Ignore:
Timestamp:
Dec 3, 2007, 5:14:11 PM (14 years ago)
Author:
mbayer
Message:
  • have tidied up the interface to the point where it is usable as it is
  • have provided defaults for every field in every form for testing
Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
3 added
8 edited
1 moved

Legend:

Unmodified
Added
Removed
  • branches/uk_ac_ebi_Tab2MageImporter/build.xml

    r486 r511  
    6262
    6363  <target name="copyJSPs">
    64     <copy todir="C:\tomcat\apache-tomcat-6.0.13\webapps\base\plugins\" verbose="true">
     64    <copy todir="${tomcat.home}\webapps\base\plugins\" verbose="true">
    6565      <fileset dir="${jspDir}" />
    6666    </copy>
  • branches/uk_ac_ebi_Tab2MageImporter/html/experiment.html

    r510 r511  
    1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
    21<html>
     2
    33<head>
    4 <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
    5 <title>Insert title here</title>
     4<title>Tab2MAGE Importer -- Experiment</title>
     5<link rel="stylesheet" type="text/css" href="styles.css" />
     6
     7<script type="text/javascript">
     8
     9    //function to display or hide a given element
     10    function showHideItems(myItem, myButton)
     11    {
     12       //this is the ID of the hidden item
     13      var myItem = document.getElementById(myItem);
     14
     15      //this is the ID of the plus/minus button image
     16      var myButton = document.getElementById(myButton);
     17
     18        if (myItem.style.display != "none")
     19        {
     20            //items are currently displayed, so hide them
     21            myItem.style.display = "none";
     22            swapImage(myButton,"plus");
     23        }
     24        else
     25        {
     26            //items are currently hidden, so display them
     27            myItem.style.display = "block";
     28            swapImage(myButton,"minus");
     29        }
     30    }
     31
     32    //function to swap an image based on its current state
     33    function swapImage(myImage, state)
     34    {
     35        if (state == "minus")
     36        {
     37            myImage.src = "hide.gif";
     38        }
     39
     40        else
     41        {
     42            myImage.src = "show.gif";
     43      }
     44    }
     45
     46</script>
     47
    648</head>
     49
    750<body>
     51
     52<h2>Tab2MAGE Importer -- Your Experiment</h2>
     53Page 1 of 3
     54<p>
     55
     56Please configure your experiment for upload by answering the questions on this and the following two pages.
     57<br>
     58The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
     59into this.
     60<p>
     61
     62<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
     63<input type="hidden" name="ID" value="<%=ID%>">
     64
     65<table cellpadding="10">
     66
     67  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     68  <tr>
     69    <td class="boldText">Domain:</td>
     70    <td class="input"><input type="text" size="45" name="domain" value="" /></td>
     71    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
     72    any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
     73  </tr>
     74  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     75  <tr>
     76    <td class="boldText">Accession:</td>
     77    <td class="input"><input type="text" size="45" name="accession" value="" /></td>
     78    <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
     79    experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
     80  </tr>
     81  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     82  <tr>
     83    <td  class="boldText">Quality Control:</td>
     84    <td class="input">
     85
     86    <table class="noBorder" cellpadding="1">
     87
     88      <tr class="noBorder">
     89        <td>biological replicate</td>
     90        <td><input type="checkbox" name="biological replicate" value="biological replicate" /></td>
     91      </tr>
     92
     93      <tr class="noBorder">
     94        <td>dye swap quality control</td>
     95        <td><input type="checkbox" name="dye swap quality control" value="dye swap quality control" /></td>
     96      </tr>
     97
     98      <tr class="noBorder">
     99        <td>peer review quality control</td>
     100        <td><input type="checkbox" name="peer review quality control" value="peer review quality control" /></td>
     101      </tr>
     102
     103      <tr class="noBorder">
     104        <td>real time PCR quality control</td>
     105        <td><input type="checkbox" name="real time PCR quality control" value="real time PCR quality control" /></td>
     106      </tr>
     107
     108      <tr class="noBorder">
     109        <td>reverse transcription PCR quality control</td>
     110        <td><input type="checkbox" name="reverse transcription PCR quality control"
     111          value="reverse transcription PCR quality control" /></td>
     112      </tr>
     113
     114      <tr class="noBorder">
     115        <td>spike quality control</td>
     116        <td><input type="checkbox" name="spike quality control" value="spike quality control" /></td>
     117      </tr>
     118
     119      <tr class="noBorder">
     120        <td>technical replicate</td>
     121        <td><input type="checkbox" name="technical replicate" value="technical replicate" /></td>
     122      </tr>
     123
     124    </table>
     125
     126  </td>
     127  <td>A list of terms taken from the MGED ontology. Multiple values can be selected.</td>
     128  </tr>
     129  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     130  <tr>
     131    <td class="boldText">Experiment Design Type:</td>
     132    <td class="input">
     133
     134    <table class="noBorder" cellpadding="3>
     135
     136      <tr class="noBorder">
     137        <td valign="top">Biological Property<br/>
     138        </td>
     139        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
     140          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
     141          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
     142        <div id="BiologicalProperty" style="display:none"><select multiple="multiple">
