" value="<%=inputDataBean.getFileList()%>" />
     123<input type="hidden"name="parameter:subjectList" value="<%=inputDataBean.getSubjectList()%>" />
     124<input type="hidden"name="parameter:tissueList" value="<%=inputDataBean.getTissueList()%>" />
     125<input type="hidden"name="parameter:useWizard" value="<%=inputDataBean.getUseWizard()%>" />
     126<input type="hidden"name="parameter:legacyData" value="<%=inputDataBean.getLegacyData()%>" />
     127<input type="hidden"name="parameter:mappingsMode" value="<%=inputDataBean.getMappingsMode()%>" />
     128<input type="hidden"name="parameter:fileList" value=""/>
     129<input type="hidden"name="parameter:subjectList" value=""/>
     130<input type="hidden"name="parameter:tissueList" value=""/>
    97131
    98132
     133</form>
     134
     135<p>
     136  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
     137  <tr class="noBorder">
     138    <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Submit</td></tr></table></div></div></td>
     139    <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td>  </tr>
     140  </table>
     141
     142
     143</body>
     144</html>
     145
     146
     147
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/userchoice1.jsp

    r539 r543  
    1212final String ID = sc.getId();
    1313final String requestId = request.getParameter("requestId");
     14
     15System.out.println("userchoice1.jsp: inputDataBean = " + inputDataBean.toString());
     16System.out.println("userchoice1.jsp: ID = " + ID);
    1417 %>
    1518 
     
    3134  var form =document.getElementById("importerMode");
    3235 
     36  if(document.getElementById("useWizardNo").checked)
     37  {
     38    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/configureImporter.jsp?ID=<%=ID%>";
     39  }
    3340  if(document.getElementById("useWizardYes").checked)
    3441  {
    35     form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/configureImporter.jsp";
    36   }
    37   if(document.getElementById("useWizardNo").checked)
    38   {
    39     form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/experiment.jsp";
     42    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/experiment.jsp?ID=<%=ID%>";
    4043  }
    4144
     
    5962<table cellpadding="10">
    6063  <tr>
    61     <td>Do you have an existing tab2mage file and would you like this to be used for importing your data into BASE?</td>
     64    <td>Would you like the Tab2MAGE Wizard to generate a Tab2MAGE file for you?</td>
    6265    <td class="input">
    6366
     
    7881</table>
    7982
    80 
    81 <p>If you choose 'yes' you will simply have to provide a zip file containing your raw data files and a Tab2MAGE file, and the import of your data will proceed automatically.
    82 </p>
    83 <p>If you choose 'no' the Tab2MAGE Wizard will first assist you in gathering the information required for full Tab2MAGE/MIAME compliant experimental data and your data will then be imported
    84 automatically into BASE.
     83<p>If you choose 'yes' the Tab2MAGE Wizard will first assist you in gathering the information required for full Tab2MAGE/MIAME compliant experimental data and your data will then be imported
     84automatically into BASE.</p>
     85<p>If you choose 'no' you will simply have to provide a zip file containing your raw data files and a Tab2MAGE file, and the import of your data will proceed automatically.
    8586</p>
    8687
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/userchoice2.jsp

    r539 r543  
    3737  if(document.getElementById("legacyDataYes").checked)
    3838  {
    39     form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice3.jsp";
     39    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice3.jsp?ID=<%=ID%>";
    4040  }
    4141  if(document.getElementById("legacyDataNo").checked)
    4242  {
    43     form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp";
     43    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/submit.jsp?ID=<%=ID%>";
    4444  }
    4545
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/userchoice3.jsp

    r539 r543  
    3333  if(document.getElementById("mappingsModeManual").checked)
    3434  {
    35     form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/mappings.jsp";
     35    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/mappings.jsp?ID=<%=ID%>";
    3636  }
    3737  if(document.getElementById("mappingsModePaste").checked)
    3838  {
    39     form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/spreadsheetdata.jsp";
     39    form.action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/spreadsheetdata.jsp?ID=<%=ID%>";
    4040  }
    4141
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

    r540 r543  
    158158        //print out current values
    159159        System.out.println("=================================================================");
    160         System.out.println("current parameter values:");
     160        System.out.println("current parameter values in Tab2MageImporter.configure():");
    161161        PluginConfigurationRequest pcRequest = (PluginConfigurationRequest) sc.getSessionSetting("plugin.configure.request");
    162162        for(PluginParameter<?> param : params)
     
    341341
    342342      String tab2MageFileName= "tab2mage.txt";
    343       String zipFileName = (String)job.getValue("zipFile");
     343      String zipFileName = (String)job.getValue("path");
    344344
    345345      File zipFile = File.getByPath(dc, new Path(zipFileName, Path.Type.FILE), false);
     
