Changeset 524


Ignore:
Timestamp:
Dec 20, 2007, 6:14:57 PM (14 years ago)
Author:
mbayer
Message:

have made more changes to the UI to satisfy IE requirements
also fixed a couple of minor bugs relating to the UI

Location:
branches/uk_ac_ebi_Tab2MageImporter
Files:
1 deleted
7 edited

Legend:

Unmodified
Added
Removed
  • branches/uk_ac_ebi_Tab2MageImporter/html/experiment.html

    r511 r524  
    33<head>
    44<title>Tab2MAGE Importer -- Experiment</title>
    5 <link rel="stylesheet" type="text/css" href="styles.css" />
     5<link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" />
    66
    77<script type="text/javascript">
     
    6363<input type="hidden" name="ID" value="<%=ID%>">
    6464
    65 <table cellpadding="10">
     65<table cellpadding="0" cellspacing="0">
    6666
    6767  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    68   <tr>
     68  <tr >
    6969    <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>
     70    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
     71    <td class="helpText">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>
    7373  </tr>
     74 
    7475  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    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>
     76  <tr >
     77    <td class="boldText">Array Acession:</td>
     78
    8479    <td class="input">
    8580
    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>
     81    <div id="accession" class="selectionlist required">
     82    <table class="noBorder"  cellspacing="0" cellpadding="5">
     83      <tr>
     84        <td style="border-style: none;"><select name="accession" onchange="arrayDesignOnChange()"></select></td>
     85        <td style="border-style: none;">
     86        <div class="buttonclass"
     87          onmouseover="this.className='buttonclass_hover';"
     88          onmouseout="this.className='buttonclass';"
     89          onclick="selectArrayDesignOnClick()">
     90        <div class="buttonclass_inner">Select&hellip;</div>
     91        </div>
    16092        </td>
    16193      </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 
    26194    </table>
    262 
    263 
     95    </div>
    26496    </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>
     97
     98    <td class="helpText">Please select an existing array design from BASE or create a
     99    new one. For ArrayExpress submissions, the array design name becomes
     100    the array accession identifier. Accession numbers for experiments
     101    submitted to ArrayExpress should have the format E-XXXX-n.</td>
     102
    269103  </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>
     104
     105
     106
    331107      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    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 
     108    <tr >
     109      <td class="boldText">Quality Control:</td>
     110      <td class="input"><select multiple name="qualityControl">
     111        <option selected="selected">biological replicate</option>
     112        <option>dye swap quality control</option>
     113        <option>peer review quality control</option>
     114        <option>real time PCR quality control</option>
     115        <option>reverse transcription PCR quality control</option>
     116        <option selected="selected">spike quality control</option>
     117        <option>technical replicate</option>
     118      </select></td>
     119      <td class="helpText">A list of terms taken from the <a
     120        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
     121        target="_blank">MGED ontology</a>. Multiple values can be selected
     122      by holding down the Ctrl key and clicking on items.</td>
     123    </tr>
     124
     125    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     126    <tr>
     127      <td class="boldText">Experiment Design Type:</td>
     128      <td class="input">
     129
     130      <table class="noBorder" cellpadding="3">
     131
     132        <tr>
     133          <td valign="top" style="border-style: none;">Biological Property<br />
     134          </td>
     135          <td colspan="2" style="border-style: none;"><a
     136            onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
     137            title="Show/hide items"> <img
     138            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     139            border="0" id="buttonBiologicalProperty"
     140            name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
     141          <div id="BiologicalProperty" style="display:none"><select
     142            multiple="multiple" name="biologicalProperty">
     143            <option selected="selected">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>
     164          <td style="border-style: none;">BioMolecular Annotation</td>
     165          <td style="border-style: none;"><a
     166            onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
     167            title="Show/hide items"> <img
     168            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     169            border="0" id="buttonBioMolecularAnnotation"
     170            name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
     171          <div id="BioMolecularAnnotation" style="display:none"><select
     172            multiple="multiple" name="bioMolecularAnnotation">
     173            <option selected="selected">RNA_stability_design</option>
     174            <option>binding_site_identification_design</option>
     175            <option>co-expression_design</option>
     176            <option>comparative_genome_hybridization_design</option>
