Ignore:
Timestamp:
Dec 4, 2007, 3:46:31 PM (14 years ago)
Author:
mbayer
Message:
  • have tied the interface to the importer plugin class now -- all parameters get picked up fine by the plugin
Location:
branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins
Files:
3 edited

Legend:

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

    r511 r512  
    9999  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    100100  <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  
     101    <td class="boldText">Quality Control:</td>
     102    <td class="input"><select multiple name="qualityControl">
     103      <option selected="selected">biological replicate</option>
     104      <option>dye swap quality control</option>
     105      <option>peer review quality control</option>
     106      <option>real time PCR quality control</option>
     107      <option>reverse transcription PCR quality control</option>
     108      <option selected="selected">spike quality control</option>
     109      <option>technical replicate</option>
     110    </select></td>
     111    <td>A list of terms taken from the <a href="http://mged.sourceforge.net/ontologies/MGEDontology.php" target="new">MGED
     112    ontology</a>. Multiple values can be selected by holding down the Ctrl key and clicking on items.</td>
     113  </tr>
     114
    148115  <!-- ------------------------------------------------------------------------------------------------------------------------------------------------ -->
    149116  <tr>
     
    159126          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBiologicalProperty"
    160127          name="buttonBiologicalProperty" /></a> <!-- begin div containing hidden items -->
    161         <div id="BiologicalProperty" style="display:none"><select multiple="multiple">
     128        <div id="BiologicalProperty" style="display:none"><select multiple="multiple" name="biologicalProperty">
    162129          <option selected="selected">cell_component_comparison_design</option>
    163130          <option>cell_cycle_design</option>
     
    185152          title="Show/hide items"> <img src="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/show.gif" border="0" id="buttonBioMolecularAnnotation"
    186153          name="buttonBioMolecularAnnotation" /></a> <!-- begin div containing hidden items -->
    187         <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple">
     154        <div id="BioMolecularAnnotation" style="display:none"><select multiple="multiple" name="bioMolecularAnnotation">
    188155          <option selected="selected">RNA_stability_design</option>
    189156          <option>binding_site_identification_design</option>
     
    205172        <td><a onclick="showHideItems('EpidemiologicalDesign', 'buttonEpidemiologicalDesign');" title="Show/hide items">
    206173        <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">
     174        <div id="EpidemiologicalDesign" style="display:none"><select multiple="multiple" name="epidemiologicalDesign">
    208175          <option>clinical_history_design</option>
    209176          <option>disease_state_design</option>
     
    218185        <td><a onclick="showHideItems('MethodologicalDesign', 'buttonMethodologicalDesign');" title="Show/hide items">
    219186        <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">
     187        <div id="MethodologicalDesign" style="display:none"><select multiple="multiple" name="methodologicalDesign">
    221188          <option>all_pairs</option>
    222189          <option>array_platform_variation_design</option>
     
    245212        <td><a onclick="showHideItems('PerturbationalDesign', 'buttonPerturbationalDesign');" title="Show/hide items">
    246213        <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">
     214        <div id="PerturbationalDesign" style="display:none"><select multiple="multiple" name="perturbationalDesign">
    248215          <option>cellular_modification_design</option>
    249216          <option>compound_treatment_design</option>
     
    266233        <td><a onclick="showHideItems('TechnologicalDesign', 'buttonTechnologicalDesign');" title="Show/hide items">
    267234        <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">
     235        <div id="TechnologicalDesign" style="display:none"><select multiple="multiple" name="technologicalDesign">
    269236          <option>binding_site_identification_design</option>
    270237          <option>cellular_modification_design</option>
     
    280247    </td>
    281248    <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.
    283249    <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.
     250    Multiple values can be selected by holding down the Ctrl key and clicking on items.
    285251    </td>
    286252  </tr>
     
    307273  <tr>
    308274    <td class="boldText">Release Date:</td>
    309     <td class="input"><input type="text" size="10" name="" value="2007-12-03" /></td>
     275    <td class="input"><input type="text" size="10" name="releaseDate" value="2007-12-03" /></td>
    310276    <td>Date for public release, in the format YYYY-MM-DD.</td>
    311277  </tr>
     