    380380      }
    381381
    382 
    383382      //if we are in wizard mode, generate the tab2mage file automatically
     383      Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc,paramNames);
    384384      if(useWizard.equals("yes"))
    385385      {
    386386        //now write the tab2mage file to the user's home dir on the server so it can be consumed by the plugin
    387387        //this takes all the inputs provided by the user on the custom interface (input.jsp)
    388         //give the file a unique name so we don't get any conflicts
    389         Tab2MageWriter t2mWriter = new Tab2MageWriter(job, dir,sc,paramNames);
    390         t2mWriter.writeTab2MageFile();
    391         t2mWriter.writeStatusFile();
    392       }
    393 
    394 
    395 
     388        //give the file a unique name so we don't get any conflicts         
     389        t2mWriter.writeTab2MageFile();       
     390      }
     391      t2mWriter.writeStatusFile();
    396392      File statusFile = File.getByPath(dc, new Path(dir.getPath()+"/statusReport.txt",Path.Type.FILE ), false);
    397393      System.out.println("statusFile = "+ statusFile.getPath());
    398394
    399 
    400 
    401 
     395     
     396     
    402397      //VALIDATION MODULE
    403398
     
    533528    catch(Throwable tr)
    534529    {
     530      tr.printStackTrace();
    535531      response.setError(tr.getMessage(), Arrays.asList(tr));
    536532    }
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriter.java

    r532 r543  
    3232  String [] tissueNames;
    3333
     34  public String experimentId;
    3435  public String domain;
    3536  public String accession;
     
    7071  public String tissues;
    7172  public String pooling;
    72   public String zipFile;
    73   public String experimentId;
     73  public String path;
    7474  public String fileList;
    7575  public String subjectList;
    7676  public String tissueList;
     77  public String useWizard;
     78  public String legacyData;
     79  public String mappingsMode;
    7780
    7881
     
    106109      {
    107110        Field field = cls.getDeclaredField(paramNames[i]);
    108         field.set(this, job.getValue(paramNames[i]));
     111        try
     112        {
     113          field.set(this, job.getValue(paramNames[i]));
     114        }
     115        catch (IllegalArgumentException e)
     116        {
     117        }
    109118      }
    110119
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageWriterTest.java

    r532 r543  
    6262      writer.tissues = "whole_organism";
    6363      writer.pooling = "no";
    64       writer.zipFile = "/home/michab/gen2.zip";
     64      writer.path = "/home/michab/gen2.zip";
    6565      writer.fileList ="Tue-10h-1.CEL\tTue-10h-2.CEL\tTue-11.7h-1.CEL\tTue-11.7h-2.CEL\tTue-14d-1.CEL\tTue-14d-2.CEL\tTue-16h-1.CEL\tTue-16h-2.CEL\tTue-1c-1.CEL\tTue-1c-2.CEL\tTue-24h-1.CEL\tTue-24h-2.CEL\tTue-30d-1.CEL\tTue-30d-2.CEL\tTue-32h-1.CEL\tTue-32h-2.CEL\tTue-48h-1.CEL\tTue-48h-2.CEL\tTue-4d-1.CEL\tTue-4d-2.CEL\tTue-5d-1.CEL\tTue-5d-2.CEL\tTue-6h-1.CEL\tTue-6h-2.CEL\tTue-8h-1.CEL\tTue-8h-2.CEL\tTue-90d-1.CEL\tTue-90d-2.CEL\tTue-9h-1.CEL\tTue-9h-2.CEL\t";
    6666      writer.subjectList = "Danio rerio Tuebingen wildtype_10h-1\tDanio rerio Tuebingen wildtype_10h-2\tDanio rerio Tuebingen wildtype_11.7h-1\tDanio rerio Tuebingen wildtype_11.7h-2\tDanio rerio Tuebingen wildtype_14d-1\tDanio rerio Tuebingen wildtype_14d_2\tDanio rerio Tuebingen wildtype_16h-1\tDanio rerio Tuebingen wildtype_16h-2\tDanio rerio Tuebingen wildtype_1c-1\tDanio rerio Tuebingen wildtype_1c-2\tDanio rerio Tuebingen wildtype_24h-1\tDanio rerio Tuebingen wildtype_24h-2\tDanio rerio Tuebingen wildtype_30d-1\tDanio rerio Tuebingen wildtype_30d-2\tDanio rerio Tuebingen wildtype_32h-1\tDanio rerio Tuebingen wildtype_32h-2\tDanio rerio Tuebingen wildtype_48h-1\tDanio rerio Tuebingen wildtype_48h-2\tDanio rerio Tuebingen wildtype_4d-1\tDanio rerio Tuebingen wildtype_4d-2\tDanio rerio Tuebingen wildtype_5d-1\tDanio rerio Tuebingen wildtype_5d-2\tDanio rerio Tuebingen wildtype_6h-1\tDanio rerio Tuebingen wildtype_6h-2\tDanio rerio Tuebingen wildtype_8h-1\tDanio rerio Tuebingen wildtype_8h-2\tDanio rerio Tuebingen wildtype_90d-1\tDanio rerio Tuebingen wildtype_90d-2\tDanio rerio Tuebingen wildtype_9h-1\tDanio rerio Tuebingen wildtype_9h-2\t";
Note: See TracChangeset for help on using the changeset viewer.