Changeset 522


Ignore:
Timestamp:
Dec 14, 2007, 6:07:34 PM (15 years ago)
Author:
mbayer
Message:

made a number of tweaks to the interface

Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
1 deleted
8 edited

Legend:

Unmodified
Added
Removed

  • branches/uk_ac_ebi_Tab2MageImporter/html/hybridizations.html

    r521 r522  
    55<title>Tab2MAGE Importer -- Hybridizations</title>
    66
    7 <link rel="stylesheet" type="text/css" href="styles.css" />
     7<link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" />
    88
    99</head>
    … …  
    1616<form>
    1717
     18<!--  table with the input form -->
    1819<table cellpadding="15">
    1920
    2021  <!-- question 1 -->
    2122  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
    22     <td class="boldText">Microarray platform used:</td>
    23     <td class="input">
    24     <select name="parameter:platform">
    25     </select>
    26     </td>
     23    <td class="boldText">Microarray platform:</td>
     24    <td class="input"><select name="parameter:platform">
     25    <option >Affymetrix</option>
     26    <option >Agilent</option>
     27    <option >AIDA</option>
     28    <option >BZScan</option>
     29    <option >ChipSkipper</option>
     30    <option >GenePix</option>
     31    <option >GeneTAC</option>
     32    <option >Illumina</option>
     33    <option >Imagene</option>
     34    <option >QuantArray Biotin</option>
     35    <option >QuantArray Cy</option>
     36    <option >Spotfinder</option>
     37    <option ><i>Custom</i></option>
     38    </select></td>
     39    <td>The manufacturer of the microarray chip used.</td>
    2740  </tr>
    2841
    2942  <!-- question 2 -->
    3043  <tr>
    31     <td class="boldText">Name of the experimental organism:</td>
    32     <td class="input"><input type="text" size="60" name="parameter:organism"/></td>
     44    <td class="boldText">Experimental organism:</td>
     45    <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td>
     46    <td>The full scientific name of the experimental organism used.</td>
    3347  </tr>
    3448
    … …  
    3650  <tr>
    3751    <td class="boldText">Number of different arrays designs used:</td>
    38     <td class="input"><input type="text" size="3" name="parameter:numDesigns"/></td>
     52    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
     53    <td>If more than one array design was used in parallel, please specify the number here.</td>
    3954  </tr>
    4055
    4156  <!-- question 4 -->
    4257  <tr>
    43     <td class="boldText">Was dye-swap used?</td>
    44     <td class="input">yes <input type="radio" name="parameter:dyeswap" value="yes"> no <input type="radio" name="parameter:dyeswap" value="no">
    45     <br>
     58    <td class="boldText">Dye-swap</td>
     59    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
     60      name="parameter:dyeSwap" value="no" checked="checked"> <br>
     61     
    4662    </td>
     63    <td>If you used a dye-swap design please indicate this here.</td>
    4764  </tr>
    4865
    4966  <!-- question 5 -->
    5067  <tr>
    51     <td class="boldText">Was a reference sample used?</td>
    52     <td class="input">yes <input type="radio" name="parameter:refSample" value="yes"> no <input type="radio" name="parameter:refSample"
    53       value="no"></td>
     68    <td class="boldText">Reference sample</td>
     69    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
     70      name="parameter:refSample" value="no" checked="checked"></td>
     71    <td>If you used a reference sample please indicate this here.</td>
    5472  </tr>
    5573
    5674  <!-- question 6 -->
    5775  <tr>
    58     <td class="boldText">Number of treatments used:</td>
    59     <td class="input"><input type="text" size="3" name="parameter:numTreatments"/></td>
     76    <td class="boldText">Number of treatment groups:</td>
     77    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td>
     78    <td>The number of permutations of factor values. <p>
     79    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
     80    </td>
    6081  </tr>
    6182
    6283  <!-- question 7 -->
    6384  <tr>
    64     <td class="boldText">Please list your experimental factors and value ranges using the following format (one per line):<br>
    65     <i>Factor 1(value1,value2,...valueN)<br>