     143          <option>cell_component_comparison_design</option>
     144          <option>cell_cycle_design</option>
     145          <option>cell_type_comparison_design</option>
     146          <option>cellular_process_design</option>
     147          <option>development_or_differentiation_design</option>
     148          <option>imprinting_design</option>
     149          <option>individual_genetic_characteristics_design</option>
     150          <option>innate_behavior_design</option>
     151          <option>is_expressed_design</option>
     152          <option>organism_part_comparison_design</option>
     153          <option>organism_status_design</option>
     154          <option>physiological_process_design</option>
     155          <option>sex_design</option>
     156          <option>species_design</option>
     157          <option>strain_or_line_design</option>
     158          <option>unknown_experiment_design_type</option>
     159        </select></div>
     160        </td>
     161      </tr>
     162
     163      <tr class="noBorder">
     164        <td>BioMolecular Annotation</td>
     165        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
     166          title="Show/hide items"> <img src="show.gif" border="0" id="buttonBioMolecularAnnotation"
     167          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
     168        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple">
     169          <option>RNA_stability_design</option>
     170          <option>binding_site_identification_design</option>
     171          <option>co-expression_design</option>
     172          <option>comparative_genome_hybridization_design</option>
     173          <option>genotyping_design</option>
     174          <option>operon_identification_design</option>
     175          <option>secreted_protein_identification_design</option>
     176          <option>tiling_path_design</option>
     177          <option>transcript_identification_design</option>
     178          <option>translational_bias_design</option>
     179          <option>unknown_experiment_design_type</option>
     180        </select></div>
     181        </td>
     182      </tr>
     183
     184      <tr class="noBorder">
     185        <td>Epidemiological Design</td>
     186        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
     187        <img src="show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
     188        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple">
     189          <option>clinical_history_design</option>
     190          <option>disease_state_design</option>
     191          <option>family_history_design</option>
     192          <option>unknown_experiment_design_type</option>
     193          </option>
     194        </select></div>
     195        </td>
     196      </tr>
     197
     198      <tr class="noBorder">
     199        <td>Methodological Design</td>
     200        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
     201        <img src="show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
     202        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple">
     203          <option>all_pairs</option>
     204          <option>array_platform_variation_design</option>
     205          <option>dye_swap_design</option>
     206          <option>ex_vivo_design</option>
     207          <option>hardware_variation_design</option>
     208          <option>in_vitro_design</option>
     209          <option>in_vivo_design</option>
     210          <option>loop_design</option>
     211          <option>normalization_testing_design</option>
     212          <option>operator_variation_design</option>
     213          <option>optimization_design</option>
     214          <option>quality_control_testing_design</option>
     215          <option>reference_design</option>
     216          <option>replicate_design</option>
     217          <option>self_vs_self_design</option>
     218          <option>software_variation_design</option>
     219          <option>time_series_design</option>
     220          <option>unknown_experiment_design_type</option>
     221          </option>
     222        </select></div>
     223        </td>
     224      </tr>
     225
     226      <tr class="noBorder">
     227        <td>Perturbational Design</td>
     228        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
     229        <img src="show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
     230        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple">
     231          <option>cellular_modification_design</option>
     232          <option>compound_treatment_design</option>
     233          <option>disease_state_design</option>
     234          <option>dose_response_design</option>
     235          <option>genetic_modification_design</option>
     236          <option>growth_condition_design</option>
     237          <option>injury_design</option>
     238          <option>non-targeted_transgenic_variation_design</option>
     239          <option>pathogenicity_design</option>
     240          <option>stimulated_design_type</option>
     241          <option>stimulus_or_stress_design</option>
     242          <option>unknown_experiment_design_type</option>
     243        </select></div>
     244        </td>
     245      </tr>
     246
     247      <tr class="noBorder">
     248        <td>Technological Design</td>
     249        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
     250        <img src="show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
     251        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple">
     252          <option>binding_site_identification_design</option>
     253          <option>cellular_modification_design</option>
     254          <option>comparative_genome_hybridization_design</option>
     255          <option>transcript_identification_design</option>
     256          </option>
     257        </select></div>
     258        </td>
     259      </tr>
     260
     261    </table>
     262
     263
     264    </td>
     265    <td>A list of terms taken from the MGED ontology. Multiple values can be selected.
     266    <p>Click "expand" for an item to see list boxes with specific choices.<br>
