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
Added
Removed
  • 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
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