    66     Factor 2(value1,value2,...valueN)</i>
    67     <p>Example: <i><br>Compound(aspirin,ibuprofen,acetaminophen)
    68                   <br>Dose(control,low,medium,high)</i>
     85    <td class="boldText">Experimental factors:
    6986    </td>
    70     <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors"></textarea></td>
     87    <td class="input"><textarea rows="7" cols="35" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
     88    <td>Please list all experimental factors and value ranges using the following format (one per
     89    line):<br>
     90    <i>Factor 1(value1,value2,...valueN)<br></i>
     91    <p>Example: <i><br>
     92    Compound(aspirin,ibuprofen,acetaminophen) <br>
     93    Dose(control,low,medium,high)</i></td>
    7194  </tr>
    7295
    7396  <!-- question 8 -->
    7497  <tr>
    75     <td  class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
    76     <td class="input"><input type="text" size="3" name="parameter:numReplicates"/></td>
     98    <td class="boldText">Number of subjects per group:</td>
     99    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
     100    <td>This is the number of biological replicates in each treatment group.</td>
    77101  </tr>
     102 
    78103  <!-- question 9 -->
    79104  <tr>
    80     <td class="boldText">List all target tissues (as a comma separated list).<br>
    81     Example: liver,heart,adipose tissue
    82     </td>
    83     <td class="input"><textarea rows="2" cols="40" name="parameter:tissues"></textarea></td>
     105    <td class="boldText">Target tissues:</td>
     106    <td class="input"><textarea rows="2" cols="35" name="parameter:tissues">stem</textarea></td>
     107    <td>List all target tissues (as a comma separated list).<br>
     108    Example: liver,heart,adipose tissue</td>
    84109  </tr>
     110 
    85111  <!-- question 10 -->
    86112  <tr>
    87     <td class="boldText">Were samples pooled?</td>
    88     <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio" name="parameter:pooling" value="no">
    89     </td>
     113    <td class="boldText">Sample pooling:</td>
     114    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
     115      name="parameter:pooling" value="no" checked="checked"></td>
     116    <td>If the samples were pooled please indicate this here.</td>
    90117  </tr>
    91  
    92  
     118
     119
    93120  <!-- file upload -->
    94121  <tr>
    95     <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
     122    <td class="boldText">Zip file:</td>
    96123
    97     <td>
    98     <table border="0" cellspacing="0" cellpadding="0" class="noBorder">
    99       <tr class="noBorder">
    100         <td><input type="text" class="text required" name="path" size="50" value="">&nbsp;</td>
     124    <td class="input">
     125    <table class="noBorder" border="0" cellspacing="0" cellpadding="0">
     126      <tr class="noBorder" valign="middle">
     127     
     128        <td ><input type="text" name="path" size="40" value="">&nbsp;</td>
     129       
    101130        <td>
    102         <div class="buttonclass" onmouseover="this.className='buttonclass_hover';"
    103           onmouseout="this.className='buttonclass';" onclick="browseOnClick()">
     131        <div class="buttonclass"
     132          onmouseover="this.className='buttonclass_hover';"
     133          onmouseout="this.className='buttonclass';"
     134          onclick="browseOnClick()">
    104135        <div class="buttonclass_inner">
    105         <table border="0" cellspacing="0" cellpadding="0">
    106           <tr>
    107             <td><img src="browse.png" border="0"></td>
     136
     137        <table class="noBorder" cellspacing="0" cellpadding="0">
     138          <tr class="noBorder">
     139            <td>&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
    108140            <td>Browse&hellip;</td>
    109141          </tr>
    110142        </table>
     143
    111144        </div>
    112145        </div>
    113146        </td>
    114 
     147       
    115148      </tr>
    116149    </table>
    117150    </td>
     151
     152    <td>Please select the zip file on your local disk that contains the data files for import.
     153   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
    118154  </tr>
     155
     156
    119157
    120158</table>

