biosample.plan

<alvisnlp-plan id="biosample">

  <read class="XMLReader">
    <sourcePath>biosample-split</sourcePath>
    <xslTransform>res://XMLReader/biosample2alvisnlp.xslt</xslTransform> <!-- since alvisnlp commit 363df429a80b960febfb5022182b9d2743e4398b -->
  </read>

  <habitat-attributes class="FileMapper">
    <mappingFile>etc/biosample-habitat-attributes.txt</mappingFile>
    <targetFeatures>habitat-attribute</targetFeatures>
    <target>documents.sections</target>
    <form>@name</form>
  </habitat-attributes>

  <table class="TabularExport">
    <outDir>.</outDir>
    <corpusFile>biosample-table.txt</corpusFile>
    <lines>documents</lines>
    <columns>
      @id,
      sections:Title.contents,
      sections:Organism.@taxid,
      sections:Organism.contents,
      sections:biotic_relationship.contents,
      sections:disease.contents,
      sections:env_biome.contents,
      sections:env_feature.contents,
      sections:env_material.contents,
      sections:env_package.contents,
      sections:host.contents,
      sections:host_sex.contents,
      sections:host_tissue_sampled.contents,
      sections:isolation_source.contents,
      sections:pathogenicity.contents,
      sections:plant_product.contents,
      sections:rel_to_oxygen.contents,
      sections:sample_type.contents,
      sections:tissue.contents,
      sections:trophic_level.contents
    </columns>
    <headers>
      "ACCESSION",
      "TITLE",
      "TAXID",
      "ORGANISM",
      "BIOTIC_RELATIONSHIP",
      "DISEASE",
      "ENV_BIOME",
      "ENV_FEATURE",
      "ENV_MATERIAL",
      "ENV_PACKAGE",
      "HOST",
      "HOST_SEX",
      "HOST_TISSUE_SAMPLED",
      "ISOLATION_SOURCE",
      "PATHOGENICITY",
      "PLANT_PRODUCT",
      "REL_TO_OXYGEN",
      "SAMPLE_TYPE",
      "TISSUE",
      "TROPHIC_LEVEL"
    </headers>
  </table>
</alvisnlp-plan>