     267    Hold down the 'Ctrl' key and click to select multiple options.
     268    </td>
     269  </tr>
     270  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     271  <tr>
     272    <td class="boldText">Experiment Name:</td>
     273    <td class="input"> 
     274    <textarea rows="2" cols="30" name="experimentName">my first experiment</textarea>
     275    </td>
     276    <td>The name you have chosen for the Experiment.</td>
     277  </tr>
     278  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     279  <tr>
     280    <td class="boldText">Experiment Description:</td>
     281    <td class="input">
     282    <textarea rows="2" cols="30" name="description">description</textarea>
     283    </td>
     284    <td>A short paragraph describing the purpose of the experiment.</td>
     285  </tr>
     286  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     287  <tr>
     288    <td class="boldText">Release Date:</td>
     289    <td class="input"><input type="text" size="10" name="" value="2007-12-03" /></td>
     290    <td>Date for public release, in the format YYYY-MM-DD.</td>
     291  </tr>
     292  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     293  <tr>
     294    <td class="boldText">Submission Date:</td>
     295    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
     296    <td>Date of submission, in the format YYYY-MM-DD.</td>
     297  </tr>
     298  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     299  <tr>
     300    <td class="boldText">Submitter:</td>
     301    <td class="input"><input type="text" size="45" name="submitter" value="Micha Bayer" /></td>
     302    <td>The name of the person responsible for submitting the experiment to the database.</td>
     303  </tr>
     304  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     305  <tr>
     306    <td class="boldText">Organization:</td>
     307    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
     308    <td>The organization to which the submitter is affiliated.</td>
     309  </tr>
     310  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     311
     312  <tr class="noBorder">
     313    <td class="boldText">Publication Details:</td>
     314    <td  class="input"></td>
     315    <td></td>
     316  </tr>
     317
     318  <tr class="noBorder">
     319    <td>Title:</td>
     320    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">publicationTitle</textarea></td>
     321
     322    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
     323    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
     324  </tr>
     325  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     326      <tr class="noBorder">
     327        <td>Authors:</td>
     328        <td class="input"><textarea rows="2" cols="30" name="authors">authors</textarea></td>
     329        <td></td>
     330      </tr>
     331      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     332      <tr class="noBorder">
     333        <td>Journal:</td>
     334        <td class="input"><textarea rows="2" cols="30" name="journal">journal</textarea></td>
     335        <td></td>
     336      </tr>
     337      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     338      <tr class="noBorder">
     339        <td>Volume:</td>
     340        <td class="input"><input type="text" size="10" name="volume" value="" /></td>
     341        <td></td>
     342      </tr>
     343      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     344      <tr class="noBorder">
     345        <td>Issue:</td>
     346        <td class="input"><input type="text" size="10" name="issue" value="" /></td>
     347        <td></td>
     348      </tr>
     349      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     350      <tr class="noBorder">
     351        <td>Pages:</td>
     352        <td class="input"><input type="text" size="10" name="pages" value="" /></td>
     353        <td></td>
     354      </tr>
     355      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     356      <tr class="noBorder">
     357        <td>Year:</td>
     358        <td class="input"><input type="text" size="10" name="year" value="" /></td>
     359        <td></td>
     360      </tr>
     361      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     362      <tr class="noBorder">
     363        <td>Pubmed ID:</td>
     364        <td class="input"><input type="text" size="30" name="pubmedId" value="" /></td>
     365        <td></td>
     366
     367  </tr>
     368
     369  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     370</table>
     371
     372<p>
     373
     374<table class="noBorder" width="100%">
     375<tr class="noBorder" ><td class="centered">
     376<input type="submit"  value="Continue"/>
     377</td>
     378</tr>
     379</table>
     380
     381</form>
    8382
    9383</body>
  • branches/uk_ac_ebi_Tab2MageImporter/html/hybridizations.html

    r510 r511  
    33<head>
    44<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
    5 <title>Tab2MAGE Importer -- Experiment Configuration</title>
     5<title>Tab2MAGE Importer -- Hybridizations</title>
    66
    7 <style type="text/css">   
    8 table   {border-color: #6E94B7;border-style: solid; border-width: 1px;border-collapse: collapse}
    9 tr {border-color: #6E94B7;border-style: solid;border-width: 1px}
    10 </style>
     7<link rel="stylesheet" type="text/css" href="styles.css" />
    118
    129</head>
    1310<body>
    1411
    15 <h2>Tab2MAGE Importer -- Experiment Configuration</h2>
     12<h2>Tab2MAGE Importer -- Your Hybridizations</h2>
     13Page 3 of 3
     14<p>
    1615
    17 Please configure your experiment for upload by answering the questions below.
    18 <br>
    19 The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
    20 into this.
    21 <p>
    2216<form>
     17
    2318<table cellpadding="15">
    24 
    25 
    26   <tr>
    27   <td>Please select the zip file on your local disk that contains the data files for import:</td>
    28     <td><INPUT type="file" name="parameter:zipFile" size="50"></td>
    29   </tr>
    30 
    3119
    3220  <!-- question 1 -->
    3321  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
    34     <td>Please select the microarray platform used in the experiment:</td>
    35     <td>
     22    <td class="boldText">Microarray platform used:</td>
     23    <td class="input">
    3624    <select name="parameter:platform">
    3725    </select>
     
    4129  <!-- question 2 -->
    4230  <tr>
    43     <td>Please enter the name of the experimental organism:</td>
    44     <td><input type="text" size="50" name="parameter:organism"/></td>
     31    <td class="boldText">Name of the experimental organism:</td>
     32    <td class="input"><input type="text" size="60" name="parameter:organism"/></td>
    4533  </tr>
    4634
    4735  <!-- question 3 -->
    4836  <tr>
    49     <td>How many different arrays designs were used ?</td>
    50     <td><input type="text" size="3" name="parameter:numDesigns"/></td>
     37    <td class="boldText">Number of different arrays designs used:</td>
     38    <td class="input"><input type="text" size="3" name="parameter:numDesigns"/></td>
    5139  </tr>
    5240
    5341  <!-- question 4 -->
    5442  <tr>
    55     <td>Was dye-swap used?</td>
    56     <td>yes <input type="radio" name="parameter:dyeswap" value="yes"> no <input type="radio" name="parameter:dyeswap" value="no">
     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">
    5745    <br>
    5846    </td>
     
    6149  <!-- question 5 -->
    6250  <tr>
    63     <td>Was a reference sample used?</td>
    64     <td>yes <input type="radio" name="parameter:refSample" value="yes"> no <input type="radio" name="parameter:refSample"
     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"
    6553      value="no"></td>
    6654  </tr>
     
    6856  <!-- question 6 -->
    6957  <tr>
    70     <td>How many study groups (= treatment groups) were defined in the experiment?</td>
    71     <td><input type="text" size="3" name="parameter:numTreatments"/></td>
     58    <td class="boldText">Number of treatments used:</td>
     59    <td class="input"><input type="text" size="3" name="parameter:numTreatments"/></td>
    7260  </tr>
    7361
    7462  <!-- question 7 -->
    7563  <tr>
    76     <td>What were the study factors (= independent variables /experimental factors) ?