  • branches/uk_ac_ebi_Tab2MageImporter/html/protocols.html

    r511 r522  
    55<title>Tab2MAGE Importer -- Protocols</title>
    66
    7 <link rel="stylesheet" type="text/css" href="styles.css" />
     7<link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" />
    88
    99</head>

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

    r521 r522  
    44<%@ page import="java.util.*"%>
    55
    6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session"/>
     6<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application"/>
    77<!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
    88<jsp:setProperty name="inputDataBean" property="*"/>
    … …  
    1414
    1515<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
    16 
     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 language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script>
    1720
    1821<script type="text/javascript">
     22    function getScale()
     23    {
     24      return 1.0;
     25    }
     26    function selectArrayDesignOnClick()
     27    {
     28      var frm = document.forms['experimentData'];
     29      var url = '<%= request.getContextPath()%>/lims/arraydesigns/index.jsp?ID=b8c5fcee801ca39c&cmd=UpdateContext&mode=selectone&callback=setArrayDesignCallback';
     30      if (frm.accession.length > 0)
     31      {
     32        var id = Math.abs(parseInt(frm.accession[0].value));       
     33        url += '&item_id='+id;
     34      }
     35      Main.openPopup(url, 'SelectArrayDesign', 1000, 700);
     36    }
     37    function setArrayDesignCallback(id, name)
     38    {
     39      var frm = document.forms['experimentData'];
     40      var list = frm.accession;
     41      if (list.length < 1 || list[0].value == '0') // >
     42      {
     43        Forms.addListOption(list, 0, new Option());
     44      }
     45      list[0].value = name;
     46      list[0].text = name;
     47      list.selectedIndex = 0;
     48      parentsChanged = true;
     49    }
     50  //submits form
     51  function submit()
     52  {
     53    document.experimentData.submit();
     54  }
    1955
    2056    //function to display or hide a given element
    … …  
    5995</head>
    6096
     97<!-- /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// -->
     98
    6199<body>
     100
    62101
    63102<%
    … …  
    84123
    85124Please configure your experiment for upload by answering the questions on this and the following two pages.
    86 <br>
    87125The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
    88 into this.
     126into this. All the associated objects (Hybridizations, Scans, Extracts etc.) will also be created.
    89127<p>
    90128
    91 <form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
     129<form name="experimentData" action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
    92130<input type="hidden" name="ID" value="<%=ID%>">
    93131
    … …  
    99137    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
    100138    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
    101     any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
     139    any suitable string, such as the originating internet domain name (e.g. "ebi.ac.uk").</td>
    102140  </tr>
    103141 
    104142  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    105143  <tr>
    106     <td class="boldText">Accession:</td>
    107     <td class="input"><input type="text" size="45" name="accession" value="E-SCRI-001" /></td>
    108     <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
    109     experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
    110   </tr>
    111  
    112   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    113   <tr>
    114     <td class="boldText">Quality Control:</td>
    115     <td class="input"><select multiple name="qualityControl">
    116       <option selected="selected">biological replicate</option>
    117       <option>dye swap quality control</option>
    118       <option>peer review quality control</option>
    119       <option>real time PCR quality control</option>
    120       <option>reverse transcription PCR quality control</option>
    121       <option selected="selected">spike quality control</option>
    122       <option>technical replicate</option>
    123     </select></td>
    124     <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED
    125     ontology</a>. Multiple values can be selected by holding down the Ctrl key and clicking on items.</td>
    126   </tr>
    127 
    128   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    129   <tr>
    130     <td class="boldText">Experiment Design Type:</td>
     144    <td class="boldText">Array Acession:</td>
     145
    131146    <td class="input">
    132147
    133     <table class="noBorder" cellpadding="3" >
    134 
     148    <div id="accession" class="selectionlist required">
     149    <table class="noBorder"  cellspacing="0" cellpadding="5">
    135150      <tr class="noBorder">
    136         <td valign="top">Biological Property<br/>
    137         </td>
    138         <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
    139           title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
    140           name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
    141         <div id="BiologicalProperty" style="display:none"><select multiple="multiple" name="biologicalProperty">
    142           <option selected="selected">cell_component_comparison_design</option>
    143           <option>cell_cycle_design</option>
    144           <option>cell_type_comparison_design</option>
    145           <option>cellular_process_design</option>
    146           <option>development_or_differentiation_design</option>
    147           <option>imprinting_design</option>
    148           <option>individual_genetic_characteristics_design</option>
    149           <option>innate_behavior_design</option>
    150           <option>is_expressed_design</option>
    151           <option>organism_part_comparison_design</option>
    152           <option>organism_status_design</option>
    153           <option>physiological_process_design</option>
    154           <option>sex_design</option>
    155           <option>species_design</option>
    156           <option>strain_or_line_design</option>
    157           <option>unknown_experiment_design_type</option>
    158         </select></div>
     151        <td><select name="accession" onchange="arrayDesignOnChange()"></select></td>
     152        <td>
     153        <div class="buttonclass"
     154          onmouseover="this.className='buttonclass_hover';"
     155          onmouseout="this.className='buttonclass';"
     156          onclick="selectArrayDesignOnClick()">
     157        <div class="buttonclass_inner">Select&hellip;</div>
     158        </div>
    159159        </td>
    160160      </tr>
    161 
    162       <tr class="noBorder">
    163         <td>BioMolecular Annotation</td>
    164         <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
    165           title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
    166           name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
    167         <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple" name="bioMolecularAnnotation">
    168           <option selected="selected">RNA_stability_design</option>
    169           <option>binding_site_identification_design</option>
    170           <option>co-expression_design</option>
    171           <option>comparative_genome_hybridization_design</option>
    172           <option>genotyping_design</option>
    173           <option>operon_identification_design</option>
    174           <option>secreted_protein_identification_design</option>
    175           <option>tiling_path_design</option>
    176           <option>transcript_identification_design</option>
    177           <option>translational_bias_design</option>
    178           <option>unknown_experiment_design_type</option>
    179         </select></div>
    180         </td>
    181       </tr>
    182 
    183       <tr class="noBorder">
    184         <td>Epidemiological Design</td>
    185         <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