     177            <option>genotyping_design</option>
     178            <option>operon_identification_design</option>
     179            <option>secreted_protein_identification_design</option>
     180            <option>tiling_path_design</option>
     181            <option>transcript_identification_design</option>
     182            <option>translational_bias_design</option>
     183            <option>unknown_experiment_design_type</option>
     184          </select></div>
     185          </td>
     186        </tr>
     187
     188        <tr>
     189          <td style="border-style: none;">Epidemiological Design</td>
     190          <td style="border-style: none;"><a
     191            onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');"
     192            title="Show/hide items"> <img
     193            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     194            border="0" id="buttonEpidemiologicalDesign"
     195            name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
     196          <div id="EpidemiologicalDesign" style="display:none"><select
     197            multiple="multiple" name="epidemiologicalDesign">
     198            <option>clinical_history_design</option>
     199            <option>disease_state_design</option>
     200            <option selected="selected">family_history_design</option>
     201            <option>unknown_experiment_design_type</option>
     202          </select></div>
     203          </td>
     204        </tr>
     205
     206        <tr>
     207          <td style="border-style: none;">Methodological Design</td>
     208          <td style="border-style: none;"><a
     209            onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');"
     210            title="Show/hide items"> <img
     211            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     212            border="0" id="buttonMethodologicalDesign"
     213            name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
     214          <div id="MethodologicalDesign" style="display:none"><select
     215            multiple="multiple" name="methodologicalDesign">
     216            <option>all_pairs</option>
     217            <option>array_platform_variation_design</option>
     218            <option>dye_swap_design</option>
     219            <option>ex_vivo_design</option>
     220            <option>hardware_variation_design</option>
     221            <option>in_vitro_design</option>
     222            <option>in_vivo_design</option>
     223            <option>loop_design</option>
     224            <option>normalization_testing_design</option>
     225            <option>operator_variation_design</option>
     226            <option>optimization_design</option>
     227            <option>quality_control_testing_design</option>
     228            <option>reference_design</option>
     229            <option>replicate_design</option>
     230            <option>self_vs_self_design</option>
     231            <option>software_variation_design</option>
     232            <option>time_series_design</option>
     233            <option>unknown_experiment_design_type</option>
     234          </select></div>
     235          </td>
     236        </tr>
     237
     238        <tr>
     239          <td style="border-style: none;">Perturbational Design</td>
     240          <td style="border-style: none;"><a
     241            onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');"
     242            title="Show/hide items"> <img
     243            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     244            border="0" id="buttonPerturbationalDesign"
     245            name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
     246          <div id="PerturbationalDesign" style="display:none"><select
     247            multiple="multiple" name="perturbationalDesign">
     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>
     265          <td style="border-style: none;">Technological Design</td>
     266          <td style="border-style: none;"><a
     267            onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');"
     268            title="Show/hide items"> <img
     269            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
     270            border="0" id="buttonTechnologicalDesign"
     271            name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
     272          <div id="TechnologicalDesign" style="display:none"><select
     273            multiple="multiple" name="technologicalDesign">
     274            <option>binding_site_identification_design</option>
     275            <option>cellular_modification_design</option>
     276            <option>comparative_genome_hybridization_design</option>
     277            <option>transcript_identification_design</option>
     278          </select></div>
     279          </td>
     280        </tr>
     281
     282      </table>
     283
     284
     285      </td>
     286      <td class="helpText">A list of terms taken from the <a
     287        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
     288        target="_blank">MGED ontology</a>.
     289      <p>Click "expand" for an item to see list boxes with specific
     290      choices.<br />
     291      <br />
     292      Multiple values can be selected by holding down the Ctrl key and
     293      clicking on items.
     294      </td>
     295    </tr>
     296
     297    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     298    <tr>
     299      <td class="boldText">Experiment Name:</td>