    77     <p>List Study Factors and Value ranges using the following format (one per line):<br>
    78     Factor 1(value1,value2,...valueN)<br>
    79     Factor 2(value1,value2,...valueN)
    80     <p>Example: <br>Compound(aspirin,ibuprofen,acetaminophen)
    81                   <br>Dose(control,low,medium,high)
     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>
    8269    </td>
    83     <td><textarea rows="8" cols="40" name="parameter:expFactors"></textarea></td>
     70    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors"></textarea></td>
    8471  </tr>
    8572
    8673  <!-- question 8 -->
    8774  <tr>
    88     <td>How many subjects per study group (i.e. number of biological replicates)?</td>
    89     <td><input type="text" size="3" name="parameter:numReplicates"/></td>
     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>
    9077  </tr>
    9178  <!-- question 9 -->
    9279  <tr>
    93     <td>List all target tissues (as a comma separated list).<br>
     80    <td class="boldText">List all target tissues (as a comma separated list).<br>
    9481    Example: liver,heart,adipose tissue
    9582    </td>
    96     <td><textarea rows="8" cols="40" name="parameter:tissues"></textarea></td>
     83    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues"></textarea></td>
    9784  </tr>
    9885  <!-- question 10 -->
    9986  <tr>
    100     <td>Were samples pooled?</td>
    101     <td>yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio" name="parameter:pooling" value="no">
     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">
    10289    </td>
    10390  </tr>
    104 
     91 
     92 
     93  <!-- file upload -->
    10594  <tr>
    106     <td colspan="2" align="center">
    107     <p><input type="submit" value="Continue" name="continue"/> &nbsp; &nbsp; &nbsp;
    108     </p>
    109 
    110     <input type="submit" value="Cancel" name="cancel" />
    111     </form>
    112     </td>
     95  <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
     96    <td class="input"><INPUT type="file" name="parameter:zipFile" size="50"></td>
    11397  </tr>
    11498
     99</table>
    115100
     101<p>
     102<table class="noBorder" width="100%">
     103<tr class="noBorder" ><td class="centered">
     104<input type="submit"  value="Run Import"/>
     105</td>
     106</tr>
    116107</table>
    117108
  • branches/uk_ac_ebi_Tab2MageImporter/html/protocols.html

    r510 r511  
    33<head>
    44<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
    5 <title>Insert title here</title>
     5<title>Tab2MAGE Importer -- Protocols</title>
     6
     7<link rel="stylesheet" type="text/css" href="styles.css" />
     8
    69</head>
    710<body>
    811
     12<h2>Tab2MAGE Importer -- Your Protocols</h2>
     13Page 2 of 3
     14<p>
     15<table cellpadding="10">
     16
     17  <tr>
     18    <td class="header">
     19    <h3>Protocol name</h3>
     20    </td>
     21    <td class="header">
     22    <h3>Protocol Text</h3>
     23    <p>The full text of the protocol.
     24    </td>
     25    <td class="header">
     26    <h3>Parameters</h3>
     27    <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'. <br />
     28    Each parameter name should be unique within this form.<br />
     29    Leave blank if the protocol is unparameterized.
     30    </p>
     31    </td>
     32  </tr>
     33
     34  <tr>
     35    <td  class="boldText">Treatment</td>
     36    <td class="input"><textarea rows="8" cols="35" id="" name=""> </textarea></td>
     37    <td><textarea rows="4" cols="35" id="" name=""> </textarea></td>
     38  </tr>
     39 
     40  <tr>
     41    <td  class="boldText">Extraction</td>
     42    <td class="input"><textarea rows="8" cols="35" id="" name=""> </textarea></td>
     43    <td><textarea rows="4" cols="35" id="" name=""> </textarea></td>
     44  </tr>
     45 
     46  <tr>
     47    <td  class="boldText">Labeling</td>
     48    <td class="input"><textarea rows="8" cols="35" id="" name=""> </textarea></td>
     49    <td><textarea rows="4" cols="35" id="" name=""> </textarea></td>
     50  </tr>
     51 
     52  <tr>
     53    <td  class="boldText">Hybridization</td>
     54    <td class="input"><textarea rows="8" cols="35" id="" name=""> </textarea></td>
     55    <td><textarea rows="4" cols="35" id="" name=""> </textarea></td>
     56  </tr>
     57 
     58  <tr>
     59    <td  class="boldText">Scanning</td>
     60    <td class="input"><textarea rows="8" cols="35" id="" name=""> </textarea></td>
     61    <td><textarea rows="4" cols="35" id="" name=""> </textarea></td>
     62  </tr>
     63
     64</table>
     65
     66<p>
     67
     68<table class="noBorder" width="100%">
     69<tr class="noBorder" ><td class="centered">
     70<input type="submit"  value="Continue"/>
     71</td>
     72</tr>
     73</table>
     74
    975</body>
    1076</html>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp

    r497 r511  
    1010
    1111<html>
     12
    1213<head>
     14
     15<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
     16
     17<script type="text/javascript">
     18
     19    //function to display or hide a given element
     20    function showHideItems(myItem, myButton)
     21    {
     22       //this is the ID of the hidden item
     23      var myItem = document.getElementById(myItem);
     24
     25      //this is the ID of the plus/minus button image
     26      var myButton = document.getElementById(myButton);
     27
     28        if (myItem.style.display != "none")
     29        {
     30            //items are currently displayed, so hide them
     31            myItem.style.display = "none";
     32            swapImage(myButton,"plus");
     33        }
     34        else
     35        {
     36            //items are currently hidden, so display them
     37            myItem.style.display = "block";
     38            swapImage(myButton,"minus");
     39        }
     40    }
     41
     42    //function to swap an image based on its current state
     43    function swapImage(myImage, state)
     44    {
     45        if (state == "minus")
     46        {
     47            myImage.src = "<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hide.gif";
     48        }
     49
     50        else
     51        {
     52            myImage.src = "<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif";
     53      }
     54    }
     55
     56</script>
     57
    1358</head>
     59
    1460<body>
    1561
     
    2066 %>
    2167
    22 <h2>Tab2MAGE Importer -- Experiment Configuration</h2>
    23 
    24 <form action="../../plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
     68<h2>Tab2MAGE Importer -- Your Experiment</h2>
     69Page 1 of 3
     70<p>
     71
     72Please configure your experiment for upload by answering the questions on this and the following two pages.