    352318      <tr class="noBorder">
    353319        <td>Journal:</td>
    354         <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Unreproducible Results</textarea></td>
     320        <td class="input"><textarea rows="2" cols="30" name="journal">The Journal of Irreproducible Results</textarea></td>
    355321        <td></td>
    356322      </tr>
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/hybridizations.jsp

    r511 r512  
    2727<form action="<%= request.getContextPath()%>/common/plugin/index.jsp" method="post">
    2828<input type="hidden" name="ID" value="<%=ID%>"> <input type="hidden" name="cmd" value="SetParameters">
    29   <input type="hidden"name="requestID" value="<%=requestID%>">
    30   <input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>">
    31   <input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>">
     29<input type="hidden"name="requestID" value="<%=requestID%>">
     30<!-- these are the parameters from the input pages; need to pick them up individually from the bean here; ugly as hell but can't be done any other way -->
     31<input type="hidden" name="parameter:domain" value="<%=inputDataBean.getDomain()%>">
     32<input type="hidden" name="parameter:accession" value="<%=inputDataBean.getAccession()%>">
     33<input type="hidden" name="parameter:qualityControl" value="<%=inputDataBean.getQualityControl()%>">
     34<input type="hidden" name="parameter:experimentalDesign" value="<%=inputDataBean.getExperimentalDesign()%>">
     35<input type="hidden" name="parameter:experimentName" value="<%=inputDataBean.getExperimentName()%>">
     36<input type="hidden" name="parameter:description" value="<%=inputDataBean.getDescription()%>">
     37<input type="hidden" name="parameter:releaseDate" value="<%=inputDataBean.getReleaseDate()%>">
     38<input type="hidden" name="parameter:submissionDate" value="<%=inputDataBean.getSubmissionDate()%>">
     39<input type="hidden" name="parameter:submitter" value="<%=inputDataBean.getSubmitter()%>">
     40<input type="hidden" name="parameter:organization" value="<%=inputDataBean.getOrganization()%>">
     41<input type="hidden" name="parameter:publicationTitle" value="<%=inputDataBean.getPublicationTitle()%>">
     42<input type="hidden" name="parameter:authors" value="<%=inputDataBean.getAuthors()%>">
     43<input type="hidden" name="parameter:journal" value="<%=inputDataBean.getJournal()%>">
     44<input type="hidden" name="parameter:volume" value="<%=inputDataBean.getVolume()%>">
     45<input type="hidden" name="parameter:issue" value="<%=inputDataBean.getIssue()%>">
     46<input type="hidden" name="parameter:pages" value="<%=inputDataBean.getPages()%>">
     47<input type="hidden" name="parameter:year" value="<%=inputDataBean.getYear()%>">
     48<input type="hidden" name="parameter:pubmedId" value="<%=inputDataBean.getPubmedId()%>">
     49<input type="hidden" name="parameter:treatmentProtocol" value="<%=inputDataBean.getTreatmentProtocol()%>">
     50<input type="hidden" name="parameter:extractionProtocol" value="<%=inputDataBean.getExtractionProtocol()%>">
     51<input type="hidden" name="parameter:labelingProtocol" value="<%=inputDataBean.getLabelingProtocol()%>">
     52<input type="hidden" name="parameter:hybridizationProtocol" value="<%=inputDataBean.getHybridizationProtocol()%>">
     53<input type="hidden" name="parameter:scanningProtocol" value="<%=inputDataBean.getScanningProtocol()%>">
     54<input type="hidden" name="parameter:treatmentProtocolParams" value="<%=inputDataBean.getTreatmentProtocolParams()%>">
     55<input type="hidden" name="parameter:extractionProtocolParams" value="<%=inputDataBean.getExtractionProtocolParams()%>">
     56<input type="hidden" name="parameter:labelingProtocolParams" value="<%=inputDataBean.getLabelingProtocolParams()%>">
     57<input type="hidden" name="parameter:hybridizationProtocolParams" value="<%=inputDataBean.getHybridizationProtocolParams()%>">
     58<input type="hidden" name="parameter:scanningProtocolParams" value="<%=inputDataBean.getScanningProtocolParams()%>">
    3259
     60<!-- 
     61<input type="hidden" name="parameter:platform" value="<%=inputDataBean.getPlatform()%>">
     62<input type="hidden" name="parameter:organism" value="<%=inputDataBean.getOrganism()%>">
     63<input type="hidden" name="parameter:numDesigns" value="<%=inputDataBean.getNumDesigns()%>">
     64<input type="hidden" name="parameter:dyeSwap" value="<%=inputDataBean.getDyeSwap()%>">
     65<input type="hidden" name="parameter:refSample" value="<%=inputDataBean.getRefSample()%>">
     66<input type="hidden" name="parameter:numTreatments" value="<%=inputDataBean.getNumTreatments()%>">
     67<input type="hidden" name="parameter:expFactors" value="<%=inputDataBean.getExpFactors()%>">
     68<input type="hidden" name="parameter:numReplicates" value="<%=inputDataBean.getNumReplicates()%>">
     69<input type="hidden" name="parameter:tissues" value="<%=inputDataBean.getTissues()%>">
     70<input type="hidden" name="parameter:pooling" value="<%=inputDataBean.getPooling()%>">
     71<input type="hidden" name="parameter:zipFile" value="<%=inputDataBean.getZipFile()%>">
     72-->
     73
     74<!--  table with the input form -->
    3375<table cellpadding="15">
    3476
     