     300      <td class="input"><textarea rows="2" cols="30"
     301        name="experimentName"><%=expName %></textarea></td>
     302      <td class="helpText">The name you have chosen for the Experiment.</td>
     303    </tr>
     304
     305    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     306    <tr>
     307      <td class="boldText">Experiment Description:</td>
     308      <td class="input"><textarea rows="2" cols="30"
     309        name="description">description goes here</textarea></td>
     310      <td class="helpText">A short paragraph describing the purpose of the experiment.</td>
     311    </tr>
     312
     313    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     314    <tr>
     315      <td class="boldText">Release Date:</td>
     316      <td class="input"><input type="text" size="10"
     317        name="releaseDate" value="2007-12-03" /></td>
     318      <td class="helpText">Date for public release, in the format YYYY-MM-DD.</td>
     319    </tr>
     320    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     321    <tr>
     322      <td class="boldText">Submission Date:</td>
     323      <td class="input"><input type="text" size="10"
     324        name="submissionDate" value="2007-12-03" /></td>
     325      <td class="helpText">Date of submission, in the format YYYY-MM-DD.</td>
     326    </tr>
     327    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     328    <tr>
     329      <td class="boldText">Submitter:</td>
     330      <td class="input"><input type="text" size="45" name="submitter"
     331        value="Joe Bloggs" /></td>
     332      <td class="helpText">The name of the person responsible for submitting the
     333      experiment to the database.</td>
     334    </tr>
     335    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     336    <tr>
     337      <td class="boldText">Organization:</td>
     338      <td class="input"><input type="text" size="45"
     339        name="organization" value="SCRI" /></td>
     340      <td class="helpText">The organization to which the submitter is affiliated.</td>
     341    </tr>
     342    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     343
     344    <tr>
     345      <td class="boldText">Publication Details:</td>
     346      <td class="input"></td>
     347      <td class="helpText">Publication details for any manuscript
     348      associated with the experiment.</td>
     349    </tr>
     350
     351    <tr>
     352      <td class="plainLabel" style="border-style: none;">Title:</td>
     353      <td class="input" style="border-style: none;"><textarea rows="2" cols="30"
     354        name="publicationTitle" >My Ropey Paper</textarea></td>
     355      <td style="border-style: none;"></td>
     356    </tr>
     357    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     358    <tr>
     359      <td class="plainLabel" style="border-style: none;">Authors:</td>
     360      <td class="input" style="border-style: none;"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
     361      <td  class="helpText" style="border-style: none;">The authors list is a semicolon-delimited list of names.</td>
     362    </tr>
     363    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     364    <tr>
     365      <td class="plainLabel" style="border-style: none;">Journal:</td>
     366      <td class="input" style="border-style: none;"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
     367      <td  class="helpText" style="border-style: none;">The journal field should contain a standard Pubmed journal
     368      abbreviated name. </td>
     369    </tr>
     370    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     371    <tr>
     372      <td class="plainLabel" style="border-style: none;">Volume:</td>
     373      <td class="input" style="border-style: none;"><input type="text" size="10" name="volume"
     374        value="5" /></td>
     375      <td style="border-style: none;"></td>
     376    </tr>
     377    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     378    <tr>
     379      <td class="plainLabel" style="border-style: none;">Issue:</td>
     380      <td class="input" style="border-style: none;"><input type="text" size="10" name="issue"
     381        value="2" /></td>
     382      <td style="border-style: none;"></td>
     383    </tr>
     384    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     385    <tr>
     386      <td class="plainLabel" style="border-style: none;">Pages:</td>
     387      <td class="input" style="border-style: none;"><input type="text" size="10" name="pages"
     388        value="1234-1235" /></td>
     389      <td style="border-style: none;"></td>
     390    </tr>
     391    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     392    <tr>
     393      <td class="plainLabel" style="border-style: none;">Year:</td>
     394      <td class="input" style="border-style: none;"><input type="text" size="10" name="year"
     395        value="2007" /></td>
     396      <td style="border-style: none;"></td>
     397    </tr>
     398    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     399    <tr>
     400      <td class="plainLabel" style="border-style: none;">Pubmed ID:</td>
     401      <td class="input" style="border-style: none;"><input type="text" size="30" name="pubmedId"
     402        value="11009762" /></td>
     403      <td style="border-style: none;"></td>
     404
     405    </tr>
     406
     407    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     408  </table>
    372409<p>
    373410
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/experiment.jsp