    186         <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
    187         <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple" name="epidemiologicalDesign">
    188           <option>clinical_history_design</option>
    189           <option>disease_state_design</option>
    190           <option selected="selected">family_history_design</option>
    191           <option>unknown_experiment_design_type</option>
    192         </select></div>
    193         </td>
    194       </tr>
    195 
    196       <tr class="noBorder">
    197         <td>Methodological Design</td>
    198         <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
    199         <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
    200         <div id="MethodologicalDesign" style="display:none"><select multiple="multiple" name="methodologicalDesign">
    201           <option>all_pairs</option>
    202           <option>array_platform_variation_design</option>
    203           <option>dye_swap_design</option>
    204           <option>ex_vivo_design</option>
    205           <option>hardware_variation_design</option>
    206           <option>in_vitro_design</option>
    207           <option>in_vivo_design</option>
    208           <option>loop_design</option>
    209           <option>normalization_testing_design</option>
    210           <option>operator_variation_design</option>
    211           <option>optimization_design</option>
    212           <option>quality_control_testing_design</option>
    213           <option>reference_design</option>
    214           <option>replicate_design</option>
    215           <option>self_vs_self_design</option>
    216           <option>software_variation_design</option>
    217           <option>time_series_design</option>
    218           <option>unknown_experiment_design_type</option>
    219         </select></div>
    220         </td>
    221       </tr>
    222 
    223       <tr class="noBorder">
    224         <td>Perturbational Design</td>
    225         <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
    226         <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
    227         <div id="PerturbationalDesign" style="display:none"><select multiple="multiple" name="perturbationalDesign">
    228           <option>cellular_modification_design</option>
    229           <option>compound_treatment_design</option>
    230           <option>disease_state_design</option>
    231           <option>dose_response_design</option>
    232           <option>genetic_modification_design</option>
    233           <option>growth_condition_design</option>
    234           <option>injury_design</option>
    235           <option>non-targeted_transgenic_variation_design</option>
    236           <option>pathogenicity_design</option>
    237           <option>stimulated_design_type</option>
    238           <option>stimulus_or_stress_design</option>
    239           <option>unknown_experiment_design_type</option>
    240         </select></div>
    241         </td>
    242       </tr>
    243 
    244       <tr class="noBorder">
    245         <td>Technological Design</td>
    246         <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
    247         <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
    248         <div id="TechnologicalDesign" style="display:none"><select multiple="multiple" name="technologicalDesign">
    249           <option>binding_site_identification_design</option>
    250           <option>cellular_modification_design</option>
    251           <option>comparative_genome_hybridization_design</option>
    252           <option>transcript_identification_design</option>
    253         </select></div>
    254         </td>
    255       </tr>
    256 
    257161    </table>
    258 
    259 
     162    </div>
    260163    </td>
    261     <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>.
    262     <p>Click "expand" for an item to see list boxes with specific choices.<br>
    263     Multiple values can be selected by holding down the Ctrl key and clicking on items.
    264     </td>
     164
     165    <td>Please select an existing array design from BASE or create a
     166    new one. For ArrayExpress submissions, the array design name becomes
     167    the array accession identifier. Accession numbers for experiments
     168    submitted to ArrayExpress should have the format E-XXXX-n.</td>
     169
    265170  </tr>
    266  
    267   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     171
     172
    268173  <tr>
    269     <td class="boldText">Experiment Name:</td>
    270     <td class="input"> 
    271     <textarea rows="2" cols="30" name="experimentName"><%=expName %></textarea>
    272     </td>
    273     <td>The name you have chosen for the Experiment.</td>
    274   </tr>
    275  
    276   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    277   <tr>
    278     <td class="boldText">Experiment Description:</td>
    279     <td class="input">
    280     <textarea rows="2" cols="30" name="description">description goes here</textarea>
    281     </td>
    282     <td>A short paragraph describing the purpose of the experiment.</td>
    283   </tr>
    284  
    285   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    286   <tr>
    287     <td class="boldText">Release Date:</td>
    288     <td class="input"><input type="text" size="10" name="releaseDate" value="2007-12-03" /></td>
    289     <td>Date for public release, in the format YYYY-MM-DD.</td>
    290   </tr>
    291   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    292   <tr>
    293     <td class="boldText">Submission Date:</td>
    294     <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
    295     <td>Date of submission, in the format YYYY-MM-DD.</td>
    296   </tr>
    297   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    298   <tr>
    299     <td class="boldText">Submitter:</td>
    300     <td class="input"><input type="text" size="45" name="submitter" value="Joe Bloggs" /></td>
    301     <td>The name of the person responsible for submitting the experiment to the database.</td>
    302   </tr>
    303   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    304   <tr>
    305     <td class="boldText">Organization:</td>
    306     <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
    307     <td>The organization to which the submitter is affiliated.</td>
    308   </tr>
    309   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    310 
     174
     175      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     176    <tr>
     177      <td class="boldText">Quality Control:</td>
     178      <td class="input"><select multiple name="qualityControl">
     179        <option selected="selected">biological replicate</option>
     180        <option>dye swap quality control</option>
     181        <option>peer review quality control</option>
     182        <option>real time PCR quality control</option>
     183        <option>reverse transcription PCR quality control</option>
     184        <option selected="selected">spike quality control</option>
     185        <option>technical replicate</option>
     186      </select></td>
     187      <td>A list of terms taken from the <a
     188        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
     189        target="_blank">MGED ontology</a>. Multiple values can be selected
     190      by holding down the Ctrl key and clicking on items.</td>
     191    </tr>
     192
     193    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     194    <tr>
     195      <td class="boldText">Experiment Design Type:</td>
     196      <td class="input">
     197
     198      <table class="noBorder" cellpadding="3">
     199
     200        <tr class="noBorder">
     201          <td valign="top">Biological Property<br />
     202          </td>
     203          <td colspan="2"><a
     204            onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
     205            title="Show/hide items"> <img
     206            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     207            border="0" id="buttonBiologicalProperty"
     208            name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