     73<br>
     74The answers you provide will be used to automatically create a new experiment in BASE and your raw data will be imported
     75into this.
     76<p>
     77
     78<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/protocols.jsp" method="post">
    2579<input type="hidden" name="ID" value="<%=ID%>">
    2680
    27 Please enter the name of your experiment:<br>
    28 <input type="text" size="30" name="experimentName" value="my first Experiment" />
    29 
    30 <input type="submit" value="Continue" />
     81<table cellpadding="10">
     82
     83  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     84  <tr>
     85    <td class="boldText">Domain:</td>
     86    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
     87    <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
     88    any suitable string, such as the originating internet domain name (e.g., "ebi.ac.uk").</td>
     89  </tr>
     90 
     91  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     92  <tr>
     93    <td class="boldText">Accession:</td>
     94    <td class="input"><input type="text" size="45" name="accession" value="E-SCRI-001" /></td>
     95    <td >The experiment accession number is a unique identifier assigned to each experiment. Accession numbers for
     96    experiments submitted to ArrayExpress have the format E-XXXX-n.</td>
     97  </tr>
     98 
     99  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     100  <tr>
     101    <td  class="boldText">Quality Control:</td>
     102    <td class="input">
     103
     104    <table class="noBorder" cellpadding="1">
     105
     106      <tr class="noBorder">
     107        <td>biological replicate</td>
     108        <td><input type="checkbox" name="biological replicate" value="biological replicate" checked="checked"/></td>
     109      </tr>
     110
     111      <tr class="noBorder">
     112        <td>dye swap quality control</td>
     113        <td><input type="checkbox" name="dye swap quality control" value="dye swap quality control" /></td>
     114      </tr>
     115
     116      <tr class="noBorder">
     117        <td>peer review quality control</td>
     118        <td><input type="checkbox" name="peer review quality control" value="peer review quality control" /></td>
     119      </tr>
     120
     121      <tr class="noBorder">
     122        <td>real time PCR quality control</td>
     123        <td><input type="checkbox" name="real time PCR quality control" value="real time PCR quality control" /></td>
     124      </tr>
     125
     126      <tr class="noBorder">
     127        <td>reverse transcription PCR quality control</td>
     128        <td><input type="checkbox" name="reverse transcription PCR quality control"
     129          value="reverse transcription PCR quality control" /></td>
     130      </tr>
     131
     132      <tr class="noBorder">
     133        <td>spike quality control</td>
     134        <td><input type="checkbox" name="spike quality control" value="spike quality control" /></td>
     135      </tr>
     136
     137      <tr class="noBorder">
     138        <td>technical replicate</td>
     139        <td><input type="checkbox" name="technical replicate" value="technical replicate" /></td>
     140      </tr>
     141
     142    </table>
     143
     144  </td>
     145  <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>. Multiple values can be selected.</td>
     146  </tr>
     147 
     148  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     149  <tr>
     150    <td class="boldText">Experiment Design Type:</td>
     151    <td class="input">
     152
     153    <table class="noBorder" cellpadding="3" >
     154
     155      <tr class="noBorder">
     156        <td valign="top">Biological Property<br/>
     157        </td>
     158        <td colspan="2"><a onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
     159          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
     160          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
     161        <div id="BiologicalProperty" style="display:none"><select multiple="multiple">
     162          <option selected="selected">cell_component_comparison_design</option>
     163          <option>cell_cycle_design</option>
     164          <option>cell_type_comparison_design</option>
     165          <option>cellular_process_design</option>
     166          <option>development_or_differentiation_design</option>
     167          <option>imprinting_design</option>
     168          <option>individual_genetic_characteristics_design</option>
     169          <option>innate_behavior_design</option>
     170          <option>is_expressed_design</option>
     171          <option>organism_part_comparison_design</option>
     172          <option>organism_status_design</option>
     173          <option>physiological_process_design</option>
     174          <option>sex_design</option>
     175          <option>species_design</option>
     176          <option>strain_or_line_design</option>
     177          <option>unknown_experiment_design_type</option>
     178        </select></div>
     179        </td>
     180      </tr>
     181
     182      <tr class="noBorder">
     183        <td>BioMolecular Annotation</td>
     184        <td><a onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
     185          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
     186          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
     187        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple">
     188          <option selected="selected">RNA_stability_design</option>
     189          <option>binding_site_identification_design</option>
     190          <option>co-expression_design</option>
     191          <option>comparative_genome_hybridization_design</option>
     192          <option>genotyping_design</option>
     193          <option>operon_identification_design</option>
     194          <option>secreted_protein_identification_design</option>
     195          <option>tiling_path_design</option>
     196          <option>transcript_identification_design</option>
