{
    "version":"0.1.0",
    "id":"check-names",
    "use_case":"BOKU",
    "title":"Check species names in biodiversity data from separate sources",
    "description":"This process XYZ HERE PLEASE, from the sources GBIF, iNaturalist and VertNet, with data provided by the user or other sources. For more details, please ask BOKU.",
    "jobControlOptions":[
        "sync-execute",
        "async-execute"
    ],
    "keywords":[
        "pan-european use case",
        "AquaINFRA",
        "R"
    ],
    "links":[
        {
            "type":"text/html",
            "rel":"about",
            "title":"GitHub repo",
            "href":"https://github.com/AnthonyBasooma/specleanr",
            "hreflang":"en-US"
        },
        {
            "type":"application/json",
            "rel":"self",
            "href":"https://aquainfra.ogc.igb-berlin.de/pygeoapi/processes/check-names?f=json",
            "title":"Process description as JSON",
            "hreflang":"en-US"
        },
        {
            "type":"text/html",
            "rel":"alternate",
            "href":"https://aquainfra.ogc.igb-berlin.de/pygeoapi/processes/check-names?f=html",
            "title":"Process description as HTML",
            "hreflang":"en-US"
        },
        {
            "type":"text/html",
            "rel":"http://www.opengis.net/def/rel/ogc/1.0/job-list",
            "href":"https://aquainfra.ogc.igb-berlin.de/pygeoapi/jobs?f=html",
            "title":"Jobs list as HTML",
            "hreflang":"en-US"
        },
        {
            "type":"application/json",
            "rel":"http://www.opengis.net/def/rel/ogc/1.0/job-list",
            "href":"https://aquainfra.ogc.igb-berlin.de/pygeoapi/jobs?f=json",
            "title":"Jobs list as JSON",
            "hreflang":"en-US"
        },
        {
            "type":"application/json",
            "rel":"http://www.opengis.net/def/rel/ogc/1.0/execute",
            "href":"https://aquainfra.ogc.igb-berlin.de/pygeoapi/processes/check-names/execution?f=json",
            "title":"Execution for this process as JSON",
            "hreflang":"en-US"
        }
    ],
    "inputs":{
        "species_names_list":{
            "title":"Species names (List of species)",
            "description":"List of species names to check from the standard database (FishBase).",
            "schema":{
                "type":"string"
            },
            "minOccurs":0,
            "maxOccurs":1,
            "keywords":[]
        },
        "species_names_url":{
            "title":"Species names to check",
            "description":"URL to a table containing the occurrences from any source. This can be the outcome of the match-data process.",
            "schema":{
                "type":"string"
            },
            "minOccurs":0,
            "maxOccurs":1,
            "keywords":[
                "csv"
            ]
        },
        "colname_species":{
            "title":"Column name including species names",
            "description":"Column name that indicate the Species in the provided dataset. Only required you provide tabular occurrence data. Example: \"species\"",
            "schema":{
                "type":"string"
            },
            "minOccurs":0,
            "maxOccurs":1,
            "keywords":[]
        },
        "percent_correctness":{
            "title":"Species name correctness in percent",
            "description":"An number indicating the percentage of species name correctness that should be allowed to be replaced. High values ensure a perfect match from the standard database.",
            "schema":{
                "type":"number"
            },
            "minOccurs":1,
            "maxOccurs":1,
            "keywords":[]
        },
        "bool_merge":{
            "title":"Merge checked species names on the dataset",
            "description":"If a dataframe with species names is provided and this is YES, then all columns are returned. For only one species, the merge will be set automatically to false.",
            "schema":{
                "type":"boolean"
            },
            "minOccurs":1,
            "maxOccurs":1,
            "keywords":[]
        },
        "bool_synonym":{
            "title":"Synonym checks",
            "description":"Return synonym checks from FishBase.",
            "schema":{
                "type":"boolean"
            },
            "minOccurs":1,
            "maxOccurs":1,
            "keywords":[]
        },
        "bool_ecosystem_type":{
            "title":"Output ecosytem types",
            "description":"Return ecoystem checks for species from FishBase including marine, freshwater, and brackish.",
            "schema":{
                "type":"boolean"
            },
            "minOccurs":1,
            "maxOccurs":1,
            "keywords":[]
        },
        "bool_rm_duplicates":{
            "title":"Remove duplicates",
            "description":"Remove duplicates from the dataset.",
            "schema":{
                "type":"boolean"
            },
            "minOccurs":1,
            "maxOccurs":1,
            "keywords":[]
        }
    },
    "outputs":{
        "cleannames_df":{
            "title":"Dataframe with checked or quality controlled species data.",
            "description":"A table containing a column speciescheck with names checked with databases for consistency. For fish species, FishBase is used as a standard database.",
            "schema":{
                "type":"object",
                "contentMediaType":"application/json"
            }
        }
    },
    "example":{
        "inputs":{
            "input_data":"https://localhost:5000/download/out/matched-biodiv-data.csv",
            "colname_species":"species",
            "percent_correctness":90,
            "bool_merge":true,
            "bool_synonym":true,
            "bool_ecosystem_type":true,
            "bool_rm_duplicates":true
        }
    },
    "outputTransmission":[
        "value"
    ]
}