Changeset 512


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
Files:
7 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
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/DataBean.java

    r497 r512  
    33public class DataBean
    44{
     5
     6  String domain;
     7  String accession;
     8  String qualityControl;
     9  String experimentalDesign;
     10  String experimentName;
     11  String description;
     12  String releaseDate;
     13  String submissionDate;
     14  String submitter;
     15  String organization;
     16  String publicationTitle;
     17  String authors;
     18  String journal;
     19  String volume;
     20  String issue;
     21  String pages;
     22  String year;
     23  String pubmedId;
     24  String treatmentProtocol;
     25  String extractionProtocol;
     26  String labelingProtocol;
     27  String hybridizationProtocol;
     28  String scanningProtocol;
     29  String treatmentProtocolParams;
     30  String extractionProtocolParams;
     31  String labelingProtocolParams;
     32  String hybridizationProtocolParams;
     33  String scanningProtocolParams;
     34  String platform;
     35  String organism;
     36  String numDesigns;
     37  String dyeSwap;
     38  String refSample;
     39  String numTreatments;
     40  String expFactors;
     41  String numReplicates;
     42  String tissues;
     43  String pooling;
     44  String zipFile;
    545 
    6   String experimentName;
    7   String treatmentProtocol;
    8 
     46 
     47  public String getAccession()
     48  {
     49    return accession;
     50  }
     51  public void setAccession(String accession)
     52  {
     53    this.accession = accession;
     54  }
     55  public String getAuthors()
     56  {
     57    return authors;
     58  }
     59  public void setAuthors(String authors)
     60  {
     61    this.authors = authors;
     62  }
     63  public String getDescription()
     64  {
     65    return description;
     66  }
     67  public void setDescription(String description)
     68  {
     69    this.description = description;
     70  }
     71  public String getDomain()
     72  {
     73    return domain;
     74  }
     75  public void setDomain(String domain)
     76  {
     77    this.domain = domain;
     78  }
     79  public String getDyeSwap()
     80  {
     81    return dyeSwap;
     82  }
     83  public void setDyeSwap(String dyeSwap)
     84  {
     85    this.dyeSwap = dyeSwap;
     86  }
     87  public String getExperimentalDesign()
     88  {
     89    return experimentalDesign;
     90  }
     91  public void setExperimentalDesign(String experimentalDesign)
     92  {
     93    this.experimentalDesign = experimentalDesign;
     94  }
    995  public String getExperimentName()
    1096  {
    1197    return experimentName;
    1298  }
    13 
    1499  public void setExperimentName(String experimentName)
    15100  {
    16     System.out.println("setting experimentName to " + experimentName);
    17101    this.experimentName = experimentName;
    18102  }
    19 
     103  public String getExpFactors()
     104  {
     105    return expFactors;
     106  }
     107  public void setExpFactors(String expFactors)
     108  {
     109    this.expFactors = expFactors;
     110  }
     111  public String getExtractionProtocol()
     112  {
     113    return extractionProtocol;
     114  }
     115  public void setExtractionProtocol(String extractionProtocol)
     116  {
     117    this.extractionProtocol = extractionProtocol;
     118  }
     119  public String getExtractionProtocolParams()
     120  {
     121    return extractionProtocolParams;
     122  }
     123  public void setExtractionProtocolParams(String extractionProtocolParams)
     124  {
     125    this.extractionProtocolParams = extractionProtocolParams;
     126  }
     127  public String getHybridizationProtocol()
     128  {
     129    return hybridizationProtocol;
     130  }
     131  public void setHybridizationProtocol(String hybridizationProtocol)
     132  {
     133    this.hybridizationProtocol = hybridizationProtocol;
     134  }
     135  public String getHybridizationProtocolParams()
     136  {
     137    return hybridizationProtocolParams;
     138  }
     139  public void setHybridizationProtocolParams(String hybridizationProtocolParams)
     140  {
     141    this.hybridizationProtocolParams = hybridizationProtocolParams;
     142  }
     143  public String getIssue()
     144  {
     145    return issue;
     146  }
     147  public void setIssue(String issue)
     148  {
     149    this.issue = issue;
     150  }
     151  public String getJournal()
     152  {
     153    return journal;
     154  }
     155  public void setJournal(String journal)
     156  {
     157    this.journal = journal;
     158  }
     159  public String getLabelingProtocol()
     160  {
     161    return labelingProtocol;
     162  }
     163  public void setLabelingProtocol(String labelingProtocol)
     164  {
     165    this.labelingProtocol = labelingProtocol;
     166  }
     167  public String getLabelingProtocolParams()
     168  {
     169    return labelingProtocolParams;
     170  }
     171  public void setLabelingProtocolParams(String labelingProtocolParams)
     172  {
     173    this.labelingProtocolParams = labelingProtocolParams;