     209          <div id="BiologicalProperty" style="display:none"><select
     210            multiple="multiple" name="biologicalProperty">
     211            <option selected="selected">cell_component_comparison_design</option>
     212            <option>cell_cycle_design</option>
     213            <option>cell_type_comparison_design</option>
     214            <option>cellular_process_design</option>
     215            <option>development_or_differentiation_design</option>
     216            <option>imprinting_design</option>
     217            <option>individual_genetic_characteristics_design</option>
     218            <option>innate_behavior_design</option>
     219            <option>is_expressed_design</option>
     220            <option>organism_part_comparison_design</option>
     221            <option>organism_status_design</option>
     222            <option>physiological_process_design</option>
     223            <option>sex_design</option>
     224            <option>species_design</option>
     225            <option>strain_or_line_design</option>
     226            <option>unknown_experiment_design_type</option>
     227          </select></div>
     228          </td>
     229        </tr>
     230
     231        <tr class="noBorder">
     232          <td>BioMolecular Annotation</td>
     233          <td><a
     234            onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
     235            title="Show/hide items"> <img
     236            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     237            border="0" id="buttonBioMolecularAnnotation"
     238            name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
     239          <div id="BioMolecularAnnotation" style="display:none"><select
     240            multiple="multiple" name="bioMolecularAnnotation">
     241            <option selected="selected">RNA_stability_design</option>
     242            <option>binding_site_identification_design</option>
     243            <option>co-expression_design</option>
     244            <option>comparative_genome_hybridization_design</option>
     245            <option>genotyping_design</option>
     246            <option>operon_identification_design</option>
     247            <option>secreted_protein_identification_design</option>
     248            <option>tiling_path_design</option>
     249            <option>transcript_identification_design</option>
     250            <option>translational_bias_design</option>
     251            <option>unknown_experiment_design_type</option>
     252          </select></div>
     253          </td>
     254        </tr>
     255
     256        <tr class="noBorder">
     257          <td>Epidemiological Design</td>
     258          <td><a
     259            onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');"
     260            title="Show/hide items"> <img
     261            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     262            border="0" id="buttonEpidemiologicalDesign"
     263            name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
     264          <div id="EpidemiologicalDesign" style="display:none"><select
     265            multiple="multiple" name="epidemiologicalDesign">
     266            <option>clinical_history_design</option>
     267            <option>disease_state_design</option>
     268            <option selected="selected">family_history_design</option>
     269            <option>unknown_experiment_design_type</option>
     270          </select></div>
     271          </td>
     272        </tr>
     273
     274        <tr class="noBorder">
     275          <td>Methodological Design</td>
     276          <td><a
     277            onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');"
     278            title="Show/hide items"> <img
     279            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     280            border="0" id="buttonMethodologicalDesign"
     281            name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
     282          <div id="MethodologicalDesign" style="display:none"><select
     283            multiple="multiple" name="methodologicalDesign">
     284            <option>all_pairs</option>
     285            <option>array_platform_variation_design</option>
     286            <option>dye_swap_design</option>
     287            <option>ex_vivo_design</option>
     288            <option>hardware_variation_design</option>
     289            <option>in_vitro_design</option>
     290            <option>in_vivo_design</option>
     291            <option>loop_design</option>
     292            <option>normalization_testing_design</option>
     293            <option>operator_variation_design</option>
     294            <option>optimization_design</option>
     295            <option>quality_control_testing_design</option>
     296            <option>reference_design</option>
     297            <option>replicate_design</option>
     298            <option>self_vs_self_design</option>
     299            <option>software_variation_design</option>
     300            <option>time_series_design</option>
     301            <option>unknown_experiment_design_type</option>
     302          </select></div>
     303          </td>
     304        </tr>
     305
     306        <tr class="noBorder">
     307          <td>Perturbational Design</td>
     308          <td><a
     309            onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');"
     310            title="Show/hide items"> <img
     311            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     312            border="0" id="buttonPerturbationalDesign"
     313            name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
     314          <div id="PerturbationalDesign" style="display:none"><select
     315            multiple="multiple" name="perturbationalDesign">
     316            <option>cellular_modification_design</option>
     317            <option>compound_treatment_design</option>
     318            <option>disease_state_design</option>
     319            <option>dose_response_design</option>
     320            <option>genetic_modification_design</option>
     321            <option>growth_condition_design</option>
     322            <option>injury_design</option>
     323            <option>non-targeted_transgenic_variation_design</option>
     324            <option>pathogenicity_design</option>
     325            <option>stimulated_design_type</option>
     326            <option>stimulus_or_stress_design</option>
     327            <option>unknown_experiment_design_type</option>
     328          </select></div>
     329          </td>
     330        </tr>
     331
     332        <tr class="noBorder">
     333          <td>Technological Design</td>
     334          <td><a
     335            onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');"
     336            title="Show/hide items"> <img
     337            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     338            border="0" id="buttonTechnologicalDesign"
     339            name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
     340          <div id="TechnologicalDesign" style="display:none"><select
     341            multiple="multiple" name="technologicalDesign">
     342            <option>binding_site_identification_design</option>
     343            <option>cellular_modification_design</option>
     344            <option>comparative_genome_hybridization_design</option>
     345            <option>transcript_identification_design</option>
     346          </select></div>
     347          </td>
     348        </tr>
     349
     350      </table>
     351
     352
     353      </td>
     354      <td>A list of terms taken from the <a
     355        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
     356        target="_blank">MGED ontology</a>.
     357      <p>Click "expand" for an item to see list boxes with specific
     358      choices.<br />
     359      <br />
     360      Multiple values can be selected by holding down the Ctrl key and
     361      clicking on items.
     362      </td>
     363    </tr>
     364
     365    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     366    <tr>