    5799  <tr>
    58100    <td class="boldText">Was dye-swap used?</td>
    59     <td class="input">yes <input type="radio" name="parameter:dyeswap" value="yes"> no <input type="radio"
    60       name="parameter:dyeswap" value="no" checked="checked"> <br>
     101    <td class="input">yes <input type="radio" name="parameter:dyeSwap" value="yes"> no <input type="radio"
     102      name="parameter:dyeSwap" value="no" checked="checked"> <br>
    61103    </td>
    62104  </tr>
     
    85127    Dose(control,low,medium,high)</i>
    86128    </td>
    87     <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Factor 1(value1,value2,...valueN)<br>Factor 2(value1,value2,...valueN)</textarea></td>
     129    <td class="input"><textarea rows="7" cols="40" name="parameter:expFactors">Factor 1(value1,value2,...valueN)</textarea></td>
    88130  </tr>
    89131
  • branches/uk_ac_ebi_Tab2MageImporter/jsp/uk/ac/ebi/nugo/plugins/protocols.jsp

    r511 r512  
    33<%@ page import="net.sf.basedb.util.*"%>
    44<%@ page import="java.util.*"%>
     5<%@ page import="java.lang.*"%>
    56
    67<jsp:useBean id="inputDataBean" class="uk.ac.ebi.nugo.plugins.DataBean" scope="session" />
     
    2021final String ID = sc.getId();
    2122final String requestID = request.getParameter("requestId");
     23
     24
     25//here we also need to deal with the multiple select inputs from the previous page
     26//their selected values need to be extracted from the request and concatenated into a single String
     27
     28//first deal with quality control input
     29String[] items = request.getParameterValues("qualityControl");
     30StringBuilder qualControl = new StringBuilder();
     31for(int i = 0; i< items.length; i++)
     32{
     33    qualControl.append(items[i] );
     34    //last one does not get a comma
     35    if(i!=items.length-1)
     36    {
     37    qualControl.append(",");
     38    }
     39}
     40//store this in the bean
     41inputDataBean.setQualityControl(qualControl.toString());
     42
     43//next deal with the experiment design type
     44//this is slightly more complex as we are dealing with six separate list boxes and we need to combine all their inputs
     45StringBuilder experimentalDesign = new StringBuilder();
     46
     47String [] biologicalPropertyItems = request.getParameterValues("biologicalProperty");
     48if(biologicalPropertyItems !=null)
     49{
     50  for(int i = 0; i< biologicalPropertyItems.length; i++)
     51  {
     52    experimentalDesign.append(biologicalPropertyItems[i] +",");
     53  }
     54}
     55
     56String [] bioMolecularAnnotationItems = request.getParameterValues("bioMolecularAnnotation");
     57if(bioMolecularAnnotationItems !=null)
     58{
     59  for(int i = 0; i<bioMolecularAnnotationItems.length; i++)
     60  {
     61    experimentalDesign.append(bioMolecularAnnotationItems[i] +",");
     62  }
     63}
     64
     65String [] epidemiologicalDesignItems = request.getParameterValues("epidemiologicalDesign");
     66if(epidemiologicalDesignItems !=null)
     67{
     68  for(int i = 0; i< epidemiologicalDesignItems.length; i++)
     69  {
     70    experimentalDesign.append(epidemiologicalDesignItems[i] +",");
     71  }
     72}
     73
     74String [] methodologicalDesignItems = request.getParameterValues("methodologicalDesign");
     75if(methodologicalDesignItems !=null)
     76{
     77  for(int i = 0; i< methodologicalDesignItems.length; i++)
     78  {
     79    experimentalDesign.append(methodologicalDesignItems[i] +",");
     80  }
     81}
     82
     83String [] perturbationalDesignItems = request.getParameterValues("perturbationalDesign");
     84if(perturbationalDesignItems !=null)
     85{
     86  for(int i = 0; i< perturbationalDesignItems.length; i++)
     87  {
     88    experimentalDesign.append(perturbationalDesignItems[i] +",");
     89  }
     90}
     91
     92String [] technologicalDesignItems = request.getParameterValues("technologicalDesign");
     93if(technologicalDesignItems !=null)
     94{
     95  for(int i = 0; i< technologicalDesignItems.length; i++)
     96  {
     97    experimentalDesign.append(technologicalDesignItems[i]+",");
     98  }
     99}
     100
     101//store the combined String in the bean
     102inputDataBean.setExperimentalDesign(experimentalDesign.toString());
     103
    22104 %>
    23105
     