    r523 r524  
    88<jsp:setProperty name="inputDataBean" property="*"/>
    99
     10<%
     11final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
     12final String ID = sc.getId();
     13final String requestID = request.getParameter("requestId");
     14
     15//we also need to figure out the name/id of the currently selected experiment that this import is getting initiated from
     16ItemContext cc = sc.getCurrentContext(Item.EXPERIMENT);
     17int experimentID = cc.getId();
     18DbControl dc = sc.newDbControl();
     19Experiment experiment = Experiment.getById(dc,experimentID);
     20String expName = experiment.getName();
     21dc.close();
     22
     23//set the experiment id in the bean so we can get at it later in the plugin
     24inputDataBean.setExperimentId(new Integer(experimentID).toString());
     25 %>
    1026
    1127<html>
     
    2743    {
    2844      var frm = document.forms['experimentData'];
    29       var url = '<%= request.getContextPath()%>/lims/arraydesigns/index.jsp?ID=b8c5fcee801ca39c&cmd=UpdateContext&mode=selectone&callback=setArrayDesignCallback';
     45      var url = '<%= request.getContextPath()%>/lims/arraydesigns/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setArrayDesignCallback';
    3046      if (frm.accession.length > 0)
    3147      {
     
    100116
    101117
    102 <%
    103 final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
    104 final String ID = sc.getId();
    105 final String requestID = request.getParameter("requestId");
    106 
    107 //we also need to figure out the name/id of the currently selected experiment that this import is getting initiated from
    108 ItemContext cc = sc.getCurrentContext(Item.EXPERIMENT);
    109 int experimentID = cc.getId();
    110 DbControl dc = sc.newDbControl();
    111 Experiment experiment = Experiment.getById(dc,experimentID);
    112 String expName = experiment.getName();
    113 dc.close();
    114 
    115 //set the experiment id in the bean so we can get at it later in the plugin
    116 inputDataBean.setExperimentId(new Integer(experimentID).toString());
    117  %>
     118
    118119 
    119120
     
    130131<input type="hidden" name="ID" value="<%=ID%>">
    131132
    132 <table cellpadding="10">
     133<table cellpadding="0" cellspacing="0">
    133134
    134135  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    135   <tr class="border" >
     136  <tr >
    136137    <td class="boldText">Domain:</td>
    137138    <td class="input"><input type="text" size="45" name="domain" value="scri.ac.uk" /></td>
    138     <td >The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
     139    <td class="helpText">The domain tag provides information on the originator of the output MAGE-ML document. This field can contain
    139140    any suitable string, such as the originating internet domain name (e.g. "ebi.ac.uk").</td>
    140141  </tr>
    141142 
    142143  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    143   <tr class="border" >
     144  <tr >
    144145    <td class="boldText">Array Acession:</td>
    145146
     
    149150    <table class="noBorder"  cellspacing="0" cellpadding="5">
    150151      <tr class="noBorder">
    151         <td><select name="accession" onchange="arrayDesignOnChange()"></select></td>
    152         <td>
     152        <td style="border-style: none;"><select name="accession" onchange="arrayDesignOnChange()"></select></td>
     153        <td style="border-style: none;">
    153154        <div class="buttonclass"
    154155          onmouseover="this.className='buttonclass_hover';"
     
    163164    </td>
    164165
    165     <td>Please select an existing array design from BASE or create a
     166    <td class="helpText">Please select an existing array design from BASE or create a
    166167    new one. For ArrayExpress submissions, the array design name becomes
    167168    the array accession identifier. Accession numbers for experiments
     
    171172
    172173
    173   <tr>
    174174
    175175      <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    176176    <tr >
    177177      <td class="boldText">Quality Control:</td>
    178       <td class="input"><select multiple name="qualityControl">
     178      <td class="input"><select multiple name="qualityControl" size="7">
    179179        <option selected="selected">biological replicate</option>
    180180        <option>dye swap quality control</option>
     
    185185        <option>technical replicate</option>
    186186      </select></td>
    187       <td>A list of terms taken from the <a
     187      <td class="helpText">A list of terms taken from the <a
    188188        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
    189189        target="_blank">MGED ontology</a>. Multiple values can be selected
     