     367      <td class="boldText">Experiment Name:</td>
     368      <td class="input"><textarea rows="2" cols="30"
     369        name="experimentName"><%=expName %></textarea></td>
     370      <td>The name you have chosen for the Experiment.</td>
     371    </tr>
     372
     373    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     374    <tr>
     375      <td class="boldText">Experiment Description:</td>
     376      <td class="input"><textarea rows="2" cols="30"
     377        name="description">description goes here</textarea></td>
     378      <td>A short paragraph describing the purpose of the experiment.</td>
     379    </tr>
     380
     381    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     382    <tr>
     383      <td class="boldText">Release Date:</td>
     384      <td class="input"><input type="text" size="10"
     385        name="releaseDate" value="2007-12-03" /></td>
     386      <td>Date for public release, in the format YYYY-MM-DD.</td>
     387    </tr>
     388    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     389    <tr>
     390      <td class="boldText">Submission Date:</td>
     391      <td class="input"><input type="text" size="10"
     392        name="submissionDate" value="2007-12-03" /></td>
     393      <td>Date of submission, in the format YYYY-MM-DD.</td>
     394    </tr>
     395    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     396    <tr>
     397      <td class="boldText">Submitter:</td>
     398      <td class="input"><input type="text" size="45" name="submitter"
     399        value="Joe Bloggs" /></td>
     400      <td>The name of the person responsible for submitting the
     401      experiment to the database.</td>
     402    </tr>
     403    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     404    <tr>
     405      <td class="boldText">Organization:</td>
     406      <td class="input"><input type="text" size="45"
     407        name="organization" value="SCRI" /></td>
     408      <td>The organization to which the submitter is affiliated.</td>
     409    </tr>
     410    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     411
     412    <tr class="noBorder">
     413      <td class="boldText">Publication Details:</td>
     414      <td class="input"></td>
     415      <td></td>
     416    </tr>
     417
     418    <tr class="noBorder">
     419      <td>Title:</td>
     420      <td class="input"><textarea rows="2" cols="30"
     421        name="publicationTitle">My Ropey Paper</textarea></td>
     422
     423      <td rowspan="4">Publication details for any manuscript
     424      associated with the experiment. <p>
     425      The authors list is a semicolon-delimited list of names.<p>
     426      The journal field should contain a standard Pubmed journal
     427      abbreviated name. </td>
     428    </tr>
     429    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     430    <tr class="noBorder">
     431      <td>Authors:</td>
     432      <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
     433      <td></td>
     434    </tr>
     435    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     436    <tr class="noBorder">
     437      <td>Journal:</td>
     438      <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
     439      <td></td>
     440    </tr>
     441    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     442    <tr class="noBorder">
     443      <td>Volume:</td>
     444      <td class="input"><input type="text" size="10" name="volume"
     445        value="5" /></td>
     446      <td></td>
     447    </tr>
     448    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     449    <tr class="noBorder">
     450      <td>Issue:</td>
     451      <td class="input"><input type="text" size="10" name="issue"
     452        value="2" /></td>
     453      <td></td>
     454    </tr>
     455    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     456    <tr class="noBorder">
     457      <td>Pages:</td>
     458      <td class="input"><input type="text" size="10" name="pages"
     459        value="1234-1235" /></td>
     460      <td></td>
     461    </tr>
     462    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     463    <tr class="noBorder">
     464      <td>Year:</td>
     465      <td class="input"><input type="text" size="10" name="year"
     466        value="2007" /></td>
     467      <td></td>
     468    </tr>
     469    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     470    <tr class="noBorder">
     471      <td>Pubmed ID:</td>
     472      <td class="input"><input type="text" size="30" name="pubmedId"
     473        value="11009762" /></td>
     474      <td></td>
     475
     476    </tr>
     477
     478    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     479  </table>
     480
     481  <p>
     482
     483
     484  <table align="center" class="noBorder"  cellpadding="5">
    311485  <tr class="noBorder">
    312     <td class="boldText">Publication Details:</td>
    313     <td  class="input"></td>
    314     <td></td>
    315   </tr>
    316 
    317   <tr class="noBorder">
    318     <td>Title:</td>
    319     <td class="input"><textarea rows="2" cols="30" name="publicationTitle">My Ropey Paper</textarea></td>
    320 
    321     <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
    322     contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
    323   </tr>
    324   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    325       <tr class="noBorder">
    326         <td>Authors:</td>
    327         <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
    328         <td></td>
    329       </tr>
    330       <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    331       <tr class="noBorder">
    332         <td>Journal:</td>
    333         <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
    334         <td></td>
    335       </tr>
    336       <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    337       <tr class="noBorder">
    338         <td>Volume:</td>
    339         <td class="input"><input type="text" size="10" name="volume" value="5" /></td>
    340         <td></td>
    341       </tr>
    342       <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    343       <tr class="noBorder">
    344         <td>Issue:</td>
    345         <td class="input"><input type="text" size="10" name="issue" value="2" /></td>
    346         <td></td>
    347       </tr>
    348       <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    349       <tr class="noBorder">
    350         <td>Pages:</td>
    351         <td class="input"><input type="text" size="10" name="pages" value="1234-1235" /></td>
    352         <td></td>
    353       </tr>
    354       <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    355       <tr class="noBorder">
    356         <td>Year:</td>
    357         <td class="input"><input type="text" size="10" name="year" value="2007" /></td>
    358         <td></td>
    359       </tr>
    360       <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    361       <tr class="noBorder">
    362         <td>Pubmed ID:</td>
    363         <td class="input"><input type="text" size="30" name="pubmedId" value="11009762" /></td>
    364         <td></td>
    365 
    366   </tr>
    367 
    368   <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    369 </table>
    370 
    371 <p>
    372 
    373 <table class="noBorder" width="100%">
    374 <tr class="noBorder" ><td class="centered">
    375 <input type="submit"  value="Continue"/>
    376 </td>
    377 </tr>
    378 </table>
    379 
    380   <table align="center">
    381   <tr>
    382     <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td>
    383     <td id="close" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="window.close();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>
     486    <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit()"><div class="buttonclass_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td>
     487    <td id="close" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="window.close()"><div class="buttonclass_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>
    384488  </tr>
    385489  </table>