     197          <option>translational_bias_design</option>
     198          <option>unknown_experiment_design_type</option>
     199        </select></div>
     200        </td>
     201      </tr>
     202
     203      <tr class="noBorder">
     204        <td>Epidemiological Design</td>
     205        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
     206        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonEpidemiologicalDesign" name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
     207        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple">
     208          <option>clinical_history_design</option>
     209          <option>disease_state_design</option>
     210          <option selected="selected">family_history_design</option>
     211          <option>unknown_experiment_design_type</option>
     212        </select></div>
     213        </td>
     214      </tr>
     215
     216      <tr class="noBorder">
     217        <td>Methodological Design</td>
     218        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
     219        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonMethodologicalDesign" name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
     220        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple">
     221          <option>all_pairs</option>
     222          <option>array_platform_variation_design</option>
     223          <option>dye_swap_design</option>
     224          <option>ex_vivo_design</option>
     225          <option>hardware_variation_design</option>
     226          <option>in_vitro_design</option>
     227          <option>in_vivo_design</option>
     228          <option>loop_design</option>
     229          <option>normalization_testing_design</option>
     230          <option>operator_variation_design</option>
     231          <option>optimization_design</option>
     232          <option>quality_control_testing_design</option>
     233          <option>reference_design</option>
     234          <option>replicate_design</option>
     235          <option>self_vs_self_design</option>
     236          <option>software_variation_design</option>
     237          <option>time_series_design</option>
     238          <option>unknown_experiment_design_type</option>
     239        </select></div>
     240        </td>
     241      </tr>
     242
     243      <tr class="noBorder">
     244        <td>Perturbational Design</td>
     245        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
     246        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonPerturbationalDesign" name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
     247        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple">
     248          <option>cellular_modification_design</option>
     249          <option>compound_treatment_design</option>
     250          <option>disease_state_design</option>
     251          <option>dose_response_design</option>
     252          <option>genetic_modification_design</option>
     253          <option>growth_condition_design</option>
     254          <option>injury_design</option>
     255          <option>non-targeted_transgenic_variation_design</option>
     256          <option>pathogenicity_design</option>
     257          <option>stimulated_design_type</option>
     258          <option>stimulus_or_stress_design</option>
     259          <option>unknown_experiment_design_type</option>
     260        </select></div>
     261        </td>
     262      </tr>
     263
     264      <tr class="noBorder">
     265        <td>Technological Design</td>
     266        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
     267        <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonTechnologicalDesign" name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
     268        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple">
     269          <option>binding_site_identification_design</option>
     270          <option>cellular_modification_design</option>
     271          <option>comparative_genome_hybridization_design</option>
     272          <option>transcript_identification_design</option>
     273        </select></div>
     274        </td>
     275      </tr>
     276
     277    </table>
     278
     279
     280    </td>
     281    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED ontology</a>.
     282     Multiple values can be selected.
     283    <p>Click "expand" for an item to see list boxes with specific choices.<br>
     284    Hold down the 'Ctrl' key and click to select multiple options.
     285    </td>
     286  </tr>
     287 
     288  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     289  <tr>
     290    <td class="boldText">Experiment Name:</td>
     291    <td class="input"> 
     292    <textarea rows="2" cols="30" name="experimentName">my numpty experiment</textarea>
     293    </td>
     294    <td>The name you have chosen for the Experiment.</td>
     295  </tr>
     296 
     297  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     298  <tr>
     299    <td class="boldText">Experiment Description:</td>
     300    <td class="input">
     301    <textarea rows="2" cols="30" name="description">description goes here</textarea>
     302    </td>
     303    <td>A short paragraph describing the purpose of the experiment.</td>
     304  </tr>
     305 
     306  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     307  <tr>
     308    <td class="boldText">Release Date:</td>
     309    <td class="input"><input type="text" size="10" name="" value="2007-12-03" /></td>
     310    <td>Date for public release, in the format YYYY-MM-DD.</td>
     311  </tr>
     312  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     313  <tr>
     314    <td class="boldText">Submission Date:</td>
     315    <td class="input"><input type="text" size="10" name="submissionDate" value="2007-12-03" /></td>
     316    <td>Date of submission, in the format YYYY-MM-DD.</td>
     317  </tr>
     318  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     319  <tr>
     320    <td class="boldText">Submitter:</td>