    198198      <table class="noBorder" cellpadding="3">
    199199
    200         <tr class="noBorder">
    201           <td valign="top">Biological Property<br />
    202           </td>
    203           <td colspan="2"><a
     200        <tr>
     201          <td valign="top" style="border-style: none;">Biological Property<br />
     202          </td>
     203          <td colspan="2" style="border-style: none;"><a
    204204            onclick="showHideItems('BiologicalProperty', 'buttonBiologicalProperty');"
    205205            title="Show/hide items"> <img
     
    208208            name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
    209209          <div id="BiologicalProperty" style="display:none"><select
    210             multiple="multiple" name="biologicalProperty">
     210            multiple="multiple" name="biologicalProperty" size="16">
    211211            <option selected="selected">cell_component_comparison_design</option>
    212212            <option>cell_cycle_design</option>
     
    229229        </tr>
    230230
    231         <tr class="noBorder">
    232           <td>BioMolecular Annotation</td>
    233           <td><a
     231        <tr>
     232          <td style="border-style: none;">BioMolecular Annotation</td>
     233          <td style="border-style: none;"><a
    234234            onclick="showHideItems('BioMolecularAnnotation', 'buttonBioMolecularAnnotation');"
    235235            title="Show/hide items"> <img
     
    238238            name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
    239239          <div id="BioMolecularAnnotation" style="display:none"><select
    240             multiple="multiple" name="bioMolecularAnnotation">
     240            multiple="multiple" name="bioMolecularAnnotation"  size="11">
    241241            <option selected="selected">RNA_stability_design</option>
    242242            <option>binding_site_identification_design</option>
     
    254254        </tr>
    255255
    256         <tr class="noBorder">
    257           <td>Epidemiological Design</td>
    258           <td><a
     256        <tr>
     257          <td style="border-style: none;">Epidemiological Design</td>
     258          <td style="border-style: none;"><a
    259259            onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');"
    260260            title="Show/hide items"> <img
     
    263263            name="buttonEpidemiologicalDesign" /></a> <!-- begin div containing hidden items -->
    264264          <div id="EpidemiologicalDesign" style="display:none"><select
    265             multiple="multiple" name="epidemiologicalDesign">
     265            multiple="multiple" name="epidemiologicalDesign"  size="4">
    266266            <option>clinical_history_design</option>
    267267            <option>disease_state_design</option>
     
    272272        </tr>
    273273
    274         <tr class="noBorder">
    275           <td>Methodological Design</td>
    276           <td><a
     274        <tr>
     275          <td style="border-style: none;">Methodological Design</td>
     276          <td style="border-style: none;"><a
    277277            onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');"
    278278            title="Show/hide items"> <img
     
    281281            name="buttonMethodologicalDesign" /></a> <!-- begin div containing hidden items -->
    282282          <div id="MethodologicalDesign" style="display:none"><select
    283             multiple="multiple" name="methodologicalDesign">
     283            multiple="multiple" name="methodologicalDesign" size="18">
    284284            <option>all_pairs</option>
    285285            <option>array_platform_variation_design</option>
     
    304304        </tr>
    305305
    306         <tr class="noBorder">
    307           <td>Perturbational Design</td>
    308           <td><a
     306        <tr>
     307          <td style="border-style: none;">Perturbational Design</td>
     308          <td style="border-style: none;"><a
    309309            onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');"
    310310            title="Show/hide items"> <img
     
    313313            name="buttonPerturbationalDesign" /></a> <!-- begin div containing hidden items -->
    314314          <div id="PerturbationalDesign" style="display:none"><select
    315             multiple="multiple" name="perturbationalDesign">
     315            multiple="multiple" name="perturbationalDesign" size="12">
    316316            <option>cellular_modification_design</option>
    317317            <option>compound_treatment_design</option>
     
    330330        </tr>
    331331
    332         <tr class="noBorder">
    333           <td>Technological Design</td>
    334           <td><a
     332        <tr>
     333          <td style="border-style: none;">Technological Design</td>
     334          <td style="border-style: none;"><a
    335335            onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');"
    336336            title="Show/hide items"> <img
    337337            src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif"
    338338            border="0" id="buttonTechnologicalDesign"
    339             name="TechnologicalDesign" /></a> <!-- begin div containing hidden items -->
     339            name="buttonTechnologicalDesign" /></a> <!-- begin div containing hidden items -->
    340340          <div id="TechnologicalDesign" style="display:none"><select
    341             multiple="multiple" name="technologicalDesign">
     341            multiple="multiple" name="technologicalDesign" size="4">
    342342            <option>binding_site_identification_design</option>
    343343            <option>cellular_modification_design</option>
     