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

    r521 r522  
    44<%@ page import="java.util.*"%>
    55
    6 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
     6<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
    77<!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
    88<jsp:setProperty name="inputDataBean" property="*" />
    … …  
    2020
    2121<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
    22 <link rel="stylesheet" type="text/css" href="/base/include/styles/main.css">
    23 <link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css">
     22
    2423
    2524<script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script>
    2625
    2726<script language="JavaScript" type="text/javascript">
     27  //submits form
     28  function submit()
     29  {
     30    document.hybridizations.submit();
     31  }
    2832    function getRoot()
    2933    {
    … …  
    125129  <!-- question 1 -->
    126130  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
    127     <td class="boldText">Microarray platform used:</td>
     131    <td class="boldText">Microarray platform:</td>
    128132    <td class="input"><select name="parameter:platform">
    129133    <option >Affymetrix</option>
    … …  
    139143    <option >QuantArray Cy</option>
    140144    <option >Spotfinder</option>
     145    <option ><i>Custom</i></option>
    141146    </select></td>
     147    <td>The manufacturer of the microarray chip used.</td>
    142148  </tr>
    143149
    144150  <!-- question 2 -->
    145151  <tr>
    146     <td class="boldText">Name of the experimental organism:</td>
    147     <td class="input"><input type="text" size="60" name="parameter:organism" value="Solanum tuberosum"/></td>
     152    <td class="boldText">Experimental organism:</td>
     153    <td class="input"><input type="text" size="50" name="parameter:organism" value="Solanum tuberosum"/></td>
     154    <td>The full scientific name of the experimental organism used.</td>
    148155  </tr>
    149156
    … …  
    152159    <td class="boldText">Number of different arrays designs used:</td>
    153160    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
     161    <td>If more than one array design was used in parallel, please specify the number here.
     162    We assume that all samples are applied once to each array design</td>
    154163  </tr>
    155164
    156165  <!-- question 4 -->
    157166  <tr>
    158     <td class="boldText">Was dye-swap used?</td>
     167    <td class="boldText">Dye-swap</td>
    159168    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
    160169      name="parameter:dyeSwap" value="no" checked="checked"> <br>
    161     </td>
     170     
     171    </td>
     172    <td>If you used a dye-swap design please indicate this here.</td>
    162173  </tr>
    163174
    164175  <!-- question 5 -->
    165176  <tr>
    166     <td class="boldText">Was a reference sample used?</td>
     177    <td class="boldText">Reference sample</td>
    167178    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
    168179      name="parameter:refSample" value="no" checked="checked"></td>
     180    <td>If you used a reference sample please indicate this here.</td>
    169181  </tr>
    170182
    … …  
    173185    <td class="boldText">Number of treatment groups:</td>
    174186    <td class="input"><input type="text" size="3" name="parameter:numTreatmentGroups" value="2"/></td>
     187    <td>The number of permutations of factor values. <p>
     188    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
     189    </td>
    175190  </tr>
    176191
    177192  <!-- question 7 -->
    178193  <tr>
    179     <td class="boldText">Please list your experimental factors and value ranges using the following format (one per
     194    <td class="boldText">Experimental factors:
     195    </td>
     196    <td class="input"><textarea rows="7" cols="35" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
     197    <td>Please list all experimental factors and value ranges using the following format (one per
    180198    line):<br>
    181199    <i>Factor 1(value1,value2,...valueN)<br></i>
    182200    <p>Example: <i><br>
    183201    Compound(aspirin,ibuprofen,acetaminophen) <br>
    184     Dose(control,low,medium,high)</i>
    185     </td>
    186     <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Strain(mutant,wildtype)</textarea></td>
     202    Dose(control,low,medium,high)</i></td>
    187203  </tr>
    188204
    189205  <!-- question 8 -->
    190206  <tr>
    191     <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
     207    <td class="boldText">Number of subjects per group:</td>
    192208    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="2"/></td>
     209    <td>This is the number of biological replicates in each treatment group.</td>
    193210  </tr>
    194211 
    195212  <!-- question 9 -->
    196213  <tr>
    197     <td class="boldText">List all target tissues (as a comma separated list).<br>
     214    <td class="boldText">Target tissues:</td>
     215    <td class="input"><textarea rows="2" cols="35" name="parameter:tissues">stem</textarea></td>
     216    <td>List all target tissues (as a comma separated list).<br>
    198217    Example: liver,heart,adipose tissue</td>
    199     <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">stem</textarea></td>
    200218  </tr>
    201219 
    202220  <!-- question 10 -->
    203221  <tr>
    204     <td class="boldText">Were samples pooled?</td>
     222    <td class="boldText">Sample pooling:</td>
    205223    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
    206224      name="parameter:pooling" value="no" checked="checked"></td>
     225    <td>If the samples were pooled please indicate this here.</td>
    207226  </tr>
    208227
    209228
    210229  <!-- file upload -->
    211   <tr >
    212     <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
    213     <td>
    214 
    215     <table class="noBorder" border="0" cellspacing="0" cellpadding="0">
    216       <tr class="noBorder">
    217         <td><input type="text" class="text required" name="path" size="50" value="">&nbsp;</td>
    218         <td>
     230  <tr>
     231    <td class="boldText">Zip file:</td>
     232
     233    <td class="input">
     234    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
     235      <tr class="noBorder" >
     236     
     237        <td style="vertical-align: middle"><input type="text" name="path" size="35" value=""></td>
    219238       
    220         <div class="buttonclass" onmouseover="this.className='buttonclass_hover';"
    221           onmouseout="this.className='buttonclass';" onclick="browseOnClick()">
    222         <div class="buttonclass_inner">
    223        
    224         <table border="0" cellspacing="0" cellpadding="0">
    225           <tr>
     239        <td  style="vertical-align: middle">
     240        <div class="buttons"
     241          onmouseover="this.className='buttons_hover';"
     242          onmouseout="this.className='buttons';"
     243          onclick="browseOnClick()">
     244        <div class="buttons_inner">
     245
     246        <table class="noBorder" cellspacing="0" cellpadding="0">
     247          <tr class="noBorder">
    226248            <td>&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
    227249            <td>Browse&hellip;</td>
    … …  
    232254        </div>
    233255        </td>
     256       
    234257      </tr>
    235258    </table>
    236   </td>
    237   </tr>
    238 
    239 
     259    </td>
     260
     261    <td>Please select the zip file on your local disk that contains the data files for import.
     262   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
     263  </tr>
    240264
    241265</table>
    242266
    243267<p>
    244 <table class="noBorder" width="100%">
     268
     269  <table align="center" class="noBorder" cellpadding="5">
    245270  <tr class="noBorder">
    246     <td class="centered"><input type="submit" value="Run Import" /></td>
    247   </tr>
    248 </table>
    249 
    250   <table align="center">
    251   <tr>
    252     <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/gonext.gif" border="0"></td><td>Submit</td></tr></table></div></div></td>
    253     <td id="close" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="window.close();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>
    254   </tr>
     271    <td id="next" width="50%"><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><img src="/base/images/gonext.gif" border="0"></td><td>Run Import</td></tr></table></div></div></td>
     272    <td id="close" width="50%"><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><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>  </tr>
    255273  </table>
    256274