     174  }
     175  public String getNumDesigns()
     176  {
     177    return numDesigns;
     178  }
     179  public void setNumDesigns(String numDesigns)
     180  {
     181    this.numDesigns = numDesigns;
     182  }
     183  public String getNumReplicates()
     184  {
     185    return numReplicates;
     186  }
     187  public void setNumReplicates(String numReplicates)
     188  {
     189    this.numReplicates = numReplicates;
     190  }
     191  public String getNumTreatments()
     192  {
     193    return numTreatments;
     194  }
     195  public void setNumTreatments(String numTreatments)
     196  {
     197    this.numTreatments = numTreatments;
     198  }
     199  public String getOrganism()
     200  {
     201    return organism;
     202  }
     203  public void setOrganism(String organism)
     204  {
     205    this.organism = organism;
     206  }
     207  public String getOrganization()
     208  {
     209    return organization;
     210  }
     211  public void setOrganization(String organization)
     212  {
     213    this.organization = organization;
     214  }
     215  public String getPages()
     216  {
     217    return pages;
     218  }
     219  public void setPages(String pages)
     220  {
     221    this.pages = pages;
     222  }
     223  public String getPlatform()
     224  {
     225    return platform;
     226  }
     227  public void setPlatform(String platform)
     228  {
     229    this.platform = platform;
     230  }
     231  public String getPooling()
     232  {
     233    return pooling;
     234  }
     235  public void setPooling(String pooling)
     236  {
     237    this.pooling = pooling;
     238  }
     239  public String getPublicationTitle()
     240  {
     241    return publicationTitle;
     242  }
     243  public void setPublicationTitle(String publicationTitle)
     244  {
     245    this.publicationTitle = publicationTitle;
     246  }
     247  public String getPubmedId()
     248  {
     249    return pubmedId;
     250  }
     251  public void setPubmedId(String pubmedId)
     252  {
     253    this.pubmedId = pubmedId;
     254  }
     255  public String getQualityControl()
     256  {
     257    return qualityControl;
     258  }
     259  public void setQualityControl(String qualityControl)
     260  {
     261    this.qualityControl = qualityControl;
     262  }
     263  public String getRefSample()
     264  {
     265    return refSample;
     266  }
     267  public void setRefSample(String refSample)
     268  {
     269    this.refSample = refSample;
     270  }
     271  public String getReleaseDate()
     272  {
     273    return releaseDate;
     274  }
     275  public void setReleaseDate(String releaseDate)
     276  {
     277    this.releaseDate = releaseDate;
     278  }
     279  public String getScanningProtocol()
     280  {
     281    return scanningProtocol;
     282  }
     283  public void setScanningProtocol(String scanningProtocol)
     284  {
     285    this.scanningProtocol = scanningProtocol;
     286  }
     287  public String getScanningProtocolParams()
     288  {
     289    return scanningProtocolParams;
     290  }
     291  public void setScanningProtocolParams(String scanningProtocolParams)
     292  {
     293    this.scanningProtocolParams = scanningProtocolParams;
     294  }
     295  public String getSubmissionDate()
     296  {
     297    return submissionDate;
     298  }
     299  public void setSubmissionDate(String submissionDate)
     300  {
     301    this.submissionDate = submissionDate;
     302  }
     303  public String getSubmitter()
     304  {
     305    return submitter;
     306  }
     307  public void setSubmitter(String submitter)
     308  {
     309    this.submitter = submitter;
     310  }
     311  public String getTissues()
     312  {
     313    return tissues;
     314  }
     315  public void setTissues(String tissues)
     316  {
     317    this.tissues = tissues;
     318  }
    20319  public String getTreatmentProtocol()
    21320  {
    22321    return treatmentProtocol;
    23322  }
    24 
    25323  public void setTreatmentProtocol(String treatmentProtocol)
    26324  {
    27     System.out.println("setting treatmentProtocol to " + treatmentProtocol);
    28325    this.treatmentProtocol = treatmentProtocol;
    29326  }
    30 
     327  public String getTreatmentProtocolParams()
     328  {
     329    return treatmentProtocolParams;
     330  }
     331  public void setTreatmentProtocolParams(String treatmentProtocolParams)
     332  {
     333    this.treatmentProtocolParams = treatmentProtocolParams;
     334  }
     335  public String getVolume()
     336  {
     337    return volume;
     338  }
     339  public void setVolume(String volume)
     340  {
     341    this.volume = volume;
     342  }
     343  public String getYear()
     344  {
     345    return year;
     346  }
     347  public void setYear(String year)
     348  {
     349    this.year = year;
     350  }
     351  public String getZipFile()
     352  {
     353    return zipFile;
     354  }
     355  public void setZipFile(String zipFile)
     356  {
     357    this.zipFile = zipFile;
     358  }
     359 
     360 
    31361
    32362}
  • branches/uk_ac_ebi_Tab2MageImporter/src/uk/ac/ebi/nugo/plugins/Tab2MageImporter.java

