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fusion.json5
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fusion.json5
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{
datasets: {
PMLS: {
name: "Pacific Marine Life Surveys (1968-2019)",
input: "%imerss-bioinfo/data/Galiano PMLS/PMLS_Records_Galiano_2021-07-27-dataPaper.csv",
map: "%imerss-bioinfo/data/Galiano PMLS/PMLS-map.json",
outMap: "%imerss-bioinfo/data/Galiano PMLS/PMLS-out-map.json",
colour: "#931362",
observationId: "%datasetId:%rowNumber"
},
iNat: {
name: "iNaturalist (2005-2021)",
input: "%imerss-bioinfo/data/iNaturalist/Galiano_Catalogue_Animalia_2023_04_16.csv",
map: "%imerss-bioinfo/data/iNaturalist/iNaturalist-obs-map-new.json",
outMap: "%imerss-bioinfo/data/iNaturalist/iNaturalist-obs-out-map.json",
colour: "#2C8C99",
observationId: "%datasetId:%id"
},
RBCM: {
name: "Royal British Columbia Museum (1893-2011)",
input: "%imerss-bioinfo/data/RBCM/RBCM_GBIF_records_intersected_with_Galiano_polygon_2021_03_08_unscrewed.csv",
map: "%imerss-bioinfo/data/RBCM/RBCM-map.json",
// input: "%imerss-bioinfo/data/RBCM/RBCM_records_Galiano_2019-10-25.csv",
// map: "%imerss-bioinfo/data/RBCM/RBCM-map-old.json",
outMap: "%imerss-bioinfo/data/RBCM/RBCM-out-map.json",
observationId: "%datasetId:%gbifID",
colour: "#29a329"
},
BCCSN: {
name: "British Columbia Cetacean Sightings Network (2001-2020)",
input: "%imerss-bioinfo/data/BCCSN/BC_Cetacean_Sightings_Network_galiano_biodiversity_catalogue_2021_08_25_withTaxa.csv",
map: "%imerss-bioinfo/data/BCCSN/BCCSN-map.json",
outMap: "%imerss-bioinfo/data/BCCSN/BCCSN-out-map.json",
colour: "#55a329",
observationId: "%datasetId:%id"
},
CMN: {
name: "Canadian Museum of Nature (1928-1982)",
input: "%imerss-bioinfo/data/CMN/CMN_Galiano_Island_Marine_fauna_2020_09_11.csv",
map: "%imerss-bioinfo/data/CMN/CMN-map.json",
outMap: "%imerss-bioinfo/data/CMN/CMN-out-map.json",
colour: "#a7a329",
observationId: "%datasetId:%catalogNumber"
},
"Gal-Salm": {
name: "Erickson (2000)",
input: "%imerss-bioinfo/data/Galiano Salmonids/Galiano_Salmonids_Erickson_2000_dated_2021-04-21.csv",
map: "%imerss-bioinfo/data/Galiano Salmonids/Gal-Salm-map.json",
outMap: "%imerss-bioinfo/data/Galiano Salmonids/Gal-Salm-out-map.json",
colour: "#c7a329",
observationId: "%datasetId:%rowNumber"
},
CHU2010: {
name: "Chu and Leys (2010)",
input: "%imerss-bioinfo/data/Chu/CHU_2010_ROV_Marine_occurrence_records_2020_10_07_unscrambled.csv",
map: "%imerss-bioinfo/data/Chu/Chu-map.json",
outMap: "%imerss-bioinfo/data/Chu/Chu-out-map.json",
colour: "#f7a329",
observationId: "%datasetId:%rowNumber"
},
CHU2012: {
name: "Chu and Leys (2012)",
input: "%imerss-bioinfo/data/Chu/CHU_2012_dorids_catalogue_2020_10_08.csv",
map: "%imerss-bioinfo/data/Chu/Chu-2012-map.json",
outMap: "%imerss-bioinfo/data/Chu/Chu-2012-out-map.json",
colour: "#f7a329",
observationId: "%datasetId:%rowNumber"
}
},
patches: {
Deprivatise: {
processor: "hortis.deprivatise"
},
PhaseICoordinates: {
type: "hortis.pipe.CSVInput",
input: "%imerss-bioinfo/data/dataPaper-I/Corrected_georeferencing_marine_animal_occurrence_records_corrected_2021-01-13-plus-round-8.csv",
map: "%imerss-bioinfo/data/dataPaper-I/correctedGeoreferencing-map.json",
processor: "hortis.processCoordinatePatch"
},
RoundCoordinates: {
type: "hortis.pipe",
processor: "hortis.roundCoordinates",
places: 6
},
GalianoRegion: {
type: "hortis.pipe.JSONInput",
input: "%imerss-bioinfo/data/Galiano/Galiano_Island_Project_Boundary_Chu_final_2021-02-23.json",
processor: "hortis.processRegionFilter",
logRejection: true
}
},
summarise: true,
applySwaps: true, // TODO: Naturally, should be an actual pipeline element
output: "%imerss-bioinfo/data/dataPaper-I/reintegrated.csv",
combinedOutMap: "%imerss-bioinfo/data/dataPaper-I/combinedOutMap.json",
filters: {
Plantae: {
field: "kingdom", // Recall that these are before outMap is applied
equals: "Plantae",
exclude: true
},
Chromista: {
field: "kingdom", // Recall that these are before outMap is applied
equals: "Chromista",
exclude: true
},
Eupulmonata: {
field: "superorder", // Land snails and slugs
equals: "Eupulmonata",
exclude: true
},
Myosotella: {
field: "genus", // That blasted saltwater snail in the mix!
