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Routine for taxonomic validation, modified from Ricardo Ortiz & Camila Plata: "Script Taxonomic Validation using GBIF's API" from SiB Colombia scripts for Biodiversity data validation and cleaning in OPEN REFINE
https://github.com/SIB-Colombia/data-quality-open-refine
Originally published by Zermoglio, PF, Plata Corredor, CA, Wieczorek, JR, Ortiz Gallego, R & Buitrago, L (2021). Guía para la limpieza de datos sobre biodiversidad con OpenRefine. Versión 3. Copenhagen: GBIF Secretariat. DOI: https://doi.org/10.15468/doc-gzjg-af18

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[
  {
    "op": "core/text-transform",
    "description": "Text transform on cells in column scientificName using expression grel:value.trim().replace(/\\u00A0/,' ').replace(/\\s+/,' ')",
    "engineConfig": {
      "facets": [],
      "mode": "row-based"
    },
    "columnName": "scientificName",
    "expression": "grel:value.trim().replace(/\\u00A0/,' ').replace(/\\s+/,' ')",
    "onError": "keep-original",
    "repeat": false,
    "repeatCount": 10
  },
 {
    "op": "core/column-addition",
    "description": "Create column NomAPI at index 6 based on column scientificName using expression grel:value.replace(\" \",\"%20\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "NomAPI",
    "columnInsertIndex": 6,
    "baseColumnName": "scientificName",
    "expression": "grel:value.replace(\" \",\"%20\")",
    "onError": "set-to-blank"
  },
   {
    "op": "core/column-addition-by-fetching-urls",
    "description": "Create column callAPI at index 6 by fetching URLs based on column NomAPI using expression grel:\"http://api.gbif.org/v1/species/match?strict=true&name=\"+value+\"&kingdom=\"+cells['kingdom'].value",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "callAPI",
    "columnInsertIndex": 6,
    "baseColumnName": "NomAPI",
    "urlExpression": "grel:\"http://api.gbif.org/v1/species/match?strict=true&name=\"+value+\"&kingdom=\"+cells['kingdom'].value",
    "onError": "set-to-blank",
    "delay": 5,
    "cacheResponses": true
  },
  {
    "op": "core/column-move",
    "description": "Move column infraspecificEpithet to position 6",
    "columnName": "infraspecificEpithet",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column specificEpithetSuggested at index 6 based on column callAPI using expression grel:split(value.parseJson().get(\"canonicalName\"),' ')[1]",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "specificEpithetSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:split(value.parseJson().get(\"canonicalName\"),' ')[1]",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column specificEpithet to position 6",
    "columnName": "specificEpithet",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedGenus at index 6 based on column callAPI using expression grel:if(value.parseJson().get(\"status\")=='SYNONYM',(split(value.parseJson().get(\"canonicalName\"),' ')[0]),value.parseJson().get(\"genus\"))",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "genusSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:if(value.parseJson().get(\"status\")=='SYNONYM',(split(value.parseJson().get(\"canonicalName\"),' ')[0]),value.parseJson().get(\"genus\"))",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column family to position 6",
    "columnName": "genus",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedFamily at index 6 based on column callAPI using expression grel:value.parseJson().get(\"family\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "familySuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"family\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column family to position 6",
    "columnName": "family",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedOrder at index 6 based on column callAPI using expression grel:value.parseJson().get(\"order\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "orderSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"order\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column order to position 6",
    "columnName": "order",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedClass at index 6 based on column callAPI using expression grel:value.parseJson().get(\"class\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "classSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"class\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column class to position 6",
    "columnName": "class",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedPhylum at index 6 based on column callAPI using expression grel:value.parseJson().get(\"phylum\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "phylumSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"phylum\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column phylum to position 6",
    "columnName": "phylum",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggstedKingdom at index 6 based on column callAPI using expression grel:value.parseJson().get(\"kingdom\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "kingdomSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"kingdom\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-addition",
    "description": "Create column kingdomValidation at index 6 based on column suggstedKingdom using expression grel:if(value==cells[\"kingdom\"].value,'1','0').toString()",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "kingdomValidation",
    "columnInsertIndex": 6,
    "baseColumnName": "kingdomSuggested",
    "expression": "grel:if(value==cells[\"kingdom\"].value,'1','0').toString()",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column kingdom to position 6",
    "columnName": "kingdom",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedTaxonomicStatus at index 6 based on column callAPI using expression grel:value.parseJson().get(\"status\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "taxonomicStatusSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"status\")",
    "onError": "set-to-blank"
  },  
  {
    "op": "core/column-addition",
    "description": "Create column suggestedRank at index 6 based on column callAPI using expression grel:value.parseJson().get(\"rank\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "taxonRankSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"rank\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-addition",
    "description": "Create column canonicalNameSuggested at index 6 based on column callAPI using expression grel:value.parseJson().get(\"canonicalName\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "canonicalNameSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"canonicalName\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-addition",
    "description": "Create column acceptedScientificName(species) at index 6 based on column callAPI using expression grel:value.parseJson().get(\"species\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "acceptedScientificName",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"species\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-addition",
    "description": "Create column suggestedScientificName at index 6 based on column callAPI using expression grel:value.parseJson().get(\"scientificName\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "scientificNameSuggested",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"scientificName\")",
    "onError": "set-to-blank"
  },
   {
    "op": "core/column-addition",
    "description": "Create column suggestedscientificNameAuthorship at index 6 based on column suggestedScientificName using expression grel:value.partition(cells[\"canonicalNameSuggested\"].value)[2]",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },

    "newColumnName": "scientificNameAuthorshipSuggested",
    "columnInsertIndex": 9,
    "baseColumnName": "scientificNameSuggested",
    "expression": "grel:value.partition(cells[\"canonicalNameSuggested\"].value)[2].trim()",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-addition",
    "description": "Create column authorshipValidation at index 6 based on column suggstedAuthorship using expression grel:if(value==cells[\"scientificNameAuthorship\"].value,'1','0').toString()",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "scientificNameAuthorshipValidation",
    "columnInsertIndex": 9,
    "baseColumnName": "scientificNameAuthorship",
    "expression": "grel:if(value==cells['scientificNameAuthorshipSuggested'].value,1,0).toString()",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-move",
    "description": "Move column scientificNameAuthorship to position 9",
    "columnName": "scientificNameAuthorship",
    "index": 9
  },
  
   {
    "op": "core/column-move",
    "description": "Move column scientificName to position 6",
    "columnName": "scientificName",
    "index": 6
  },
  {
    "op": "core/column-addition",
    "description": "Create column taxonMatchType at index 6 based on column callAPI using expression grel:value.parseJson().get(\"matchType\")",
    "engineConfig": {
      "mode": "row-based",
      "facets": []
    },
    "newColumnName": "taxonMatchType",
    "columnInsertIndex": 6,
    "baseColumnName": "callAPI",
    "expression": "grel:value.parseJson().get(\"matchType\")",
    "onError": "set-to-blank"
  },
  {
    "op": "core/column-removal",
    "description": "Remove column scientificNameSuggested",
    "columnName": "scientificNameSuggested"
  }
  {
    "op": "core/column-removal",
    "description": "Remove column callAPI",
    "columnName": "callAPI"
  }
  {
    "op": "core/column-removal",
    "description": "Remove column NomAPI",
    "columnName": "NomAPI"
  }
]