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
File:
1 edited

Legend:

Unmodified
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  • 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);
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     15      //this is the ID of the plus/minus button image
     16      var myButton = document.getElementById(myButton);
     17
     18        if (myItem.style.display != "none")
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     24        else
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     31
     32    //function to swap an image based on its current state
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     39
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     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>
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