Protist taxonomy issues from N-ICE2015

[cnrdh]

Common: "Genus sp1/sp2" => "cf. sp1/sp2" ? Chaetoceros convolutus/concavicornis

Some problems:

"var." "Bacillaria paxillifer var.tumidula"
32 ["aff Catenula",null,null]
"Chrysophyceae cyst 1"
Cocal sphere
67 Spora
1 "Deformed Ciliophora with endosymbionts
1 ["Empty dinophyceae",null,"spores"]
1 ["Empty unknown",null,"cysts"]
1 ["Encysting protist on stem",null,null]
5 ["Fragilariopsis cylindrus/F. Reginae-jahniae",null,null]
99 Incertains taxa
5 ["Unknown",null,"cysts"]
2 ["Unknown",null,"spores"]
11 ["Unknown taxon",null,null]

[cnrdh]

ndjson-join --left 'd.scientificName' data/deposit/2015/N-ICE2015/biodiversity/n-ice2015-ice-algae-taxonomy.ndjson data/master/taxonomy/taxonomy-db.ndjson | ndjson-filter '!d[1]' | ndjson-map 'd[0]' | ./bin/ndjson-transform --tsv | ./bin/gbif-validate-species

[cnrdh]

cat data/deposit/iopan/protist-biodiversity/n-ice2015_phytopl_micrpl_taxonomy-iopan.tsv | ./bin/dwc-occurrence-csv-transform 2> /tmp/e |ndjson-filter d.errors | ndjson-split d.errors | sort | ndjson-map '[d.dataPath,d.value]' | sort | uniq
[".individualCount","#DIV/0!"]
[".maximumDepthInMeters","in log does not exist"]
[".organismQuantity","#DIV/0!"]
[".organismQuantity","#VERDI!"]
[".scientificName","Autotrophic flagellates"]
[".scientificName","Bifagellates"]
[".scientificName","Chrysophycean"]
[".scientificName","Cocal sphere"]
[".scientificName","Ebria tripartita"]
[".scientificName","Entomoneis kjellmanii var kariana"]
[".scientificName","Fagellatae"]
[".scientificName","Gonyaulax gracilis (aff. Poulin)"]
[".scientificName","Gymndinium arcticum"]
[".scientificName","Gymndinium galeatum"]
[".scientificName","Gymndinium gracilentum"]
[".scientificName","Gymndinium/Gyrodinium"]
[".scientificName","Gymndinium simplex"]
[".scientificName","Oligotrichea"]
[".scientificName","Pennales"]
[".scientificName","Spora"]
[".scientificName","Symbiont Mesodinium rubrum"]

[cnrdh]

$ ndjson-join --left 'd.scientificName' data/input/iopan/protist-biodiversity/ndjson/n-ice2015_pht.ndjson data/master/taxonomy/taxonomy-db.ndjson | ndjson-filter '!d[1]' | ndjson-map 'd[0]' | ./bin/gbif-validate-taxon | ./bin/gbif-validate-taxon | grep Chromista

[cnrdh]

See #57