equals: "Myosotella",
exclude: false
},
Hygrophila: {
field: "superorder", // Freshwater snails
equals: "Hygrophila",
exclude: true
},
Collembola: {
field: "subclass", // Springtails
equals: "Collembola",
exclude: true
},
Myriapoda: {
field: "subphylum", // Millipedes
equals: "Myriapoda",
exclude: true
},
Oniscidea: {
field: "suborder", // Woodlice
equals: "Oniscidea",
exclude: true
},
Branchiopoda: {
field: "class", // Two freshwater exports from RBCM
equals: "Branchiopoda",
exclude: true
},
Phylactolaemata: { // The freshwater bryozoan (Pectinatella magnifica) needs to be removed from our iNaturalist catalogue
field: "class", // AS of 24/12/20
equals: "Phylactolaemata",
exclude: true
},
Cypriniformes: {
field: "order", // Goldfish
equals: "Cypriniformes",
exclude: true
},
// Following: All terrestrial animals as listed in AS' R script
Aves: {
field: "class",
equals: "Aves",
exclude: true
},
Arachnida: {
field: "class",
equals: "Arachnida",
exclude: true
},
Insecta: {
field: "class",
equals: "Insecta",
exclude: true
},
Amphibia: {
field: "class",
equals: "Amphibia",
exclude: true
},
Reptilia: {
field: "class",
equals: "Reptilia",
exclude: true
},
Diplopoda: {
field: "class",
equals: "Diplopoda",
exclude: true
},
Chiroptera: {
field: "order",
equals: "Chiroptera",
exclude: true
},
Eulipotyphla: {
field: "order",
equals: "Eulipotyphla",
exclude: true
},
Felidae: { // CATTs
field: "family",
equals: "Felidae",
exclude: true
},
Rodentia: { // MMIACE
field: "order",
equals: "Rodentia",
exclude: true
},
Armadillidiidae: {
field: "family",
equals: "Armadillidiidae",
exclude: true
},
Bovidae: {
field: "family",
equals: "Bovidae",
exclude: true
},
Cervidae: {
field: "family",
equals: "Cervidae",
exclude: true
},
Oniscidae: {
field: "family",
equals: "Oniscidae",
exclude: true
},
Porcellionidae: {
field: "family",
equals: "Porcellionidae",
exclude: true
},
Procyonidae: { // Raccoons
field: "family",
equals: "Procyonidae",
exclude: true
},
BadRBCMHemigrapsus: { // Review point 2 from technical reviewer
field: "gbifOccurrenceID",
equals: "49c162e1-b19e-499c-863a-7c3ae208f9ac",
exclude: true
},
iNatDup1: {
field: "id",
equals: "2854812",
exclude: true
},
iNatDup2: {
field: "id",
equals: "84943919",
exclude: true
},
// WARNING! PMLS has no unique ids. These are meant to hit two obs of Cadlina luteomarginata complex
// If PMLS is reissued the ids may need to be remapped by looking at materials-duplicates-PMLS.csv output by arphify.js
PMLSDup1: {
field: "observationId",
equals: "PMLS:3437",
exclude: true
},
PMLSDup2: {
field: "observationId",
equals: "PMLS:18231",
exclude: true
},
/* Adocia: { // Donna Gibbs has requested this PMLS record be deleted as it is now undeterminable
field: "genus",
equals: "Adocia",
exclude: true
},*/
}
}