    48130  <tr>
    49131    <td class="boldText">Treatment</td>
    50     <td class="input"><textarea rows="8" cols="35" id="" name="">my treatment protocol text </textarea></td>
    51     <td><textarea rows="4" cols="25" id="" name="">param1</textarea></td>
     132    <td class="input"><textarea rows="8" cols="35" name="treatmentProtocol">my treatment protocol text </textarea></td>
     133    <td><textarea rows="4" cols="25" name="treatmentProtocolParams">param1</textarea></td>
    52134  </tr>
    53135
    54136  <tr>
    55137    <td class="boldText">Extraction</td>
    56     <td class="input"><textarea rows="8" cols="35" id="" name=""> my extraction protocol text  </textarea></td>
    57     <td><textarea rows="4" cols="25" id="" name="">param2</textarea></td>
     138    <td class="input"><textarea rows="8" cols="35" name="extractionProtocol"> my extraction protocol text  </textarea></td>
     139    <td><textarea rows="4" cols="25" name="extractionProtocolParams">param2</textarea></td>
    58140  </tr>
    59141
    60142  <tr>
    61143    <td class="boldText">Labeling</td>
    62     <td class="input"><textarea rows="8" cols="35" id="" name=""> my labeling protocol text  </textarea></td>
    63     <td><textarea rows="4" cols="25" id="" name="">param3</textarea></td>
     144    <td class="input"><textarea rows="8" cols="35" name="labelingProtocol"> my labeling protocol text  </textarea></td>
     145    <td><textarea rows="4" cols="25" name="labelingProtocolParams">param3</textarea></td>
    64146  </tr>
    65147
    66148  <tr>
    67149    <td class="boldText">Hybridization</td>
    68     <td class="input"><textarea rows="8" cols="35" id="" name="">my hybs protocol text   </textarea></td>
    69     <td><textarea rows="4" cols="25" id="" name="">param4</textarea></td>
     150    <td class="input"><textarea rows="8" cols="35" name="hybridizationProtocol">my hybs protocol text   </textarea></td>
     151    <td><textarea rows="4" cols="25" name="hybridizationProtocolParams">param4</textarea></td>
    70152  </tr>
    71153
    72154  <tr>
    73155    <td class="boldText">Scanning</td>
    74     <td class="input"><textarea rows="8" cols="35" id="" name=""> my scanning protocol text </textarea></td>
    75     <td><textarea rows="4" cols="25" id="" name=""> param5</textarea></td>
     156    <td class="input"><textarea rows="8" cols="35"name="scanningProtocol"> my scanning protocol text </textarea></td>
     157    <td><textarea rows="4" cols="25" name="scanningProtocolParams"> param5</textarea></td>
    76158  </tr>
    77159
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