    352352
    353353      </td>
    354       <td>A list of terms taken from the <a
     354      <td class="helpText">A list of terms taken from the <a
    355355        href="http://mged.sourceforge.net/ontologies/MGEDontology.php"
    356356        target="_blank">MGED ontology</a>.
     
    366366    <tr>
    367367      <td class="boldText">Experiment Name:</td>
    368       <td class="input"><textarea rows="2" cols="30"
     368      <td class="input"><textarea rows="4" cols="30"
    369369        name="experimentName"><%=expName %></textarea></td>
    370       <td>The name you have chosen for the Experiment.</td>
     370      <td class="helpText">The name you have chosen for the Experiment.</td>
    371371    </tr>
    372372
     
    374374    <tr>
    375375      <td class="boldText">Experiment Description:</td>
    376       <td class="input"><textarea rows="2" cols="30"
     376      <td class="input"><textarea rows="4" cols="30"
    377377        name="description">description goes here</textarea></td>
    378       <td>A short paragraph describing the purpose of the experiment.</td>
     378      <td class="helpText">A short paragraph describing the purpose of the experiment.</td>
    379379    </tr>
    380380
     
    384384      <td class="input"><input type="text" size="10"
    385385        name="releaseDate" value="2007-12-03" /></td>
    386       <td>Date for public release, in the format YYYY-MM-DD.</td>
     386      <td class="helpText">Date for public release, in the format YYYY-MM-DD.</td>
    387387    </tr>
    388388    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     
    391391      <td class="input"><input type="text" size="10"
    392392        name="submissionDate" value="2007-12-03" /></td>
    393       <td>Date of submission, in the format YYYY-MM-DD.</td>
     393      <td class="helpText">Date of submission, in the format YYYY-MM-DD.</td>
    394394    </tr>
    395395    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     
    398398      <td class="input"><input type="text" size="45" name="submitter"
    399399        value="Joe Bloggs" /></td>
    400       <td>The name of the person responsible for submitting the
     400      <td class="helpText">The name of the person responsible for submitting the
    401401      experiment to the database.</td>
    402402    </tr>
     