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

    r521 r522  
    55<%@ page import="java.lang.*"%>
    66
    7 <jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
     7<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="application" />
    88<!-- submits the form data back to the bean assuming that each form element is matched to a variable in the bean by the same name -->
    99<jsp:setProperty name="inputDataBean" property="*" />
    … …  
    1111
    1212<html>
     13
    1314<head>
     15
    1416<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
     17<link rel="stylesheet" type="text/css" href="/base/include/styles/main.css">
     18<link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css">
     19
     20<script language="JavaScript" type="text/javascript">
     21  //submits form
     22  function submit()
     23  {
     24    document.protocols.submit();
     25  }
     26</script>
     27
    1528</head>
     29
    1630<body>
    1731
    … …  
    104118 %>
    105119
    106 <form 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" method="post">
    107121<input type="hidden" name="ID" value="<%=ID%>">
    108122
    … …  
    122136    <td class="header">
    123137    <h3>Parameters</h3>
    124     <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'. <br />
    125     Each parameter name should be unique within this form.<br />
     138    <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'.
     139    Each parameter name must be unique within this form.<br /><br />
    126140    Leave blank if the protocol is unparameterized.</p>
    127141    </td>
    … …  
    131145    <td class="boldText">Treatment</td>
    132146    <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">my treatment protocol text </textarea></td>
    133     <td><textarea rows="4" cols="25" name="treatmentProtocolParams">param1</textarea></td>
     147    <td class="input_topaligned"><textarea rows="3" cols="35" name="treatmentProtocolParams">param1</textarea></td>
    134148  </tr>
    135149
    … …  
    137151    <td class="boldText">Extraction</td>
    138152    <td class="input"><textarea rows="8" cols="35" name="extractionProtocol"> my extraction protocol text  </textarea></td>
    139     <td><textarea rows="4" cols="25" name="extractionProtocolParams">param2</textarea></td>
     153    <td class="input_topaligned"><textarea rows="3" cols="35" name="extractionProtocolParams">param2</textarea></td>
    140154  </tr>
    141155
    … …  
    143157    <td class="boldText">Labeling</td>
    144158    <td class="input"><textarea rows="8" cols="35" name="labelingProtocol"> my labeling protocol text  </textarea></td>
    145     <td><textarea rows="4" cols="25" name="labelingProtocolParams">param3</textarea></td>
     159    <td class="input_topaligned"><textarea rows="3" cols="35" name="labelingProtocolParams">param3</textarea></td>
    146160  </tr>
    147161
    … …  
    149163    <td class="boldText">Hybridization</td>
    150164    <td class="input"><textarea rows="8" cols="35" name="hybridizationProtocol">my hybs protocol text   </textarea></td>
    151     <td><textarea rows="4" cols="25" name="hybridizationProtocolParams">param4</textarea></td>
     165    <td class="input_topaligned"><textarea rows="3" cols="35" name="hybridizationProtocolParams">param4</textarea></td>
    152166  </tr>
    153167
    … …  
    155169    <td class="boldText">Scanning</td>
    156170    <td class="input"><textarea rows="8" cols="35"name="scanningProtocol"> my scanning protocol text </textarea></td>
    157     <td><textarea rows="4" cols="25" name="scanningProtocolParams"> param5</textarea></td>
     171    <td class="input_topaligned"><textarea rows="3" cols="35" name="scanningProtocolParams"> param5</textarea></td>
    158172  </tr>
    159173
    … …  
    161175
    162176<p>
    163 <table class="noBorder" width="100%">
    164   <tr class="noBorder">
    165     <td class="centered"><input type="submit" value="Continue" /></td>
    166   </tr>
    167 </table>
    168177
    169   <table align="center">
    170   <tr>
    171     <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td>
    172     <td id="close" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="window.close();"><div class="buttonclass_inner"><table border="0" cellspacing="0" cellpadding="0"><tr><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>
    173   </tr>
     178  <table align="center"  class="noBorder"  cellpadding="5">
     179  <tr  class="noBorder">
     180    <td id="next" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="submit()"><div class="buttonclass_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Continue</td></tr></table></div></div></td>
     181    <td id="close" width="50%"><div class="buttonclass" onmouseover="this.className='buttonclass_hover';" onmouseout="this.className='buttonclass';" onclick="window.close()"><div class="buttonclass_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>  </tr>
    174182  </table>
    175183

  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/styles.css

    r521 r522  
    4444tr.noBorder {
    4545  border-style: none;
     46  vertical-align: middle;
    4647}
    4748
    … …  
    6768}
    6869
     70td.input_topaligned {
     71  vertical-align: top;
     72  text-align: left;
     73  align: left; #
     74  white-space: nowrap;
     75  background-color: rgb(240, 240, 240);
     76}
     77
    6978img {
    70   vertical-align: bottom;
     79  vertical-align: middle;
    7180}
     81
     82.buttons{
     83  background: #E0E0E0;
     84  border-top: 1px solid #333333;
     85  border-left: 1px solid #333333;
     86  border-right: 1px solid #333333;
     87  border-bottom: 1px solid #333333;
     88  vertical-align: middle;
     89}
     90
     91
     92.buttons_inner {
     93  border-top: 1px solid #FFFFFF;
     94  border-left: 1px solid #FFFFFF;
     95  border-bottom: 1px solid #999999;
     96  border-right: 1px solid #999999;
     97  padding: 1px 5px 2px 5px;
     98  text-align: center;
     99  white-space: nowrap;
     100  vertical-align: middle;
     101}
     102
     103.buttons_hover {
     104  background: #F0F0F0;
     105  border-top: 1px solid #333333;
     106  border-left: 1px solid #333333;
     107  border-right: 1px solid #333333;
     108  border-bottom: 1px solid #333333;
     109  cursor: pointer;
     110  vertical-align: middle;
     111}
     112
     113.form tr {
     114  vertical-align: middle;
     115}
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