userDatasetRecord.xml

<?xml version="1.0" encoding="UTF-8"?>

<wdkModel>

    <constant name="datasetRecordDisplayName" includeProjects="ClinEpiDB">User Study</constant>
  <constant name="datasetRecordDisplayNamePlural" includeProjects="ClinEpiDB">User Studies</constant>

  <constant name="datasetRecordDisplayName" excludeProjects="ClinEpiDB">User Dataset</constant>
  <constant name="datasetRecordDisplayNamePlural" excludeProjects="ClinEpiDB">User Datasets</constant>


  <recordClassSet name="UserDatasetRecordClasses">

    <!-- ======================================= USER DATASET RECORD CLASS =========================================================== -->

    <recordClass name="UserDatasetRecordClass" displayName="%%datasetRecordDisplayName%%" displayNamePlural="%%datasetRecordDisplayNamePlural%%" urlName="userdataset" useBasket="false" >
      <testParamValues>
        <paramValue name="dataset_id">test123</paramValue>
      </testParamValues>

      <!-- Primary key definition -->
      <primaryKey aliasQueryRef="UserDatasetAttributes.DatasetAlias">
        <columnRef>dataset_id</columnRef>
      </primaryKey>

      <idAttribute name="primary_key" displayName="User Dataset"
                   help="Click a user dataset to go to the full dataset record">
        <text>
          <![CDATA[ $$name$$ ]]>
        </text>
      </idAttribute>

      <!-- =============================================================== -->
      <!--   Reporters -->
      <!-- =============================================================== -->

      <reporter name="attributesTabular" displayName="Summary - tab delimited" scopes="results"
                implementation="org.gusdb.wdk.model.report.reporter.AttributesTabularReporter">
        <property name="page_size">500</property>
      </reporter>

      <reporter name="tableTabular" displayName="%%tableReporterDisplayName%%" scopes="results"
                implementation="org.gusdb.wdk.model.report.reporter.TableTabularReporter">
        <property name="page_size">1000000</property>
      </reporter>

      <reporter name="fullRecord" displayName="%%fullReporterDisplayName%%" scopes="record"
                implementation="org.gusdb.wdk.model.report.reporter.FullRecordReporter">
      </reporter>

      <reporter name="xml" displayName="XML: choose from columns and/or tables" scopes=""
                implementation="org.gusdb.wdk.model.report.reporter.XMLReporter">
      </reporter>

      <reporter name="json" displayName="json: choose from columns and/or tables" scopes=""
                implementation="org.gusdb.wdk.model.report.reporter.JSONReporter">
      </reporter>

      <!-- =============================================================== -->
      <!--   Core Attributes -->
      <!-- =============================================================== -->

      <attributeQueryRef ref="UserDatasetAttributes.CoreMetadata">
        <columnAttribute name="owner" displayName="Owner ID" help="User ID of the dataset owner"/>
        <columnAttribute name="type_name" displayName="Type" help="Dataset type"/>
        <columnAttribute name="type_version" displayName="Type Version" help="Dataset type version"/>
        <columnAttribute name="category" displayName="Category" help="Dataset category"/>
        <columnAttribute name="deleted_status" displayName="Deleted Status"
                         help="0 = Active, 1 = Deleted and Uninstalled, 2 = Deleted but not yet Uninstalled"/>
        <columnAttribute name="is_public" displayName="Public" help="Whether the dataset is public"/>
        <columnAttribute name="accessibility" displayName="Accessibility"
                         help="Access level: public, protected, or private"/>
        <columnAttribute name="days_for_approval" displayName="Days for approval"
                         help="Number of days required for approval"/>
        <columnAttribute name="creation_date" displayName="Created" help="Dataset creation date"/>
      </attributeQueryRef>

      <attributeQueryRef ref="UserDatasetAttributes.DescriptiveMetadata">
        <columnAttribute name="name" displayName="Name" help="Dataset name"/>
        <columnAttribute name="summary" displayName="Summary" sortable="false" help="Brief dataset summary"/>
        <columnAttribute name="description" displayName="Description" sortable="false"
                         help="Detailed dataset description"/>
        <columnAttribute name="program_name" displayName="Program" help="Program name"/>
        <columnAttribute name="project_name" displayName="Project" help="Project name"/>
        <columnAttribute name="short_attribution" displayName="Attribution" help="Short attribution text"/>
        <columnAttribute name="short_name" displayName="Short name" help="Abbreviated dataset name"/>
      </attributeQueryRef>

      <attributeQueryRef ref="UserDatasetAttributes.EdaStudyMapping">
        <columnAttribute name="eda_study_id" displayName="EDA Study ID" help="EDA study identifier"/>
      </attributeQueryRef>

      <attributeQueryRef ref="UserDatasetAttributes.PrimaryContact">
        <columnAttribute name="primary_contact_name" displayName="Primary contact name" help=""/>
        <columnAttribute name="primary_affiliation" displayName="Primary contact affiliation" help=""/>
        <columnAttribute name="primary_email" displayName="Primary contact email" help=""/>
        <columnAttribute name="primary_country" displayName="Primary contact country" help=""/>
      </attributeQueryRef>

      <attributesList summary="name,owner,type_name,accessibility,creation_date,summary"/>

      <!-- =============================================================== -->
      <!--   Tables -->
      <!-- =============================================================== -->

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- References --> 
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- TODO will return search , name hardcoded based on dataset type