    406406      <td class="input"><input type="text" size="45"
    407407        name="organization" value="SCRI" /></td>
    408       <td>The organization to which the submitter is affiliated.</td>
    409     </tr>
    410     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    411 
    412     <tr class="noBorder">
     408      <td class="helpText">The organization to which the submitter is affiliated.</td>
     409    </tr>
     410    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     411
     412    <tr>
    413413      <td class="boldText">Publication Details:</td>
    414414      <td class="input"></td>
    415       <td></td>
    416     </tr>
    417 
    418     <tr class="noBorder">
    419       <td>Title:</td>
    420       <td class="input"><textarea rows="2" cols="30"
    421         name="publicationTitle">My Ropey Paper</textarea></td>
    422 
    423       <td rowspan="4">Publication details for any manuscript
    424       associated with the experiment. <p>
    425       The authors list is a semicolon-delimited list of names.<p>
    426       The journal field should contain a standard Pubmed journal
     415      <td class="helpText">Publication details for any manuscript
     416      associated with the experiment.</td>
     417    </tr>
     418
     419    <tr>
     420      <td class="plainLabel" style="border-style: none;">Title:</td>
     421      <td class="input" style="border-style: none;"><textarea rows="3" cols="30"
     422        name="publicationTitle" >My Ropey Paper</textarea></td>
     423      <td style="border-style: none;"></td>
     424    </tr>
     425    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     426    <tr>
     427      <td class="plainLabel" style="border-style: none;">Authors:</td>
     428      <td class="input" style="border-style: none;"><textarea rows="3" cols="30" name="authors">Bloggs, Joe</textarea></td>
     429      <td  class="helpText" style="border-style: none;">The authors list is a semicolon-delimited list of names.</td>
     430    </tr>
     431    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     432    <tr>
     433      <td class="plainLabel" style="border-style: none;">Journal:</td>
     434      <td class="input" style="border-style: none;"><textarea rows="3" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
     435      <td  class="helpText" style="border-style: none;">The journal field should contain a standard Pubmed journal
    427436      abbreviated name. </td>
    428437    </tr>
    429438    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    430     <tr class="noBorder">
    431       <td>Authors:</td>
    432       <td class="input"><textarea rows="2" cols="30" name="authors">Bloggs, Joe</textarea></td>
    433       <td></td>
    434     </tr>
    435     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    436     <tr class="noBorder">
    437       <td>Journal:</td>
    438       <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
    439       <td></td>
    440     </tr>
    441     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    442     <tr class="noBorder">
    443       <td>Volume:</td>
    444       <td class="input"><input type="text" size="10" name="volume"
     439    <tr>
     440      <td class="plainLabel" style="border-style: none;">Volume:</td>
     441      <td class="input" style="border-style: none;"><input type="text" size="10" name="volume"
    445442        value="5" /></td>
    446       <td></td>
    447     </tr>
    448     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    449     <tr class="noBorder">
    450       <td>Issue:</td>
    451       <td class="input"><input type="text" size="10" name="issue"
     443      <td style="border-style: none;"></td>
     444    </tr>
     445    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     446    <tr>
     447      <td class="plainLabel" style="border-style: none;">Issue:</td>
     448      <td class="input" style="border-style: none;"><input type="text" size="10" name="issue"
    452449        value="2" /></td>
    453       <td></td>
    454     </tr>
    455     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    456     <tr class="noBorder">
    457       <td>Pages:</td>
    458       <td class="input"><input type="text" size="10" name="pages"
     450      <td style="border-style: none;"></td>
     451    </tr>
     452    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     453    <tr>
     454      <td class="plainLabel" style="border-style: none;">Pages:</td>
     455      <td class="input" style="border-style: none;"><input type="text" size="10" name="pages"
    459456        value="1234-1235" /></td>
    460       <td></td>
    461     </tr>
    462     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    463     <tr class="noBorder">
    464       <td>Year:</td>
    465       <td class="input"><input type="text" size="10" name="year"
     457      <td style="border-style: none;"></td>
     458    </tr>
     459    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     460    <tr>
     461      <td class="plainLabel" style="border-style: none;">Year:</td>
     462      <td class="input" style="border-style: none;"><input type="text" size="10" name="year"
    466463        value="2007" /></td>
    467       <td></td>
    468     </tr>
    469     <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    470     <tr class="noBorder">
    471       <td>Pubmed ID:</td>
    472       <td class="input"><input type="text" size="30" name="pubmedId"
     464      <td style="border-style: none;"></td>
     465    </tr>
     466    <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
     467    <tr>
     468      <td class="plainLabel" style="border-style: none;">Pubmed ID:</td>
     469      <td class="input" style="border-style: none;"><input type="text" size="30" name="pubmedId"
    473470        value="11009762" /></td>
    474       <td></td>
     471      <td style="border-style: none;"></td>
    475472
    476473    </tr>
     
    484481  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
    485482  <tr class="noBorder">
    486     <td id="next" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Next</td></tr></table></div></div></td>
    487     <td id="close" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>  </tr>
     483    <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Next</td></tr></table></div></div></td>
     484    <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td>  </tr>
    488485  </table>
    489486
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

    r523 r524  
    2020
    2121<link rel="stylesheet" type="text/css" href="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/styles.css" />
    22 
     22<link rel="stylesheet" type="text/css" href="/base/include/styles/main.css">
     23<link rel="stylesheet" type="text/css" href="/base/include/styles/size_m.css">
    2324
    2425<script language="JavaScript" src="<%= request.getContextPath()%>/include/scripts/main.js" type="text/javascript"></script>
     
    8384
    8485
    85 <h2>Tab2MAGE Importer -- Your Hybridizations</h2>
    86 Page 3 of 3
    87 <p>
     86
    8887<form name="hybridizations"action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
    8988<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters">
     