    r497 r512  
    9393  private PluginParameter<Boolean> validationParameter;
    9494
    95   // parameters from custom input page (input.jsp)
    96   PluginParameter zipFile;
    97   PluginParameter platform;
    98   PluginParameter organism;
    99   PluginParameter numDesigns;
    100   PluginParameter dyeSwap;
    101   PluginParameter refSample;
    102   PluginParameter numTreatments;
    103   PluginParameter expFactors;
    104   PluginParameter numReplicates;
    105   PluginParameter tissues;
    106   PluginParameter pooling;
    107   PluginParameter experimentName;
    108   PluginParameter treatmentProtocol;
    109 
    11095  //holds the plugin/job config parameters
    11196  LinkedList<PluginParameter<?>> params;
     
    134119  private void initParams()
    135120  {   
    136     // first create the parameter types
     121    //add all the parameter names to a String array for processing
     122    String [] paramNames = new String []{"domain","accession","qualityControl","experimentalDesign",
     123            "experimentName","description","releaseDate","submissionDate","submitter","organization",
     124            "publicationTitle","authors","journal","volume","issue","pages","year","pubmedId","treatmentProtocol",
     125            "extractionProtocol","labelingProtocol","hybridizationProtocol","scanningProtocol",
     126            "treatmentProtocolParams","extractionProtocolParams","labelingProtocolParams",
     127            "hybridizationProtocolParams","scanningProtocolParams","platform","organism",
     128            "numDesigns","dyeSwap","refSample","numTreatments","expFactors","numReplicates",
     129            "tissues","pooling","zipFile"};
     130       
     131    // next create the parameter type
    137132    StringParameterType stringPT = new StringParameterType(255, null, true);
    138 
    139     // create the plugin parameter objects here
    140     experimentName = new PluginParameter<String>("experimentName", "experimentName", "experimentName", stringPT);
    141     treatmentProtocol = new PluginParameter<String>("treatmentProtocol", "treatmentProtocol", "treatmentProtocol", stringPT);
    142 //    zipFile = new PluginParameter<String>("zipFile", " Zip file", "Contains raw data files", stringPT);
    143     platform = new PluginParameter<String>("platform", "Platform", "chip platform used", stringPT);
    144 //    organism = new PluginParameter<String>("organism", "Organism", "First string", stringPT);
    145 //    numDesigns = new PluginParameter<String>("numDesigns", "NumDesigns", "Second string", stringPT);
    146 //    dyeSwap = new PluginParameter<String>("dyeSwap", "dyeSwap", "dyeSwap", stringPT);
    147 //    refSample = new PluginParameter<String>("refSample","refSample","refSample", stringPT);
    148 //    numTreatments = new PluginParameter<String>("numTreatments","numTreatments","numTreatments", stringPT);
    149 //    expFactors = new PluginParameter<String>("expFactors","expFactors","expFactors",stringPT);
    150 //    numReplicates = new PluginParameter<String>("numReplicates","numReplicates","numReplicates", stringPT);
    151 //    tissues = new PluginParameter<String>("tissues","tissues","tissues", stringPT);
    152 //    pooling = new PluginParameter<String>("pooling","pooling","pooling",stringPT);
    153 
    154     //add them all to a list
     133   
     134    //a list to add the parameters to
    155135    params = new LinkedList<PluginParameter<?>>();
    156     params.add(experimentName);
    157     params.add(treatmentProtocol);
    158 //    params.add(zipFile);
    159     params.add(platform);
    160 //    params.add(organism);
    161 //    params.add(numDesigns);
    162 //    params.add(dyeSwap);
    163 //    params.add(refSample);
    164 //    params.add(numTreatments);
    165 //    params.add(expFactors);
    166 //    params.add(numReplicates);
    167 //    params.add(tissues);
    168 //    params.add(pooling);
     136
     137    // create the plugin parameter objects here and add them to the list
     138    for (int i = 0; i < paramNames.length; i++)
     139    {
     140      PluginParameter<String> param = new PluginParameter<String>(paramNames[i],paramNames[i],paramNames[i],stringPT);
     141      params.add(param);
     142    }
    169143  }
    170144
     
    203177
    204178        //print out current values
     179        System.out.println("=================================================================");
    205180        System.out.println("current parameter values:");
    206181        PluginConfigurationRequest pcRequest = (PluginConfigurationRequest) sc.getSessionSetting("plugin.configure.request");
     
    210185          System.out.println(param.getName() + " = " + value);
    211186        }
     187        System.out.println("=================================================================");
    212188      }
    213189    }
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