      <table name="References" excludeProjects="ClinEpiDB,MicrobiomeDB"
             displayName="Explore this Data Set within this Website"
             queryRef="GenomeDatasetTables.References">
        <columnAttribute name="dataset_id"  inReportMaker="false" internal="true"/>
        <columnAttribute name="dataset_name"  inReportMaker="false" internal="true"/>
        <columnAttribute name="text" inReportMaker="false" internal="true"/>
        <columnAttribute name="url" inReportMaker="false" internal="true"/>
        <columnAttribute name="description" inReportMaker="false" internal="true"/>
        <columnAttribute name="record_type" displayName="Record Type" />
        <columnAttribute name="target_type" displayName="Type of Reference"/>
        <columnAttribute name="target_name" displayName="Name"/>
        <columnAttribute name="link_type" displayName="link_type"/>
      </table>   
-->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Publications -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Publications"
             displayName="Publications"
             queryRef="UserDatasetTables.Publications">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="external_id" displayName="ID" internal="true"/>
        <columnAttribute name="type" displayName="Type"/>
        <columnAttribute name="citation" displayName="Citation" internal="true"/>
        <columnAttribute name="is_primary" displayName="Primary"/>
        <columnAttribute name="url" internal="true"/>

        <linkAttribute name="publication_link" displayName="Link">
          <displayText>
            <![CDATA[
              $$citation$$
            ]]>
          </displayText>
          <url>
            <![CDATA[
              $$url$$
            ]]>
          </url>
        </linkAttribute>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Contacts -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Contacts"
             displayName="Contacts"
             queryRef="UserDatasetTables.Contacts">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="contact_name" displayName="Name"/>
        <columnAttribute name="affiliation" displayName="Affiliation"/>
        <columnAttribute name="email" displayName="Email"/>
        <columnAttribute name="country" displayName="Country"/>
        <columnAttribute name="is_primary" displayName="Primary contact"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Organisms -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Organisms"
             displayName="Organisms"
             queryRef="UserDatasetTables.Organisms">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="organism_type" displayName="Type"
                         help="experimental or host"/>
        <columnAttribute name="species" displayName="Species"/>
        <columnAttribute name="strain" displayName="Strain"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Hyperlinks -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="HyperLinks"
             displayName="External Links"
             queryRef="UserDatasetTables.HyperLinks">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="url" internal="true"/>
        <columnAttribute name="description" internal="true"/>

        <linkAttribute name="hyper_link" displayName="Link">
          <displayText>
            <![CDATA[
              $$description$$
            ]]>
          </displayText>
          <url>
            <![CDATA[
              $$url$$
            ]]>
          </url>
        </linkAttribute>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Funding Awards -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="FundingAwards"
             displayName="Funding Awards"
             queryRef="UserDatasetTables.FundingAwards">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="agency" displayName="Funding agency"/>
        <columnAttribute name="award_number" displayName="Award number"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Countries -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Countries"
             displayName="Countries"
             queryRef="UserDatasetTables.Countries">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="country" displayName="Country"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Outcome -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Outcome"
             displayName="Outcome"
             queryRef="UserDatasetTables.Outcome">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="outcome" displayName="Outcome"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Diseases -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Diseases"
             displayName="Diseases"
             queryRef="UserDatasetTables.Diseases">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="disease" displayName="Disease"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Study Characteristics -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Characteristics"
             displayName="Study Characteristics"
             queryRef="UserDatasetTables.Characteristics">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="study_design" displayName="Study design"/>
        <columnAttribute name="study_type" displayName="Study type"/>
        <columnAttribute name="participant_ages" displayName="Participant ages"/>
        <columnAttribute name="sample_year_start" displayName="Sample year start"/>
        <columnAttribute name="sample_year_end" displayName="Sample year end"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Projects -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="Projects"
             displayName="Associated Projects"
             queryRef="UserDatasetTables.Projects">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="project_id" displayName="Project ID"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- External Identifiers -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="ExternalIds"
             displayName="External Identifiers"
             queryRef="UserDatasetTables.ExternalIds">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="identifier_type" displayName="Type"/>
        <columnAttribute name="identifier_value" displayName="Identifier"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Dependencies -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- not needed in UI
      <table name="Dependencies"
             displayName="Dependencies"
             queryRef="UserDatasetTables.Dependencies">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="identifier" displayName="Identifier"/>
        <columnAttribute name="display_name" displayName="Name"/>
        <columnAttribute name="version" displayName="Version"/>
      </table>
-->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Associated Factors -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="AssociatedFactors"
             displayName="Associated Factors"
             queryRef="UserDatasetTables.AssociatedFactors">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="factor" displayName="Factor"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Sample Types -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="SampleTypes"
             displayName="Sample Types"
             queryRef="UserDatasetTables.SampleTypes">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="type" displayName="Sample Type"/>
      </table>

      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <!-- Dataset Links -->
      <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
      <table name="DatasetLinks"
             displayName="Dataset Links"
             queryRef="UserDatasetTables.DatasetLinks">
        <columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
        <columnAttribute name="dataset_uri" displayName="URI" internal="true"/>
        <columnAttribute name="shares_records" displayName="Shares Records"/>

        <linkAttribute name="dataset_link" displayName="Link">
          <displayText>
            <![CDATA[
              $$dataset_uri$$
            ]]>
          </displayText>
          <url>
            <![CDATA[
              $$dataset_uri$$
            ]]>
          </url>
        </linkAttribute>
      </table>

    </recordClass>

  </recordClassSet>

</wdkModel>