    123122<input type="hidden" name="parameter:zipFile" value=""  id="zipFile">
    124123
    125 
     124<h2>Tab2MAGE Importer -- Your Hybridizations</h2>
     125Page 3 of 3
     126<p>
    126127<!--  table with the input form -->
    127128<table cellpadding="15">
    128129
    129130  <!-- question 1 -->
    130   <tr style="border-color: #6E94B7;border-style: solid;border-width: 1px">
     131  <tr >
    131132    <td class="boldText">Microarray platform:</td>
    132133    <td class="input"><select name="parameter:platform">
     
    235236      <tr class="noBorder" >
    236237     
    237         <td style="vertical-align: middle"><input type="text" name="path" size="35" value=""></td>
     238        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
    238239       
    239         <td  style="vertical-align: middle">
     240        <td  style="vertical-align: middle;border-style: none;">
    240241        <div class="buttons"
    241242          onmouseover="this.className='buttons_hover';"
     
    246247        <table class="noBorder" cellspacing="0" cellpadding="0">
    247248          <tr class="noBorder">
    248             <td>&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
    249             <td>Browse&hellip;</td>
     249            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
     250            <td style="border-style: none;">Browse&hellip;</td>
    250251          </tr>
    251252        </table>
     
    269270  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
    270271  <tr class="noBorder">
    271     <td id="next" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Run Import</td></tr></table></div></div></td>
    272     <td id="close" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>  </tr>
     272    <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Run Import</td></tr></table></div></div></td>
     273    <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td>  </tr>
    273274  </table>
    274275
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r523 r524  
    177177  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
    178178  <tr class="noBorder">
    179     <td id="next" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/gonext.gif" border="0"></td><td>Next</td></tr></table></div></div></td>
    180     <td id="close" width="50%"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td><img src="/base/images/cancel.gif" border="0"></td><td>Cancel</td></tr></table></div></div></td>  </tr>
     179    <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Next</td></tr></table></div></div></td>
     180    <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td>  </tr>
    181181  </table>
    182182
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/styles.css

    r523 r524  
    1111}
    1212
    13 td.header
    14   {
    15   vertical-align: top;
    16   background-color: #F9F7F0;
    17   }
    18 
    19 td.boldText
    20   {
    21   font-weight: bold;
    22   vertical-align: middle;
    23   color: #274D70;
    24   }
    25 
    2613table {
    2714  border-color: #6E94B7;
    2815  border-style: solid;
    2916  border-width: 1px;
    30   border-collapse: separate;
     17  border-collapse: collapse;
    3118}
    3219
    3320tr {
    34   border-color: #6E94B7;
    35   border-style: solid;
    36   border-width: 1px;
    3721  vertical-align: middle;
    3822}
    3923
    40 tr.border {
    41   border-color: #6E94B7;
    42   border-style: solid;
    43   border-width: 1px;
     24td {
    4425  vertical-align: middle;
     26  text-align: left;
     27  align: left;
     28  border-top: 1px solid #6E94B7;
    4529}
    46 
    4730
    4831table.noBorder {
     
    5033}
    5134
    52 tr.noBorder {
     35
     36td.noBorder {
    5337  border-style: none;
    54   vertical-align: middle;
    5538}
    5639
    57 td {
    58   vertical-align: top;
    59   text-align: left;
    60   align: left; #
     40td.plainLabel {
     41  padding: 10px;
     42}
     43
     44td.helpText {
     45  padding: 10px;
    6146}
    6247
     
    7055  vertical-align: middle;
    7156  text-align: left;
    72   align: left; 
     57  align: left;
    7358  background-color: rgb(240, 240, 240);
     59  padding: 10px;
    7460}
    7561
     
    8167}
    8268
     69td.header {
     70  vertical-align: top;
     71  background-color: #F9F7F0;
     72}
     73
     74td.boldText {
     75  font-weight: bold;
     76  vertical-align: middle;
     77  color: #274D70;
     78  padding: 10px;
     79}
     80
    8381img {
    8482  vertical-align: middle;
    8583}
    8684
    87 .buttons{
     85.buttons {
    8886  background: #E0E0E0;
    8987  border-top: 1px solid #333333;
     
    9391  vertical-align: middle;
    9492}
    95 
    9693
    9794.buttons_inner {
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