     321    <td class="input"><input type="text" size="45" name="submitter" value="Joe Bloggs" /></td>
     322    <td>The name of the person responsible for submitting the experiment to the database.</td>
     323  </tr>
     324  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     325  <tr>
     326    <td class="boldText">Organization:</td>
     327    <td class="input"><input type="text" size="45" name="organization" value="SCRI" /></td>
     328    <td>The organization to which the submitter is affiliated.</td>
     329  </tr>
     330  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     331
     332  <tr class="noBorder">
     333    <td class="boldText">Publication Details:</td>
     334    <td  class="input"></td>
     335    <td></td>
     336  </tr>
     337
     338  <tr class="noBorder">
     339    <td>Title:</td>
     340    <td class="input"><textarea rows="2" cols="30" name="publicationTitle">My Ropey Paper</textarea></td>
     341
     342    <td rowspan="4">Publication details for any manuscript associated with the experiment. The journal field should
     343    contain a standard Pubmed journal abbreviated name. The authors list is a semicolon-delimited list of names.</td>
     344  </tr>
     345  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     346      <tr class="noBorder">
     347        <td>Authors:</td>
     348        <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
     349        <td></td>
     350      </tr>
     351      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     352      <tr class="noBorder">
     353        <td>Journal:</td>
     354        <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Unreproducible Results</textarea></td>
     355        <td></td>
     356      </tr>
     357      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     358      <tr class="noBorder">
     359        <td>Volume:</td>
     360        <td class="input"><input type="text" size="10" name="volume" value="5" /></td>
     361        <td></td>
     362      </tr>
     363      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     364      <tr class="noBorder">
     365        <td>Issue:</td>
     366        <td class="input"><input type="text" size="10" name="issue" value="2" /></td>
     367        <td></td>
     368      </tr>
     369      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     370      <tr class="noBorder">
     371        <td>Pages:</td>
     372        <td class="input"><input type="text" size="10" name="pages" value="1234-1235" /></td>
     373        <td></td>
     374      </tr>
     375      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     376      <tr class="noBorder">
     377        <td>Year:</td>
     378        <td class="input"><input type="text" size="10" name="year" value="2007" /></td>
     379        <td></td>
     380      </tr>
     381      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     382      <tr class="noBorder">
     383        <td>Pubmed ID:</td>
     384        <td class="input"><input type="text" size="30" name="pubmedId" value="11009762" /></td>
     385        <td></td>
     386
     387  </tr>
     388
     389  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     390</table>
     391
     392<p>
     393
     394<table class="noBorder" width="100%">
     395<tr class="noBorder" ><td class="centered">
     396<input type="submit"  value="Continue"/>
     397</td>
     398</tr>
     399</table>
     400
     401
     402
    31403</form>
    32404
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

    r497 r511  
    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="session" />
    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 -->
    8 <jsp:setProperty name="inputDataBean" property="*"/>
     8<jsp:setProperty name="inputDataBean" property="*" />
    99
    1010
    1111<html>
    1212<head>
     13<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
    1314</head>
    1415<body>
     16
    1517
    1618<%
     
    2022 %>
    2123
    22 <h2>Tab2MAGE Importer -- Hybridizations Configuration</h2>
    23 
    24 <form action="../../../../../../common/plugin/index.jsp" method="post">
    25 <input type="hidden" name="ID" value="<%=ID%>">
    26 <input type="hidden" name="cmd" value="SetParameters">
    27 <input type="hidden" name="requestID" value="<%=requestID%>">
    28 <input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>">
    29 <input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>">
     24<h2>Tab2MAGE Importer -- Your Hybridizations</h2>
     25Page 3 of 3
     26<p>
     27<form action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
     28<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters">
     29  <input type="hidden"name="requestID" value="<%=requestID%>">
     30  <input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>">
     31  <input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>">
    3032
    3133<table cellpadding="15">
     34
    3235  <!-- question 1 -->
    3336  <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
    34     <td>Please select the microarray platform used in the experiment:</td>
    35     <td><select name="parameter:platform">
    36       <option>Affymetrix</option>
    37       <option selected="selected">Genepix</option>
     37    <td class="boldText">Microarray platform used:</td>
     38    <td class="input"><select name="parameter:platform">
     39    <option >Genepix</option>
     40    <option >Affymetrix</option>
    3841    </select></td>
    3942  </tr>
     43
     44  <!-- question 2 -->
     45  <tr>
     46    <td class="boldText">Name of the experimental organism:</td>
     47    <td class="input"><input type="text" size="60" name="parameter:organism" value="barley"/></td>
     48  </tr>
     49
     50  <!-- question 3 -->
     51  <tr>
     52    <td class="boldText">Number of different arrays designs used:</td>
     53    <td class="input"><input type="text" size="3" name="parameter:numDesigns" value="1"/></td>
     54  </tr>
     55
     56  <!-- question 4 -->
     57  <tr>
     58    <td class="boldText">Was dye-swap used?</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    </td>
     62  </tr>
     63
     64  <!-- question 5 -->
     65  <tr>
     66    <td class="boldText">Was a reference sample used?</td>
     67    <td class="input">yes <input type="radio" name="parameter:refSample" value="yes" > no <input type="radio"
     68      name="parameter:refSample" value="no" checked="checked"></td>
     69  </tr>
     70
     71  <!-- question 6 -->
     72  <tr>
     73    <td class="boldText">Number of treatments used:</td>
     74    <td class="input"><input type="text" size="3" name="parameter:numTreatments" value="2"/></td>
     75  </tr>
     76
     77  <!-- question 7 -->
     78  <tr>
     79    <td class="boldText">Please list your experimental factors and value ranges using the following format (one per
     80    line):<br>
     81    <i>Factor 1(value1,value2,...valueN)<br>
     82    Factor 2(value1,value2,...valueN)</i>
     83    <p>Example: <i><br>
     84    Compound(aspirin,ibuprofen,acetaminophen) <br>
     85    Dose(control,low,medium,high)</i>
     86    </td>
     87    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Factor 1(value1,value2,...valueN)<br>Factor 2(value1,value2,...valueN)</textarea></td>
     88  </tr>
     89
     90  <!-- question 8 -->
     91  <tr>
     92    <td class="boldText">Number of subjects per group (i.e. number of biological replicates):</td>
     93    <td class="input"><input type="text" size="3" name="parameter:numReplicates" value="3"/></td>
     94  </tr>
    4095 
    41   </table>
     96  <!-- question 9 -->
     97  <tr>
     98    <td class="boldText">List all target tissues (as a comma separated list).<br>
     99    Example: liver,heart,adipose tissue</td>
     100    <td class="input"><textarea rows="2" cols="40" name="parameter:tissues">tissues1,tissue2</textarea></td>
     101  </tr>
     102 
     103  <!-- question 10 -->
     104  <tr>
     105    <td class="boldText">Were samples pooled?</td>
     106    <td class="input">yes <input type="radio" name="parameter:pooling" value="yes"> no <input type="radio"
     107      name="parameter:pooling" value="no" checked="checked"></td>
     108  </tr>
    42109
    43 <input type="submit" value="Continue" />
     110
     111  <!-- file upload -->
     112  <tr>
     113    <td class="boldText">Please select the zip file on your local disk that contains the data files for import:</td>
     114    <td class="input"><INPUT type="file" name="parameter:zipFile" size="50" value="test.txt"></td>
     115  </tr>
     116
     117</table>
     118
     119<p>
     120<table class="noBorder" width="100%">
     121  <tr class="noBorder">
     122    <td class="centered"><input type="submit" value="Run Import" /></td>
     123  </tr>
     124</table>
     125
     126
    44127</form>
    45128
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r497 r511  
    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="session" />
    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 -->
    8 <jsp:setProperty name="inputDataBean" property="*"/>
     8<jsp:setProperty name="inputDataBean" property="*" />
    99
    1010
    1111<html>
    1212<head>
     13<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
    1314</head>
    1415<body>
     16
    1517
    1618<%
     
    2022 %>
    2123
    22 <h2>Tab2MAGE Importer -- Protocol Configuration</h2>
     24<form action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/hybridizations.jsp" method="post">
     25<input type="hidden" name="ID" value="<%=ID%>">
    2326
    24 <form action="hybridizations.jsp" method="post">
    25 <input type="hidden" name="ID" value="<%=ID%>">
     27<h2>Tab2MAGE Importer -- Your Protocols</h2>
     28Page 2 of 3
     29<p>
     30<table cellpadding="10">
    2631
    27 Please enter the details of your protocol:<br>
    28 <input type="text" size="30" name="treatmentProtocol" value="my treatment protocol" />
     32  <tr>
     33    <td class="header">
     34    <h3>Protocol name</h3>
     35    </td>
     36    <td class="header">
     37    <h3>Protocol Text</h3>
     38    <p>The full text of the protocol.
     39    </td>
     40    <td class="header">
     41    <h3>Parameters</h3>
     42    <p>A list of parameters for this protocol, separated by semicolons, in the format 'name(units)'. <br />
     43    Each parameter name should be unique within this form.<br />
     44    Leave blank if the protocol is unparameterized.</p>
     45    </td>
     46  </tr>
    2947
    30 <input type="submit" value="Continue" />
     48  <tr>
     49    <td class="boldText">Treatment</td>
     50    <td class="input"><textarea rows="8" cols="35" id="" name="">my treatment protocol text </textarea></td>
     51    <td><textarea rows="4" cols="25" id="" name="">param1</textarea></td>
     52  </tr>
     53
     54  <tr>
     55    <td class="boldText">Extraction</td>
     56    <td class="input"><textarea rows="8" cols="35" id="" name=""> my extraction protocol text  </textarea></td>
     57    <td><textarea rows="4" cols="25" id="" name="">param2</textarea></td>
     58  </tr>
     59
     60  <tr>
     61    <td class="boldText">Labeling</td>
     62    <td class="input"><textarea rows="8" cols="35" id="" name=""> my labeling protocol text  </textarea></td>
     63    <td><textarea rows="4" cols="25" id="" name="">param3</textarea></td>
     64  </tr>
     65
     66  <tr>
     67    <td class="boldText">Hybridization</td>
     68    <td class="input"><textarea rows="8" cols="35" id="" name="">my hybs protocol text   </textarea></td>
     69    <td><textarea rows="4" cols="25" id="" name="">param4</textarea></td>
     70  </tr>
     71
     72  <tr>
     73    <td class="boldText">Scanning</td>
     74    <td class="input"><textarea rows="8" cols="35" id="" name=""> my scanning protocol text </textarea></td>
     75    <td><textarea rows="4" cols="25" id="" name=""> param5</textarea></td>
     76  </tr>
     77
     78</table>
     79
     80<p>
     81<table class="noBorder" width="100%">
     82  <tr class="noBorder">
     83    <td class="centered"><input type="submit" value="Continue" /></td>
     84  </tr>
     85</table>
     86
     87
     88
    3189</form>
    3290
Note: See TracChangeset for help on using the changeset viewer.